Long range moves for high density polymer simulations

Deutsch, J.M.
June 1997
Journal of Chemical Physics;6/1/1997, Vol. 106 Issue 21, p8849
Academic Journal
Develops long-range moves that are compatible with high density polymer p protein simulations traditionally done using the Monte Carlo method. Effectiveness in reaching random heteropolymers; Discussion of the results of 48-mer systems where the ground state is known exactly.


Related Articles

  • A Monte Carlo simulation study on the collapse transition of model polymers: Possible solvent effect and relevance to protein folding. Sen, Srikanta // Journal of Chemical Physics;4/1/1996, Vol. 104 Issue 13, p5304 

    A clear theoretical understanding of the protein folding problem both in kinetic as well as in thermodynamic aspects, has not yet been achieved. In this context, we have studied here the possible role of solvent on the equilibrium collapse transition characteristics of a polymer that serves as a...

  • Origin of scaling behavior of protein packing density: A sequential Monte Carlo study of compact long chain polymers. Zhang, Jinfeng; Chen, Rong; Tang, Chao; Liang, Jie // Journal of Chemical Physics;4/1/2003, Vol. 118 Issue 13, p6102 

    Single domain proteins are thought to be tightly packed. The introduction of voids by mutations is often regarded as destabilizing. In this study we show that packing density for single domain proteins decreases with chain length. We find that the radius of gyration provides a poor description...

  • Observation of the molten globule state in a Monte Carlo simulation of the coil-to-globule... Haojun Liang // Journal of Chemical Physics;5/22/1999, Vol. 110 Issue 20, p10212 

    Discusses the observation of the molten globule state in a Monte Carlo simulation of the coil-to-globule transition of a homopolymer chain. Implication of the existence of the special state on the process of the melting of the globule; Resemblance of the sate to the molten globule state of a...

  • Kinetic and thermodynamic analysis of proteinlike heteropolymers: Monte Carlo histogram technique. Socci, Nicholas D.; Onuchic, José Nelson // Journal of Chemical Physics;9/15/1995, Vol. 103 Issue 11, p4732 

    Using Monte Carlo dynamics and the Monte Carlo histogram method, the simple three-dimensional 27 monomer lattice copolymer is examined in depth. The thermodynamic properties of various sequences are examined contrasting the behavior of good and poor folding sequences. The good (fast folding)...

  • Density-of-States Based Monte Carlo Techniques for Simulation of Proteins and Polymers. Rathore, Nitin; Knotts IV, Thomas Allen; de Pablo, Juan José // AIP Conference Proceedings;2003, Vol. 690 Issue 1, p289 

    Monte Carlo methods are reaching a level of sophistication that permits study of relatively complex fluids or materials. Over the past few years our research group at the University of Wisconsin has concentrated its efforts on the development and application of these methods for the study of...

  • Brownian dynamics algorithm for entangled wormlike threads. Ramanathan, Shriram; Morse, David C. // Journal of Chemical Physics;3/7/2007, Vol. 126 Issue 9, p094906 

    The authors present a hybrid Brownian dynamics/Monte Carlo algorithm for simulating solutions of highly entangled semiflexible polymers or filaments. The algorithm combines a Brownian dynamics time-stepping approach with an efficient scheme for rejecting moves that cause chains to cross or that...

  • Monte Carlo update for chain molecules: Biased Gaussian steps in torsional space. Favrin, Giorgio; Irba¨ck, Anders; Sjunnesson, Fredrik // Journal of Chemical Physics;5/8/2001, Vol. 114 Issue 18 

    We develop a new elementary move for simulations of polymer chains in torsion angle space. The method is flexible and easy to implement. Tentative updates are drawn from a (conformation-dependent) Gaussian distribution that favors approximately local deformations of the chain. The degree of bias...

  • A theoretical method to compute sequence dependent configurational properties in charged polymers and proteins. Sawle, Lucas; Ghosh, Kingshuk // Journal of Chemical Physics;2015, Vol. 143 Issue 8, p1 

    A general formalism to compute configurational properties of proteins and other heteropolymers with an arbitrary sequence of charges and non-uniform excluded volume interaction is presented. A variational approach is utilized to predict average distance between any two monomers in the chain. The...

  • Conformational properties of a polymer chain confined between two plates. Ishinabe, Takao // Journal of Chemical Physics;7/1/1985, Vol. 83 Issue 1, p423 

    The behavior of a polymer chain confined between parallel plates a distance D apart is studied by Monte Carlo calculations of self-avoiding walks for up to 100 steps on the tetrahedral lattice. Scaling predictions of Daoud and de Gennes are tested using the data obtained; they are consistent...


Read the Article


Sorry, but this item is not currently available from your library.

Try another library?
Sign out of this library

Other Topics