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Theory of simulation

Michael B Liu, Christopher Y Ko, Zhen Song, Alan Garfinkel, James N Weiss, Zhilin Qu
Ventricular myocytes are excitable cells whose voltage threshold for action potential (AP) excitation is ∼-60 mV at which INa is activated to give rise to a fast upstroke. Therefore, for a short stimulus pulse to elicit an AP, a stronger stimulus is needed if the resting potential lies further away from the INa threshold, such as in hypokalemia. However, for an AP elicited by a long duration stimulus or a diastolic spontaneous calcium release, we observed that the stimulus needed was lower in hypokalemia than in normokalemia in both computer simulations and experiments of rabbit ventricular myocytes...
December 6, 2016: Biophysical Journal
A Umemoto, C B Holroyd
Anterior cingulate cortex (ACC) is involved in cognitive control and decision-making but its precise function is still highly debated. Based on evidence from lesion, neurophysiological, and neuroimaging studies, we have recently proposed a critical role for ACC in motivating extended behaviors according to learned task values (Holroyd and Yeung, 2012). Computational simulations based on this theory suggest a hierarchical mechanism in which a caudal division of ACC selects and applies control over task execution, and a rostral division of ACC facilitates switches between tasks according to a higher task strategy (Holroyd and McClure, 2015)...
2016: Progress in Brain Research
Jie Luo, Yuting Yang, Zhongqi Yao, Weixin Lu, Bo Hou, Zhi Hong Hang, C T Chan, Yun Lai
By using pure dielectric photonic crystals, we demonstrate the realization of ultratransparent media, which allow near 100% transmission of light for all incident angles and create aberration-free virtual images. The ultratransparency effect is well explained by spatially dispersive effective medium theory for photonic crystals, and verified by both simulations and proof-of-principle microwave experiments. Designed with shifted elliptical equal frequency contours, such ultratransparent media not only provide a low-loss and feasible platform for transformation optics devices at optical frequencies, but also enable new freedom for phase manipulation beyond the local medium framework...
November 25, 2016: Physical Review Letters
Lorenzo Zino, Alessandro Rizzo, Maurizio Porfiri
Activity-driven networks are a powerful paradigm to study epidemic spreading over time-varying networks. Despite significant advances, most of the current understanding relies on discrete-time computer simulations, in which each node is assigned an activity potential from a continuous distribution. Here, we establish a continuous-time discrete-distribution framework toward an analytical treatment of the epidemic spreading, from its onset to the endemic equilibrium. In the thermodynamic limit, we derive a nonlinear dynamical system to accurately model the epidemic spreading and leverage techniques from the fields of differential inclusions and adaptive estimation to inform short- and long-term predictions...
November 25, 2016: Physical Review Letters
Andreas Kaesler, Peter C Schlanstein, Felix Hesselmann, Martin Büsen, Michael Klaas, Dorothee Roggenkamp, Thomas Schmitz-Rode, Ulrich Steinseifer, Jutta Arens
Flow distribution is key in artificial lungs, as it directly influences gas exchange performance as well as clot forming and blood damaging potential. The current state of computational fluid dynamics (CFD) in artificial lungs can only give insight on a macroscopic level due to model simplification applied to the fiber bundle. Based on our recent work on wound fiber bundles, we applied particle image velocimetry (PIV) to the model of an artificial lung prototype intended for neonatal use to visualize flow distribution in a stacked fiber bundle configuration to (i) evaluate the feasibility of PIV for artificial lungs, (ii) validate CFD in the fiber bundle of artificial lungs, and (iii) give a suggestion how to incorporate microscopic aspects into mainly macroscopic CFD studies...
December 7, 2016: Artificial Organs
Guillermo Iván Guerrero-García, Francisco J Solis, Kalyan Raidongia, Andrew Robert Koltonow, Jiaxing Huang, Mónica Olvera de la Cruz
The current rectification displayed by solid-state p-n semiconductor diodes relies on the abundance of electrons and holes near the interface between the p-n junction. In analogy to this electronic device, we propose here the construction of a purely ionic liquid-state electric rectifying heterojunction displaying an excess of monovalent cations and anions near the interface between two immiscible solvents with different dielectric properties. This system does not need any physical membrane or material barrier to show preferential ion transfer but relies on the ionic solvation energy between the two immiscible solvents...
November 23, 2016: ACS Central Science
Li-Kun Yang, Xia-Guang Zhang, Fang-Zu Yang, De-Yin Wu, Zhong-Qun Tian, Xiang-Yang Liu
Density functional theory calculations have been used to elucidate the mechanism of the addition reaction of acetaldehyde to the positively charged hydrogenated silicene (H-silicene). We find that the positively charged H-silicene plane could be partially restructured to form a vacant Si site, enabling a further nucleophilic addition reaction. After acetaldehyde molecule attached to the H-silicene plane, two competing pathways are involved in hydrogen abstraction process: a random reaction mechanism and a chain reaction mechanism...
December 6, 2016: Chemphyschem: a European Journal of Chemical Physics and Physical Chemistry
F A Braeu, A Seitz, R C Aydin, C J Cyron
Constrained mixture models for soft tissue growth and remodeling have attracted increasing attention over the last decade. They can capture the effects of the simultaneous presence of multiple constituents that are continuously deposited and degraded at in general different rates, which is important to understand essential features of living soft tissues that cannot be captured by simple kinematic growth models. Recently the novel concept of homogenized constrained mixture models was introduced. It was shown that these models produce results which are very similar (and in certain limit cases even identical) to the ones of constrained mixture models based on multi-network theory...
December 5, 2016: Biomechanics and Modeling in Mechanobiology
Javier Segarra-Martí, Antonio Francés-Monerris, Daniel Roca-Sanjuán, Manuela Merchán
The present study provides new insights into the topography of the potential energy hypersurfaces (PEHs) of the thymine nucleobase in order to rationalize its main ultrafast photochemical decay paths by employing two methodologies based on the complete active space self-consistent field (CASSCF) and the complete active space second-order perturbation theory (CASPT2) methods: (i) CASSCF optimized structures and energies corrected with the CASPT2 method at the CASSCF geometries and (ii) CASPT2 optimized geometries and energies...
December 3, 2016: Molecules: a Journal of Synthetic Chemistry and Natural Product Chemistry
Matias R Fagiani, Xiaowei Song, Petko Petkov, Sreekanta Debnath, Sandy Gewinner, Wieland Schöllkopf, Thomas Heine, André Fielicke, Knut R Asmis
We use cryogenic ion vibrational spectroscopy to characterize the structure and fluxionality of the magic number boron cluster B13(+) . The infrared photodissociation (IRPD) spectrum of the D2 -tagged all-(11) B isotopologue of B13(+) is reported in the spectral range from 435 to 1790 cm(-1) and unambiguously assigned to a planar boron double wheel structure based on a comparison to simulated IR spectra of low energy isomers from density-functional-theory (DFT) computations. Born-Oppenheimer DFT molecular dynamics simulations show that B13(+) exhibits internal quasi-rotation already at 100 K...
December 5, 2016: Angewandte Chemie
Priyanka Tavhare, Amol Deshmukh, Ajay Chaudhari
We have performed an ab initio and density functional theory study of the hydrogen adsorption on a lithium (Li)-decorated pentalene (C8H6Li2) complex. The C8H6Li2 complex can interact with a maximum of two hydrogen molecules with a H2 uptake capacity of 3.36 wt%. The effect of the number and position of boron atom substitution in the C8H6Li2 complex on the H2 uptake capacity is also studied. Two and four carbon atoms are substituted by boron atoms in the C8H6Li2 complex. Two different structures are considered for each of the two and four boron atom substitutions...
December 5, 2016: Physical Chemistry Chemical Physics: PCCP
Javier D Fuhr, Maarten W van der Meijden, Lucila J Cristina, Luis M Rodríguez, Richard M Kellogg, J Esteban Gayone, Hugo Ascolani, Magalí Lingenfelder
The chiral expression of a molecule on a surface is driven from a random solid solution on Cu(100) to a racemic crystal on a Sn/Cu(100) alloy. Density functional theory simulations reveal how the growth of the racemate is influenced by the underlying surface.
December 5, 2016: Chemical Communications: Chem Comm
Nieves Amat Camacho, Amy Hughes, Frederick M Burkle, Pier Luigi Ingrassia, Luca Ragazzoni, Anthony Redmond, Ian Norton, Johan von Schreeb
An increasing number of international emergency medical teams are deployed to assist disaster-affected populations worldwide. Since Haiti earthquake those teams have been criticised for ill adapted care, lack of preparedness in addition to not coordinating with the affected country healthcare system. The Emergency Medical Teams (EMTs) initiative, as part of the Word Health Organization's Global Health Emergency Workforce program, aims to address these shortcomings by improved EMT coordination, and mechanisms to ensure quality and accountability of national and international EMTs...
October 21, 2016: PLoS Currents
Andrea Zen, Loïc M Roch, Stephen J Cox, Xiao Liang Hu, Sandro Sorella, Dario Alfè, Angelos Michaelides
Clay minerals are ubiquitous in nature, and the manner in which they interact with their surroundings has important industrial and environmental implications. Consequently, a molecular-level understanding of the adsorption of molecules on clay surfaces is crucial. In this regard computer simulations play an important role, yet the accuracy of widely used empirical force fields (FF) and density functional theory (DFT) exchange-correlation functionals is often unclear in adsorption systems dominated by weak interactions...
November 23, 2016: Journal of Physical Chemistry. C, Nanomaterials and Interfaces
Romain de Monchy, François Destrempes, Ratan K Saha, Guy Cloutier, Emilie Franceschini
The effective medium theory (EMT) was recently developed to model the ultrasound backscatter from aggregating red blood cells [Franceschini, Metzger, and Cloutier, IEEE Trans. Ultrason. Ferroelectr. Freq. Control 58, 2668-2679 (2011)]. The EMT assumes that aggregates can be treated as homogeneous effective scatterers, which have effective properties determined by the aggregate compactness and the acoustical characteristics of the cells and the surrounding medium. In this study, the EMT is further developed to decompose the differential backscattering cross section of a single cell aggregate into coherent and incoherent components...
September 2016: Journal of the Acoustical Society of America
Chuanlin He, Kunde Yang, Yuanliang Ma, Bo Lei
The arriving-angle structure for the forward scattered wave on a vertical line array is obtained upon a modified scattering model in the Pekeris waveguide. The structure is investigated and interpreted by the array invariant theory combined with target induced modal coupling effect. Compared with that of the direct blast, the arriving-angle structure of the forward scattering wave owns multi-striations as well as an increased vertical array invariant. The forward scattered angle structure is dependent on the target position on the source-receiver line...
September 2016: Journal of the Acoustical Society of America
Shang Xiang, Weikang Jiang, Hao Jiang, Jianzheng Gao
An acoustic source identification technique with single layer pressure measurement is presented to reconstruct normal velocities of target sources in noisy environments. The theory for this reconstruction is developed from the inverse patch transfer functions method which is supposed to combine measurements of pressure and velocity on a surface surrounding the source. The rigid microphone array is called an acoustic mask, which is designed to obtain pressure on the Neumann boundary condition and realized by microphones flush mounted on the aluminum plate...
September 2016: Journal of the Acoustical Society of America
Jie Gao, Peiyong Zhu, Ahmed Alsaedi, Fuad E Alsaadi, Tasawar Hayat
In this paper, finite-time synchronization (FTS) of memristor-based recurrent neural networks (MNNs) with time-varying delays is investigated by designing a new switching controller. First, by using the differential inclusions theory and set-valued maps, sufficient conditions to ensure FTS of MNNs are obtained under the two cases of 0<α<1 and α=0, and it is derived that α=0 is the critical value of 0<α<1. Next, it is discussed deeply on the relation between the parameter α and the synchronization time...
November 4, 2016: Neural Networks: the Official Journal of the International Neural Network Society
Jie Li, Patrice Koehl
Computational protein sequence design is the rational design based on computer simulation of new protein molecules to fold to target three-dimensional structures, with the ultimate goal of designing novel functions. It requires a good understanding of the thermodynamic equilibrium properties of the protein of interest. Here, we consider the contribution of the solvent to the stability of the protein. We describe implicit solvent models, focusing on approximations of their nonpolar components using geometric potentials...
2017: Methods in Molecular Biology
Efrath Barta
Long-chain fatty acids cross a few membranes on their way from the capillary blood to the cardiomyocyte cytosol, where they are utilized as an essential source of energy. Details of the transport mechanism across those membranes remained elusive despite decades of laboratory and theoretical work. Here we inspect several optional scenarios for the crossing of the luminal membrane of the endothelial cell, the first barrier that should be crossed: a passive diffusion, facilitation by receptors for albumin and facilitation by fatty acids transporters...
December 3, 2016: Journal of Membrane Biology
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