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https://www.readbyqxmd.com/read/28228023/reconciling-transition-path-time-and-rate-measurements-in-reactions-with-large-entropic-barriers
#1
Dmitrii E Makarov
Recent experiments and simulation studies showed that protein/DNA folding barriers inferred from folding rates or from potentials of mean force are often much higher than the barriers estimated from the distributions of transition path times. Here a toy model is used to explain a possible origin of this effect: It is shown that when the transition in question involves an entropic barrier, the one-dimensional Langevin model commonly used to interpret experimental data, while adequately predicting the transition rate, fails to describe the properties of the subset of the trajectories that form the transition path ensemble; the latter may still be describable in terms of a one-dimensional model, but with a different potential, just as observed experimentally...
February 21, 2017: Journal of Chemical Physics
https://www.readbyqxmd.com/read/28228020/coarse-grained-simulations-of-cis-and-trans-polybutadiene-a-bottom-up-approach
#2
Claire A Lemarchand, Marc Couty, Bernard Rousseau
We apply the dissipative particle dynamics strategy proposed by Hijón et al. [Faraday Discuss. 144, 301-322 (2010)] and based on an exact derivation of the generalized Langevin equation to cis- and trans-1,4-polybutadiene. We prove that it is able to reproduce not only the structural but also the dynamical properties of these polymers without any fitting parameter. A systematic study of the effect of the level of coarse-graining is done on cis-1,4-polybutadiene. We show that as the level of coarse-graining increases, the dynamical properties are better and better reproduced while the structural properties deviate more and more from those calculated in molecular dynamics (MD) simulations...
February 21, 2017: Journal of Chemical Physics
https://www.readbyqxmd.com/read/28208482/aging-underdamped-scaled-brownian-motion-ensemble-and-time-averaged-particle-displacements-nonergodicity-and-the-failure-of-the-overdamping-approximation
#3
Hadiseh Safdari, Andrey G Cherstvy, Aleksei V Chechkin, Anna Bodrova, Ralf Metzler
We investigate both analytically and by computer simulations the ensemble- and time-averaged, nonergodic, and aging properties of massive particles diffusing in a medium with a time dependent diffusivity. We call this stochastic diffusion process the (aging) underdamped scaled Brownian motion (UDSBM). We demonstrate how the mean squared displacement (MSD) and the time-averaged MSD of UDSBM are affected by the inertial term in the Langevin equation, both at short, intermediate, and even long diffusion times...
January 2017: Physical Review. E
https://www.readbyqxmd.com/read/28208481/escape-rate-of-active-particles-in-the-effective-equilibrium-approach
#4
A Sharma, R Wittmann, J M Brader
The escape rate of a Brownian particle over a potential barrier is accurately described by the Kramers theory. A quantitative theory explicitly taking the activity of Brownian particles into account has been lacking due to the inherently out-of-equilibrium nature of these particles. Using an effective equilibrium approach [Farage et al., Phys. Rev. E 91, 042310 (2015)PLEEE81539-375510.1103/PhysRevE.91.042310] we study the escape rate of active particles over a potential barrier and compare our analytical results with data from direct numerical simulation of the colored noise Langevin equation...
January 2017: Physical Review. E
https://www.readbyqxmd.com/read/28208477/bifurcation-induced-by-the-aspect-ratio-in-a-turbulent-von-k%C3%A3-rm%C3%A3-n-swirling-flow
#5
Olivier Liot, Javier Burguete
We evaluate the effect of the aspect ratio, i.e., the distance between the propellers H divided by the diameter D, on the slow dynamics of a von Kármán swirling flow driven by two propellers in a closed cylinder. We use a cell with a fixed diameter D but where the distance between the propellers can be turned continuously and where the inertia from the propellers can also be changed using different gears. No change on the dynamics is observed when the momentum of inertia is modified. Some dramatic changes of the shear layer position are observed modifying the aspect ratio Γ=H/D...
January 2017: Physical Review. E
https://www.readbyqxmd.com/read/28208460/self-confined-particle-pairs-in-complex-plasmas
#6
I I Lisina, E A Lisin, O S Vaulina, O F Petrov
The liquid-crystal type of phase transition in complex plasmas has been observed repeatedly. However, more studies need to be done on the liquid-vapor transition in complex plasmas. In this paper, the phenomenon of coupling (condensation) of particles into self-confined particle pairs in an anisotropic plasma medium with ion flow is considered analytically and numerically using the Langevin molecular dynamics method. We obtain the stability conditions of the pair (bound) state depending on the interaction parameters and particle kinetic energy...
January 2017: Physical Review. E
https://www.readbyqxmd.com/read/28208451/mori-zwanzig-theory-for-dissipative-forces-in-coarse-grained-dynamics-in-the-markov-limit
#7
Sergei Izvekov
We derive alternative Markov approximations for the projected (stochastic) force and memory function in the coarse-grained (CG) generalized Langevin equation, which describes the time evolution of the center-of-mass coordinates of clusters of particles in the microscopic ensemble. This is done with the aid of the Mori-Zwanzig projection operator method based on the recently introduced projection operator [S. Izvekov, J. Chem. Phys. 138, 134106 (2013)10.1063/1.4795091]. The derivation exploits the "generalized additive fluctuating force" representation to which the projected force reduces in the adopted projection operator formalism...
January 2017: Physical Review. E
https://www.readbyqxmd.com/read/28208409/thermal-transport-in-dimerized-harmonic-lattices-exact-solution-crossover-behavior-and-extended-reservoirs
#8
Chih-Chun Chien, Said Kouachi, Kirill A Velizhanin, Yonatan Dubi, Michael Zwolak
We present a method for calculating analytically the thermal conductance of a classical harmonic lattice with both alternating masses and nearest-neighbor couplings when placed between individual Langevin reservoirs at different temperatures. The method utilizes recent advances in analytic diagonalization techniques for certain classes of tridiagonal matrices. It recovers the results from a previous method that was applicable for alternating on-site parameters only, and extends the applicability to realistic systems in which masses and couplings alternate simultaneously...
January 2017: Physical Review. E
https://www.readbyqxmd.com/read/28208404/efficient-simulation-of-semiflexible-polymers-with-stiff-bonds
#9
Gerard T Barkema, J M J van Leeuwen
We investigate the simulation of stiff (extensible) and rigid (inextensible) semiflexible polymers in solution. In particular, we focus on polymers represented as chains of beads, interconnected by bonds with a low to zero extensibility, and significant persistence in the bond orientations along the chain, whose dynamical behavior is described by the Langevin equation. We review the derivation of the pseudopotential needed for rigid bonds. The efficiency of a number of routines for such simulations is determined...
January 2017: Physical Review. E
https://www.readbyqxmd.com/read/28208380/inferring-hidden-states-in-langevin-dynamics-on-large-networks-average-case-performance
#10
B Bravi, M Opper, P Sollich
We present average performance results for dynamical inference problems in large networks, where a set of nodes is hidden while the time trajectories of the others are observed. Examples of this scenario can occur in signal transduction and gene regulation networks. We focus on the linear stochastic dynamics of continuous variables interacting via random Gaussian couplings of generic symmetry. We analyze the inference error, given by the variance of the posterior distribution over hidden paths, in the thermodynamic limit and as a function of the system parameters and the ratio α between the number of hidden and observed nodes...
January 2017: Physical Review. E
https://www.readbyqxmd.com/read/28208313/diffusion-of-a-rouse-chain-in-porous-media-a-mode-coupling-theory-study
#11
Huai Ding, Huijun Jiang, Nanrong Zhao, Zhonghuai Hou
We use a kinetic mode-coupling theory (MCT) combining with generalized Langevin equation (GLE) to study the diffusion and conformational dynamics of a bead-spring Rouse chain (RC) dissolved in porous media. The media contains fluid particles and immobile matrix ones wherein the latter leads to the lack of translational invariance. The friction kernel ζ(t) used in the GLE can be obtained directly by adopting a simple density-functional approach in which the density correlators calculated by MCT equations of porous media serve as inputs...
January 2017: Physical Review. E
https://www.readbyqxmd.com/read/28193897/simulating-the-dynamics-of-the-mechanochemical-cycle-of-myosin-v
#12
Shayantani Mukherjee, Raphael Alhadeff, Arieh Warshel
The detailed dynamics of the cycle of myosin-V are explored by simulation approaches, examining the nature of the energy-driven motion. Our study started with Langevin dynamics (LD) simulations on a very coarse landscape with a single rate-limiting barrier and reproduced the stall force and the hand-over-hand dynamics. We then considered a more realistic landscape and used time-dependent Monte Carlo (MC) simulations that allowed trajectories long enough to reproduce the force/velocity characteristic sigmoidal correlation, while also reproducing the hand-over-hand motion...
February 13, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28178815/unfolding-dna-condensates-produced-by-dna-like-charged-depletants-a-force-spectroscopy-study
#13
C H M Lima, M S Rocha, E B Ramos
In this work, we have measured, by means of optical tweezers, forces acting on depletion-induced DNA condensates due to the presence of the DNA-like charged protein bovine serum albumin (BSA). The stretching and unfolding measurements performed on the semi-flexible DNA chain reveal (1) the softening of the uncondensed DNA contour length and (2) a mechanical behavior strikingly different from those previously observed: the force-extension curves of BSA-induced DNA condensates lack the "saw-tooth" pattern and applied external forces as high as ≈80 pN are unable to fully unfold the condensed DNA contour length...
February 7, 2017: Journal of Chemical Physics
https://www.readbyqxmd.com/read/28157200/revisiting-metallization-boundary-of-warm-dense-helium-in-a-wide-%C3%AF-t-regime-from-ab-initio-study
#14
Wei Zhang, Zhiguo Li, Zhijian Fu, Jiayu Dai, Qifeng Chen, Lingcang Cai
The knowledge of the metallization of warm dense helium has important implications for understanding the thermal histories, stellar structure and magnetic field environment of giant planets. However, it is also a pendent scientific topic. For a revisiting into the properties of warm dense helium, we performed extensive quantum Langevin molecular dynamic simulations and electronic structure calculations to study helium over a very wide range of density (ρ = 1~24 g/cm(3)) and temperature (T = 10~160 kK)...
February 3, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28155731/-development-of-multidisciplinary-community-based-health-care-centres-in-germany
#15
Claire Imbaud, Paul Garassus, Jean-Marie André, François Langevin
MVZ provide community-based health care services improving integrated primary care and specialist care and allow hospital to outsource outpatient activities. They also provide patient-centered care and promote internal and external multidisciplinary coordination.</ce:para> <ce:para>MVZ can provide an example for possible changes to private specialist organisation and structuring of hospital services in France, while MSP mainly focus on primary care and only a few specialist CS have been created...
November 25, 2016: Santé Publique: Revue Multidisciplinaire Pour la Recherche et L'action
https://www.readbyqxmd.com/read/28147543/langevin-poisson-eqt-a-dipolar-solvent-based-quasi-continuum-approach-for-electric-double-layers
#16
S Y Mashayak, N R Aluru
Water is a highly polar solvent. As a result, electrostatic interactions of interfacial water molecules play a dominant role in determining the distribution of ions in electric double layers (EDLs). Near a surface, an inhomogeneous and anisotropic arrangement of water molecules gives rise to pronounced variations in the electrostatic and hydration energies of ions. Therefore, a detailed description of the structural and dielectric properties of water is important to study EDLs. However, most theoretical models ignore the molecular effects of water and treat water as a background continuum with a uniform dielectric permittivity...
January 28, 2017: Journal of Chemical Physics
https://www.readbyqxmd.com/read/28134338/a-strong-diffusive-ion-mode-in-dense-ionized-matter-predicted-by-langevin-dynamics
#17
P Mabey, S Richardson, T G White, L B Fletcher, S H Glenzer, N J Hartley, J Vorberger, D O Gericke, G Gregori
The state and evolution of planets, brown dwarfs and neutron star crusts is determined by the properties of dense and compressed matter. Due to the inherent difficulties in modelling strongly coupled plasmas, however, current predictions of transport coefficients differ by orders of magnitude. Collective modes are a prominent feature, whose spectra may serve as an important tool to validate theoretical predictions for dense matter. With recent advances in free electron laser technology, X-rays with small enough bandwidth have become available, allowing the investigation of the low-frequency ion modes in dense matter...
January 30, 2017: Nature Communications
https://www.readbyqxmd.com/read/28120904/escape-rate-and-diffusion-of-a-stochastically-driven-particle
#18
Antonio Piscitelli, Massimo Pica Ciamarra
The dynamical properties of a tracer repeatedly colliding with heat bath particles can be described within a Langevin framework provided that the tracer is more massive than the bath particles, and that the collisions are frequent. Here we consider the escape of a particle from a potential well, and the diffusion coefficient in a periodic potential, without making these assumptions. We have thus investigated the dynamical properties of a Stochastically Driven particle that moves under the influence of the confining potential in between successive collisions with the heat bath...
January 25, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28119544/effect-of-wall-mediated-hydrodynamic-fluctuations-on-the-kinetics-of-a-brownian-nanoparticle
#19
Hsiu-Yu Yu, David M Eckmann, Portonovo S Ayyaswamy, Ravi Radhakrishnan
The reactive flux formalism (Chandler 1978 J. Chem. Phys.68, 2959-2970. (doi:10.1063/1.436049)) and the subsequent development of methods such as transition path sampling have laid the foundation for explicitly quantifying the rate process in terms of microscopic simulations. However, explicit methods to account for how the hydrodynamic correlations impact the transient reaction rate are missing in the colloidal literature. We show that the composite generalized Langevin equation (Yu et al. 2015 Phys. Rev. E91, 052303...
December 2016: Proceedings. Mathematical, Physical, and Engineering Sciences
https://www.readbyqxmd.com/read/28112932/simulating-energy-relaxation-in-pump-probe-vibrational-spectroscopy-of-hydrogen-bonded-liquids
#20
Riccardo Dettori, Michele Ceriotti, Johannes Hunger, Claudio Melis, Luciano Colombo, Davide Donadio
We introduce a nonequilibrium molecular dynamics simulation approach, based on the generalized Langevin equation, to study vibrational energy relaxation in pump-probe spectroscopy. A colored noise thermostat is used to selectively excite a set of vibrational modes, leaving the other modes nearly unperturbed, to mimic the effect of a monochromatic laser pump. Energy relaxation is probed by analyzing the evolution of the system after excitation in the microcanonical ensemble, thus providing direct information about the energy redistribution paths at the molecular level and their time scale...
February 6, 2017: Journal of Chemical Theory and Computation
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