Rheology of Granular Materials: Dynamics in a Stress Landscape

We present a framework for analyzing the rheology of dense driven granular materials, based on a recent proposal of a stress-based ensemble. In this ensemble fluctuations in a granular system near jamming are controlled by a temperature-like parameter, the angoricity, which is conjugate to the stress of the system. In this paper, we develop a model for slowly driven granular materials based on the stress ensemble and the idea of a landscape in stress space. The idea of an activated process driven by the angoricity has been shown by Behringer et al (2008) to describe the logarithmic strengthening of granular materials. Just as in the Soft Glassy Rheology (SGR) picture, our model represents the evolution of a small patch of granular material (a mesoscopic region) in a stress-based trap landscape. The angoricity plays the role of the fluctuation temperature in SGR. We determine (a) the constitutive equation, (b) the yield stress, and (c) the distribution of stress dissipated during granular shearing experiments, and compare these predictions to experiments of Hartley & Behringer (2003).Comment: 17 pages, 4 figure

Pinpointing dynamic coupling in enzymes for efficient drug design

Enzymes are proteins that catalyze almost every chemical reaction in living systems, achieving rate enhancements of up to 21 orders of magnitude relative to the uncatalyzed reactions. However, despite a century of intense investigation, the biophysical basis of the enormous catalytic power of enzymes is not completely understood. Enzymes are not only central to living systems, but also to many industrial processes such as the production of food, textiles, detergents, pharmaceuticals and other chemicals where environmentally friendly, green methods are of ever increasing importance. Because of their central role for life, enzymes are key drug targets and enzyme inhibition is a central strategy in the design of new drugs. Acetylsalicylic acid, azidothymidine, acyclovir, allopurinol, chloramphenicol, exemestane, fosfomycin, isoniazid, methotrexate, profens, proguanil, statins, thiouracil and warfarin are but a small subset of approved drug substances that are used in the clinic to treat, among others, pain, fever, inflammation, malaria, cancer, HIV, bacterial and viral infections, rheumatoid arthritis, osteoarthritis and heart disease, through the inhibition of key enzymes

Self-learning Kinetic Monte-Carlo method: application to Cu(111)

We present a novel way of performing kinetic Monte Carlo simulations which does not require an {\it a priori} list of diffusion processes and their associated energetics and reaction rates. Rather, at any time during the simulation, energetics for all possible (single or multi-atom) processes, within a specific interaction range, are either computed accurately using a saddle point search procedure, or retrieved from a database in which previously encountered processes are stored. This self-learning procedure enhances the speed of the simulations along with a substantial gain in reliability because of the inclusion of many-particle processes. Accompanying results from the application of the method to the case of two-dimensional Cu adatom-cluster diffusion and coalescence on Cu(111) with detailed statistics of involved atomistic processes and contributing diffusion coefficients attest to the suitability of the method for the purpose.Comment: 18 pages, 9 figure

Improved modelling of liquid GeSe2_2: the impact of the exchange-correlation functional

The structural properties of liquid GeSe$_2$ are studied by using first-principles molecular dynamics in conjuncton with the Becke, Lee, Yang and Parr (BLYP) generalized gradient approximation for the exchange and correlation energy. The results on partial pair correlation functions, coordination numbers, bond angle distributions and partial structure factors are compared with available experimental data and with previous first-principle molecular dynamics results obtained within the Perdew and Wang (PW) generalized gradient approximation for the exchange and correlation energy. We found that the BLYP approach substantially improves upon the PW one in the case of the short-range properties. In particular, the Ge$-$Ge pair correlation function takes a more structured profile that includes a marked first peak due to homopolar bonds, a first maximum exhibiting a clear shoulder and a deep minimum, all these features being absent in the previous PW results. Overall, the amount of tetrahedral order is significantly increased, in spite of a larger number of Ge$-$Ge homopolar connections. Due to the smaller number of miscoordinations, diffusion coefficients obtained by the present BLYP calculation are smaller by at least one order of magnitude than in the PW case.Comment: 6 figure

Transition from a simple yield stress fluid to a thixotropic material

From MRI rheometry we show that a pure emulsion can be turned from a simple yield stress fluid to a thixotropic material by adding a small fraction of colloidal particles. The two fluids have the same behavior in the liquid regime but the loaded emulsion exhibits a critical shear rate below which no steady flows can be observed. For a stress below the yield stress, the pure emulsion abruptly stops flowing, whereas the viscosity of the loaded emulsion continuously increases in time, which leads to an apparent flow stoppage. This phenomenon can be very well represented by a model assuming a progressive increase of the number of droplet links via colloidal particles.Comment: Published in Physical Review E. http://pre.aps.org/abstract/PRE/v76/i5/e05140

Thermonuclear burn-up in deuterated methane CD4CD_4

The thermonuclear burn-up of highly compressed deuterated methane CD$_4$ is considered in the spherical geometry. The minimal required values of the burn-up parameter $x = \rho_0 \cdot r_f$ are determined for various temperatures $T$ and densities $\rho_0$. It is shown that thermonuclear burn-up in $CD_4$ becomes possible in practice if its initial density $\rho_0$ exceeds $\approx 5 \cdot 10^3$ $g \cdot cm^{-3}$. Burn-up in CD$_2$T$_2$ methane requires significantly ($\approx$ 100 times) lower compressions. The developed approach can be used in order to compute the critical burn-up parameters in an arbitrary deuterium containing fuel

Bottlenecks to vibrational energy flow in OCS: Structures and mechanisms

Finding the causes for the nonstatistical vibrational energy relaxation in the planar carbonyl sulfide (OCS) molecule is a longstanding problem in chemical physics: Not only is the relaxation incomplete long past the predicted statistical relaxation time, but it also consists of a sequence of abrupt transitions between long-lived regions of localized energy modes. We report on the phase space bottlenecks responsible for this slow and uneven vibrational energy flow in this Hamiltonian system with three degrees of freedom. They belong to a particular class of two-dimensional invariant tori which are organized around elliptic periodic orbits. We relate the trapping and transition mechanisms with the linear stability of these structures.Comment: 13 pages, 13 figure

Driven translocation of a polynucleotide chain through a nanopore--A continuous time Monte-Carlo study

Using continuous time Monte-Carlo method we simulated the translocation of a polynucleotide chain driven through a nanopore by an electric field. We have used two models of driven diffusion due to the electric field. The chain may have strong interaction with the pore, and depends on which end of the chain first enters the pore. Depending on this interaction, in both cases, the distribution of times for the chain to pass through the pore in our model is found to have three peaks, as observed in the experiment of Kasianowicz, Brandin, Branton and Deamer (KBBD).Comment: 26 pages, 6 figure

Deformation and flow of a two-dimensional foam under continuous shear

We investigate the flow properties of a two-dimensional aqueous foam submitted to a quasistatic shear in a Couette geometry. A strong localization of the flow (shear banding) at the edge of the moving wall is evidenced, characterized by an exponential decay of the average tangential velocity. Moreover, the analysis of the rapid velocity fluctuations reveals self-similar dynamical structures consisting of clusters of bubbles rolling as rigid bodies. To relate the instantaneous (elastic) and time-averaged (plastic) components of the strain, we develop a stochastic model where irreversible rearrangements are activated by local stress fluctuations originating from the rubbing of the wall. This model gives a complete description of our observations and is also consistent with data obtained on granular shear bands by other groups.Comment: 5 pages, 2 figure

Surface diffusion coefficients by thermodynamic integration: Cu on Cu(100)

The rate of diffusion of a Cu adatom on the Cu(100) surface is calculated using thermodynamic integration within the transition state theory. The results are found to be in excellent agreement with the essentially exact values from molecular-dynamics simulations. The activation energy and related entropy are shown to be effectively independent of temperature, thus establishing the validity of the Arrhenius law over a wide range of temperatures. Our study demonstrates the equivalence of diffusion rates calculated using thermodynamic integration within the transition state theory and direct molecular-dynamics simulations.Comment: 4 pages (revtex), two figures (postscript