Related papers: Probing vibrational energy relaxation in proteins …
We describe a two-step approach for combining interactive molecular dynamics in virtual reality (iMD-VR) with free energy (FE) calculation to explore the dynamics of biological processes at the molecular level. We refer to this combined…
Polarizable Quantum Mechanics/Molecular Mechanics (QM/MM) approaches based on fluctuating charges and dipoles (QM/FQ(F$\mu$)) are formulated within the state-specific Vertical Excitation Model (VEM) to compute vertical excitation energies…
In this paper, an enhanced Virtual Element Method (VEM) formulation is proposed for plane elasticity. It is based on the improvement of the strain representation within the element, without altering the degree of the displacement…
We present results of extensive computer simulations and theoretical analysis of vibrational phase relaxation of a nitrogen molecule along the critical isochore and also along the gas-liquid coexistence. The simulation includes all the…
The viscous and thermal relaxation rates of an interacting fermion gas are calculated as functions of temperature and scattering length, using a many-body scattering matrix which incorporates medium effects due to Fermi blocking of…
The Virtual Element Method (VEM) is a well-established framework for solving partial differential equations on polygonal and polyhedral meshes. In this paper, we introduce a novel hybrid VEM that integrates both conforming and nonconforming…
We study a nonconforming virtual element method (VEM) for advection-diffusion-reaction problems with continuous interior penalty (CIP) stabilization. The design of the method is based on a standard variational formulation of the problem (no…
Curvilinear kinetic energy models are developed for variational nuclear motion computations including the inter- and the low-frequency intra-molecular degrees of freedom of the formic acid dimer. The coupling of the inter- and…
We present a Virtual Element Method (VEM) for a nonlocal reaction-diffusion system of the cardiac electric field. To this system, we analyze an $H^1(\Omega)$-conforming discretization by means of VEM which can make use of general polygonal…
A model calculation is given for the energy relaxation of a non-equilibrium distribution of hot electrons prepared in a metallic sample that has been subjected to homogeneous photo-excitation by a femtosecond laser pulse. The model assumes…
A time-dependent vibrational electronic coupled-cluster (VECC) approach is proposed to simulate photoelectron/ UV-VIS absorption spectra, as well as time-dependent properties for non-adiabatic vibronic models, going beyond the…
We present results of a hole burning study with thermal cycling and waiting time spectral diffusion experiments on a modified cytochrome - c protein in its native as well as in its denatured state. The experiments show features which seem…
The stress as a response to strain prescribed as a harmonic excitation is examined in both transient and steady state regime for the viscoelastic body modeled by thermodynamically consistent fractional anti-Zener and Zener models by the use…
The vibrational dynamics of formic acid monomer (FAM) and dimer (FAD) is investigated from machine-learned potential energy surfaces at the MP2 (PES$_{\rm MP2}$) and transfer-learned (PES$_{\rm TL}$) to the CCSD(T) levels of theory. The…
Collisional relaxation rates of collective modes in nuclei are calculated using the Levinson equation for the reduced density matrix with a memory dependent collision term. Linearizing the collision integral two contribution have to be…
In the present work, we provide a dielectric study on two differently concentrated aqueous lysozyme solutions in the frequency range from 1 MHz to 40 GHz and for temperatures from 275 to 330 K. We analyze the three dispersion regions,…
We study the intramolecular vibrational energy redistribution (IVR) dynamics of an effective spectroscopic Hamiltonian describing the four coupled high frequency modes of CDBrClF. The IVR dynamics ensuing from nearly isoenergetic…
In a two-part publication, we propose and analyze a formal foundation for practical calculations of vibrational mode lifetimes in solids. The approach is based on a recursion method analysis of the Liouvillian. In the first part, we derived…
A spectroscopic method is applied to measure the inelastic quasi-particle relaxation rate in a disordered Fermi liquid. The quasi-particle relaxation rate, $\gamma$ is deduced from the magnitude of fluctuations in the local density of…
In the present paper the resonances of vibrational modes in one-dimensional random Morse lattice are found and analyzed. The resonance energy exchange is observed at some values of elongation. Resonance $2 \omega_1 = \omega_2$ is…