相关论文: Vibrational energy relaxation in proteins
Vibrational energy relaxation (VER) of a selected mode in cytochrome c (hemeprotein) in vacuum is studied using two theoretical approaches: One is the equilibrium simulation approach with quantum correction factors, and the other is the…
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…
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…
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…
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…
The physics of vibrational kinetics in nitrogen-containing plasma produced by collisions with electrons is studied on the basis of recently derived cross sections and rate coefficients for the resonant vibrational-excitation by…
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…
Vibrational spectroscopy is a powerful technique to characterize the near-equilibrium dynamics of molecules in the gas- and the condensed-phase. This contribution summarizes efforts from computer-based methods to gain insight into the…
We present a theoretical analysis that associates the resonances of extraordinary acoustic Raman (EAR) spectroscopy [Wheaton et al., Nat Photon 9, 68 (2015)] with the collective modes of proteins. The theory uses the anisotropic elastic…
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…
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…
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…
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…
In the present paper we address the problem of the energy downconversion of the light absorbed by a protein into its internal vibrational modes. We consider the case in which the light receptors are fluorophores either naturally…
The theory of biochemical processes needs simple but realistic models of phenomena underlying microscopic dynamics of proteins. Many experiments performed in the 1980s have demonstrated that within the protein native state, apart from usual…
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…
A full set of vibrationally-resolved cross sections for electron impact excitation of NO(X2{\Pi}, v) molecules is calculated from ab initio molecular dynamics, in the framework of the local-complex-potential approach. Electron-vibration…