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Ruben Perez-Carrasco, Pilar Guerrero, James Briscoe, Karen M Page
During tissue development, patterns of gene expression determine the spatial arrangement of cell types. In many cases, gradients of secreted signalling molecules-morphogens-guide this process by controlling downstream transcriptional networks. A mechanism commonly used in these networks to convert the continuous information provided by the gradient into discrete transitions between adjacent cell types is the genetic toggle switch, composed of cross-repressing transcriptional determinants. Previous analyses have emphasised the steady state output of these mechanisms...
October 2016: PLoS Computational Biology
Haidong Tian, Yinfeng Zhang, Jingzhi Han, Zhuang Xu, Xiaodong Zhang, Shunquan Liu, Changsheng Wang, Yingchang Yang, Li Han, Jinbo Yang
Nd2Fe14B/α-Fe nanocomposite magnets are prepared through electron beam exposure with a greatly reduced annealing time of 0.1 s. This is by far the most effective approach due to the effect of an extremely high heating rate featuring a rapid thermal process. The impact that the rapid thermal process has on crystallization is expounded by the introduction of the Landau model and Langevin dynamical simulations. The change of crystallization sequence from the α-Fe phase preceding the Nd2Fe14B phase under conventional annealing conditions, to synergetic crystallization under electron beam conditions is investigated...
October 19, 2016: Nanoscale
Rolf E Isele-Holder, Julia Jäger, Guglielmo Saggiorato, Jens Elgeti, Gerhard Gompper
Worm-like filaments, which are propelled by a tangential homogeneous force along their contour, are studied as they push loads of different shapes and sizes. The resulting dynamics is investigated using Langevin dynamics simulations. The effects of size and shape of the load, propulsion strength, and thermal noise are systematically explored. The propulsive force and hydrodynamic friction of the load cause a compression in the filament that results in a buckling instability and versatile motion. Distinct regimes of elongated filaments, curved filaments, beating filaments, and filaments with alternating beating and circular motion are identified, and a phase diagram depending on the propulsion strength and the size of the load is constructed...
October 19, 2016: Soft Matter
Cheng Jiang, Yuanshun Cui, Guibin Chen
We explore theoretically the dynamics of an optomechanical system in which a resonantly driven cavity mode is quadratically coupled to the displacement of a mechanical resonator. Considering the first order correction to adiabatic elimination, we obtain the analytical expression of optomechanical damping rate which is negative and depends on the position of the mechanical resonator. After comparing the numerical results between the full simulation of Langevin equations, adiabatic elimination, and first order correction to adiabatic elimination, we explain the dynamics of the system in terms of overall mechanical potential and optomechanical damping rate...
October 18, 2016: Scientific Reports
Timur V Tscherbul, Paul Brumer, Alexei A Buchachenko
We present accurate ab initio and quantum scattering calculations on a prototypical hybrid ion-atom system Yb^{+}-Rb, recently suggested as a promising candidate for the experimental study of open quantum systems, quantum information processing, and quantum simulation. We identify the second-order spin-orbit (SO) interaction as the dominant source of hyperfine relaxation in cold Yb^{+}-Rb collisions. Our results are in good agreement with recent experimental observations [L. Ratschbacher et al., Phys. Rev...
September 30, 2016: Physical Review Letters
Giacomo Di Gesù, Tony Lelièvre, Dorian Le Peutrec, Boris Nectoux
We are interested in the connection between a metastable continuous state space Markov process (satisfying e.g. the Langevin or overdamped Langevin equation) and a jump Markov process in a discrete state space. More precisely, we use the notion of quasi-stationary distribution within a metastable state for the continuous state space Markov process to parametrize the exit event from the state. This approach is useful to analyze and justify methods which use the jump Markov process underlying a metastable dynamics as a support to efficiently sample the state-to-state dynamics (accelerated dynamics techniques)...
October 14, 2016: Faraday Discussions
Mesfin Asfaw Taye
We derive general expressions for the free energy, entropy production, and entropy extraction rates for a Brownian particle that walks in a viscous medium where the dynamics of its motion is governed by the Langevin equation. It is shown that, when the system is out of equilibrium, it constantly produces entropy and at the same time extracts entropy out of the system. Its entropy production and extraction rates decrease in time and saturate to a constant value. In the long-time limit, the rate of entropy production balances the rate of entropy extraction and, at equilibrium, both entropy production and extraction rates become zero...
September 2016: Physical Review. E
J I Jiménez-Aquino, M Romero-Bastida
In this paper we derive the non-Markovian barotropic-type and Hall-type fluctuation relations for noninteracting charged Brownian particles embedded in a memory heat bath and under the action of crossed electric and magnetic fields. We first obtain a more general non-Markovian fluctuation relation formulated within the context of a generalized Langevin equation with arbitrary friction memory kernel and under the action of a constant magnetic field and an arbitrary time-dependent electric field. It is shown that this fluctuation relation is related to the total amount of an effective work done on the charged particle as it is driven out of equilibrium by the applied time-dependent electric field...
September 2016: Physical Review. E
Anoosheh Yazdi, Matthias Sperl
We consider a two-dimensional model system of Brownian particles in which slow particles are accelerated while fast particles are damped. The motion of the individual particles is described by a Langevin equation with Rayleigh-Helmholtz velocity-dependent friction. In the case of noninteracting particles, the time evolution equations lead to a non-Gaussian velocity distribution. The velocity-dependent friction allows negative values of the friction or energy intakes by slow particles, which we consider active motion, and also causes breaking of the fluctuation dissipation relation...
September 2016: Physical Review. E
Roman Belousov, E G D Cohen, Lamberto Rondoni
In this paper, we generalize the theory of Brownian motion and the Onsager-Machlup theory of fluctuations for spatially symmetric systems to equilibrium and nonequilibrium steady-state systems with a preferred spatial direction, due to an external force. To do this, we extend the Langevin equation to include a bias, which is introduced by an external force and alters the Gaussian structure of the system's fluctuations. In addition, by solving this extended equation, we provide a physical interpretation for the statistical properties of the fluctuations in these systems...
September 2016: Physical Review. E
A B Duncan, S Kalliadasis, G A Pavliotis, M Pradas
We consider the problem of an overdamped Brownian particle moving in multiscale potential with N+1 characteristic length scales: the macroscale and N separated microscales. We show that the coarse-grained dynamics is given by an overdamped Langevin equation with respect to the free energy and with a space-dependent diffusion tensor, the calculation of which requires the solution of N fully coupled Poisson equations. We study in detail the structure of the bifurcation diagram for one-dimensional problems, and we show that the multiscale structure in the potential leads to hysteresis effects and to noise-induced transitions...
September 2016: Physical Review. E
Sunghan Ro, Juyeon Yi, Yong Woon Kim
Separation of enantiomers by flows is a promising chiral resolution method using cost-effective microfluidics. Notwithstanding a number of experimental and numerical studies, a fundamental understanding still remains elusive, and an important question as to whether it is possible to specify common physical properties of flows that induce separation has not been addressed. Here, we study the separation of rigid chiral objects of an arbitrary shape induced by a linear flow field at low Reynolds numbers. Based on a symmetry property under parity inversion, we show that the rate-of-strain field is essential to drift the objects in opposite directions according to chirality...
October 14, 2016: Scientific Reports
Catherine M Wright, Paula J Duquesnay, Stephanie Anzman-Frasca, Virginia R Chomitz, Kenneth Chui, Christina D Economos, Elizabeth G Langevin, Miriam E Nelson, Jennifer M Sacheck
BACKGROUND: Physical activity (PA) is critical to preventing childhood obesity and contributes to children's overall physical and cognitive health, yet fewer than half of all children achieve the recommended 60 min per day of moderate-to-vigorous physical activity (MVPA). Schools are an ideal setting to meeting PA guidelines, but competing demands and limited resources have impacted PA opportunities. The Fueling Learning through Exercise (FLEX) Study is a randomized controlled trial that will evaluate the impact of two innovative school-based PA programs on children's MVPA, cognitive function, and academic outcomes...
October 13, 2016: BMC Public Health
Helene M Langevin, Patricia Keely, Jun Mao, Lisa M Hodge, Robert Schleip, Gary Deng, Boris Hinz, Melody A Swartz, Beverley A de Valois, Suzanna Zick, Thomas Findley
Complementary and integrative treatments, such as massage, acupuncture, and yoga, are used by increasing numbers of cancer patients to manage symptoms and improve their quality of life. In addition, such treatments may have other important and currently overlooked benefits by reducing tissue stiffness and improving mobility. Recent advances in cancer biology are underscoring the importance of connective tissue in the local tumor environment. Inflammation and fibrosis are well-recognized contributors to cancer, and connective tissue stiffness is emerging as a driving factor in tumor growth...
October 11, 2016: Cancer Research
Hai-Yun Xiao, Scott H Watterson, Charles M Langevine, Anurag S Srivastava, Soo S Ko, Yanlei Zhang, Robert Joseph Cherney, Weiwei Guo, John L Gilmore, James E Sheppeck, Dauh-Rurng Wu, Peng Li, Duraisamy Ramasamy, Pirama Nayagam Arunachalam, Arvind Mathur, Tracy L Taylor, David J Shuster, Kim W McIntyre, Ding Ren Shen, Melissa Yarde, Mary Ellen Cvijic, Anthony M Marino, Praveen V Balimane, Zheng Yang, Dana M Banas, Georgia Cornelius, Celia J D Arienzo, Bethanne M Warrack, Lois D Lehman-McKeeman, Luisa M Salter-Cid, Jenny H Xie, Joel C Barrish, Percy H Carter, Alaric J Dyckman, T G Murali Dhar
Fingolimod (1) is the first approved oral therapy for the treatment of relapsing remitting multiple sclerosis. While the phosphorylated metabolite of fingolimod was found to be a non-selective S1P receptor agonist, agonism specifically of S1P1 is responsible for the peripheral blood lymphopenia believed to be key to its efficacy. Identification of modulators that maintain activity on S1P1 while sparing activity on other S1P receptors could offer equivalent efficacy with reduced liabilities. We disclose in this paper a ligand based drug design approach that led to the discovery of a series of potent tricyclic agonists of S1P1 with selectivity over S1P3 and were efficacious in a pharmacodynamic model of suppression of circulating lymphocytes...
October 11, 2016: Journal of Medicinal Chemistry
Joshua S Kretchmer, Thomas F Miller Iii
We investigate the performance of the recently developed kinetically-constrained ring polymer molecular dynamics (KC-RPMD) method for the description of model condensed-phase electron transfer (ET) reactions in which solvent and donor-acceptor dynamics play an important role. Comparison of KC-RPMD with results from Golden-Rule rate theories and numerically exact quantum dynamics calculations demonstrates that KC-RPMD accurately captures the combination of electronic- and nuclear-dynamical effects throughout the Marcus (intermediate solvent friction) and Zusman (large solvent friction) regimes of ET...
October 7, 2016: Faraday Discussions
Denis S Tikhonov, Dmitry I Sharapa, Jan Schwabedissen, Vladimir V Rybkin
In this study, we investigate the ability of classical molecular dynamics (MD) and Monte-Carlo (MC) simulations for modeling the intramolecular vibrational motion. These simulations were used to compute thermally-averaged geometrical structures and infrared vibrational intensities for a benchmark set previously studied by gas electron diffraction (GED): CS2, benzene, chloromethylthiocyanate, pyrazinamide and 9,12-I2-1,2-closo-C2B10H10. The MD sampling of NVT ensembles was performed using chains of Nose-Hoover thermostats (NH) as well as the generalized Langevin equation thermostat (GLE)...
October 12, 2016: Physical Chemistry Chemical Physics: PCCP
Danielle Lefebvre, Lisa Marie Langevin, Natalia Jaworska, Ashley D Harris, R Marc Lebel, Yamile Jasaui, Adam Kirton, T Christopher Wilkes, Mariko Sembo, Rose Swansburg, Frank P MacMaster
BACKGROUND: Smaller hippocampal volumes, as assessed by magnetic resonance imaging (MRI), and proton magnetic resonance spectroscopy ((1)H-MRS) indexed alterations in brain metabolites have been identified in adults with major depressive disorder (MDD). Our group has found similar effects in MDD youth. However, this has not been studied in youth with treatment resistant MDD (TRD), nor has the interaction between regional N-acetyl-aspartate and volume deficits. N-acetyl-aspartate is an amino acid in the synthesis pathway of glutamate, and serves a marker of neuronal viability/number...
October 1, 2016: Journal of Affective Disorders
Bo-Kai Zhang, Hui-Shu Li, Jian Li, Kang Chen, Wen-de Tian, Yu-Qiang Ma
Bond length is generally not considered as a controllable variable for molecular polymers. Hence, no experimental, simulation or theoretical research, to our knowledge, has examined the influence of bond length on the glassy dynamics of polymers. Recently, a new class of assembling materials called "colloidal polymers" has been synthesized. These colloidal polymers have advantages over molecular polymers in the visibility and flexibility of tuning, for example, the size and shape of the "monomers", the interaction, and the bond length...
October 4, 2016: Soft Matter
Wei Chien, Yeng-Long Chen
We investigate polymer diffusion in a quasi-two-dimensional environment decorated with attractive cylindrical posts using Langevin dynamics simulation. We find that the polymer diffusivity has non-monotonic dependence on the post array density. This diffusive behavior strongly depends on the adsorption-desorption transition and the critical adsorption strength εc. For ε < εc, the polymer undergoes normal diffusion and the diffusivity decreases as the post density increases due to the reduction of the void volume...
September 28, 2016: Soft Matter
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