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