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Publications

Most recent list is available on a Google Scholar profile.

    2025

  1. Falsifiability Test for Classical Nucleation Theory
    Phys. Rev. Lett. (2025); arxiv preprint
    Camilla Beneduce, Diogo EP Pinto, Lorenzo Rovigatti, Flavio Romano, Petr Šulc, Francesco Sciortino, John Russo
  2. Mismatch-Assisted Toehold Exchange Cascades for Magnetic Nanoparticle-Based Nucleic Acid Diagnostics
    bioarxiv preprint
    Rebecca Sack, Joshua Evans, Florian Wolgast, Meinhard Schilling, Thilo Viereck, Petr Šulc, Aidin Lak
  3. How we simulate DNA origami
    Small Methods (2025); arxiv preprint
    Sarah Haggenmueller, Michael Matthies, Matthew Sample, Petr Šulc
  4. Automating Blueprints for Colloidal Quasicrystal Assembly
    ACS Nano (2025) arxiv preprint
    Diogo Pinto, Petr Šulc, Francesco Sciortino, John Russo

    2024

  5. Inverse design of a pyrochlore lattice of DNA origami through model-driven experiments
    Science, 384, 6697, (741-742), (2024); arxiv preprint
    covered by Perspective in the same issue of Science
    Hao Liu, Michael Matthies, John Russo, Lorenzo Rovigatti, Raghu Pradeep Narayanan, Thong Diep, Daniel McKeen, Oleg Gang, Nicholas Stephanopoulos, Francesco Sciortino, Hao Yan, Flavio Romano, Petr Šulc
  6. Hairygami: Analysis of DNA Nanostructures' Conformational Change Driven by Functionalizable Overhangs
    ACS Nano, 2024
    arxiv preprint
    Matthew Sample, Thong Diep, Hao Liu, Michael Matthies, Petr Šulc
  7. Combination of Coevolutionary Information and Supervised Learning Enables Generation of Cyclic Peptide Inhibitors with Enhanced Potency from a Small Data Set
    ACS Central Science, 2024
    Ylenia Mazzocato, Nicola Frasson, Matthew Sample, Cristian Fregonese, Angela Pavan, Alberto Caregnato, Marta Simeoni, Alessandro Scarso, Laura Cendron, Petr Šulc, Alessandro Angelini
  8. Evolving to find optimizations humans miss: using evolutionary computation to improve GPU code for bioinformatics applications
    ACM Transactions on Evolutionary Learning (2024)
    Jhe-Yu Liou, Muaaz Awan, Kirtus Leyba, Petr Šulc, Steven Hofmeyr, Carole-Jean Wu, Stephanie Forrest
  9. ANNaMo: Coarse-grained modeling for folding and assembly of RNA and DNA systems
    J. Chem. Phys. 160, 205102 (2024); arxiv preprint
    F. Tosti Guerra, E. Poppleton, P. Šulc, L. Rovigatti
  10. A rhythmically pulsing leaf-spring nanoengine that drives a passive follower
    Nature Nanotechnology 19, 226-236 (2024) ; biorxiv preprint
    M. Centola, E. Poppleton, M. Centola, J. Valero, S. Ray, R. Welty, Nils G. Walter, P. Šulc, M. Famulok
  11. Coarse-grained modeling of DNA-protein interactions helps elucidate DNA compaction
    New and Notable perspective for Biophysical journal
    Petr Sulc
  12. Coarse-grained modelling of DNA-RNA hybrids
    J. Chem. Phys. 160, 115101 (2024); article was featured in Scilight ; arxiv preprint;
    Eryk J. Ratajczyk, Petr Šulc, Andrew J. Turberfield, Jonathan P.K. Doye, Ard A. Louis
  13. Inverse design of self-folding 3D shells
    Phys. Rev. Lett. 132, 118201 (2024) ; arxiv preprint
    Diogo Pinto, Nuno Araújo, Petr Šulc, John Russo
  14. RNA-induced allosteric coupling drives viral capsid assembly
    PRX Life (2024), article selected for spotlight in Physics Magazine
    Sean Hamilton, Tushar Modi, Petr Šulc, Banu Ozkan
  15. Designing 3D multicomponent self-assembling systems with signal-passing building blocks
    J. Chem. Phys. 160, 084902 (2024): Emerging Investigators Special Collection; selected as "Editor's Pick" ; arxiv preprint
    Joshua Evans, Petr Šulc
  16. DNA-Nanostructure-Guided Assembly of Proteins into Programmable Shapes
    Nano Lett. (2024)
    Qinyi Lu, Yang Xu, Erik Poppleton, Kun Zhou, Petr Sulc, Nicholas Stephanopoulos, Yonggang Ke
  17. Single-Molecule Force Spectroscopy of Toehold-Mediated Strand Displacement
    Nature Communications 15 (2024); biorXiv preprint
    Andreas Walbrun, Tianhe Wang, Michael Matthies, Petr Šulc, Friedrich Simmel, Matthias Rief
  18. Controlling DNA-RNA strand displacement kinetics with base distribution
    bioRxiv preprint
    Eryk Ratajczyk, Jonathan Bath, Petr Sulc, Jonathan Doye, Ard Louis, Andrew Turberfield

    2023

  19. CytoDirect: A Nucleic Acid Nanodevice for Specific and Efficient Delivery of Functional Payloads to the Cytoplasm
    JACS (2023)
    Lu Yu, Yang Xu, Md Al-Amin, Shuoxing Jiang, Matthew Sample, Abhay Prasad, Nicholas Stephanopoulos, Petr Šulc, and Hao Yan
  20. Engineering Azeotropy to Optimize the Self-Assembly of Colloidal Mixtures
    ACS Nano (2023); arxiv preprint
    Camilla Beneduce, Francesco Sciortino, Petr Šulc, John Russo
  21. High-affinity binding to the SARS-CoV-2 spike trimer by a nanostructured, trivalent protein-DNA synthetic antibody
    biorxiv preprint (2023)
    Yang Xu, Rong Zheng, Abhay Prasad, Minghui Liu, Zijian Wan, Xiaoyan Zhou, Ryan M Porter, Matthew Sample, Erik Poppleton, Jonah Procyk, Hao Liu, Yize Li, Shaopeng Wang, Hao Yan, Petr Šulc, Nicholas Stephanopoulos
  22. High-speed 3D DNA-PAINT and unsupervised clustering for unlocking 3D DNA origami cryptography
    biorxiv preprint (2023)
    G. Bimananda M. Wisna, Daria Sukhareva, Jonathan Zhao, Deeksha Satyabola, Michael Matthies, Subhajit Roy, Petr Šulc, Hao Yan, Rizal F. Hariadi
  23. Coarse-grained simulations of DNA and RNA systems with oxDNA and oxRNA models: Introductory tutorial
    Proceedings of Winter Simulation Conference (2023)
    arxiv preprint
    Michael Matthies, Matthew Sample, Petr Šulc
  24. DNA Origami Tessellations
    J. Am. Chem. Soc., 145, 25 (2023)
    Yue Tang, Hao Liu, Qi Wang, Xiaodong Qi, Lu Yu, Petr Šulc, Fei Zhang, Hao Yan, Shuoxing Jiang
  25. Atomistic Picture of Opening–Closing Dynamics of DNA Holliday Junction Obtained by Molecular Simulations
    Journal of Chemical Information and Modeling (2023)
    Zhengyue Zhang, Jiří Šponer, Giovanni Bussi, Vojtěch Mlýnský, Petr Šulc, Chad R Simmons, Nicholas Stephanopoulos, Miroslav Krepl
  26. Design strategies for the self-assembly of polyhedral shells
    Proceedings of the National Academy of Sciences 120 (16), (2023)
    Diogo E. P. Pinto; Petr Šulc; Francesco Sciortino; John Russo
  27. Designing the self-assembly of arbitrary shapes using minimal complexity building blocks
    ACS Nano (2023) (featured on the cover) ; arxiv preprint
    Joakim Bohlin, Andrew Turberfield, Ard Louis, Petr Šulc
  28. Two-step nucleation in a binary mixture of Patchy Particles
    J. Chem. Phys. (2023); selected as "Editor's pick"
    Camilla Beneduce, Diogo Pinto, Petr Šulc, Francesco Sciortino, John Russo
  29. oxDNA: coarse-grained simulations of nucleic acids made simple
    Journal of Open Source Software (2023)
    Erik Poppleton, Michael Matthies, Debesh Mandal, Flavio Romano, Petr Šulc, Lorenzo Rovigatti

    2022

  30. Biomotors, viral assembly, and RNA nanobiotechnology: Current achievements and future directions
    Computational and Structural Biotechnology Journal (2022)
    L. Rolband et al
  31. Coarse-Grained Simulations for the Characterization and Optimization of Hybrid Protein–DNA Nanostructures
    ACS Nano (2022)
    Raghu Pradeep Narayanan, Jonah Procyk, Purbasha Nandi, Abhay Prasad, Yang Xu, Erik Poppleton, Dewight Williams, Fei Zhang, Hao Yan, Po-Lin Chiu, Nicholas Stephanopoulos, Petr Šulc
  32. 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
  33. 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
  34. A simple solution to the problem of self-assembling cubic diamond crystals
    Nanoscale 14 (2022), arxiv preprint
    Lorenzo Rovigatti, John Russo, Flavio Romano, Michael Matthies, Lukáš Kroc, Petr Šulc
  35. 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
  36. Generative and interpretable machine learning for aptamer design and analysis of in vitro sequence selection
    PLOS Comp. Biology (2022);
    Andrea Di Gioacchino, Jonah Procyk, Marco Molari, John S. Schreck, Yu Zhou, Yan Liu, Rémi Monasson, Simona Cocco, Petr Šulc
  37. 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
  38. Unified Nanotechnology Format: One Way to Store Them All
    Molecules, 27 (2022)
    David Kuťák, Erik Poppleton, Haichao Miao, Petr Šulc, Ivan Barišić
  39. 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
  40. 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
  41. Y-RNAs Lead an Endogenous Program of RIG-I Agonism Mobilized upon RNA Virus Infection and Targeted by HIV
    iScience 2022
    Nicolas Vabret, Valérie Najburg, Alexander Solovyov, Ramya Gopal, Christopher McClain, Petr Šulc, Sreekumar Balan, Yannis Rahou, Guillaume Beauclair, Maxime Chazal, Hugo Varet, Rachel Legendre, Odile Sismeiro, Raul Y Sanchez David, Lise Chauveau, Nolwenn Jouvenet, Martin Markowitz, Sylvie van der Werf, Olivier Schwartz, Frédéric Tangy, Nina Bhardwaj, Benjamin D Greenbaum, Anastassia V Komarova

    42. 2021

  42. 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
  43. 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
  44. 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
  45. 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
  46. DNA Nanodevices as Mechanical Probes of Protein Structure and Function
    Applied Sciences 11 (6), 2802 (2021)
    Nicholas Stephanopoulos, Petr Šulc
  47. Coarse-grained nucleic acid–protein model for hybrid nanotechnology
    Soft Matter (2021) ; arXiv preprint
    Jonah Procyk, Erik Poppleton, Petr Šulc
  48. 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
  49. 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
  50. 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

    2020

  51. 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
  52. 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
  53. The multiscale future of RNA modeling
    Biophysical Journal (2020)
    Petr Šulc
  54. Understanding DNA interactions in crowded environments with a coarse-grained model
    Nucleic Acids Research, Vol. 48, 19 (2020)
    Fan Hong, John Schreck, Petr Šulc
  55. 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

    2019

  56. 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
  57. An emergent understanding of strand displacement in RNA biology
    Journal of Structural Biology 207 (3), 241-249 (2019)
    Fan Hong, Petr Šulc
  58. 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

    2018

  59. 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
  60. 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

    61. prior 2018

  61. Self-assembling DNA nanotubes to connect molecular landmarks
     Nature Nanotechnology, 2017
    AM Mohammed, P Šulc, J Zenk, R Schulman
  62. Coarse-grained modelling of supercoiled RNA
    preprint: arXiv:1506.02539
    C. Matek, P. Šulc, F. Randisi, J.P.K. Doye, A. A. Louis
  63. 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
  64. 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
  65. 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
  66. 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
  67. 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
  68. 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
  69. 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
  70. 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
  71. 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
  72. 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
  73. 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
  74. 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
  75. 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
  76. Local Control of Reactive Power by Distributed Photovoltaic Generators
    IEEE SmartGridComm 2010, preprint: arXiv:1006.0160
    K. Turitsyn, P. Šulc, S. Backhaus, M. Chertkov
  77. Belief propagation for graph partitioning
    Journal of Physics A: Math. & Theor. (2010), preprint: arXiv:0912.3563
    P. Šulc, L. Zdeborová
  78. 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
  79. 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
  80. 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
  81. 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
    DNA and RNA Origami: Methods and Protocols, Methods in Molecular Biology, Humana Press, (2023), preprint: arxiv
    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