相关论文: Computational study of small molecule binding for …
We consider membranes adhered through specific receptor-ligand bonds. Thermal undulations of the membrane induce effective interactions between adhesion sites. We derive an upper bound to the free energy that is independent of interaction…
We use Metropolis Monte Carlo and umbrella sampling to calculate the free energies of interaction of two methane molecules and their charged derivatives in cylindrical water-filled pores. Confinement strongly alters the interactions between…
The lattice fluid model of the system with short range and long range Coulomb interactions is suggested. In the framework of the collective variables method, the screening of the Coulomb interactions in the bulk is considered. It is shown…
Every time a chemical reaction occurs, an energy exchange between reactants and environment exists, which is defined as the enthalpy of the reaction. In the last decades, research has resulted in an increasing number of devices at the…
We introduce a simulation technique to compute the free energy difference between two hydrate structures of different stoichiometry connected to a reservoir of gas molecules at a prescribed pressure. The method permits the determination of…
The static and dynamical properties of heavy water have been studied at ambient conditions with extensive Car-Parrinello molecular-dynamics simulations in the canonical ensemble, with temperatures ranging between 325 K and 400 K.…
This work addresses the question of whether it is possible to define simple pair-wise interaction terms to approximate free energies of proteins or polymers. Rather than ask how reliable a potential of mean force is, one can ask how…
Understanding the stabilities of proteins in nanopores requires a quantitative description of confinement induced interactions between amino acid side chains. We use molecular dynamics simulations to study the nature of interactions between…
The free energy of mixing and the entropy of mixing for Cu$_{x}$Al$_{1-x}$ liquid binary alloys have been systematically investigated by using the electronic theory of metals along with the perturbation approach at a thermodynamic state…
Melt-quenched AsxGexSe1-2x glasses over the composition range, 0 < x < 0.26, are examined in Raman scattering, T-modulated Differential Scanning Calorimetry (MDSC), and 119Sn Mossbauer spectroscopy measurements. The non-reversing enthalpy…
The tethered-particle method is a single-molecule technique that has been used to explore the dynamics of a variety of macromolecules of biological interest. We give a theoretical analysis of the particle motions in such experiments. Our…
The NEXT experiment aims at searching for the hypothetical neutrinoless double-beta decay from the ${}^{136}$Xe isotope using a high-purity xenon TPC. Efficient discrimination of the events through pattern recognition of the topology of…
Thermodynamical features of Xe system is investigated as functions of temperature and freeze-out density in the frame of lattice gas model. The calculation shows different temperature dependence of physical observables at different…
Molecular dynamics simulations are performed for a supercooled simple liquid with changing the system size from N=108 to $10^4$ to examine possible finite-size effects. Although almost no systematic deviation is detected in the static pair…
Polymers confined to a narrow channel are subject to strong entropic forces that tend to drive the molecules apart. In this study, we use Monte Carlo computer simulations to study the segregation behavior of two flexible hard-sphere…
In the free energy of hydration of a solute, the chemical contribution is given by the free energy required to expel water molecules from the coordination sphere and the packing contribution is given by the free energy required to create…
The electric density profile along the normal to the phase interface between aromatic hydrocarbon toluene and water has been studied by X-ray reflectometry using synchrotron radiation. According to the experimental data, the width of the…
Binding energies calculated from using the Bethe-Salpeter equation in the simplest ladder approximation significantly differ from those obtained in the non-relativistic standard instantaneous approximation. While they should a priori be…
We present a quantum Monte Carlo study of the hydrogen-benzene system where binding is very weak. We demonstrate that the binding is well described at both variational Monte Carlo (VMC) and diffusion Monte Carlo (DMC) levels by a Jastrow…
In this study, we propose a theoretical framework to investigate the interactions between flexible polymer chains, specifically polyelectrolytes (PEs). By calculating the system's free energy while considering position-dependent mutual…