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https://www.readbyqxmd.com/read/28106448/accelerating-ab%C3%A2-initio-molecular-dynamics-and-probing-the-weak-dispersive-forces-in-dense-liquid-hydrogen
#1
Guglielmo Mazzola, Sandro Sorella
We propose an ab initio molecular dynamics method, capable of dramatically reducing the autocorrelation time required for the simulation of classical and quantum particles at finite temperatures. The method is based on an efficient implementation of a first order Langevin dynamics modified by means of a suitable, position dependent acceleration matrix S. Here, we apply this technique to both Lennard-Jones models, to demonstrate the accuracy and speeding-up of the sampling, and within a quantum Monte Carlo based wave function approach, for determining the phase diagram of high-pressure hydrogen with simulations much longer than the autocorrelation time...
January 6, 2017: Physical Review Letters
https://www.readbyqxmd.com/read/28095200/stdp-as-presynaptic-activity-times-rate-of-change-of-postsynaptic-activity-approximates-backpropagation
#2
Yoshua Bengio, Thomas Mesnard, Asja Fischer, Saizheng Zhang, Yuhuai Wu
We show that Langevin Monte Carlo Markov chain inference in an energy-based model with latent variables has the property that the early steps of inference, starting from a stationary point, correspond to propagating error gradients into internal layers, similar to backpropagation. The backpropagated error is with respect to output units that have received an outside driving force pushing them away from the stationary point. Backpropagated error gradients correspond to temporal derivatives with respect to the activation of hidden units...
January 17, 2017: Neural Computation
https://www.readbyqxmd.com/read/28090613/expedient-and-modular-access-to-2-azabicyclic-architectures-by-iron-catalyzed-dehydrative-coupling-of-alcohol-bearing-allylic-lactams
#3
Katie Hovenkotter, Hannah Braunstein, Spencer Langevin, Timothy K Beng
A high-yielding, cost-effective, modular and environmentally benign approach to [5,5]- or [6,5]-2-azabicyclic architectures bearing vicinal stereocenters, by Fe-catalyzed intramolecular dehydrative coupling of readily affordable alcohol-bearing allylic lactams is presented.
January 16, 2017: Organic & Biomolecular Chemistry
https://www.readbyqxmd.com/read/28063444/computing-the-non-markovian-coarse-grained-interactions-derived-from-the-mori-zwanzig-formalism-in-molecular-systems-application-to-polymer-melts
#4
Zhen Li, Hee Sun Lee, Eric Darve, George Em Karniadakis
Memory effects are often introduced during coarse-graining of a complex dynamical system. In particular, a generalized Langevin equation (GLE) for the coarse-grained (CG) system arises in the context of Mori-Zwanzig formalism. Upon a pairwise decomposition, GLE can be reformulated into its pairwise version, i.e., non-Markovian dissipative particle dynamics (DPD). GLE models the dynamics of a single coarse particle, while DPD considers the dynamics of many interacting CG particles, with both CG systems governed by non-Markovian interactions...
January 7, 2017: Journal of Chemical Physics
https://www.readbyqxmd.com/read/28059440/langevin-dynamcis-simulations-of-driven-polymer-translocation-into-a-crosslinked-gel
#5
David Sean, Gary W Slater
We investigate the dynamics of driving a polyelectrolyte such as DNA though a nanopore and into a crosslinked gel. Placing the gel on the trans-side of the nanopore can increase the translocation time while not negatively affecting the capture rates. This setup thus combines the mechanics of gel electrophoresis with nanopore translocation. However, contrary to typical gel electrophoresis scenarios, the effect of the field is localized in the immediate vicinity of the nanopore and becomes negligible inside the gel matrix...
January 6, 2017: Electrophoresis
https://www.readbyqxmd.com/read/28059372/contribution-of-off-resonant-states-to-the-phase-noise-of-quantum-dot-lasers
#6
Cheng Wang, Jun-Ping Zhuang, Frédéric Grillot, Sze-Chun Chan
The phase noise of quantum dot lasers is investigated theoretically by coupling the Langevin noise sources into the rate equations. The off-resonant populations in the excited state and in the carrier reservoir contribute to the phase noise of ground-state emission lasers through the phase-amplitude coupling effect. This effect arises from the optical-noise induced carrier fluctuations in the off-resonant states. In addition, the phase noise has low sensitivity to the carrier scattering rates.
December 26, 2016: Optics Express
https://www.readbyqxmd.com/read/28049339/relocking-of-intrinsic-angular-momenta-in-collisions-of-diatoms-with-ions-capture-of-h2-j-0-1-by-h2
#7
E I Dashevskaya, I Litvin, E E Nikitin, J Troe
Rate coefficients for capture of H2(j = 0,1) by H2(+) are calculated in perturbed rotor approximation, i.e., at collision energies considerably lower than Bhc (where B denotes the rotational constant of H2). The results are compared with the results from an axially nonadiabatic channel (ANC) approach, the latter providing a very good approximation from the low-temperature Bethe-Wigner to the high temperature Langevin limit. The classical ANC approximation performs satisfactorily at temperatures above 0.1 K...
December 28, 2016: Journal of Chemical Physics
https://www.readbyqxmd.com/read/28049336/observation-of-enhanced-rate-coefficients-in-the-h2-h2%C3%A2-h3-h-reaction-at-low-collision-energies
#8
Pitt Allmendinger, Johannes Deiglmayr, Katharina Höveler, Otto Schullian, Frédéric Merkt
The energy dependence of the rate coefficient of the H2(+)+H2→H3(+)+H reaction has been measured in the range of collision energies between kB⋅10K and kB⋅300mK. A clear deviation of the rate coefficient from the value expected on the basis of the classical Langevin-capture behavior has been observed at collision energies below kB⋅1K, which is attributed to the joint effects of the ion-quadrupole and Coriolis interactions in collisions involving ortho-H2 molecules in the  j = 1 rotational level, which make up 75% of the population of the neutral H2 molecules in the experiments...
December 28, 2016: Journal of Chemical Physics
https://www.readbyqxmd.com/read/28047123/we-h-207a-09-theoretical-limits-to-molecular-biomarker-detection-using-magnetic-nanoparticles
#9
J Weaver
PURPOSE: Estimate the limits of molecular biomarker detection using magnetic nanoparticle methods like in vivo ELISA. METHODS: Magnetic nanoparticles in an alternating magnetic field produce a magnetization that can be detected at exceedingly low levels because the signal at the harmonic frequencies is uniquely produced by the nanoparticles. Because the magnetization can also be used to characterize the nanoparticle rotational freedom, the bound state can be found...
June 2016: Medical Physics
https://www.readbyqxmd.com/read/28035168/computational-models-for-nanoscale-fluid-dynamics-and-transport-inspired-by-nonequilibrium-thermodynamics
#10
Ravi Radhakrishnan, Hsiu-Yu Yu, David M Eckmann, Portonovo S Ayyaswamy
Traditionally, the numerical computation of particle motion in a fluid is resolved through computational fluid dynamics (CFD). However, resolving the motion of nanoparticles poses additional challenges due to the coupling between the Brownian and hydrodynamic forces. Here, we focus on the Brownian motion of a nanoparticle coupled to adhesive interactions and confining-wall-mediated hydrodynamic interactions. We discuss several techniques that are founded on the basis of combining CFD methods with the theory of nonequilibrium statistical mechanics in order to simultaneously conserve thermal equipartition and to show correct hydrodynamic correlations...
March 2017: Journal of Heat Transfer
https://www.readbyqxmd.com/read/28009205/dynamics-of-a-ground-state-cooled-ion-colliding-with-ultracold-atoms
#11
Ziv Meir, Tomas Sikorsky, Ruti Ben-Shlomi, Nitzan Akerman, Yehonatan Dallal, Roee Ozeri
Ultracold atom-ion mixtures are gaining increasing interest due to their potential applications in ultracold and state-controlled chemistry, quantum computing, and many-body physics. Here, we studied the dynamics of a single ground-state cooled ion during few, to many, Langevin (spiraling) collisions with ultracold atoms. We measured the ion's energy distribution and observed a clear deviation from the Maxwell-Boltzmann distribution, characterized by an exponential tail, to a power-law distribution best described by a Tsallis function...
December 9, 2016: Physical Review Letters
https://www.readbyqxmd.com/read/28009178/translocation-time-through-a-nanopore-with-an-internal-cavity-is-minimal-for-polymers-of-intermediate-length
#12
Martin Magill, Cory Falconer, Ed Waller, Hendrick W de Haan
The translocation of polymers through nanopores with large internal cavities bounded by two narrow pores is studied via Langevin dynamics simulations. The total translocation time is found to be a nonmonotonic function of polymer length, reaching a minimum at intermediate length, with both shorter and longer polymers taking longer to translocate. The location of the minimum is shown to shift with the magnitude of the applied force, indicating that the pore can be dynamically tuned to favor different polymer lengths...
December 9, 2016: Physical Review Letters
https://www.readbyqxmd.com/read/28002047/the-modified-langevin-description-for-probes-in-a-nonlinear-medium
#13
Matthias Krüger, Christian Maes
When the motion of a probe strongly disturbs the thermal equilibrium of the solvent or bath, the nonlinear response of the latter must enter the probe's effective evolution equation. We derive that induced stochastic dynamics using second order response around the bath thermal equilibrium. We discuss the nature of the new term in the evolution equation which is no longer purely dissipative, and the appearance of a novel time-scale for the probe related to changes in the dynamical activity of the bath. A major application for the obtained nonlinear generalized Langevin equation is in the study of colloid motion in a visco-elastic medium...
February 15, 2017: Journal of Physics. Condensed Matter: An Institute of Physics Journal
https://www.readbyqxmd.com/read/27990313/deep-brain-stimulation-of-a-patient-with-psychogenic-movement-disorder
#14
Jean-Philippe Langevin, Jesse M Skoch, Scott J Sherman
BACKGROUND: The long-term safety of deep brain stimulation (DBS) is an important issue because new applications are being investigated for a variety of disorders. Studying instances where DBS was inadvertently implanted in patients without a movement disorder may provide information about the safety of the therapy. We report the case of a patient with a psychogenic movement disorder treated with deep brain stimulation (DBS). CASE DESCRIPTION: The patient presented at our clinic after 5 years of chronic DBS of the subthalamic nucleus (STN) for presumed Parkinson's disease...
2016: Surgical Neurology International
https://www.readbyqxmd.com/read/27984878/uncertainty-quantification-for-generalized-langevin-dynamics
#15
Eric J Hall, Markos A Katsoulakis, Luc Rey-Bellet
We present efficient finite difference estimators for goal-oriented sensitivity indices with applications to the generalized Langevin equation (GLE). In particular, we apply these estimators to analyze an extended variable formulation of the GLE where other well known sensitivity analysis techniques such as the likelihood ratio method are not applicable to key parameters of interest. These easily implemented estimators are formed by coupling the nominal and perturbed dynamics appearing in the finite difference through a common driving noise or common random path...
December 14, 2016: Journal of Chemical Physics
https://www.readbyqxmd.com/read/27983858/interaction-of-charged-patchy-protein-models-with-like-charged-polyelectrolyte-brushes
#16
Cemil Yigit, Matej Kanduč, Matthias Ballauff, Joachim Dzubiella
We study the adsorption of charged patchy particle models (CPPMs) on a thin film of a like-charged and dense polyelectrolyte (PE) brush (of 50 monomers per chain) by means of implicit-solvent, explicit-salt Langevin dynamics computer simulations. Our previously introduced set of CPPMs embraces well-defined one- and two-patched spherical globules, each of the same net charge and (nanometer) size, with mono- and multipole moments comparable to those of small globular proteins. We focus on electrostatic effects on the adsorption far away from the isoelectric point of typical proteins, i...
December 16, 2016: Langmuir: the ACS Journal of Surfaces and Colloids
https://www.readbyqxmd.com/read/27980509/sec-sans-size-exclusion-chromatography-combined-in-situ-with-small-angle-neutron-scattering
#17
Ashley Jordan, Mark Jacques, Catherine Merrick, Juliette Devos, V Trevor Forsyth, Lionel Porcar, Anne Martel
The first implementation and use of an in situ size exclusion chromatography (SEC) system on a small-angle neutron scattering instrument (SANS) is described. The possibility of deploying such a system for biological solution scattering at the Institut Laue-Langevin (ILL) has arisen from the fact that current day SANS instruments at ILL now allow datasets to be acquired using small sample volumes with exposure times that are often shorter than a minute. This capability is of particular importance for the study of unstable biological macromolecules where aggregation or denaturation issues are a major problem...
December 1, 2016: Journal of Applied Crystallography
https://www.readbyqxmd.com/read/27973887/ballistic-diffusion-in-polyaromatic-hydrocarbons-on-graphite
#18
Irene Calvo-Almazán, Marco Sacchi, Anton Tamtögl, Emanuel Bahn, Marek M Koza, Salvador Miret-Artés, Peter Fouquet
This work presents an experimental picture of molecular ballistic diffusion on a surface, a process that is difficult to pinpoint because it generally occurs on very short length scales. By combining neutron time-of-flight data with molecular dynamics simulations and density functional theory calculations, we provide a complete description of the ballistic translations and rotations of a polyaromatic hydrocarbon (PAH) adsorbed on the basal plane of graphite. Pyrene, C16H10, adsorbed on graphite is a unique system, where at relative surface coverages of about 10-20% its mean free path matches the experimentally accessible time/space scale of neutron time-of-flight spectroscopy (IN6 at the Institut Laue-Langevin)...
December 15, 2016: Journal of Physical Chemistry Letters
https://www.readbyqxmd.com/read/27967200/suppressing-membrane-height-fluctuations-leads-to-a-membrane-mediated-interaction-among-proteins
#19
Kayla Sapp, Lutz Maibaum
Membrane-induced interactions can play a significant role in the spatial distribution of membrane-bound proteins. We develop a model that combines a continuum description of lipid bilayers with a discrete particle model of proteins to probe the emerging structure of the combined membrane-protein system. Our model takes into account the membrane's elastic behavior, the steric repulsion between proteins, and the quenching of membrane shape fluctuations due to the presence of the proteins. We employ coupled Langevin equations to describe the dynamics of the system...
November 2016: Physical Review. E
https://www.readbyqxmd.com/read/27967182/heat-dissipation-and-information-flow-for-delayed-bistable-langevin-systems-near-coherence-resonance
#20
Tiejun Xiao
In this paper, stochastic thermodynamics of delayed bistable Langevin systems near coherence resonance is discussed. We calculate the heat dissipation rate and the information flow of a delayed bistable Langevin system under various noise intensities. Both the heat dissipation rate and the information flow are found to be bell-shaped functions of the noise intensity, which implies that coherence resonance manifests itself in the thermodynamic properties.
November 2016: Physical Review. E
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