Publications
Most recent list is available on a
Google Scholar profile.
- Design and simulation of DNA, RNA and hybrid protein–nucleic acid nanostructures with oxView
Nature Protocols (2022)
Joakim Bohlin, Michael Matthies, Erik Poppleton, Jonah Procyk, Aatmik Mallya, Hao Yan, Petr Šulc
- The influence of Holliday junction sequence and dynamics on DNA crystal self-assembly
Nature Communications 13 (2022)
Chad R. Simmons, Tara MacCulloch, Miroslav Krepl, Michael Matthies, Alex Buchberger, Ilyssa Crawford, Jiří Šponer, Petr Šulc, Nicholas Stephanopoulos, Hao Yan
- A simple solution to the problem of self-assembling cubic diamond crystals
arXiv preprint (2022)
Lorenzo Rovigatti, John Russo, Flavio Romano, Michael Matthies, Lukáš Kroc, Petr Šulc
- A localized DNA finite-state machine with temporal resolution
Science Advances 8 (12) (2022)
Lan Liu, Fan Hong, Hao Liu, Xu Zhou, Shuoxing Jiang, Petr Šulc, Jian-Hui Jiang, Hao Yan
- Generative and interpretable machine learning for aptamer design and analysis of in vitro sequence selection
bioRxiv preprint (2022)
Andrea Di Gioacchino, Jonah Procyk, Marco Molari, John S. Schreck, Yu Zhou, Yan Liu, Rémi Monasson, Simona Cocco, Petr Šulc
- SAT-assembly: A new approach for designing self-assembling systems
Journal of Physics: Cond. Matter (2022); arxiv preprint
John Russo, Flavio Romano, Lukáš Kroc, Francesco Sciortino, Lorenzo Rovigatti, Petr Šulc
- Unified Nanotechnology Format: One Way to Store Them All
Molecules, 27 (2022)
David Kuťák, Erik Poppleton, Haichao Miao, Petr Šulc, Ivan Barišić
- ExpertRNA: A new framework for RNA structure prediction
Informs Journal on Computing (2022); bioRxiv preprint
M. Liu, G. Pedrielli, E. Poppleton, P. Šulc, D. P. Bertsekas
- Nanobase.org: a repository for DNA and RNA nanostructures
Nucleic Acids Research, (2022), article featured on the front cover
Erik Poppleton, Aatmik Mallya, Swarup Dey, Joel Joseph, Petr Šulc
- A rhythmically pulsing leaf-spring nanoengine that drives a passive follower
bioRxiv preprint (2021)
Mathias Centola, Erik Poppleton, Martin Centola, Julian Valero, Petr Šulc, Michael Famulok
- Repeats Mimic Immunostimulatory Viral Features Across a Vast Evolutionary Landscape
bioRxiv preprint (2021)
Petr Šulc, Alexander Solovyov, Sajid A. Marhon, Siyu Sun, John LaCava, Omar Abdel-Wahab, Nicolas Vabret, Daniel D. De Carvalho, Rémi Monasson, Simona Cocco, Benjamin D. Greenbaum
- Kinetics of RNA and RNA:DNA hybrid strand displacement
ACS Synthetic Biology (2021)
H. Liu, F. Hong, F. Smith, J. Goertz, T. E. Ouldridge, M. Stevens, H. Yan, P. Šulc
- A Self-Regulating DNA Rotaxane Linear Actuator Driven by Chemical Energy
J. Am. Chem. Soc. 143. 13292 (2021)
Z. Yu, M. Centola, J. Valero, M. Matthies, P. Šulc, M. Famulok
- OxDNA.org: a public webserver for coarse-grained simulations of DNA and RNA nanostructures
Nucleic Acids Research, (2021)
Erik Poppleton, Roger Romero, Aatmik Mallya, Lorenzo Rovigatti, Petr Šulc
- DNA Nanodevices as Mechanical Probes of Protein Structure and Function
Applied Sciences 11 (6), 2802 (2021)
Nicholas Stephanopoulos, Petr Šulc
- Coarse-grained nucleic acid–protein model for hybrid nanotechnology
Soft Matter (2021) ; arXiv preprint
Jonah Procyk, Erik Poppleton, Petr Šulc
- The heterogeneous landscape and early evolution of pathogen-associated CpG dinucleotides in SARS-CoV-2
Molecular Biology and Evolution (2021)
Andrea Di Gioacchino, Petr Šulc, Anastassia V. Komarova, Benjamin D. Greenbaum, Rémi Monasson, Simona Cocco
- A primer on the oxDNA model of DNA: When to use it, how to simulate it and how to interpret the results
Front. Mol. Biosci., 17 June 2021 (2021)
A. Sengar, T. E. Ouldridge, O. Henrich, L. Rovigatti, P. Šulc
- Phenotype bias determines how RNA structures occupy the morphospace of all possible shapes
Molecular Biology and Evolution (2021)
K. Dingle, F. Ghaddar, P. Šulc, A.A. Louis
- Designing patchy interactions to self-assemble arbitrary structures
Phys. Rev. Lett., Vol. 125, 118003, (2020) ; arXiv preprint
Flavio Romano, John Russo, Lukáš Kroc, Petr Šulc
- Meta-DNA structures
Nature Chemistry (2020)
Guangbao Yao, Fei Zhang, Fei Wang, Tianhuan Peng, Hao Liu, Erik Poppleton, Petr Šulc, Shuoxing Jiang, Lan Liu, Chen Gong, Xinxin Jing, Xiaoguo Liu, Lihua Wang, Yan Liu, Chunhai Fan, Hao Yan
- The multiscale future of RNA modeling
Biophysical Journal (2020)
Petr Šulc
- Understanding DNA interactions in crowded environments with a coarse-grained model
Nucleic Acids Research, Vol. 48, 19 (2020)
Fan Hong, John Schreck, Petr Šulc
- Design, optimization, and analysis of large DNA and RNA nanostructures through interactive visualization, editing, and molecular simulation
Nucleic Acids Research, Volume 48, Issue 12, (2020)
Erik Poppleton, Joakim Bohlin, Michael Matthies, Shuchi Sharma, Fei Zhang, Petr Šulc
- TacoxDNA: A user‐friendly web server for simulations of complex DNA structures, from single strands to origami
Journal of computational chemistry 40 (29), 2586-2595 (2019); article was featured on the front cover
Antonio Suma, Erik Poppleton, Michael Matthies, Petr Šulc, Flavio Romano, Ard A Louis, Jonathan PK Doye, Cristian Micheletti, Lorenzo Rovigatti
- An emergent understanding of strand displacement in RNA biology
Journal of Structural Biology 207 (3), 241-249 (2019)
Fan Hong, Petr Šulc
- Triangulated Wireframe Structures Assembled Using Single-Stranded DNA Tiles
ACS nano 13 (2), 1839-1848 (2019)
Michael Matthies, Nayan P Agarwal, Erik Poppleton, Foram M Joshi, Petr Šulc, Thorsten L Schmidt
- Y-RNAs Lead an Endogenous Program of RIG-I Agonism Mobilized upon RNA Virus Infection and Targeted by HIV
bioArxiv preprint (2019)
Nicolas Vabret, Valérie Najburg, Alexander Solovyov, Petr Šulc, Sreekumar Balan, Guillaume Beauclair, Maxime Chazal, Hugo Varet, Rachel Legendre, Odile Sismeiro, Raul Y Sanchez David, Christopher McClain, Ramya Gopal, Lise Chauveau, Olivier Schwartz, Nolwenn Jouvenet, Martin Markowitz, Frédéric Tangy, Nina Bhardwaj, Benjamin D Greenbaum, Anastasia V Komarova
- Layered-crossover tiles with precisely tunable angles for 2D and 3D DNA crystal engineering
Journal of the American Chemical Society 140 (44), 14670-14676 (2018)
Fan Hong, Shuoxing Jiang, Xiang Lan, Raghu Pradeep Narayanan, Petr Šulc, Fei Zhang, Yan Liu, Hao Yan
- Rapid Photoactuation of a DNA nanostructure using an internal photocaged trigger strand
Angewandte Chemie International Edition 57 (30), 9341-9345 (2018)
M Liu, S Jiang, O Loza, NE Fahmi, P Šulc, N Stephanopoulos
- Self-assembling DNA nanotubes to connect molecular landmarks
Nature Nanotechnology, 2017
AM Mohammed, P Šulc, J Zenk, R Schulman
- Coarse-grained modelling of supercoiled RNA
preprint: arXiv:1506.02539
C. Matek, P. Šulc, F. Randisi, J.P.K. Doye, A. A. Louis
- Introducing Improved Structural Properties and Salt Dependence into a Coarse-Grained Model of DNA
J. Chem. Phys., 142, 234901 (2015) (article featured on the journal cover)
, preprint: arXiv:1504.00821
B. E. K. Snodin, F. Randisi, M. Mosayebi, P. Šulc, J. S. Schreck, F. Romano, T. E. Ouldridge, R. Tsukanov, E. Nir, A. A. Louis, J. P. K. Doye
- Modelling toehold-mediated RNA strand displacement
Biophys. J. 108, iss. 5, 1238-1247 (2015) (article featured on the front cover), preprint: arXiv:1411.3239
P. Šulc, T. E. Ouldridge, F. Romano, J. P. K. Doye, A. A. Louis
- DNA hairpins primarily promote duplex melting rather than inhibiting hybridization
Nucleic Acids Res. (2015)
preprint: arXiv:1408.4401
J. S. Schreck, T. E. Ouldridge, F. Romano, P. Šulc, L. Shaw, A. A. Louis, J. P. K. Doye
- A nucleotide-level coarse-grained model of RNA
J. Chem. Phys. 140, 235102 (2014) (article featured on the front cover), preprint: arXiv:1403.4180
P. Šulc, F. Romano, T. E. Ouldridge, J. P. K. Doye, A. A. Louis
- A comparison between parallelization approaches in molecular dynamics simulations on GPUs
J. Comp. Chem 36 (2015), (article featured on the front cover) preprint: arXiv:1401.4350
L. Rovigatti, P. Šulc, István Z. Reguly, F. Romano
- Optimal Distributed Control of Reactive Power via the Alternating Direction Method of Multipliers
IEEE Transactions on Energy Conversion 29 (2014), preprint: arXiv:1310.5748
P. Šulc, S. Backhaus, M. Chertkov
- Coarse-graining DNA for simulations of DNA nanotechnology
Phys. Chem. Chem. Phys. (2013), preprint: arxiv:1308.3843
J.P.K. Doye, T. E. Ouldridge, A. A. Louis, F. Romano, P. Šulc, C. Matek, B.E.K. Snodin, L. Rovigatti, J. S. Schreck, R.M. Harrison, W.P.J. Smith
- On the biophysics and kinetics of toehold-mediated DNA strand displacement
Nucleic Acids Res. (2013)
N. Srinivas, T.E. Ouldridge, P. Šulc, J.M. Schaeffer, B. Yurke, A.A. Louis, J.P.K. Doye, E. Winfree
- DNA hybridization kinetics: zippering, internal displacement and sequence dependence
Nucleic Acids Res. (2013), preprint: arxiv:1303.3370
T.E. Ouldridge, P. Šulc, F. Romano, J.P.K. Doye, A.A. Louis
- Simulating a burnt-bridges DNA motor with a coarse-grained DNA model
Natural Computing (2014), preprint: arxiv:1212.4536
P. Šulc, T.E. Ouldridge, F. Romano, J.P.K. Doye, A.A. Louis
- Sequence-dependent thermodynamics of a coarse-grained DNA model
J. Chem. Phys. (2012), (article featured on the front cover) preprint: arxiv:1207.3391
P. Šulc, F. Romano, T.E. Ouldridge, L. Rovigatti, J.P.K. Doye, A.A. Louis
- Non-Gaussianity in single-particle tracking: Use of kurtosis to learn the characteristics of a cage-type potential
Phys. Rev. E (2012), preprint: arXiv:1102.2290
P. Lushnikov, P. Šulc, K. Turitsyn
- Options for Control of Reactive Power by Distributed Photovoltaic Generators
Proceedings of the IEEE (2011), preprint: arXiv:1008.0878
K. Turitsyn, P. Šulc, S. Backhaus, M. Chertkov
- Local Control of Reactive Power by Distributed Photovoltaic Generators
IEEE SmartGridComm 2010, preprint: arXiv:1006.0160
K. Turitsyn, P. Šulc, S. Backhaus, M. Chertkov
- Belief propagation for graph partitioning
Journal of Physics A: Math. & Theor. (2010), preprint: arXiv:0912.3563
P. Šulc, L. Zdeborová
- Distributed control of reactive power flow in a radial distribution circuit with high photovoltaic penetration
IEEE Power and Energy Society General Meeting 2010, preprint: arXiv:0912.3281
K. Turitsyn, P. Šulc, S. Backhaus, M. Chertkov
- Quantifying Slow Evolutionary Dynamics in RNA Fitness Landscapes
Journal of Bioinformatics and Computational Biology, (2010), preprint: arXiv:0911.5366
P. Šulc, O. C. Martin, A. Wagner
- Random walk return probabilities and hitting times on sparse Erdos-Renyi graphs
Phys. Rev. E 81, (2010), preprint: arXiv:0902.2173
O. C. Martin, P. Šulc
- Group theoretical construction
of mutually unbiased bases in Hilbert spaces of prime dimensions
Journal of Physics A: Math. & Theor. (2007), preprint: arXiv:0708.4114
P. Šulc, J. Tolar
Book Chapters:
- Introduction to Molecular simulation
"Quantitative Biology: Theory, Computational Methods and Models", ed. B. Munsky, W.S. Hlavacek and L.S. Tsimring
MIT Press, 2018, pp. 179-208
Petr Sulc, Jonathan P.K. Doye, and Ard A. Louis
- The oxDNA coarse-grained model as a tool to simulate DNA origami
Methods in Molecular Biology, Humana Press, in press
Jonathan PK Doye, Hannah Fowler, Domen Prešern, Joakim Bohlin, Lorenzo Rovigatti, Flavio Romano, Petr Šulc, Chak Kui Wong, Ard A Louis, John S Schreck, Megan C Engel, Michael Matthies, Erik Benson, Erik Poppleton, Benedict EK Snodin