Related papers: Modelling proton transfer in water molecule chains
Water is an associated liquid in which the main intermolecular interaction is the hydrogen bond (HB) which is limited to four per atom, independently of the number of neighbours. We have considered a hydrogen bond net superposed on Bernal's…
A simple model of globular proteins which incorporates anisotropic attractions is proposed. It is closely related to models used to model simple hydrogen-bonding molecules such as water. Theories for both the fluid and solid phases are…
The goal of this paper is to set up a framework designed to take into account the characteristics of sediment particles when transported by water. Our protocol consists in describing the characteristics of sediment particles via an…
Molecular fluids show rich and complicated dynamics close to the glass transition. Some of these observations are related to the fact that translational and orientational degrees of freedom couple in nontrivial ways. A model system which…
The understanding of dynamics and functioning of biological membranes and in particular of membrane embedded proteins is one of the most fundamental problems and challenges in modern biology and biophysics. In particular the impact of…
Transport of molecular motors along protein filaments in a half-closed geometry is a common feature of biologically relevant processes in cellular protrusions. Using a lattice gas model we study how the interplay between active and…
Monte Carlo simulation is used to study the dynamical crossover from single file diffusion to normal diffusion in fluids confined to narrow channels. We show that the long time diffusion coefficients for a series of systems involving hard…
We have mapped the molecular-atomic transition in liquid hydrogen using first principles molecular dynamics. We predict that a molecular phase with short-range orientational order exists at pressures above 100 GPa. The presence of this…
Novel experimental and computational studies have uncovered the proton momentum distribution in hydrogen bonded systems. In this work, we utilize recently developed open path integral Car-Parrinello molecular dynamics methodology in order…
Understanding the dynamic nature of the semiconductor-water interface is crucial for developing efficient photoelectrochemical water splitting catalysts, as it governs reactivity through charge and mass transport. In this study, we employ…
Dynamical systems having many coexisting attractors present interesting properties from both fundamental theoretical and modelling points of view. When such dynamics is under bounded random perturbations, the basins of attraction are no…
The generalized transport equations for a consistent description of kinetic and hydrodynamic processes in dense gases and liquids are considered. The inner structure of the generalized transport kernels for these equations is established.…
We present an ab initio molecular dynamics (MD) investigation of the tautomeric equilibrium for aqueous solutions of glycine and acetone at realistic experimental conditions. Metadynamics is used to accelerate proton migration among…
Aqueous radiation chemistry emerges through ultrafast proton transfer and ion-radical formation with unexplored energy-redistribution dynamics steering the subsequent reactions. We performed time-resolved disruptive probing on pure water…
The hopping model for cargo transport by molecular motors introduced in Refs. goldman1, goldman2, is extended here in order to incorporate the movement of cargo-motor complexes. In this context, hopping process expresses the possibility for…
Aquaporins (AQPs) are a family of transmembrane channels that are found from archaea, eubacteria, and fungi kingdoms to plants and animals. These proteins play a major role in water and small solutes transport across biological cell…
We discuss a model of motion of substance through the nodes of a channel of a network. The channel can be modeled by a chain of urns where each urn can exchange substance with the neighboring urns. In addition the urns can exchange…
Knotted proteins, when forced through the pores, can get stuck if the knots in their backbone tighten under force. Alternatively, the knot can slide off the chain, making translocation possible. We construct a simple energy landscape model…
We propose a simple model of cytochrome c oxidase, including four redox centers and four protonable sites, to study the time evolution of electrostatically coupled electron and proton transfers initiated by the injection of a single…
Heat dissipation is ubiquitous in living systems, which constantly convert distinct forms of energy into each other. The transport of thermal energy in liquids and even within proteins is well understood but kinetic energy transfer across a…