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H H Katkar, M Muthukumar
One of the major theoretical methods in understanding polymer translocation through a nanopore is the Fokker-Planck formalism based on the assumption of quasi-equilibrium of polymer conformations. The criterion for applicability of the quasi-equilibrium approximation for polymer translocation is that the average translocation time per Kuhn segment, ⟨τ⟩/NK, is longer than the relaxation time τ0 of the polymer. Toward an understanding of conditions that would satisfy this criterion, we have performed coarse-grained three dimensional Langevin dynamics and multi-particle collision dynamics simulations...
January 14, 2018: Journal of Chemical Physics
Pei-Yang Chen, Mark E Tuckerman
Enhanced sampling techniques that target a set of collective variables and that use molecular dynamics as the driving engine have seen widespread application in the computational molecular sciences as a means to explore the free-energy landscapes of complex systems. The use of molecular dynamics as the fundamental driver of the sampling requires the introduction of a time step whose magnitude is limited by the fastest motions in a system. While standard multiple time-stepping methods allow larger time steps to be employed for the slower and computationally more expensive forces, the maximum achievable increase in time step is limited by resonance phenomena, which inextricably couple fast and slow motions...
January 14, 2018: Journal of Chemical Physics
Youjiro Tamura
A muscle model that uses a modified Langevin equation with actomyosin potentials was used to describe the residual force enhancement after active stretching. Considering that the new model uses cross-bridge theory to describe the residual force enhancement, it is different from other models that use passive stretching elements. Residual force enhancement was simulated using a half sarcomere comprising 100 myosin molecules. In this paper, impulse is defined as the integral of an excess force from the steady isometric force over the time interval for which a stretch is applied...
January 12, 2018: Computer Methods in Biomechanics and Biomedical Engineering
Juan I Garaycoechea, Gerry P Crossan, Frédéric Langevin, Lee Mulderrig, Sandra Louzada, Fentang Yang, Guillaume Guilbaud, Naomi Park, Sophie Roerink, Serena Nik-Zainal, Michael R Stratton, Ketan J Patel
Haematopoietic stem cells renew blood. Accumulation of DNA damage in these cells promotes their decline, while misrepair of this damage initiates malignancies. Here we describe the features and mutational landscape of DNA damage caused by acetaldehyde, an endogenous and alcohol-derived metabolite. This damage results in DNA double-stranded breaks that, despite stimulating recombination repair, also cause chromosome rearrangements. We combined transplantation of single haematopoietic stem cells with whole-genome sequencing to show that this damage occurs in stem cells, leading to deletions and rearrangements that are indicative of microhomology-mediated end-joining repair...
January 11, 2018: Nature
Julian Kappler, Jan O Daldrop, Florian N Brünig, Moritz D Boehle, Roland R Netz
We study the mean first-passage time τMFP for the barrier crossing of a single massive particle with non-Markovian memory by Langevin simulations in one dimension. In the Markovian limit of short memory time τΓ, the expected Kramers turnover between the overdamped (high-friction) and the inertial (low-friction) limits is recovered. Compared to the Markovian case, we find barrier crossing to be accelerated for intermediate memory time, while for long memory time, barrier crossing is slowed down and τMFP increases with τΓ as a power law τMFP∼τΓ2...
January 7, 2018: Journal of Chemical Physics
A M Reynolds
In contrast to bird flocks, fish schools and animal herds, midge swarms maintain cohesion but do not possess global order. High-speed imaging techniques are now revealing that these swarms have surprising properties. Here, I show that simple models found on the Langevin equation are consistent with this wealth of recent observations. The models predict correctly that large accelerations, exceeding 10 g, will be common and they predict correctly the coexistence of core condensed phases surrounded by dilute vapour phases...
January 2018: Journal of the Royal Society, Interface
Yuta Yoshimoto, Zhen Li, Ikuya Kinefuchi, George Em Karniadakis
We propose a new coarse-grained (CG) molecular simulation technique based on the Mori-Zwanzig (MZ) formalism along with the iterative Boltzmann inversion (IBI). Non-Markovian dissipative particle dynamics (NMDPD) taking into account memory effects is derived in a pairwise interaction form from the MZ-guided generalized Langevin equation. It is based on the introduction of auxiliary variables that allow for the replacement of a non-Markovian equation with a Markovian one in a higher dimensional space. We demonstrate that the NMDPD model exploiting MZ-guided memory kernels can successfully reproduce the dynamic properties such as the mean square displacement and velocity autocorrelation function of a Lennard-Jones system, as long as the memory kernels are appropriately evaluated based on the Volterra integral equation using the force-velocity and velocity-velocity correlations...
December 28, 2017: Journal of Chemical Physics
Zhi Wei Tay, Daniel W Hensley, Erika C Vreeland, Bo Zheng, Steven M Conolly
Magnetic Particle Imaging (MPI) is a promising new tracer modality with zero attenuation in tissue, high contrast and sensitivity, and an excellent safety profile. However, the spatial resolution of MPI is currently around 1 mm in small animal scanners. Especially considering tradeoffs when scaling up MPI scanning systems to human size, this resolution needs to be improved for clinical applications such as angiography and brain perfusion. One method to improve spatial resolution is to increase the magnetic core size of the superparamagnetic nanoparticle tracers...
June 2017: Biomedical Physics & Engineering Express
Shaopeng Liu, Wen-Xing Yang, Tao Shui, Zhonghu Zhu, Ai-Xi Chen
We propose an efficient scheme for the controllable amplification of two-phonon higher-order sidebands in a quadratically coupled optomechanical system. In this scheme, a strong control field and a weak probe pulse are injected into the cavity, and the membrane located at the middle position of the cavity is driven resonantly by a weak coherent mechanical pump. Beyond the conventional linearized approximation, we derive analytical expressions for the output transmission of probe pulse and the amplitude of second-order sideband by adding the nonlinear coefficients into the Heisenberg-Langevin formalism...
December 15, 2017: Scientific Reports
R L Davidchack, T E Ouldridge, M V Tretyakov
We introduce new Langevin-type equations describing the rotational and translational motion of rigid bodies interacting through conservative and non-conservative forces and hydrodynamic coupling. In the absence of non-conservative forces, the Langevin-type equations sample from the canonical ensemble. The rotational degrees of freedom are described using quaternions, the lengths of which are exactly preserved by the stochastic dynamics. For the proposed Langevin-type equations, we construct a weak 2nd order geometric integrator that preserves the main geometric features of the continuous dynamics...
December 14, 2017: Journal of Chemical Physics
Chenyu Jin, Babak Vajdi Hokmabad, Kyle Anthony Baldwin, Corinna Charlotte Maass
Chemotaxis and auto-chemotaxis are key mechanisms in the dynamics of micro-organisms, e.g. in the acquisition of nutrients and in the communication between individuals, influencing the collective behaviour. However, chemical signalling and the natural environment of biological swimmers are generally complex, making them hard to access analytically. We present a well-controlled, tunable artificial model to study chemotaxis and autochemotaxis in complex geometries, using microfluidic assays of self-propelling oil droplets in an aqueous surfactant solution...
December 15, 2017: Journal of Physics. Condensed Matter: An Institute of Physics Journal
Stephanie Langevin, Jean Proulx, Eric Lacourse
This study investigated the day-to-day deviant and nondeviant sexuality of a sample of Canadian sexual aggressors against women ( N = 160). Using latent class analysis, three latent classes were identified: internalized deviant (ID), low sexual problem (LSP), and hypersexual deviant (HD). Following the latent class analysis, the developmental, physiological, cognitive, and criminological correlates of these lifestyles were analyzed. ID ( n = 31) aggressors were characterized by sexual dissatisfaction, sexual deviance, and a bland sexual life...
February 1, 2017: International Journal of Offender Therapy and Comparative Criminology
Juergen Weizenecker
Calculating the dynamic properties of magnetization of single-domain particles is of great importance for the tomographic imaging modality known as magnetic particle imaging (MPI). Although the assumption of instantaneous thermodynamic equilibrium (Langevin function) after application of time-dependent magnetic fields is sufficient for understanding the fundamental behavior, it is essential to consider the finite response times of magnetic particles for optimizing or analyzing various aspects, e.g., interpreting spectra, optimizing MPI sequences, developing new contrasts, and evaluating simplified models...
December 13, 2017: Physics in Medicine and Biology
João Batista Souza, Laudemir Carlos Varanda
A synthetic procedure is described to obtain superparamagnetic Co nanoparticles (NPs) via hot-injection method in the presence of sodium borohydride. The Co NPs obtained have an average diameter of 5.3 nm and saturation magnetization of 115 emu g<sup>-1</sup>. A modified Langevin equation is fitted to the magnetization curves using a lognormal distribution for the particles diameter and an effective field to account for dipolar interactions. The calculated magnetic diameter of the Co NPs is 0.6 nm smaller than TEM-derived values, implying a magnetic dead layer of 0...
December 11, 2017: Nanotechnology
Hugues Meyer, Thomas Voigtmann, Tanja Schilling
In molecular dynamics simulations and single molecule experiments, observables are usually measured along dynamic trajectories and then averaged over an ensemble ("bundle") of trajectories. Under stationary conditions, the time-evolution of such averages is described by the generalized Langevin equation. By contrast, if the dynamics is not stationary, it is not a priori clear which form the equation of motion for an averaged observable has. We employ the formalism of time-dependent projection operator techniques to derive the equation of motion for a non-equilibrium trajectory-averaged observable as well as for its non-stationary auto-correlation function...
December 7, 2017: Journal of Chemical Physics
Ravi Bhadauria, N R Aluru
We present a multiscale model describing the electroosmotic flow (EOF) in nanoscale channels involving high surface charge liquid-solid interfaces. The departure of the EOF velocity profiles from classical predictions is explained by the non-classical charge distribution in the confined direction including charge inversion, reduced mobility of interfacial counter-ions, and subsequent enhancement of the local viscosity. The excess component of the local solvent viscosity is modeled by the local application of the Fuoss-Onsager theory and the Hubbard-Onsager electro-hydrodynamic equation based dielectric friction theory...
December 7, 2017: Journal of Chemical Physics
Pierre Gaspard, Raymond Kapral
Microscopic dynamical aspects of the propulsion of nanomotors by self-phoretic mechanisms are considered. Propulsion by self-diffusiophoresis relies on the mechanochemical coupling between the fluid velocity field and the concentration fields induced by asymmetric catalytic reactions on the motor surface. The consistency between the thermodynamics of this coupling and the microscopic reversibility of the underlying molecular dynamics is investigated. For this purpose, a mechanochemical fluctuation theorem for the joint probability to find the motor at position r after n reactive events have occurred during the time interval t is derived, starting from coupled Langevin equations for the translational, rotational, and chemical fluctuations of self-phoretic motors...
December 7, 2017: Journal of Chemical Physics
Ulf D Schiller, Timm Krüger, Oliver Henrich
The deformability of soft condensed matter often requires modelling of hydrodynamical aspects to gain quantitative understanding. This, however, requires specialised methods that can resolve the multiscale nature of soft matter systems. We review a number of the most popular simulation methods that have emerged, such as Langevin dynamics, dissipative particle dynamics, multi-particle collision dynamics, sometimes also referred to as stochastic rotation dynamics, and the lattice-Boltzmann method. We conclude this review with a short glance at current compute architectures for high-performance computing and community codes for soft matter simulation...
December 6, 2017: Soft Matter
Bappa Ghosh, Srabanti Chaudhury
We probe the influence of polymer pore interactions on the translocation dynamics using Langevin dynamics simulations. We investigate the effect of the strength and location of the polymer- pore interaction using nanopores that are partially charged either at the entry or the exit or on both sides of the pore. We study the change of the translocation time as a function of the strength of the polymer-pore interaction for a given chain length and under the effect of an externally applied field. Under a moderate driving force and a chain length longer than the length of the pore, the translocation time shows a non-monotonic increase with an increase in the attractive interaction...
December 5, 2017: Journal of Physical Chemistry. B
Ching-Cher Sanders Yan, Surendhar Reddy Chepyala, Chao-Ming Yen, Chao-Ping Hsu
Gene expression involves bursts of production of both mRNA and protein, and the fluctuations in their number are increased due to such bursts. The Langevin equation is an efficient and versatile means to simulate such number fluctuation. However, how to include these mRNA and protein bursts in the Langevin equation is not intuitively clear. In this work, we estimated the variance in burst production from a general gene expression model and introduced such variation in the Langevin equation. Our approach offers different Langevin expressions for either or both transcriptional and translational bursts considered and saves computer time by including many production events at once in a short burst time...
December 4, 2017: Scientific Reports
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