Related papers: Temperature- and Force-Induced beta-Sheet Unfoldin…
We describe a class of "bare bones" models of homopolymers which undergo coil-globule collapse and proteins which fold into their native states in free space or into denatured states when captured by an attractive substrate as the…
We investigate the sequence-dependent properties of proteins that determine the dual requirements of stability of the native state and its kinetic accessibility using simple cubic lattice models. Three interaction schemes are used to…
The thermodynamic formalism expresses chaotic properties of dynamical systems in terms of the Ruelle pressure $\psi(\beta)$. The inverse-temperature like variable $\beta$ allows one to scan the structure of the probability distribution in…
Energetic correlations due to polymeric constraints and the locality of interactions, in conjunction with the apriori specification of the existence of a particularly low energy state, provides a method of introducing the aspect of minimal…
Mechanical stretching of secondary structures is studied through molecular dynamics simulations of a Go-like model. Force vs. displacement curves are studied as a function of the stiffness and velocity of the pulling device. The succession…
We consider the Ising model on the two-dimensional square lattice where on each horizontal line, called "layer", the interaction is given by a ferromagnetic Kac potential with coupling strength $J_\gamma(x,y)=\gamma J(\gamma(x-y))$, where…
Protein sequences are believed to have been selected to provide the stability of, and reliable renaturation to, an encoded unique spatial fold. In recently proposed theoretical schemes, this selection is modeled as ``minimal frustration,''…
We study the aggregation of peptides using the discrete molecular dynamics simulations. At temperatures above the alpha-helix melting temperature of a single peptide, the model peptides aggregate into a multi-layer parallel beta-sheet…
We study the evolution of prior columnar $\beta$ phase, interface $L$ phase, and $\alpha$ phase during directional solidification of a Ti-6Al-4V melt pool. Finite element simulations estimate the solidification temperature and velocity…
The dynamic and static properties of a supercooled (non-entangled) polymer melt are investigated via molecular dynamics (MD) simulations. The system is confined between two completely smooth and purely repulsive walls. The wall-to-wall…
A joint experimental / theoretical investigation of the elastin-like octapeptide GVG(VPGVG) was carried out. In this paper a comprehensive molecular dynamics study of the temperature dependent folding and unfolding of the octapeptide is…
Monte Carlo simulations and finite-size scaling analysis have been carried out to study the critical behavior in a two-dimensional system of particles with two bonding sites that, by decreasing temperature or increasing density, polymerize…
Mechanical unfolding of several domains of calmodulin and titin is studied using a Go-like model with a realistic contact map and Lennard-Jones contact interactions. It is shown that this simple model captures the experimentally observed…
We analyze the dependence of thermal denaturation transition and folding rates of globular proteins on the number of amino acid residues, N. Using lattice Go models we show that DeltaT/T_F ~ N^-1, where T_F is the folding transition…
By quantitative studies of statistics of polymer stretching in a random flow and of a flow field we demonstrate that the stretching of polymer molecules in a 3D random flow occurs rather sharply via the coil-stretch transition at the value…
We study the structural and thermodynamic properties of bilayer graphene, a prototype two-layer membrane, by means of Monte Carlo simulations based on the empirical bond order potential LCBOPII. We present the temperature dependence of…
Intermolecular forces are known to precipitate adhesion events between solid bodies. Inspired by a macro-scale experiment showing the hysteretic adhesion of a piece of flexible tape over a plastic substrate, we develop here a model of…
Semiflexible polymer models are widely used as a paradigm to understand structural phases in biomolecules including folding of proteins. Since stable knots are not so common in real proteins, the existence of stable knots in semiflexible…
We report the first observation of temperature-controlled reentrant transition in simulations of mixtures of small and big particles interacting via soft repulsive potential in 2D. As temperature increases, the system passes from a fluid…
Combined tearing-thermal evolution plays an important role in the disruption of current sheets, and formation of cool condensations within the solar atmosphere. However, this has received limited attention to date. We numerically explore a…