Related papers: Modelling proton transfer in water molecule chains
We present theory for ion and water transport through reverse osmosis membranes based on a Maxwell-Stefan framework combined with hydrodynamic theory for the reduced motion of particles in thin pores. We include all driving forces and…
The frequency dependence of dynamical conductivity of the quasi-one-dimensional structures with hydrogen bonds is studied on the basis of pseudospin-electron model. It takes into account the proton-electron interaction, external…
The hypersphere model is a simple one-parameter model of the potential energy landscape of viscous liquids, which is defined as a percolating system of same-radius hyperspheres randomly distributed in $\mathbb{R}^{3N}$ in which $N$ is the…
Molecular dynamics simulations are performed to study the temperature-dependent dynamics and structures of the hydration shells of elastin-like and collagen-like peptides. For both model peptides, it is consistently observed that, upon…
The formation of polaron and its migration in a DNA chain are studied within a semiclassical Peyrard-Biship-Holstein polaron model. Comparing the energetics of the polaron system found from the quantum chemical and semiclassical…
We discuss the electronic transport through molecules in the Kondo regime. We concentrate here on the influence of molecular vibrations. Two types of vibrations are investigated: (i) the breathing internal molecular modes, where the…
A recent description of the motion of atoms in a classical monatomic system in liquid and supercooled liquid states divides the motion into two parts: oscillations within a given many-particle potential valley, and transit motion which…
The microscopic description of the local structure of water remains an open challenge. Here, we adopt an agnostic approach to understanding water's hydrogen bond network using data harvested from molecular dynamics simulations of an…
Superconducting circuits constitute a promising platform for future implementation of quantum processors and simulators. Arrays of capacitively coupled transmon qubits naturally implement the Bose-Hubbard model with attractive on-site…
One of the most important topics in molecular biology is the genetic stability of DNA. One threat to this stability is proton transfer along the hydrogen bonds of DNA that could lead to tautomerisation, hence creating point mutations. We…
We study multiple ionization in proton collisions with water, methane, and ammonia molecules using an independent-atom model. Previous work on total (net) capture and ionization cross sections is extended to treat the multiple ionization…
Channel proteins, that selectively conduct molecules across cell membranes, often exhibit an asymmetric structure. By means of a stochastic model, we argue that channel asymmetry in the presence of non-equilibrium fluctuations, fueled by…
Two models involving particles moving by ``hopping'' in disordered media are investigated: I) A model glass-forming liquid is investigated by molecular dynamics under (pseudo-) equilibrium conditions. ``Standard'' results such as mean…
We present a model of proton tunnelling across DNA hydrogen bonds, compute the characteristic tunnelling time (CTT) from donor to acceptor and discuss its biological implications. The model is a double oscillator characterised by three…
The transport of deformable objects including polymer particles, vesicles and cells, has been a subject of interest for several decades where the majority of experimental and theoretical studies have been focused on circular tubes. Due to…
I have investigated the structural and dynamic properties of water by performing a series of molecular dynamic simulations in the range of temperatures from 213 K to 360 K, using the Simple Point Charge-Extended (SPC/E) model. I performed…
Recent years have seen a surge of interest in nanopores because such structures show a strong potential for characterizing nanoparticles, proteins, DNA, and even single molecules. These systems have been extensively studied in experiment as…
Studies of the transport of wet water vapour are relevant for various areas of human activity, including the construction and production of building materials, mining, agriculture, environmental safety of technological processes, scientific…
Molecular dynamics simulations have been performed on pure liquid water, aqueous solutions of sodium chloride, and polymer solutions exposed to a strong external electric field with the goal to gain molecular insight into the structural…
We have studied by Molecular Dynamics computer simulations the dynamics of water confined in ionic surfactants phases, ranging from well ordered lamellar structures to micelles at low and high water loading, respectively. We have analysed…