630 research outputs found
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 (,
is the barrier height, is the Boltzmann constant, is the
bath temperature). The bath-induced relaxation is treated within the Rayleigh
model (a heavy particle of mass in the bath of light particles of mass
) up to the terms of the order of ,
. The term is equivalent to the Fokker-Planck
dissipative operator, and the term is responsible for the
velocity dependence of friction. As expected, the correction to the Kramers
escape rate in the overdamped limit is proportional to and is
small. The corresponding correction in the underdamped limit is proportional to
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 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 intraÂmolecular C—H⋯O interÂaction. SupraÂmolecular layers, two molÂecules 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 interÂactions between the components of the fused ring system and the phenyl ring of inversion-related molÂecules [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
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