146 research outputs found
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
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
Fluctuation-Driven Molecular Transport in an Asymmetric Membrane Channel
Channel proteins, that selectively conduct molecules across cell membranes,
often exhibit an asymmetric structure. By means of a stochastic model, we argue
that channel asymmetry in the presence of non-equilibrium fluctuations, fueled
by the cell's metabolism as observed recently, can dramatically influence the
transport through such channels by a ratchet-like mechanism. For an
aquaglyceroporin that conducts water and glycerol we show that a previously
determined asymmetric glycerol potential leads to enhanced inward transport of
glycerol, but for unfavorably high glycerol concentrations also to enhanced
outward transport that protects a cell against poisoning.Comment: REVTeX4, 4 pages, 3 figures; Accepted for publication in Phys. Rev.
Let
Comment on "T-dependence of the magnetic penetration depth in unconventional superconductors at low temperatures: Can it be linear?"
We show that the clean superconductor with line of gap nodes is not in
conflict with the Nernst theorem. The answer to the question in the title of
the Schopohl-Dolgov paper in Phys. Rev. Lett. 80 (1998) 4761 (cond-mat/9802264)
is yes.Comment: Comment to the paper by Schopohl and Dolgov in Phys. Rev. Lett. 80
(1998) 4761 (cond-mat/9802264), RevTex file, 1 page, no figures, typos are
corrected, submitted to Phys. Rev. Let
Pairing Fluctuation Theory of Superconducting Properties in Underdoped to Overdoped Cuprates
We propose a theoretical description of the superconducting state of under-
to overdoped cuprates, based on the short coherence length of these materials
and the associated strong pairing fluctuations. The calculated and the
zero temperature excitation gap , as a function of hole
concentration , are in semi-quantitative agreement with experiment. Although
the ratio has a strong dependence, different from the
universal BCS value, and deviates significantly from the BCS
prediction, we obtain, quite remarkably, quasi-universal behavior, for the
normalized superfluid density and the Josephson critical
current , as a function of . While experiments on
are consistent with these results, future measurements on
are needed to test this prediction.Comment: 4 pages, 3 figures, REVTeX, submitted to Phys. Rev. Let
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
Comment on "Is the nonlinear Meissner effect unobservable?"
In a recent Letter (Phys. Rev. Lett. 81, p.5640 (1998), cond-mat/9808249 v3),
it was suggested that nonlocal effects may prevent observation of the nonlinear
Meissner effect in YBCO. We argue that this claim is incorrect with regards to
measurements of the nonlinear transverse magnetic moment, and that the most
likely reason for a null result lies elsewhere.Comment: 1 pag
Non-Locality and Strong Coupling in the Heavy Fermion Superconductor CeCoIn: A Penetration Depth Study
We report measurements of the magnetic penetration depth in single
crystals of CeCoIn down to 0.14 K using a tunnel-diode based,
self-inductive technique at 28 MHz. While the in-plane penetration depth tends
to follow a power law, , the data are better
described as a crossover between linear ({\it T} ) and
quadratic ({\it T} ) behavior, with the
crossover temperature in the strong-coupling limit. The {\it c}-axis
penetration depth is linear in {\it T}, providing evidence
that CeCoIn is a {\it d}-wave superconductor with line nodes along the
{\it c}-axis. The different temperature dependences of and
rule out impurity effects as the source of .Comment: 4 pages, 3 figure
On the T-dependence of the magnetic penetration depth in unconventional superconductors at low temperatures: can it be linear?
We present a thermodynamics argument against a strictly linear temperature
dependence of the magnetic penetration depth, which applies to superconductors
with arbitrary pairing symmetry at low temperatures.Comment: 5 pages, expanded version of cond-mat/971102
Absence of non-linear Meissner effect in YBa2Cu3O6.95
We present measurements the field and temperature dependence of the
penetration depth (lambda) in high purity, untwinned single crystals of
YBa2Cu3O6.95 in all three crystallographic directions. The temperature
dependence of lambda is linear down to low temperatures, showing that our
crystals are extremely clean. Both the magnitude and temperature dependence of
the field dependent correction to lambda however, are considerably different
from that predicted from the theory of the non-linear Meissner effect for a
d-wave superconductor (Yip-Sauls theory). Our results suggest that the
Yip-Sauls effect is either absent or is unobservably small in the Meissner
state of YBa2Cu3O6.95.Comment: 4 pages, 4 figures (Latex file + Postscipt figures
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