Path I - Biological Systems

Introduction

banner path i

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.

Investigators
Overall Goal + Justification

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.

Research Approach

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 Regeneration

An 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 signals

This 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 Systems

Both 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 Classification

Engineering 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 group

We 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.
Our work draws inspiration from physics, information theory, and engineering; likewise, we seek to excite bio-inspired applications of biological information processing in these fields.

 

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.

 

Recent Achievements

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.
Publications

  • 2018

  • 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]
  • Meik Dörpinghaus, Izaak Neri, Édgar Roldán, Heinrich Meyr, Frank Jülicher, "Testing Optimality of Sequential Decision-Making" , pp. , 01/2018. [Bibtex & Downloads]
  • Samata Chaudhuri, Till Korten, Slobodanka Korten, Gloria Milani, Tobia Lana, Geertruy te Kronnie, Stefan Diez, "Label-Free Detection of Microvesicles and Proteins by the Bundling of Gliding Microtubules" , In Nano Letters, vol. 18, no. 1, pp. 117-123, 2018. [doi] [Bibtex & Downloads]
  • 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]
  • S. Singh, É. Roldán, I. Neri, I. M. and Khaymovich, "Records of entropy production in an electronic double dot" , In ArXiv e-prints, Dec 2017. [Bibtex & Downloads]
  • Josué Nava-Sedeño, Haralambos Hatzikirou, Rainer Klages, Andreas Deutsch, "Cellular automaton models for time-correlated random walks: Derivation and analysis" , vol. 7, pp. , 12/2017. [Bibtex & Downloads]
  • 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]
  • Katrin Talkenberger, Elisabetta Cavalcanti-Adam, Anja Voß-Böhme, Andreas Deutsch, "Amoeboid-mesenchymal migration plasticity promotes invasion only in complex heterogeneous microenvironments" , vol. 7, pp. , 12/2017. [Bibtex & Downloads]
  • Josefine Asmus, Christian Müller, Ivo Sbalzarini, "L p -Adaptation: Simultaneous Design Centering and Robustness Estimation of Electronic and Biological Systems" , vol. 7, pp. , 12/2017. [Bibtex & Downloads]
  • J. A. Kromer, S. Märcker, S. Lange, C. and Baier, "Optimal decision making for sperm chemotaxis in the presence of noise" , In ArXiv e-prints, Nov 2017. [Bibtex & Downloads]
  • D. Aguilar Hidalgo, S. Werner, O. and Wartlick, "Dynamic gradient scaling as a critical point of growth control" , In ArXiv e-prints, Nov 2017. [Bibtex & Downloads]
  • 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]
  • 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]
  • David "Reher, "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]
  • J. Karschau, M. Zimmerling, B. M. Friedrich, "Renormalization group theory for percolation in time-varying networks" , In ArXiv e-prints, Jul 2017. [Bibtex & Downloads]
  • 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]
  • 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]
  • 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]
  • 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]
  • I. Neri, É. Roldán, F. Jülicher, "Statistics of Infima and Stopping Times of Entropy Production and Applications to Active Molecular Processes" , In Physical Review X, vol. 7, no. 1, pp. 011019, Jan 2017. [doi] [Bibtex & Downloads]
  • 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]
  • 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]
  • 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]
  • 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]
  • 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, 2017. [doi] [Bibtex & Downloads]
  • 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, 2017. [doi] [Bibtex & Downloads]
  • 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, 2017. [doi] [Bibtex & Downloads]
  • 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]
  • 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]
  • 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]
  • Daniel Aguilar Hidalgo, Steffen Werner, Ortrud Wartlick, Marcos González-Gaitán, Benjamin Friedrich, Frank Julicher, "Dynamic gradient scaling as a critical point of growth control" , In arXiv preprint arXiv:1711.02021, 2017. [Bibtex & Downloads]
  • Benjamin M Friedrich, "The load response of shape-changing microswimmers scales with their energy efficiency" , In arXiv preprint arXiv:1711.03597, 2017. [Bibtex & Downloads]
  • 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]
  • 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]
  • 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]
  • J. C. L. Alfonso, A. Köhn-Luque, T. and Stylianopoulos, "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]
  • 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, pp. , 10/2016. [Bibtex & Downloads]
  • Dan Nicolau, Mercy Lard, Till Korten, Falco Van Delft, Malin Persson, Elina Bengtsson, Alf Mansson, Stefan Diez, Heiner Linke, "Parallel computation with molecular-motor-propelled agents in nanofabricated networks" , vol. 113, pp. , 02/2016. [Bibtex & Downloads]
  • 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]
  • 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]
  • 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]
  • G. Stoychev and C. Reuther and S. Diez and L. Ionov, "Controlled retention and release of biomolecular transport systems using shape-changing polymer bilayers" , In Angewandte Chemie, 2016. [Bibtex & Downloads]
  • 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]
  • B M Friedrich, "Hydrodynamic synchronization of flagellar oscillators" , In Eur. Phys. J. Special Topics, vol. 225, pp. 2353–2368, 2016. [doi] [Bibtex & Downloads]
  • 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]
  • 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]
  • 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]
  • 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]
  • 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]
  • 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]
  • 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]
  • 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]
  • 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]
  • Till Korten, Samata Chaudhuri, Elena Tavkin, Marcus Braun, Stefan Diez, "Kinesin-1 Expressed in Insect Cells Improves Microtubule in Vitro Gliding Performance, Long-Term Stability and Guiding Efficiency in Nanostructures" , In IEEE Transactions on NanoBioscience, vol. 15, pp. 62-69, 2016. [Bibtex & Downloads]
  • 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]
  • 2015

  • M. Dörpinghaus, É. Roldán, I. and Neri, "An Information Theoretic Analysis of Sequential Decision-Making" , In ArXiv e-prints, Oct 2015. [Bibtex & Downloads]
  • 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]
  • 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]
  • 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]
  • 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]
  • 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]
  • 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]
  • 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]
  • 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]
  • 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]
  • 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]
  • 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]
  • 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]
  • 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]
  • 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]
  • 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]
  • 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]
  • 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]
  • 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]
  • 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]
  • Rajesh Ramaswamy, George Bourantas, Frank Jülicher, Ivo F Sbalzarini, "A hybrid particle-mesh method for incompressible active polar viscous gels" , In Journal of Computational Physics, Elsevier, vol. 291, pp. 334–361, 2015. [Bibtex & Downloads]
  • 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]
  • 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]
  • 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]
  • 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]
  • 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]
  • Eduard A Jorswieck, Andreas I Reppas, Haralampos Hatzikirou, "Encoding of cellular positional information and maximum capacity of parallel coupled channels" , In Proceeding: Information Theory and Applications Workshop (ITA), 2014, pp. 1–8, 2014. [Bibtex & Downloads]
  • 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]
  • 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]
  • 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]
  • 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]
  • 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]
  • 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]
  • 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]
  • 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]
  • 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]
  • 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]
  • Michel Ludwig, Boris Konev, "Practical Uniform Interpolation and Forgetting for ALC TBoxes with Applications to Logical Difference." , In Proceeding: KR, 2014. [Bibtex & Downloads]
  • Michel Ludwig, Dirk Walther, "Detecting Conjunctive Query Differences between ELHr-Terminologies using Hypergraphs." , In Proceeding: Description Logics, pp. 287–298, 2014. [Bibtex & Downloads]
  • 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]
  • Michel Ludwig, Rafael Penaloza, "Brave and Cautious Reasoning in EL." , In Proceeding: Description Logics, pp. 274–286, 2014. [Bibtex & Downloads]
  • 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]
  • Michel Ludwig, "Just: a Tool for Computing Justifications wrt ELH Ontologies." , In ORE, vol. 1207, pp. 1–7, 2014. [Bibtex & Downloads]
  • 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]
  • 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]
  • 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]
  • 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]
  • 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]
  • 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]
  • 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]
  • Andreas Herzig, Emiliano Lorini, Faustine Maffre, Dirk Walther, "Alternating-time temporal logic with explicit programs" , LAMAS, 2014. [Bibtex & Downloads]
  • 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]
  • 2013

  • Andreas Ecke, Michel Ludwig, Dirk Walther, "The Concept Difference for EL-Terminologies using Hypergraphs." , In Proceeding: DChanges, 2013. [Bibtex & Downloads]
  • 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]
  • 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]
  • 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]
  • Andreas Herzig, Emiliano Lorini, Dirk Walther, "Reasoning about actions meets strategic logics" , In Proceeding: International Workshop on Logic, Rationality and Interaction, pp. 162–175, 2013. [Bibtex & Downloads]
  • 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]
  • 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]
  • 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]
  • 0

  • 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]
  • Meik Dörpinghaus, Édgar Roldán, Izaak Neri, Heinrich Meyr, Frank Jülicher, "Information Density and Optimality of Sequential Decision-Making" . [Bibtex & Downloads]
  • Yuanhao Gong, Ivo Sbalzarini, "A Natural-Scene Gradient Distribution Prior for Light-Microscopy Image Processing" , IEEE. [Bibtex & Downloads]
  • Vasiliki Tsikourkitoudi, George Lolas, George Bourantas, Panagiotis Gavriliadis, Tao Zhang, "Mathematical modeling of particle dynamics in spray flames" . [Bibtex & Downloads]
  • Sven Karol, Pietro Incardona, Yaser Afshar, Ivo F Sbalzarini, Jeronimo Castrillon, "Towards a Next-Generation Parallel Particle-Mesh" . [Bibtex & Downloads]