Related papers: Influence of Protein Electromagnetic Field on Hydr…
The interactions of a protein, its phase behavior, and ultimately, its ability to function, are all influenced by the interactions between the protein and its hydration waters. Here we study proteins with a variety of sizes, shapes,…
Phylogenetic studies show that horizontal gene transfer (HGT) is a significant contributor to genetic variability of prokaryotes, and was perhaps even more abundant during early evolution. Hitherto, research of natural HGT has mainly…
We used cold helium droplets as nano-scale reactors to form and ionize, by electron bombardment and charge transfer, aromatic amino acid heterodimers of histidine with tryptophan, methyl-tryptophan, and indole. The molecular interaction…
The effect of sequence heterogeneity on polynucleotide translocation across a pore and on simple models of molecular motors such as helicases, DNA polymerase/exonuclease and RNA polymerase is studied in detail. Pore translocation of RNA or…
Quantum proton tunneling (QPT) in the two representative multi-electron/-proton transfer electrode processes, i.e. hydrogen evolution reaction (HER) and oxygen reduction reaction (ORR), was investigated by using polycrystalline platinum…
Nuclear quantum effects of protons on electronic excitations in hydrogen-bonded organic materials remains underexplored. In theoretical studies, modeling excitons in these extended systems is particularly difficult because they tend to have…
We describe a model of electron transfer reactions affected by local binding to the donor or acceptor sites of a particle in equilibrium with the solution. The statistics of fluctuations of the donor-acceptor energy gap caused by…
Mechanochemically active enzymes change their shapes within every turnover cycle. Therefore, they induce circulating flows in the solvent around them and behave as oscillating hydrodynamic force dipoles. Because of non-equilibrium…
Engineering molecular systems that exhibit complex behavior requires the design of kinetic barriers. For example, an effective catalytic pathway must have a large barrier when the catalyst is absent. While programming such energy barriers…
Ammonia has strong poisoning effects on cathode catalyst layers of proton exchange membrane (PEM) fuel cells, but the poisoning mechanism is still unclear. In this study, all-atom molecular dynamics simulations are employed to investigate…
The interaction between protons and graphene is attracting a large interest due to recent experiments showing that these charged species permeate through the 2D material following a low barrier (~ 0.8 eV) activated process. A possible…
Molecular hydrogen (H$_2$) plays a critical role in astrophysical processes from galaxy evolution to the formation of planets. While the dominant formation channel in the interstellar medium is considered as dust-catalyzed H$_2$ formation,…
We study the formation of molecular states in a two-electron quantum dot as a function of the barrier potential dividing the dot. The increasing barrier potential drives the two electron system from an artificial helium atom to an…
Cooperativity plays an important role in the action of proteins bound to DNA. A simple, mechanical mechanism for cooperativity, in the form of a tension-mediated interaction between proteins bound to DNA at two different locations is…
Low-energy cosmic rays ($E\lesssim 1$ GeV) are responsible for the ionisation and heating of molecular clouds. While the role of supra-thermal electrons produced in the ionisation process in inducing excitation of the ambient gas (mostly…
We propose a mechanism in which two molecular knots pass through each other and swap positions along a polymer strand. Associated free energy barriers in our simulations only amount to a few $k_{B}T$, which may enable the interchange of…
All living systems can function only far away from equilibrium, and for this reason chemical kinetic methods are critically important for uncovering the mechanisms of biological processes. Here we present a new theoretical method of…
We study electron transfer between two separated nuclei using local control theory. By conditioning the algorithm in a symmetric system formed by two protons, one can favored slow transfer processes, where tunneling is the main mechanism,…
The experimental conditions by which electromagnetic signals (EMS) of low frequency can be emitted by diluted aqueous solutions of some bacterial and viral DNAs are described. That the recorded EMS and nanostructures induced in water carry…
The mechanisms of cold- and pressure-denaturation of proteins are matter of debate and are commonly understood as due to water-mediated interactions. Here we study several cases of proteins, with or without a unique native state, with or…