Related papers: Probing vibrational energy relaxation in proteins …
An overview of theories related to vibrational energy relaxation (VER) in proteins is presented. VER of a selected mode in cytochrome c is studied using two theoretical approaches. One is the equilibrium simulation approach with quantum…
We first review how to determine the rate of vibrational energy relaxation (VER) using perturbation theory. We then apply those theoretical results to the problem of VER of a CD stretching mode in the protein cytochrome c. We model…
Using a time-dependent perturbation theory, vibrational energy relaxation (VER) of isotopically labeled amide I modes in cytochrome c solvated with water is investigated. Contributions to the VER are decomposed into two contributions from…
Energy transfer (relaxation) phenomena are ubiquitous in nature. At a macroscopic level, the phenomenological theory of heat (Fourier law) successfully describes heat transfer and energy flow. However, its microscopic origin is still under…
A numerical simulation of vibrational excitation of molecules was devised, and used to excite computational models of common molecules into a prescribed, pure, normal vibration mode in the ground electronic state, with varying, controlable…
Without invoking the Markov approximation, we derive formulas for vibrational energy relaxation (VER) and dephasing for an anharmonic system oscillator using a time-dependent perturbation theory. The system-bath Hamiltonian contains more…
We have investigated the relaxational dynamics for a protein model at various temperatures. Theoretical analysis of this model in conjunction with numerical simulations suggests several relaxation regimes, including a single exponential, a…
We carry out a theoretical study of the vibrational and relaxation properties of naturally-occurring proteins with the purpose of characterizing both the folding and equilibrium thermodynamics. By means of a suitable model we provide a full…
Representation of molecular vibrational degrees of freedom by independent harmonic oscillators, when describing electronic spectra or electronic excitation energy transport, raises unfavourable effects as vibrational energy relaxation…
We present a priori and a posteriori error analysis of a Virtual Element Method (VEM) to approximate the vibration frequencies and modes of an elastic solid. We analyze a variational formulation relying only on the solid displacement and…
At room temperature, low frequency vibrations at far-infrared frequencies are thermally excited ($k_B T > h \nu$) and not restricted to harmonic fluctuations around a single potential energy minimum. For folded proteins, these intrinsically…
Rotational and vibrational energy relaxation (RER and VER) of N$_2$O embedded in xenon and SF$_6$ environments ranging from the gas phase to the liquid, including the supercritical regime, is studied at a molecular level. Calibrated…
This paper devises a novel lowest-order conforming virtual element method (VEM) for planar linear elasticity with the pure displacement/traction boundary condition. The main trick is to view a generic polygon $K$ as a new one…
Within the framework of the displacement-based Virtual Element Method (VEM) for plane elasticity a significant problem is represented by an accurate evaluation of the stress field. In particular, in the classical VEM formulation, a suitable…
A robust $C^0$-continuous nonconforming virtual element method (VEM) is developed for a boundary value problem arising from strain gradient elasticity in two dimensions, with the family of polygonal meshes satisfying a very general…
The aim of this paper is to develop a virtual element method (VEM) for the vibration problem of thin plates on polygonal meshes. We consider a variational formulation relying only on the transverse displacement of the plate and propose an…
The relaxation of Fourier modes of hamiltonian chains close to equilibrium is studied in the framework of a simple mode-coupling theory. Explicit estimates of the dependence of relevant time scales on the energy density (or temperature) and…
Vibrationally resolved electronic absorption spectra including the effect of vibrational pre-excitation are computed in order to interpret and predict vibronic transitions that are probed in the Vibrationally Promoted Electronic Resonance…
A simple model to predict the directionality of vibrational energy flow at molecular level is presented. This model is based on a vibrational energy propagation analysis using ab intio molecular dynamics and the Fukui function and local…
A computational approach to describe the energy relaxation of a high-frequency vibrational mode in a fluctuating heterogeneous environment is outlined. Extending previous work [H. Fujisaki, Y. Zhang, and J.E. Straub, J. Chem. Phys. {\bf…