Related papers: A Multicanonical Molecular Dynamics Study on a Sim…
We discuss general thermodynamic properties of molecular structure formation processes like protein folding by means of simplified, coarse-grained models. The conformational transitions accompanying these processes exhibit similarities to…
A model to describe the mechanism of conformational dynamics in protein based on matter interactions using lagrangian approach and imposing certain symmetry breaking is proposed. Both conformation changes of proteins and the injected…
Using molecular dynamics simulations we study the slow dynamics of a colloidal fluid annealed within a matrix of obstacles quenched from an equilibrated colloidal fluid. We choose all particles to be of the same size and to interact as hard…
We introduce an exactly solvable statistical-mechanical model of the hydration of non-polar compounds, based on grouping water molecules in clusters where hydrogen bonds and isotropic interactions occur; interactions between clusters are…
We review a molecular dynamics method for nucleon many-body systems called the quantum molecular dynamics (QMD) and our studies using this method. These studies address the structure and the dynamics of nuclear matter relevant to the…
We analyze a bubble forming system composed of particles with competing long range repulsive and short range attractive interactions driven over a quasi-one-dimensional periodic substrate. We find various pinned and sliding phases as a…
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…
We propose a protein model based on a hierarchy of constraints that force the protein to follow certain pathways when changing conformation. The model exhibits a first order phase transition, cooperativity and is exactly solvable. It also…
A hybrid mesoscopic multi-particle collision model is used to study diffusion-influenced reaction kinetics. The mesoscopic particle dynamics conserves mass, momentum and energy so that hydrodynamic effects are fully taken into account.…
A comprehensive, semi-quantitative model for the thermodynamics of hydrophobic solvation is presented. The model is based on a very simple premise suggested by the scaled particle theory and treats both solute and solvent molecules as hard…
For a system of two spatially separated monoatomic graphene layers encapsulated in hexagonal boron nitride, we consider the drag effect between charge carriers in the Fermi liquid regime. Commonly, the phenomenon is described in terms of an…
Wang-Landau sampling has been applied to investigate the thermodynamics and structural properties of a lattice hydrophobic-polar heteropolymer (the HP protein model) interacting with an attractive substrate. For simplicity, we consider a…
Studies of liquid water in its supercooled region have led to many insights into the structure and behavior of water. While bulk water freezes at its homogeneous nucleation temperature of approximately 235 K, for protein hydration water,…
The mechanisms of cold- and pressure-denaturation of proteins are matter of debate and are commonly understood as due to water-mediated interactions. Here we study several cases of proteins, with or without a unique native state, with or…
In a similar way in which the folding of single--domain proteins provide an important test in the study of self--organization, the folding of homodimers constitute a basic challenge in the quest for the mechanisms which are at the basis of…
We use molecular dynamic simulations to investigate the relation between the presence of packing defects in a glass-former and the spontaneous cooperative motions called dynamic heterogeneity. For that purpose we use a simple diatomic…
We investigate theoretically the behavior of proteins as well as other large macromolecules which are incorporated into amphiphilic monolayers at the air-water interface. We assume the monolayer to be in the coexistence region of the…
The internal dynamics of strongly interacting systems and that of biomolecules such as proteins display several important analogies, despite the huge difference in their characteristic energy and length scales. For example, in all such…
A protein's function depends critically on its conformational ensemble, a collection of energy weighted structures whose balance depends on temperature and environment. Though recent deep learning (DL) methods have substantially advanced…
A reliable prediction of 3D protein structures from sequence data remains a big challenge due to both theoretical and computational difficulties. We have previously shown that our kinetostatic compliance method (KCM) implemented into the…