Related papers: Probing vibrational energy relaxation in proteins …
The bottleneck in enhanced sampling lies in finding collective variables (CVs) that can effectively accelerate protein conformational changes. True reaction coordinates (tRCs) that can predict the committor are considered the optimal CVs,…
The velocity relaxation of an impulsively forced spherical particle in a fluid confined by two parallel plane walls is studied using a direct numerical simulation approach. During the relaxation process, the momentum of the particle is…
Normal mode analysis is a widely used technique for reconstructing conformational changes of proteins from the knowledge of native structures. In this Letter, we investigate to what extent normal modes capture the salient features of the…
The vibrational spectra of simple CH$_3^+$-Rg (Rg=He, Ne, Ar, Kr) complexes have been studied by vibrational configuration interaction (VCI) theory relying on multidimensional potential energy surfaces (PES) obtained from explicitly…
We propose and analyze an $H^2$-conforming Virtual Element Method (VEM) for the simplest linear elliptic PDEs in nondivergence form with Cordes coefficients. The VEM hinges on a hierarchical construction valid for any dimension $d \ge 2$.…
The scaling property of the thermodynamic free energy ($\Phi$) of a system at global equilibrium has been examined using a real-time method known as the virial theorem. We demonstrate these scaling properties through a derived relation…
This article presents a priori error estimates of the miscible displacement of one incompressible fluid by another through a porous medium characterized by a coupled system of nonlinear elliptic and parabolic equations. The study utilizes…
We theoretically investigate normal-state properties of a unitary Bose-Fermi mixture. Including strong hetero-pairing fluctuations, we evaluate the Bose and Fermi chemical potential, internal energy, pressure, entropy, as well as specific…
A method is presented for determining second virial coefficients B_2 of protein solutions from retention time measurements in size exclusion chromatography (SEC). We determine B_2 by analyzing the concentration dependance of the…
In a recent review by Anderson and coworkers\cite{Vanilla}, it was pointed out that an early resonating valence bond (RVB) theory is able to explain a number of unusual properties of high temperature superconducting (SC) Cu-oxides. Here we…
In this work, we present a proof-of-concept investigation of non-equilibrium chemical reaction dynamics at a molecule-electrode interface, driven out of equilibrium by an applied votage bias and mediated by a confined, enhanced vacuum…
Color transparency (CT) in high momentum transfer $(e,e' \vec p)$ reactions is explored. The spin of the proton and photon are treated explicitly, hence the name ``Vector CT". The Dirac distorted wave impulse approximation is used as a…
This work presents a Virtual Element Method (VEM) formulation tailored for two-dimensional axisymmetric problems in linear elasticity. By exploiting the rotational symmetry of the geometry and loading conditions, the problem is reduced to a…
When the energy content of a resonant mode of a crystalline solid in thermodynamic equilibrium is directly measured, assuming that quantum effects can be neglected it coincides with temperature except for a proportionality factor. This is…
The dielectric spectra of the twist bend nematic phase of the bent shaped achiral liquid crystal dimer are studied for the determination of the different relaxation modes. The two molecular processes were assigned one to the precessional…
A sum rule approach is used to calculate the zero temperature oscillation frequencies of a two component trapped atomic Fermi gas in the BCS-Bose Einstein condensation crossover region. These sum rules are evaluated using a local density…
Vibrational modes of molecules are fundamental properties determined by intramolecular bonding, atomic masses, and molecular geometry, and often serve as important channels for dissipation in nanoscale processes. Although single-molecule…
The time sequences of the molecular dynamics simulation for the folding process of a protein is analyzed with the inherent structure landscape which focuses on configurational dynamics of the system. Time dependent energy and entropy for…
By means of the Boltzmann-Vlasov kinetic equation we investigate dynamical properties of a trapped, one-component Fermi gas at zero temperature, featuring the anisotropic and long-range dipole-dipole interaction. To this end, we determine…
The path probability method (PPM), which is a natural extension of the cluster variation method (CVM) to a time domain, has been employed in a relaxation process of atomic configurations in alloy systems. Although the vacancy mechanism is…