Related papers: Folding and form: Insights from lattice simulation…
The extent of coupling between the folding of a protein and its binding to a substrate varies from protein to protein. Some proteins have highly structured native states in solution, while others are natively disordered and only fold fully…
The relevance of various residue positions for the stability and the folding characteristics of the prion protein are investigated by using molecular dynamics simulations of models exploiting the topology of the native state. Highly…
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…
A system of optimal biaxial molecules placed at the sites of a cubic lattice is studied in an extended Lebwohl-Lasher model. Molecules interact only with their nearest neighbors through the pair potential that depends on the molecule…
The self-avoid random walk algorithm has been extensively used in the study of polymers. In this work we study the basic properties of the trajectories generated with this algorithm when two interactions are added to it: contact and folding…
Mitsumatsu constructed leafwise symplectic structures of certain codimension one foliations of the 5-sphere. This inspired the present author to improve his result on convergence of contact structure to foliation. We describe convergence of…
Lattices and their underlying symmetries play a central role in determining the physical properties and applications of many natural and engineered materials. By bridging the lattice geometry and rigid-folding kinematics, this study…
At low temperatures, some lattice spin models with simple ferromagnetic or antiferromagnetic interactions (for example nearest-neighbour interaction being isotropic in spin space on a bipartite three-dimensional lattice) produce…
A vertex model introduced by M. Bowick, P. Di Francesco, O. Golinelli, and E. Guitter (cond-mat/9502063) describing the folding of the triangular lattice onto the face centered cubic lattice has been studied in the hexagon approximation of…
Cotranslational folding depends on the folding speed and stability of the nascent protein. It remains difficult, however, to predict which proteins cotranslationally fold. Here, we simulate evolution of model proteins to investigate how…
The dynamical chaos in Lennard-Jones toy models of heteropolymers is studied by molecular dynamics simulations. It is shown that two nearby trajectories quickly diverge from each other if the heteropolymer corresponds to a random sequence.…
We present results of Monte-Carlo simulations for finite 2D single and bilayer systems. Strong Coulomb correlations lead to arrangement of particles in configurations resembling a crystal lattice. For binary layers, there exists a…
The aqueous solvent profoundly influences protein folding, yet its effects are relatively poorly understood. In this study, we investigate the impact of solvation on the folding of lattice proteins by using Monte Carlo simulations. The…
We study the stationary properties of the two-dimensional pair contact process, a nonequilibrium lattice model exhibiting a phase transition to an absorbing state with an infinite number of configurations. The critical probability and…
We study the collective dynamics of a lattice model of stochastically interacting agents with a weighted field of vision. We assume that agents preferentially interact with neighbours, depending on their relative location, through velocity…
The equilibrium properties of hard rod monolayers are investigated in a lattice model (where position and orientation of a rod are restricted to discrete values) as well as in an off--lattice model featuring spherocylinders with continuous…
Pressure-induced phase transitions of spin-crossover materials were simulated by a Monte Carlo simulation in the constant pressure ensemble for the first time. Here, as the origin of the cooperative interaction, we adopt elastic interaction…
In structure-based models of proteins, one often assumes that folding is accomplished when all contacts are established. This assumption may frequently lead to a conceptual problem that folding takes place in a temperature region of very…
Motivated by recent developments in magnetic materials, frustrated nanoarrays and cold atomic systems, we investigate the behaviour of dipolar spins on the frustrated two-dimensional kagome lattice. By combining the Luttinger-Tisza…
What energetic and solvation effects underlie the remarkable two-state thermodynamics and folding/unfolding kinetics of small single-domain proteins? To address this question, we investigate the folding and unfolding of a hierarchy of…