相关论文: Dipolar response of hydrated proteins

Recent experiments have reported lower critical solution temperature (LCST) phase behavior of aqueous solutions of proteins induced by multivalent ions, where the solution phase separates upon heating. This phenomenon is linked to complex…

A novel combination of discontinuous molecular dynamics and the Langevin equation, together with an intermediate-resolution model, are used to carry out long (several $\mu$s) simulation and study folding transition and transport of proteins…

A theoretical approach is developed to quantify hydrophobic hydration and interactions on a molecular scale, with the goal of gaining insight into the molecular origins of hydrophobic effects. The model is based on the fundamental relation…

Protein-protein interactions (protein functionalities) are mediated by water, which compacts individual proteins and promotes close and temporarily stable large-area protein-protein interfaces. In their classic paper Kyte and Doolittle (KD)…

We investigate dynamical coupling between water and amino acid side-chain residues in solvation dynamics by selecting residues often used as natural probes, namely tryptophan, tyrosine and histidine, located at different positions on…

Electrostatic interactions between point charges embedded into interfaces separating dielectric media are omnipresent in soft matter systems and often control their stability. Such interactions are typically complicated and do not resemble…

The dielectric response of nano-confined fluids is crucial across technologies and biological systems, yet its calculation and interpretation from molecular simulations are often muddled by unclear boundary conditions. We re-derive the…

Combining elastic incoherent neutron scattering experiments at different resolutions with molecular dynamics simulations, we report the observation of a protein-like dynamical transition in linear chains of Poly(N-isopropylacrylamide). We…

The response of polar solvents to ions and polar molecules dictates many fundamental molecular processes. To understand such electrostatically-driven solvation processes, one ideally would probe the dielectric response of a solvent to an…

An exact integral formula for the Kirkwood correlation factor of isotropic polar fluids $g_K$ is derived from the equilibrium averaged rotational Dean equation, which as compared to previous approaches easily lends itself to further…

We refine a protein model that reproduces fundamental aspects of protein thermodynamics. The model exhibits two transitions, hot and cold unfolding. The number of relevant parameters is reduced to three: 1) binding energy of folding…

We present a computational study on the folding and aggregation of proteins in aqueous environment, as function of its concentration. We show how the increase of the concentration of individual protein species can induce a partial unfolding…

We present a complete calculation, fully accounting for quantum effects and for molecular flexibility, of the first dielectric virial coefficient of water and its isotopologues. The contribution of the electronic polarizability is computed…

Biological forces govern essential cellular and molecular processes in all living organisms. Many cellular forces, e.g. those generated in cyclic conformational changes of biological machines, have repetitive components. However, little is…

The mechanism of cold- and pressure-denaturation are matter of debate. Some models propose that when denaturation occurs more hydrogen bonds between the molecules of hydration water are formed. Other models identify the cause in the density…

Non-local electrostatic interactions associated with the finite solvent size and ion polarizability are investigated within the mean-field linear response theory. To this end, we introduce a field theoretic model of a polar liquid composed…

Quantum mechanical calculations are performed on 116 conformers of the protein ubiquitin (Lange et al., Science 2008, 320, 1471-1475). The results indicate that the heat of formation (HOF), dipole moment, energy of the frontier orbitals…

Hydrophobic thickness mismatch between integral membrane proteins and the surrounding lipid bilayer can produce lipid bilayer thickness deformations. Experiment and theory have shown that protein-induced lipid bilayer thickness deformations…

Molecular dynamics simulations are used to study the mechanism and kinetics of hydrated electron diffusion. The electron center of mass is found to exhibit Brownian-type behavior with a diffusion coefficient considerably greater than that…

The effect of the applied trajectory length on the convergence of the static dielectric constant and the self-diffusion coefficient were examined for the SPC/E water model in the NVT ensemble with different system size at 293 K. Very long…