Bibliografic database on Semiconductors, Heterostructures and Biophysics

Method Monte Carlo

• Reentrant Condensation of Proteins in Solution Induced by Multivalent Counterions
  F. Zhang, M. W. A. Skoda, R. M. J. Jacobs, S. Zorn, R. A. Martin, C. M. Martin, G. F. Clark, S. Weggler, A. Hildebrandt, O. Kohlbacher, and F. Schreiber
  Phys. Rev. Lett. 101, 148101 (2008)
• Microcanonical versus Canonical Analysis of Protein Folding
  J. Hernández-Rojas and J. M. Gomez Llorente
  Phys. Rev. Lett. 100, 258104 (2008)
• Unbiased Sampling of Globular Lattice Proteins in Three Dimensions
  Jesper Lykke Jacobsen
  Phys. Rev. Lett. 100, 118102 (2008)
• Mechanisms and Dynamics of Protein Clustering on a Solid Surface
  P. A. Mulheran, D. Pellenc, R. A. Bennett, R. J. Green, and M. Sperrin
  Phys. Rev. Lett. 100, 068102 (2008)
• Conformation of a coarse-grained protein chain (an aspartic acid protease) model in effective solvent by a bond-fluctuating Monte Carlo simulation
  R. B. Pandey and B. L. Farmer
  Phys. Rev. E 77, 031902 (2008)
• Stochastic dynamics and denaturation of thermalized DNA
  Mao Lin Deng and Wei Qiu Zhu
  Phys. Rev. E 77, 021918 (2008)
• Nonequilibrium-Driven Motion in Actin Networks: Comet Tails and Moving Beads
  N. J. Burroughs and D. Marenduzzo
  Phys. Rev. Lett. 98, 238302 (2007)
• Combined Effect of Pore Radius and Protein Dielectric Coefficient on the Selectivity of a Calcium Channel
  Dezső Boda, Mónika Valiskó, Bob Eisenberg, Wolfgang Nonner, Douglas Henderson, and Dirk Gillespie
  Phys. Rev. Lett. 98, 168102 (2007)
• Separation of Suspended Particles by Arrays of Obstacles in Microfluidic Devices
  Zhigang Li and German Drazer
  Phys. Rev. Lett. 98, 050602 (2007)
• Two-State Folding, Folding through Intermediates, and Metastability in a Minimalistic Hydrophobic-Polar Model for Proteins
  Stefan Schnabel, Michael Bachmann, and Wolfhard Janke
  Phys. Rev. Lett. 98, 048103 (2007)
• Stochastic simulations of the repressilator circuit
  Adiel Loinger and Ofer Biham
  Phys. Rev. E 76, 051917 (2007)
• Link and subgraph likelihoods in random undirected networks with fixed and partially fixed degree sequences
  Jacob G. Foster, David V. Foster, Peter Grassberger, and Maya Paczuski
  Phys. Rev. E 76, 046112 (2007)
• How the excluded volume architecture influences ion-mediated forces between proteins
  V. Dahirel, M. Jardat, J.-F. Dufrêche, and P. Turq
  Phys. Rev. E 76, 040902 (2007)
• Simulation via direct computation of partition functions
  Cheng Zhang and Jianpeng Ma
  Phys. Rev. E 76, 036708 (2007)
• Graph animals, subgraph sampling, and motif search in large networks
  Kim Baskerville, Peter Grassberger, and Maya Paczuski
  Phys. Rev. E 76, 036107 (2007)
• Accuracy and convergence of the Wang-Landau sampling algorithm
  Alexander N. Morozov and Sheng Hsien Lin
  Phys. Rev. E 76, 026701 (2007)
• Wang-Landau molecular dynamics technique to search for low-energy conformational space of proteins
  Takehiro Nagasima, Akira R. Kinjo, Takashi Mitsui, and Ken Nishikawa
  Phys. Rev. E 75, 066706 (2007)
• Simulation studies of a phenomenological model for elongated virus capsid formation
  Ting Chen and Sharon C. Glotzer
  Phys. Rev. E 75, 051504 (2007)
• Solutions of burnt-bridge models for molecular motor transport
  Alexander Yu. Morozov, Ekaterina Pronina, Anatoly B. Kolomeisky, and Maxim N. Artyomov
  Phys. Rev. E 75, 031910 (2007)
• Stochastic simulations of genetic switch systems
  Adiel Loinger, Azi Lipshtat, Nathalie Q. Balaban, and Ofer Biham
  Phys. Rev. E 75, 021904 (2007)
• Inferring DNA sequences from mechanical unzipping data: the large-bandwidth case
  V. Baldazzi, S. Bradde, S. Cocco, E. Marinari, and R. Monasson
  Phys. Rev. E 75, 011904 (2007)
• Fragmentation cross sections of 290 and 400 MeV/nucleon 12C beams on elemental targets
  C. Zeitlin, S. Guetersloh, L. Heilbronn, J. Miller, A. Fukumura, Y. Iwata, and T. Murakami
  Phys. Rev. C 76, 014911 (2007)
• Effect of Confinement on the Interaction between Two Like-Charged Rods
  G. Odriozola, F. Jiménez-Ángeles, and M. Lozada-Cassou
  Phys. Rev. Lett. 97, 018102 (2006)
• Probing the Mechanical Unzipping of DNA
  N. K. Voulgarakis, A. Redondo, A. R. Bishop, and K. Ø. Rasmussen
  Phys. Rev. Lett. 96, 248101 (2006)
• Weight matrices for protein-DNA binding sites from a single co-crystal structure
  Robert G. Endres and Ned S. Wingreen
  Phys. Rev. E 73, 061921 (2006)
• Monte Carlo simulation of chromatin stretching
  Frank Aumann, Filip Lankas, Maïwen Caudron, and Jörg Langowski
  Phys. Rev. E 73, 041927 (2006)
• Monte Carlo simulations of polyelectrolytes inside viral capsids
  Daniel George Angelescu, Robijn Bruinsma, and Per Linse
  Phys. Rev. E 73, 041921 (2006)
• Electron spectroscopy in proton collisions with dry gas-phase uracil base
  Patrick Moretto-Capelle and Arnaud Le Padellec
  Phys. Rev. A 74, 062705 (2006)
• Coupled Dynamics of RNA Folding and Nanopore Translocation
  Ralf Bundschuh and Ulrich Gerland
  Phys. Rev. Lett. 95, 208104 (2005)
• Bubble Nucleation and Cooperativity in DNA Melting
  S. Ares, N. K. Voulgarakis, K. Ø. Rasmussen, and A. R. Bishop
  Phys. Rev. Lett. 94, 035504 (2005)
• Mesoscopic modeling for nucleic acid chain dynamics
  M. Sales-Pardo, R. Guimerà, A. A. Moreira, J. Widom, and L. A. Amaral
  Phys. Rev. E 71, 051902 (2005)
• Clustered Bottlenecks in mRNA Translation and Protein Synthesis
  Tom Chou and Greg Lakatos
  Phys. Rev. Lett. 93, 198101 (2004)
• DNA -DNA interaction beyond the ground state
  D. J. Lee, A. Wynveen, and A. A. Kornyshev
  Phys. Rev. E 70, 051913 (2004)
• Nucleosome interactions in chromatin: Fiber stiffening and hairpin formation
  Boris Mergell, Ralf Everaers, and Helmut Schiessel
  Phys. Rev. E 70, 011915 (2004)
• Density functional study on the structures and thermodynamic properties of small ions around polyanionic DNA
  Ke Wang, Yang-Xin Yu, and Guang-Hua Gao
  Phys. Rev. E 70, 011912 (2004)
• Semiphenomenological model for the dispersion of DNA during electrophoresis in a microfluidic array of posts
  Kevin D. Dorfman and Jean-Louis Viovy
  Phys. Rev. E 69, 011901 (2004)
• Statistical mechanics of RNA folding: A lattice approach
  P. Leoni and C. Vanderzande
  Phys. Rev. E 68, 051904 (2003)
• Structure formation, melting, and optical properties of gold/DNA nanocomposites: Effects of relaxation time
  Sung Yong Park and D. Stroud
  Phys. Rev. B 68, 224201 (2003)
• Roles of Stiffness and Excluded Volume in DNA Denaturation
  Enrico Carlon, Enzo Orlandini, and Attilio L. Stella
  Phys. Rev. Lett. 88, 198101 (2002)
• Scaling in DNA unzipping models: Denaturated loops and end segments as branches of a block copolymer network
  Marco Baiesi, Enrico Carlon, and Attilio L. Stella
  Phys. Rev. E 66, 021804 (2002)
• Approach to Monte Carlo calculation of the buckling of supercoiled DNA loops
  Yang Zhang
  Phys. Rev. E 62, R5923 (2000)
• Diffusion constant for the repton model of gel electrophoresis
  M. E. Newman and G. T. Barkema
  Phys. Rev. E 56, 3468 (1997)
• Hydrodynamics of a DNA molecule in a flow field
  R. G. Larson, T. T. Perkins, D. E. Smith, and S. Chu
  Phys. Rev. E 55, 1794 (1997)
• Radial Distribution Function of Semiflexible Polymers
  Jan Wilhelm and Erwin Frey
  Phys. Rev. Lett. 77, 2581 (1996)
• Lattice ribbons: A model of double-stranded polymers
  E.J. Janse van Rensburg, E. Orlandini, D.W Sumners, M.C. Tesi, and S.G. Whittington
  Phys. Rev. E 50, R4279 (1994)
• Monte Carlo simulation of the unwinding of cholesteric twist
  Arunava Chatterjee and David H. Van Winkle
  Phys. Rev. E 49, 1450 (1994)
• Computation of the fraction of RNA sequences that fold sequentially into a unique free-energy minimum
  Ariel Fernández
  Phys. Rev. A 46, R4524 (1992)
• Fluctuations and resulting competing pathways in RNA folding: The activation of splicing
  Ariel Fernández
  Phys. Rev. A 43, 1138 (1991)
• Random energy model for the kinetics of RNA folding
  Ariel Fernández
  Phys. Rev. Lett. 65, 2259 (1990)
• Glassy kinetic barriers between conformational substates in RNA
  Ariel Fernández
  Phys. Rev. Lett. 64, 2328 (1990)
• Activation-energy landscape for metastable RNA folding
  Ariel Fernández and Eugene I. Shakhnovich
  Phys. Rev. A 42, 3657 (1990)