Interaction and Concerted Diffusion of Lithium in a (5,5) Carbon Nanotube

The interaction and diffusion of lithium atoms in a (5,5) carbon nanotube is studied using density-functional theory. The Li-nanotube interaction perpendicular to the tube axis for a single Li inside and outside the tube is calculated and compared with the Li-graphene interaction obtained using the same technique. Both interactions are similar in the repulsive region but exhibit differences in their attractive part. Nevertheless, they can be described using a common parametrization. The Li-Li interaction is calculated as a function of their separation inside the tube. This interaction is similar to a screened repulsive Coulomb potential at small separations. However, at larger separations, the Li-Li interaction does not vanish and shows residual oscillations. This repulsive long-ranged interaction favors concerted diffusion of many Li atoms compared to the independent diffusion of individual Li inside the tube

Dynamics of Viscoplastic Deformation in Amorphous Solids

We propose a dynamical theory of low-temperature shear deformation in amorphous solids. Our analysis is based on molecular-dynamics simulations of a two-dimensional, two-component noncrystalline system. These numerical simulations reveal behavior typical of metallic glasses and other viscoplastic materials, specifically, reversible elastic deformation at small applied stresses, irreversible plastic deformation at larger stresses, a stress threshold above which unbounded plastic flow occurs, and a strong dependence of the state of the system on the history of past deformations. Microscopic observations suggest that a dynamically complete description of the macroscopic state of this deforming body requires specifying, in addition to stress and strain, certain average features of a population of two-state shear transformation zones. Our introduction of these new state variables into the constitutive equations for this system is an extension of earlier models of creep in metallic glasses. In the treatment presented here, we specialize to temperatures far below the glass transition, and postulate that irreversible motions are governed by local entropic fluctuations in the volumes of the transformation zones. In most respects, our theory is in good quantitative agreement with the rich variety of phenomena seen in the simulations.Comment: 16 pages, 9 figure

Interaction of Hydrogen with Graphitic Surfaces, Clean and Doped with Metal Clusters

Producción CientíficaHydrogen is viewed as a possible alternative to the fossil fuels in transportation. The technology of fuel-cell engines is fully developed, and the outstanding remaining problem is the storage of hydrogen in the vehicle. Porous materials, in which hydrogen is adsorbed on the pore walls, and in particular nanoporous carbons, have been investigated as potential onboard containers. Furthermore, metallic nanoparticles embedded in porous carbons catalyze the dissociation of hydrogen in the anode of the fuel cells. For these reasons the interaction of hydrogen with the surfaces of carbon materials is a topic of high technological interest. Computational modeling and the density functional formalism (DFT) are helping in the task of discovering the basic mechanisms of the interaction of hydrogen with clean and doped carbon surfaces. Planar and curved graphene provide good models for the walls of porous carbons. We first review work on the interaction of molecular and atomic hydrogen with graphene and graphene nanoribbons, and next we address the effects due to the presence of metal clusters on the surface because of the evidence of their role in enhancing hydrogen storage.Ministerio de Economía, Industria y Competitividad (Grant MAT2014-54378-R

Non-equilibrium statistical mechanics: From a paradigmatic model to biological transport

Unlike equilibrium statistical mechanics, with its well-established foundations, a similar widely-accepted framework for non-equilibrium statistical mechanics (NESM) remains elusive. Here, we review some of the many recent activities on NESM, focusing on some of the fundamental issues and general aspects. Using the language of stochastic Markov processes, we emphasize general properties of the evolution of configurational probabilities, as described by master equations. Of particular interest are systems in which the dynamics violate detailed balance, since such systems serve to model a wide variety of phenomena in nature. We next review two distinct approaches for investigating such problems. One approach focuses on models sufficiently simple to allow us to find exact, analytic, non-trivial results. We provide detailed mathematical analyses of a one-dimensional continuous-time lattice gas, the totally asymmetric exclusion process (TASEP). It is regarded as a paradigmatic model for NESM, much like the role the Ising model played for equilibrium statistical mechanics. It is also the starting point for the second approach, which attempts to include more realistic ingredients in order to be more applicable to systems in nature. Restricting ourselves to the area of biophysics and cellular biology, we review a number of models that are relevant for transport phenomena. Successes and limitations of these simple models are also highlighted.Comment: 72 pages, 18 figures, Accepted to: Reports on Progress in Physic

The mechanism of DNA unwinding by the eukaryotic replicative helicase

Accurate DNA replication is tightly regulated in eukaryotes to ensure genome stability during cell division and is performed by the multi-protein replisome. At the core an AAA+ hetero-hexameric complex, Mcm2-7, together with GINS and Cdc45 form the active replicative helicase Cdc45/Mcm2-7/GINS (CMG). It is not clear how this replicative ring helicase translocates on, and unwinds, DNA. We measure real-time dynamics of purified recombinant Drosophila melanogaster CMG unwinding DNA with single-molecule magnetic tweezers. Our data demonstrates that CMG exhibits a biased random walk, not the expected unidirectional motion. Through building a kinetic model we find CMG may enter up to three paused states rather than unwinding, and should these be prevented, in vivo fork rates would be recovered in vitro. We propose a mechanism in which CMG couples ATP hydrolysis to unwinding by acting as a lazy Brownian ratchet, thus providing quantitative understanding of the central process in eukaryotic DNA replication

Reflection principles for biased random walks and application to escape time distributions

We present a reflection principle for an arbitrarybiased continuous time random walk (comprising both Markovian and non-Markovian processes) in the presence of areflecting barrier on semi-infinite and finite chains. For biased walks in the presence of a reflecting barrier this principle (which cannot be derived from combinatorics) is completely different from its familiar form in the presence of an absorbing barrier. The result enables us to obtain closed-form solutions for the Laplace transform of the conditional probability for biased walks on finite chains for all three combinations of absorbing and reflecting barriers at the two ends. An important application of these solutions is the calculation of various first-passage-time and escape-time distributions. We obtain exact results for the characteristic functions of various kinds of escape time distributions for biased random walks on finite chains. For processes governed by a long-tailed event-time distribution we show that the mean time of escape from bounded regions diverges even in the presence of a bias-suggesting, in a sense, the absence of true long-range diffusion in such frozen processes