相关论文: The structural order of protein hydration water

In equilibrium and supercooled liquids, polymorphism is manifested by thermodynamic regions defined in the phase diagram, which are predominantly of different short- and medium-range order (local structure). It is found that on the phase…

The mechanism behind mutual recognition of homologous DNA sequences prior to genetic recombination is one of the remaining puzzles in molecular biology. Leading models of homology recognition, based on classical electrostatics, neglect the…

Water plays a crucial role in geological, biological, and technological processes. Nanoscale water confinement occurs in many of these settings, including sedimentary rocks, water channel proteins, and applications like desalination and…

The mobility of water molecules confined in a silica pore is studied by computer simulation in the low hydration regime, where most of the molecules reside close to the hydrophilic substrate. A layer analysis of the single particle dynamics…

Water and water-mediated interactions determine thermodynamic and kinetics of protein folding, protein aggregation and self-assembly in confined spaces. To obtain insights into the role of water in the context of folding problems, we…

Surface effects could play a dominant role in modifying the natural liquid order. In some cases, the effects of the surface interactions can propagate inwards, and even can interfere with a similar propagation from opposite surfaces. This…

Isotopic substitution, which can be realized both in experiment and computer simulations, is a direct approach to assess the role of nuclear quantum effects on the structure and dynamics of matter. Yet, the impact of nuclear quantum effects…

Proteins play a central role in biology from immune recognition to brain activity. While major advances in machine learning have improved our ability to predict protein structure from sequence, determining protein function from structure…

The swimming behavior of bacteria and other microorganisms is sensitive to the physical properties of the fluid in which they swim. Mucus, biofilms, and artificial liquid-crystalline solutions are all examples of fluids with some degree of…

A reduced model, which can fold both helix and sheet structures, is proposed to study the problem of protein folding. The goal of this model is to find an unbiased effective potential that has included the effects of water and at the same…

We present a probabilistic approach to water-water hydrogen bonding that allows one to obtain an analytic expression for the number of bonds per water molecule as a function of both its distance to a hydrophobic particle and hydrophobe…

Hydroxide ion transport and structure in aqueous media is fundamental to many chemical and biological processes. Research on hydroxide behavior has primarily focused on a single fully solvated hydroxide, either as an isolated cluster or in…

Water provides the driving force for the assembly and stability of many cellular components. Despite its impact on biological functions, a nanoscale understanding of the relationship between its structure and dynamics under soft confinement…

The covalent-like characteristics of hydrogen bonds offer a new perspective on intermolecular interactions. Here, using density functional theory and post-Hartree-Fock methods, we reveal that there are two bonding molecular orbitals (MOs)…

We have employed molecular dynamics simulations based on the TIP4P/2005 water model to investigate the local structural, dynamical, and dielectric properties of the two recently reported body-centered-cubic and face-centered-cubic plastic…

The microscopic description of the local structure of water remains an open challenge. Here, we adopt an agnostic approach to understanding water's hydrogen bond network using data harvested from molecular dynamics simulations of an…

The zero point kinetic energy of protons in water is large on the scale of chemical interaction energies(29 Kj/mol in bulk room temperature water). Its value depends upon the structure of the hydrogen bond network, and can change as the…

We consider the hydrodynamics of lipid bilayers containing transmembrane proteins of arbitrary shape. This biologically-motivated problem is relevant to the cell membrane, whose fluctuating dynamics play a key role in phenomena ranging from…

Water is the main component of interstellar ice mantles, is abundant in the solar system and is a crucial ingredient for life. The formation of this molecule in the interstellar medium cannot be explained by gas-phase chemistry only and its…

S-nitrosylation, the covalent addition of NO to the thiol side chain of cysteine, is an important post-transitional modification (PTM) that can affect the function of proteins. As such, PTMs extend and diversify protein functions and thus…