218 research outputs found
Tumbling of polymers in semidilute solution under shear flow
The tumbling dynamics of individual polymers in semidilute solution is
studied by large-scale non-equilibrium mesoscale hydrodynamic simulations. We
find that the tumbling time is equal to the non-equilibrium relaxation time of
the polymer end-to-end distance along the flow direction and strongly depends
on concentration. In addition, the normalized tumbling frequency as well as the
widths of the alignment distribution functions for a given
concentration-dependent Weissenberg number exhibit a weak concentration
dependence in the cross-over regime from a dilute to a semidilute solution. For
semidilute solutions a universal behavior is obtained. This is a consequence of
screening of hydrodynamic interactions at polymer concentrations exceeding the
overlap concentration
Instantaneous Normal Mode analysis of liquid HF
We present an Instantaneous Normal Modes analysis of liquid HF aimed to
clarify the origin of peculiar dynamical properties which are supposed to stem
from the arrangement of molecules in linear hydrogen-bonded network. The
present study shows that this approach is an unique tool for the understanding
of the spectral features revealed in the analysis of both single molecule and
collective quantities. For the system under investigation we demonstrate the
relevance of hydrogen-bonding ``stretching'' and fast librational motion in the
interpretation of these features.Comment: REVTeX, 7 pages, 5 eps figures included. Minor changes in the text
and in a figure. Accepted for publication in Phys. Rev. Let
Phase Behavior of Columnar DNA Assemblies
The pair interaction between two stiff parallel linear DNA molecules depends
not only on the distance between their axes but on their azimuthal orientation.
The positional and orientational order in columnar B-DNA assemblies in solution
is investigated, based on the DNA-DNA electrostatic pair potential that takes
into account DNA helical symmetry and the amount and distribution of adsorbed
counterions. A phase diagram obtained by lattice sum calculations predicts a
variety of positionally and azimuthally ordered phases and bundling transitions
strongly depending on the counterion adsorption patterns.Comment: 4 pages, 3 figures, submitted to PR
Towards Blood Flow in the Virtual Human: Efficient Self-Coupling of HemeLB
Many scientific and medical researchers are working towards the creation of a
virtual human - a personalised digital copy of an individual - that will assist
in a patient's diagnosis, treatment and recovery. The complex nature of living
systems means that the development of this remains a major challenge. We
describe progress in enabling the HemeLB lattice Boltzmann code to simulate 3D
macroscopic blood flow on a full human scale. Significant developments in
memory management and load balancing allow near linear scaling performance of
the code on hundreds of thousands of computer cores. Integral to the
construction of a virtual human, we also outline the implementation of a
self-coupling strategy for HemeLB. This allows simultaneous simulation of
arterial and venous vascular trees based on human-specific geometries.Comment: 30 pages, 10 figures, To be published in Interface Focus
(https://royalsocietypublishing.org/journal/rsfs
Oscillations and waves in solar spicules
Since their discovery, spicules have attracted increased attention as energy/mass bridges between the dense and dynamic photosphere and the tenuous hot solar corona. Mechanical energy of photospheric random and coherent motions can be guided by magnetic field lines, spanning from the interior to the upper parts of the solar atmosphere, in the form of waves and oscillations. Since spicules are one of the most pronounced features of the chromosphere, the energy transport they participate in can be traced by the observations of their oscillatory motions. Oscillations in spicules have been observed for a long time. However the recent high-resolutions and high-cadence space and ground based facilities with superb spatial, temporal and spectral capacities brought new aspects in the research of spicule dynamics. Here we review the progress made in imaging and spectroscopic observations of waves and oscillations in spicules. The observations are accompanied by a discussion on theoretical modelling and interpretations of these oscillations. Finally, we embark on the recent developments made on the presence and role of Alfven and kink waves in spicules. We also address the extensive debate made on the Alfven versus kink waves in the context of the explanation of the observed transverse oscillations of spicule axes
Kinetic Monte Carlo modelling of dipole blockade in Rydberg excitation experiment
We present a method to model the interaction and the dynamics of atoms
excited to Rydberg states. We show a way to solve the optical Bloch equations
for laser excitation of the frozen gas in good agreement with the experiment. A
second method, the Kinetic Monte Carlo method gives an exact solution of rate
equations. Using a simple N-body integrator (Verlet), we are able to describe
dynamical processes in space and time. Unlike more sophisticated methods, the
Kinetic Monte Carlo simulation offers the possibility of numerically following
the evolution of tens of thousands of atoms within a reasonable computation
time. The Kinetic Monte Carlo simulation gives good agreement with
dipole-blockade type of experiment. The role of ions and the individual
particle effects are investigated.Comment: 23 pages. Submitted to New Journal of Physic
Molecular dynamics simulation of humic substances
© 2014, Orsi. Humic substances (HS) are complex mixtures of natural organic material which are found almost everywhere in the environment, and particularly in soils, sediments, and natural water. HS play key roles in many processes of paramount importance, such as plant growth, carbon storage, and the fate of contaminants in the environment. While most of the research on HS has been traditionally carried out by conventional experimental approaches, over the past 20 years complementary investigations have emerged from the application of computer modeling and simulation techniques. This paper reviews the literature regarding computational studies of HS, with a specific focus on molecular dynamics simulations. Significant achievements, outstanding issues, and future prospects are summarized and discussed
Multigrid method based on transformation-free high-order scheme for solving 2D Helmholtz equation on nonuniform grids
Scaling of the Memory Function and Brownian Motion
It has been recently shown that the velocity autocorrelation function of a tracer particle immersed in a simple liquid scales approximately with the inverse of its mass. With increasing mass the amplitude is systematically reduced and the velocity autocorrelation function tends to a slowly decaying exponential, which is characteristic for Brownian motion. We give here an analytical proof for this behavior and comment on the usual explanation for Brownian dynamics which is based on the assumption that the memory function is proportional to a Dirac distribution. We also derive conditions for Brownian dynamics of a tracer particle which are entirely based on properties of its memory function
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