Velocity dependence of friction and Kramers relaxation rates

We study the influence of the velocity dependence of friction on the escape of a Brownian particle from the deep potential well ($E_{b} \gg k_{B}T$, $E_{b}$ is the barrier height, $k_{B}$ is the Boltzmann constant, $T$ is the bath temperature). The bath-induced relaxation is treated within the Rayleigh model (a heavy particle of mass $M$ in the bath of light particles of mass $m\ll M$) up to the terms of the order of $O(\lambda^{4})$, $\lambda^{2}=m/M\ll1$. The term $\sim 1$ is equivalent to the Fokker-Planck dissipative operator, and the term $\sim \lambda^{2}$ is responsible for the velocity dependence of friction. As expected, the correction to the Kramers escape rate in the overdamped limit is proportional to $\lambda^{2}$ and is small. The corresponding correction in the underdamped limit is proportional to $\lambda^{2}E_{b}/(k_{B}T)$ and is not necessarily small. We thus suggest that the effects due to the velocity-dependent friction may be of considerable importance in determining the rate of escape of an under- and moderately damped Brownian particle from a deep potential well, while they are of minor importance for an overdamped particle

Exact quantum master equation for a molecular aggregate coupled to a harmonic bath

We consider a molecular aggregate consisting of $N$ identical monomers. Each monomer comprises two electronic levels and a single harmonic mode. The monomers interact with each other via dipole-dipole forces. The monomer vibrational modes are bilinearly coupled to a bath of harmonic oscillators. This is a prototypical model for the description of coherent exciton transport, from quantum dots to photosynthetic antennae. We derive an exact quantum master equation for such systems. Computationally, the master equation may be useful for the testing of various approximations employed in theories of quantum transport. Physically, it offers a plausible explanation of the origins of long-lived coherent optical responses of molecular aggregates in dissipative environments

Angular momentum dependent friction slows down rotational relaxation under non-equilibrium conditions

It has recently been shown that relaxation of the rotational energy of hot non-equlibrium photofragments (i) slows down significantly with the increase of their initial rotational temperature and (ii) differs dramatically from the relaxation of the equilibrium rotational energy correlation function, manifesting thereby breakdown of the linear response description [Science 311, 1907 (2006)]. We demonstrate that this phenomenon may be caused by the angular momentum dependence of rotational friction. We have developed the generalized Fokker-Planck equation whose rotational friction depends upon angular momentum algebraically. The calculated rotational correlation functions correspond well to their counterparts obtained via molecular dynamics simulations in a broad range of initial non-equilibrium conditions. It is suggested that the angular momentum dependence of friction should be taken into account while describing rotational relaxation far from equilibrium

Manifestation of nonequilibrium initial conditions in molecular rotation: the generalized J-diffusion model

In order to adequately describe molecular rotation far from equilibrium, we have generalized the J-diffusion model by allowing the rotational relaxation rate to be angular momentum dependent. The calculated nonequilibrium rotational correlation functions (CFs) are shown to decay much slower than their equilibrium counterparts, and orientational CFs of hot molecules exhibit coherent behavior, which persists for several rotational periods. As distinct from the results of standard theories, rotational and orientational CFs are found to dependent strongly on the nonequilibrium preparation of the molecular ensemble. We predict the Arrhenius energy dependence of rotational relaxation times and violation of the Hubbard relations for orientational relaxation times. The standard and generalized J-diffusion models are shown to be almost indistinguishable under equilibrium conditions. Far from equilibrium, their predictions may differ dramatically

3,6-Dimethyl-1-phenyl-1H,4H-pyrano[2,3-c]pyrazol-4-one

The title compound, C14H12N2O2, is almost planar with an r.m.s. deviation for all non-H atoms of 0.038 Å. The observed planarity is rationalized in terms of a close intra­molecular C—H⋯O inter­action. Supra­molecular layers, two mol­ecules thick and with a step topology, are formed in the crystal packing via C—H⋯O contacts involving the carbonyl O atom, which accepts two such bonds, and π–π inter­actions between the components of the fused ring system and the phenyl ring of inversion-related mol­ecules [centroid–centroid distances = 3.6819 (13) and 3.6759 (12) Å]

Role of the Subunits Interactions in the Conformational Transitions in Adult Human Hemoglobin: an Explicit Solvent Molecular Dynamics Study

Hemoglobin exhibits allosteric structural changes upon ligand binding due to the dynamic interactions between the ligand binding sites, the amino acids residues and some other solutes present under physiological conditions. In the present study, the dynamical and quaternary structural changes occurring in two unligated (deoxy-) T structures, and two fully ligated (oxy-) R, R2 structures of adult human hemoglobin were investigated with molecular dynamics. It is shown that, in the sub-microsecond time scale, there is no marked difference in the global dynamics of the amino acids residues in both the oxy- and the deoxy- forms of the individual structures. In addition, the R, R2 are relatively stable and do not present quaternary conformational changes within the time scale of our simulations while the T structure is dynamically more flexible and exhibited the T\rightarrow R quaternary conformational transition, which is propagated by the relative rotation of the residues at the {\alpha}1{\beta}2 and {\alpha}2{\beta}1 interface.Comment: Reprinted (adapted) with permission from J. Phys. Chem. B DOI:10.1021/jp3022908. Copyright (2012) American Chemical Societ