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Petr Sulc

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Center for Biological Physics
Assistant Professor
Faculty, TEMPE Campus, Mailcode 7301
Biodesign Center for Biocomputing, Security and Society
Faculty Member
Faculty, TEMPE Campus, Mailcode 7301
School of Molecular Sciences
Assistant Professor
Faculty, TEMPE Campus, Mailcode 7301
Biodesign Center for Molecular Design & Biomimetics
Asst Professor
Faculty, TEMPE Campus, Mailcode 7301
Biography
  • 2017- now: Assistant Professor, The Biodesign Institute, Arizona State University, Tempe, AZ, USA
  • 2014-2017: Fellow in Physics and Biology, The Rockefeller University, New York, USA
  • 2009-2010: Graduate Research Assistant, Center for Nonlinear Studies, Los Alamos National Laboratory, New Mexico, USA
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Education
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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
  1. Self-assembling DNA nanotubes to connect molecular landmarks
    Nature Nanotechnology (2017) 
    A. M. Mohammed, P. Šulc, J. Zenk, R. Schulman
  2. Introduction to molecular simulation
    to appear in Quantitative Biology: Computational Methods and Examples, ed. B. Munsky, W.S. Hlavacek and L.S. Tsimring, MIT Press (2018)
    P. Šulc, J.P.K. Doye and A. A. Louis
  3. 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
  4. 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
  5. 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
  6. 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
  7. 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
  8. 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
  9. 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
  10. 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
  11. 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
  12. 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 
  13. 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 
  14. 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
  15. 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
  16. 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
  17. Local Control of Reactive Power by Distributed Photovoltaic Generators 
    IEEE SmartGridComm 2010, preprint: arXiv:1006.0160 
    K. Turitsyn, P. Šulc, S. Backhaus, M. Chertkov
  18. Belief propagation for graph partitioning 
    Journal of Physics A: Math. & Theor. (2010), preprint: arXiv:0912.3563 
    P. Šulc, L. Zdeborová
  19. 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
  20. 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
  21. 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
  22. 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
  23. Intruduction to Molecular Simulation 
    Quantitative Biology (2018), a book chapter
    P. Šulc, J. Doye, A. Louis
  24. Triangulated Wireframe Structure Assembled Using Single-Stranded DNA Tiles 
    ACS Nano (2019)
    M. Matthies, N.P. Agarwal, E. Poppleton, F.M. Joshi, P. Šulc*, T.L. Schmidt*
  25. 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
  26. Rapid Photoactuation of a DNA nanostructure using an internal photocaged trigger strand 
    Angewandte Chemie (2018)
    M. Liu, S. Jiang, O. Loza, N.E. Fahmi, P. Šulc, N. Stephanopoulos
Fall 2019
Course NumberCourse Title
CHM 501Current Topics in Chemistry
CHM 598Special Topics
Spring 2019
Course NumberCourse Title
CHM 240Math Methods in Chemistry
BDE 792Research
BDE 799Dissertation
Spring 2018
Course NumberCourse Title
CHM 240Math Methods in Chemistry
Expertise Areas
Molecular Biophysics
Physics
Chemistry
Computational Modeling
Computational Biology