1,952 research outputs found
Efficient multiple time scale molecular dynamics: using colored noise thermostats to stabilize resonances
Multiple time scale molecular dynamics enhances computational efficiency by
updating slow motions less frequently than fast motions. However, in practice
the largest outer time step possible is limited not by the physical forces but
by resonances between the fast and slow modes. In this paper we show that this
problem can be alleviated by using a simple colored noise thermostatting scheme
which selectively targets the high frequency modes in the system. For two
sample problems, flexible water and solvated alanine dipeptide, we demonstrate
that this allows the use of large outer time steps while still obtaining
accurate sampling and minimizing the perturbation of the dynamics. Furthermore,
this approach is shown to be comparable to constraining fast motions, thus
providing an alternative to molecular dynamics with constraints.Comment: accepted for publication by the Journal of Chemical Physic
Multi-speckle diffusing wave spectroscopy with a single mode detection scheme
We present a detection scheme for diffusing wave spectroscopy (DWS) based on
a two cell geometry that allows efficient ensemble averaging. This is achieved
by putting a fast rotating diffuser in the optical path between laser and
sample. We show that the recorded (multi-speckle) correlation echoes provide an
ensemble averaged signal that does not require additional time averaging. We
find the performance of our experimental scheme comparable or even superior to
camera based multi-speckle techniques that rely on direct spatial averaging.
Furthermore, combined with traditional two-cell DWS, the full intensity
autocorrelation function can be measured with a single experimental setup
covering more than 10 decades in correlation time.Comment: Submitted to PR
Aggregates relaxation in a jamming colloidal suspension after shear cessation
The reversible aggregates formation in a shear thickening, concentrated
colloidal suspension is investigated through speckle visibility spectroscopy, a
dynamic light scattering technique recently introduced [P.K. Dixon and D.J.
Durian, Phys. Rev. Lett. 90, 184302 (2003)]. Formation of particles aggregates
is observed in the jamming regime, and their relaxation after shear cessation
is monitored as a function of the applied shear stress. The aggregates
relaxation time increases when a larger stress is applied. Several phenomena
have been proposed to interpret this behavior: an increase of the aggregates
size and volume fraction, or a closer packing of the particles in the
aggregates.Comment: 7 pages, 7 figures; added figures included in the pdf versio
Multiangle static and dynamic light scattering in the intermediate scattering angle range
We describe a light scattering apparatus based on a novel optical scheme
covering the scattering angle range 0.5\dg \le \theta \le 25\dg, an
intermediate regime at the frontier between wide angle and small angle setups
that is difficult to access by existing instruments. Our apparatus uses
standard, readily available optomechanical components. Thanks to the use of a
charge-coupled device detector, both static and dynamic light scattering can be
performed simultaneously at several scattering angles. We demonstrate the
capabilities of our apparatus by measuring the scattering profile of a variety
of samples and the Brownian dynamics of a dilute colloidal suspension
Orientational relaxation in a discotic liquid crystal
We investigate orientational relaxation of a model discotic liquid crystal,
consists of disc-like molecules, by molecular dynamics simulations along two
isobars starting from the high temperature isotropic phase. The two isobars
have been so chosen that (A) the phase sequence isotropic (I)-nematic
(N)-columnar (C) appears upon cooling along one of them and (B) the sequence
isotropic (I)-columnar (C) along the other. While the orientational relaxation
in the isotropic phase near the I-N phase transition in system (A) shows a
power law decay at short to intermediate times, such power law relaxation is
not observed in the isotropic phase near the I-C phase boundary in system (B).
In order to understand this difference (the existence or the absence of the
power law decay), we calculated the the growth of the orientational pair
distribution functions (OPDF) near the I-N phase boundary and also near the I-C
phase boundary. We find that OPDF shows a marked growth in long range
correlation as the I-N phase boundary is approached in the I-N-C system (A),
but such a growth is absent in the I-C system, which appears to be consistent
with the result that I-N phase transition in the former is weakly first order
while the the I-C phase transition in the later is not weak. As the system
settles into the nematic phase, the decay of the single-particle second-rank
orientational OTCF follows a pattern that is similar to what is observed with
calamitic liquid crystals and supercooled molecular liquids.Comment: 16 pages and 4 figure
Binding branched and linear DNA structures: from isolated clusters to fully bonded gels
The proper design of DNA sequences allows for the formation of well defined
supramolecular units with controlled interactions via a consecution of
self-assembling processes. Here, we benefit from the controlled DNA
self-assembly to experimentally realize particles with well defined valence,
namely tetravalent nanostars (A) and bivalent chains (B). We specifically focus
on the case in which A particles can only bind to B particles, via
appropriately designed sticky-end sequences. Hence AA and BB bonds are not
allowed. Such a binary mixture system reproduces with DNA-based particles the
physics of poly-functional condensation, with an exquisite control over the
bonding process, tuned by the ratio, r, between B and A units and by the
temperature, T. We report dynamic light scattering experiments in a window of
Ts ranging from 10{\deg}C to 55{\deg}C and an interval of r around the
percolation transition to quantify the decay of the density correlation for the
different cases. At low T, when all possible bonds are formed, the system
behaves as a fully bonded network, as a percolating gel and as a cluster fluid
depending on the selected r.Comment: 15 pages, 11 figure
Modelling a Dune Field
We present a model to describe the collective motion of barchan dunes in a
field. Our model is able to reproduce the observation that a typical dune stays
confined within a stripe. We also obtain some of the pattern structures which
ressemble those observed from aerial photos which we do analyse and compare
with the specific field of La\^ayounne.Comment: 15 pages, 13 figure
Speckle visibility spectroscopy and variable granular fluidization
We introduce a dynamic light scattering technique capable of resolving motion
that changes systematically, and rapidly, with time. It is based on the
visibility of a speckle pattern for a given exposure duration. Applying this to
a vibrated layer of glass beads, we measure the granular temperature and its
variation with phase in the oscillation cycle. We observe several transitions
involving jammed states, where the grains are at rest during some portion of
the cycle. We also observe a two-step decay of the temperature on approach to
jamming.Comment: 4 pages, 4 figures, experimen
Differential Dynamic Microscopy to characterize Brownian motion and bacteria motility
We have developed a lab work module where we teach undergraduate students how
to quantify the dynamics of a suspension of microscopic particles, measuring
and analyzing the motion of those particles at the individual level or as a
group. Differential Dynamic Microscopy (DDM) is a relatively recent technique
that precisely does that and constitutes an alternative method to more
classical techniques such as dynamics light scattering (DLS) or video particle
tracking (VPT). DDM consists in imaging a particle dispersion with a standard
light microscope and a camera. The image analysis requires the students to code
and relies on digital Fourier transform to obtain the intermediate scattering
function, an autocorrelation function that characterizes the dynamics of the
dispersion. We first illustrate DDM on the textbook case of colloids where we
measure the diffusion coefficient. Then we show that DDM is a pertinent tool to
characterize biologic systems such as motile bacteria i.e.bacteria that can
self propel, where we not only determine the diffusion coefficient but also the
velocity and the fraction of motile bacteria. Finally, so that our paper can be
used as a tutorial to the DDM technique, we have joined to this article movies
of the colloidal and bacterial suspensions and the DDM algorithm in both Matlab
and Python to analyze the movies
Liquid Transport Due to Light Scattering
Using experiments and theory, we show that light scattering by
inhomogeneities in the index of refraction of a fluid can drive a large-scale
flow. The experiment uses a near-critical, phase-separated liquid, which
experiences large fluctuations in its index of refraction. A laser beam
traversing the liquid produces a large-scale deformation of the interface and
can cause a liquid jet to form. We demonstrate that the deformation is produced
by a scattering-induced flow by obtaining good agreements between the measured
deformations and those calculated assuming this mechanism.Comment: 4 pages, 5 figures, submitted to Physical Review Letters v2: Edited
based on comments from referee
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