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Meng-Bo Luo, Dessalegne A Tsehay, Li-Zhen Sun
The forced translocation of a polymer chain through repulsive nanopores was studied by using Langevin dynamics simulations. The polymer is in the compact globule state at low temperature and in the random coil state at high temperature. Simulation results show that the mean translocation time 〈τ〉 is highly dependent on the temperature T and the minimal 〈τ〉 is located near the coil-globule transition temperature. Moreover, the scaling behaviors 〈τ〉 ∼ N(α) and 〈τ〉 ∼ F(-δ) are studied, with N the polymer length and F the driving force inside the nanopore...
July 21, 2017: Journal of Chemical Physics
Kai Szuttor, Tamal Roy, Steffen Hardt, Christian Holm, Jens Smiatek
We use mesoscopic lattice-Boltzmann/molecular dynamics simulations to study the stretching behavior of a single tethered polymer in micro- and nanochannels. In particular, we are interested in the connection between fluid flow properties and the force on the polymer chain. An analytical expression for the stretching force is proposed, which linearly depends on the number of monomers and the boundary shear rate. In agreement with theory, the numerical findings reveal that the influence of hydrodynamic interactions can be ignored, which is also supported by results of additional Langevin dynamics simulations...
July 21, 2017: Journal of Chemical Physics
W T Coffey, M Zarifakis, Y P Kalmykov, S V Titov, W J Dowling, A S Titov
The itinerant oscillator model describing rotation of a dipole about a fixed axis inside a cage formed by its surrounding polar molecules is revisited in the context of modeling the dielectric relaxation of a polar fluid via the Langevin equation. The dynamical properties of the model are studied by averaging the Langevin equations describing the complex orientational dynamics of two bodies (molecule-cage) over their realizations in phase space so that the problem reduces to solving a system of three index linear differential-recurrence relations for the statistical moments...
July 21, 2017: Journal of Chemical Physics
Zhijun Zhang, Xinzijian Liu, Zifei Chen, Haifeng Zheng, Kangyu Yan, Jian Liu
We show a unified second-order scheme for constructing simple, robust, and accurate algorithms for typical thermostats for configurational sampling for the canonical ensemble. When Langevin dynamics is used, the scheme leads to the BAOAB algorithm that has been recently investigated. We show that the scheme is also useful for other types of thermostats, such as the Andersen thermostat and Nosé-Hoover chain, regardless of whether the thermostat is deterministic or stochastic. In addition to analytical analysis, two 1-dimensional models and three typical real molecular systems that range from the gas phase, clusters, to the condensed phase are used in numerical examples for demonstration...
July 21, 2017: Journal of Chemical Physics
Geert-Jan Kroes, J I Juaristi, M Alducin
In scattering of H2 from Cu(111), vibrational excitation has so far defied an accurate theoretical description. To expose the causes of the large discrepancies with experiment, we investigate how the feature due to vibrational excitation (the "gain peak") in the simulated time-of-flight spectrum of (v = 1, j = 3) H2 scattering from Cu(111) depends on the surface temperature (Ts) and the possibility of energy exchange with surface phonons and electron-hole pairs (ehp's). Quasi-classical dynamics calculations are performed on the basis of accurate semiempirical density functionals for the interaction with H2 + Cu(111)...
June 29, 2017: Journal of Physical Chemistry. C, Nanomaterials and Interfaces
Avinava Dubey, Sashank J Reddi, Barnabás Póczos, Alexander J Smola, Eric P Xing, Sinead A Williamson
Stochastic gradient-based Monte Carlo methods such as stochastic gradient Langevin dynamics are useful tools for posterior inference on large scale datasets in many machine learning applications. These methods scale to large datasets by using noisy gradients calculated using a mini-batch or subset of the dataset. However, the high variance inherent in these noisy gradients degrades performance and leads to slower mixing. In this paper, we present techniques for reducing variance in stochastic gradient Langevin dynamics, yielding novel stochastic Monte Carlo methods that improve performance by reducing the variance in the stochastic gradient...
December 2016: Advances in Neural Information Processing Systems
Alexandre Roulet, Stefan Nimmrichter, Juan Miguel Arrazola, Stella Seah, Valerio Scarani
The triumph of heat engines is their ability to convert the disordered energy of thermal sources into useful mechanical motion. In recent years, much effort has been devoted to generalizing thermodynamic notions to the quantum regime, partly motivated by the promise of surpassing classical heat engines. Here, we instead adopt a bottom-up approach: we propose a realistic autonomous heat engine that can serve as a test bed for quantum effects in the context of thermodynamics. Our model draws inspiration from actual piston engines and is built from closed-system Hamiltonians and weak bath coupling terms...
June 2017: Physical Review. E
Saurav Talukdar, Shreyas Bhaban, Murti V Salapaka
We study the thermodynamics of a Brownian particle under the influence of a time-multiplexed harmonic potential of finite width. The memory storage mechanism and the erasure protocol based on time-multiplexed potentials are utilized to experimentally realize erasure with work performed close to Landauer's bound. We quantify the work performed on the system with respect to the duty ratio of time multiplexing, which also provides a handle for approaching reversible erasures. A Langevin dynamics based simulation model is developed for the proposed memory bit and the erasure protocol, which guides the experimental realization...
June 2017: Physical Review. E
Neelam Yadav, V P Panov, V Swaminathan, S P Sreenilayam, J K Vij, T S Perova, R Dhar, A Panov, D Rodriguez-Lojo, P J Stevenson
Infrared and dielectric spectroscopic techniques are used to investigate the characteristics of two chiral smectics, namely, 1,1,3,3,5,5,5-heptamethyltrisiloxane 1-[4^{'}-(undecyl-1-oxy)-4-biphenyl(S,S)-2-chloro-3-methylpentanoate] (MSi_{3}MR_{11}) and tricarbosilane-hexyloxy-benzoic acid (S)-4'-(1-methyl-hexyloxy)-3'-nitro-biphenyl-4-yl ester (W599). The orientational features and the field dependencies of the apparent tilt angle and the dichroic ratio for homogeneous planar-aligned samples were calculated from the absorbance profiles obtained at different temperatures especially in the smectic-A* phase of these liquid crystals...
June 2017: Physical Review. E
Dan Pirjol, Farshid Jafarpour, Srividya Iyer-Biswas
Stochastic exponential growth is observed in a variety of contexts, including molecular autocatalysis, nuclear fission, population growth, inflation of the universe, viral social media posts, and financial markets. Yet literature on modeling the phenomenology of these stochastic dynamics has predominantly focused on one model, geometric Brownian motion (GBM), which can be described as the solution of a Langevin equation with linear drift and linear multiplicative noise. Using recent experimental results on stochastic exponential growth of individual bacterial cell sizes, we motivate the need for a more general class of phenomenological models of stochastic exponential growth, which are consistent with the observation that the mean-rescaled distributions are approximately stationary at long times...
June 2017: Physical Review. E
De-Ming Deng, Yi-Ta Lu, Cheng-Hung Chang
The legality of using simple kinetic schemes to determine the stochastic properties of a complex system depends on whether the fluctuations generated from hierarchical equivalent schemes are consistent with one another. To analyze this consistency, we perform lumping processes on the stochastic differential equations and the generalized fluctuation-dissipation theorem and apply them to networks with the frequently encountered Arrhenius-type transition rates. The explicit Langevin force derived from those networks enables us to calculate the state fluctuations caused by the intrinsic and extrinsic noises on the free energy surface and deduce their relations between kinetically equivalent networks...
June 2017: Physical Review. E
Hiroki Tutu, Katsuya Ouchi, Takehiko Horita
With a model for two-dimensional (2D) Brownian rotary ratchets being capable of producing a net torque under athermal random forces, its optimization for mean angular momentum (L), mean angular velocity (ω), and efficiency (η) is considered. In the model, supposing that such a small ratchet system is placed in a thermal bath, the motion of the rotor in the stator is described by the Langevin dynamics of a particle in a 2D ratchet potential, which consists of a static and a time-dependent interaction between rotor and stator; for the latter, we examine a force [randomly directed dc field (RDDF)] for which only the direction is instantaneously updated in a sequence of events in a Poisson process...
June 2017: Physical Review. E
Michael Hohmann, Farina Kindermann, Tobias Lausch, Daniel Mayer, Felix Schmidt, Eric Lutz, Artur Widera
We report on the experimental investigation of individual Cs atoms impinging on a dilute cloud of ultracold Rb atoms with variable density. We study the relaxation of the initial nonthermal state and detect the effect of single collisions which has so far eluded observation. We show that, after few collisions, the measured spatial distribution of the tracer atoms is correctly described by a Langevin equation with a velocity-dependent friction coefficient, over a large range of Knudsen numbers. Our results extend the simple and effective Langevin treatment to the realm of light particles in dilute gases...
June 30, 2017: Physical Review Letters
T Secker, N Ewald, J Joger, H Fürst, T Feldker, R Gerritsma
We theoretically study trapped ions that are immersed in an ultracold gas of Rydberg-dressed atoms. By off-resonant coupling on a dipole-forbidden transition, the adiabatic atom-ion potential can be made repulsive. We study the energy exchange between the atoms and a single trapped ion and find that Langevin collisions are inhibited in the ultracold regime for these repulsive interactions. Therefore, the proposed system avoids recently observed ion heating in hybrid atom-ion systems caused by coupling to the ion's radio frequency trapping field and retains ultracold temperatures even in the presence of excess micromotion...
June 30, 2017: Physical Review Letters
Zhenzhen Qiao, Lise Pingault, Prince Zogli, Micaela Langevin, Niccole Rech, Andrew Farmer, Marc Libault
A comparative transcriptomic and genomic analysis between Arabidopsis thaliana and Glycine max root hair genes reveals the evolution of the expression of plant genes after speciation and whole genome duplication. Our understanding of the conservation and divergence of the expression patterns of genes between plant species is limited by the quality of the genomic and transcriptomic resources available. Specifically, the transcriptomes generated from plant organs are the reflection of the contribution of the different cell types composing the samples weighted by their relative abundances in the sample...
July 7, 2017: Plant Molecular Biology
Uzma Alim, Duane Bates, Ashten Langevin, Denise Werry, Deonne Dersch-Mills, Robert J Herman, Marcy Mintz, Sunita Ghosh
BACKGROUND: Thiamine (vitamin B1) is an essential cofactor responsible for the breakdown of glucose, and its deficiency is associated with Wernicke encephalopathy (WE). There is a lack of evidence from systematic studies on the optimal dosing of thiamine for WE. Objectives: The primary objective was to describe the prescribing patterns for IV thiamine in adult patients admitted to a large teaching hospital. The secondary objective was to evaluate the clinical resolution of WE symptoms (confusion, ataxia, and/or ocular motor abnormalities) in relation to the dose of IV thiamine prescribed...
May 2017: Canadian Journal of Hospital Pharmacy
Abdolreza Javidialesaadi, George Stan
Powerful AAA+ biological nanomachines, such as ClpY, form hexameric ring structures, which selectively process abnormal proteins targeted for degradation by unfolding and threading them through a narrow central channel. The molecular details of this process are not yet fully understood. We perform Langevin dynamics simulations using a coarse-grained model of substrate proteins (SPs), Titin I27 and its V13P variant, threading through the ClpY pore. We probe the effect of ClpY surface heterogeneity and changes in pore width on SP orientation and the direction of applied force during SP unfolding...
July 18, 2017: Journal of Physical Chemistry. B
Gonzalo Angulo, Jakub Jedrak, Anna Ochab-Marcinek, Pakorn Pasitsuparoad, Czesław Radzewicz, Paweł Wnuk, Arnulf Rosspeintner
The dynamics of unimolecular photo-triggered reactions can be strongly affected by the surrounding medium for which a large number of theoretical descriptions have been used in the past. An accurate description of these reactions requires knowing the potential energy surface and the friction felt by the reactants. Most of these theories start from the Langevin equation to derive the dynamics, but there are few examples comparing it with experiments. Here we explore the applicability of a Generalized Langevin Equation (GLE) with an arbitrary potential and a non-Markovian friction...
June 28, 2017: Journal of Chemical Physics
Xujun Zhao, Jiyuan Li, Xikai Jiang, Dmitry Karpeev, Olle Heinonen, Barry Smith, Juan P Hernandez-Ortiz, Juan J de Pablo
An efficient parallel Stokes' solver has been developed for complete description of hydrodynamic interactions between Brownian particles in bulk and confined geometries. A Langevin description of the particle dynamics is adopted, where the long-range interactions are included using a Green's function formalism. A scalable parallel computational approach is presented, where the general geometry Stokeslet is calculated following a matrix-free algorithm using the general geometry Ewald-like method. Our approach employs a highly efficient iterative finite-element Stokes' solver for the accurate treatment of long-range hydrodynamic interactions in arbitrary confined geometries...
June 28, 2017: Journal of Chemical Physics
Matthieu Caruel, Lev Truskinovsky
We present an overview of the recent attempts to complement the chemistry-centered microscopic models of skeletal muscles by the purely mechanical models. The force generation phenomena of interest can be divided into two classes and their mechanisms are usually modeled in dierent ways. Models in the rst class deal with fast force recovery, which does not require detachment of myosin crossbridges and is believed to be a passive process. It can be viewed as collective folding in the system of interacting bi-stable units and is modeled by equilibrium statistical mechanics and Langevin kinetics...
June 26, 2017: Reports on Progress in Physics
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