Petr Sulc
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Phone: 480-965-9601
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Mail code: 7301Campus: Tempe
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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 assistant 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.
- 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
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.
- Nanobase.org: a repository for DNA and RNA nanostructures. Nucleic Acids Research (2022). E. Poppleton, A. Mallya, S. Dey, J. Joseph, P. Šulc.
- Unified Nanotechnology Format: One Way to Store Them All. Molecules (2021). D. Kuťák, E. Poppleton, H. Miao, P. Šulc, I. Barišić.
- Kinetics of RNA and RNA:DNA Hybrid Strand Displacement. ACS Synth. Biol. (2021). H. Liu, F. Hong, F. Smith, J. Goertz, T. Ouldridge, M.M. Stevens, H. Yan, P. Šulc.
- A Self-Regulating DNA Rotaxane Linear Actuator Driven by Chemical Energy. J. Am. Chem. Soc. (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). E. Poppleton, R. Romero, A. Mallya, L. Rovigatti, P. Šulc.
- A Primer on the oxDNA Model of DNA: When to Use it, How to Simulate it and How to Interpret the Results. Frontiers in Molecular Biosciences (2021). A. Sengar, T.E. Ouldridge, O. Henrich, L. Rovigatti, P. Šulc.
- The Heterogeneous Landscape and Early Evolution of Pathogen-Associated CpG Dinucleotides in SARS-CoV-2. Cell Reports Physical Science (2021). A. Di Gioacchino, P. Šulc, A.V. Komarova, B.D. Greenbaum, R. Monasson, S. Cocco.
- Coarse-grained nucleic acid–protein model for hybrid nanotechnology. Soft Matter (2021). J. Procyk, E. Poppleton, P. Šulc.
- DNA Nanodevices as Mechanical Probes of Protein Structure and Function. Applied Sciences (2021). N. Stephanopoulos, P. Šulc.
- Meta-DNA Structures. Nature Chemistry (2020). G. Yao, F. Zhang, F. Wang, T. Peng, H. Liu, E. Poppleton, P. Šulc, S. Jiang, L. Liu, C. Gong, X. Jing, X. Liu, L. Wang, Y. Liu, C. Fan, H. Yan.
- The Multiscale Future of RNA Modeling. Biophysical Journal (2020). P. Šulc.
- Design, optimization and analysis of large DNA and RNA nanostructures through interactive visualization, editing and molecular simulation. Nucleic Acids Research (2020). E. Poppleton, J. Bohlin, M. Matthies, S. Sharma, F. Zhang, P. Sulc.
- Designing Patchy Interactions to Self-Assemble Arbitrary Structures. Physical Review Letters (2020). F. Romano, J. Russo, L. Kroc, P. Sulc.
- Triangulated Wireframe Structures Assembled Using Single-Stranded DNA Tiles. ACS Nano (2019). M. Matthies, N.P. Agarwal, E. Poppleton, F.M. Joshi, P. Sulc, T.L. Schmidt.
- An emergent understanding of strand displacement in RNA biology. Journal of Structural Biology (2019). F. Hong, P. Sulc.
- Triangulated Wireframe Structures Assembled Using Single-Stranded DNA Tiles. ACS Nano (2019). M. Matthies, N.P. Agarwal, E. Poppleton, F.M. Joshi, P. Sulc, T.L. Schmidt.
- Introduction to Molecular Simulation. Quantitative Biology (2018), a book chapter. P. Šulc, J. Doye, A. Louis
- Layered-crossover tiles with precisely tunable angles for 2D and 3D DNA crystal engineering. Journal of the American Chemical Society (2018). F. Hong, S. Jiang, X. Lan, R.P. Narayanan, P. Šulc, F. Zhang, Y. Liu, H. Yan.
- Rapid Photoactuation of a DNA nanostructure using an internal photocaged trigger stand. Angewandte Chemie (2018). M. Liu, S. Jiang, O. Loza, N.E. Fahmi, P. Šulc, N. Stephanopoulos.
- Layered-Crossover Tiles with Precisely Tunable Angles for 2D and 3D DNA Crystal Engineering. Journal of American Chemical Society (2018) F. Hong, S. Jiang, X. Lan, R.P. Narayanan, P. Sulc, F. Zhang, Y. Liu, H. Yan.
- Self-assembling DNA nanotube to connect molecular landmark. Nature nanotechnology (2017). A. M. Mohammed, P. Šulc, J. Zenk, R. Schulman.
- Coarse-grained modelling of supercoiled RNA. J. Chem. Phys., 143 243122 (2015) 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.
- Modeling 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-leve 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 Directon 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 course-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.
Courses
2025 Spring
Course Number | Course Title |
---|---|
PHY 792 | Research |
BDE 799 | Dissertation |
BDE 792 | Research |
BDE 792 | Research |
BDE 795 | Continuing Registration |
BDE 799 | Dissertation |
BCH 341 | Physical Chem with Bio Focus |
BCH 341 | Physical Chem with Bio Focus |
2024 Fall
Course Number | Course Title |
---|---|
BCH 392 | Intro to Research Techniques |
BCH 492 | Honors Directed Study |
BCH 493 | Honors Thesis |
CHM 392 | Intro to Research Techniques |
CHM 492 | Honors Directed Study |
PHY 792 | Research |
BDE 792 | Research |
BDE 799 | Dissertation |
CHM 598 | Special Topics |
CHM 493 | Honors Thesis |
BCH 392 | Intro to Research Techniques |
CHM 598 | Special Topics |
CHM 494 | Special Topics |
CHM 494 | Special Topics |
BDE 792 | Research |
CHM 392 | Intro to Research Techniques |
2024 Summer
Course Number | Course Title |
---|---|
BDE 792 | Research |
PHY 792 | Research |
2024 Spring
Course Number | Course Title |
---|---|
PHY 792 | Research |
BDE 799 | Dissertation |
BDE 792 | Research |
BDE 792 | Research |
BDE 795 | Continuing Registration |
BDE 799 | Dissertation |
BCH 341 | Physical Chem with Bio Focus |
BCH 341 | Physical Chem with Bio Focus |
2023 Fall
Course Number | Course Title |
---|---|
PHY 792 | Research |
BDE 792 | Research |
BDE 799 | Dissertation |
CHM 501 | Current Topics in Chemistry |
2023 Summer
Course Number | Course Title |
---|---|
BDE 792 | Research |
BDE 795 | Continuing Registration |
2023 Spring
Course Number | Course Title |
---|---|
BDE 799 | Dissertation |
BDE 792 | Research |
BCH 341 | Physical Chem with Bio Focus |
BCH 341 | Physical Chem with Bio Focus |
BDE 795 | Continuing Registration |
BDE 799 | Dissertation |
2022 Fall
Course Number | Course Title |
---|---|
BDE 792 | Research |
BDE 799 | Dissertation |
2022 Summer
Course Number | Course Title |
---|---|
BDE 792 | Research |
BDE 795 | Continuing Registration |
2022 Spring
Course Number | Course Title |
---|---|
CHM 341 | Elementary Physical Chemistry |
BDE 799 | Dissertation |
BDE 792 | Research |
BDE 792 | Research |
BDE 795 | Continuing Registration |
BDE 799 | Dissertation |
2021 Fall
Course Number | Course Title |
---|---|
BDE 792 | Research |
BDE 799 | Dissertation |
CHM 598 | Special Topics |
CHM 598 | Special Topics |
CHM 494 | Special Topics |
CHM 494 | Special Topics |
BDE 799 | Dissertation |
2021 Summer
Course Number | Course Title |
---|---|
BDE 792 | Research |
2021 Spring
Course Number | Course Title |
---|---|
CHM 341 | Elementary Physical Chemistry |
BDE 799 | Dissertation |
BDE 792 | Research |
2020 Fall
Course Number | Course Title |
---|---|
CHM 341 | Elementary Physical Chemistry |
2020 Summer
Course Number | Course Title |
---|---|
BDE 792 | Research |
2020 Spring
Course Number | Course Title |
---|---|
CHM 240 | Math Methods in Chemistry |
CHM 240 | Math Methods in Chemistry |
CHM 240 | Math Methods in Chemistry |
BDE 799 | Dissertation |
BDE 792 | Research |
2019 Fall
Course Number | Course Title |
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CHM 501 | Current Topics in Chemistry |
CHM 598 | Special Topics |