Publications

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2018

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


2017

Self-assembling DNA nanotubes to connect molecular landmarks. Nature Nanotechnology (2017), A. M. Mohammed, P. Šulc, J. Zenk, R. Schulman


2015

  1. 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 
  2. 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
  3. 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
  4. 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
  5. 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

2014

  1. 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 
  2. 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
  3. 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 

2013

  1. 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 
  2. 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
  3. 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 

2012

  1. 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 
  2. 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

2011

  1. 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 

2010

  1. Local Control of Reactive Power by Distributed Photovoltaic Generators IEEE SmartGridComm 2010, preprint: arXiv:1006.0160 K. Turitsyn, P. Šulc, S. Backhaus, M. Chertkov 
  2. Belief propagation for graph partitioning Journal of Physics A: Math. & Theor. (2010), preprint: arXiv:0912.3563 P. Šulc, L. Zdeborová
  3. 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
  4. 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
  5. 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

2007

  1. 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