300 research outputs found
Theoretical prediction of spectral and optical properties of bacteriochlorophylls in thermally disordered LH2 antenna complexes
A general approach for calculating spectral and optical properties of
pigment-protein complexes of known atomic structure is presented. The method,
that combines molecular dynamics simulations, quantum chemistry calculations
and statistical mechanical modeling, is demonstrated by calculating the
absorption and circular dichroism spectra of the B800-B850 BChls of the LH2
antenna complex from Rs. molischianum at room temperature. The calculated
spectra are found to be in good agreement with the available experimental
results. The calculations reveal that the broadening of the B800 band is mainly
caused by the interactions with the polar protein environment, while the
broadening of the B850 band is due to the excitonic interactions. Since it
contains no fitting parameters, in principle, the proposed method can be used
to predict optical spectra of arbitrary pigment-protein complexes of known
structure.Comment: ReVTeX4, 11 pages, 9 figures, submitted to J. Chem. Phy
Calculating potentials of mean force and diffusion coefficients from nonequilibirum processes without Jarzynski's equality
In general, the direct application of the Jarzynski equality (JE) to
reconstruct potentials of mean force (PMFs) from a small number of
nonequilibrium unidirectional steered molecular dynamics (SMD) paths is
hindered by the lack of sampling of extremely rare paths with negative
dissipative work. Such trajectories, that transiently violate the second law,
are crucial for the validity of JE. As a solution to this daunting problem, we
propose a simple and efficient method, referred to as the FR method, for
calculating simultaneously both the PMF U(z) and the corresponding diffusion
coefficient D(z) along a reaction coordinate z for a classical many particle
system by employing a small number of fast SMD pullings in both forward (F) and
time reverse (R) directions, without invoking JE. By employing Crook's
transient fluctuation theorem (that is more general than JE) and the stiff
spring approximation, we show that: (i) the mean dissipative work W_d in the F
and R pullings are equal, (ii) both U(z) and W_d can be expressed in terms of
the easily calculable mean work of the F and R processes, and (iii) D(z) can be
expressed in terms of the slope of W_d. To test its viability, the FR method is
applied to determine U(z) and D(z) of single-file water molecules in
single-walled carbon nanotubes (SWNTs). The obtained U(z) is found to be in
very good agreement with the results from other PMF calculation methods, e.g.,
umbrella sampling. Finally, U(z) and D(z) are used as input in a stochastic
model, based on the Fokker-Planck equation, for describing water transport
through SWNTs on a mesoscopic time scale that in general is inaccessible to MD
simulations.Comment: ReVTeX4, 13 pages, 6 EPS figures, Submitted to Journal of Chemical
Physic
Early signatures of ozone trend reversal over the Antarctic
We report on a detailed time series analysis of long total column ozone (TO) records based on multi-satellite observations of daily resolution. We concentrate on three geographic latitudes over and around the Antarctic area, specifically on three circles at 58.5 degrees S, 59.5 degrees S, and 79.5 degrees S. Almost continuous observations are available at the two former latitudes; however, data are lacking during the polar winter periods at 79.5 degrees S, because the measurement technique requires sunlight. The methodology is motivated by level-crossing statistics, where subsets of the records above or below particular threshold levels are evaluated. Long-term trend reversal at around the turn of the century is already detectable for low TO levels in the raw time series in the "ozone-hole" region (79.5 degrees S). In order to overcome the apparent non-stationarities of the time series, we determined daily TO differences (Delta TO) belonging to the same geographic longitudes between the different latitudinal circles. The result is a stable, stationary behavior for small (absolute) Delta TO values in the period January-February-March without any significant detectable trends. The high absolute value Delta TO subsets (September-October-November) indicate a robust trend reversal in the middle of the 1990s. The observed trend reversal in the total column ozone time series is consistent with the temporal development of the stratospheric halogen loading. However, a close correspondence of ozone and halogen turnaround years is not expected because of the statistical uncertainties in the determination of the ozone turnaround, and the many factors contributing to ozone depletion processes
Kinetic Monte Carlo and Cellular Particle Dynamics Simulations of Multicellular Systems
Computer modeling of multicellular systems has been a valuable tool for
interpreting and guiding in vitro experiments relevant to embryonic
morphogenesis, tumor growth, angiogenesis and, lately, structure formation
following the printing of cell aggregates as bioink particles. Computer
simulations based on Metropolis Monte Carlo (MMC) algorithms were successful in
explaining and predicting the resulting stationary structures (corresponding to
the lowest adhesion energy state). Here we present two alternatives to the MMC
approach for modeling cellular motion and self-assembly: (1) a kinetic Monte
Carlo (KMC), and (2) a cellular particle dynamics (CPD) method. Unlike MMC,
both KMC and CPD methods are capable of simulating the dynamics of the cellular
system in real time. In the KMC approach a transition rate is associated with
possible rearrangements of the cellular system, and the corresponding time
evolution is expressed in terms of these rates. In the CPD approach cells are
modeled as interacting cellular particles (CPs) and the time evolution of the
multicellular system is determined by integrating the equations of motion of
all CPs. The KMC and CPD methods are tested and compared by simulating two
experimentally well known phenomena: (1) cell-sorting within an aggregate
formed by two types of cells with different adhesivities, and (2) fusion of two
spherical aggregates of living cells.Comment: 11 pages, 7 figures; submitted to Phys Rev
Analysis of Transient Processes in a Radiophysical Flow System
Transient processes in a third-order radiophysical flow system are studied
and a map of the transient process duration versus initial conditions is
constructed and analyzed. The results are compared to the arrangement of
submanifolds of the stable and unstable cycles in the Poincare section of the
system studied.Comment: 3 pages, 2 figure
A Method for Determining the Transient Process Duration in Dynamic Systems in the Regime of Chaotic Oscillations
We describe a method for determining the transient process duration in a
standard two-dimensionaldynamic system with discrete time (Henon map),
occurring in the regime of chaotic oscillationsComment: 4 pages, 2 figure
Collision induced spatial organization of microtubules
The dynamic behavior of microtubules in solution can be strongly modified by
interactions with walls or other structures. We examine here a microtubule
growth model where the increase in size of the plus-end is perturbed by
collisions with other microtubules. We show that such a simple mechanism of
constrained growth can induce ordered structures and patterns from an initially
isotropic and homogeneous suspension. First, microtubules self-organize locally
in randomly oriented domains that grow and compete with each other. By imposing
even a weak orientation bias, external forces like gravity or cellular
boundaries may bias the domain distribution eventually leading to a macroscopic
sample orientation.Comment: Submitted to Biophysical Journa
Symmetries and Fixed Point Stability of Stochastic Differential Equations Modeling Self-Organized Criticality
A stochastic nonlinear partial differential equation is built for two
different models exhibiting self-organized criticality, the Bak, Tang, and
Wiesenfeld (BTW) sandpile model and the Zhang's model. The dynamic
renormalization group (DRG) enables to compute the critical exponents. However,
the nontrivial stable fixed point of the DRG transformation is unreachable for
the original parameters of the models. We introduce an alternative
regularization of the step function involved in the threshold condition, which
breaks the symmetry of the BTW model. Although the symmetry properties of the
two models are different, it is shown that they both belong to the same
universality class. In this case the DRG procedure leads to a symmetric
behavior for both models, restoring the broken symmetry, and makes accessible
the nontrivial fixed point. This technique could also be applied to other
problems with threshold dynamics.Comment: 19 pages, RevTex, includes 6 PostScript figures, Phys. Rev. E (March
97?
Simulation study of the inhomogeneous Olami-Feder-Christensen model of earthquakes
Statistical properties of the inhomogeneous version of the
Olami-Feder-Christensen (OFC) model of earthquakes is investigated by numerical
simulations. The spatial inhomogeneity is assumed to be dynamical. Critical
features found in the original homogeneous OFC model, e.g., the
Gutenberg-Richter law and the Omori law are often weakened or suppressed in the
presence of inhomogeneity, whereas the characteristic features found in the
original homogeneous OFC model, e.g., the near-periodic recurrence of large
events and the asperity-like phenomena persist.Comment: Shortened from the first version. To appear in European Physical
Journal
Statistics of extremal intensities for Gaussian interfaces
The extremal Fourier intensities are studied for stationary
Edwards-Wilkinson-type, Gaussian, interfaces with power-law dispersion. We
calculate the probability distribution of the maximal intensity and find that,
generically, it does not coincide with the distribution of the integrated power
spectrum (i.e. roughness of the surface), nor does it obey any of the known
extreme statistics limit distributions. The Fisher-Tippett-Gumbel limit
distribution is, however, recovered in three cases: (i) in the non-dispersive
(white noise) limit, (ii) for high dimensions, and (iii) when only
short-wavelength modes are kept. In the last two cases the limit distribution
emerges in novel scenarios.Comment: 15 pages, including 7 ps figure
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