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https://www.readbyqxmd.com/read/29775635/enhanced-sampling-of-interdomain-motion-using-map-restrained-langevin-dynamics-and-nmr-application-to-pin1
#1
Jill J Bouchard, Junchao Xia, David A Case, Jeffrey W Peng
Many signaling proteins consist of globular domains connected by flexible linkers that allow for substantial domain motion. Because these domains often serve as complementary functional modules, the possibility of functionally important domain motions arises. To explore this possibility, we require knowledge of the ensemble of protein conformations sampled by interdomain motion. Measurements of NMR residual dipolar couplings (RDCs) of backbone NH bonds offer a per-residue characterization of interdomain dynamics, as the couplings are sensitive to domain orientation...
May 15, 2018: Journal of Molecular Biology
https://www.readbyqxmd.com/read/29775371/langevin-dynamics-with-spatial-correlations-as-a-model-for-electron-phonon-coupling
#2
A Tamm, M Caro, A Caro, G Samolyuk, M Klintenberg, A A Correa
Stochastic Langevin dynamics has been traditionally used as a tool to describe nonequilibrium processes. When utilized in systems with collective modes, traditional Langevin dynamics relaxes all modes indiscriminately, regardless of their wavelength. We propose a generalization of Langevin dynamics that can capture a differential coupling between collective modes and the bath, by introducing spatial correlations in the random forces. This allows modeling the electronic subsystem in a metal as a generalized Langevin bath endowed with a concept of locality, greatly improving the capabilities of the two-temperature model...
May 4, 2018: Physical Review Letters
https://www.readbyqxmd.com/read/29764135/fast-forward-langevin-dynamics-with-momentum-flips
#3
Mahdi Hijazi, David M Wilkins, Michele Ceriotti
Stochastic thermostats based on the Langevin equation, in which a system is coupled to an external heat bath, are popular methods for temperature control in molecular dynamics simulations due to their ergodicity and their ease of implementation. Traditionally, these thermostats suffer from sluggish behavior in the limit of high friction, unlike thermostats of the Nosé-Hoover family whose performance degrades more gently in the strong coupling regime. We propose a simple and easy-to-implement modification to the integration scheme of the Langevin algorithm that addresses the fundamental source of the overdamped behavior of high-friction Langevin dynamics: if the action of the thermostat causes the momentum of a particle to change direction, it is flipped back...
May 14, 2018: Journal of Chemical Physics
https://www.readbyqxmd.com/read/29764123/the-folding-pathways-and-thermodynamics-of-semiflexible-polymers
#4
Jing Wu, Chenqian Cheng, Gaoyuan Liu, Ping Zhang, Tao Chen
Inspired by the protein folding and DNA packing, we have systematically studied the thermodynamic and kinetic behaviors of single semiflexible homopolymers by Langevin dynamics simulations. In line with experiments, a rich variety of folding products, such as rod-like bundles, hairpins, toroids, and a mixture of them, are observed in the complete diagram of states. Moreover, knotted structures with a significant population are found in a certain range of bending stiffness in thermal equilibrium. As the solvent quality becomes poorer, the population of the intermediate occurring in the folding process increases, which leads to a severe chevron rollover for the folding arm...
May 14, 2018: Journal of Chemical Physics
https://www.readbyqxmd.com/read/29762567/chemical-elemental-analysis-of-single-acoustic-levitated-water-droplets-by-laser-induced-breakdown-spectroscopy
#5
Victor Contreras, Ricardo Valencia, Jairo Peralta, H Sobral, M A Meneses-Nava, Horacio Martinez
Laser-induced breakdown spectroscopy is presented for trace element detection of liquid samples by analyzing a single droplet levitated by ultrasonic waves. A single liquid droplet is placed in the node of a standing acoustic wave produced by a uniaxial levitator for further chemical analysis. The acoustic levitator consists of a commercial Langevin-type transducer, attached to a concave mechanical amplifier, and a concave reflector. A micro-syringe was used to manually place individual liquid droplet samples in the acoustic levitation system...
May 15, 2018: Optics Letters
https://www.readbyqxmd.com/read/29761184/tuning-thin-film-bijels-with-applied-external-electric-fields
#6
Joseph M Carmack, Paul C Millett
The tunability of thin-film bijels using applied external electric fields is explored using a Cahn-Hilliard Langevin dynamics computational model. Dielectric contrast between liquid domains governs liquid domain alignment and was varied in the simulations. Dielectric contrast between colloidal particles and liquid matrix induces dipolar particle interactions and was also varied in the simulations. The study reveals unique internal morphologies including those with through-thickness liquid domains. Significant results include identification of electric field effects on phase evolution and final morphology as well as relevant mechanisms...
May 15, 2018: Soft Matter
https://www.readbyqxmd.com/read/29758679/role-of-sufficient-statistics-in-stochastic-thermodynamics-and-its-implication-to-sensory-adaptation
#7
Takumi Matsumoto, Takahiro Sagawa
A sufficient statistic is a significant concept in statistics, which means a probability variable that has sufficient information required for an inference task. We investigate the roles of sufficient statistics and related quantities in stochastic thermodynamics. Specifically, we prove that for general continuous-time bipartite networks, the existence of a sufficient statistic implies that an informational quantity called the sensory capacity takes the maximum. Since the maximal sensory capacity imposes a constraint that the energetic efficiency cannot exceed one-half, our result implies that the existence of a sufficient statistic is inevitably accompanied by energetic dissipation...
April 2018: Physical Review. E
https://www.readbyqxmd.com/read/29758659/statistics-of-zero-crossings-in-rough-interfaces-with-fractional-elasticity
#8
Arturo L Zamorategui, Vivien Lecomte, Alejandro B Kolton
We study numerically the distribution of zero crossings in one-dimensional elastic interfaces described by an overdamped Langevin dynamics with periodic boundary conditions. We model the elastic forces with a Riesz-Feller fractional Laplacian of order z=1+2ζ, such that the interfaces spontaneously relax, with a dynamical exponent z, to a self-affine geometry with roughness exponent ζ. By continuously increasing from ζ=-1/2 (macroscopically flat interface described by independent Ornstein-Uhlenbeck processes [Phys...
April 2018: Physical Review. E
https://www.readbyqxmd.com/read/29739223/effects-of-surface-motion-and-electron-hole-pair-excitations-in-co-2-dissociation-and-scattering-on-ni-100
#9
Xuan Luo, Xueyao Zhou, Bin Jiang
The energy transfer between different channels is an important aspect in chemical reactions at surfaces. We investigate here in detail the energy transfer dynamics in a prototypical system, i.e., reactive and nonreactive scattering of CO2 on Ni(100), which is related to heterogeneous catalytic processes with Ni-based catalysts for CO2 reduction. On the basis of our earlier nine-dimensional potential energy surface for CO2 /Ni(100), dynamical calculations have been done using the generalized Langevin oscillator (GLO) model combined with local density friction approximation (LDFA), in which the former accounts for the surface motion and the latter accounts for the low-energy electron-hole pair (EHP) excitation...
May 7, 2018: Journal of Chemical Physics
https://www.readbyqxmd.com/read/29738461/characterization-of-nanoparticle-batch-to-batch-variability
#10
Sonja Mülhopt, Silvia Diabaté, Marco Dilger, Christel Adelhelm, Christopher Anderlohr, Thomas Bergfeldt, Johan Gómez de la Torre, Yunhong Jiang, Eugenia Valsami-Jones, Dominique Langevin, Iseult Lynch, Eugene Mahon, Inge Nelissen, Jordi Piella, Victor Puntes, Sikha Ray, Reinhard Schneider, Terry Wilkins, Carsten Weiss, Hanns-Rudolf Paur
A central challenge for the safe design of nanomaterials (NMs) is the inherent variability of NM properties, both as produced and as they interact with and evolve in, their surroundings. This has led to uncertainty in the literature regarding whether the biological and toxicological effects reported for NMs are related to specific NM properties themselves, or rather to the presence of impurities or physical effects such as agglomeration of particles. Thus, there is a strong need for systematic evaluation of the synthesis and processing parameters that lead to potential variability of different NM batches and the reproducible production of commonly utilized NMs...
May 8, 2018: Nanomaterials
https://www.readbyqxmd.com/read/29736534/langevin-equations-for-the-run-and-tumble-of-swimming-bacteria
#11
G Fier, D Hansmann, R C Buceta
The run and tumble motions of a swimming bacterium are well characterized by two stochastic variables: the speed v(t) and the change of direction or deflection x(t) = cos φ(t), where φ(t) is the turning angle at time t. Recently, we have introduced [G. Fier, D. Hansmann and R. C. Buceta, A stochastic model for directional changes of swimming bacteria, Soft Matter, 2017, 13, 3385-3394.] a single stochastic model for the deflection x(t) of an E. coli bacterium performing both types of movement in isotropic media without taxis, based on available experimental data...
May 8, 2018: Soft Matter
https://www.readbyqxmd.com/read/29716220/deviation-from-equilibrium-conditions-in-molecular-dynamic-simulations-of-homogeneous-nucleation
#12
Roope Halonen, Evgeni Zapadinsky, Hanna Vehkamäki
We present a comparison between Monte Carlo (MC) results for homogeneous vapour-liquid nucleation of Lennard-Jones clusters and previously published values from molecular dynamics (MD) simulations. Both the MC and MD methods sample real cluster configuration distributions. In the MD simulations, the extent of the temperature fluctuation is usually controlled with an artificial thermostat rather than with more realistic carrier gas. In this study, not only a primarily velocity scaling thermostat is considered, but also Nosé-Hoover, Berendsen, and stochastic Langevin thermostat methods are covered...
April 28, 2018: Journal of Chemical Physics
https://www.readbyqxmd.com/read/29716219/sequencing-of-semiflexible-polymers-of-varying-bending-rigidity-using-patterned-pores
#13
Rajneesh Kumar, Abhishek Chaudhuri, Rajeev Kapri
We study the translocation of a semiflexible polymer through extended pores with patterned stickiness, using Langevin dynamics simulations. We find that the consequence of pore patterning on the translocation time dynamics is dramatic and depends strongly on the interplay of polymer stiffness and pore-polymer interactions. For heterogeneous polymers with periodically varying stiffness along their lengths, we find that variation of the block size of the sequences and the orientation results in large variations in the translocation time distributions...
April 28, 2018: Journal of Chemical Physics
https://www.readbyqxmd.com/read/29714359/corrigendum-environmental-impacts-of-plant-based-diets-how-does-organic-food-consumption-contribute-to-environmental-sustainability
#14
Camille Lacour, Louise Seconda, Benjamin Allès, Serge Hercberg, Brigitte Langevin, Philippe Pointereau, Denis Lairon, Julia Baudry, Emmanuelle Kesse-Guyot
[This corrects the article on p. 8 in vol. 5, PMID: 29479530.].
2018: Frontiers in Nutrition
https://www.readbyqxmd.com/read/29694225/derivation-of-the-boltzmann-equation-for-financial-brownian-motion-direct-observation-of-the-collective-motion-of-high-frequency-traders
#15
Kiyoshi Kanazawa, Takumi Sueshige, Hideki Takayasu, Misako Takayasu
A microscopic model is established for financial Brownian motion from the direct observation of the dynamics of high-frequency traders (HFTs) in a foreign exchange market. Furthermore, a theoretical framework parallel to molecular kinetic theory is developed for the systematic description of the financial market from microscopic dynamics of HFTs. We report first on a microscopic empirical law of traders' trend-following behavior by tracking the trajectories of all individuals, which quantifies the collective motion of HFTs but has not been captured in conventional order-book models...
March 30, 2018: Physical Review Letters
https://www.readbyqxmd.com/read/29686374/publisher-correction-spin-controlled-atom-ion-chemistry
#16
Tomas Sikorsky, Ziv Meir, Ruti Ben-Shlomi, Nitzan Akerman, Roee Ozeri
The original version of this Article contained an error in the third sentence of the first paragraph of the 'Spin polarizing the Sr+ ion with ultracold atoms' section of the Results, which incorrectly read 'The Langevin collision rate is 1.' The correct version adds 'kHz' after '1.' The fifth sentence of this same paragraph originally read as "Although 87 Rb has a I = 3/2 nuclear spin and a hyperfine-split ground-state manifold, 88 Sr has no nuclear spin and a Zeeman split two-fold ground state", which is incorrect...
April 23, 2018: Nature Communications
https://www.readbyqxmd.com/read/29681861/coupling-langevin-dynamics-with-continuum-mechanics-exposing-the-role-of-sarcomere-stretch-activation-mechanisms-to-cardiac-function
#17
Takumi Washio, Seiryo Sugiura, Ryo Kanada, Jun-Ichi Okada, Toshiaki Hisada
High-performance computing approaches that combine molecular-scale and macroscale continuum mechanics have long been anticipated in various fields. Such approaches may enrich our understanding of the links between microscale molecular mechanisms and macroscopic properties in the continuum. However, there have been few successful examples to date owing to various difficulties associated with overcoming the large spatial (from 1 nm to 10 cm) and temporal (from 1 ns to 1 ms) gaps between the two scales. In this paper, we propose an efficient parallel scheme to couple a microscopic model using Langevin dynamics for a protein motor with a finite element continuum model of a beating heart...
2018: Frontiers in Physiology
https://www.readbyqxmd.com/read/29681251/behavior-problems-in-sexually-abused-preschoolers-over-a-1-year-period-the-mediating-role-of-attachment-representations
#18
Florence Charest, Martine Hébert, Annie Bernier, Rachel Langevin, Raphaële Miljkovitch
According to the developmental psychopathology framework, adverse childhood experiences, including child sexual abuse (CSA), may alter the course of normal development in children. Attachment security has been identified as a protective factor against psychopathology and may thus play a critical role in predicting victims' adaptation. The main objective of the present study was to investigate the mediating effect of attachment representations in the relation between CSA and behavior problems over a 1-year period...
April 23, 2018: Development and Psychopathology
https://www.readbyqxmd.com/read/29679973/isomorph-theory-of-physical-aging
#19
Jeppe C Dyre
This paper derives and discusses the configuration-space Langevin equation describing a physically aging R-simple system and the corresponding Smoluchowski equation. Externally controlled thermodynamic variables like temperature, density, and pressure enter the description via the single parameter Ts /T, in which T is the bath temperature and Ts is the "systemic" temperature defined at any time t as the thermodynamic equilibrium temperature of the state point with density ρ(t) and potential energy U(t)...
April 21, 2018: Journal of Chemical Physics
https://www.readbyqxmd.com/read/29626886/committor-of-elementary-reactions-on-multistate-systems
#20
Péter Király, Dóra Judit Kiss, Gergely Tóth
In our study, we extend the committor concept on multi-minima systems, where more than one reaction may proceed, but the feasible data evaluation needs the projection onto partial reactions. The elementary reaction committor and the corresponding probability density of the reactive trajectories are defined and calculated on a three-hole two-dimensional model system explored by single-particle Langevin dynamics. We propose a method to visualize more elementary reaction committor functions or probability densities of reactive trajectories on a single plot that helps to identify the most important reaction channels and the nonreactive domains simultaneously...
April 7, 2018: Journal of Chemical Physics
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