Equilibrium thermodynamics of homopolymers and clusters: Molecular dynamics and Monte Carlo simulations of systems with square-well interactions

Abstract

The thermodynamics of homopolymers and clusters with square-well interactions of up to 64 particles are studied with constant-temperature discontinuous molecular dynamics ͑DMD͒ simulations; for comparison Monte Carlo ͑MC͒ simulations are also reported. Homopolymers composed of more than five beads are found to exhibit two or more equilibrium transitions. In the long chain limit, these multiple transitions correspond to gas-to-liquid, liquid-to-solid, and solid-to-solid transitions. In particular, the liquid-to-solid-like disorder-to-order transition for isolated 32mers and 64mers is strongly first order ͑bimodal energy distribution͒ at the reduced square-well diameter ϭ1.5. As decreases from 1.5 to 1.3, the bimodal distribution becomes unimodal. The use of Lindemann's rule for solids indicates that the structure formed right below the liquid-to-solid transition temperature has a solid core but a liquid surface. Comparing the homopolymer results with those for square-well clusters indicates that the bonding constraint in homopolymers increases the temperatures of transitions but decreases their strength. The solid structure of an isolated 64mer is nearly identical to that of a cluster of 64 beads. Possible approaches to the experimental observation of the solid-state for an isolated chain are discussed.

Is there an en route folding intermediate for cold shock proteins?

“…The total energy of any given conformation is calculated as the sum of all pairwise energies for nonlocal atoms. Discrete molecular dynamics with constant temperature 43,51 is used in both thermodynamic sampling and the studies of folding kinetics. As shown in Figure 1, residues 2-10, 14-19, 26-29, 44-53, and 58-66 are defined as strands b1-b5, respectively.…”

Helical Structures from an Isotropic Homopolymer Model

“…Across the temperature range studied, no ordered low temperature structures are observed for σ/l < 1.475. For σ/l = 1, the globule should freeze into an ordered crystalline phase [10,11] at sufficiently low temperature. For other values of σ/l, however, the low temperature structure is still unclear.…”

“…Zhou and coworkers discovered [10,11] a freezing transition for linear homopolymers composed of tangenthard spheres that interact with each other through an attractive square-well potential. During this discontinuous transition, the collapsed "molten" globule state freezes into a highly symmetric crystalline-like state.…”

Simple but predictive protein models

“…We describe the use of simplified protein models in conjunction with the rapid simulations methodology, discrete molecular dynamics (DMD). Despite the use of DMD in simulating polymer fluids [6,7], single homopolymers [7,8], proteins [9][10][11][12][13][14][15][16][17][18][19][20][21][22][23][24][25], protein aggregates [13,17,23,24,26], and gases and liquids [27,28], we believe it is significantly underutilized in the molecular-modeling field.…”