Related papers: Characterizing Hydration Properties Based on the O…
Despite recent breakthroughs in understanding how protein sequence relates to structure and function, considerably less attention has been paid to the general features of protein surfaces beyond those regions involved in binding and…
We apply a phenomenological theory of polar liquids to calculate the interaction energy between two plane surfaces at nm-distances. We show that depending on the properties of the surface-liquid interfaces, the interacting surfaces induce…
We report here how the hydration of complex surfaces can be efficiently studied thanks to recent advances in classical molecular density functional theory. This is illustrated on the example of the pyrophylite clay. After presenting the…
Simplified, classical models of water are an integral part of atomistic molecular simulations, especially in biology and chemistry where hydration effects are critical. Yet, despite several decades of effort, these models are still far from…
As a common view the hydrophobic association between molecular-scale binding partners is supposed to be dominantly driven by entropy. Recent calorimetric experiments and computer simulations heavily challenge this established paradigm by…
Ionic liquids are widely used as electrolytes in electrochemical devices. In this context, many experimental and theoretical approaches have been recently developed for characterizing their interface with electrodes. In this perspective…
We develop a simple correspondence between hydrophobic surface topology of globular proteins and and an effective protein-protein adhesiveness parameter of the Baxter type. We discuss within this framework analytical interpretation of the…
The interface between hemoglobin (Hb) and its environment, in particular water, is of great physiological relevance. Here, results from {\it in vitro}, {\it in vivo}, and computational experiments (molecular dynamics simulations) are…
We simulate a hard-sphere liquid in confined geometry where the separation of the two parallel, hard walls is smaller than two particle diameters. By systematically reducing the wall separation we analyze the behavior of structural and…
We introduce fluctuating hydrodynamics approaches on surfaces for capturing the drift-diffusion dynamics of particles and microstructures immersed within curved fluid interfaces of spherical shape. We take into account the interfacial…
We construct a Hamiltonian for a single domain protein where the contact enthalpy and the chain entropy decrease linearly with the number of native contacts. The hydration effect upon protein unfolding is included by modeling water as ideal…
Molecules at the air-water interface often form inhomogeneous layers in which domains of different densities are separated by sharp interfaces. Complex interfacial pattern formation may occur through the competition of short- and long-range…
We present a new methodology to analyze complicated multi-physics simulations by introducing a fictitious parameter. Using the method, we study quantum mechanical aspects of an organic molecule in water. The simulation is variationally…
We develop a graph-based model of the hydrogen bond network in water, with a view towards quantitatively modeling the molecular-level correlational structure of the network. The networks are formed are studied by the constructing the model…
The interaction between surface patches of proteins with different surface properties has a vital role to play driving conformational changes of proteins in different salt solutions. We demonstrate the existence of ion-specific attractive…
In situ interfacial rheology and numerical simulations are used to investigate microgel monolayers in a wide range of packing fractions, $\zeta_{2D}$. The heterogeneous particle compressibility determines two flow regimes characterized by…
Topological properties of native folds are obtained from statistical analysis of 160 low homology proteins covering the four structural classes. This is done analysing one, two and three-vertex joint distribution of quantities related to…
Acid solutions exhibit a variety of complex structural and dynamical features arising from the presence of multiple interacting reactive proton defects and counterions. However, disentangling the transient structural motifs of proton…
The density of a protein molecule is a key property within a variety of experimental techniques. We present a computational method for determining protein mass density that explicitly incorporates hydration effects. Our approach uses…
Using molecular dynamics simulations, we reveal emergent properties of hydrated electrode interfaces that while molecular in origin are integral to the behavior of the system across long times scales and large length scales. Specifically,…