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Huan Lei, Nathan A Baker, Xiantao Li
We present a data-driven approach to determine the memory kernel and random noise in generalized Langevin equations. To facilitate practical implementations, we parameterize the kernel function in the Laplace domain by a rational function, with coefficients directly linked to the equilibrium statistics of the coarse-grain variables. We show that such an approximation can be constructed to arbitrarily high order and the resulting generalized Langevin dynamics can be embedded in an extended stochastic model without explicit memory...
November 29, 2016: Proceedings of the National Academy of Sciences of the United States of America
Lina Ma, Xiantao Li, Chun Liu
We present a derivation of a coarse-grained description, in the form of a generalized Langevin equation, from the Langevin dynamics model that describes the dynamics of bio-molecules. The focus is placed on the form of the memory kernel function, the colored noise, and the second fluctuation-dissipation theorem that connects them. Also presented is a hierarchy of approximations for the memory and random noise terms, using rational approximations in the Laplace domain. These approximations offer increasing accuracy...
November 28, 2016: Journal of Chemical Physics
Guillaume Copie, Fabrizio Cleri, Ralf Blossey, Marc F Lensink
Interfacial waters are increasingly appreciated as playing a key role in protein-protein interactions. We report on a study of the prediction of interfacial water positions by both Molecular Dynamics and explicit solvent-continuum electrostatics based on the Dipolar Poisson-Boltzmann Langevin (DPBL) model, for three test cases: (i) the barnase/barstar complex (ii) the complex between the DNase domain of colicin E2 and its cognate Im2 immunity protein and (iii) the highly unusual anti-freeze protein Maxi which contains a large number of waters in its interior...
December 1, 2016: Scientific Reports
Xiaolong Lu, Junhui Hu, Hanmin Peng, Yuan Wang
In this paper, a new topological structure for the Langevin-type ultrasonic transducer is proposed and investigated. The two cylindrical terminal blocks are conically shaped with four supporting plates each, and two cooling fins are disposed at the bottom of terminal blocks, adjacent to the piezoelectric rings. Experimental results show that it has larger vibration velocity, lower temperature rise and higher electroacoustic energy efficiency than the conventional Langevin transducer. The reasons for the phenomena can be well explained by the change of mass, heat dissipation surface and force factor of the transducer...
November 16, 2016: Ultrasonics
Pamela Madu, Jennifer T Hau, Kathy Langevin
No abstract text is available yet for this article.
November 2016: Pediatric Dermatology
Fredrik Lindén, Henrik Cederquist, Henning Zettergren
We present exact analytical solutions for charge transfer reactions between two arbitrarily charged hard dielectric spheres. These solutions, and the corresponding exact ones for sphere-sphere interaction energies, include sums that describe polarization effects to infinite orders in the inverse of the distance between the sphere centers. In addition, we show that these exact solutions may be approximated by much simpler analytical expressions that are useful for many practical applications. This is exemplified through calculations of Langevin type cross sections for forming a compound system of two colliding spheres and through calculations of electron transfer cross sections...
November 21, 2016: Journal of Chemical Physics
Pedro E Ramírez-González, Luis E Sanchéz-Díaz, Magdaleno Medina-Noyola, Yanting Wang
The recent predictions of the self-consistent generalized Langevin equation theory, describing the existence of unusual partially arrested states in the context of ionic liquids, were probed using all-atom molecular dynamics simulations of a room-temperature ionic liquid. We have found a slower diffusion of the smaller anions compared with the large cations for a wide range of temperatures. The arrest mechanism consists on the formation of a strongly repulsive glass by the anions, stabilized by the long range electrostatic potential...
November 21, 2016: Journal of Chemical Physics
R Dhavalikar, D Hensley, L Maldonado-Camargo, L R Croft, S Ceron, P W Goodwill, S M Conolly, C Rinaldi
Magnetic Particle Imaging (MPI) is an emerging tomographic imaging technology that detects magnetic nanoparticle tracers by exploiting their non-linear magnetization properties. In order to predict the behavior of nanoparticles in an imager, it is possible to use a non-imaging MPI relaxometer or spectrometer to characterize the behavior of nanoparticles in a controlled setting. In this paper we explore the use of ferrohydrodynamic magnetization equations for predicting the response of particles in an MPI relaxometer...
August 3, 2016: Journal of Physics D: Applied Physics
Pitt Allmendinger, Johannes Deiglmayr, Otto Schullian, Katharina Höveler, Josef A Agner, Hansjürg Schmutz, Frédéric Merkt
Studies of ion-molecule reactions at low temperatures are difficult because stray electric fields in the reaction volume affect the kinetic energy of charged reaction partners. We describe a new experimental approach to study ion-molecule reactions at low temperatures and present, as example, a measurement of the H2++H2→H3++H reaction with the H2+ ion prepared in a single rovibrational state at collision energies in the range Ecol /kB =5-60 K. To reach such low-collision energies, we use a merged-beam approach and observe the reaction within the orbit of a Rydberg electron, which shields the ions from stray fields...
November 16, 2016: Chemphyschem: a European Journal of Chemical Physics and Physical Chemistry
Simon P Rittmeyer, David J Ward, Patrick Gütlein, John Ellis, William Allison, Karsten Reuter
Helium spin echo experiments combined with ab initio based Langevin molecular dynamics simulations are used to quantify the adsorbate-substrate coupling during the thermal diffusion of Na atoms on Cu(111). An analysis of trajectories within the local density friction approximation allows the contribution from electron-hole pair excitations to be separated from the total energy dissipation. Despite the minimal electronic friction coefficient of Na and the relatively small mass mismatch to Cu promoting efficient phononic dissipation, about (20±5)% of the total energy loss is attributable to electronic friction...
November 4, 2016: Physical Review Letters
Kang Qiu, Li-Fang Wang, Jian Shen, Alssadig A M Yousif, Peng He, Dan-Dan Shao, Xiao-Min Zhang, John B Kirunda, Ya Jia
Based on a deterministic continuous model of cell populations dynamics in the colonic crypt and in colorectal cancer, we propose four combinations of feedback mechanisms in the differentiations from stem cells (SCs) to transit cells (TCs) and then to differentiated cells (DCs), the four combinations include the double linear (LL), the linear and saturating (LS), the saturating and linear (SL), and the double saturating (SS) feedbacks, respectively. The relative fluctuations of the population of SCs, TCs, and DCs around equilibrium states with four feedback mechanisms are studied by using the Langevin method...
November 18, 2016: Scientific Reports
G Filacchione, A Raponi, F Capaccioni, M Ciarniello, F Tosi, M T Capria, M C De Sanctis, A Migliorini, G Piccioni, P Cerroni, M A Barucci, S Fornasier, B Schmitt, E Quirico, S Erard, D Bockelee-Morvan, C Leyrat, G Arnold, V Mennella, E Ammannito, G Bellucci, J Benkhoff, J P Bibring, A Blanco, M I Blecka, R Carlson, U Carsenty, L Colangeli, M Combes, M Combi, J Crovisier, P Drossart, T Encrenaz, C Federico, U Fink, S Fonti, M Fulchignoni, W H Ip, P Irwin, R Jaumann, E Kuehrt, Y Langevin, G Magni, T McCord, L Moroz, S Mottola, E Palomba, U Schade, K Stephan, F Taylor, D Tiphene, G P Tozzi, P Beck, N Biver, L Bonal, J-Ph Combe, D Despan, E Flamini, M Formisano, A Frigeri, D Grassi, M S Gudipati, D Kappel, A Longobardo, F Mancarella, K Markus, F Merlin, R Orosei, G Rinaldi, M Cartacci, A Cicchetti, Y Hello, F Henry, S Jacquinod, J M Reess, R Noschese, R Politi, G Peter
Carbon dioxide is one of the most abundant species in cometary nuclei, but due to its high volatility CO2 ice is generally only found beneath the surface. We report the infrared spectroscopic identification of a CO2 ice-rich surface area, located in the Anhur region of comet 67P/Churyumov-Gerasimenko. Spectral modeling shows that about 0.1% of the 80×60 m area is CO2 ice. This exposed ice was observed a short time after exiting from local winter; following the increased illumination, the CO2 ice completely disappeared over about three weeks...
November 17, 2016: Science
E R Smith, E A Müller, R V Craster, O K Matar
Molecular dynamics simulations are employed to develop a theoretical model to predict the fluid-solid contact angle as a function of wall-sliding speed incorporating thermal fluctuations. A liquid bridge between counter-sliding walls is studied, with liquid-vapour interface-tracking, to explore the impact of wall-sliding speed on contact angle. The behaviour of the macroscopic contact angle varies linearly over a range of capillary numbers beyond which the liquid bridge pinches off, a behaviour supported by experimental results...
November 17, 2016: Soft Matter
Norbert Schaudinnus, Benjamin Lickert, Mithun Biswas, Gerhard Stock
Molecular dynamics simulations of biomolecular processes are often discussed in terms of diffusive motion on a low-dimensional free energy landscape F(
November 14, 2016: Journal of Chemical Physics
Frank P MacMaster, Jordan Cohen, Waqar Waheed, Emilie Magaud, Mariko Sembo, Lisa Marie Langevin, Katherine Rittenbach
BACKGROUND: Research activity is especially critical in the field of psychiatry as it is evolving rapidly thanks to advances in neuroscience. RESULTS: We administered a 34-item survey regarding research experiences targeted at psychiatry residents and postgraduate residency program directors in Canada. One hundred and nineteen participants answered the survey (16 program directors, 103 residents) allowing for a margin of error of 8.4% at a 95% confidence interval...
November 14, 2016: BMC Research Notes
Ken-Ichi Inoue, Kazuya Watanabe, Toshiki Sugimoto, Yoshiyasu Matsumoto, Tomokazu Yasuike
Hot carriers at metal surfaces can drive nonthermal reactions of adsorbates. Characterizing nonequilibrium statistics among various degrees of freedom in an ultrafast time scale is crucial to understand and develop hot carrier-driven chemistry. Here we demonstrate multidimensional vibrational dynamics of carbon monoxide (CO) on Cu(100) along hot-carrier induced desorption studied by using time-resolved vibrational sum-frequency generation with phase-sensitive detection. Instantaneous frequency and amplitude of the CO internal stretching mode are tracked with a subpicosecond time resolution that is shorter than the vibrational dephasing time...
October 28, 2016: Physical Review Letters
Pierre Boudinot, Christelle Langevin, Christopher J Secombes, Jean-Pierre Levraud
Antiviral type I interferons (IFNs) have been discovered in fish. Genomic studies revealed their considerable number in many species; some genes encode secreted and non-secreted isoforms. Based on cysteine motifs, fish type I IFNs fall in two subgroups, which use two different receptors. Mammalian type I IFN genes are intronless while type III have introns; in fish, all have introns, but structurally, both subgroups belong to type I. Type I IFNs likely appeared early in vertebrates as intron containing genes, and evolved in parallel in tetrapods and fishes...
November 2, 2016: Viruses
Mingfeng Pu, Huijun Jiang, Zhonghuai Hou
Polymer translocation through nanopores into a crowded environment is of ubiquitous importance in many biological processes. Here we investigate polymer translocation through a nanopore into an active bath of self-propelled particles in two-dimensional space using Langevin dynamics simulations. Interestingly, we find that the mean translocation time τ can show a bell-shape dependence on the particle activity Fa at a fixed volume fraction ϕ, indicating that the translocation process may become slower for small activity compared to the case of the passive media, and only when the particle activity becomes large enough can the translocation process be accelerated...
November 7, 2016: Journal of Chemical Physics
Alex Pauvolid-Corrêa, Owen Solberg, Dinair Couto-Lima, Rita Maria Nogueira, Stanley Langevin, Nicholas Komar
Genomic sequences are described from five novel viruses and divergent strains of Brejeira and Guaico Culex viruses from mosquitoes collected in Pantanal, Brazil, in 2010.
November 3, 2016: Genome Announcements
V Hutanu, W Luberstetter, E Bourgeat-Lami, M Meven, A Sazonov, A Steffen, G Heger, G Roth, E Lelièvre-Berna
A new polarized neutron single crystal diffractometer POLI (Polarization Investigator) has been developed at the Maier-Leibnitz Zentrum, Garching, Germany. After reviewing existing devices, spherical neutron polarimetry has been implemented on POLI as a main experimental technique using a third-generation cryogenic polarization analysis device (Cryopad) built in cooperation between RWTH University and Institut Laue-Langevin. In this report we describe the realization and present the performance of the new Cryopad on POLI...
October 2016: Review of Scientific Instruments
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