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Theory of simulation

Parnian Kianfar, Nabiollah Abolfathi, Navid Zarif Karimi
This study investigated the adhesion behavior of Contactin4 (CNTN4), a member of Immunoglobulin Super Family (Ig-SF) of cell adhesion molecules. Contactin4 plays a crucial role in the formation, maintenance, and plasticity of neuronal networks. Contactin in its complex configuration with protein tyrosine phosphatase gamma (PTPRG) was selected for simulation. By utilizing Steered Molecular Dynamics (SMD), the uniaxial force was applied to induce unbinding of the complex, and the force-induced detachment of complex components was probed...
June 2, 2017: Journal of Molecular Graphics & Modelling
Yulun Han, Qingguo Meng, Bakhtiyor Rasulev, P Stanley May, Mary T Berry, Dmitri S Kilin
This study compares two competing pathways of photoexcitations in gas-phase metal-organic complexes: first, a sequence of phonon-assisted electronic transitions leading to dissipation of the energy of photoexcitations and second, a sequence of light-driven electronic transitions leading to photolysis. Phonon-assisted charge carrier dynamics is investigated by combination of the density matrix formalism and on-the-fly nonadiabatic couplings. Light-driven fragmentation is modeled by a time-dependent excited-state molecular dynamics (TDESMD) algorithm based on Rabi theory and principles similar to the trajectory surface hopping approximation...
June 26, 2017: Journal of Chemical Theory and Computation
Lin Guo, Xiaotian Wang, Wenxiong Shi, Zhao Jin, Weifeng Huang, Jie Lin, Guanshui Ma, Shuzhou Li
Here, by developing amorphous ZnO nanocages (a-ZnO NCs), we successfully obtained an ultrahigh enhancement factor up to 6.62×105. This remarkable SERS sensitivity can be attributed to high-efficiency ICTP within a-ZnO NCs-molecules system, which is caused by metastable electronic states of a-ZnO NCs. First-principles density functional theory (DFT) simulation further confirmed stronger ICTP in a-ZnO NCs than the crystalline counterpart. The efficient ICTP can even generate π bonding in Zn-S bonds peculiar to the mercapto molecule adsorbed a-ZnO NCs, which has been verified through the X-ray absorption near edge structure (XANES) characterization...
June 26, 2017: Angewandte Chemie
Yang Li, Tian-Shu Chu
By using density functional theory (DFT) and time-dependent density functional theory (TDDFT) methods, the sensing mechanism of a fluorescent probe 2-(2-hydroxyphenyl) benzothiazole (HBT) derivative HBTPP-S for hydrogen sulfide has been thoroughly studied. The thiolysis reaction has a moderate reaction barrier of 18.40 kcal mol-1, which indicates that the hydrogen sulfide sensing process has a favorable response speed. Due to the non-radiative donor-excited photoinduced electron transfer (d-PET, fluorophore as the electron donor) from the excited HBTPP group to the electron-withdrawing 2,4-dinitrophenyl group, as well as the inhibition of the proton transfer (PT) and the excited state intramolecular proton transfer (ESIPT) process by 2,4-dinitrophenyl group, the probe HBTPP-S is essentially non-fluorescent...
June 26, 2017: Journal of Physical Chemistry. A
H George E Hentschel, Prabhat K Jaiswal, Chandana Mondal, Itamar Procaccia, Jacques Zylberg
We revisit the problem of the stress distribution in a frictional sandpile with both normal and tangential (frictional) inter-granular forces, under gravity, equipped with a new numerical method of generating such assemblies. Numerical simulations allow a determination of the spatial dependence of all the components of the stress field, principle stress axis, angle of repose, as a function of systems size, the coefficient of static friction and the frictional interaction with the bottom surface. We compare these results with the predictions of a theory based on continuum equilibrium mechanics...
June 26, 2017: Soft Matter
Matti Gralka, Diana Fusco, Stephen Martis, Oskar Hallatschek
Since penicillin was discovered about 90 years ago, we have become used to using drugs to eradicate unwanted pathogenic cells. However, using drugs to kill bacteria, viruses or cancer cells has the serious side effect of selecting for mutant types that survive the drug attack. A key question therefore is how one could eradicate as many cells as possible for a given acceptable risk of drug resistance evolution. We address this general question in a model of drug resistance evolution in spatial drug gradients, which recent experiments and theories have suggested as key drivers of drug resistance...
June 26, 2017: Physical Biology
Stefano Bellucci, Yuri Shunin, Viktor Gopejenko, Tamara Lobanova-Shunina, Natalya Burlutskaya, Yuri Zhukovskii
Functionalized CNTs and GNRs nanostructures, serving as the basis for the creation of physical pressure and temperature nanosensors, are considered as tools for ecological monitoring and medical applications. Fragments of nanocarbon inclusions with different morphologies, presenting a disordered system, are regarded as models for nanocomposite materials based on carbon nanoсluster suspension in dielectric polymer environments (e.g., epoxy resins). We have formulated the approach of conductivity calculations for carbon-based polymer nanocomposites using the effective media cluster approach, disordered systems theory and conductivity mechanisms analysis, and obtained the calibration dependences...
June 26, 2017: Nanotechnology
Suzanne M O'Regan
Anticipating critical transitions in spatially extended systems is a key topic of interest to ecologists. Gradually declining metapopulations are an important example of a spatially extended biological system that may exhibit a critical transition. Theory for spatially extended systems approaching extinction that accounts for environmental stochasticity and coupling is currently lacking. Here, we develop spatially implicit two-patch models with additive and multiplicative forms of environmental stochasticity that are slowly forced through population collapse, through changing environmental conditions...
June 25, 2017: Journal of Biological Dynamics
Yuta Saito, Kotaro Makino, Paul Fons, Alexander V Kolobov, Junji Tominaga
The bulk band structures of a variety of artificially constructed van der Waals chalcogenide heterostructures IVTe/V2VI3 (IV: C, Si, Ge, Sn, Pb; V: As, Sb, Bi; VI: S, Se, Te) have been systematically examined using ab initio simulations based on density functional theory. The crystal structure and the electronic band structure of the heterostructures were found to strongly depend on the choice of elements as well as the presence of van der Waals corrections. Furthermore, it was found that the use of the modified Becke-Johnson local density approximation functional demonstrated that a Dirac cone is formed when tensile stress is applied to a GeTe/Sb2Te3 heterostructure and the band gap can be controlled by tuning the stress...
June 26, 2017: ACS Applied Materials & Interfaces
Micah B Goldwater
This paper argues that grammatical constructions, specifically argument structure constructions that determine the "who did what to whom" part of sentence meaning and how this meaning is expressed syntactically, can be considered a kind of relational category. That is, grammatical constructions are represented as the abstraction of the syntactic and semantic relations of the exemplar utterances that are expressed in that construction, and it enables the generation of novel exemplars. To support this argument, I review evidence that there are parallel behavioral patterns between how children learn relational categories generally and how they learn grammatical constructions specifically...
June 26, 2017: Topics in Cognitive Science
Gregory L Mutumi, David S Jacobs, Henning Winker
Natural selection and drift can act on populations individually, simultaneously or in tandem and our understanding of phenotypic divergence depends on our ability to recognize the contribution of each. According to the quantitative theory of evolution, if an organism has diversified through neutral evolutionary processes (mutation and drift), variation of phenotypic characteristics between different geographic localities (B) should be directly proportional to the variation within localities (W), that is, B ∝ W...
June 2017: Ecology and Evolution
Edwin Pos, Juan Ernesto Guevara Andino, Daniel Sabatier, Jean-François Molino, Nigel Pitman, Hugo Mogollón, David Neill, Carlos Cerón, Gonzalo Rivas-Torres, Anthony Di Fiore, Raquel Thomas, Milton Tirado, Kenneth R Young, Ophelia Wang, Rodrigo Sierra, Roosevelt García-Villacorta, Roderick Zagt, Walter Palacios Cuenca, Milton Aulestia, Hans Ter Steege
With many sophisticated methods available for estimating migration, ecologists face the difficult decision of choosing for their specific line of work. Here we test and compare several methods, performing sanity and robustness tests, applying to large-scale data and discussing the results and interpretation. Five methods were selected to compare for their ability to estimate migration from spatially implicit and semi-explicit simulations based on three large-scale field datasets from South America (Guyana, Suriname, French Guiana and Ecuador)...
June 2017: Ecology and Evolution
Theoni Photopoulou, Ines M Ferreira, Peter B Best, Toshio Kasuya, Helene Marsh
BACKGROUND: A substantial period of life after reproduction ends, known as postreproductive lifespan (PRLS), is at odds with classical life history theory and its causes and mechanisms have puzzled evolutionary biologists for decades. Prolonged PRLS has been confirmed in only two non-human mammals, both odontocete cetaceans in the family Delphinidae. We investigate the evidence for PRLS in a third species, the false killer whale, Pseudorca crassidens, using a quantitative measure of PRLS and morphological evidence from reproductive tissues...
2017: Frontiers in Zoology
Ali O Altun, Tiziana Bond, Wouter Pronk, Hyung Gyu Park
Surface adsorption plays a critical role in a wide variety of fields from surface catalysis to molecular separation. Despite the importance, limited access to a simultaneously sensitive and selective detection mechanisms has hampered the acquisition of comprehensive and versatile experimental data needed to understand the complex aspects of mixture adsorption, calling for a molecular detection method capable of obtaining the surface adsorption isotherms over a wide range of concentrations as well as distinguishing the competitive adsorption of different adsorbates...
June 25, 2017: Langmuir: the ACS Journal of Surfaces and Colloids
Xin Ye, Dongyuan Chu, Yaoyin Lou, Zhi-Long Ye, Ming Kuang Wang, Shaohua Chen
Phosphorus recovery in the form of struvite has been aroused in recent decades for its dual advantages in eutrophication control and resource protection. The usage of the struvite products is normally determined by the size which is largely depended on the hydrodynamics. In this study, flow behavior of struvite pellets was simulated by means of Eulerian-Eulerian two-fluid model combining with kinetic theory of granular flow in a liquid-solid fluidized bed reactor (FBR). A parametric study including the mesh size, time step, discretization strategy, turbulent model and drag model was first developed, followed by the evaluations of crucial operational conditions, particle characteristics and reactor shapes...
July 2017: Journal of Environmental Sciences (China)
Javier Monroy, Victor Hernandez-Bennets, Han Fan, Achim Lilienthal, Javier Gonzalez-Jimenez
This work presents a simulation framework developed under the widely used Robot Operating System (ROS) to enable the validation of robotics systems and gas sensing algorithms under realistic environments. The framework is rooted in the principles of computational fluid dynamics and filament dispersion theory, modeling wind flow and gas dispersion in 3D real-world scenarios (i.e., accounting for walls, furniture, etc.). Moreover, it integrates the simulation of different environmental sensors, such as metal oxide gas sensors, photo ionization detectors, or anemometers...
June 23, 2017: Sensors
Arthur C Newton, T Anh Nguyen, Sandra J Veen, Daniela J Kraft, Peter Schall, Peter G Bolhuis
Colloidal particles suspended in a binary liquid mixture can interact via solvent mediated interactions, known as critical Casimir forces. For anisotropic colloids this interaction becomes directional, which leads to rich phase behavior. While experimental imaging and particle tracking techniques allow determination of isotropic effective potentials via Boltzmann inversion, the modeling of effective interaction in anisotropic systems is non-trivial precisely because of this directionality. Here we extract effective interaction potentials for non-spherical dumbbell particles from observed radial and angular distributions, by employing reference interaction site model (RISM) theory and direct Monte Carlo simulations...
June 23, 2017: Soft Matter
Rumen Manolov, José L Losada
Observational studies entail making several decisions before data collection, such as the observational design to use, the sampling of sessions within the observational period, the need for time sampling within the observation sessions, as well as the observation recording procedures to use. The focus of the present article is on observational recording procedures different from continuous recording (i.e., momentary time sampling, partial and whole interval recording). The main aim is to develop an online software application, constructed using R and the Shiny package, on the basis of simulations using the alternating renewal process (a model implemented in the ARPobservation package)...
2017: Frontiers in Psychology
Graeme J Ackland, Mihindra Dunuwille, Miguel Martinez-Canales, Ingo Loa, Rong Zhang, Stanislav Sinogeikin, Weizhao Cai, Shanti Deemyad
The crystal structure of elements at zero pressure and temperature is the most fundamental information in condensed matter physics. For decades it has been believed that lithium, the simplest metallic element, has a complicated ground-state crystal structure. Using synchrotron x-ray diffraction in diamond anvil cells and multiscale simulations with density functional theory and molecular dynamics, we show that the previously accepted martensitic ground state is metastable. The actual ground state is face-centered cubic (fcc)...
June 23, 2017: Science
Anja Aarva, Tomi Laurila, Miguel A Caro
In this work, we study the adsorption characteristics of dopamine (DA), ascorbic acid (AA), and dopaminequinone (DAox) on carbonaceous electrodes. Our goal is to obtain a better understanding of the adsorption behavior of these analytes in order to promote the development of new carbon-based electrode materials for sensitive and selective detection of dopamine in vivo. Here we employ density functional theory-based simulations to reach a level of detail that cannot be achieved experimentally. To get a broader understanding of carbonaceous surfaces with different morphological characteristics, we compare three materials: graphene, diamond, and amorphous carbon (a-C)...
June 21, 2017: Journal of Chemical Physics
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