Path D - Biomolecular-Assembled Circuits

Introduction

banner path d

Compared to the other paths, a more unconventional approach is followed by the Biomolecular-Assembled Circuits Path (BAC). In our approach, complex biomolecular structures will serve as templates to achieve devices with a large variety of materials, functionalities and (1, 2 and 3-dimensional) geometrical arrangements which are not easily accessible by standard lithography techniques.

In particular, complex, three-dimensional DNA-based (deoxyribonucleic acid) scaffolds are used to create plasmonic, optoelectronic and electronic structures in a cost-effective and highly parallel manner. By integrating such components into established silicon-based electronics, functionalities and systems far beyond current boundaries will be enabled.

Investigators
Overall Goal + Justification

Most microelectronic components are fabricated by lithographic means. Despite the continuing miniaturization of components, there are a number of limitations to conventional lithography. For example, only few materials such as metals or certain semiconductors can be fabricated. Integrating more diverse functional materials such as plasmonically active metal or semiconducting nanoparticles, photonic crystals, or biomolecules is challenging. Next, only flat structures can be produced with lithography. Several layers can be stacked, but for example spherical nanoparticles or complex three-dimensional arrangements of components are difficult to produce. Finally, techniques such as electron-beam lithography or ion beam milling are sequential techniques and therefore expensive and not scalable.

Chemical synthesis on the other hand enables the cheap and scalable production of a large variety of functional nanomaterials including metallic and semiconducting nanoparticles, carbon nanotubes, silicon nanowires or (macro-) molecules.

To achieve functional devices, such materials need to be arranged and interconnected. For this, we are exploring the power of DNA (deoxyribonucleic acid) based self-assembly.

Our goal is to employ structural DNA nanotechnology for a massively parallelized low-cost fabrication of nanophotonic, optoelectronic and electronic devices for future electronics and communication. To achieve integrated devices and systems, larger complex and high-precision self-assembled structures may in the next step patterned with cheaper low-resolution lithographic techniques.

Research Approach

The BAC path covers 5 different topics areas:

Self-assembled plasmonic waveguides

Light will be guided through metallic nanoparticles arranged on DNA structures to demonstrate sub-wavelength optical short-range communication.

Plasmonic antennas

Top-down and bottom-up techniques will be combined to build optical antennas to enable coupling between near- and far-field effects.

DNA-templated heterostructures

Programmable/hierarchical self-assembly of nanostructures from different materials (e.g. polymers, metallic, semiconducting nanoparticles)

Modelling

Theoretical support for the design and optimization of optical devices.

Micro-nano interfacing

Most potential devices, require electrical and/or optical interfacing of the self-assembled nanostructures with the outside world to bridge the gap from nano to micro (to macro). For this, a selective and well-ordered deposition of the DNA-based structures is required.

The BAC path is working in close collaboration with the Carbon, Si-NW and HAEC paths.

Recent News and Achievements

June 22, 2016:

BAC reatreat in Lohmen.

BAC Retreat Lohmen

 

May 2016:

Paper by Gür et al. in ACS Nano: Toward Self-Assembled Plasmonic devices: High-Yield Arrangement of Gold Nanoparticles on DNA Origami Templates

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February 2016:

Paper by Matthies et al in Nano Letters: Design and Synthesis of Triangulated DNA Origami Trusses

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Dec. 11, 2015:

Fatih Gür (Schmidt lab) wins the poster prize at "DNA meets Plasmonics" in Bad Honnef for his poster "High yield assembly of DNA based plasmonic waveguides". Congratulations, Fatih!

 

Nov. 2015:

An enzymic oligonucleotide synthesis method developed at the Wyss Institute (Harvard) and the cfaed may radically decrease the price of oligonucleotides necessary to increase the complexity of DNA nanostructures or for applications in synthetic biology.

Read more: T. L. Schmidt et al. Nature Communications 2015.

 

Sept. 2015: BAC general assemblyBAC PI meeting Sept 2015

Publications

  • 2017

  • Inna Dewald, Andreas Fery, "Polymeric Micelles and Vesicles in Polyelectrolyte Multilayers: Introducing Hierarchy and Compartmentalization" , In Advanced Materials Interfaces, Wiley Online Library, vol. 4, no. 1, 2017. [Bibtex & Downloads]
  • 2016

  • Michael Matthies, Nayan P Agarwal, Thorsten L Schmidt, "Design and synthesis of triangulated DNA origami trusses" , In Nano letters, ACS Publications, vol. 16, no. 3, pp. 2108–2113, 2016. [Bibtex & Downloads]
  • Jonas F Nawroth, Claudia Neisser, Artur Erbe, Rainer Jordan, "Nanopatterned polymer brushes by reactive writing" , In Nanoscale, Royal Society of Chemistry, vol. 8, no. 14, pp. 7513–7522, 2016. [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]
  • Richard Weichelt, Susanne Leubner, Anja Henning-Knechtel, Michael Mertig, Nikolai Gaponik, Thorsten-Lars Schmidt, Alexander Eychmüller, "Methods to Characterize the Oligonucleotide Functionalization of Quantum Dots" , In Small, Wiley Online Library, vol. 12, no. 34, pp. 4763–4771, 2016. [Bibtex & Downloads]
  • Tao Zhang, Dan Gieseler, Rainer Jordan, "Lights on! A significant photoenhancement effect on ATRP by ambient laboratory light" , In Polymer Chemistry, Royal Society of Chemistry, 2016. [Bibtex & Downloads]
  • Till Korten, Samata Chaudhuri, Elena Tavkin, Marcus Braun, Stefan Diez, "Kinesin-1 Expressed in Insect Cells Improves Microtubule Gliding Performance, Long-Term Stability and Guiding Efficiency in Nanostructures" , IEEE, 2016. [Bibtex & Downloads]
  • Dan V Nicolau, Mercy Lard, Till Korten, Falco CMJM van Delft, Malin Persson, Elina Bengtsson, Alf Månsson, Stefan Diez, Heiner Linke, "Parallel computation with molecular-motor-propelled agents in nanofabricated networks" , In Proceedings of the National Academy of Sciences, National Acad Sciences, pp. 201510825, 2016. [Bibtex & Downloads]
  • Fatih N Gür, Friedrich W Schwarz, Jingjing Ye, Stefan Diez, Thorsten L Schmidt, "Towards Self-Assembled Plasmonic Devices: High-Yield Arrangement of Gold Nanoparticles on DNA Origami Templates" , In ACS nano, ACS Publications, 2016. [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, IEEE, vol. 15, no. 1, pp. 62–69, 2016. [Bibtex & Downloads]
  • Vera Fiehler, Fabian Patrovsky, Lisa Ortmann, Susan Derenko, Andreas Hille, Lukas M Eng, "Plasmonic Nanorod Antenna Array: Analysis in Reflection and Transmission" , In The Journal of Physical Chemistry C, ACS Publications, 2016. [Bibtex & Downloads]
  • G. Stoychev, C. Reuther, S. Diez, L. Ionov, "Controlled retention and release of biomolecular transport systems using shape-changing polymer bilayers" , In Angewandte Chemie, 2016. [Bibtex & Downloads]
  • Daniel Hafner, Lisa Ziegler, Muhammad Ichwan, Tao Zhang, Maximilian Schneider, Michael Schiffmann, Claudia Thomas, Karsten Hinrichs, Rainer Jordan, Ihsan Amin, "Polymer Brushes: Mussel-Inspired Polymer Carpets: Direct Photografting of Polymer Brushes on Polydopamine Nanosheets for Controlled Cell Adhesion (Adv. Mater. 7/2016)" , In Advanced Materials, Wiley Online Library, vol. 28, no. 7, pp. 1330–1330, 2016. [Bibtex & Downloads]
  • Roland PM Höller, Martin Dulle, Sabrina Thomä, Martin Mayer, Anja Maria Steiner, Stephan Förster, Andreas Fery, Christian Kuttner, Munish Chanana, "Protein-Assisted Assembly of Modular 3D Plasmonic Raspberry-like Core/Satellite Nanoclusters: Correlation of Structure and Optical Properties" , In ACS nano, ACS Publications, 2016. [Bibtex & Downloads]
  • Martin Mayer, Moritz Tebbe, Christian Kuttner, Max J Schnepf, Tobias AF Koenig, Andreas Fery, "Template-Assisted Colloidal Self-Assembly of Macroscopic Magnetic Metasurfaces" , In Faraday Discussions, Royal Society of Chemistry, 2016. [Bibtex & Downloads]
  • Vladimir Sayevich, Bin Cai, Albrecht Benad, Danny Haubold, Luisa Sonntag, Nikolai Gaponik, Vladimir Lesnyak, Alexander Eychmüller, "3D Assembly of All-Inorganic Colloidal Nanocrystals into Gels and Aerogels" , In Angewandte Chemie International Edition, Wiley Online Library, vol. 55, no. 21, pp. 6334–6338, 2016. [Bibtex & Downloads]
  • Franz Selzer, Carlo Floresca, David Kneppe, Ludwig Bormann, Christoph Sachse, Nelli Weiß, Alexander Eychmüller, Aram Amassian, Lars Müller-Meskamp, Karl Leo, "Electrical limit of silver nanowire electrodes: Direct measurement of the nanowire junction resistance" , In Applied Physics Letters, AIP Publishing, vol. 108, no. 16, pp. 163302, 2016. [Bibtex & Downloads]
  • T. Kämpfe, A. Haußmann, LM Eng, P. Reichenbach, A. Thiessen, T. Woike, R. Steudtner, "Time-resolved photoluminescence spectroscopy of Nb Nb 4+ and O- polarons in LiNbO 3 single crystals" , In Physical Review B, APS, vol. 93, no. 17, pp. 174116, 2016. [Bibtex & Downloads]
  • Ralf Schneider, Florian Weigert, Vladimir Lesnyak, Susanne Leubner, Tommy Lorenz, Thomas Behnke, Aliaksei Dubavik, Jan-Ole Joswig, Ute Resch-Genger, Nikolai Gaponik, others, "pH and Concentration Dependence of the Optical Properties of Thiol-Capped CdTe Nanocrystals in Water and D 2 O" , In Physical Chemistry Chemical Physics, Royal Society of Chemistry, 2016. [Bibtex & Downloads]
  • Christian Kuttner, Munish Chanana, Matthias Karg, Andreas Fery, "Macromolecular Decoration of Nanoparticles for Guiding Self-Assembly in 2D and 3D" , Wiley-VCH, 2016. [Bibtex & Downloads]
  • Jens W Neubauer, Longjian Xue, Johann Erath, Dirk-M Drotlef, Aránzazu del Campo, Andreas Fery, "Monitoring the Contact Stress Distribution of Gecko-Inspired Adhesives Using Mechano-Sensitive Surface Coatings" , In ACS Applied Materials & Interfaces, ACS Publications, vol. 8, no. 28, pp. 17870–17877, 2016. [Bibtex & Downloads]
  • Inna Dewald, Julia Gensel, Eva Betthausen, Oleg V Borisov, Axel HE Müller, Felix H Schacher, Andreas Fery, "Splitting of Surface-Immobilized Multicompartment Micelles into Clusters upon Charge Inversion" , In ACS nano, ACS Publications, vol. 10, no. 5, pp. 5180–5188, 2016. [Bibtex & Downloads]
  • Stefan Diez, Rahul Grover, Janine Fischer, Friedrich Schwarz, Wilhelm J Walter, Petra Schwille, "Transport efficiency of membrane-anchored kinesin-1 motors depends on motor density and diffusivity" , In bioRxiv, Cold Spring Harbor Labs Journals, pp. 064246, 2016. [Bibtex & Downloads]
  • Fatih N Gür, Friedrich W Schwarz, Jingjing Ye, Stefan Diez, Thorsten L Schmidt, "Toward self-assembled plasmonic devices: High-yield arrangement of gold nanoparticles on dna origami templates" , In ACS nano, ACS Publications, vol. 10, no. 5, pp. 5374–5382, 2016. [Bibtex & Downloads]
  • Alexander Haußmann, André Gemeinhardt, Mathias Schröder, Thomas Kämpfe, Lukas M Eng, "Bottom-up assembly of molecular nanostructures by means of ferroelectric lithography" , In Langmuir, ACS Publications, 2016. [Bibtex & Downloads]
  • 2015

  • Thorsten L. Schmidt, Brian J. Beliveau, Yavuz O. Uca, Mark Theilmann, Felipe Da Cruz, Chao-Ting Wu, William M. Shih, "Scalable amplification of strand subsets from chip-synthesized oligonucleotide libraries" , In Nat Commun, vol. 6, pp. 8634, Nov 2015. [doi] [Bibtex & Downloads]
  • Chun-Hua Lu, Alessandro Cecconello, Xiu-Juan Qi, Na Wu, Stefan-Sven Jester, Michael Famulok, Michael Matthies, Thorsten-Lars Schmidt, Itamar Willner, "Switchable Reconfiguration of a Seven-Ring Interlocked DNA Catenane Nanostructure" , In Nano Letters, vol. 15, no. 10, pp. 7133–7137, Oct 2015. [doi] [Bibtex & Downloads]
  • Alfred Kick, Michael Mertig, "Characterization of pH-sensitive polymer layers by surface plasmon resonance and quartz crystal microbalance" , In physica status solidi (a), Wiley Online Library, 2015. [doi] [Bibtex & Downloads]
  • Anna A Makarova, Elena V Grachova, Vera S Neudachina, Lada V Yashina, Anja Blüher, Serguei L Molodtsov, Michael Mertig, Hermann Ehrlich, Vera K Adamchuk, Clemens Laubschat, others, "Insight into Bio-metal Interface Formation in vacuo: Interplay of S-layer Protein with Copper and Iron" , In Scientific reports, Nature Publishing Group, vol. 5, 2015. [doi] [Bibtex & Downloads]
  • Franziska Fischer, Anja Henning-Knechtel, Michael Mertig, "Investigating the aggregation behaviour of DNA origami frames" , In physica status solidi (a), Wiley Online Library, 2015. [doi] [Bibtex & Downloads]
  • Evgeni Sperling, Mandy Hohlfeld, Michael Mertig, "Soft-lithographically fabricated nanofluidic channels for single-DNA measurements" , In physica status solidi (a), Wiley Online Library, 2015. [Bibtex & Downloads]
  • Patrick Seiler, Bernhard Klein, Dirk Plettemeier, "Analytical and Experimental Investigation of Substrate Permittivity and Loss up to 67 GHz" , In ECTI Transactions on Electrical Engineering, Electronics, and Communications, vol. 13, no. 1, pp. 26–34, 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. [doi] [Bibtex & Downloads]
  • Sheng-Chieh Yang, Ji-Ling Hou, Andreas Finn, Amit Kumar, Yang Ge, Wolf-Joachim Fischer, "Synthesis of multifunctional plasmonic nanopillar array using soft thermal nanoimprint lithography for highly sensitive refractive index sensing" , In Nanoscale, Royal Society of Chemistry, vol. 7, no. 13, pp. 5760–5766, 2015. [doi] [Bibtex & Downloads]
  • Aniruddha Mitra, Felix Ruhnow, Bert Nitzsche, Stefan Diez, "Impact-Free Measurement of Microtubule Rotations on Kinesin and Cytoplasmic-Dynein Coated Surfaces" , In PloS one, Public Library of Science, vol. 10, no. 9, pp. e0136920, 2015. [Bibtex & Downloads]
  • René Schneider, Till Korten, Wilhelm J Walter, Stefan Diez, "Kinesin-1 Motors Can Circumvent Permanent Roadblocks by Side-Shifting to Neighboring Protofilaments" , In Biophysical journal, Elsevier, vol. 108, no. 9, pp. 2249–2257, 2015. [Bibtex & Downloads]
  • Chengzhou Zhu, Dan Wen, Susanne Leubner, Martin Oschatz, Wei Liu, Matthias Holzschuh, Frank Simon, Stefan Kaskel, Alexander Eychmüller, "Nickel cobalt oxide hollow nanosponges as advanced electrocatalysts for the oxygen evolution reaction" , In Chemical Communications, Royal Society of Chemistry, vol. 51, no. 37, pp. 7851–7854, 2015. [Bibtex & Downloads]
  • A. Thiessen, E. Beyreuther, R. Werner, D. Koelle, R. Kleiner, LM Eng, "Quantifying the electrical transport characteristics of electron-doped La 0.7 Ce 0.3 MnO 3 thin films through hopping energies, Mn valence, and carrier localization length" , In Journal of Physics and Chemistry of Solids, Elsevier, vol. 80, pp. 26–33, 2015. [Bibtex & Downloads]
  • Marco Braun, Andreas P Bregulla, Katrin Günther, Michael Mertig, Frank Cichos, "Single Molecules Trapped by Dynamic Inhomogeneous Temperature Fields" , In Nano letters, ACS Publications, vol. 15, no. 8, pp. 5499–5505, 2015. [Bibtex & Downloads]
  • AI Reppas, JCL Alfonso, H. Hatzikirou, "In silico tumor control induced via alternating immunostimulating and immunosuppressive phases" , In Virulence, Taylor & Francis, no. just-accepted, pp. 00–00, 2015. [Bibtex & Downloads]
  • Krzysztof Sozański, Felix Ruhnow, Agnieszka Wi\ sniewska, Marcin Tabaka, Stefan Diez, Robert Hołyst, "Small Crowders Slow Down Kinesin-1 Stepping by Hindering Motor Domain Diffusion" , In Physical review letters, APS, vol. 115, no. 21, pp. 218102, 2015. [Bibtex & Downloads]
  • Felix E Kemmerich, Marko Swoboda, Dominik J Kauert, M Svea Grieb, Steffen Hahn, Friedrich W Schwarz, Ralf Seidel, Michael Schlierf, "Simultaneous single-molecule force and fluorescence sampling of DNA nanostructure conformations using magnetic tweezers" , In Nano letters, ACS Publications, vol. 16, no. 1, pp. 381–386, 2015. [Bibtex & Downloads]
  • Andreas I Reppas, Konstantinos Spiliotis, Constantinos I Siettos, "Tuning the average path length of complex networks and its influence to the emergent dynamics of the majority-rule model" , In Mathematics and Computers in Simulation, Elsevier, vol. 109, pp. 186–196, 2015. [Bibtex & Downloads]
  • 2014

  • Bernhard Klein, Michael Jenning, Patrick Seiler, Dirk Plettemeier, "Wideband half-cloverleaf shaped on-chip antenna for 160 GHz–200 GHz applications" , In Proceeding: Antennas and Propagation Society International Symposium (APSURSI), 2014 IEEE, pp. 364–365, 2014. [doi] [Bibtex & Downloads]
  • Bernhard Klein, Michael Jenning, Patrick Seiler, Klaus Wolf, Dirk Plettemeier, "Verification and demonstration up to 67 GHz of an on-chip antenna pattern measurement setup" , In Proceeding: Antenna Measurements & Applications (CAMA), 2014 IEEE Conference on, pp. 1–4, 2014. [doi] [Bibtex & Downloads]
  • S. Leubner, R. Schneider, A. Dubavik, S. Hatami, N. Gaponik, U. Resch-Genger, A. Eychmüller, "Influence of the stabilizing ligand on the quality, signal-relevant optical properties, and stability of near-infrared emitting Cd 1- x Hg x Te nanocrystals" , In Journal of Materials Chemistry C, Royal Society of Chemistry, vol. 2, no. 25, pp. 5011–5018, 2014. [doi] [Bibtex & Downloads]
  • Cordula Reuther, Robert Tucker, Leonid Ionov, Stefan Diez, "Programmable Patterning of Protein Bioactivity by Visible Light" , In Nano letters, ACS Publications, vol. 14, no. 7, pp. 4050–4057, 2014. [Bibtex & Downloads]
  • Patrick Seiler, Bernhard Klein, Dirk Plettemeier, "Broadband characterization of planar transmission line substrate permittivity up to 67 GHz" , In Proceeding: Antennas and Propagation (ISAP), 2014 International Symposium on, pp. 373–374, 2014. [Bibtex & Downloads]
  • Niels Neumann, Tobias Schuster, Dirk Plettemeier, "Novel approach for simultaneous wireless transmission and evaluation of optical sensors" , In Proceeding: SPIE/COS Photonics Asia, pp. 927402–927402, 2014. [Bibtex & Downloads]
  • Christian Mayr, Johannes Partzsch, Marko Noack, Stefan Hanzsche, Stefan Scholze, Sebastian Hoppner, Georg Ellguth, Rene Schuffny, "A biological-realtime neuromorphic system in 28 nm CMOS using low-leakage switched capacitor circuits" , IEEE, 2014. [Bibtex & Downloads]
  • 2013

  • Frieder Ostermaier, Michael Mertig, "Sorting of CVD-grown single-walled carbon nanotubes by means of gel column chromatography" , In physica status solidi (b), Wiley Online Library, vol. 250, no. 12, pp. 2564–2568, 2013. [doi] [Bibtex & Downloads]
  • KL Jiménez-Monroy, A. Kick, Kasper Eersels, Bart van Grinsven, Patrick Wagner, M. Mertig, "Surface plasmon resonance-based DNA microarrays: Comparison of thiol and phosphorothioate modified oligonucleotides" , In physica status solidi (a), Wiley Online Library, vol. 210, no. 5, pp. 918–925, 2013. [doi] [Bibtex & Downloads]
  • Rodney R Agayan, Robert Tucker, Takahiro Nitta, Felix Ruhnow, Wilhelm J Walter, Stefan Diez, Henry Hess, "Optimization of isopolar microtubule arrays" , In Langmuir, ACS Publications, vol. 29, no. 7, pp. 2265–2272, 2013. [doi] [Bibtex & Downloads]
  • René Schneider, Tilman Glaser, Michael Berndt, Stefan Diez, "Using a quartz paraboloid for versatile wide-field TIR microscopy with sub-nanometer localization accuracy" , In Optics express, Optical Society of America, vol. 21, no. 3, pp. 3523–3539, 2013. [doi] [Bibtex & Downloads]
  • Susanne Leubner, Soheil Hatami, Nehir Esendemir, Tommy Lorenz, Jan-Ole Joswig, Vladimir Lesnyak, Sebastian Recknagel, Nikolai Gaponik, Ute Resch-Genger, Alexander Eychmüller, "Experimental and theoretical investigations of the ligand structure of water-soluble CdTe nanocrystals" , In Dalton Transactions, Royal Society of Chemistry, vol. 42, no. 35, pp. 12733–12740, 2013. [doi] [Bibtex & Downloads]
  • Tobias Schuster, Christian Schaeffer, Michael Mertig, Dirk Plettemeier, "Entwicklung eines kompakten faseroptischen Oberflächenplasmonenresonanz-Sensors" , In tm-Technisches Messen Plattform für Methoden, Systeme und Anwendungen der Messtechnik, vol. 80, no. 7-8, pp. 221–228, 2013. [doi] [Bibtex & Downloads]
  • Viktor Schroeder, Till Korten, Heiner Linke, Stefan Diez, Ivan Maximov, "Dynamic guiding of motor-driven microtubules on electrically heated, smart polymer tracks" , In Nano letters, ACS Publications, vol. 13, no. 7, pp. 3434–3438, 2013. [doi] [Bibtex & Downloads]
  • Wolfgang Pompe, Gerhard Rödel, Hans-Jürgen Weiss, Michael Mertig, "Bio-nanomaterials: designing materials inspired by nature" , John Wiley & Sons, 2013. [Bibtex & Downloads]
  • Tomáš Kuba\vr, Rafael Gutiérrez, Ulrich Kleinekathöfer, Gianaurelio Cuniberti, Marcus Elstner, "Modeling charge transport in DNA using multi-scale methods" , In physica status solidi (b), Wiley Online Library, vol. 250, no. 11, pp. 2277–2287, 2013. [Bibtex & Downloads]