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Publications

Most recent list is available on a Google Scholar profile.
  1. 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
  2. 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
  3. 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
  4. 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
  5. 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
  6. 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
  7. Unified Nanotechnology Format: One Way to Store Them All
    Molecules, 27 (2022)
    David Kuťák, Erik Poppleton, Haichao Miao, Petr Šulc, Ivan Barišić
  8. 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
  9. 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
  10. 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
  11. 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
  12. 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
  13. 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
  14. 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
  15. DNA Nanodevices as Mechanical Probes of Protein Structure and Function
    Applied Sciences 11 (6), 2802 (2021)
    Nicholas Stephanopoulos, Petr Šulc
  16. Coarse-grained nucleic acid–protein model for hybrid nanotechnology
    Soft Matter (2021) ; arXiv preprint
    Jonah Procyk, Erik Poppleton, Petr Šulc
  17. 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
  18. 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
  19. 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
  20. 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
  21. 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
  22. The multiscale future of RNA modeling
    Biophysical Journal (2020)
    Petr Šulc
  23. Understanding DNA interactions in crowded environments with a coarse-grained model
    Nucleic Acids Research, Vol. 48, 19 (2020)
    Fan Hong, John Schreck, Petr Šulc
  24. 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
  25. 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
  26. An emergent understanding of strand displacement in RNA biology
    Journal of Structural Biology 207 (3), 241-249 (2019)
    Fan Hong, Petr Šulc
  27. 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
  28. 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
  29. 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
  30. 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
  31. Self-assembling DNA nanotubes to connect molecular landmarks
     Nature Nanotechnology, 2017
    AM Mohammed, P Šulc, J Zenk, R Schulman
  32. Coarse-grained modelling of supercoiled RNA
    preprint: arXiv:1506.02539
    C. Matek, P. Šulc, F. Randisi, J.P.K. Doye, A. A. Louis
  33. 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
  34. 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
  35. 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
  36. 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
  37. 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
  38. 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
  39. 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
  40. 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
  41. 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
  42. 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
  43. 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
  44. 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
  45. 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
  46. Local Control of Reactive Power by Distributed Photovoltaic Generators
    IEEE SmartGridComm 2010, preprint: arXiv:1006.0160
    K. Turitsyn, P. Šulc, S. Backhaus, M. Chertkov
  47. Belief propagation for graph partitioning
    Journal of Physics A: Math. & Theor. (2010), preprint: arXiv:0912.3563
    P. Šulc, L. Zdeborová
  48. 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
  49. 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
  50. 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
  51. 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:

  1. 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
  2. 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