2,039 research outputs found
GPU-accelerated simulation of colloidal suspensions with direct hydrodynamic interactions
Solvent-mediated hydrodynamic interactions between colloidal particles can
significantly alter their dynamics. We discuss the implementation of Stokesian
dynamics in leading approximation for streaming processors as provided by the
compute unified device architecture (CUDA) of recent graphics processors
(GPUs). Thereby, the simulation of explicit solvent particles is avoided and
hydrodynamic interactions can easily be accounted for in already available,
highly accelerated molecular dynamics simulations. Special emphasis is put on
efficient memory access and numerical stability. The algorithm is applied to
the periodic sedimentation of a cluster of four suspended particles. Finally,
we investigate the runtime performance of generic memory access patterns of
complexity for various GPU algorithms relying on either hardware cache
or shared memory.Comment: to appear in a special issue of Eur. Phys. J. Special Topics on
"Computer Simulations on GPUs
A study of pre-validation
Given a predictor of outcome derived from a high-dimensional dataset,
pre-validation is a useful technique for comparing it to competing predictors
on the same dataset. For microarray data, it allows one to compare a newly
derived predictor for disease outcome to standard clinical predictors on the
same dataset. We study pre-validation analytically to determine if the
inferences drawn from it are valid. We show that while pre-validation generally
works well, the straightforward "one degree of freedom" analytical test from
pre-validation can be biased and we propose a permutation test to remedy this
problem. In simulation studies, we show that the permutation test has the
nominal level and achieves roughly the same power as the analytical test.Comment: Published in at http://dx.doi.org/10.1214/07-AOAS152 the Annals of
Applied Statistics (http://www.imstat.org/aoas/) by the Institute of
Mathematical Statistics (http://www.imstat.org
Anomalous transport in the crowded world of biological cells
A ubiquitous observation in cell biology is that diffusion of macromolecules
and organelles is anomalous, and a description simply based on the conventional
diffusion equation with diffusion constants measured in dilute solution fails.
This is commonly attributed to macromolecular crowding in the interior of cells
and in cellular membranes, summarising their densely packed and heterogeneous
structures. The most familiar phenomenon is a power-law increase of the MSD,
but there are other manifestations like strongly reduced and time-dependent
diffusion coefficients, persistent correlations, non-gaussian distributions of
the displacements, heterogeneous diffusion, and immobile particles. After a
general introduction to the statistical description of slow, anomalous
transport, we summarise some widely used theoretical models: gaussian models
like FBM and Langevin equations for visco-elastic media, the CTRW model, and
the Lorentz model describing obstructed transport in a heterogeneous
environment. Emphasis is put on the spatio-temporal properties of the transport
in terms of 2-point correlation functions, dynamic scaling behaviour, and how
the models are distinguished by their propagators even for identical MSDs.
Then, we review the theory underlying common experimental techniques in the
presence of anomalous transport: single-particle tracking, FCS, and FRAP. We
report on the large body of recent experimental evidence for anomalous
transport in crowded biological media: in cyto- and nucleoplasm as well as in
cellular membranes, complemented by in vitro experiments where model systems
mimic physiological crowding conditions. Finally, computer simulations play an
important role in testing the theoretical models and corroborating the
experimental findings. The review is completed by a synthesis of the
theoretical and experimental progress identifying open questions for future
investigation.Comment: review article, to appear in Rep. Prog. Phy
Structure and dynamics of binary liquid mixtures near their continuous demixing transitions
The dynamic and static critical behavior of five binary Lennard-Jones liquid
mixtures, close to their continuous demixing points (belonging to the so-called
model H' dynamic universality class), are studied computationally by combining
semi-grand canonical Monte Carlo simulations and large-scale molecular dynamics
(MD) simulations, accelerated by graphic processing units (GPU). The symmetric
binary liquid mixtures considered cover a variety of densities, a wide range of
compressibilities, and various interactions between the unlike particles. The
static quantities studied here encompass the bulk phase diagram (including both
the binodal and the -line), the correlation length, the concentration
susceptibility, the compressibility of the finite-sized systems at the bulk
critical temperature , and the pressure. Concerning the collective
transport properties, we focus on the Onsager coefficient and the shear
viscosity. The critical power-law singularities of these quantities are
analyzed in the mixed phase (above ) and non-universal critical amplitudes
are extracted. Two universal amplitude ratios are calculated. The first one
involves static amplitudes only and agrees well with the expectations for the
three-dimensional Ising universality class. The second ratio includes also
dynamic critical amplitudes and is related to the Einstein--Kawasaki relation
for the interdiffusion constant. Precise estimates of this amplitude ratio are
difficult to obtain from MD simulations, but within the error bars our results
are compatible with theoretical predictions and experimental values for model
H'. Evidence is reported for an inverse proportionality of the pressure and the
isothermal compressibility at the demixing transition, upon varying either the
number density or the repulsion strength between unlike particles.Comment: 15 pages, 12 figure
Interband cascade lasers with room temperature threshold current densities below 100 A/cm(2)
Interband Cascade Lasers (ICLs) with threshold current densities below 100 A/cm(2) in pulsed operation at room temperature are presented. The laser structure comprises 10 active stages of 41 nm length, each stage containing a W-quantum well active region for emission in the spectral region around 3.6 mu m. A comparison of devices with 6 and 10 stages shows that the latter have a reduced threshold due to an increased optical confinement factor, very competitive threshold power densities of 428 W cm(-2) despite an increased threshold voltage and large differential slope efficiencies of 1390 mW/A. For a narrow ridge device, continuous wave operation is observed up to 65 degrees C.Publisher PDFPeer reviewe
Anomalous transport resolved in space and time by fluorescence correlation spectroscopy
A ubiquitous observation in crowded cell membranes is that molecular
transport does not follow Fickian diffusion but exhibits subdiffusion. The
microscopic origin of such a behaviour is not understood and highly debated.
Here we discuss the spatio-temporal dynamics for two models of subdiffusion:
fractional Brownian motion and hindered motion due to immobile obstacles. We
show that the different microscopic mechanisms can be distinguished using
fluorescence correlation spectroscopy (FCS) by systematic variation of the
confocal detection area. We provide a theoretical framework for space-resolved
FCS by generalising FCS theory beyond the common assumption of spatially
Gaussian transport. We derive a master formula for the FCS autocorrelation
function, from which it is evident that the beam waist of an FCS experiment is
a similarly important parameter as the wavenumber of scattering experiments.
These results lead to scaling properties of the FCS correlation for both
models, which are tested by in silico experiments. Further, our scaling
prediction is compatible with the FCS half-value times reported by Wawrezinieck
et al. [Biophys. J. 89, 4029 (2005)] for in vivo experiments on a transmembrane
protein.Comment: accepted for publication in Soft Matte
Enhanced Diffusion of a Needle in a Planar Course of Point Obstacles
The transport of an infinitely thin, hard rod in a random, dense array of
point obstacles is investigated by molecular dynamics simulations. Our model
mimics the sterically hindered dynamics in dense needle liquids. The
center-of-mass diffusion exhibits a minimum, and transport becomes increasingly
fast at higher densities. The diffusion coefficient diverges according to a
power law in the density with an approximate exponent of 0.8. This observation
is connected with a new divergent time scale, reflected in a zig-zag motion of
the needle, a two-step decay of the velocity-autocorrelation function, and a
negative plateau in the non-Gaussian parameter.Comment: accepted for publication in Phys. Rev. Let
Localization phenomena in models of ion-conducting glass formers
The mass transport in soft-sphere mixtures of small and big particles as well
as in the disordered Lorentz gas (LG) model is studied using molecular dynamics
(MD) computer simulations. The soft-sphere mixture shows anomalous
small-particle diffusion signifying a localization transition separate from the
big-particle glass transition. Switching off small-particle excluded volume
constraints slows down the small-particle dynamics, as indicated by incoherent
intermediate scattering functions. A comparison of logarithmic time derivatives
of the mean-squared displacements reveals qualitative similarities between the
localization transition in the soft-sphere mixture and its counterpart in the
LG. Nevertheless, qualitative differences emphasize the need for further
research elucidating the connection between both models.Comment: to appear in Eur. Phys. J. Special Topic
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