Long Bio
Petr Šulc’s research focuses on application of computational modeling and statistical physics approaches to complex systems. In particular, his group uses computational models to study problems in biology, and bio-inspired nanotechnology systems. He is mainly interested in nucleic acids modeling (DNA and RNA) using coarse-grained models, which allow for simulations of longer time-scales and larger systems than if fully-atomistic representation is used. Such an approach is allows for efficient studies of nanotechnology system, as well as biologically relevant interactions between nucleic acids.
His research group is furthermore interested in applying computer simulations and statistical physics analysis to study properties of RNA molecules in vivo, in relation to RNAs expressed in tumor cells and viral genomes. The research is done in active collaboration with experimental groups.
He is an associate professor at ASU. Prior to ASU, he was a fellow in physics and biology with The Rockefeller University (2014-2017) and served as a graduate research assistant with the Center for Nonlinear Studies at the Los Alamos National Laboratory, New Mexico (2009-2010). His prior research also involved mathematical modeling and optimization of smart-grid systems.
Education
D.Phil. Theoretical Physics, University of Oxford 2010-2014
Master's degree. Fundamental Concepts of Physics: Quantum Physics, Ecole Polytechnique , Palaiseau, France 2009
Master's degree. Mathematical Physics, Faculty of Nuclear Sciences and Physical Engineering, Czech Technical University in Prague , Czech Republic 2009
Bachelor's degree. Mathematical Physics, Faculty of Nuclear Sciences and Physical Engineering, Czech Technical University in Prague , Czech Republic 2006
Research Interests
Petr Sulc's research focuses on application of computational modeling / statistical physics approaches to complex systems. In particular, his group uses computational models to study problems in biology, and bio-inspired nanotechnology systems. He is mainly interested in nucleic acids modeling (DNA and RNA) using coarse-grained models, which allow for simulations of longer time-scales and larger systems than if fully-atomistic representation is used. Such an approach is allows for efficient studies of nanotechnology system, as well as biologically relevant interactions between nucleic acids.
His research group is furthermore interested in applying computer simulations and statistical physics analysis to study properties of RNA molecules in vivo, in relation to RNAs expressed in tumor cells and viral genomes. The research is done in active collaboration with experimental groups.
His prior research also involved mathematical modeling and optimization of smart-grid systems.
Publications
How we simulate DNA origami Small Methods (2025); arxiv preprint Sarah Haggenmueller, Michael Matthies, Matthew Sample, Petr Šulc
2024
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
Automating Blueprints for Colloidal Quasicrystal Assembly ACS Nano (2024) arxiv preprint Diogo Pinto, Petr Šulc, Francesco Sciortino, John Russo
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
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
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
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
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
Coarse-grained modeling of DNA-protein interactions helps elucidate DNA compaction New and Notable perspective for Biophysical journal Petr Sulc
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
Inverse design of self-folding 3D shells Phys. Rev. Lett. 132, 118201 (2024) ; arxiv preprint Diogo Pinto, Nuno Araújo, Petr Šulc, John Russo
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
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
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
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
Controlling DNA-RNA strand displacement kinetics with base distribution bioRxiv preprint Eryk Ratajczyk, Jonathan Bath, Petr Sulc, Jonathan Doye, Ard Louis, Andrew Turberfield
2023
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
Engineering Azeotropy to Optimize the Self-Assembly of Colloidal Mixtures ACS Nano (2023); arxiv preprint Camilla Beneduce, Francesco Sciortino, Petr Šulc, John Russo
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
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
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
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
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
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
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
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
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
Biomotors, viral assembly, and RNA nanobiotechnology: Current achievements and future directions Computational and Structural Biotechnology Journal (2022) L. Rolband et al
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
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 Nanoscale 14 (2022), arxiv preprint 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 PLOS Comp. Biology (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
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
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
2020
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
2019
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
2018
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
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 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
Courses
2025 Summer
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2025 Spring
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2024 Fall
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2024 Summer
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2024 Spring
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2023 Fall
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2023 Summer
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2023 Spring
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2022 Fall
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2022 Summer
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2022 Spring
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2021 Fall
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2021 Summer
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Course Number
Course Title
BDE 792
Research
2021 Spring
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2020 Fall
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2020 Summer
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Course Number
Course Title
BDE 792
Research
2020 Spring
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