Related papers: Allosteric Communication Pathways and Thermal Rect…
Allosteric regulation is a widespread strategy employed by several proteins to transduce chemical signals and perform biological functions. Metal sensor proteins are exemplary in this respect, e.g., in that they selectively bind and unbind…
Diffusion, transport of mass in response to concentration and thermal energy gradient, is an important transport property, vital in material science and life science. In the present work classical molecular dynamics study of diffusion of…
Molecular transport maintains cellular structures and functions. For example, lipid and protein diffusion sculpts the dynamic shapes and structures on the cell membrane that perform essential cellular functions, such as cell signaling.…
We consider Lagrangian coherent structures (LCSs) as the boundaries of material subsets whose advective evolution is metastable under weak diffusion. For their detection, we first transform the Eulerian advection-diffusion equation to…
The thermodynamic properties for three different types of off-lattice four-strand beta-sheet protein models interacting via a hybrid Go-type potential have been investigated. Discontinuous molecular dynamic simulations have been performed…
Low thermal conductivity is favorable for preserving the temperature gradient between the two ends of a thermoelectric material in order to ensure continuous electron current generation. In high-performance thermoelectric materials, there…
In cell membranes, proteins and lipids diffuse in a highly crowded and heterogeneous landscape, where aggregates and dense domains of proteins or lipids obstruct the path of diffusing molecules. In general, hindered motion gives rise to…
The point defect thermodynamics in a general family of binary compounds, including B2 compounds as a specific representative, are classified by way of two non-trivial energy parameters. The scheme is applied to published ab initio defect…
This work relaxes the assumption of point particles prevalent in the study of thermal transport characteristics in $\Phi^4$ chains. The particles of the modified chain, henceforth termed as the $\Phi^{4C}$ chain, can collide with each…
Understanding interfacial heat transfer between polymers and water is crucial for the design of biomaterials, drug delivery platforms, and nanofluidic systems. In this study, we employed all atom molecular dynamics (MD) simulations to…
Consider anomalous energy spread in solid phases, i.e., $MSD= \int (x -{\langle x \rangle}_E)^2 \rho_E(x,t)dx \propto t^{\beta}$, as induced by a small initial excess energy perturbation distribution $\rho_{E}(x,t=0)$ away from equilibrium.…
In this work we study the asymmetric heat flow, i.e., thermal rectification, of a one-dimensional, mass-graded system consisting of acoupled harmonic oscillator lattice (ballistic spacer) and two diffusive leads attached to the boundaries…
Heat-transport mechanism mediated by near-field interactions in plasmonic nanostructures networks is shown to be analogous to a generalized random-walk process. Existence of superdiffusive regimes is demonstrated both in linear ordered…
In the course of evolution, proteins undergo important changes in their amino acid sequences, while their three-dimensional folded structure and their biological function remain remarkably conserved. Thanks to modern sequencing techniques,…
Allosteric regulation is often viewed as thermodynamic in nature. However protein internal motions during an enzymatic reaction cycle can be slow hopping processes over numerous potential barriers. We propose that regulating molecules may…
Using analytical calculations and computer simulations we consider both the lateral diffusion of a membrane protein and the fluctuation spectrum of the membrane in which the protein is embedded. The membrane protein interacts with the…
The low-frequency collective vibrational modes in proteins as well as the protein-water interface have been suggested as dominant factors controlling the efficiency of biochemical reactions and biological energy transport. It is thus…
The Anderson metal-insulator transition is a fundamental phenomenon in condensed matter physics, describing the transition from a conducting (metallic) to a non-conducting (insulating) state driven by disorder in a material. At the critical…
Heat transport can be modelled with a variety of approaches in real space (using molecular dynamics) or in reciprocal space (using the Boltzmann transport equation). Employing two conceptually different approaches of each type, we study…
The thermodynamics of proteins indicate that folding/unfolding takes place either through stable intermediates or through a two-state process without intermediates. The rather short folding times of the two-state process indicate that…