- Silicon Nanowire Path
- Carbon Path
- Organic / Polymer Path
- Biomolecular-Assembled Circuits
- Chemical Information Processing Path
- Orchestration Path
- Resilience Path
- CRC 912 (HAEC)
- Biological Systems Path
Path I - Biological Systems
The mission of the Path is to study emergent behavior and information processing in biological systems and identify principles that underlie biological function and could be beneficial for engineering applications. This is pursued in close cooperation between biologists, engineers, physicists, computer scientists, and mathematicians, combining concepts from the various disciplines. Important challenges are to understand the emergence of robustness, parallelism, convergence, and self-organization in information-processing systems. The goal is to deepen the understanding of the biological systems and to inspire novel engineering applications.
Path Leader: Prof. Marino Zerial
Path Co-Leader: Prof. Marc Timme
Investigators:
- Prof. Dr.-Ing. Dr. h.c. Gerhard Fettweis
- Dr. Benjamin Friedrich (RGL Biological Algorithms Group)
- Prof. Dr. Frank Jülicher
- Prof. Dr.-Ing. habil. Christian Georg Mayr
- Prof. Dr. Ivo Sbalzarini
- Prof. Dr. Marc Timme
- Prof. Dr. Marino Zerial
Previous members:
The goal of the Biological Systems Path is to study emergent behavior of biological systems, such as resilience, parallelism, scalability, self-organization, and energy efficiency, from an information-processing (computation and communication) viewpoint, and to make available this knowledge for innovative engineering applications. We analyze biological examples of information processing where such properties emerge from simple interactions at smaller scales. Examples of such interactions include signals changing from analog to digital (e.g., a cell-fate decision was made), from digital to analog (e.g., turning on a finite set of genes leads to a graded protein concentration), or from stationary to oscillatory (e.g., triggering a cellular oscillation within the ear). How robust (reliable) are these transformations? How is robustness achieved with small numbers of unreliable components? And how can a biological system “solve” complex combinatorial problems with a small number of components? These are some of the key information-processing questions that are addressed in this Path.
Electronic information-processing systems also use different modes of computation (analog/digital) and different scales of implementation. For instance, analog transistors on a chip are used to make digital decisions on the circuit level. In communication systems, digital information is carried by analog signals that are processed by both analog and digital components, before being decoded back to information. Hence, it seems promising to apply some of these concepts to biological information-processing systems, and to compare biological systems with electronic systems in terms of their complexity and (energy) efficiency. Biological systems are among the most complex systems known, and it is possible that universal principles emerge that can provide insight into the increasingly complex engineering systems of the future.
The Bio Path is the outreach and innovation Path of cfaed. It bi-directionally combines two areas where Dresden is strong: microelectronics and the life sciences. As a trans-disciplinary Path, we integrate researchers from both disciplines and allow them to mutually learn from each other. In this, biologists import new concepts and knowledge from engineers and computer scientists, and vice versa. This is fundamentally different from the often-cited “bio-inspired engineering” approaches. Here, the study of the biological system using engineering principles is the driving force, and concepts are imported from the other disciplines. The Biological Systems Path consists of seven interdisciplinary projects, aiming at transferring knowledge bi-directionally between biology and engineering.
Specific biological information-processing systems are analyzed using tools from engineering, computer science, and mathematics. The systems are “reverse engineered” to determine the underlying algorithms and design principles. We quantify the speed, resilience, and efficiency of a broad range of systems from cell, tissue, and developmental biology. The strong emphasis on quantitative data in the biological labs, in combination with the theoretical expertise in the engineering, computer science, and mathematics groups, allows us to obtain definitive answers to key questions concerning biological computing and information processing. Ultimately, we seek to know how closely biological systems approach the theoretical limits set by physics and information theory.
In parallel, new theoretical methods are developed that are applicable to a number of biological problems. These methods include logic-based modeling, communication theory, agent-based simulations, optimization theory, and non-linear dynamics. Because each theoretical approach can be used to analyze different biological problems, the theoretical groups provide important connections between the various projects.
As a bi-directional Path, the engineering principles identified in biological systems are made available to the other Paths in numerous inter-Path collaborations. They may inspire novel ways of thinking about the engineering systems of the future.
The list below provides an overview of all current projects and the participating investigators.
No. |
Investigator |
Topic |
2 |
Zerial, Deutsch/Brusch, Sbalzarini |
Maintenance of Function During Repair and RegenerationAn outstanding technological challenge is the interrupt-free maintenance of system function despite random failures of the constituent parts. In biological systems, individual cells grow old and die, yet the organs made of such cells function without interruption. We focus on the liver and aim at discovering decentral load balancing and network regeneration algorithms. Immediate applications include the balancing of computing load within the parallel particle mesh library. |
4 |
Zerial, Jülicher, Fettweis |
How cells compute biochemical signalsThis proposal aims at transferring knowledge from cell-based into engineering-based computing. Cells receive instructions (e.g. to divide) in the form of signalling molecules that bind to receptors on the surface and transduce information to the nucleus. Cells integrate multiple signals over time, filter noise and reliably compute a fate decision. Remarkably, signalling ligand-receptor complexes are packaged in endosomes at constant amount, which can be viewed as an analog-to-digital conversion. We will 1) develop models of signaling complexes distribution in the endosomal network; 2) learn from engineering the design principles of the cellular computer; 3) study possible applications to nanocomputers |
5 |
Fettweis, Jülicher(Schüffny, Siegmund) |
Robust Self-organized Synchronization of Separate Electronic Clocks inspired by Biological SystemsBoth in biology and in engineering, synchronization of many autonomously oscillating parts is an important concept; think of flashing fireflies, cardiac pacemaker cells, or multi-core systems. In electronic systems consisting of hundreds of autonomous cores with separate clocks, state-of-the-art techniques of synchronization can become highly inefficient. Understanding synchronization strategies in biological systems can provide novel approaches for synchronization in electronic systems. The project's goal is to seek for biologically inspired synchronization techniques for large systems of electronic clocks to support concerted operations. Using theories of coupled oscillators that capture the effects of signal transmission delays and signal filtering we analyze the synchronization properties of such systems. In parallel, we test our theoretical results with experiments on mutually delay-coupled electronic clocks. |
6 |
Sbalzarini, Howard, Baader |
Bioinspired Computing and Optimization Problem ClassificationEngineering and biology share the challenge of solving hard optimization problems in noisy environments. Biology has evolved different solution strategies that engineers mimic in bioinspired algorithms. But which algorithms work well on what problems? How should one classify optimization problems? Why do birds look for food in swarms, but squirrels don’t? We aim at learning a problem classification from biology, using it to provide a theoretical understanding of bioinspired algorithms, and applying these algorithms to circuit design, chemical computing, and systems biology |
8 |
Friedrich |
Mission of the Biological Algorithms groupWe seek to theoretically understand biological solutions for motility control and self-organization in cells and tissues. A special emphasis is on principles that make biological function robust in the presence of strong fluctuations. We combine dynamical systems theory, statistical physics, and image analysis to reverse-engineer physical mechanisms of robust feedback control. We want to understand emergent dynamics from simple rules. We enjoy close collaborations with biologists with rapid iteration loops between quantitative theory and experiment. Motility control: At the cellular scale, we study how noisy sensory information controls motion. Our model system are flagellated microswimmers, where we study swimming, steering, and synchronization, e.g. in sperm navigation for the egg. Pattern control: At the tissue scale, we study elementary rules of self-organized pattern formation during self-repair and adaptation to fluctuating environments. In the past, we have studied self-organized scaling of developmental patterns. Current project address design principles and transport in 3-dimensional tissues such as the liver. |
Previous Projects
Project 1
A Logic of Aggregation and Emerging Functionality (Baader)
In biological systems, new functionalities may emerge when small components (e.g., cells) are aggregated into larger entities (e.g., tissue). The purpose of this project is to develop a logic-based modelling language that is expressive enough to describe such phenomena, but still allows effective reasoning. The development of the formalism will be guided by examples found in biological systems, and the resulting formalism evaluated by comparing it to known models from systems biology.
Project 3
Strategies for Controlling Protein Concentrations (Siegmund, Beyer, Gross)
Cellular regulatory processes can be seen as ‘biological computing’. The goal of this project is to understand the processes controlling protein concentrations and to evaluate different regulatory strategies using mathematical models. This work should improve our understanding about which strategies are used in which context in order to meet conflicting optimization goals (e.g. resource efficiency versus speed). Ultimately, this should yield new strategies for implementation in engineered computing systems.
Project 7
Cell fate decision making in multicellular systems: a multiscale approach (Hatzikirou)
Our goal is the profound understanding of cell decision-making in multicellular systems by means of multiscale mathematical modeling. Single cell decision-making has been a major focus of biology. However, in a multicellular system, cell decisions influence and get influenced by its own micro-environment, consisted of homotypic and heterotypic components. This dialogue makes the system dynamics extremely complex.
Replacing the word “cell” by “agent”, we can draw a useful analogy between biological multicellular systems and technical multi-agent ones. The remarkable way that biological system process information can be a source of inspiration for novel engineering ideas.
I.5 project (Robust Synchronisation of Separate Clock Signals on Massively Multi-Core Chips inspired by Biological Systems)
The I.5 project aims at finding novel synchronization strategies for high performance multi-core architectures at low power consumption using concepts developed in the study of biological systems. To this point, the project has obtained interesting new results for networks of mutually coupled electronic oscillators. It has shown how two factors that individually hinder synchronization in such systems will together enable robustly synchronized states. On this basis, novel architectures that allow efficient and robust synchronization are under investigation. The theory is now being tested comparing analytic model predictions to Matlab/Simulink simulations and to experiments with electronic oscillator units, assembled in our group. Compared to prior architectures for globally synchronous operating applications our approach reduces wiring between the oscillators, drops the Master clock and thereby reduces power consumption and production cost. We expect applications in high performance Multiprocessor System-on-Chips (MPSoCs) architectures, distributed antenna arrays, and other large-scale electronic clocking systems communicating by means of time-continuous signals.
I.6 project (Bio-inspired Computing and Optimization Problem Classification)
Optimization problems are ubiquitous in engineering, ranging from parameter estimation to robust design optimization. In practical applications, the function to be optimized is usually not known in mathematical form, but candidate solutions can only be evaluated for quality. Such optimization problems are called "black-box problems". Evaluating the quality of a proposed design or solution in a black-box problem may involve running a computer simulation, performing experimental measurements, or asking an expert.
Due to the practical importance of black-box optimization problems in engineering, hundreds of heuristics and algorithms have been developed, including genetic algorithms, evolution strategies, particle-swarm optimization, simulated annealing, etc. It is a known fact that no algorithm outperforms any other on all possible problems. In practical applications, it is hence of utmost importance to pick a well-suited algorithm for a given problem.
Which algorithm performs well on what type of problems, however, is unknown. It is not even clear how problem "types" or "classes" should be defined such that they predict algorithm performance. This project addresses this shortcoming. It is the goal of this project to develop a recommender system that would suggest a suitable algorithm for a given problem using only the solution evaluations collected. We follow a two-tier strategy: one the one hand, we exploit extensive databases of performance measurements of hundreds of algorithms tested on a standard set of test problems. We use machine-learning methods and tools from computational logic to extract patterns and implications from these data. On the other hand, we seek inspiration in how biology has evolved different optimization strategies for different types of problems. This is motivated by the fact that most black-box heuristics are biologically inspired themselves.
- We have published the idea of a recommender system based on formal concept analysis from logic. The prototype of this system successfully reproduced known recommendations, and suggested new ones.
- We have performed hierarchical bi-clustering analysis of the benchmark database and discovered groups of algorithms that perform similarly well on groups of problems. We currently investigate in what sense these problems are different.
- We generated a catalog of optimization problems and strategies from biology, and are currently relating them to engineering problems and the benchmark problems used in the black-box optimization community
- Applications in other cfAED Paths (parameter estimation in compact models of Carbon Nanotube transistors; robust design centering of flexible thin-film electronics) have shown the potential and challenges of our approach.
2020
- Justus A Kromer, Noelia de la Cruz, Benjamin M Friedrich, "Chemokinetic Scattering, Trapping, and Avoidance of Active Brownian Particles", In Physical Review Letters, APS, vol. 124, no. 11, pp. 118101, 2020. [Bibtex & Downloads]
Chemokinetic Scattering, Trapping, and Avoidance of Active Brownian Particles
Reference
Justus A Kromer, Noelia de la Cruz, Benjamin M Friedrich, "Chemokinetic Scattering, Trapping, and Avoidance of Active Brownian Particles", In Physical Review Letters, APS, vol. 124, no. 11, pp. 118101, 2020.
Bibtex
@article{kromer2020chemokinetic,
title={Chemokinetic Scattering, Trapping, and Avoidance of Active Brownian Particles},
author={Kromer, Justus A and de la Cruz, Noelia and Friedrich, Benjamin M},
journal={Physical Review Letters},
volume={124},
number={11},
pages={118101},
year={2020},
publisher={APS}
}Downloads
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2019
- Marc Timme, Jan Nagler, "Propagation patterns unravelled", In Nature Physics, Springer Nature, Jan 2019. [doi] [Bibtex & Downloads]
Propagation patterns unravelled
Reference
Marc Timme, Jan Nagler, "Propagation patterns unravelled", In Nature Physics, Springer Nature, Jan 2019. [doi]
Bibtex
@article{Timme_2019,
doi = {10.1038/s41567-019-0424-9},
url = {https://doi.org/10.1038%2Fs41567-019-0424-9},
year = 2019,
month = {jan},
publisher = {Springer Nature},
author = {Marc Timme and Jan Nagler},
title = {Propagation patterns unravelled},
journal = {Nature Physics}
}Downloads
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- Jens Karschau, Andre Scholich, Jonathan Wise, Hernán Morales-Navarette, Yannis Kalaidzidis, Marino Zerial, Benjamin M Friedrich, "Resilience of three-dimensional sinusoidal networks in liver tissue", In arXiv preprint arXiv:1912.09929, 2019. [Bibtex & Downloads]
Resilience of three-dimensional sinusoidal networks in liver tissue
Reference
Jens Karschau, Andre Scholich, Jonathan Wise, Hernán Morales-Navarette, Yannis Kalaidzidis, Marino Zerial, Benjamin M Friedrich, "Resilience of three-dimensional sinusoidal networks in liver tissue", In arXiv preprint arXiv:1912.09929, 2019.
Bibtex
@article{karschau2019resilience,
title={Resilience of three-dimensional sinusoidal networks in liver tissue},
author={Karschau, Jens and Scholich, Andre and Wise, Jonathan and Morales-Navarette, Hern{\'a}n and Kalaidzidis, Yannis and Zerial, Marino and Friedrich, Benjamin M},
journal={arXiv preprint arXiv:1912.09929},
year={2019}
}Downloads
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- Hernan Morales-Navarrete, Hidenori Nonaka, André Scholich, Fabian Segovia-Miranda, Walter de Back, Kirstin Meyer, Roman L Bogorad, Victor Koteliansky, Lutz Brusch, Yannis Kalaidzidis, others, "Liquid-crystal organization of liver tissue", In Elife, eLife Sciences Publications Limited, vol. 8, pp. e44860, 2019. [Bibtex & Downloads]
Liquid-crystal organization of liver tissue
Reference
Hernan Morales-Navarrete, Hidenori Nonaka, André Scholich, Fabian Segovia-Miranda, Walter de Back, Kirstin Meyer, Roman L Bogorad, Victor Koteliansky, Lutz Brusch, Yannis Kalaidzidis, others, "Liquid-crystal organization of liver tissue", In Elife, eLife Sciences Publications Limited, vol. 8, pp. e44860, 2019.
Bibtex
@article{morales2019liquid,
title={Liquid-crystal organization of liver tissue},
author={Morales-Navarrete, Hernan and Nonaka, Hidenori and Scholich, Andr{\'e} and Segovia-Miranda, Fabian and de Back, Walter and Meyer, Kirstin and Bogorad, Roman L and Koteliansky, Victor and Brusch, Lutz and Kalaidzidis, Yannis and others},
journal={Elife},
volume={8},
pages={e44860},
year={2019},
publisher={eLife Sciences Publications Limited}
}Downloads
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- Steffen Lange, Benjamin M Friedrich, "Fertilization in the sea: sperm chemotaxis in physiological shear flows", In arXiv preprint arXiv:1912.09112, 2019. [Bibtex & Downloads]
Fertilization in the sea: sperm chemotaxis in physiological shear flows
Reference
Steffen Lange, Benjamin M Friedrich, "Fertilization in the sea: sperm chemotaxis in physiological shear flows", In arXiv preprint arXiv:1912.09112, 2019.
Bibtex
@article{lange2019fertilization,
title={Fertilization in the sea: sperm chemotaxis in physiological shear flows},
author={Lange, Steffen and Friedrich, Benjamin M},
journal={arXiv preprint arXiv:1912.09112},
year={2019}
}Downloads
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2018
- Jose Casadiego, Dimitra Maoutsa, Marc Timme, "Inferring Network Connectivity from Event Timing Patterns", In Physical Review Letters, American Physical Society (APS), vol. 121, no. 5, Aug 2018. [doi] [Bibtex & Downloads]
Inferring Network Connectivity from Event Timing Patterns
Reference
Jose Casadiego, Dimitra Maoutsa, Marc Timme, "Inferring Network Connectivity from Event Timing Patterns", In Physical Review Letters, American Physical Society (APS), vol. 121, no. 5, Aug 2018. [doi]
Bibtex
@article{Casadiego_2018,
doi = {10.1103/physrevlett.121.054101},
url = {https://doi.org/10.1103%2Fphysrevlett.121.054101},
year = 2018,
month = {aug},
publisher = {American Physical Society ({APS})},
volume = {121},
number = {5},
author = {Jose Casadiego and Dimitra Maoutsa and Marc Timme},
title = {Inferring Network Connectivity from Event Timing Patterns},
journal = {Physical Review Letters}
}Downloads
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- Farnaz Basiri, Jose Casadiego, Marc Timme, Dirk Witthaut, "Inferring power-grid topology in the face of uncertainties", In Physical Review E, American Physical Society (APS), vol. 98, no. 1, Jul 2018. [doi] [Bibtex & Downloads]
Inferring power-grid topology in the face of uncertainties
Reference
Farnaz Basiri, Jose Casadiego, Marc Timme, Dirk Witthaut, "Inferring power-grid topology in the face of uncertainties", In Physical Review E, American Physical Society (APS), vol. 98, no. 1, Jul 2018. [doi]
Bibtex
@article{Basiri_2018,
doi = {10.1103/physreve.98.012305},
url = {https://doi.org/10.1103%2Fphysreve.98.012305},
year = 2018,
month = {jul},
publisher = {American Physical Society ({APS})},
volume = {98},
number = {1},
author = {Farnaz Basiri and Jose Casadiego and Marc Timme and Dirk Witthaut},
title = {Inferring power-grid topology in the face of uncertainties},
journal = {Physical Review E}
}Downloads
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- Samuel Krüger, Christoph A Weber, Jens-Uwe Sommer, Frank Jülicher, "Discontinuous switching of position of two coexisting phases", In New Journal of Physics, IOP Publishing, vol. 20, no. 7, pp. 075009, Jul 2018. [doi] [Bibtex & Downloads]
Discontinuous switching of position of two coexisting phases
Reference
Samuel Krüger, Christoph A Weber, Jens-Uwe Sommer, Frank Jülicher, "Discontinuous switching of position of two coexisting phases", In New Journal of Physics, IOP Publishing, vol. 20, no. 7, pp. 075009, Jul 2018. [doi]
Bibtex
@article{Kr_ger_2018,
doi = {10.1088/1367-2630/aad173},
url = {https://doi.org/10.1088%2F1367-2630%2Faad173},
year = 2018,
month = {jul},
publisher = {{IOP} Publishing},
volume = {20},
number = {7},
pages = {075009},
author = {Samuel Krüger and Christoph A Weber and Jens-Uwe Sommer and Frank Jülicher},
title = {Discontinuous switching of position of two coexisting phases},
journal = {New Journal of Physics}
}Downloads
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- Malte Schröder, Jan Nagler, Marc Timme, Dirk Witthaut, "Hysteretic Percolation from Locally Optimal Individual Decisions", In Physical Review Letters, American Physical Society (APS), vol. 120, no. 24, Jun 2018. [doi] [Bibtex & Downloads]
Hysteretic Percolation from Locally Optimal Individual Decisions
Reference
Malte Schröder, Jan Nagler, Marc Timme, Dirk Witthaut, "Hysteretic Percolation from Locally Optimal Individual Decisions", In Physical Review Letters, American Physical Society (APS), vol. 120, no. 24, Jun 2018. [doi]
Bibtex
@article{Schr_der_2018,
doi = {10.1103/physrevlett.120.248302},
url = {https://doi.org/10.1103%2Fphysrevlett.120.248302},
year = 2018,
month = {jun},
publisher = {American Physical Society ({APS})},
volume = {120},
number = {24},
author = {Malte Schröder and Jan Nagler and Marc Timme and Dirk Witthaut},
title = {Hysteretic Percolation from Locally Optimal Individual Decisions},
journal = {Physical Review Letters}
}Downloads
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- Justine Wolter, Benedict Lünsmann, Xiaozhu Zhang, Malte Schröder, Marc Timme, "Quantifying transient spreading dynamics on networks", In Chaos: An Interdisciplinary Journal of Nonlinear Science, AIP Publishing, vol. 28, no. 6, pp. 063122, Jun 2018. [doi] [Bibtex & Downloads]
Quantifying transient spreading dynamics on networks
Reference
Justine Wolter, Benedict Lünsmann, Xiaozhu Zhang, Malte Schröder, Marc Timme, "Quantifying transient spreading dynamics on networks", In Chaos: An Interdisciplinary Journal of Nonlinear Science, AIP Publishing, vol. 28, no. 6, pp. 063122, Jun 2018. [doi]
Bibtex
@article{Wolter_2018,
doi = {10.1063/1.5000996},
url = {https://doi.org/10.1063%2F1.5000996},
year = 2018,
month = {jun},
publisher = {{AIP} Publishing},
volume = {28},
number = {6},
pages = {063122},
author = {Justine Wolter and Benedict Lünsmann and Xiaozhu Zhang and Malte Schröder and Marc Timme},
title = {Quantifying transient spreading dynamics on networks},
journal = {Chaos: An Interdisciplinary Journal of Nonlinear Science}
}Downloads
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- Niklas Biere, Mehmood Ghaffar, Anja Doebbe, Daniel Jäger, Nils Rothe, Benjamin M. Friedrich, Ralf Hofestädt, Falk Schreiber, Olaf Kruse, Björn Sommer, "Heuristic Modeling and 3D Stereoscopic Visualization of a Chlamydomonas reinhardtii Cell", In Journal of Integrative Bioinformatics, Walter de Gruyter GmbH, vol. 15, no. 2, Jun 2018. [doi] [Bibtex & Downloads]
Heuristic Modeling and 3D Stereoscopic Visualization of a Chlamydomonas reinhardtii Cell
Reference
Niklas Biere, Mehmood Ghaffar, Anja Doebbe, Daniel Jäger, Nils Rothe, Benjamin M. Friedrich, Ralf Hofestädt, Falk Schreiber, Olaf Kruse, Björn Sommer, "Heuristic Modeling and 3D Stereoscopic Visualization of a Chlamydomonas reinhardtii Cell", In Journal of Integrative Bioinformatics, Walter de Gruyter GmbH, vol. 15, no. 2, Jun 2018. [doi]
Bibtex
@article{Biere_2018,
doi = {10.1515/jib-2018-0003},
url = {https://doi.org/10.1515%2Fjib-2018-0003},
year = 2018,
month = {jun},
publisher = {Walter de Gruyter {GmbH}},
volume = {15},
number = {2},
author = {Niklas Biere and Mehmood Ghaffar and Anja Doebbe and Daniel Jäger and Nils Rothe and Benjamin M. Friedrich and Ralf Hofestädt and Falk Schreiber and Olaf Kruse and Björn Sommer},
title = {Heuristic Modeling and 3D Stereoscopic Visualization of a Chlamydomonas reinhardtii Cell},
journal = {Journal of Integrative Bioinformatics}
}Downloads
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- Benjamin Schäfer, Dirk Witthaut, Marc Timme, Vito Latora, "Dynamically induced cascading failures in power grids", In Nature Communications, Springer Nature, vol. 9, no. 1, May 2018. [doi] [Bibtex & Downloads]
Dynamically induced cascading failures in power grids
Reference
Benjamin Schäfer, Dirk Witthaut, Marc Timme, Vito Latora, "Dynamically induced cascading failures in power grids", In Nature Communications, Springer Nature, vol. 9, no. 1, May 2018. [doi]
Bibtex
@article{Sch_fer_2018,
doi = {10.1038/s41467-018-04287-5},
url = {https://doi.org/10.1038%2Fs41467-018-04287-5},
year = 2018,
month = {may},
publisher = {Springer Nature},
volume = {9},
number = {1},
author = {Benjamin Schäfer and Dirk Witthaut and Marc Timme and Vito Latora},
title = {Dynamically induced cascading failures in power grids},
journal = {Nature Communications}
}Downloads
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- Matthias Rank, Aniruddha Mitra, Louis Reese, Stefan Diez, Erwin Frey, "Limited Resources Induce Bistability in Microtubule Length Regulation", In Physical Review Letters, American Physical Society (APS), vol. 120, no. 14, Apr 2018. [doi] [Bibtex & Downloads]
Limited Resources Induce Bistability in Microtubule Length Regulation
Reference
Matthias Rank, Aniruddha Mitra, Louis Reese, Stefan Diez, Erwin Frey, "Limited Resources Induce Bistability in Microtubule Length Regulation", In Physical Review Letters, American Physical Society (APS), vol. 120, no. 14, Apr 2018. [doi]
Bibtex
@article{Rank_2018,
doi = {10.1103/physrevlett.120.148101},
url = {https://doi.org/10.1103%2Fphysrevlett.120.148101},
year = 2018,
month = {apr},
publisher = {American Physical Society ({APS})},
volume = {120},
number = {14},
author = {Matthias Rank and Aniruddha Mitra and Louis Reese and Stefan Diez and Erwin Frey},
title = {Limited Resources Induce Bistability in Microtubule Length Regulation},
journal = {Physical Review Letters}
}Downloads
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- Benjamin M. Friedrich, "Load response of shape-changing microswimmers scales with their swimming efficiency", In Physical Review E, American Physical Society (APS), vol. 97, no. 4, Apr 2018. [doi] [Bibtex & Downloads]
Load response of shape-changing microswimmers scales with their swimming efficiency
Reference
Benjamin M. Friedrich, "Load response of shape-changing microswimmers scales with their swimming efficiency", In Physical Review E, American Physical Society (APS), vol. 97, no. 4, Apr 2018. [doi]
Bibtex
@article{Friedrich_2018,
doi = {10.1103/physreve.97.042416},
url = {https://doi.org/10.1103%2Fphysreve.97.042416},
year = 2018,
month = {apr},
publisher = {American Physical Society ({APS})},
volume = {97},
number = {4},
author = {Benjamin M. Friedrich},
title = {Load response of shape-changing microswimmers scales with their swimming efficiency},
journal = {Physical Review E}
}Downloads
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- Justus A. Kromer, Steffen Märcker, Steffen Lange, Christel Baier, Benjamin M. Friedrich, "Decision making improves sperm chemotaxis in the presence of noise", In PLOS Computational Biology (Sarah D Olson), Public Library of Science (PLoS), vol. 14, no. 4, pp. e1006109, Apr 2018. [doi] [Bibtex & Downloads]
Decision making improves sperm chemotaxis in the presence of noise
Reference
Justus A. Kromer, Steffen Märcker, Steffen Lange, Christel Baier, Benjamin M. Friedrich, "Decision making improves sperm chemotaxis in the presence of noise", In PLOS Computational Biology (Sarah D Olson), Public Library of Science (PLoS), vol. 14, no. 4, pp. e1006109, Apr 2018. [doi]
Bibtex
@article{Kromer_2018,
doi = {10.1371/journal.pcbi.1006109},
url = {https://doi.org/10.1371%2Fjournal.pcbi.1006109},
year = 2018,
month = {apr},
publisher = {Public Library of Science ({PLoS})},
volume = {14},
number = {4},
pages = {e1006109},
author = {Justus A. Kromer and Steffen Märcker and Steffen Lange and Christel Baier and Benjamin M. Friedrich},
editor = {Sarah D Olson},
title = {Decision making improves sperm chemotaxis in the presence of noise},
journal = {{PLOS} Computational Biology}
}Downloads
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- Sven Karol, Tobias Nett, Jeronimo Castrillon, Ivo F. Sbalzarini, "A Domain-Specific Language and Editor for Parallel Particle Methods", In ACM Transactions on Mathematical Software (TOMS), ACM, vol. 44, no. 3, pp. 32, New York, NY, USA, Mar 2018. [doi] [Bibtex & Downloads]
A Domain-Specific Language and Editor for Parallel Particle Methods
Reference
Sven Karol, Tobias Nett, Jeronimo Castrillon, Ivo F. Sbalzarini, "A Domain-Specific Language and Editor for Parallel Particle Methods", In ACM Transactions on Mathematical Software (TOMS), ACM, vol. 44, no. 3, pp. 32, New York, NY, USA, Mar 2018. [doi]
Abstract
Domain-specific languages (DSLs) are of increasing importance in scientific high-performance computing to reduce development costs, raise the level of abstraction and, thus, ease scientific programming. However, designing DSLs is not easy, as it requires knowledge of the application domain and experience in language engineering and compilers. Consequently, many DSLs follow a weak approach using macros or text generators, which lack many of the features that make a DSL comfortable for programmers. Some of these features –e.g., syntax highlighting, type inference, error reporting– are easily provided by language workbenches, which combine language engineering techniques and tools in a common ecosystem. In this paper, we present the Parallel Particle-Mesh Environment (PPME), a DSL and development environment for numerical simulations based on particle methods and hybrid particle-mesh methods. PPME uses the Meta Programming System (MPS), a projectional language workbench. PPME is the successor of the Parallel Particle-Mesh Language, a Fortran-based DSL that uses conventional implementation strategies. We analyze and compare both languages and demonstrate how the programmer’s experience is improved using static analyses and projectional editing, i.e., code-structure editing, constrained by syntax, as opposed to free-text editing. We present an explicit domain model for particle abstractions and the first formal type system for partircle methods.
Bibtex
@Article{karol_toms18,
author = {Karol, Sven and Nett, Tobias and Castrillon, Jeronimo and Sbalzarini, Ivo F.},
title = {A Domain-Specific Language and Editor for Parallel Particle Methods},
journal = {ACM Transactions on Mathematical Software (TOMS)},
issue_date = {March 2018},
volume = {44},
number = {3},
month = mar,
year = {2018},
issn = {0098-3500},
pages = {34:1--34:32},
articleno = {34},
numpages = {32},
url = {http://doi.acm.org/10.1145/3175659},
doi = {10.1145/3175659},
acmid = {3175659},
publisher = {ACM},
address = {New York, NY, USA},
pages = {32},
abstract = {
Domain-specific languages (DSLs) are of increasing importance in scientific high-performance computing to reduce development costs, raise the level of abstraction and, thus, ease scientific programming. However, designing DSLs is not easy, as it requires knowledge of the application domain and experience in language engineering and compilers. Consequently, many DSLs follow a weak approach using macros or text generators, which lack many of the features that make a DSL comfortable for programmers. Some of these features --e.g., syntax highlighting, type inference, error reporting-- are easily provided by language workbenches, which combine language engineering techniques and tools in a common ecosystem. In this paper, we present the Parallel Particle-Mesh Environment (PPME), a DSL and development environment for numerical simulations based on particle methods and hybrid particle-mesh methods. PPME uses the Meta Programming System (MPS), a projectional language workbench. PPME is the successor of the Parallel Particle-Mesh Language, a Fortran-based DSL that uses conventional implementation strategies. We analyze and compare both languages and demonstrate how the programmer’s experience is improved using static analyses and projectional editing, i.e., code-structure editing, constrained by syntax, as opposed to free-text editing. We present an explicit domain model for particle abstractions and the first formal type system for partircle methods.},
}Downloads
1709_Karol_TOMS-arxiv [PDF]
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- Adilson E. Motter, Marc Timme, "Antagonistic Phenomena in Network Dynamics", In Annual Review of Condensed Matter Physics, Annual Reviews, vol. 9, no. 1, pp. 463–484, Mar 2018. [doi] [Bibtex & Downloads]
Antagonistic Phenomena in Network Dynamics
Reference
Adilson E. Motter, Marc Timme, "Antagonistic Phenomena in Network Dynamics", In Annual Review of Condensed Matter Physics, Annual Reviews, vol. 9, no. 1, pp. 463–484, Mar 2018. [doi]
Bibtex
@article{Motter_2018,
doi = {10.1146/annurev-conmatphys-033117-054054},
url = {https://doi.org/10.1146%2Fannurev-conmatphys-033117-054054},
year = 2018,
month = {mar},
publisher = {Annual Reviews},
volume = {9},
number = {1},
pages = {463--484},
author = {Adilson E. Motter and Marc Timme},
title = {Antagonistic Phenomena in Network Dynamics},
journal = {Annual Review of Condensed Matter Physics}
}Downloads
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- Meik Dörpinghaus, Izaak Neri, Édgar Roldán, Heinrich Meyr, Frank Jülicher, "Testing Optimality of Sequential Decision-Making", 01/2018. [Bibtex & Downloads]
Testing Optimality of Sequential Decision-Making
Reference
Meik Dörpinghaus, Izaak Neri, Édgar Roldán, Heinrich Meyr, Frank Jülicher, "Testing Optimality of Sequential Decision-Making", 01/2018.
Bibtex
@article{article,
author = {Dörpinghaus, Meik and Neri, Izaak and Roldán, Édgar and Meyr, Heinrich and Jülicher, Frank},
year = {2018},
month = {01},
pages = {},
title = {Testing Optimality of Sequential Decision-Making},
url={https://arxiv.org/pdf/1801.01574.pdf}
}Downloads
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- Matthias Reis, Justus A. Kromer, Edda Klipp, "General solution of the chemical master equation and modality of marginal distributions for hierarchic first-order reaction networks", In Journal of Mathematical Biology, Springer Nature, vol. 77, no. 2, pp. 377–419, Jan 2018. [doi] [Bibtex & Downloads]
General solution of the chemical master equation and modality of marginal distributions for hierarchic first-order reaction networks
Reference
Matthias Reis, Justus A. Kromer, Edda Klipp, "General solution of the chemical master equation and modality of marginal distributions for hierarchic first-order reaction networks", In Journal of Mathematical Biology, Springer Nature, vol. 77, no. 2, pp. 377–419, Jan 2018. [doi]
Bibtex
@article{Reis_2018,
doi = {10.1007/s00285-018-1205-2},
url = {https://doi.org/10.1007%2Fs00285-018-1205-2},
year = 2018,
month = {jan},
publisher = {Springer Nature},
volume = {77},
number = {2},
pages = {377--419},
author = {Matthias Reis and Justus A. Kromer and Edda Klipp},
title = {General solution of the chemical master equation and modality of marginal distributions for hierarchic first-order reaction networks},
journal = {Journal of Mathematical Biology}
}Downloads
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- Benjamin Schäfer, Christian Beck, Kazuyuki Aihara, Dirk Witthaut, Marc Timme, "Non-Gaussian power grid frequency fluctuations characterized by Lévy-stable laws and superstatistics", In Nature Energy, Nature Publishing Group, vol. 3, no. 2, pp. 119–126, 2018. [Bibtex & Downloads]
Non-Gaussian power grid frequency fluctuations characterized by Lévy-stable laws and superstatistics
Reference
Benjamin Schäfer, Christian Beck, Kazuyuki Aihara, Dirk Witthaut, Marc Timme, "Non-Gaussian power grid frequency fluctuations characterized by Lévy-stable laws and superstatistics", In Nature Energy, Nature Publishing Group, vol. 3, no. 2, pp. 119–126, 2018.
Bibtex
@article{schafer2018non,
title={Non-Gaussian power grid frequency fluctuations characterized by L{\'e}vy-stable laws and superstatistics},
author={Sch{\"a}fer, Benjamin and Beck, Christian and Aihara, Kazuyuki and Witthaut, Dirk and Timme, Marc},
journal={Nature Energy},
volume={3},
number={2},
pages={119--126},
year={2018},
publisher={Nature Publishing Group}
}Downloads
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2017
- Jose Casadiego, Mor Nitzan, Sarah Hallerberg, Marc Timme, "Model-free inference of direct network interactions from nonlinear collective dynamics", In Nature Communications, Nature Publishing Group, vol. 8, no. 1, pp. 2192, 12/2017. [doi] [Bibtex & Downloads]
Model-free inference of direct network interactions from nonlinear collective dynamics
Reference
Jose Casadiego, Mor Nitzan, Sarah Hallerberg, Marc Timme, "Model-free inference of direct network interactions from nonlinear collective dynamics", In Nature Communications, Nature Publishing Group, vol. 8, no. 1, pp. 2192, 12/2017. [doi]
Abstract
Network dynamical systems can represent the interactions involved in the collective dynamics of gene regulatory networks or metabolic circuits. Here Casadiego et al. present a method for inferring these types of interactions directly from observed time series without relying on their model.
Bibtex
@article{casadiego2017model-free,
author = {Casadiego, Jose and Nitzan, Mor and Hallerberg, Sarah and Timme, Marc},
year = {2017},
title = {Model-free inference of direct network interactions from nonlinear collective dynamics},
journal = {Nature Communications},
publisher = {Nature Publishing Group},
issn = {2041-1723},
doi = {10.1038/s41467-017-02288-4},
volume = {8},
month = {12},
pages = {2192},
number = {1},
url = {http:https://doi.org/10.1038/s41467-017-02288-4},
abstract = {Network dynamical systems can represent the interactions involved in the collective dynamics of gene regulatory networks or metabolic circuits. Here Casadiego et al. present a method for inferring these types of interactions directly from observed time series without relying on their model.
}
}Downloads
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- S. Singh, É. Roldán, I. Neri, I. M. andGolubev Khaymovich, V. F. Maisi, J. T. andJülicher Peltonen, J. P. Pekola, "Records of entropy production in an electronic double dot", In ArXiv e-prints, Dec 2017. [Bibtex & Downloads]
Records of entropy production in an electronic double dot
Reference
S. Singh, É. Roldán, I. Neri, I. M. andGolubev Khaymovich, V. F. Maisi, J. T. andJülicher Peltonen, J. P. Pekola, "Records of entropy production in an electronic double dot", In ArXiv e-prints, Dec 2017.
Bibtex
@ARTICLE{2017arXiv171201693S,
author = {{Singh}, S. and {Rold{\'a}n}, {\'E}. and {Neri}, I. and {Khaymovich}, I.~M. and
{Golubev}, D.~S. and {Maisi}, V.~F. and {Peltonen}, J.~T. and
{J{\"u}licher}, F. and {Pekola}, J.~P.},
title = "{Records of entropy production in an electronic double dot}",
journal = {ArXiv e-prints},
archivePrefix = "arXiv",
eprint = {1712.01693},
primaryClass = "cond-mat.stat-mech",
keywords = {Condensed Matter - Statistical Mechanics, Condensed Matter - Mesoscale and Nanoscale Physics},
year = 2017,
month = dec,
adsurl = {http://adsabs.harvard.edu/abs/2017arXiv171201693S},
adsnote = {Provided by the SAO/NASA Astrophysics Data System}
}Downloads
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- Josué Nava-Sedeño, Haralambos Hatzikirou, Rainer Klages, Andreas Deutsch, "Cellular automaton models for time-correlated random walks: Derivation and analysis", vol. 7, 12/2017. [Bibtex & Downloads]
Cellular automaton models for time-correlated random walks: Derivation and analysis
Reference
Josué Nava-Sedeño, Haralambos Hatzikirou, Rainer Klages, Andreas Deutsch, "Cellular automaton models for time-correlated random walks: Derivation and analysis", vol. 7, 12/2017.
Bibtex
@article{article,
author = {Nava-Sedeño, Josué and Hatzikirou, Haralambos and Klages, Rainer and Deutsch, Andreas},
year = {2017},
month = {12},
pages = {},
title = {Cellular automaton models for time-correlated random walks: Derivation and analysis},
volume = {7},
booktitle = {Scientific Reports}
}Downloads
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- Ostrenko, Oleksandr AND Incardona, Pietro AND Ramaswamy, Rajesh AND Brusch, Lutz AND Sbalzarini, Ivo F., "pSSAlib: The partial-propensity stochastic chemical network simulator", In PLOS Computational Biology, Public Library of Science, vol. 13, no. 12, pp. 1-15, 12/2017. [doi] [Bibtex & Downloads]
pSSAlib: The partial-propensity stochastic chemical network simulator
Reference
Ostrenko, Oleksandr AND Incardona, Pietro AND Ramaswamy, Rajesh AND Brusch, Lutz AND Sbalzarini, Ivo F., "pSSAlib: The partial-propensity stochastic chemical network simulator", In PLOS Computational Biology, Public Library of Science, vol. 13, no. 12, pp. 1-15, 12/2017. [doi]
Abstract
Chemical reaction networks are ubiquitous in biology, and their dynamics is fundamentally stochastic. Here, we present the software library pSSAlib, which provides a complete and concise implementation of the most efficient partial-propensity methods for simulating exact stochastic chemical kinetics. pSSAlib can import models encoded in Systems Biology Markup Language, supports time delays in chemical reactions, and stochastic spatiotemporal reaction-diffusion systems. It also provides tools for statistical analysis of simulation results and supports multiple output formats. It has previously been used for studies of biochemical reaction pathways and to benchmark other stochastic simulation methods. Here, we describe pSSAlib in detail and apply it to a new model of the endocytic pathway in eukaryotic cells, leading to the discovery of a stochastic counterpart of the cut-out switch motif underlying early-to-late endosome conversion. pSSAlib is provided as a stand-alone command-line tool and as a developer API. We also provide a plug-in for the SBMLToolbox. The open-source code and pre-packaged installers are freely available from http://mosaic.mpi-cbg.de.
Bibtex
@article{10.1371/journal.pcbi.1005865,
author = {Ostrenko, Oleksandr AND Incardona, Pietro AND Ramaswamy, Rajesh AND Brusch, Lutz AND Sbalzarini, Ivo F.},
journal = {PLOS Computational Biology},
publisher = {Public Library of Science},
title = {pSSAlib: The partial-propensity stochastic chemical network simulator},
year = {2017},
month = {12},
volume = {13},
url = {https://doi.org/10.1371/journal.pcbi.1005865},
pages = {1-15},
abstract = {Chemical reaction networks are ubiquitous in biology, and their dynamics is fundamentally stochastic. Here, we present the software library pSSAlib, which provides a complete and concise implementation of the most efficient partial-propensity methods for simulating exact stochastic chemical kinetics. pSSAlib can import models encoded in Systems Biology Markup Language, supports time delays in chemical reactions, and stochastic spatiotemporal reaction-diffusion systems. It also provides tools for statistical analysis of simulation results and supports multiple output formats. It has previously been used for studies of biochemical reaction pathways and to benchmark other stochastic simulation methods. Here, we describe pSSAlib in detail and apply it to a new model of the endocytic pathway in eukaryotic cells, leading to the discovery of a stochastic counterpart of the cut-out switch motif underlying early-to-late endosome conversion. pSSAlib is provided as a stand-alone command-line tool and as a developer API. We also provide a plug-in for the SBMLToolbox. The open-source code and pre-packaged installers are freely available from http://mosaic.mpi-cbg.de.},
number = {12},
doi = {10.1371/journal.pcbi.1005865}
}Downloads
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- Katrin Talkenberger, Elisabetta Cavalcanti-Adam, Anja Voß-Böhme, Andreas Deutsch, "Amoeboid-mesenchymal migration plasticity promotes invasion only in complex heterogeneous microenvironments", vol. 7, 12/2017. [Bibtex & Downloads]
Amoeboid-mesenchymal migration plasticity promotes invasion only in complex heterogeneous microenvironments
Reference
Katrin Talkenberger, Elisabetta Cavalcanti-Adam, Anja Voß-Böhme, Andreas Deutsch, "Amoeboid-mesenchymal migration plasticity promotes invasion only in complex heterogeneous microenvironments", vol. 7, 12/2017.
Bibtex
@article{article,
author = {Talkenberger, Katrin and Cavalcanti-Adam, Elisabetta and Voß-Böhme, Anja and Deutsch, Andreas},
year = {2017},
month = {12},
pages = {},
title = {Amoeboid-mesenchymal migration plasticity promotes invasion only in complex heterogeneous microenvironments},
volume = {7},
booktitle = {Scientific Reports}
}Downloads
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- Josefine Asmus, Christian Müller, Ivo Sbalzarini, "L p -Adaptation: Simultaneous Design Centering and Robustness Estimation of Electronic and Biological Systems", vol. 7, 12/2017. [Bibtex & Downloads]
L p -Adaptation: Simultaneous Design Centering and Robustness Estimation of Electronic and Biological Systems
Reference
Josefine Asmus, Christian Müller, Ivo Sbalzarini, "L p -Adaptation: Simultaneous Design Centering and Robustness Estimation of Electronic and Biological Systems", vol. 7, 12/2017.
Bibtex
@article{article,
author = {Asmus, Josefine and Müller, Christian and Sbalzarini, Ivo},
year = {2017},
month = {12},
pages = {},
title = {L p -Adaptation: Simultaneous Design Centering and Robustness Estimation of Electronic and Biological Systems},
volume = {7},
booktitle = {Scientific Reports}
}Downloads
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- D. Aguilar Hidalgo, S. Werner, O. andGonzález-Gaitán Wartlick, B. Friedrich, F. Jülicher, "Dynamic gradient scaling as a critical point of growth control", In ArXiv e-prints, Nov 2017. [Bibtex & Downloads]
Dynamic gradient scaling as a critical point of growth control
Reference
D. Aguilar Hidalgo, S. Werner, O. andGonzález-Gaitán Wartlick, B. Friedrich, F. Jülicher, "Dynamic gradient scaling as a critical point of growth control", In ArXiv e-prints, Nov 2017.
Bibtex
@ARTICLE{2017arXiv171102021A,
author = {{Aguilar Hidalgo}, D. and {Werner}, S. and {Wartlick}, O. and
{Gonz{\'a}lez-Gait{\'a}n}, M. and {Friedrich}, B. and {J{\"u}licher}, F.
},
title = "{Dynamic gradient scaling as a critical point of growth control}",
journal = {ArXiv e-prints},
archivePrefix = "arXiv",
eprint = {1711.02021},
primaryClass = "physics.bio-ph",
keywords = {Physics - Biological Physics, Quantitative Biology - Cell Behavior, Quantitative Biology - Tissues and Organs},
year = 2017,
month = nov,
adsurl = {http://adsabs.harvard.edu/abs/2017arXiv171102021A},
adsnote = {Provided by the SAO/NASA Astrophysics Data System}
}Downloads
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- Simone Pigolotti, Izaak Neri, Édgar Roldán, Frank Jülicher, "Generic Properties of Stochastic Entropy Production", In Phys. Rev. Lett., American Physical Society, vol. 119, pp. 140604, Oct 2017. [doi] [Bibtex & Downloads]
Generic Properties of Stochastic Entropy Production
Reference
Simone Pigolotti, Izaak Neri, Édgar Roldán, Frank Jülicher, "Generic Properties of Stochastic Entropy Production", In Phys. Rev. Lett., American Physical Society, vol. 119, pp. 140604, Oct 2017. [doi]
Bibtex
@article{PhysRevLett.119.140604,
title = {Generic Properties of Stochastic Entropy Production},
author = {Pigolotti, Simone and Neri, Izaak and Rold\'an, \'Edgar and J\"ulicher, Frank},
journal = {Phys. Rev. Lett.},
volume = {119},
issue = {14},
pages = {140604},
numpages = {5},
year = {2017},
month = {Oct},
publisher = {American Physical Society},
doi = {10.1103/PhysRevLett.119.140604},
url = {https://link.aps.org/doi/10.1103/PhysRevLett.119.140604}
}Downloads
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- Benedict J. Lünsmann, Christoph Kirst, Marc Timme, "Transition to reconstructibility in weakly coupled networks", In PLOS ONE (Michal Zochowski), Public Library of Science (PLoS), vol. 12, no. 10, pp. e0186624, Oct 2017. [doi] [Bibtex & Downloads]
Transition to reconstructibility in weakly coupled networks
Reference
Benedict J. Lünsmann, Christoph Kirst, Marc Timme, "Transition to reconstructibility in weakly coupled networks", In PLOS ONE (Michal Zochowski), Public Library of Science (PLoS), vol. 12, no. 10, pp. e0186624, Oct 2017. [doi]
Bibtex
@article{L_nsmann_2017,
doi = {10.1371/journal.pone.0186624},
url = {https://doi.org/10.1371%2Fjournal.pone.0186624},
year = 2017,
month = {oct},
publisher = {Public Library of Science ({PLoS})},
volume = {12},
number = {10},
pages = {e0186624},
author = {Benedict J. Lünsmann and Christoph Kirst and Marc Timme},
editor = {Michal Zochowski},
title = {Transition to reconstructibility in weakly coupled networks},
journal = {{PLOS} {ONE}}
}Downloads
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- Sven Karol, Tobias Nett, Pietro Incardona, Nesrine Khouzami, Jeronimo Castrillon, Ivo F. Sbalzarini, "A Language and Development Environment for Parallel Particle Methods", Proceedings of the 5th International Conference on Particle-based Methods. Fundamentals and Applications PARTICLES 2017 (P. Wriggers and M. Bischoff and E. Oñate and D.R.J. Owen and T. Zohdi), Sep 2017. [Bibtex & Downloads]
A Language and Development Environment for Parallel Particle Methods
Reference
Sven Karol, Tobias Nett, Pietro Incardona, Nesrine Khouzami, Jeronimo Castrillon, Ivo F. Sbalzarini, "A Language and Development Environment for Parallel Particle Methods", Proceedings of the 5th International Conference on Particle-based Methods. Fundamentals and Applications PARTICLES 2017 (P. Wriggers and M. Bischoff and E. Oñate and D.R.J. Owen and T. Zohdi), Sep 2017.
Bibtex
@InProceedings{karol_particles17,
author = {Sven Karol and Tobias Nett and Pietro Incardona and Nesrine Khouzami and Jeronimo Castrillon and Ivo F. Sbalzarini},
title = {A Language and Development Environment for Parallel Particle Methods},
booktitle = {Proceedings of the 5th International Conference on Particle-based Methods. Fundamentals and Applications PARTICLES 2017},
year = {2017},
editor = {P. Wriggers and M. Bischoff and E. O{\~n}ate and D.R.J. Owen and T. Zohdi},
url = {https://www.semanticscholar.org/paper/A-Language-and-Development-Environment-for-Paralle-Karol-Nett/2b79bd3836aeb8e2fb2a2b5d9949f9efb1bdfab7?tab=abstract},
month = sep,
}Downloads
1709_Karol_particles [PDF]
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Biological Systems Path, Orchestration Path
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- Reher, Davidand Klink, Barbaraand Deutsch, Andreasand Voss-B"ohme, Anja, "Cell adhesion heterogeneity reinforces tumour cell dissemination: novel insights from a mathematical model", In Biology Direct, vol. 12, no. 1, pp. 18, Aug 2017. [doi] [Bibtex & Downloads]
Cell adhesion heterogeneity reinforces tumour cell dissemination: novel insights from a mathematical model
Reference
Reher, Davidand Klink, Barbaraand Deutsch, Andreasand Voss-B"ohme, Anja, "Cell adhesion heterogeneity reinforces tumour cell dissemination: novel insights from a mathematical model", In Biology Direct, vol. 12, no. 1, pp. 18, Aug 2017. [doi]
Abstract
Cancer cell invasion, dissemination, and metastasis have been linked to an epithelial-mesenchymal transition (EMT) of individual tumour cells. During EMT, adhesion molecules like E-cadherin are downregulated and the decrease of cell-cell adhesion allows tumour cells to dissociate from the primary tumour mass. This complex process depends on intracellular cues that are subject to genetic and epigenetic variability, as well as extrinsic cues from the local environment resulting in a spatial heterogeneity in the adhesive phenotype of individual tumour cells. Here, we use a novel mathematical model to study how adhesion heterogeneity, influenced by intrinsic and extrinsic factors, affects the dissemination of tumour cells from an epithelial cell population. The model is a multiscale cellular automaton that couples intracellular adhesion receptor regulation with cell-cell adhesion.
Bibtex
@Article{Reher2017,
author="Reher, David
and Klink, Barbara
and Deutsch, Andreas
and Voss-B{\"o}hme, Anja",
title="Cell adhesion heterogeneity reinforces tumour cell dissemination: novel insights from a mathematical model",
journal="Biology Direct",
year="2017",
month="Aug",
day="11",
volume="12",
number="1",
pages="18",
abstract="Cancer cell invasion, dissemination, and metastasis have been linked to an epithelial-mesenchymal transition (EMT) of individual tumour cells. During EMT, adhesion molecules like E-cadherin are downregulated and the decrease of cell-cell adhesion allows tumour cells to dissociate from the primary tumour mass. This complex process depends on intracellular cues that are subject to genetic and epigenetic variability, as well as extrinsic cues from the local environment resulting in a spatial heterogeneity in the adhesive phenotype of individual tumour cells. Here, we use a novel mathematical model to study how adhesion heterogeneity, influenced by intrinsic and extrinsic factors, affects the dissemination of tumour cells from an epithelial cell population. The model is a multiscale cellular automaton that couples intracellular adhesion receptor regulation with cell-cell adhesion.",
issn="1745-6150",
doi="10.1186/s13062-017-0188-z",
url="https://doi.org/10.1186/s13062-017-0188-z"
}Downloads
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- Debsankha Manik, Marc Timme, Dirk Witthaut, "Cycle flows and multistability in oscillatory networks", In Chaos: An Interdisciplinary Journal of Nonlinear Science, AIP Publishing, vol. 27, no. 8, pp. 083123, Aug 2017. [doi] [Bibtex & Downloads]
Cycle flows and multistability in oscillatory networks
Reference
Debsankha Manik, Marc Timme, Dirk Witthaut, "Cycle flows and multistability in oscillatory networks", In Chaos: An Interdisciplinary Journal of Nonlinear Science, AIP Publishing, vol. 27, no. 8, pp. 083123, Aug 2017. [doi]
Bibtex
@article{Manik_2017,
doi = {10.1063/1.4994177},
url = {https://doi.org/10.1063%2F1.4994177},
year = 2017,
month = {aug},
publisher = {{AIP} Publishing},
volume = {27},
number = {8},
pages = {083123},
author = {Debsankha Manik and Marc Timme and Dirk Witthaut},
title = {Cycle flows and multistability in oscillatory networks},
journal = {Chaos: An Interdisciplinary Journal of Nonlinear Science}
}Downloads
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- Malte Schröder, Marc Timme, Dirk Witthaut, "A universal order parameter for synchrony in networks of limit cycle oscillators", In Chaos: An Interdisciplinary Journal of Nonlinear Science, AIP Publishing, vol. 27, no. 7, pp. 073119, Jul 2017. [doi] [Bibtex & Downloads]
A universal order parameter for synchrony in networks of limit cycle oscillators
Reference
Malte Schröder, Marc Timme, Dirk Witthaut, "A universal order parameter for synchrony in networks of limit cycle oscillators", In Chaos: An Interdisciplinary Journal of Nonlinear Science, AIP Publishing, vol. 27, no. 7, pp. 073119, Jul 2017. [doi]
Bibtex
@article{Schr_der_2017,
doi = {10.1063/1.4995963},
url = {https://doi.org/10.1063%2F1.4995963},
year = 2017,
month = {jul},
publisher = {{AIP} Publishing},
volume = {27},
number = {7},
pages = {073119},
author = {Malte Schröder and Marc Timme and Dirk Witthaut},
title = {A universal order parameter for synchrony in networks of limit cycle oscillators},
journal = {Chaos: An Interdisciplinary Journal of Nonlinear Science}
}Downloads
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- Meik Dörpinghaus, Édgar Roldán, Izaak Neri, Heinrich Meyr, Frank Jülicher, "An information theoretic analysis of sequential decision-making", In Proceeding: IEEE International Symposium on Information Theory (ISIT), Aachen, Germany, June 2017. [Bibtex & Downloads]
An information theoretic analysis of sequential decision-making
Reference
Meik Dörpinghaus, Édgar Roldán, Izaak Neri, Heinrich Meyr, Frank Jülicher, "An information theoretic analysis of sequential decision-making", In Proceeding: IEEE International Symposium on Information Theory (ISIT), Aachen, Germany, June 2017.
Bibtex
@inproceedings{dorpinghaus2017information,
title={An information theoretic analysis of sequential decision-making},
author={D{\"o}rpinghaus, Meik and Rold{\'a}n, {\'E}dgar and Neri, Izaak and Meyr, Heinrich and J{\"u}licher, Frank},
booktitle={IEEE International Symposium on Information Theory (ISIT)},
address={Aachen, Germany},
month={June},
year={2017},
}Downloads
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- Gerald Hempel, Andrés Goens, Josefine Asmus, Jeronimo Castrillon, Ivo F. Sbalzarini, "Robust Mapping of Process Networks to Many-Core Systems Using Bio-Inspired Design Centering", Proceedings of the 20th International Workshop on Software and Compilers for Embedded Systems (SCOPES '17), ACM, pp. 21–30, New York, NY, USA, Jun 2017. [doi] [Bibtex & Downloads]
Robust Mapping of Process Networks to Many-Core Systems Using Bio-Inspired Design Centering
Reference
Gerald Hempel, Andrés Goens, Josefine Asmus, Jeronimo Castrillon, Ivo F. Sbalzarini, "Robust Mapping of Process Networks to Many-Core Systems Using Bio-Inspired Design Centering", Proceedings of the 20th International Workshop on Software and Compilers for Embedded Systems (SCOPES '17), ACM, pp. 21–30, New York, NY, USA, Jun 2017. [doi]
Bibtex
@InProceedings{hempel_scopes17,
author = {Gerald Hempel and Andr\'{e}s Goens and Josefine Asmus and Jeronimo Castrillon and Ivo F. Sbalzarini},
title = {Robust Mapping of Process Networks to Many-Core Systems Using Bio-Inspired Design Centering},
booktitle = {Proceedings of the 20th International Workshop on Software and Compilers for Embedded Systems (SCOPES '17)},
year = {2017},
series = {SCOPES '17},
pages = {21--30},
address = {New York, NY, USA},
month = jun,
publisher = {ACM},
acmid = {3078667},
doi = {10.1145/3078659.3078667},
isbn = {978-1-4503-5039-6},
location = {Sankt Goar, Germany},
numpages = {10},
url = {http://doi.acm.org/10.1145/3078659.3078667}
}Downloads
1706_Hempel_SCOPES [PDF]
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- Caterina Tomba, Céline Braini, Ghislain Bugnicourt, Floriane Cohen, Benjamin Friedrich, Nir Gov, Catherine Villard, "Geometrical Determinants of Neuronal Actin Waves", vol. 11, pp. 86, 03/2017. [Bibtex & Downloads]
Geometrical Determinants of Neuronal Actin Waves
Reference
Caterina Tomba, Céline Braini, Ghislain Bugnicourt, Floriane Cohen, Benjamin Friedrich, Nir Gov, Catherine Villard, "Geometrical Determinants of Neuronal Actin Waves", vol. 11, pp. 86, 03/2017.
Bibtex
@article{article,
author = {Tomba, Caterina and Braini, Céline and Bugnicourt, Ghislain and Cohen, Floriane and Friedrich, Benjamin and Gov, Nir and Villard, Catherine},
year = {2017},
month = {03},
pages = {86},
title = {Geometrical Determinants of Neuronal Actin Waves},
volume = {11},
booktitle = {Frontiers in Cellular Neuroscience}
}Downloads
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- Wetzel, Lucas AND Jörg, David J. AND Pollakis, Alexandros AND Rave, Wolfgang AND Fettweis, Gerhard AND Jülicher, Frank, "Self-organized synchronization of digital phase-locked loops with delayed coupling in theory and experiment", In PLOS ONE, Public Library of Science, vol. 12, no. 2, pp. 1-21, 02/2017. [doi] [Bibtex & Downloads]
Self-organized synchronization of digital phase-locked loops with delayed coupling in theory and experiment
Reference
Wetzel, Lucas AND Jörg, David J. AND Pollakis, Alexandros AND Rave, Wolfgang AND Fettweis, Gerhard AND Jülicher, Frank, "Self-organized synchronization of digital phase-locked loops with delayed coupling in theory and experiment", In PLOS ONE, Public Library of Science, vol. 12, no. 2, pp. 1-21, 02/2017. [doi]
Abstract
Self-organized synchronization occurs in a variety of natural and technical systems but has so far only attracted limited attention as an engineering principle. In distributed electronic systems, such as antenna arrays and multi-core processors, a common time reference is key to coordinate signal transmission and processing. Here we show how the self-organized synchronization of mutually coupled digital phase-locked loops (DPLLs) can provide robust clocking in large-scale systems. We develop a nonlinear phase description of individual and coupled DPLLs that takes into account filter impulse responses and delayed signal transmission. Our phase model permits analytical expressions for the collective frequencies of synchronized states, the analysis of stability properties and the time scale of synchronization. In particular, we find that signal filtering introduces stability transitions that are not found in systems without filtering. To test our theoretical predictions, we designed and carried out experiments using networks of off-the-shelf DPLL integrated circuitry. We show that the phase model can quantitatively predict the existence, frequency, and stability of synchronized states. Our results demonstrate that mutually delay-coupled DPLLs can provide robust and self-organized synchronous clocking in electronic systems.
Bibtex
@article{10.1371/journal.pone.0171590,
author = {Wetzel, Lucas AND Jörg, David J. AND Pollakis, Alexandros AND Rave, Wolfgang AND Fettweis, Gerhard AND Jülicher, Frank},
journal = {PLOS ONE},
publisher = {Public Library of Science},
title = {Self-organized synchronization of digital phase-locked loops with delayed coupling in theory and experiment},
year = {2017},
month = {02},
volume = {12},
url = {https://doi.org/10.1371/journal.pone.0171590},
pages = {1-21},
abstract = {Self-organized synchronization occurs in a variety of natural and technical systems but has so far only attracted limited attention as an engineering principle. In distributed electronic systems, such as antenna arrays and multi-core processors, a common time reference is key to coordinate signal transmission and processing. Here we show how the self-organized synchronization of mutually coupled digital phase-locked loops (DPLLs) can provide robust clocking in large-scale systems. We develop a nonlinear phase description of individual and coupled DPLLs that takes into account filter impulse responses and delayed signal transmission. Our phase model permits analytical expressions for the collective frequencies of synchronized states, the analysis of stability properties and the time scale of synchronization. In particular, we find that signal filtering introduces stability transitions that are not found in systems without filtering. To test our theoretical predictions, we designed and carried out experiments using networks of off-the-shelf DPLL integrated circuitry. We show that the phase model can quantitatively predict the existence, frequency, and stability of synchronized states. Our results demonstrate that mutually delay-coupled DPLLs can provide robust and self-organized synchronous clocking in electronic systems.},
number = {2},
doi = {10.1371/journal.pone.0171590}
}Downloads
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- Cordula Reuther, Matthäus Mittasch, Sundar R. Naganathan, Stephan W. Grill, Stefan Diez, "Highly-Efficient Guiding of Motile Microtubules on Non-Topographical Motor Patterns", In Nano Letters, vol. 17, no. 9, pp. 5699-5705, 2017. [doi] [Bibtex & Downloads]
Highly-Efficient Guiding of Motile Microtubules on Non-Topographical Motor Patterns
Reference
Cordula Reuther, Matthäus Mittasch, Sundar R. Naganathan, Stephan W. Grill, Stefan Diez, "Highly-Efficient Guiding of Motile Microtubules on Non-Topographical Motor Patterns", In Nano Letters, vol. 17, no. 9, pp. 5699-5705, 2017. [doi]
Bibtex
@article{doi:10.1021/acs.nanolett.7b02606,
author = {Reuther, Cordula and Mittasch, Matthäus and Naganathan, Sundar R. and Grill, Stephan W. and Diez, Stefan},
title = {Highly-Efficient Guiding of Motile Microtubules on Non-Topographical Motor Patterns},
journal = {Nano Letters},
volume = {17},
number = {9},
pages = {5699-5705},
year = {2017},
doi = {10.1021/acs.nanolett.7b02606},
note ={PMID: 28819981},
URL = {
http://dx.doi.org/10.1021/acs.nanolett.7b02606
},
eprint = {
http://dx.doi.org/10.1021/acs.nanolett.7b02606
}
}Downloads
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- J. C. L. Alfonso, K. Talkenberger, M. Seifert, B. Klink, A. Hawkins-Daarud, K. R. Swanson, H. Hatzikirou, A. Deutsch, "The biology and mathematical modelling of glioma invasion: a review", In Journal of The Royal Society Interface, The Royal Society, vol. 14, no. 136, 2017. [doi] [Bibtex & Downloads]
The biology and mathematical modelling of glioma invasion: a review
Reference
J. C. L. Alfonso, K. Talkenberger, M. Seifert, B. Klink, A. Hawkins-Daarud, K. R. Swanson, H. Hatzikirou, A. Deutsch, "The biology and mathematical modelling of glioma invasion: a review", In Journal of The Royal Society Interface, The Royal Society, vol. 14, no. 136, 2017. [doi]
Abstract
Adult gliomas are aggressive brain tumours associated with low patient survival rates and limited life expectancy. The most important hallmark of this type of tumour is its invasive behaviour, characterized by a markedly phenotypic plasticity, infiltrative tumour morphologies and the ability of malignant progression from low- to high-grade tumour types. Indeed, the widespread infiltration of healthy brain tissue by glioma cells is largely responsible for poor prognosis and the difficulty of finding curative therapies. Meanwhile, mathematical models have been established to analyse potential mechanisms of glioma invasion. In this review, we start with a brief introduction to current biological knowledge about glioma invasion, and then critically review and highlight future challenges for mathematical models of glioma invasion.
Bibtex
@article {Alfonso20170490,
author = {Alfonso, J. C. L. and Talkenberger, K. and Seifert, M. and Klink, B. and Hawkins-Daarud, A. and Swanson, K. R. and Hatzikirou, H. and Deutsch, A.},
title = {The biology and mathematical modelling of glioma invasion: a review},
volume = {14},
number = {136},
year = {2017},
doi = {10.1098/rsif.2017.0490},
publisher = {The Royal Society},
abstract = {Adult gliomas are aggressive brain tumours associated with low patient survival rates and limited life expectancy. The most important hallmark of this type of tumour is its invasive behaviour, characterized by a markedly phenotypic plasticity, infiltrative tumour morphologies and the ability of malignant progression from low- to high-grade tumour types. Indeed, the widespread infiltration of healthy brain tissue by glioma cells is largely responsible for poor prognosis and the difficulty of finding curative therapies. Meanwhile, mathematical models have been established to analyse potential mechanisms of glioma invasion. In this review, we start with a brief introduction to current biological knowledge about glioma invasion, and then critically review and highlight future challenges for mathematical models of glioma invasion.},
issn = {1742-5689},
URL = {http://rsif.royalsocietypublishing.org/content/14/136/20170490},
eprint = {http://rsif.royalsocietypublishing.org/content/14/136/20170490.full.pdf},
journal = {Journal of The Royal Society Interface}
}Downloads
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- Karl B. Hoffmann, Anja Voss-Böhme, Jochen C. Rink, Lutz Brusch, "A dynamically diluted alignment model reveals the impact of cell turnover on the plasticity of tissue polarity patterns", In Journal of The Royal Society Interface, The Royal Society, vol. 14, no. 135, 2017. [doi] [Bibtex & Downloads]
A dynamically diluted alignment model reveals the impact of cell turnover on the plasticity of tissue polarity patterns
Reference
Karl B. Hoffmann, Anja Voss-Böhme, Jochen C. Rink, Lutz Brusch, "A dynamically diluted alignment model reveals the impact of cell turnover on the plasticity of tissue polarity patterns", In Journal of The Royal Society Interface, The Royal Society, vol. 14, no. 135, 2017. [doi]
Abstract
The polarization of cells and tissues is fundamental for tissue morphogenesis during biological development and regeneration. A deeper understanding of biological polarity pattern formation can be gained from the consideration of pattern reorganization in response to an opposing instructive cue, which we here consider using the example of experimentally inducible body axis inversions in planarian flatworms. We define a dynamically diluted alignment model linking three processes: entrainment of cell polarity by a global signal, local cell\textendashcell coupling aligning polarity among neighbours, and cell turnover replacing polarized cells by initially unpolarized cells. We show that a persistent global orienting signal determines the final mean polarity orientation in this stochastic model. Combining numerical and analytical approaches, we find that neighbour coupling retards polarity pattern reorganization, whereas cell turnover accelerates it. We derive a formula for an effective neighbour coupling strength integrating both effects and find that the time of polarity reorganization depends linearly on this effective parameter and no abrupt transitions are observed. This allows us to determine neighbour coupling strengths from experimental observations. Our model is related to a dynamic 8-Potts model with annealed site-dilution and makes testable predictions regarding the polarization of dynamic systems, such as the planarian epithelium.
Bibtex
@article {Hoffmann20170466,
author = {Hoffmann, Karl B. and Voss-B{\"o}hme, Anja and Rink, Jochen C. and Brusch, Lutz},
title = {A dynamically diluted alignment model reveals the impact of cell turnover on the plasticity of tissue polarity patterns},
volume = {14},
number = {135},
year = {2017},
doi = {10.1098/rsif.2017.0466},
publisher = {The Royal Society},
abstract = {The polarization of cells and tissues is fundamental for tissue morphogenesis during biological development and regeneration. A deeper understanding of biological polarity pattern formation can be gained from the consideration of pattern reorganization in response to an opposing instructive cue, which we here consider using the example of experimentally inducible body axis inversions in planarian flatworms. We define a dynamically diluted alignment model linking three processes: entrainment of cell polarity by a global signal, local cell{\textendash}cell coupling aligning polarity among neighbours, and cell turnover replacing polarized cells by initially unpolarized cells. We show that a persistent global orienting signal determines the final mean polarity orientation in this stochastic model. Combining numerical and analytical approaches, we find that neighbour coupling retards polarity pattern reorganization, whereas cell turnover accelerates it. We derive a formula for an effective neighbour coupling strength integrating both effects and find that the time of polarity reorganization depends linearly on this effective parameter and no abrupt transitions are observed. This allows us to determine neighbour coupling strengths from experimental observations. Our model is related to a dynamic 8-Potts model with annealed site-dilution and makes testable predictions regarding the polarization of dynamic systems, such as the planarian epithelium.},
issn = {1742-5689},
URL = {http://rsif.royalsocietypublishing.org/content/14/135/20170466},
eprint = {http://rsif.royalsocietypublishing.org/content/14/135/20170466.full.pdf},
journal = {Journal of The Royal Society Interface}
}Downloads
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- Kirstin Meyer, Oleksandr Ostrenko, Georgios Bourantas, Hernan Morales-Navarrete, Natalie Porat-Shliom, Fabian Segovia-Miranda, Hidenori Nonaka, Ali Ghaemi, Jean-Marc Verbavatz, Lutz Brusch, Ivo Sbalzarini, Yannis Kalaidzidis, Roberto Weigert, Marino Zerial, "A Predictive 3D Multi-Scale Model of Biliary Fluid Dynamics in the Liver Lobule", In Cell Systems, vol. 4, no. 3, pp. 277 - 290.e9, 2017. [doi] [Bibtex & Downloads]
A Predictive 3D Multi-Scale Model of Biliary Fluid Dynamics in the Liver Lobule
Reference
Kirstin Meyer, Oleksandr Ostrenko, Georgios Bourantas, Hernan Morales-Navarrete, Natalie Porat-Shliom, Fabian Segovia-Miranda, Hidenori Nonaka, Ali Ghaemi, Jean-Marc Verbavatz, Lutz Brusch, Ivo Sbalzarini, Yannis Kalaidzidis, Roberto Weigert, Marino Zerial, "A Predictive 3D Multi-Scale Model of Biliary Fluid Dynamics in the Liver Lobule", In Cell Systems, vol. 4, no. 3, pp. 277 - 290.e9, 2017. [doi]
Bibtex
@article{MEYER2017277,
title = "A Predictive 3D Multi-Scale Model of Biliary Fluid Dynamics in the Liver Lobule",
journal = "Cell Systems",
volume = "4",
number = "3",
pages = "277 - 290.e9",
year = "2017",
issn = "2405-4712",
doi = "https://doi.org/10.1016/j.cels.2017.02.008",
url = "http://www.sciencedirect.com/science/article/pii/S2405471217300522",
author = "Kirstin Meyer and Oleksandr Ostrenko and Georgios Bourantas and Hernan Morales-Navarrete and Natalie Porat-Shliom and Fabian Segovia-Miranda and Hidenori Nonaka and Ali Ghaemi and Jean-Marc Verbavatz and Lutz Brusch and Ivo Sbalzarini and Yannis Kalaidzidis and Roberto Weigert and Marino Zerial",
keywords = "mouse liver, bile canaliculi, multi-scale model, computational fluid dynamics, bile flow, actomyosin contractility, peristalsis, drug-induced liver injury, cholestasis, acetaminophen"
}Downloads
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- Tom Stückemann, James Patrick Cleland, Steffen Werner, Hanh Thi-Kim Vu, Robert Bayersdorf, Shang-Yun Liu, Benjamin Friedrich, Frank Jülicher, Jochen Christian Rink, "Antagonistic Self-Organizing Patterning Systems Control Maintenance and Regeneration of the Anteroposterior Axis in Planarians", In Developmental Cell, vol. 40, no. 3, pp. 248 - 263.e4, 2017. [doi] [Bibtex & Downloads]
Antagonistic Self-Organizing Patterning Systems Control Maintenance and Regeneration of the Anteroposterior Axis in Planarians
Reference
Tom Stückemann, James Patrick Cleland, Steffen Werner, Hanh Thi-Kim Vu, Robert Bayersdorf, Shang-Yun Liu, Benjamin Friedrich, Frank Jülicher, Jochen Christian Rink, "Antagonistic Self-Organizing Patterning Systems Control Maintenance and Regeneration of the Anteroposterior Axis in Planarians", In Developmental Cell, vol. 40, no. 3, pp. 248 - 263.e4, 2017. [doi]
Bibtex
@article{STUCKEMANN2017248,
title = "Antagonistic Self-Organizing Patterning Systems Control Maintenance and Regeneration of the Anteroposterior Axis in Planarians",
journal = "Developmental Cell",
volume = "40",
number = "3",
pages = "248 - 263.e4",
year = "2017",
issn = "1534-5807",
doi = "https://doi.org/10.1016/j.devcel.2016.12.024",
url = "http://www.sciencedirect.com/science/article/pii/S153458071630956X",
author = "Tom Stückemann and James Patrick Cleland and Steffen Werner and Hanh Thi-Kim Vu and Robert Bayersdorf and Shang-Yun Liu and Benjamin Friedrich and Frank Jülicher and Jochen Christian Rink",
keywords = "planaria, Wnt signaling, regeneration, patterning, self-organization, morphogen gradient, Turing pattern"
}Downloads
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- Gary S Klindt, Christian Ruloff, Christian Wagner, Benjamin M Friedrich, "In-phase and anti-phase flagellar synchronization by waveform compliance and basal coupling", In New Journal of Physics, vol. 19, no. 11, pp. 113052, 2017. [Bibtex & Downloads]
In-phase and anti-phase flagellar synchronization by waveform compliance and basal coupling
Reference
Gary S Klindt, Christian Ruloff, Christian Wagner, Benjamin M Friedrich, "In-phase and anti-phase flagellar synchronization by waveform compliance and basal coupling", In New Journal of Physics, vol. 19, no. 11, pp. 113052, 2017.
Abstract
We present a theory of flagellar synchronization in the green alga Chlamydomonas , using full treatment of flagellar hydrodynamics and measured beat patterns. We find that two recently proposed synchronization mechanisms, flagellar waveform compliance and basal coupling, stabilize anti-phase synchronization (AP) if operative in isolation. Their nonlinear superposition, however, can stabilize in-phase synchronization (IP) for suitable parameter choices, matching experimental observations. Our theory is based on a description of the flagellar beat as a limit-cycle oscillator, which was introduced and calibrated by experimental data in a recent letter (Klindt et al 2016 Phys. Rev. Lett. 117 258101). Using a minimal model of basal coupling, we identify regimes of IP, AP and even out-of-phase synchronization with spontaneous symmetry-breaking in this system of two identical coupled oscillators as a function of an effective strength of basal coupling. From our theory, we quantitatively predict different synchronization dynamics in fluids of increased viscosity or external flow, suggesting a non-invasive way to control synchronization by hydrodynamic coupling.
Bibtex
@article{1367-2630-19-11-113052,
author={Gary S Klindt and Christian Ruloff and Christian Wagner and Benjamin M Friedrich},
title={In-phase and anti-phase flagellar synchronization by waveform compliance and basal coupling},
journal={New Journal of Physics},
volume={19},
number={11},
pages={113052},
url={http://stacks.iop.org/1367-2630/19/i=11/a=113052},
year={2017},
abstract={We present a theory of flagellar synchronization in the green alga Chlamydomonas , using full treatment of flagellar hydrodynamics and measured beat patterns. We find that two recently proposed synchronization mechanisms, flagellar waveform compliance and basal coupling, stabilize anti-phase synchronization (AP) if operative in isolation. Their nonlinear superposition, however, can stabilize in-phase synchronization (IP) for suitable parameter choices, matching experimental observations. Our theory is based on a description of the flagellar beat as a limit-cycle oscillator, which was introduced and calibrated by experimental data in a recent letter (Klindt et al 2016 Phys. Rev. Lett. 117 258101). Using a minimal model of basal coupling, we identify regimes of IP, AP and even out-of-phase synchronization with spontaneous symmetry-breaking in this system of two identical coupled oscillators as a function of an effective strength of basal coupling. From our theory, we quantitatively predict different synchronization dynamics in fluids of increased viscosity or external flow, suggesting a non-invasive way to control synchronization by hydrodynamic coupling.}
}Downloads
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- Izaak Neri, Édgar Roldán, Frank Jülicher, "Statistics of Infima and Stopping Times of Entropy Production and Applications to Active Molecular Processes", In Physical Review X, APS, vol. 7, no. 1, pp. 011019, 2017. [Bibtex & Downloads]
Statistics of Infima and Stopping Times of Entropy Production and Applications to Active Molecular Processes
Reference
Izaak Neri, Édgar Roldán, Frank Jülicher, "Statistics of Infima and Stopping Times of Entropy Production and Applications to Active Molecular Processes", In Physical Review X, APS, vol. 7, no. 1, pp. 011019, 2017.
Bibtex
@article{neri2017statistics,
title={Statistics of Infima and Stopping Times of Entropy Production and Applications to Active Molecular Processes},
author={Neri, Izaak and Rold{\'a}n, {\'E}dgar and J{\"u}licher, Frank},
journal={Physical Review X},
volume={7},
number={1},
pages={011019},
year={2017},
publisher={APS}
}Downloads
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- Samata Chaudhuri, Till Korten, Stefan Diez, "Tetrazine–trans-cyclooctene Mediated Conjugation of Antibodies to Microtubules Facilitates Subpicomolar Protein Detection", In Bioconjugate Chemistry, ACS Publications, vol. 28, no. 4, pp. 918–922, 2017. [Bibtex & Downloads]
Tetrazine–trans-cyclooctene Mediated Conjugation of Antibodies to Microtubules Facilitates Subpicomolar Protein Detection
Reference
Samata Chaudhuri, Till Korten, Stefan Diez, "Tetrazine–trans-cyclooctene Mediated Conjugation of Antibodies to Microtubules Facilitates Subpicomolar Protein Detection", In Bioconjugate Chemistry, ACS Publications, vol. 28, no. 4, pp. 918–922, 2017.
Bibtex
@article{chaudhuri2017tetrazine,
title={Tetrazine--trans-cyclooctene Mediated Conjugation of Antibodies to Microtubules Facilitates Subpicomolar Protein Detection},
author={Chaudhuri, Samata and Korten, Till and Diez, Stefan},
journal={Bioconjugate Chemistry},
volume={28},
number={4},
pages={918--922},
year={2017},
publisher={ACS Publications}
}Downloads
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- Justus A Kromer, Steffen Märcker, Steffen Lange, Christel Baier, Benjamin M Friedrich, "Optimal decision making for sperm chemotaxis in the presence of noise", In arXiv preprint arXiv:1711.04858, 2017. [Bibtex & Downloads]
Optimal decision making for sperm chemotaxis in the presence of noise
Reference
Justus A Kromer, Steffen Märcker, Steffen Lange, Christel Baier, Benjamin M Friedrich, "Optimal decision making for sperm chemotaxis in the presence of noise", In arXiv preprint arXiv:1711.04858, 2017.
Bibtex
@article{kromer2017optimal,
title={Optimal decision making for sperm chemotaxis in the presence of noise},
author={Kromer, Justus A and M{\"a}rcker, Steffen and Lange, Steffen and Baier, Christel and Friedrich, Benjamin M},
journal={arXiv preprint arXiv:1711.04858},
year={2017}
}Downloads
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- Benjamin M Friedrich, "The load response of shape-changing microswimmers scales with their energy efficiency", In arXiv preprint arXiv:1711.03597, 2017. [Bibtex & Downloads]
The load response of shape-changing microswimmers scales with their energy efficiency
Reference
Benjamin M Friedrich, "The load response of shape-changing microswimmers scales with their energy efficiency", In arXiv preprint arXiv:1711.03597, 2017.
Bibtex
@article{friedrich2017load,
title={The load response of shape-changing microswimmers scales with their energy efficiency},
author={Friedrich, Benjamin M},
journal={arXiv preprint arXiv:1711.03597},
year={2017}
}Downloads
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- Jens Karschau, Marco Zimmerling, Benjamin M Friedrich, "Renormalization group theory for percolation in time-varying networks", In arXiv preprint arXiv:1708.05704, 2017. [Bibtex & Downloads]
Renormalization group theory for percolation in time-varying networks
Reference
Jens Karschau, Marco Zimmerling, Benjamin M Friedrich, "Renormalization group theory for percolation in time-varying networks", In arXiv preprint arXiv:1708.05704, 2017.
Bibtex
@article{karschau2017renormalization,
title={Renormalization group theory for percolation in time-varying networks},
author={Karschau, Jens and Zimmerling, Marco and Friedrich, Benjamin M},
journal={arXiv preprint arXiv:1708.05704},
year={2017}
}Downloads
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2016
- Gary S. Klindt, Christian Ruloff, Christian Wagner, Benjamin M. Friedrich, "Load Response of the Flagellar Beat", In Phys. Rev. Lett., American Physical Society, vol. 117, pp. 258101, Dec 2016. [doi] [Bibtex & Downloads]
Load Response of the Flagellar Beat
Reference
Gary S. Klindt, Christian Ruloff, Christian Wagner, Benjamin M. Friedrich, "Load Response of the Flagellar Beat", In Phys. Rev. Lett., American Physical Society, vol. 117, pp. 258101, Dec 2016. [doi]
Bibtex
@article{PhysRevLett.117.258101,
title = {Load Response of the Flagellar Beat},
author = {Klindt, Gary S. and Ruloff, Christian and Wagner, Christian and Friedrich, Benjamin M.},
journal = {Phys. Rev. Lett.},
volume = {117},
issue = {25},
pages = {258101},
numpages = {5},
year = {2016},
month = {Dec},
publisher = {American Physical Society},
doi = {10.1103/PhysRevLett.117.258101},
url = {http://link.aps.org/doi/10.1103/PhysRevLett.117.258101}
}Downloads
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- Fabian Rost, Aida Rodrigo Albors, Vladimir Mazurov, Lutz Brusch, Andreas Deutsch, Elly M Tanaka, Osvaldo Chara, "Accelerated cell divisions drive the outgrowth of the regenerating spinal cord in axolotls", In eLife (Bronner, Marianne), eLife Sciences Publications, Ltd, vol. 5, pp. e20357, Nov 2016. [doi] [Bibtex & Downloads]
Accelerated cell divisions drive the outgrowth of the regenerating spinal cord in axolotls
Reference
Fabian Rost, Aida Rodrigo Albors, Vladimir Mazurov, Lutz Brusch, Andreas Deutsch, Elly M Tanaka, Osvaldo Chara, "Accelerated cell divisions drive the outgrowth of the regenerating spinal cord in axolotls", In eLife (Bronner, Marianne), eLife Sciences Publications, Ltd, vol. 5, pp. e20357, Nov 2016. [doi]
Abstract
Axolotls are unique in their ability to regenerate the spinal cord. However, the mechanisms that underlie this phenomenon remain poorly understood. Previously, we showed that regenerating stem cells in the axolotl spinal cord revert to a molecular state resembling embryonic neuroepithelial cells and functionally acquire rapid proliferative divisions (Rodrigo Albors et al., 2015). Here, we refine the analysis of cell proliferation in space and time and identify a high-proliferation zone in the regenerating spinal cord that shifts posteriorly over time. By tracking sparsely-labeled cells, we also quantify cell influx into the regenerate. Taking a mathematical modeling approach, we integrate these quantitative datasets of cell proliferation, neural stem cell activation and cell influx, to predict regenerative tissue outgrowth. Our model shows that while cell influx and neural stem cell activation play a minor role, the acceleration of the cell cycle is the major driver of regenerative spinal cord outgrowth in axolotls.
Bibtex
@article {10.7554/eLife.20357,
article_type = {journal},
title = {Accelerated cell divisions drive the outgrowth of the regenerating spinal cord in axolotls},
author = {Rost, Fabian and Rodrigo Albors, Aida and Mazurov, Vladimir and Brusch, Lutz and Deutsch, Andreas and Tanaka, Elly M and Chara, Osvaldo},
editor = {Bronner, Marianne},
volume = 5,
year = 2016,
month = {nov},
pub_date = {2016-11-25},
pages = {e20357},
citation = {eLife 2016;5:e20357},
doi = {10.7554/eLife.20357},
url = {https://doi.org/10.7554/eLife.20357},
abstract = {Axolotls are unique in their ability to regenerate the spinal cord. However, the mechanisms that underlie this phenomenon remain poorly understood. Previously, we showed that regenerating stem cells in the axolotl spinal cord revert to a molecular state resembling embryonic neuroepithelial cells and functionally acquire rapid proliferative divisions (Rodrigo Albors et al., 2015). Here, we refine the analysis of cell proliferation in space and time and identify a high-proliferation zone in the regenerating spinal cord that shifts posteriorly over time. By tracking sparsely-labeled cells, we also quantify cell influx into the regenerate. Taking a mathematical modeling approach, we integrate these quantitative datasets of cell proliferation, neural stem cell activation and cell influx, to predict regenerative tissue outgrowth. Our model shows that while cell influx and neural stem cell activation play a minor role, the acceleration of the cell cycle is the major driver of regenerative spinal cord outgrowth in axolotls.},
keywords = {regeneration, modeling, cell proliferation, axolotl},
journal = {eLife},
issn = {2050-084X},
publisher = {eLife Sciences Publications, Ltd},
}Downloads
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- J. C. L. Alfonso, A. Köhn-Luque, T. andFeuerhake Stylianopoulos, A. Deutsch, H. Hatzikirou, "Why one-size-fits-all vaso-modulatory interventions fail to control glioma invasion: in silico insights", In Scientific Reports, vol. 6, pp. 37283, Nov 2016. [doi] [Bibtex & Downloads]
Why one-size-fits-all vaso-modulatory interventions fail to control glioma invasion: in silico insights
Reference
J. C. L. Alfonso, A. Köhn-Luque, T. andFeuerhake Stylianopoulos, A. Deutsch, H. Hatzikirou, "Why one-size-fits-all vaso-modulatory interventions fail to control glioma invasion: in silico insights", In Scientific Reports, vol. 6, pp. 37283, Nov 2016. [doi]
Bibtex
@ARTICLE{2016NatSR...637283A,
author = {{Alfonso}, J.~C.~L. and {K{\"o}hn-Luque}, A. and {Stylianopoulos}, T. and
{Feuerhake}, F. and {Deutsch}, A. and {Hatzikirou}, H.},
title = "{Why one-size-fits-all vaso-modulatory interventions fail to control glioma invasion: in silico insights}",
journal = {Scientific Reports},
archivePrefix = "arXiv",
eprint = {1604.05082},
primaryClass = "q-bio.TO",
year = 2016,
month = nov,
volume = 6,
eid = {37283},
pages = {37283},
doi = {10.1038/srep37283},
adsurl = {http://adsabs.harvard.edu/abs/2016NatSR...637283A},
adsnote = {Provided by the SAO/NASA Astrophysics Data System}
}Downloads
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- J. Alfonso, Nadine Schaadt, Ralf Schönmeyer, N. Brieu, Germain Forestier, Cédric Wemmert, F. Feuerhake, Haralambos Hatzikirou, "In-silico insights on the prognostic potential of immune cell infiltration patterns in the breast lobular epithelium", vol. 6, 10/2016. [Bibtex & Downloads]
In-silico insights on the prognostic potential of immune cell infiltration patterns in the breast lobular epithelium
Reference
J. Alfonso, Nadine Schaadt, Ralf Schönmeyer, N. Brieu, Germain Forestier, Cédric Wemmert, F. Feuerhake, Haralambos Hatzikirou, "In-silico insights on the prognostic potential of immune cell infiltration patterns in the breast lobular epithelium", vol. 6, 10/2016.
Bibtex
@article{article,
author = {Alfonso, J and Schaadt, Nadine and Schönmeyer, Ralf and Brieu, N and Forestier, Germain and Wemmert, Cédric and Feuerhake, F and Hatzikirou, Haralambos},
year = {2016},
month = {10},
pages = {},
title = {In-silico insights on the prognostic potential of immune cell infiltration patterns in the breast lobular epithelium},
volume = {6},
booktitle = {Scientific Reports}
}Downloads
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- Andreas I. Reppas, Georgios Lolas, Andreas Deutsch, Haralampos Hatzikirou, "The Extrinsic Noise Effect on Lateral Inhibition Differentiation Waves", In ACM Trans. Model. Comput. Simul., ACM, vol. 26, no. 3, pp. 19:1–19:18, New York, NY, USA, Jan 2016. [doi] [Bibtex & Downloads]
The Extrinsic Noise Effect on Lateral Inhibition Differentiation Waves
Reference
Andreas I. Reppas, Georgios Lolas, Andreas Deutsch, Haralampos Hatzikirou, "The Extrinsic Noise Effect on Lateral Inhibition Differentiation Waves", In ACM Trans. Model. Comput. Simul., ACM, vol. 26, no. 3, pp. 19:1–19:18, New York, NY, USA, Jan 2016. [doi]
Bibtex
@article{Reppas:2016:ENE:2876000.2832908,
author = {Reppas, Andreas I. and Lolas, Georgios and Deutsch, Andreas and Hatzikirou, Haralampos},
title = {The Extrinsic Noise Effect on Lateral Inhibition Differentiation Waves},
journal = {ACM Trans. Model. Comput. Simul.},
issue_date = {February 2016},
volume = {26},
number = {3},
month = jan,
year = {2016},
issn = {1049-3301},
pages = {19:1--19:18},
articleno = {19},
numpages = {18},
url = {http://doi.acm.org/10.1145/2832908},
doi = {10.1145/2832908},
acmid = {2832908},
publisher = {ACM},
address = {New York, NY, USA},
keywords = {Cellular automata, cell fate, differentiation wave, noise, notch/delta},
}Downloads
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- Matthias Grube, "Silicon Nanowires: Pushing Energy Storage Capacity in Li Based Battery Systems", In Proceeding: 18th International Meeting on Lithium Batteries (June 19-24, 2016), 2016. [Bibtex & Downloads]
Silicon Nanowires: Pushing Energy Storage Capacity in Li Based Battery Systems
Reference
Matthias Grube, "Silicon Nanowires: Pushing Energy Storage Capacity in Li Based Battery Systems", In Proceeding: 18th International Meeting on Lithium Batteries (June 19-24, 2016), 2016.
Bibtex
@inproceedings{grube2016silicon,
title={Silicon Nanowires: Pushing Energy Storage Capacity in Li Based Battery Systems},
author={Grube, Matthias},
booktitle={18th International Meeting on Lithium Batteries (June 19-24, 2016)},
year={2016},
organization={Ecs}
}Downloads
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Silicon Nanowire Path, Silicon Nanowire Path, Silicon Nanowire Path, Biological Systems Path
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- Aniruddha Mitra, Felix Ruhnow, Salvatore Girardo, Diez Stefan, "Three-Dimensional Motility of the Highly Processive Kinesin-8 Along the Microtubule Lattice", In Biophysical Journal, Elsevier, vol. 110, no. 3, pp. 461a, 2016. [Bibtex & Downloads]
Three-Dimensional Motility of the Highly Processive Kinesin-8 Along the Microtubule Lattice
Reference
Aniruddha Mitra, Felix Ruhnow, Salvatore Girardo, Diez Stefan, "Three-Dimensional Motility of the Highly Processive Kinesin-8 Along the Microtubule Lattice", In Biophysical Journal, Elsevier, vol. 110, no. 3, pp. 461a, 2016.
Bibtex
@article{mitra2016three,
title={Three-Dimensional Motility of the Highly Processive Kinesin-8 Along the Microtubule Lattice},
author={Mitra, Aniruddha and Ruhnow, Felix and Girardo, Salvatore and Stefan, Diez},
journal={Biophysical Journal},
volume={110},
number={3},
pages={461a},
year={2016},
publisher={Elsevier}
}Downloads
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Biomolecular-Assembled Circuits Path, Biomolecular-Assembled Circuits Path, Biological Systems Path, Biomolecular-Assembled Circuits Path
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- Henrik Klessig, David Öhmann, Andreas I Reppas, Haralampos Hatzikirou, Majid Abedi, Meryem Simsek, Gerhard P Fettweis, "From immune cells to self-organizing ultra-dense small cell networks", In IEEE Journal on Selected Areas in Communications, IEEE, vol. 34, no. 4, pp. 800–811, 2016. [Bibtex & Downloads]
From immune cells to self-organizing ultra-dense small cell networks
Reference
Henrik Klessig, David Öhmann, Andreas I Reppas, Haralampos Hatzikirou, Majid Abedi, Meryem Simsek, Gerhard P Fettweis, "From immune cells to self-organizing ultra-dense small cell networks", In IEEE Journal on Selected Areas in Communications, IEEE, vol. 34, no. 4, pp. 800–811, 2016.
Bibtex
@article{klessig2016immune,
title={From immune cells to self-organizing ultra-dense small cell networks},
author={Klessig, Henrik and {\"O}hmann, David and Reppas, Andreas I and Hatzikirou, Haralampos and Abedi, Majid and Simsek, Meryem and Fettweis, Gerhard P},
journal={IEEE Journal on Selected Areas in Communications},
volume={34},
number={4},
pages={800--811},
year={2016},
publisher={IEEE}
}Downloads
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Biological Systems Path, Biological Systems Path, Biological Systems Path
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- Veikko F. Geyer, Pablo Sartori, Benjamin M. Friedrich, Frank Jülicher, Jonathon Howard, "Independent control of the static and dynamic components of the Chlamydomonas flagellar beat", In Curr. Biol., vol. 26, pp. 1098–1103, 2016. [doi] [Bibtex & Downloads]
Independent control of the static and dynamic components of the Chlamydomonas flagellar beat
Reference
Veikko F. Geyer, Pablo Sartori, Benjamin M. Friedrich, Frank Jülicher, Jonathon Howard, "Independent control of the static and dynamic components of the Chlamydomonas flagellar beat", In Curr. Biol., vol. 26, pp. 1098–1103, 2016. [doi]
Bibtex
@article{Geyer:2016,
author = {Geyer, Veikko F. and Sartori, Pablo and Friedrich, Benjamin M. and J\"{u}licher, Frank and Howard, Jonathon},
doi = {10.1016/j.cub.2016.02.053},
issn = {09609822},
journal = {Curr. Biol.},
pages = {1098--1103},
title = ,
volume = {26},
year = {2016}
}Downloads
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- B M Friedrich, "Hydrodynamic synchronization of flagellar oscillators", In Eur. Phys. J. Special Topics, vol. 225, pp. 2353–2368, 2016. [doi] [Bibtex & Downloads]
Hydrodynamic synchronization of flagellar oscillators
Reference
B M Friedrich, "Hydrodynamic synchronization of flagellar oscillators", In Eur. Phys. J. Special Topics, vol. 225, pp. 2353–2368, 2016. [doi]
Bibtex
@article{Friedrich2016,
author = {Friedrich, B M},
doi = {10.1140/epjst/e2016-60056-4},
journal = {Eur. Phys. J. Special Topics},
pages = {2353–2368},
title = ,
volume = {225},
year = {2016}
}Downloads
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- G. S. Klindt, Ruloff C., Wagner C., B. M. Friedrich, "The load-response of the flagellar beat", In Phys. Rev. Lett., vol. in press, 2016. [Bibtex & Downloads]
The load-response of the flagellar beat
Reference
G. S. Klindt, Ruloff C., Wagner C., B. M. Friedrich, "The load-response of the flagellar beat", In Phys. Rev. Lett., vol. in press, 2016.
Bibtex
@article{Klindt2016,
author = {Klindt, G. S. and Ruloff C. and Wagner C. and Friedrich, B. M.},
journal = {Phys. Rev. Lett.},
title = ,
volume = {in press},
year = {2016}
}Downloads
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- Édgar Roldán, Ana Lisica, Daniel Sánchez-Taltavull, Stephan W Grill, "Stochastic resetting in backtrack recovery by RNA polymerases", In Physical Review E, APS, vol. 93, no. 6, pp. 062411, 2016. [Bibtex & Downloads]
Stochastic resetting in backtrack recovery by RNA polymerases
Reference
Édgar Roldán, Ana Lisica, Daniel Sánchez-Taltavull, Stephan W Grill, "Stochastic resetting in backtrack recovery by RNA polymerases", In Physical Review E, APS, vol. 93, no. 6, pp. 062411, 2016.
Bibtex
@article{roldan2016stochastic,
title={Stochastic resetting in backtrack recovery by RNA polymerases},
author={Rold{\'a}n, {\'E}dgar and Lisica, Ana and S{\'a}nchez-Taltavull, Daniel and Grill, Stephan W},
journal={Physical Review E},
volume={93},
number={6},
pages={062411},
year={2016},
publisher={APS}
}Downloads
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Biological Systems Path, other
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- Ana Lisica, Christoph Engel, Marcus Jahnel, Édgar Roldán, Eric A Galburt, Patrick Cramer, Stephan W Grill, "Mechanisms of backtrack recovery by RNA polymerases I and II", In Proceedings of the National Academy of Sciences, National Acad Sciences, vol. 113, no. 11, pp. 2946–2951, 2016. [Bibtex & Downloads]
Mechanisms of backtrack recovery by RNA polymerases I and II
Reference
Ana Lisica, Christoph Engel, Marcus Jahnel, Édgar Roldán, Eric A Galburt, Patrick Cramer, Stephan W Grill, "Mechanisms of backtrack recovery by RNA polymerases I and II", In Proceedings of the National Academy of Sciences, National Acad Sciences, vol. 113, no. 11, pp. 2946–2951, 2016.
Bibtex
@article{lisica2016mechanisms,
title={Mechanisms of backtrack recovery by RNA polymerases I and II},
author={Lisica, Ana and Engel, Christoph and Jahnel, Marcus and Rold{\'a}n, {\'E}dgar and Galburt, Eric A and Cramer, Patrick and Grill, Stephan W},
journal={Proceedings of the National Academy of Sciences},
volume={113},
number={11},
pages={2946--2951},
year={2016},
publisher={National Acad Sciences}
}Downloads
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Biological Systems Path, other, Biological Systems Path
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- Yuanhao Gong, Ivo F Sbalzarini, "A Natural-Scene Gradient Distribution Prior and its Application in Light-Microscopy Image Processing", In IEEE Journal of Selected Topics in Signal Processing, IEEE, vol. 10, no. 1, pp. 99–114, 2016. [Bibtex & Downloads]
A Natural-Scene Gradient Distribution Prior and its Application in Light-Microscopy Image Processing
Reference
Yuanhao Gong, Ivo F Sbalzarini, "A Natural-Scene Gradient Distribution Prior and its Application in Light-Microscopy Image Processing", In IEEE Journal of Selected Topics in Signal Processing, IEEE, vol. 10, no. 1, pp. 99–114, 2016.
Bibtex
@article{gong2016natural,
title={A Natural-Scene Gradient Distribution Prior and its Application in Light-Microscopy Image Processing},
author={Gong, Yuanhao and Sbalzarini, Ivo F},
journal={IEEE Journal of Selected Topics in Signal Processing},
volume={10},
number={1},
pages={99--114},
year={2016},
publisher={IEEE}
}Downloads
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Biological Systems Path, Biological Systems Path
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- Georgi Stoychev, Cordula Reuther, Stefan Diez, Leonid Ionov, "Controlled Retention and Release of Biomolecular Transport Systems Using Shape-Changing Polymer Bilayers", In Angewandte Chemie, vol. 128, no. 52, pp. 16340–16343, 2016. [doi] [Bibtex & Downloads]
Controlled Retention and Release of Biomolecular Transport Systems Using Shape-Changing Polymer Bilayers
Reference
Georgi Stoychev, Cordula Reuther, Stefan Diez, Leonid Ionov, "Controlled Retention and Release of Biomolecular Transport Systems Using Shape-Changing Polymer Bilayers", In Angewandte Chemie, vol. 128, no. 52, pp. 16340–16343, 2016. [doi]
Bibtex
@article {ANGE:ANGE201608299,
author = {Stoychev, Georgi and Reuther, Cordula and Diez, Stefan and Ionov, Leonid},
title = {Controlled Retention and Release of Biomolecular Transport Systems Using Shape-Changing Polymer Bilayers},
journal = {Angewandte Chemie},
volume = {128},
number = {52},
issn = {1521-3757},
url = {http://dx.doi.org/10.1002/ange.201608299},
doi = {10.1002/ange.201608299},
pages = {16340--16343},
keywords = {Hydrogele, Motorproteine, Selbstfaltung, Transport von Biomolekülen},
year = {2016},
}Downloads
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- David J Jörg, Andrew C Oates, Frank Jülicher, "Sequential pattern formation governed by signaling gradients", In Physical Biology, IOP Publishing, vol. 13, no. 5, pp. 05LT03, 2016. [Bibtex & Downloads]
Sequential pattern formation governed by signaling gradients
Reference
David J Jörg, Andrew C Oates, Frank Jülicher, "Sequential pattern formation governed by signaling gradients", In Physical Biology, IOP Publishing, vol. 13, no. 5, pp. 05LT03, 2016.
Bibtex
@article{jorg2016sequential,
title={Sequential pattern formation governed by signaling gradients},
author={J{\"o}rg, David J and Oates, Andrew C and J{\"u}licher, Frank},
journal={Physical Biology},
volume={13},
number={5},
pages={05LT03},
year={2016},
publisher={IOP Publishing}
}Downloads
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- DH Murray, M. Jahnel, J. Lauer, MJ Avellaneda, N. Brouilly, A. Cezanne, H. Morales-Navarrete, ED Perini, C. Ferguson, AN Lupas, Y. Kalaidzidis, RG Parton, SW Grill, M. Zerial, "An endosomal tether undergoes an entropic collapse to bring vesicles together." , In Nature, vol. 537, no. 5, pp. 107-111, 2016-09-01 00:00:00.0. [doi] [Bibtex & Downloads]
An endosomal tether undergoes an entropic collapse to bring vesicles together.
Reference
DH Murray, M. Jahnel, J. Lauer, MJ Avellaneda, N. Brouilly, A. Cezanne, H. Morales-Navarrete, ED Perini, C. Ferguson, AN Lupas, Y. Kalaidzidis, RG Parton, SW Grill, M. Zerial, "An endosomal tether undergoes an entropic collapse to bring vesicles together." , In Nature, vol. 537, no. 5, pp. 107-111, 2016-09-01 00:00:00.0. [doi]
Bibtex
@Article{27556945,
AUTHOR = { Murray, DH and Jahnel, M and Lauer, J and Avellaneda, MJ and Brouilly, N and Cezanne, A and Morales-Navarrete, H and Perini, ED and Ferguson, C and Lupas, AN and Kalaidzidis, Y and Parton, RG and Grill, SW and Zerial, M },
TITLE = {An endosomal tether undergoes an entropic collapse to bring vesicles together.},
JOURNAL = {Nature},
VOLUME = {537},
YEAR = {2016-09-01 00:00:00.0},
NUMBER = {5},
PAGES = {107-111},
DOI = {10.1038/nature19326},
ISSN = {},
}
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- Rahul Grover, Janine Fischer, Friedrich W. Schwarz, Wilhelm J. Walter, Petra Schwille, Stefan Diez, "Transport efficiency of membrane-anchored kinesin-1 motors depends on motor density and diffusivity", In Proceedings of the National Academy of Sciences, vol. 113, no. 46, pp. E7185-E7193, 2016. [doi] [Bibtex & Downloads]
Transport efficiency of membrane-anchored kinesin-1 motors depends on motor density and diffusivity
Reference
Rahul Grover, Janine Fischer, Friedrich W. Schwarz, Wilhelm J. Walter, Petra Schwille, Stefan Diez, "Transport efficiency of membrane-anchored kinesin-1 motors depends on motor density and diffusivity", In Proceedings of the National Academy of Sciences, vol. 113, no. 46, pp. E7185-E7193, 2016. [doi]
Abstract
In eukaryotic cells, membranous vesicles and organelles are transported by ensembles of motor proteins. These motors, such as kinesin-1, have been well characterized in vitro as single molecules or as ensembles rigidly attached to nonbiological substrates. However, the collective transport by membrane-anchored motors, that is, motors attached to a fluid lipid bilayer, is poorly understood. Here, we investigate the influence of motors’ anchorage to a lipid bilayer on the collective transport characteristics. We reconstituted “membrane-anchored” gliding motility assays using truncated kinesin-1 motors with a streptavidin-binding peptide tag that can attach to streptavidin-loaded, supported lipid bilayers. We found that the diffusing kinesin-1 motors propelled the microtubules in the presence of ATP. Notably, we found the gliding velocity of the microtubules to be strongly dependent on the number of motors and their diffusivity in the lipid bilayer. The microtubule gliding velocity increased with increasing motor density and membrane viscosity, reaching up to the stepping velocity of single motors. This finding is in contrast to conventional gliding motility assays where the density of surface-immobilized kinesin-1 motors does not influence the microtubule velocity over a wide range. We reason that the transport efficiency of membrane-anchored motors is reduced because of their slippage in the lipid bilayer, an effect that we directly observed using single-molecule fluorescence microscopy. Our results illustrate the importance of motor–cargo coupling, which potentially provides cells with an additional means of regulating the efficiency of cargo transport.
Bibtex
@article{Grover15112016,
author = {Grover, Rahul and Fischer, Janine and Schwarz, Friedrich W. and Walter, Wilhelm J. and Schwille, Petra and Diez, Stefan},
title = {Transport efficiency of membrane-anchored kinesin-1 motors depends on motor density and diffusivity},
volume = {113},
number = {46},
pages = {E7185-E7193},
year = {2016},
doi = {10.1073/pnas.1611398113},
abstract ={In eukaryotic cells, membranous vesicles and organelles are transported by ensembles of motor proteins. These motors, such as kinesin-1, have been well characterized in vitro as single molecules or as ensembles rigidly attached to nonbiological substrates. However, the collective transport by membrane-anchored motors, that is, motors attached to a fluid lipid bilayer, is poorly understood. Here, we investigate the influence of motors’ anchorage to a lipid bilayer on the collective transport characteristics. We reconstituted “membrane-anchored” gliding motility assays using truncated kinesin-1 motors with a streptavidin-binding peptide tag that can attach to streptavidin-loaded, supported lipid bilayers. We found that the diffusing kinesin-1 motors propelled the microtubules in the presence of ATP. Notably, we found the gliding velocity of the microtubules to be strongly dependent on the number of motors and their diffusivity in the lipid bilayer. The microtubule gliding velocity increased with increasing motor density and membrane viscosity, reaching up to the stepping velocity of single motors. This finding is in contrast to conventional gliding motility assays where the density of surface-immobilized kinesin-1 motors does not influence the microtubule velocity over a wide range. We reason that the transport efficiency of membrane-anchored motors is reduced because of their slippage in the lipid bilayer, an effect that we directly observed using single-molecule fluorescence microscopy. Our results illustrate the importance of motor–cargo coupling, which potentially provides cells with an additional means of regulating the efficiency of cargo transport.},
URL = {http://www.pnas.org/content/113/46/E7185.abstract},
eprint = {http://www.pnas.org/content/113/46/E7185.full.pdf},
journal = {Proceedings of the National Academy of Sciences}
}Downloads
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- George C. Bourantas, Bevan L. Cheeseman, Rajesh Ramaswamy, Ivo F. Sbalzarini, "Using DC PSE operator discretization in Eulerian meshless collocation methods improves their robustness in complex geometries", In Computers & Fluids, vol. 136, pp. 285 - 300, 2016. [doi] [Bibtex & Downloads]
Using DC PSE operator discretization in Eulerian meshless collocation methods improves their robustness in complex geometries
Reference
George C. Bourantas, Bevan L. Cheeseman, Rajesh Ramaswamy, Ivo F. Sbalzarini, "Using DC PSE operator discretization in Eulerian meshless collocation methods improves their robustness in complex geometries", In Computers & Fluids, vol. 136, pp. 285 - 300, 2016. [doi]
Bibtex
@article{BOURANTAS2016285,
title = "Using DC PSE operator discretization in Eulerian meshless collocation methods improves their robustness in complex geometries",
journal = "Computers & Fluids",
volume = "136",
pages = "285 - 300",
year = "2016",
issn = "0045-7930",
doi = "https://doi.org/10.1016/j.compfluid.2016.06.010",
url = "http://www.sciencedirect.com/science/article/pii/S0045793016301955",
author = "George C. Bourantas and Bevan L. Cheeseman and Rajesh Ramaswamy and Ivo F. Sbalzarini",
keywords = "Incompressible steady state, DC PSE, MLS, Meshless point collocation, Particle methods, Complex geometry, Velocity-correction, Discretization correction"
}Downloads
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- Siqi Ling, Wieland Marth, Simon Praetorius, Axel Voigt, "An adaptive finite element multi-mesh approach for interacting deformable objects in flow", In Computational Methods in Applied Mathematics, vol. 16, no. 3, pp. 475–484, 2016. [Bibtex & Downloads]
An adaptive finite element multi-mesh approach for interacting deformable objects in flow
Reference
Siqi Ling, Wieland Marth, Simon Praetorius, Axel Voigt, "An adaptive finite element multi-mesh approach for interacting deformable objects in flow", In Computational Methods in Applied Mathematics, vol. 16, no. 3, pp. 475–484, 2016.
Bibtex
@article{ling2016adaptive,
title={An adaptive finite element multi-mesh approach for interacting deformable objects in flow},
author={Ling, Siqi and Marth, Wieland and Praetorius, Simon and Voigt, Axel},
journal={Computational Methods in Applied Mathematics},
volume={16},
number={3},
pages={475--484},
year={2016}
}Downloads
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2015
- Katrin Böttger, Haralambos Hatzikirou, Anja Voss-Böhme, Elisabetta Ada Cavalcanti-Adam, Miguel A Herrero, Andreas Deutsch, "An emerging allee effect is critical for tumor initiation and persistence", In PLoS computational biology, Public Library of Science, vol. 11, no. 9, pp. e1004366, 2015. [Bibtex & Downloads]
An emerging allee effect is critical for tumor initiation and persistence
Reference
Katrin Böttger, Haralambos Hatzikirou, Anja Voss-Böhme, Elisabetta Ada Cavalcanti-Adam, Miguel A Herrero, Andreas Deutsch, "An emerging allee effect is critical for tumor initiation and persistence", In PLoS computational biology, Public Library of Science, vol. 11, no. 9, pp. e1004366, 2015.
Bibtex
@article{bottger2015emerging,
title={An emerging allee effect is critical for tumor initiation and persistence},
author={B{\"o}ttger, Katrin and Hatzikirou, Haralambos and Voss-B{\"o}hme, Anja and Cavalcanti-Adam, Elisabetta Ada and Herrero, Miguel A and Deutsch, Andreas},
journal={PLoS computational biology},
volume={11},
number={9},
pages={e1004366},
year={2015},
publisher={Public Library of Science}
}Downloads
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- Osvaldo Chara, Lutz Brusch, "Mathematical modelling of fluid transport and its regulation at multiple scales", In Biosystems, Elsevier, vol. 130, pp. 1–10, 2015. [Bibtex & Downloads]
Mathematical modelling of fluid transport and its regulation at multiple scales
Reference
Osvaldo Chara, Lutz Brusch, "Mathematical modelling of fluid transport and its regulation at multiple scales", In Biosystems, Elsevier, vol. 130, pp. 1–10, 2015.
Bibtex
@article{chara2015mathematical,
title={Mathematical modelling of fluid transport and its regulation at multiple scales},
author={Chara, Osvaldo and Brusch, Lutz},
journal={Biosystems},
volume={130},
pages={1--10},
year={2015},
publisher={Elsevier}
}Downloads
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- Shasha Feng, Michel Ludwig, Dirk Walther, "The Logical Difference for EL: From Terminologies Towards TBoxes.", In Proceeding: IWOST-1, pp. 31–41, 2015. [Bibtex & Downloads]
The Logical Difference for EL: From Terminologies Towards TBoxes.
Reference
Shasha Feng, Michel Ludwig, Dirk Walther, "The Logical Difference for EL: From Terminologies Towards TBoxes.", In Proceeding: IWOST-1, pp. 31–41, 2015.
Bibtex
@inproceedings{feng2015logical,
title={The Logical Difference for EL: From Terminologies Towards TBoxes.},
author={Feng, Shasha and Ludwig, Michel and Walther, Dirk},
booktitle={IWOST-1},
pages={31--41},
year={2015}
}Downloads
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- Thai Son Doan, Anke Kalauch, Markus Klose, Stefan Siegmund, "Stability of positive linear switched systems on ordered Banach spaces", In Systems & Control Letters, Elsevier, vol. 75, pp. 14–19, 2015. [Bibtex & Downloads]
Stability of positive linear switched systems on ordered Banach spaces
Reference
Thai Son Doan, Anke Kalauch, Markus Klose, Stefan Siegmund, "Stability of positive linear switched systems on ordered Banach spaces", In Systems & Control Letters, Elsevier, vol. 75, pp. 14–19, 2015.
Bibtex
@article{doan2015stability,
title={Stability of positive linear switched systems on ordered Banach spaces},
author={Doan, Thai Son and Kalauch, Anke and Klose, Markus and Siegmund, Stefan},
journal={Systems \& Control Letters},
volume={75},
pages={14--19},
year={2015},
publisher={Elsevier}
}Downloads
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- Édgar Roldán, Izaak Neri, Meik Dörpinghaus, Heinrich Meyr, Frank Jülicher, "Decision making in the arrow of time", In Physical Review Letters, APS, vol. 115, no. 25, pp. 250602, 2015. [Bibtex & Downloads]
Decision making in the arrow of time
Reference
Édgar Roldán, Izaak Neri, Meik Dörpinghaus, Heinrich Meyr, Frank Jülicher, "Decision making in the arrow of time", In Physical Review Letters, APS, vol. 115, no. 25, pp. 250602, 2015.
Bibtex
@article{roldan2015decision,
title={Decision making in the arrow of time},
author={Rold{\'a}n, {\'E}dgar and Neri, Izaak and D{\"o}rpinghaus, Meik and Meyr, Heinrich and J{\"u}licher, Frank},
journal={Physical Review Letters},
publisher={APS},
volume={115},
number={25},
pages={250602},
year={2015},
}Downloads
DecisionArrow15 [PDF]
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- David J Jorg, Alexandros Pollakis, Lucas Wetzel, Marvin Dropp, Wolfgang Rave, Frank Julicher, Gerhard Fettweis, "Synchronization of mutually coupled digital PLLs in massive MIMO systems", In Proceeding: Communications (ICC), 2015 IEEE International Conference on, pp. 1716–1721, 2015. [Bibtex & Downloads]
Synchronization of mutually coupled digital PLLs in massive MIMO systems
Reference
David J Jorg, Alexandros Pollakis, Lucas Wetzel, Marvin Dropp, Wolfgang Rave, Frank Julicher, Gerhard Fettweis, "Synchronization of mutually coupled digital PLLs in massive MIMO systems", In Proceeding: Communications (ICC), 2015 IEEE International Conference on, pp. 1716–1721, 2015.
Bibtex
@inproceedings{jorg2015synchronization,
title={Synchronization of mutually coupled digital PLLs in massive MIMO systems},
author={Jorg, David J and Pollakis, Alexandros and Wetzel, Lucas and Dropp, Marvin and Rave, Wolfgang and Julicher, Frank and Fettweis, Gerhard},
booktitle={Communications (ICC), 2015 IEEE International Conference on},
pages={1716--1721},
year={2015},
organization={IEEE}
}Downloads
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- A. Ramirez-Torres, R. Rodriguez-Ramos, J. Merodio, J. Bravo-Castillero, R. Guinovart-Diaz, JCL Alfonso, "Mathematical modeling of anisotropic avascular tumor growth", In Mechanics Research Communications, Elsevier, vol. 69, pp. 8–14, 2015. [Bibtex & Downloads]
Mathematical modeling of anisotropic avascular tumor growth
Reference
A. Ramirez-Torres, R. Rodriguez-Ramos, J. Merodio, J. Bravo-Castillero, R. Guinovart-Diaz, JCL Alfonso, "Mathematical modeling of anisotropic avascular tumor growth", In Mechanics Research Communications, Elsevier, vol. 69, pp. 8–14, 2015.
Bibtex
@article{ramirez2015mathematical,
title={Mathematical modeling of anisotropic avascular tumor growth},
author={Ramirez-Torres, A and Rodriguez-Ramos, R and Merodio, J and Bravo-Castillero, J and Guinovart-Diaz, R and Alfonso, JCL},
journal={Mechanics Research Communications},
volume={69},
pages={8--14},
year={2015},
publisher={Elsevier}
}Downloads
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- Sebastian Aland, Haralambos Hatzikirou, John Lowengrub, Axel Voigt, "A Mechanistic Collective Cell Model for Epithelial Colony Growth and Contact Inhibition", In Biophysical journal, Elsevier, vol. 109, no. 7, pp. 1347–1357, 2015. [Bibtex & Downloads]
A Mechanistic Collective Cell Model for Epithelial Colony Growth and Contact Inhibition
Reference
Sebastian Aland, Haralambos Hatzikirou, John Lowengrub, Axel Voigt, "A Mechanistic Collective Cell Model for Epithelial Colony Growth and Contact Inhibition", In Biophysical journal, Elsevier, vol. 109, no. 7, pp. 1347–1357, 2015.
Bibtex
@article{aland2015mechanistic,
title={A Mechanistic Collective Cell Model for Epithelial Colony Growth and Contact Inhibition},
author={Aland, Sebastian and Hatzikirou, Haralambos and Lowengrub, John and Voigt, Axel},
journal={Biophysical journal},
volume={109},
number={7},
pages={1347--1357},
year={2015},
publisher={Elsevier}
}Downloads
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- David J Jörg, "Nonlinear transient waves in coupled phase oscillators with inertia", In Chaos: An Interdisciplinary Journal of Nonlinear Science, AIP Publishing, vol. 25, no. 5, pp. 053106, 2015. [Bibtex & Downloads]
Nonlinear transient waves in coupled phase oscillators with inertia
Reference
David J Jörg, "Nonlinear transient waves in coupled phase oscillators with inertia", In Chaos: An Interdisciplinary Journal of Nonlinear Science, AIP Publishing, vol. 25, no. 5, pp. 053106, 2015.
Bibtex
@article{jorg2015nonlinear,
title={Nonlinear transient waves in coupled phase oscillators with inertia},
author={J{\"o}rg, David J},
journal={Chaos: An Interdisciplinary Journal of Nonlinear Science},
volume={25},
number={5},
pages={053106},
year={2015},
publisher={AIP Publishing}
}Downloads
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- A. Ramírez-Torres, R. Rodríguez-Ramos, J. Merodio, J. Bravo-Castillero, R. Guinovart-Díaz, JCL Alfonso, "Action of body forces in tumor growth", In International Journal of Engineering Science, Elsevier, vol. 89, pp. 18–34, 2015. [Bibtex & Downloads]
Action of body forces in tumor growth
Reference
A. Ramírez-Torres, R. Rodríguez-Ramos, J. Merodio, J. Bravo-Castillero, R. Guinovart-Díaz, JCL Alfonso, "Action of body forces in tumor growth", In International Journal of Engineering Science, Elsevier, vol. 89, pp. 18–34, 2015.
Bibtex
@article{ramirez2015action,
title={Action of body forces in tumor growth},
author={Ram{\'\i}rez-Torres, A and Rodr{\'\i}guez-Ramos, R and Merodio, J and Bravo-Castillero, J and Guinovart-D{\'\i}az, R and Alfonso, JCL},
journal={International Journal of Engineering Science},
volume={89},
pages={18--34},
year={2015},
publisher={Elsevier}
}Downloads
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- H. Hatzikirou, JCL Alfonso, S. Mühle, C. Stern, S. Weiss, Michael Meyer-Hermann, "Cancer therapeutic potential of combinatorial immuno-and vasomodulatory interventions", In Journal of The Royal Society Interface, The Royal Society, vol. 12, no. 112, pp. 20150439, 2015. [Bibtex & Downloads]
Cancer therapeutic potential of combinatorial immuno-and vasomodulatory interventions
Reference
H. Hatzikirou, JCL Alfonso, S. Mühle, C. Stern, S. Weiss, Michael Meyer-Hermann, "Cancer therapeutic potential of combinatorial immuno-and vasomodulatory interventions", In Journal of The Royal Society Interface, The Royal Society, vol. 12, no. 112, pp. 20150439, 2015.
Bibtex
@article{hatzikirou2015cancer,
title={Cancer therapeutic potential of combinatorial immuno-and vasomodulatory interventions},
author={Hatzikirou, H and Alfonso, JCL and M{\"u}hle, S and Stern, C and Weiss, S and Meyer-Hermann, Michael},
journal={Journal of The Royal Society Interface},
volume={12},
number={112},
pages={20150439},
year={2015},
publisher={The Royal Society}
}Downloads
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- Jieying Chen, Michel Ludwig, Yue Ma, Dirk Walther, "Towards Extracting Ontology Excerpts", In Proceeding: International Conference on Knowledge Science, Engineering and Management, pp. 78–89, 2015. [Bibtex & Downloads]
Towards Extracting Ontology Excerpts
Reference
Jieying Chen, Michel Ludwig, Yue Ma, Dirk Walther, "Towards Extracting Ontology Excerpts", In Proceeding: International Conference on Knowledge Science, Engineering and Management, pp. 78–89, 2015.
Bibtex
@inproceedings{chen2015towards,
title={Towards Extracting Ontology Excerpts},
author={Chen, Jieying and Ludwig, Michel and Ma, Yue and Walther, Dirk},
booktitle={International Conference on Knowledge Science, Engineering and Management},
pages={78--89},
year={2015},
organization={Springer}
}Downloads
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Biological Systems Path, Silicon Nanowire Path
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- Andreas Deutsch, "Cellular automaton models for collective cell behaviour", In Proceeding: International Workshop on Cellular Automata and Discrete Complex Systems, pp. 1–10, 2015. [Bibtex & Downloads]
Cellular automaton models for collective cell behaviour
Reference
Andreas Deutsch, "Cellular automaton models for collective cell behaviour", In Proceeding: International Workshop on Cellular Automata and Discrete Complex Systems, pp. 1–10, 2015.
Bibtex
@inproceedings{deutsch2015cellular,
title={Cellular automaton models for collective cell behaviour},
author={Deutsch, Andreas},
booktitle={International Workshop on Cellular Automata and Discrete Complex Systems},
pages={1--10},
year={2015},
organization={Springer}
}Downloads
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- Arianna Bianchi, Konstantinos Syrigos, Georgios Lolas, "Tumor-induced neoneurogenesis and perineural tumor growth: a mathematical approach", In arXiv preprint arXiv:1510.02323, 2015. [Bibtex & Downloads]
Tumor-induced neoneurogenesis and perineural tumor growth: a mathematical approach
Reference
Arianna Bianchi, Konstantinos Syrigos, Georgios Lolas, "Tumor-induced neoneurogenesis and perineural tumor growth: a mathematical approach", In arXiv preprint arXiv:1510.02323, 2015.
Bibtex
@article{bianchi2015tumor,
title={Tumor-induced neoneurogenesis and perineural tumor growth: a mathematical approach},
author={Bianchi, Arianna and Syrigos, Konstantinos and Lolas, Georgios},
journal={arXiv preprint arXiv:1510.02323},
year={2015}
}Downloads
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- Carr D Vincent, Fabian Rost, Wouter Masselink, Lutz Brusch, Elly M Tanaka, "Cellular dynamics underlying regeneration of appropriate segment number during axolotl tail regeneration", In BMC developmental biology, BioMed Central, vol. 15, no. 1, pp. 48, 2015. [Bibtex & Downloads]
Cellular dynamics underlying regeneration of appropriate segment number during axolotl tail regeneration
Reference
Carr D Vincent, Fabian Rost, Wouter Masselink, Lutz Brusch, Elly M Tanaka, "Cellular dynamics underlying regeneration of appropriate segment number during axolotl tail regeneration", In BMC developmental biology, BioMed Central, vol. 15, no. 1, pp. 48, 2015.
Bibtex
@article{vincent2015cellular,
title={Cellular dynamics underlying regeneration of appropriate segment number during axolotl tail regeneration},
author={Vincent, Carr D and Rost, Fabian and Masselink, Wouter and Brusch, Lutz and Tanaka, Elly M},
journal={BMC developmental biology},
volume={15},
number={1},
pages={48},
year={2015},
publisher={BioMed Central}
}Downloads
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- H. Hatzikirou, K. Böttger, A. Deutsch, "Model-based comparison of cell density-dependent cell migration strategies", In Mathematical Modelling of Natural Phenomena, EDP Sciences, vol. 10, no. 1, pp. 94–107, 2015. [Bibtex & Downloads]
Model-based comparison of cell density-dependent cell migration strategies
Reference
H. Hatzikirou, K. Böttger, A. Deutsch, "Model-based comparison of cell density-dependent cell migration strategies", In Mathematical Modelling of Natural Phenomena, EDP Sciences, vol. 10, no. 1, pp. 94–107, 2015.
Bibtex
@article{hatzikirou2015model,
title={Model-based comparison of cell density-dependent cell migration strategies},
author={Hatzikirou, H and B{\"o}ttger, K and Deutsch, A},
journal={Mathematical Modelling of Natural Phenomena},
volume={10},
number={1},
pages={94--107},
year={2015},
publisher={EDP Sciences}
}Downloads
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- Shasha Feng, Michel Ludwig, Dirk Walther, "Deciding Subsumers of Least Fixpoint Concepts wrt general$\backslash$mathcal $\{$EL$}$-TBoxes", In Proceeding: Joint German/Austrian Conference on Artificial Intelligence (Künstliche Intelligenz), pp. 59–71, 2015. [Bibtex & Downloads]
Deciding Subsumers of Least Fixpoint Concepts wrt general$\backslash$mathcal $\{$EL$}$-TBoxes
Reference
Shasha Feng, Michel Ludwig, Dirk Walther, "Deciding Subsumers of Least Fixpoint Concepts wrt general$\backslash$mathcal $\{$EL$}$-TBoxes", In Proceeding: Joint German/Austrian Conference on Artificial Intelligence (Künstliche Intelligenz), pp. 59–71, 2015.
Bibtex
@inproceedings{feng2015deciding,
title={Deciding Subsumers of Least Fixpoint Concepts wrt general$\backslash$mathcal $\{$EL$\}$-TBoxes},
author={Feng, Shasha and Ludwig, Michel and Walther, Dirk},
booktitle={Joint German/Austrian Conference on Artificial Intelligence (K{\"u}nstliche Intelligenz)},
pages={59--71},
year={2015},
organization={Springer}
}Downloads
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- Thomas Buder, Andreas Deutsch, Barbara Klink, Anja Voss-Böhme, "Model-based evaluation of spontaneous tumor regression in pilocytic astrocytoma", In PLoS computational biology, Public Library of Science, vol. 11, no. 12, pp. e1004662, 2015. [Bibtex & Downloads]
Model-based evaluation of spontaneous tumor regression in pilocytic astrocytoma
Reference
Thomas Buder, Andreas Deutsch, Barbara Klink, Anja Voss-Böhme, "Model-based evaluation of spontaneous tumor regression in pilocytic astrocytoma", In PLoS computational biology, Public Library of Science, vol. 11, no. 12, pp. e1004662, 2015.
Bibtex
@article{buder2015model,
title={Model-based evaluation of spontaneous tumor regression in pilocytic astrocytoma},
author={Buder, Thomas and Deutsch, Andreas and Klink, Barbara and Voss-B{\"o}hme, Anja},
journal={PLoS computational biology},
volume={11},
number={12},
pages={e1004662},
year={2015},
publisher={Public Library of Science}
}Downloads
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- Sebastian Weitz, Andreas Deutsch, Fernando Peruani, "Self-propelled rods exhibit a phase-separated state characterized by the presence of active stresses and the ejection of polar clusters", In Physical Review E, APS, vol. 92, no. 1, pp. 012322, 2015. [Bibtex & Downloads]
Self-propelled rods exhibit a phase-separated state characterized by the presence of active stresses and the ejection of polar clusters
Reference
Sebastian Weitz, Andreas Deutsch, Fernando Peruani, "Self-propelled rods exhibit a phase-separated state characterized by the presence of active stresses and the ejection of polar clusters", In Physical Review E, APS, vol. 92, no. 1, pp. 012322, 2015.
Bibtex
@article{weitz2015self,
title={Self-propelled rods exhibit a phase-separated state characterized by the presence of active stresses and the ejection of polar clusters},
author={Weitz, Sebastian and Deutsch, Andreas and Peruani, Fernando},
journal={Physical Review E},
volume={92},
number={1},
pages={012322},
year={2015},
publisher={APS}
}Downloads
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- Carsten Mente, Anja Voss-Böhme, Andreas Deutsch, "Analysis of individual cell trajectories in lattice-gas cellular automaton models for migrating cell populations", In Bulletin of mathematical biology, Springer, vol. 77, no. 4, pp. 660–697, 2015. [Bibtex & Downloads]
Analysis of individual cell trajectories in lattice-gas cellular automaton models for migrating cell populations
Reference
Carsten Mente, Anja Voss-Böhme, Andreas Deutsch, "Analysis of individual cell trajectories in lattice-gas cellular automaton models for migrating cell populations", In Bulletin of mathematical biology, Springer, vol. 77, no. 4, pp. 660–697, 2015.
Bibtex
@article{mente2015analysis,
title={Analysis of individual cell trajectories in lattice-gas cellular automaton models for migrating cell populations},
author={Mente, Carsten and Voss-B{\"o}hme, Anja and Deutsch, Andreas},
journal={Bulletin of mathematical biology},
volume={77},
number={4},
pages={660--697},
year={2015},
publisher={Springer}
}Downloads
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2014
- Alexandros Pollakis, Lucas Wetzel, David J Jörg, Wolfgang Rave, Gerhard Fettweis, Frank Jülicher, "Synchronization in networks of mutually delay-coupled phase-locked loops", In New Journal of Physics, IOP Publishing, vol. 16, no. 11, pp. 113009, 2014. [Bibtex & Downloads]
Synchronization in networks of mutually delay-coupled phase-locked loops
Reference
Alexandros Pollakis, Lucas Wetzel, David J Jörg, Wolfgang Rave, Gerhard Fettweis, Frank Jülicher, "Synchronization in networks of mutually delay-coupled phase-locked loops", In New Journal of Physics, IOP Publishing, vol. 16, no. 11, pp. 113009, 2014.
Bibtex
@article{pollakis2014synchronization,
title={Synchronization in networks of mutually delay-coupled phase-locked loops},
author={Pollakis, Alexandros and Wetzel, Lucas and J{\"o}rg, David J and Rave, Wolfgang and Fettweis, Gerhard and J{\"u}licher, Frank},
journal={New Journal of Physics},
volume={16},
number={11},
pages={113009},
year={2014},
publisher={IOP Publishing}
}Downloads
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- David Zwicker, Markus Decker, Steffen Jaensch, Anthony A Hyman, Frank Jülicher, "Centrosomes are autocatalytic droplets of pericentriolar material organized by centrioles", In Proceedings of the National Academy of Sciences, National Acad Sciences, vol. 111, no. 26, pp. E2636–E2645, 2014. [Bibtex & Downloads]
Centrosomes are autocatalytic droplets of pericentriolar material organized by centrioles
Reference
David Zwicker, Markus Decker, Steffen Jaensch, Anthony A Hyman, Frank Jülicher, "Centrosomes are autocatalytic droplets of pericentriolar material organized by centrioles", In Proceedings of the National Academy of Sciences, National Acad Sciences, vol. 111, no. 26, pp. E2636–E2645, 2014.
Bibtex
@article{zwicker2014centrosomes,
title={Centrosomes are autocatalytic droplets of pericentriolar material organized by centrioles},
author={Zwicker, David and Decker, Markus and Jaensch, Steffen and Hyman, Anthony A and J{\"u}licher, Frank},
journal={Proceedings of the National Academy of Sciences},
volume={111},
number={26},
pages={E2636--E2645},
year={2014},
publisher={National Acad Sciences}
}Downloads
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- Elisabeth Fischer-Friedrich, Anthony A Hyman, Frank Jülicher, Daniel J Müller, Jonne Helenius, "Quantification of surface tension and internal pressure generated by single mitotic cells", In Scientific reports, Nature Publishing Group, vol. 4, 2014. [Bibtex & Downloads]
Quantification of surface tension and internal pressure generated by single mitotic cells
Reference
Elisabeth Fischer-Friedrich, Anthony A Hyman, Frank Jülicher, Daniel J Müller, Jonne Helenius, "Quantification of surface tension and internal pressure generated by single mitotic cells", In Scientific reports, Nature Publishing Group, vol. 4, 2014.
Bibtex
@article{fischer2014quantification,
title={Quantification of surface tension and internal pressure generated by single mitotic cells},
author={Fischer-Friedrich, Elisabeth and Hyman, Anthony A and J{\"u}licher, Frank and M{\"u}ller, Daniel J and Helenius, Jonne},
journal={Scientific reports},
volume={4},
year={2014},
publisher={Nature Publishing Group}
}Downloads
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- F. Martin-Recuerda, Dirk Walther, "Axiom dependency hypergraphs for fast modularisation and atomic decomposition", Proceedings of the 27th International Workshop on Description Logics (DL’14), vol. 1193, pp. 299–310, 2014. [Bibtex & Downloads]
Axiom dependency hypergraphs for fast modularisation and atomic decomposition
Reference
F. Martin-Recuerda, Dirk Walther, "Axiom dependency hypergraphs for fast modularisation and atomic decomposition", Proceedings of the 27th International Workshop on Description Logics (DL’14), vol. 1193, pp. 299–310, 2014.
Bibtex
@inproceedings{martin2014axiom,
title={Axiom dependency hypergraphs for fast modularisation and atomic decomposition},
author={Martin-Recuerda, F and Walther, Dirk},
booktitle={Proceedings of the 27th International Workshop on Description Logics (DL’14)},
volume={1193},
pages={299--310},
year={2014}
}Downloads
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- Francisco Martín-Recuerda, Dirk Walther, "Fast modularisation and atomic decomposition of ontologies using axiom dependency hypergraphs", In Proceeding: International Semantic Web Conference, pp. 49–64, 2014. [Bibtex & Downloads]
Fast modularisation and atomic decomposition of ontologies using axiom dependency hypergraphs
Reference
Francisco Martín-Recuerda, Dirk Walther, "Fast modularisation and atomic decomposition of ontologies using axiom dependency hypergraphs", In Proceeding: International Semantic Web Conference, pp. 49–64, 2014.
Bibtex
@inproceedings{martin2014fast,
title={Fast modularisation and atomic decomposition of ontologies using axiom dependency hypergraphs},
author={Mart{\'\i}n-Recuerda, Francisco and Walther, Dirk},
booktitle={International Semantic Web Conference},
pages={49--64},
year={2014},
organization={Springer}
}Downloads
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- GC Bourantas, ED Skouras, VC Loukopoulos, VN Burganos, "Heat transfer and natural convection of nanofluids in porous media", In European Journal of Mechanics-B/Fluids, Elsevier, vol. 43, pp. 45–56, 2014. [Bibtex & Downloads]
Heat transfer and natural convection of nanofluids in porous media
Reference
GC Bourantas, ED Skouras, VC Loukopoulos, VN Burganos, "Heat transfer and natural convection of nanofluids in porous media", In European Journal of Mechanics-B/Fluids, Elsevier, vol. 43, pp. 45–56, 2014.
Bibtex
@article{bourantas2014heat,
title={Heat transfer and natural convection of nanofluids in porous media},
author={Bourantas, GC and Skouras, ED and Loukopoulos, VC and Burganos, VN},
journal={European Journal of Mechanics-B/Fluids},
volume={43},
pages={45--56},
year={2014},
publisher={Elsevier}
}Downloads
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- GC Bourantas, Vassilios C Loukopoulos, "Modeling the natural convective flow of micropolar nanofluids", In International Journal of Heat and Mass Transfer, Elsevier, vol. 68, pp. 35–41, 2014. [Bibtex & Downloads]
Modeling the natural convective flow of micropolar nanofluids
Reference
GC Bourantas, Vassilios C Loukopoulos, "Modeling the natural convective flow of micropolar nanofluids", In International Journal of Heat and Mass Transfer, Elsevier, vol. 68, pp. 35–41, 2014.
Bibtex
@article{bourantas2014modeling,
title={Modeling the natural convective flow of micropolar nanofluids},
author={Bourantas, GC and Loukopoulos, Vassilios C},
journal={International Journal of Heat and Mass Transfer},
volume={68},
pages={35--41},
year={2014},
publisher={Elsevier}
}Downloads
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- GC Bourantas, VC Loukopoulos, VN Burganos, GC Nikiforidis, "A meshless point collocation treatment of transient bioheat problems", In International journal for numerical methods in biomedical engineering, Wiley Online Library, vol. 30, no. 5, pp. 587–601, 2014. [Bibtex & Downloads]
A meshless point collocation treatment of transient bioheat problems
Reference
GC Bourantas, VC Loukopoulos, VN Burganos, GC Nikiforidis, "A meshless point collocation treatment of transient bioheat problems", In International journal for numerical methods in biomedical engineering, Wiley Online Library, vol. 30, no. 5, pp. 587–601, 2014.
Bibtex
@article{bourantas2014meshless,
title={A meshless point collocation treatment of transient bioheat problems},
author={Bourantas, GC and Loukopoulos, VC and Burganos, VN and Nikiforidis, GC},
journal={International journal for numerical methods in biomedical engineering},
volume={30},
number={5},
pages={587--601},
year={2014},
publisher={Wiley Online Library}
}Downloads
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- Josefine Asmus, Daniel Borchmann, Ivo F Sbalzarini, Dirk Walther, "Towards an FCA-based recommender system for black-box optimization", In Proceeding: Workshop Notes, pp. 35, 2014. [Bibtex & Downloads]
Towards an FCA-based recommender system for black-box optimization
Reference
Josefine Asmus, Daniel Borchmann, Ivo F Sbalzarini, Dirk Walther, "Towards an FCA-based recommender system for black-box optimization", In Proceeding: Workshop Notes, pp. 35, 2014.
Bibtex
@inproceedings{asmus2014towards,
title={Towards an FCA-based recommender system for black-box optimization},
author={Asmus, Josefine and Borchmann, Daniel and Sbalzarini, Ivo F and Walther, Dirk},
booktitle={Workshop Notes},
pages={35},
year={2014}
}Downloads
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- Jieying Chen, Michel Ludwig, Yue Ma, Dirk Walther, "Evaluation of Extraction Techniques for Ontology Excerpts.", In Proceeding: Description Logics, pp. 471–482, 2014. [Bibtex & Downloads]
Evaluation of Extraction Techniques for Ontology Excerpts.
Reference
Jieying Chen, Michel Ludwig, Yue Ma, Dirk Walther, "Evaluation of Extraction Techniques for Ontology Excerpts.", In Proceeding: Description Logics, pp. 471–482, 2014.
Bibtex
@inproceedings{chen2014evaluation,
title={Evaluation of Extraction Techniques for Ontology Excerpts.},
author={Chen, Jieying and Ludwig, Michel and Ma, Yue and Walther, Dirk},
booktitle={Description Logics},
pages={471--482},
year={2014}
}Downloads
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- Jörn Starruß, Walter de Back, Lutz Brusch, Andreas Deutsch, "Morpheus: a user-friendly modeling environment for multiscale and multicellular systems biology", In Bioinformatics, Oxford University Press, vol. 30, no. 9, pp. 1331–1332, 2014. [Bibtex & Downloads]
Morpheus: a user-friendly modeling environment for multiscale and multicellular systems biology
Reference
Jörn Starruß, Walter de Back, Lutz Brusch, Andreas Deutsch, "Morpheus: a user-friendly modeling environment for multiscale and multicellular systems biology", In Bioinformatics, Oxford University Press, vol. 30, no. 9, pp. 1331–1332, 2014.
Bibtex
@article{starruss2014morpheus,
title={Morpheus: a user-friendly modeling environment for multiscale and multicellular systems biology},
author={Starru{\ss}, J{\"o}rn and de Back, Walter and Brusch, Lutz and Deutsch, Andreas},
journal={Bioinformatics},
volume={30},
number={9},
pages={1331--1332},
year={2014},
publisher={Oxford University Press}
}Downloads
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- Katrin Bohl, Sabine Hummert, Sarah Werner, David Basanta, Andreas Deutsch, Stefan Schuster, Günter Theißen, Anja Schroeter, "Evolutionary game theory: molecules as players", In Molecular BioSystems, Royal Society of Chemistry, vol. 10, no. 12, pp. 3066–3074, 2014. [Bibtex & Downloads]
Evolutionary game theory: molecules as players
Reference
Katrin Bohl, Sabine Hummert, Sarah Werner, David Basanta, Andreas Deutsch, Stefan Schuster, Günter Theißen, Anja Schroeter, "Evolutionary game theory: molecules as players", In Molecular BioSystems, Royal Society of Chemistry, vol. 10, no. 12, pp. 3066–3074, 2014.
Bibtex
@article{bohl2014evolutionary,
title={Evolutionary game theory: molecules as players},
author={Bohl, Katrin and Hummert, Sabine and Werner, Sarah and Basanta, David and Deutsch, Andreas and Schuster, Stefan and Thei{\ss}en, G{\"u}nter and Schroeter, Anja},
journal={Molecular BioSystems},
volume={10},
number={12},
pages={3066--3074},
year={2014},
publisher={Royal Society of Chemistry}
}Downloads
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- Morgan Delarue, Jean-François Joanny, Frank Jülicher, Jacques Prost, "Stress distributions and cell flows in a growing cell aggregate", In Interface focus, Royal Society, vol. 4, no. 6, pp. 20140033, 2014. [Bibtex & Downloads]
Stress distributions and cell flows in a growing cell aggregate
Reference
Morgan Delarue, Jean-François Joanny, Frank Jülicher, Jacques Prost, "Stress distributions and cell flows in a growing cell aggregate", In Interface focus, Royal Society, vol. 4, no. 6, pp. 20140033, 2014.
Bibtex
@article{delarue2014stress,
title={Stress distributions and cell flows in a growing cell aggregate},
author={Delarue, Morgan and Joanny, Jean-Fran{\c{c}}ois and J{\"u}licher, Frank and Prost, Jacques},
journal={Interface focus},
volume={4},
number={6},
pages={20140033},
year={2014},
publisher={Royal Society}
}Downloads
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- Michel Ludwig, Boris Konev, "Practical Uniform Interpolation and Forgetting for ALC TBoxes with Applications to Logical Difference.", In Proceeding: KR, 2014. [Bibtex & Downloads]
Practical Uniform Interpolation and Forgetting for ALC TBoxes with Applications to Logical Difference.
Reference
Michel Ludwig, Boris Konev, "Practical Uniform Interpolation and Forgetting for ALC TBoxes with Applications to Logical Difference.", In Proceeding: KR, 2014.
Bibtex
@inproceedings{ludwig2014practical,
title={Practical Uniform Interpolation and Forgetting for ALC TBoxes with Applications to Logical Difference.},
author={Ludwig, Michel and Konev, Boris},
booktitle={KR},
year={2014}
}Downloads
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- Michel Ludwig, Dirk Walther, "Detecting Conjunctive Query Differences between ELHr-Terminologies using Hypergraphs.", In Proceeding: Description Logics, pp. 287–298, 2014. [Bibtex & Downloads]
Detecting Conjunctive Query Differences between ELHr-Terminologies using Hypergraphs.
Reference
Michel Ludwig, Dirk Walther, "Detecting Conjunctive Query Differences between ELHr-Terminologies using Hypergraphs.", In Proceeding: Description Logics, pp. 287–298, 2014.
Bibtex
@inproceedings{ludwig2014detecting,
title={Detecting Conjunctive Query Differences between ELHr-Terminologies using Hypergraphs.},
author={Ludwig, Michel and Walther, Dirk},
booktitle={Description Logics},
pages={287--298},
year={2014}
}Downloads
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- Michel Ludwig, Dirk Walther, "The logical difference for ℇLH r-terminologies using hypergraphs", Proceedings of the Twenty-first European Conference on Artificial Intelligence, pp. 555–560, 2014. [Bibtex & Downloads]
The logical difference for ℇLH r-terminologies using hypergraphs
Reference
Michel Ludwig, Dirk Walther, "The logical difference for ℇLH r-terminologies using hypergraphs", Proceedings of the Twenty-first European Conference on Artificial Intelligence, pp. 555–560, 2014.
Bibtex
@inproceedings{ludwig2014logical,
title={The logical difference for ℇLH r-terminologies using hypergraphs},
author={Ludwig, Michel and Walther, Dirk},
booktitle={Proceedings of the Twenty-first European Conference on Artificial Intelligence},
pages={555--560},
year={2014},
organization={IOS Press}
}Downloads
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- Michel Ludwig, Rafael Penaloza, "Brave and Cautious Reasoning in EL.", In Proceeding: Description Logics, pp. 274–286, 2014. [Bibtex & Downloads]
Brave and Cautious Reasoning in EL.
Reference
Michel Ludwig, Rafael Penaloza, "Brave and Cautious Reasoning in EL.", In Proceeding: Description Logics, pp. 274–286, 2014.
Bibtex
@inproceedings{ludwig2014brave,
title={Brave and Cautious Reasoning in EL.},
author={Ludwig, Michel and Penaloza, Rafael},
booktitle={Description Logics},
pages={274--286},
year={2014}
}Downloads
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- Michel Ludwig, Rafael Penaloza, "Error-Tolerant Reasoning in the Description Logic EL⋆", In Proceeding: Proc. of JELIA, vol. 14, pp. 107–121, 2014. [Bibtex & Downloads]
Error-Tolerant Reasoning in the Description Logic EL⋆
Reference
Michel Ludwig, Rafael Penaloza, "Error-Tolerant Reasoning in the Description Logic EL⋆", In Proceeding: Proc. of JELIA, vol. 14, pp. 107–121, 2014.
Bibtex
@inproceedings{ludwig2014error,
title={Error-Tolerant Reasoning in the Description Logic EL⋆},
author={Ludwig, Michel and Penaloza, Rafael},
booktitle={Proc. of JELIA},
volume={14},
pages={107--121},
year={2014},
organization={Springer}
}Downloads
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- Michel Ludwig, "Just: a Tool for Computing Justifications wrt ELH Ontologies.", In ORE, vol. 1207, pp. 1–7, 2014. [Bibtex & Downloads]
Just: a Tool for Computing Justifications wrt ELH Ontologies.
Reference
Michel Ludwig, "Just: a Tool for Computing Justifications wrt ELH Ontologies.", In ORE, vol. 1207, pp. 1–7, 2014.
Bibtex
@article{ludwig2014just,
title={Just: a Tool for Computing Justifications wrt ELH Ontologies.},
author={Ludwig, Michel},
journal={ORE},
volume={1207},
pages={1--7},
year={2014}
}Downloads
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- Nadine Hohmann, Wei Weiwei, Uta Dahmen, Olaf Dirsch, Andreas Deutsch, Anja Voss-Böhme, "How does a single cell know when the liver has reached its correct size?", In PloS one, Public Library of Science, vol. 9, no. 4, pp. e93207, 2014. [Bibtex & Downloads]
How does a single cell know when the liver has reached its correct size?
Reference
Nadine Hohmann, Wei Weiwei, Uta Dahmen, Olaf Dirsch, Andreas Deutsch, Anja Voss-Böhme, "How does a single cell know when the liver has reached its correct size?", In PloS one, Public Library of Science, vol. 9, no. 4, pp. e93207, 2014.
Bibtex
@article{hohmann2014does,
title={How does a single cell know when the liver has reached its correct size?},
author={Hohmann, Nadine and Weiwei, Wei and Dahmen, Uta and Dirsch, Olaf and Deutsch, Andreas and Voss-B{\"o}hme, Anja},
journal={PloS one},
volume={9},
number={4},
pages={e93207},
year={2014},
publisher={Public Library of Science}
}Downloads
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- Osvaldo Chara, Elly M Tanaka, Lutz Brusch, "Mathematical modeling of regenerative processes", In Curr Top Dev Biol, vol. 108, pp. 283–317, 2014. [Bibtex & Downloads]
Mathematical modeling of regenerative processes
Reference
Osvaldo Chara, Elly M Tanaka, Lutz Brusch, "Mathematical modeling of regenerative processes", In Curr Top Dev Biol, vol. 108, pp. 283–317, 2014.
Bibtex
@article{chara2014mathematical,
title={Mathematical modeling of regenerative processes},
author={Chara, Osvaldo and Tanaka, Elly M and Brusch, Lutz},
journal={Curr Top Dev Biol},
volume={108},
pages={283--317},
year={2014}
}Downloads
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- Olaf Wolkenhauer, Charles Auffray, Olivier Brass, Jean Clairambault, Andreas Deutsch, Dirk Drasdo, Francesco Gervasio, Luigi Preziosi, Philip Maini, Anna Marciniak-Czochra, others, "Enabling multiscale modeling in systems medicine", In Genome Med, vol. 6, pp. 21, 2014. [doi] [Bibtex & Downloads]
Enabling multiscale modeling in systems medicine
Reference
Olaf Wolkenhauer, Charles Auffray, Olivier Brass, Jean Clairambault, Andreas Deutsch, Dirk Drasdo, Francesco Gervasio, Luigi Preziosi, Philip Maini, Anna Marciniak-Czochra, others, "Enabling multiscale modeling in systems medicine", In Genome Med, vol. 6, pp. 21, 2014. [doi]
Bibtex
@article{wolkenhauer2014enabling,
title={Enabling multiscale modeling in systems medicine},
author={Wolkenhauer, Olaf and Auffray, Charles and Brass, Olivier and Clairambault, Jean and Deutsch, Andreas and Drasdo, Dirk and Gervasio, Francesco and Preziosi, Luigi and Maini, Philip and Marciniak-Czochra, Anna and others},
journal={Genome Med},
volume={6},
pages={21},
year={2014},
doi={10.1186/gm538}
}Downloads
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- Stathis Delivorias, Haralampos Hatzikirou, Rafael Penaloza, Dirk Walther, "Detecting Emergent Phenomena in Cellular Automata Using Temporal Description Logics", In Proceeding: International Conference on Cellular Automata, pp. 357–366, 2014. [Bibtex & Downloads]
Detecting Emergent Phenomena in Cellular Automata Using Temporal Description Logics
Reference
Stathis Delivorias, Haralampos Hatzikirou, Rafael Penaloza, Dirk Walther, "Detecting Emergent Phenomena in Cellular Automata Using Temporal Description Logics", In Proceeding: International Conference on Cellular Automata, pp. 357–366, 2014.
Bibtex
@inproceedings{delivorias2014detecting,
title={Detecting Emergent Phenomena in Cellular Automata Using Temporal Description Logics},
author={Delivorias, Stathis and Hatzikirou, Haralampos and Penaloza, Rafael and Walther, Dirk},
booktitle={International Conference on Cellular Automata},
pages={357--366},
year={2014},
organization={Springer}
}Downloads
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- Sabine Hummert, Katrin Bohl, David Basanta, Andreas Deutsch, Sarah Werner, Günter Theißen, Anja Schroeter, Stefan Schuster, "Evolutionary game theory: cells as players", In Molecular BioSystems, Royal Society of Chemistry, vol. 10, no. 12, pp. 3044–3065, 2014. [Bibtex & Downloads]
Evolutionary game theory: cells as players
Reference
Sabine Hummert, Katrin Bohl, David Basanta, Andreas Deutsch, Sarah Werner, Günter Theißen, Anja Schroeter, Stefan Schuster, "Evolutionary game theory: cells as players", In Molecular BioSystems, Royal Society of Chemistry, vol. 10, no. 12, pp. 3044–3065, 2014.
Bibtex
@article{hummert2014evolutionary,
title={Evolutionary game theory: cells as players},
author={Hummert, Sabine and Bohl, Katrin and Basanta, David and Deutsch, Andreas and Werner, Sarah and Thei{\ss}en, G{\"u}nter and Schroeter, Anja and Schuster, Stefan},
journal={Molecular BioSystems},
volume={10},
number={12},
pages={3044--3065},
year={2014},
publisher={Royal Society of Chemistry}
}Downloads
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- Yang Jiao, Timothy Lau, Haralampos Hatzikirou, Michael Meyer-Hermann, Joseph C Corbo, Salvatore Torquato, "Avian photoreceptor patterns represent a disordered hyperuniform solution to a multiscale packing problem", In Physical Review E, APS, vol. 89, no. 2, pp. 022721, 2014. [Bibtex & Downloads]
Avian photoreceptor patterns represent a disordered hyperuniform solution to a multiscale packing problem
Reference
Yang Jiao, Timothy Lau, Haralampos Hatzikirou, Michael Meyer-Hermann, Joseph C Corbo, Salvatore Torquato, "Avian photoreceptor patterns represent a disordered hyperuniform solution to a multiscale packing problem", In Physical Review E, APS, vol. 89, no. 2, pp. 022721, 2014.
Bibtex
@article{jiao2014avian,
title={Avian photoreceptor patterns represent a disordered hyperuniform solution to a multiscale packing problem},
author={Jiao, Yang and Lau, Timothy and Hatzikirou, Haralampos and Meyer-Hermann, Michael and Corbo, Joseph C and Torquato, Salvatore},
journal={Physical Review E},
volume={89},
number={2},
pages={022721},
year={2014},
publisher={APS}
}Downloads
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- Robert Müller, Marian Kampschulte, Thaqif El Khassawna, Gudrun Schlewitz, Britta Hürter, Wolfgang Böcker, Manfred Bobeth, Alexander C Langheinrich, Christian Heiss, Andreas Deutsch, others, "Change of mechanical vertebrae properties due to progressive osteoporosis: combined biomechanical and finite-element analysis within a rat model", In Medical & biological engineering & computing, Springer, vol. 52, no. 4, pp. 405–414, 2014. [Bibtex & Downloads]
Change of mechanical vertebrae properties due to progressive osteoporosis: combined biomechanical and finite-element analysis within a rat model
Reference
Robert Müller, Marian Kampschulte, Thaqif El Khassawna, Gudrun Schlewitz, Britta Hürter, Wolfgang Böcker, Manfred Bobeth, Alexander C Langheinrich, Christian Heiss, Andreas Deutsch, others, "Change of mechanical vertebrae properties due to progressive osteoporosis: combined biomechanical and finite-element analysis within a rat model", In Medical & biological engineering & computing, Springer, vol. 52, no. 4, pp. 405–414, 2014.
Bibtex
@article{muller2014change,
title={Change of mechanical vertebrae properties due to progressive osteoporosis: combined biomechanical and finite-element analysis within a rat model},
author={M{\"u}ller, Robert and Kampschulte, Marian and El Khassawna, Thaqif and Schlewitz, Gudrun and H{\"u}rter, Britta and B{\"o}cker, Wolfgang and Bobeth, Manfred and Langheinrich, Alexander C and Heiss, Christian and Deutsch, Andreas and others},
journal={Medical \& biological engineering \& computing},
volume={52},
number={4},
pages={405--414},
year={2014},
publisher={Springer}
}Downloads
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- Andreas Herzig, Emiliano Lorini, Faustine Maffre, Dirk Walther, "Alternating-time temporal logic with explicit programs", LAMAS, 2014. [Bibtex & Downloads]
Alternating-time temporal logic with explicit programs
Reference
Andreas Herzig, Emiliano Lorini, Faustine Maffre, Dirk Walther, "Alternating-time temporal logic with explicit programs", LAMAS, 2014.
Bibtex
@misc{herzig2014alternating,
title={Alternating-time temporal logic with explicit programs},
author={Herzig, Andreas and Lorini, Emiliano and Maffre, Faustine and Walther, Dirk},
year={2014},
publisher={LAMAS}
}Downloads
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- Albrecht J Fehske, Ingo Viering, Jens Voigt, Cinzia Sartori, Simone Redana, Gerhard P Fettweis, "Small-cell self-organizing wireless networks", In Proceedings of the IEEE, IEEE, vol. 102, no. 3, pp. 334–350, 2014. [Bibtex & Downloads]
Small-cell self-organizing wireless networks
Reference
Albrecht J Fehske, Ingo Viering, Jens Voigt, Cinzia Sartori, Simone Redana, Gerhard P Fettweis, "Small-cell self-organizing wireless networks", In Proceedings of the IEEE, IEEE, vol. 102, no. 3, pp. 334–350, 2014.
Bibtex
@article{fehske2014small,
title={Small-cell self-organizing wireless networks},
author={Fehske, Albrecht J and Viering, Ingo and Voigt, Jens and Sartori, Cinzia and Redana, Simone and Fettweis, Gerhard P},
journal={Proceedings of the IEEE},
volume={102},
number={3},
pages={334--350},
year={2014},
publisher={IEEE}
}Downloads
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- Eduard A Jorswieck, Andreas I Reppas, Haralampos Hatzikirou, "Encoding of cellular positional information and maximum capacity of parallel coupled channels", In Proceeding: 2014 Information Theory and Applications Workshop (ITA), pp. 1–8, 2014. [Bibtex & Downloads]
Encoding of cellular positional information and maximum capacity of parallel coupled channels
Reference
Eduard A Jorswieck, Andreas I Reppas, Haralampos Hatzikirou, "Encoding of cellular positional information and maximum capacity of parallel coupled channels", In Proceeding: 2014 Information Theory and Applications Workshop (ITA), pp. 1–8, 2014.
Bibtex
@inproceedings{jorswieck2014encoding,
title={Encoding of cellular positional information and maximum capacity of parallel coupled channels},
author={Jorswieck, Eduard A and Reppas, Andreas I and Hatzikirou, Haralampos},
booktitle={2014 Information Theory and Applications Workshop (ITA)},
pages={1--8},
year={2014},
organization={IEEE}
}Downloads
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2013
- Chiu Fan Lee, Clifford P Brangwynne, Jöbin Gharakhani, Anthony A Hyman, Frank Jülicher, "Spatial organization of the cell cytoplasm by position-dependent phase separation", In Physical review letters, APS, vol. 111, no. 8, pp. 088101, 2013. [Bibtex & Downloads]
Spatial organization of the cell cytoplasm by position-dependent phase separation
Reference
Chiu Fan Lee, Clifford P Brangwynne, Jöbin Gharakhani, Anthony A Hyman, Frank Jülicher, "Spatial organization of the cell cytoplasm by position-dependent phase separation", In Physical review letters, APS, vol. 111, no. 8, pp. 088101, 2013.
Bibtex
@article{lee2013spatial,
title={Spatial organization of the cell cytoplasm by position-dependent phase separation},
author={Lee, Chiu Fan and Brangwynne, Clifford P and Gharakhani, J{\"o}bin and Hyman, Anthony A and J{\"u}licher, Frank},
journal={Physical review letters},
volume={111},
number={8},
pages={088101},
year={2013},
publisher={APS}
}Downloads
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- Francisco Martin-Recuerda, Dirk Walther, "Towards fast Atomic Decomposition using Axiom Dependency Hypergraphs⋆", In Proc. of WoMO, vol. 13, pp. 61–72, 2013. [Bibtex & Downloads]
Towards fast Atomic Decomposition using Axiom Dependency Hypergraphs⋆
Reference
Francisco Martin-Recuerda, Dirk Walther, "Towards fast Atomic Decomposition using Axiom Dependency Hypergraphs⋆", In Proc. of WoMO, vol. 13, pp. 61–72, 2013.
Bibtex
@article{martin2013towards,
title={Towards fast Atomic Decomposition using Axiom Dependency Hypergraphs⋆},
author={Mart{\i}n-Recuerda, Francisco and Walther, Dirk},
journal={Proc. of WoMO},
volume={13},
pages={61--72},
year={2013}
}Downloads
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- Harald Kempf, Haralampos Hatzikirou, Marcus Bleicher, Michael Meyer-Hermann, "In silico analysis of cell cycle synchronisation effects in radiotherapy of tumour spheroids", In PLoS computational biology, Public Library of Science, vol. 9, no. 11, pp. e1003295, 2013. [Bibtex & Downloads]
In silico analysis of cell cycle synchronisation effects in radiotherapy of tumour spheroids
Reference
Harald Kempf, Haralampos Hatzikirou, Marcus Bleicher, Michael Meyer-Hermann, "In silico analysis of cell cycle synchronisation effects in radiotherapy of tumour spheroids", In PLoS computational biology, Public Library of Science, vol. 9, no. 11, pp. e1003295, 2013.
Bibtex
@article{kempf2013silico,
title={In silico analysis of cell cycle synchronisation effects in radiotherapy of tumour spheroids},
author={Kempf, Harald and Hatzikirou, Haralampos and Bleicher, Marcus and Meyer-Hermann, Michael},
journal={PLoS computational biology},
volume={9},
number={11},
pages={e1003295},
year={2013},
publisher={Public Library of Science}
}Downloads
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- Jeremias Epperlein, Anne-Ly Do, Thilo Gross, Stefan Siegmund, "Meso-scale obstructions to stability of 1D center manifolds for networks of coupled differential equations with symmetric Jacobian", In Physica D: Nonlinear Phenomena, Elsevier, vol. 261, pp. 1–7, 2013. [Bibtex & Downloads]
Meso-scale obstructions to stability of 1D center manifolds for networks of coupled differential equations with symmetric Jacobian
Reference
Jeremias Epperlein, Anne-Ly Do, Thilo Gross, Stefan Siegmund, "Meso-scale obstructions to stability of 1D center manifolds for networks of coupled differential equations with symmetric Jacobian", In Physica D: Nonlinear Phenomena, Elsevier, vol. 261, pp. 1–7, 2013.
Bibtex
@article{epperlein2013meso,
title={Meso-scale obstructions to stability of 1D center manifolds for networks of coupled differential equations with symmetric Jacobian},
author={Epperlein, Jeremias and Do, Anne-Ly and Gross, Thilo and Siegmund, Stefan},
journal={Physica D: Nonlinear Phenomena},
volume={261},
pages={1--7},
year={2013},
publisher={Elsevier}
}Downloads
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- Arnaud Chauvière, Haralambos Hatzikirou, Marco Tektonidis, Andreas Deutsch, "Introduction aux automates cellulaires de type" lattice-gas". Application à la croissance in vitro des gliomes et à l'identification de leurs mécanismes d'invasion", Editions matériologiques, 2013. [Bibtex & Downloads]
Introduction aux automates cellulaires de type" lattice-gas". Application à la croissance in vitro des gliomes et à l'identification de leurs mécanismes d'invasion
Reference
Arnaud Chauvière, Haralambos Hatzikirou, Marco Tektonidis, Andreas Deutsch, "Introduction aux automates cellulaires de type" lattice-gas". Application à la croissance in vitro des gliomes et à l'identification de leurs mécanismes d'invasion", Editions matériologiques, 2013.
Bibtex
@misc{chauviere2013introduction,
title={Introduction aux automates cellulaires de type" lattice-gas". Application {\`a} la croissance in vitro des gliomes et {\`a} l'identification de leurs m{\'e}canismes d'invasion},
author={Chauvi{\`e}re, Arnaud and Hatzikirou, Haralambos and Tektonidis, Marco and Deutsch, Andreas},
year={2013},
publisher={Editions mat{\'e}riologiques}
}Downloads
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2012
- Lucas Wetzel, Luis G Morelli, Andrew C Oates, Frank Julicher, Saúl Ares, "Synchronization in the presence of distributed delays", In arXiv preprint arXiv:1206.2288, 2012. [Bibtex & Downloads]
Synchronization in the presence of distributed delays
Reference
Lucas Wetzel, Luis G Morelli, Andrew C Oates, Frank Julicher, Saúl Ares, "Synchronization in the presence of distributed delays", In arXiv preprint arXiv:1206.2288, 2012.
Bibtex
@article{wetzel2012synchronization,
title={Synchronization in the presence of distributed delays},
author={Wetzel, Lucas and Morelli, Luis G and Oates, Andrew C and Julicher, Frank and Ares, Sa{\'u}l},
journal={arXiv preprint arXiv:1206.2288},
year={2012}
}Downloads
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Previous Years
- Lucas Wetzel, Alexandros Pollakis, David J Jörg, Wolfgang Rave, Gerhard Fettweis, Frank Jülicher, "Self-organized synchronisation in massive MIMO inspired by biological systems". [Bibtex & Downloads]
Self-organized synchronisation in massive MIMO inspired by biological systems
Reference
Lucas Wetzel, Alexandros Pollakis, David J Jörg, Wolfgang Rave, Gerhard Fettweis, Frank Jülicher, "Self-organized synchronisation in massive MIMO inspired by biological systems".
Bibtex
@article{wetzelself,
title={Self-organized synchronisation in massive MIMO inspired by biological systems},
author={Wetzel, Lucas and Pollakis, Alexandros and J{\"o}rg, David J and Rave, Wolfgang and Fettweis, Gerhard and J{\"u}licher, Frank}
}Downloads
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- Meik Dörpinghaus, Édgar Roldán, Izaak Neri, Heinrich Meyr, Frank Jülicher, "Information Density and Optimality of Sequential Decision-Making". [Bibtex & Downloads]
Information Density and Optimality of Sequential Decision-Making
Reference
Meik Dörpinghaus, Édgar Roldán, Izaak Neri, Heinrich Meyr, Frank Jülicher, "Information Density and Optimality of Sequential Decision-Making".
Bibtex
@article{dorpinghausinformation,
title={Information Density and Optimality of Sequential Decision-Making},
author={D{\"o}rpinghaus, Meik and Rold{\'a}n, {\'E}dgar and Neri, Izaak and Meyr, Heinrich and J{\"u}licher, Frank}
}Downloads
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Biological Systems Path, Biological Systems Path
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- Yuanhao Gong, Ivo Sbalzarini, "A Natural-Scene Gradient Distribution Prior for Light-Microscopy Image Processing", IEEE. [Bibtex & Downloads]
A Natural-Scene Gradient Distribution Prior for Light-Microscopy Image Processing
Reference
Yuanhao Gong, Ivo Sbalzarini, "A Natural-Scene Gradient Distribution Prior for Light-Microscopy Image Processing", IEEE.
Bibtex
@article{gongnatural,
title={A Natural-Scene Gradient Distribution Prior for Light-Microscopy Image Processing},
author={Gong, Yuanhao and Sbalzarini, Ivo},
publisher={IEEE}
}Downloads
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Biological Systems Path, Biological Systems Path, Biological Systems Path
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- Vasiliki Tsikourkitoudi, George Lolas, George Bourantas, Panagiotis Gavriliadis, Tao Zhang, "Mathematical modeling of particle dynamics in spray flames". [Bibtex & Downloads]
Mathematical modeling of particle dynamics in spray flames
Reference
Vasiliki Tsikourkitoudi, George Lolas, George Bourantas, Panagiotis Gavriliadis, Tao Zhang, "Mathematical modeling of particle dynamics in spray flames".
Bibtex
@article{tsikourkitoudimathematical,
title={Mathematical modeling of particle dynamics in spray flames},
author={Tsikourkitoudi, Vasiliki and Lolas, George and Bourantas, George and Gavriliadis, Panagiotis and Zhang, Tao}
}Downloads
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