Journal ArticleDOI
Molecular dynamics simulation of polymer chains with excluded volume
Reads0
Chats0
TLDR
In this article, the mean square end-to-end distance and radius of gyration are found to vary exponentially with chain length, and the results are similar to those obtained in Monte Carlo and self-avoiding walk studies.Abstract:
Molecular dynamics simulation techniques have been used to study the equilibrium configurational properties of freely moving polymer chains constructed from linked elastic spheres. The mean square end-to-end distance and radius of gyration are found to vary exponentially with chain length, and the results are similar to those obtained in Monte Carlo and self-avoiding walk studies. It is suggested that molecular dynamics is capable of yielding results of the same quality as Monte Carlo, while avoiding the inherent sampling problems.read more
Citations
More filters
Journal ArticleDOI
Molecular dynamics simulations of spontaneous fibril formation by random-coil peptides
Hung D. Nguyen,Carol K. Hall +1 more
TL;DR: Systems containing 12-96 model polyalanine peptides form fibrils at temperatures greater than a critical temperature that decreases with peptide concentration and exceeds the peptide's folding temperature, consistent with experimental findings.
Journal ArticleDOI
Deciphering the kinetic mechanism of spontaneous self-assembly of icosahedral capsids.
TL;DR: The competition between the formation of full capsids and nonidealized structures is strongly dependent upon the protein concentration and temperature, occurring kinetically as a cascade of elementary reactions in which free monomers are added to the growing oligomers on a downhill free-energy landscape.
Journal ArticleDOI
Equilibrium thermodynamics of homopolymers and clusters: Molecular dynamics and Monte Carlo simulations of systems with square-well interactions
TL;DR: The thermodynamics of homopolymers and clusters with square-well interactions of up to 64 particles are studied with constant-temperature discontinuous molecular dynamics simulations; for comparison Monte Carlo ~MC! simulations are also reported as discussed by the authors.
Journal ArticleDOI
alpha-helix formation: discontinuous molecular dynamics on an intermediate-resolution protein model.
Anne Voegler Smith,Carol K. Hall +1 more
TL;DR: The ability of the intermediate‐resolution model developed in this work to accurately mimic realistic peptide behavior is demonstrated, suggesting that simulations of very long times are possible with this model.
Journal ArticleDOI
Molecular dynamics study of a polymer chain in solution
TL;DR: In this paper, the behavior of a polymer chain in solution has been simulated by means of molecular dynamics techniques and both the equilibrium configurational properties of chains of various lengths and their time-dependent autocorrelation functions are studied.
References
More filters
Journal ArticleDOI
Studies in Molecular Dynamics. I. General Method
Berni J. Alder,T. E. Wainwright +1 more
TL;DR: A method is outlined by which it is possible to calculate exactly the behavior of several hundred interacting classical particles so that the solution of many problems in both equilibrium and nonequilibrium statistical mechanics is discussed.
Journal ArticleDOI
The statistical mechanics of polymers with excluded volume
TL;DR: In this article, the probability distribution of the configurations of a polymer consisting of freely hinged links of length l and excluded volume v is studied, and it is shown that the interaction of the polymer with itself can be represented by considering the polymer under the influence of a self-consistent field which reduces the problem to an equation like the Hartree equation for an atom.
Journal ArticleDOI
Mean square endpoint separation of off‐lattice self‐avoiding walks
TL;DR: In this paper, a new algorithm combining the features of the enrichment procedure of Wall and Erpenbeck and the dimerization procedure of Alexandrowicz was used to generate ten thousand off-lattice self-avoiding walks of 500 steps.
Journal ArticleDOI
Monte Carlo calculations on off-lattice polymer chains. The influence of variation of the excluded volume
TL;DR: In this paper, Monte Carlo calculations on off-lattice chains with various ratios lambda of bead diameter to bond length show that gamma and gamma are not 6/5 throughout but depend on lambda.
Journal ArticleDOI
Monte Carlo studies of the excluded volume problem for polymer chains in the continuum. I. Use of inversely restricted sampling techniques
N C Smith,R J Fleming +1 more
TL;DR: In this article, the use of inversely restricted sampling to generate off-lattice model chains, with either freely varying or fixed bond angles, and free rotation about bonds, is described.