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https://www.readbyqxmd.com/read/28633990/cellular-gauge-symmetry-and-the-li-organization-principle-a-mathematical-addendum-quantifying-energetic-dynamics-in-physical-and-biological-systems-through-a-simple-geometric-tool-and-geodetic-curves
#1
REVIEW
Alexander Yurkin, Arturo Tozzi, James F Peters, Pedro C Marijuán
The present Addendum complements the accompanying paper "Cellular Gauge Symmetry and the Li Organization Principle"; it illustrates a recently-developed geometrical physical model able to assess electronic movements and energetic paths in atomic shells. The model describes a multi-level system of circular, wavy and zigzag paths which can be projected onto a horizontal tape. This model ushers in a visual interpretation of the distribution of atomic electrons' energy levels and the corresponding quantum numbers through rather simple tools, such as compasses, rulers and straightforward calculations...
June 17, 2017: Progress in Biophysics and Molecular Biology
https://www.readbyqxmd.com/read/28618830/acoustic-levitation-of-an-object-larger-than-the-acoustic-wavelength
#2
Marco A B Andrade, Fábio T A Okina, Anne L Bernassau, Julio C Adamowski
Levitation and manipulation of objects by sound waves have a wide range of applications in chemistry, biology, material sciences, and engineering. However, the current acoustic levitation techniques are mainly restricted to particles that are much smaller than the acoustic wavelength. In this work, it is shown that acoustic standing waves can be employed to stably levitate an object much larger than the acoustic wavelength in air. The levitation of a large slightly curved object weighting 2.3 g is demonstrated by using a device formed by two 25 kHz ultrasonic Langevin transducers connected to an aluminum plate...
June 2017: Journal of the Acoustical Society of America
https://www.readbyqxmd.com/read/28618585/uniform-description-of-polymer-ejection-dynamics-from-capsid-with-and-without-hydrodynamics
#3
J Piili, P M Suhonen, R P Linna
We use stochastic rotation dynamics (SRD) to examine the dynamics of the ejection of an initially strongly confined flexible polymer from a spherical capsid with and without hydrodynamics. The results obtained using stochastic rotation dynamics (SRD) are compared to similar Langevin simulations. Inclusion of hydrodynamic modes speeds up the ejection but also allows the part of the polymer outside the capsid to expand closer to equilibrium. This shows as higher values of radius of gyration when hydrodynamics are enabled...
May 2017: Physical Review. E
https://www.readbyqxmd.com/read/28618517/microscopic-derivation-of-the-hydrodynamics-of-active-brownian-particle-suspensions
#4
Stefano Steffenoni, Gianmaria Falasco, Klaus Kroy
We derive the hydrodynamic equations of motion for a fluid of active particles described by underdamped Langevin equations that reduce to the active-Brownian-particle model, in the overdamped limit. The contraction into the hydrodynamic description is performed by locally averaging the particle dynamics with the nonequilibrium many-particle probability density, whose formal expression is found in the physically relevant limit of high friction through a multiple-time-scale analysis. This approach permits us to identify the conditions under which self-propulsion can be subsumed into the fluid stress tensor and thus to define systematically and unambiguously the local pressure of the active fluid...
May 2017: Physical Review. E
https://www.readbyqxmd.com/read/28612756/mobility-dependent-recombination-models-for-organic-solar-cells
#5
Alexander Wagenpfahl
Modern solar cell technologies are coined by the effort to enhance power conversion efficiencies. Limiting influences are manifold. Undoubtedly, the loss of electrical charge carriers, the charge carrier recombination, is one of the most prominent process which may lead to such limitations. In the field of organic solar cells with rather low charge carrier mobilities, the encounter of two charge carriers has turned out to be the limiting factor for charge carrier recombination. The recombination process strongly depends on the charge carrier mobilities...
June 14, 2017: Journal of Physics. Condensed Matter: An Institute of Physics Journal
https://www.readbyqxmd.com/read/28603526/ftr83-a-member-of-the-large-fish-specific-fintrim-family-triggers-ifn-pathway-and-counters-viral-infection
#6
Christelle Langevin, Elina Aleksejeva, Armel Houel, Valérie Briolat, Corinne Torhy, Aurélie Lunazzi, Jean-Pierre Levraud, Pierre Boudinot
Tripartite motif (TRIM) proteins are involved in various cellular functions and constitute key factors of the antiviral innate immune response. TRIM proteins can bind viral particles directly, sending them to degradation by the proteasome, or ubiquitinate signaling molecules leading to upregulation of innate immunity. TRIM proteins are present in across metazoans but are particularly numerous in vertebrates where genes comprising a B30.2 domain have been often duplicated. In fish, a TRIM subset named finTRIM is highly diversified, with large gene numbers and clear signatures of positive selection in the B30...
2017: Frontiers in Immunology
https://www.readbyqxmd.com/read/28576289/psychological-counseling-as-an-adjunct-to-stuttering-treatment-clients-experiences-and-perceptions
#7
Alanna Lindsay, Marilyn Langevin
PURPOSE: Stuttering can trigger anxiety and other psychological and emotional reactions, and limit participation in society. It is possible that psychological counseling could enhance stuttering treatment outcomes; however, little is known about how clients view such counseling. The purpose of this study was to gain an understanding of clients' experiences with, and perceptions of, a psychological counseling service that was offered as an optional adjunct to speech therapy for stuttering...
June 2017: Journal of Fluency Disorders
https://www.readbyqxmd.com/read/28571611/incorporation-of-ion-and-solvent-structure-into-mean-field-modeling-of-the-electric-double-layer
#8
REVIEW
Klemen Bohinc, Guilherme Volpe Bossa, Sylvio May
An electric double layer forms when the small mobile ions of an electrolyte interact with an extended charged object, a macroion. The competition between electrostatic attraction and translational entropy loss of the small ions results in a diffuse layer of partially immobilized ions in the vicinity of the macroion. Modeling structure and energy of the electric double layer has a long history that has lead to the classical Poisson-Boltzmann theory and numerous extensions that account for ion-ion correlations and structural ion and solvent properties...
May 5, 2017: Advances in Colloid and Interface Science
https://www.readbyqxmd.com/read/28571330/influence-of-chemistry-interfacial-width-and-non-isothermal-conditions-on-spatially-heterogeneous-activated-relaxation-and-elasticity-in-glass-forming-free-standing-films
#9
Stephen Mirigian, Kenneth S Schweizer
We employ the Elastically Collective Nonlinear Langevin Equation (ECNLE) theory of activated relaxation to study several questions in free standing thin films of glass-forming molecular and polymer liquids. The influence of non-universal chemical aspects on dynamical confinement effects is found to be relatively weak, but with the caveat that for the systems examined, the bulk ECNLE polymer theory does not predict widely varying fragilities. Allowing the film model to have a realistic vapor interfacial width significantly enhances the reduction of the film-averaged glass transition temperature, Tg, in a manner that depends on whether a dynamic or pseudo-thermodynamic averaging of the spatial mobility gradient is adopted...
May 28, 2017: Journal of Chemical Physics
https://www.readbyqxmd.com/read/28555683/foamed-emulsion-drainage-flow-and-trapping-of-drops
#10
Maxime Schneider, Ziqiang Zou, Dominique Langevin, Anniina Salonen
Foamed emulsions are ubiquitous in our daily life but the ageing of such systems is still poorly understood. In this study we investigate foam drainage and measure the evolution of the gas, liquid and oil volume fractions inside the foam. We evidence three regimes of ageing. During an initial period of fast drainage, both bubbles and drops are very mobile. As the foam stabilises drainage proceeds leading to a gradual decrease of the liquid fraction and slowing down of drainage. Clusters of oil drops are less sheared, their dynamic viscosity increases and drainage slows down even further, until the drops become blocked...
June 7, 2017: Soft Matter
https://www.readbyqxmd.com/read/28554975/mechanical-and-electrostatic-experiments-with-dust-particles-collected-in-the-inner-coma-of-comet-67p-by-cosima-onboard-rosetta
#11
Martin Hilchenbach, Henning Fischer, Yves Langevin, Sihane Merouane, John Paquette, Jouni Rynö, Oliver Stenzel, Christelle Briois, Jochen Kissel, Andreas Koch, Rita Schulz, Johan Silen, Nicolas Altobelli, Donia Baklouti, Anais Bardyn, Herve Cottin, Cecile Engrand, Nicolas Fray, Gerhard Haerendel, Hartmut Henkel, Herwig Höfner, Klaus Hornung, Harry Lehto, Eva Maria Mellado, Paola Modica, Lena Le Roy, Sandra Siljeström, Wolfgang Steiger, Laurent Thirkell, Roger Thomas, Klaus Torkar, Kurt Varmuza, Boris Zaprudin
The in situ cometary dust particle instrument COSIMA (COmetary Secondary Ion Mass Analyser) onboard ESA's Rosetta mission has collected about 31 000 dust particles in the inner coma of comet 67P/Churyumov-Gerasimenko since August 2014. The particles are identified by optical microscope imaging and analysed by time-of-flight secondary ion mass spectrometry. After dust particle collection by low speed impact on metal targets, the collected particle morphology points towards four families of cometary dust particles...
July 13, 2017: Philosophical Transactions. Series A, Mathematical, Physical, and Engineering Sciences
https://www.readbyqxmd.com/read/28553494/molecular-dynamics-and-charge-transport-in-organic-semiconductors-a-classical-approach-to-modeling-electron-transfer
#12
Kenley M Pelzer, Álvaro Vázquez-Mayagoitia, Laura E Ratcliff, Sergei Tretiak, Raymond A Bair, Stephen K Gray, Troy Van Voorhis, Ross E Larsen, Seth B Darling
Organic photovoltaics (OPVs) are a promising carbon-neutral energy conversion technology, with recent improvements pushing power conversion efficiencies over 10%. A major factor limiting OPV performance is inefficiency of charge transport in organic semiconducting materials (OSCs). Due to strong coupling with lattice degrees of freedom, the charges form polarons, localized quasi-particles comprised of charges dressed with phonons. These polarons can be conceptualized as pseudo-atoms with a greater effective mass than a bare charge...
April 1, 2017: Chemical Science
https://www.readbyqxmd.com/read/28548147/reentrant-phase-separation-behavior-of-active-particles-with-anisotropic-janus-interaction
#13
Mingfeng Pu, Huijun Jiang, Zhonghuai Hou
Recent studies showed substantial evidence of dynamic clustering and phase separation in active particle systems, but the role of anisotropic interaction between the particles has not been addressed yet. Here we investigate the phase separation of active particles that experience an anisotropic Janus interaction with tunable strength in two dimensional space by using Langevin dynamics simulations. Interestingly, we find that phase separation shows a re-entrance behavior with variation of the Janus interaction strength: while small Janus interaction can enhance the formation of living clusters and phase separation, large Janus interaction would destroy the large cluster...
June 7, 2017: Soft Matter
https://www.readbyqxmd.com/read/28548089/finding-multiple-reaction-pathways-via-global-optimization-of-action
#14
Juyong Lee, In-Ho Lee, InSuk Joung, Jooyoung Lee, Bernard R Brooks
Global searching for reaction pathways is a long-standing challenge in computational chemistry and biology. Most existing approaches perform only local searches due to computational complexity. Here we present a computational approach, Action-CSA, to find multiple diverse reaction pathways connecting fixed initial and final states through global optimization of the Onsager-Machlup action using the conformational space annealing (CSA) method. Action-CSA successfully overcomes large energy barriers via crossovers and mutations of pathways and finds all possible pathways of small systems without initial guesses on pathways...
May 26, 2017: Nature Communications
https://www.readbyqxmd.com/read/28505709/causal-influence-in-linear-langevin-networks-without-feedback
#15
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
https://www.readbyqxmd.com/read/28505440/iterative-reconstruction-of-memory-kernels
#16
Gerhard Jung, Martin Hanke, Friederike Schmid
In recent years, it has become increasingly popular to construct coarse-grained models with non-Markovian dynamics 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 article, we propose an iterative method for memory reconstruction from dynamical correlation functions. Compared to previously proposed noniterative 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 30, 2017: Journal of Chemical Theory and Computation
https://www.readbyqxmd.com/read/28484333/robust-identification-of-harmonic-oscillator-parameters-using-the-adjoint-fokker-planck-equation
#17
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
https://www.readbyqxmd.com/read/28483796/imaging-of-viral-neuroinvasion-in-the-zebrafish-reveals-that-sindbis-and-chikungunya-viruses-favour-different-entry-routes
#18
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
https://www.readbyqxmd.com/read/28465594/crowding-facilitated-macromolecular-transport-in-attractive-micropost-arrays
#19
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
https://www.readbyqxmd.com/read/28465433/chemotaxis-and-autochemotaxis-of-self-propelling-droplet-swimmers
#20
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 16, 2017: Proceedings of the National Academy of Sciences of the United States of America
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