Related papers: Ion Binding Sites and their Representations by Qua…
A statistical thermodynamic development is given of a new implicit solvent model that avoids the traditional system size limitations of computer simulation of macromolecular solutions with periodic boundary conditions. This implicit solvent…
The tight binding model is a minimal electronic structure model for molecular modelling and simulation. We show that the total energy in this model can be decomposed into site energies, that is, into contributions from each atomic site…
Metal ions play numerous important roles in biological systems being central to the function of biomolecules. In this letter we show that the absorption of X-rays by these ions leads to a complicated chain of ultrafast relaxation steps…
A tight binding model for scanning tunneling microscopy images of a molecule adsorbed on a metal surface is described. The model is similar in spirit to that used to analyze conduction along molecular wires connecting two metal leads and…
Protein-ligand binding is the process by which a small molecule (drug or inhibitor) attaches to a target protein. Binding affinity, which characterizes the strength of biomolecular interactions, is essential for tackling diverse challenges…
Structural and thermodynamic properties of ionic fluids are related to those of a simpler ``mimic'' system with short ranged intermolecular interactions in a spatially varying effective field by use of Local Molecular Field (LMF) theory,…
Solvation of ions is ubiquitous on our planet. Solvated ions have a profound effect on the behavior of ionic solutions, which is crucial in nature and technology. Experimentally, ions have been classified into "structure makers" or…
Ion channels are of major interest and form an area of intensive research in the fields of biophysics and medicine since they control many vital physiological functions. The aim of this work is on one hand to propose a fully stochastic and…
Most elemental metals under ambient conditions adopt simple structures such as BCC, FCC and HCP in specific groupings across the Periodic Table, and on compression, many of these elements undergo transitions to surprisingly complex…
The rich novel materials class of iron based superconductors turned out to exhibit a very complex electronic structure, despite of the simplicity of their crystal structures. For various approaches to study the instability against magnetic…
Charge regulation is a fundamental mechanism in most chemical, geochemical, and biochemical systems. Various minerals surfaces and proteins are well-known to change their charge state as a function of the activity of the hydronium ions,…
Proteins need to selectively interact with specific targets among a multitude of similar molecules in the cell. But despite a firm physical understanding of binding interactions, we lack a general theory of how proteins evolve high…
Basic problems of the semiclassical microscopic modelling of strongly interactingsystems are discussed within the framework of Quantum Molecular Dynamics (QMD). This model allows to study the influence of several types of nucleonic…
Binding and unbinding of ligands to specific sites of a macromolecule are one of the most elementary molecular interactions inside the cell that embody the computational processes of biological regulations. The interaction between…
A key starting assumption in many classical interatomic potential models for materials is a site energy decomposition of the potential energy surface into contributions that only depend on a small neighbourhood. Under a natural stability…
Transition metal ions play crucial roles in the structure and function of numerous proteins, contributing to essential biological processes such as catalysis, electron transfer, and oxygen binding. However, accurately modeling the…
The association of ions in electrolyte solutions at very low concentration and low temperature is studied using computer simulations and quasi-chemical ion-pairing theory. The specific case of the restricted primitive model (charged hard…
Metal coordination is ubiquitous in Nature and central in many applications ranging from nanotechnology to catalysis and environmental chemistry. Complex formation results from the subtle interplay between different thermodynamic, kinetic,…
We developed a new physical model to predict macroscopic properties of inorganic molten systems using a realistic description of inter-atomic interactions. Unlike the conventional approach, which tends to overestimate viscosity by several…
Inferring properties of macroscopic solutions from molecular simulations is complicated by the limited size of systems that can be feasibly examined with a computer. When long-ranged electrostatic interactions are involved, the resulting…