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Universal properties of the Coulomb interaction energy apply to all many-electron systems. Bounds on the exchange-correlation energy, inparticular, are important for the construction of improved density functionals. Here we investigate one…
Biological adhesion often involves several pairs of specific receptor-ligand molecules. Using rate equations, we study theoretically the rupture of such multiple parallel bonds under dynamic loading assisted by thermal activation. For a…
Myoglobin modulates the binding of diatomic molecules to its heme group via hydrogen-bonding and steric interactions with neighboring residues, and is an important benchmark for computational studies of biomolecules. We have performed…
We report on a combined atomistic molecular dynamics simulation and implicit solvent analysis of a generic hydrophobic pocket-ligand (host-guest) system. The approaching ligand induces complex wetting/dewetting transitions in the weakly…
The efficacy of drug treatments depends on how tightly small molecules bind to their target proteins. The rapid and accurate quantification of the strength of these interactions (as measured by binding affinity) is a grand challenge of…
In this paper, the authors study the limit of a sharp interface model for the solvation of charged molecules in an implicit solvent as the number of solute molecules and the size of the surrounding box tend to infinity. The energy is given…
A quantitative model of the mobility of functionalized particles at the interface is pivotal to understanding important systems in biology and nanotechnology. In this work, we investigate the emerging dynamics of particles anchored through…
While all the information required for the folding of a protein is contained in its amino acid sequence, one has not yet learned how to extract this information to predict the three--dimensional, biologically active, native conformation of…
The percentage and sequence of AT and GC base pairs and charges on the DNA backbone contribute significantly to the stiffness of DNA. This elastic property of DNA also changes with small interacting ligands. The single-molecule force…
Molecular bonds can be divided into four primary types: ionic, covalent, van der Waals and hydrogen bonds. At ultralow temperatures a novel binding type emerges paving the way for novel molecules and ultracold chemistry [1,2]. The…
In recent years machine learning (ML) took bio- and cheminformatics fields by storm, providing new solutions for a vast repertoire of problems related to protein sequence, structure, and interactions analysis. ML techniques, deep neural…
Molecular recognition, which is essential in processing information in biological systems, takes place in a crowded noisy biochemical environment and requires the recognition of a specific target within a background of various similar…
The adhesion of biological membranes is controlled by various types of receptor and ligand molecules. In this letter, we present a statistical-mechanical model for membranes that interact via receptor/ligand bonds of two different lengths.…
The behaviour of molecules in space is to a large extent governed by where they freeze out or sublimate. The molecular binding energy is thus an important parameter for many astrochemical studies. This parameter is usually determined with…
Molecular docking plays a crucial role in predicting the binding mode of ligands to target proteins, and covalent interactions, which involve the formation of a covalent bond between the ligand and the target, are particularly valuable due…
The binding of small metal ions to complex macromolecular structures is typically dominated by strong local interactions of the ion with its nearest ligands. For this reason, it is often possible to understand the microscopic origin of ion…
The crucial problem for better understanding the nature of glass transition and related relaxation phenomena is to find proper interrelations between molecular dynamics and thermodynamics of viscous systems. To gain this aim the recently…
Applications of machine learning in chemistry are often limited by the scarcity and expense of labeled data, restricting traditional supervised methods. In this work, we introduce a framework for molecular reasoning using general-purpose…
Despite decades of research, the modeling of moving contact lines has remained a formidable challenge in fluid dynamics whose resolution will impact numerous industrial, biological, and daily life applications. On the one hand, molecular…
Bimolecular binding rate constants are often used to describe the association of large molecules, such as proteins. In this paper, we analyze a model for such binding rates that includes the fact that pairs of molecules can bind only in…