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Spencer Langevin, Jonathan S Chang, Stanley Chang
BACKGROUND/PURPOSE: To describe a case of serous retinopathy and associated photoreceptor atrophy after intravenous cisplatin therapy. METHODS: Evaluation was performed using electroretinogram, optical coherence tomography, fundus autofluorescence, and funduscopic examinations to assess the extent of retinal disease, toxicity, and eventual atrophy. RESULTS: A 56 year-old man with metastatic small cell carcinoma with vision changes after initiation of cisplatin therapy...
March 22, 2017: Retinal Cases & Brief Reports
Adithya Vijaykumar, Thomas E Ouldridge, Pieter Rein Ten Wolde, Peter G Bolhuis
The modeling of complex reaction-diffusion processes in, for instance, cellular biochemical networks or self-assembling soft matter can be tremendously sped up by employing a multiscale algorithm which combines the mesoscopic Green's Function Reaction Dynamics (GFRD) method with explicit stochastic Brownian, Langevin, or deterministic molecular dynamics to treat reactants at the microscopic scale [A. Vijaykumar, P. G. Bolhuis, and P. R. ten Wolde, J. Chem. Phys. 143, 214102 (2015)]. Here we extend this multiscale MD-GFRD approach to include the orientational dynamics that is crucial to describe the anisotropic interactions often prevalent in biomolecular systems...
March 21, 2017: Journal of Chemical Physics
Jennifer T Hau, Kathy Langevin
Juvenile xanthogranuloma (JXG) is a benign, non-Langerhans cell histiocytosis, which commonly manifests as a solitary papule or nodule in infants and young children. However, other less common clinical presentations have been reported including clustered, agminated or plaque-like. It is important to recognize these variants, as diagnosis is often clinical. We highlight a case of juvenile xanthogranuloma presenting as nodules on the trunk of an infant that gradually coalesced to form a larger plaque.
October 15, 2016: Dermatology Online Journal
Miljko V Sataric, Dalibor L Sekulic, Slobodan Zdravkovic, Nebojsa M Ralevic
It appears that so-called post-translational modifications of tubulin heterodimers are mostly focussed at positions of amino acid sequences of carboxy-terminal tails. These changes have very profound effects on microtubule functions especially in connection with cellular traffic in terms of motor proteins. In this study, we elaborated the biophysical model aimed to explain the strategy governing these subtle interplays between structural and functional properties of microtubules. We relied onto Langevin equations including fluctuation-dissipation processes...
March 12, 2017: Journal of Theoretical Biology
Patrick Figliozzi, Nishant Sule, Zijie Yan, Ying Bao, Stanislav Burov, Stephen K Gray, Stuart A Rice, Suriyanarayanan Vaikuntanathan, Norbert F Scherer
To date investigations of the dynamics of driven colloidal systems have focused on hydrodynamic interactions and often employ optical (laser) tweezers for manipulation. However, the optical fields that provide confinement and drive also result in electrodynamic interactions that are generally neglected. We address this issue with a detailed study of interparticle dynamics in an optical ring vortex trap using 150-nm diameter Ag nanoparticles. We term the resultant electrodynamically interacting nanoparticles a driven optical matter system...
February 2017: Physical Review. E
M L Rosinberg, G Tarjus, T Munakata
This paper is the second in a series devoted to the study of Langevin systems subjected to a continuous time-delayed feedback control. The goal of our previous paper [Phys. Rev. E 91, 042114 (2015)PLEEE81539-375510.1103/PhysRevE.91.042114] was to derive second-law-like inequalities that provide bounds to the average extracted work. Here we study stochastic fluctuations of time-integrated observables such as the heat exchanged with the environment, the extracted work, or the (apparent) entropy production. We use a path-integral formalism and focus on the long-time behavior in the stationary cooling regime, stressing the role of rare events...
February 2017: Physical Review. E
Bingyu Cui, Rico Milkus, Alessio Zaccone
We compute the dielectric response of glasses starting from a microscopic system-bath Hamiltonian of the Zwanzig-Caldeira-Leggett type and using an ansatz from kinetic theory for the memory function in the resulting generalized Langevin equation. The resulting framework requires the knowledge of the vibrational density of states (DOS) as input, which we take from numerical evaluation of a marginally stable harmonic disordered lattice, featuring a strong boson peak (excess of soft modes over Debye ∼ω_{p}^{2} law)...
February 2017: Physical Review. E
S Chung, S Samin, C Holm, J G Malherbe, S Amokrane
We study, using Langevin dynamics simulations, the change in composition of a binary colloidal mixture confined in a finite-length channel, induced by an external field. The field-induced transition from a near-bulk composition to an inverted population is studied as a function of time, for different field strengths and system parameters. For state points corresponding to reversible field cycles, the cyclic filling and emptying of the channel by the minority species are compared. Extrapolation of the physical relaxation times to the colloidal regime is performed through a series of simulations at increasing value of the damping parameter...
February 2017: Physical Review. E
Weixin Qian, Kentaro Doi, Satoyuki Kawano
Electrokinetic phenomena in micro/nanofluidic channels have attracted considerable attention because precise control of molecular transport in liquids is required to optically and electrically capture the behavior of single molecules. However, the detailed mechanisms of polymer transport influenced by electroosmotic flows and electric fields in micro/nanofluidic channels have not yet been elucidated. In this study, a Langevin dynamics simulation was used to investigate the electrokinetic transport of single-stranded DNA (ssDNA) in a cylindrical nanochannel, employing a coarse-grained bead-spring model that quantitatively reproduced the radius of gyration, diffusion coefficient, and electrophoretic mobility of the polymer...
March 14, 2017: Biophysical Journal
Franck Plouraboué, E Ibrahima Thiam, Blaise Delmotte, Eric Climent
In this paper, we address the identifiability of constitutive parameters of passive or active micro-swimmers. We first present a general framework for describing fibres or micro-swimmers using a bead-model description. Using a kinematic constraint formulation to describe fibres, flagellum or cilia, we find explicit linear relationship between elastic constitutive parameters and generalized velocities from computing contact forces. This linear formulation then permits one to address explicitly identifiability conditions and solve for parameter identification...
January 2017: Proceedings. Mathematical, Physical, and Engineering Sciences
Ying Xiong, Lisbeth Berrueta, Katia Urso, Sara Olenich, Igla Muskaj, Gary J Badger, Antonios Aliprantis, Robert Lafyatis, Helene M Langevin
OBJECTIVE: Although physical therapy can help preserve mobility in patients with systemic sclerosis (SSc), stretching has not been used systematically as a treatment to prevent or reverse the disease process. We previously showed in rodent models that stretching promotes the resolution of connective tissue inflammation and reduces new collagen formation after injury. Here, we tested the hypothesis that stretching would impact scleroderma development using a mouse sclerodermatous graft-versus-host disease (sclGvHD) model...
2017: Frontiers in Immunology
Gilles Thomas, Marco Aurelio Andrade, Julio Adamowski, Emilio Silva
A linear acoustic levitation transportation system based on a ring-type vibrator is presented. The system is composed by two 21 kHz Langevin transducers connected to a ring-shaped structure formed by two semicircular sections and two flat plates. In this system, a flexural standing wave is generated along the ring structure, producing an acoustic standing wave between the vibrating ring and a plane reflector located at a distance of approximately a half wavelength from the ring. The acoustic standing wave in air has a series of pressure nodes, where small particles can be levitated and transported...
February 23, 2017: IEEE Transactions on Ultrasonics, Ferroelectrics, and Frequency Control
J M Nava-Sedeño, H Hatzikirou, F Peruani, A Deutsch
Cellular automata (CA) are discrete time, space, and state models which are extensively used for modeling biological phenomena. CA are "on-lattice" models with low computational demands. In particular, lattice-gas cellular automata (LGCA) have been introduced as models of single and collective cell migration. The interaction rule dictates the behavior of a cellular automaton model and is critical to the model's biological relevance. The LGCA model's interaction rule has been typically chosen phenomenologically...
February 27, 2017: Journal of Mathematical Biology
Hans Vandebroek, Carlo Vanderzande
Inspired by recent experiments on the dynamics of particles and polymers in artificial cytoskeletons and in cells, we introduce a modified Langevin equation for a particle in an environment that is a viscoelastic medium and that is brought out of equilibrium by the action of active fluctuations caused by molecular motors. We show that within such a model, the motion of a free particle crosses over from superdiffusive to subdiffusive as observed for tracer particles in an in vitro cytoskeleton or in a cell. We investigate the dynamics of a particle confined by a harmonic potential as a simple model for the motion of the tethered head of kinesin-1...
February 27, 2017: Soft Matter
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
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
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
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
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
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
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