Related papers: Rethinking hydrogen-bond kinetics
One of the main applications of atomistic computer simulations is the calculation of ligand binding energies. The accuracy of these calculations depends on the force field quality and on the thoroughness of configuration sampling. Sampling…
Conventional hydrodynamics describes systems with few long-lived excitations. In one dimension, however, many experimentally relevant systems feature a large number of long-lived excitations even at high temperature, because they are…
The resistance of hydrogen-bond networks to ambient flow in water produces viscoelectric stresses and contributes to electrostrictive pressure. Within Onsager's nonequilibrium thermodynamic framework, a lattice-gas description of aqueous…
Using modified Arrhenius approximations, the activation energies of water, alcohols, and hexane structure rearrangement reactions responsible for temperature dependences of their dynamic and dielectric characteristics were determined. The…
We develop a general kinetic theory framework to describe the hydrodynamics of strongly interacting, nonequilibrium quantum systems in which integrability is weakly broken, leaving a few residual conserved quantities. This framework is…
Inspired by dense contractile tissues, where cells are subject to periodic deformation, we formulate and study a generic hydrodynamic theory of pulsating active liquids. Combining mechanical and phenomenological arguments, we postulate that…
We propose a dynamical model depicting the interactions between DNA and a specific binding protein involving long range transmissions. The dynamics rely on the coupling between Hydrogen bonds formed between DNA and protein and between the…
Elastic network models (ENM) and constraint-based, topological rigidity analysis are two distinct, coarse-grained approaches to study conformational flexibility of macromolecules. In the two decades since their introduction, both have…
A gaussian distribution of binding energies, but conditioned to exploit generally available information on packing in liquids, provides a statistical-thermodynamic theory of liquid water that is structurally non-committal, molecularly…
Many atomic liquids can form transient covalent bonds reminiscent of those in the corresponding solid states. These directional interactions dictate many important properties of the liquid state, necessitating a quantitative, atomic-scale…
The hydrogen bond is usually described within the clamped nucleus approximation in which electronic and vibrational motions are considered separately. This approach leads to a double-well potential which facilitates proton tunnelling. In…
While the water molecule is simple, its condensed phase liquid behavior is so complex that no consensus description has emerged despite three centuries of effort. Here we identify features of its behavior that are the most peculiar, hence…
We have investigated thermodynamic and dynamic properties as well as the dielectric constant of water-metha\-nol model mixtures in the entire range of composition by using constant pressure molecular dynamics simulations at ambient…
The hydrodynamic interpretation of quantum mechanics treats a system of particles in an effective manner. In this work, we investigate squeezed coherent states within the hydrodynamic interpretation. The Hamiltonian operator in question is…
Simulation techniques based on accurate and efficient representations of potential energy surfaces are urgently needed for the understanding of complex aqueous systems such as solid-liquid interfaces. Here, we present a machine learning…
Hydrogen bonding is modeled in terms of virtual exchange of protons between water molecules. A simple lattice model is analyzed, using ideas and techniques from the theory of correlated electrons in metals. Reasonable parameters reproduce…
Fluids under extreme confinement exhibit unique structures and intermolecular bonding, distinct from their bulk analogs, driving innovative applications at the water-energy nexus. Probing confined water experimentally at the length scale of…
In order to understand the nature and dynamics of interfacial water molecules on the surface of complex systems, large scale molecular dynamics simulations of an aqueous micelle of cesium perfluorooctanoate surfactant molecules have been…
The hydrogen-bond network of water is characterized by the presence of coordination defects relative to the ideal tetrahedral network of ice, whose fluctuations determine the static and time-dependent properties of the liquid. Because of…
By solving a simple kinetic equation, in the relaxation time approximation, and for a particular set of moments of the distribution function, we establish a set of equations which, on the one hand, capture exactly the dynamics of the…