Related papers: Ion Binding Sites and their Representations by Qua…
Thermochemistry of gas-phase ion-water clusters together with estimates of the hydration free energy of the clusters and the water ligands are used to calculate the hydration free energy of the ion. Often the hydration calculations use a…
Studying chemical reactions at very low temperatures is of importance for the understanding of fundamental physical and chemical processes. At very low energies, collisions are dominated by only a few partial waves. Thus, studies in this…
Biochemical networks are used in computational biology, to model the static and dynamical details of systems involved in cell signaling, metabolism, and regulation of gene expression. Parametric and structural uncertainty, as well as…
Electrolytes play an important role in a plethora of applications ranging from energy storage to biomaterials. Notwithstanding this, the structure of concentrated electrolytes remains enigmatic. Many theoretical approaches attempt to model…
In biology, ligand mediated transitions (LMT), where the binding of a molecular ligand onto the binding site of a receptor molecule leads to a well-defined change in the conformation of the receptor, are often referred to as 'the second…
A method for generating angular forces around $\sigma$-bonded transition metal ions is generalized to treat $\pi$-bonded configurations. The theoretical approach is based on an analysis of a ligand-field Hamiltonian based on the moments of…
Fusion reactions of heavy ions are investigated by employing a simple stochastic semi-classical model which includes the coupling between relative motion and low frequency collective surface modes of colliding ions similarly to the quantal…
Ion transport in biological tissues is crucial in the study of many biological and pathological problems. Some multi-cellular structures, like smooth muscles on the vessel walls, could be treated as periodic bi-domain structures, which…
Ion transport in concentrated electrolytes plays a fundamental role in electrochemical systems such as lithium ion batteries. Nonetheless, the mechanism of transport amid strong ion-ion interactions remains enigmatic. A key question is…
Ion channels are specific proteins present in the membranes of living cells. They control the flow of specific ions through a cell, initiated by an ion channel's electrochemical gradient. In doing so, they control important physiological…
The features of heavy ion collisions that suggest the relevance of collective dynamics, as opposed to mere superpositions of nucleon-nucleon or even parton-parton collisions, are reviewed. The surprise of these studies is that bulk…
Proteins' fuzziness are features for communicating changes in cell signaling instigated by binding with secondary messengers, such as calcium ions, associated with the coordination of muscle contraction, neurotransmitter release, and gene…
We consider a simple working hypothesis that all permeation properties of open ionic channels can be predicted by understanding electrodiffusion in fixed structures, without invoking conformation changes, or changes in chemical bonds. We…
Ions transiting biomembranes might pass readily from water through ion-specific membrane proteins if those protein channels provide environments similar to the aqueous solution hydration environment. Indeed, bulk aqueous solution is an…
We introduce a statistical and linear response theory of selective conduction in biological ion channels with multiple binding sites and possible point mutations. We derive an effective grand-canonical ensemble and generalised Einstein…
A simple "trick" is proposed, which allows to perform exactly the site-averaging procedure required when developing integral equation theories of interaction site models of macromolecular fluids. It shows that no approximation is involved…
In this paper, we consider the problem of model order reduction of stochastic biochemical networks. In particular, we reduce the order of (the number of equations in) the Linear Noise Approximation of the Chemical Master Equation, which is…
We develop a model of molecular binding based on the Bohr-Sommerfeld description of atoms together with a constraint taken from conventional quantum mechanics. The model can describe the binding energy curves of H2, H3 and other molecules…
We explore an idealized theoretical model for the transport of ions within highly asymmetric ionic liquid mixtures. A primitive model (PM)-inspired system serves as a representative for asymmetric ionic materials (such as liquid crystalline…
In concentrated electrolytes with asymmetric or irregular ions, such as ionic liquids and solvent-in-salt electrolytes, ion association is more complicated than simple ion-pairing. Large branched aggregates can form at significant…