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Andrea Auconi, Andrea Giansanti, Edda Klipp
The intuition of causation is so fundamental that almost every research study in life sciences refers to this concept. However, a widely accepted formal definition of causal influence between observables is still missing. In the framework of linear Langevin networks without feedback (linear response models) we propose a measure of causal influence based on a new decomposition of information flows over time. We discuss its main properties and we compare it with other information measures like the transfer entropy...
April 2017: Physical Review. E
Gerhard Jung, Martin Hanke, Friederike Schmid
In recent years it has become increasingly popular to construct coarse-grained models with non-Markovian dynamics in order to account for an incomplete separation of time scales. One challenge of a systematic coarse-graining procedure is the extraction of the dynamical properties, namely the memory kernel, from equilibrium all-atom simulations. In this paper we propose an iterative method for memory reconstruction from dynamical correlation functions. Compared to previously proposed non-iterative techniques, it ensures by construction that the target correlation functions of the original fine-grained systems are reproduced accurately by the coarse-grained system, regardless of time step and discretization effects...
May 15, 2017: Journal of Chemical Theory and Computation
E Boujo, N Noiray
We present a model-based output-only method for identifying from time series the parameters governing the dynamics of stochastically forced oscillators. In this context, suitable models of the oscillator's damping and stiffness properties are postulated, guided by physical understanding of the oscillatory phenomena. The temporal dynamics and the probability density function of the oscillation amplitude are described by a Langevin equation and its associated Fokker-Planck equation, respectively. One method consists in fitting the postulated analytical drift and diffusion coefficients with their estimated values, obtained from data processing by taking the short-time limit of the first two transition moments...
April 2017: Proceedings. Mathematical, Physical, and Engineering Sciences
Gabriella Passoni, Christelle Langevin, Nuno Palha, Bryan C Mounce, Valérie Briolat, Pierre Affaticati, Elodie De Job, Jean-Stéphane Joly, Marco Vignuzzi, Maria-Carla Saleh, Philippe Herbomel, Pierre Boudinot, Jean-Pierre Levraud
Alphaviruses, such as chikungunya (CHIKV) and Sindbis virus (SINV), are vector‑borne pathogens that cause acute illnesses in humans and are sometimes associated with neuropathies, especially in infants and elderly patients. Little is known about their entry mechanism in the central nervous system (CNS), even for SINV, which has been used extensively as a model for viral encephalopathies. We previously established a CHIKV infection model in the optically transparent zebrafish larva; here we describe a new SINV infection model in this host...
May 8, 2017: Disease Models & Mechanisms
Fan-Tso Chien, Po-Keng Lin, Wei Chien, Cheng-Hsiang Hung, Ming-Hung Yu, Chia-Fu Chou, Yeng-Long Chen
Our study of DNA dynamics in weakly attractive nanofabricated post arrays revealed crowding enhances polymer transport, contrary to hindered transport in repulsive medium. The coupling of DNA diffusion and adsorption to the microposts results in more frequent cross-post hopping and increased long-term diffusivity with increased crowding density. We performed Langevin dynamics simulations and found maximum long-term diffusivity in post arrays with gap sizes comparable to the polymer radius of gyration. We found that macromolecular transport in weakly attractive post arrays is faster than in non-attractive dense medium...
May 2, 2017: Scientific Reports
Chenyu Jin, Carsten Krüger, Corinna C Maass
Chemotaxis and autochemotaxis play an important role in many essential biological processes. We present a self-propelling artificial swimmer system that exhibits chemotaxis as well as negative autochemotaxis. Oil droplets in an aqueous surfactant solution are driven by interfacial Marangoni flows induced by micellar solubilization of the oil phase. We demonstrate that chemotaxis along micellar surfactant gradients can guide these swimmers through a microfluidic maze. Similarly, a depletion of empty micelles in the wake of a droplet swimmer causes negative autochemotaxis and thereby trail avoidance...
May 2, 2017: Proceedings of the National Academy of Sciences of the United States of America
Tingting Sun, Yunxin Gen, Hujun Xie, Zhouting Jiang, Zhiyong Yang
The translocation of a polymer chain through a crowded cylindrical channel is studied using the Langevin dynamics simulations. The influences of the field strength F, the chain length N, and the crowding extent ρ on the translocation time are evaluated, respectively. Scaling relation τ ~ F(-α) is observed. With the crowding extent ρ increasing, the scaling exponent α becomes large. It is found that, for noncrowded channel, translocation probability drops when the field strength becomes large. However, for high-crowded channel, it is the opposite...
2017: BioMed Research International
H Ness, L Stella, C D Lorenz, L Kantorovich
We use a generalised Langevin equation scheme to study the thermal transport of low dimensional systems. In this approach, the central classical region is connected to two realistic thermal baths kept at two different temperatures [H. Ness et al., Phys. Rev. B 93, 174303 (2016)]. We consider model Al systems, i.e., one-dimensional atomic chains connected to three-dimensional baths. The thermal transport properties are studied as a function of the chain length N and the temperature difference ΔT between the baths...
April 28, 2017: Journal of Chemical Physics
Jason P Koski, Robert A Riggleman
Block copolymers, due to their ability to self-assemble into periodic structures with long range order, are appealing candidates to control the ordering of functionalized nanoparticles where it is well-accepted that the spatial distribution of nanoparticles in a polymer matrix dictates the resulting material properties. The large parameter space associated with block copolymer nanocomposites makes theory and simulation tools appealing to guide experiments and effectively isolate parameters of interest. We demonstrate a method for performing field-theoretic simulations in a constant volume-constant interfacial tension ensemble (nVγT) that enables the determination of the equilibrium properties of block copolymer nanocomposites, including when the composites are placed under tensile or compressive loads...
April 28, 2017: Journal of Chemical Physics
Félix Mouhat, Sandro Sorella, Rodolphe Vuilleumier, Antonino Marco Saitta, Michele Casula
We introduce a novel approach for a fully quantum description of coupled electron-ion systems from first principles. It combines the variational quantum Monte Carlo solution of the electronic part with the path integral formalism for the quantum nuclear dynamics. On the one hand, the path integral molecular dynamics includes nuclear quantum effects by adding a set of fictitious classical particles (beads) aimed at reproducing nuclear quantum fluctuations via a harmonic kinetic term. On the other hand, variational quantum Monte Carlo can provide Born-Oppenheimer potential energy surfaces with a precision comparable to the most advanced post Hartree-Fock approaches, and with a favorable scaling with the system size...
April 25, 2017: Journal of Chemical Theory and Computation
G Fier, D Hansmann, R C Buceta
In this work we introduce a stochastic model to describe directional changes in the movement of swimming bacteria. We use the probability density function (PDF) of turn angles, measured on tumbling wild-type E. coli, to build a Langevin equation for the deflection of the bacterial body swimming in isotropic media. We have solved this equation analytically by means of the Green function method and shown that three parameters are sufficient to describe the movement: the characteristic time, the steady-state solution and the control parameter...
May 11, 2017: Soft Matter
Yoji Kawamura
We formulate a theory for the collective phase reduction of globally coupled noisy dynamical elements exhibiting macroscopic rhythms. We first transform the Langevin-type equation that represents a group of globally coupled noisy dynamical elements into the corresponding nonlinear Fokker-Planck equation and then develop the phase reduction method for limit-cycle solutions to the nonlinear Fokker-Planck equation. The theory enables us to describe the collective dynamics of a group of globally coupled noisy dynamical elements by a single degree of freedom called the collective phase...
March 2017: Physical Review. E
Serena di Santo, Pablo Villegas, Raffaella Burioni, Miguel A Muñoz
We revisit the problem of deriving the mean-field values of avalanche exponents in systems with absorbing states. These are well known to coincide with those of unbiased branching processes. Here we show that for at least four different universality classes (directed percolation, dynamical percolation, the voter model or compact directed percolation class, and the Manna class of stochastic sandpiles) this common result can be obtained by mapping the corresponding Langevin equations describing each of them into a random walker confined to the origin by a logarithmic potential...
March 2017: Physical Review. E
Andrey A Kuznetsov, Alexander F Pshenichnikov
Langevin dynamics simulation is used to study the suspension of interacting magnetic nanoparticles (dipolar spheres) in a zero applied magnetic field and in the presence of a gravitational (centrifugal) field. A particular emphasis is placed on the equilibrium vertical distribution of particles in the infinite horizontal slab. An increase in the dipolar coupling constant λ (the ratio of dipole-dipole interaction energy to thermal energy) from zero to seven units causes an increase in the particle segregation coefficient by several orders of magnitude...
March 2017: Physical Review. E
Debarshee Bagchi
We study the thermal transport properties of the one-dimensional Fermi-Pasta-Ulam model (β type) with long-range interactions. The strength of the long-range interaction decreases with the (shortest) distance between the lattice sites as distance^{-δ}, where δ≥0. Two Langevin heat baths at unequal temperatures are connected to the ends of the one-dimensional lattice via short-range harmonic interactions that drive the system away from thermal equilibrium. In the nonequilibrium steady state the heat current, thermal conductivity, and temperature profiles are computed by solving the equations of motion numerically...
March 2017: Physical Review. E
Jia-Ming Zhang, Jing-Dong Bao
We study a frequency-dependent damping model of hyperdiffusion within the generalized Langevin equation. The model allows for the colored noise defined by its spectral density, assumed to be proportional to ω^{δ-1} at low frequencies with 0<δ<1 (sub-Ohmic damping) or 1<δ<2 (super-Ohmic damping), where the frequency-dependent damping is deduced from the noise by means of the fluctuation-dissipation theorem. It is shown that for super-Ohmic damping and certain parameters, the diffusive process of the particle in a titled periodic potential undergos sequentially four time regimes: thermalization, hyperdiffusion, collapse, and asymptotical restoration...
March 2017: Physical Review. E
Jacopo Grilli, Matteo Osella, Andrew S Kennard, Marco Cosentino Lagomarsino
A recent burst of dynamic single-cell data makes it possible to characterize the stochastic dynamics of cell division control in bacteria. Different models were used to propose specific mechanisms, but the links between them are poorly explored. The lack of comparative studies makes it difficult to appreciate how well any particular mechanism is supported by the data. Here, we describe a simple and generic framework in which two common formalisms can be used interchangeably: (i) a continuous-time division process described by a hazard function and (ii) a discrete-time equation describing cell size across generations (where the unit of time is a cell cycle)...
March 2017: Physical Review. E
S P Sreenilayam, D M Agra-Kooijman, V P Panov, V Swaminathan, J K Vij, Yu P Panarin, A Kocot, A Panov, D Rodriguez-Lojo, P J Stevenson, Michael R Fisch, Satyendra Kumar
A heptamethyltrisiloxane liquid crystal (LC) exhibiting I-SmA^{*}-SmC^{*} phases has been characterized by calorimetry, polarizing microscopy, x-ray diffraction, electro-optics, and dielectric spectroscopy. Observations of a large electroclinic effect, a large increase in the birefringence (Δn) with electric field, a low shrinkage in the layer thickness (∼1.75%) at 20 °C below the SmA^{*}-SmC^{*} transition, and low values of the reduction factor (∼0.40) suggest that the SmA^{*} phase in this material is of the de Vries type...
March 2017: Physical Review. E
Tomasz Srokowski
The random walk process in a nonhomogeneous medium, characterized by a Lévy stable distribution of jump length, is discussed. The width depends on a position: either before the jump or after that. In the latter case, the density slope is affected by the variable width and the variance may be finite; then all kinds of the anomalous diffusion are predicted. In the former case, only the time characteristics are sensitive to the variable width. The corresponding Langevin equation with different interpretations of the multiplicative noise is discussed...
March 2017: Physical Review. E
T Sakaue, J-C Walter, E Carlon, C Vanderzande
We develop a theoretical description of the critical zipping dynamics of a self-folding polymer. We use tension propagation theory and the formalism of the generalized Langevin equation applied to a polymer that contains two complementary parts which can bind to each other. At the critical temperature, the (un)zipping is unbiased and the two strands open and close as a zipper. The number of broken base pairs n(t) displays a subdiffusive motion characterized by a variance growing as 〈Δn(2)(t)〉 ∼ t(α) with α < 1 at long times...
May 3, 2017: Soft Matter
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