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Theory of simulation

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https://www.readbyqxmd.com/read/28334943/effects-of-prefrontal-cortex-damage-on-emotion-understanding-eeg-and-behavioural-evidence
#1
Anat Perry, Samantha N Saunders, Jennifer Stiso, Callum Dewar, Jamie Lubell, Torstein R Meling, Anne-Kristin Solbakk, Tor Endestad, Robert T Knight
Humans are highly social beings that interact with each other on a daily basis. In these complex interactions, we get along by being able to identify others' actions and infer their intentions, thoughts and feelings. One of the major theories accounting for this critical ability assumes that the understanding of social signals is based on a primordial tendency to simulate observed actions by activating a mirror neuron system. If mirror neuron regions are important for action and emotion recognition, damage to regions in this network should lead to deficits in these domains...
February 22, 2017: Brain: a Journal of Neurology
https://www.readbyqxmd.com/read/28334369/isotropic-failure-criteria-are-not-appropriate-for-anisotropic-fibrous-biological-tissues
#2
Christopher E Korenczuk, Lauren E Votava, Rohit Y Dhume, Shannen B Kizilski, George E Brown, Rahul Narain, Victor H Barocas
The von Mises (VM) stress is a common stress measure for finite-element models of tissue mechanics. The VM failure criterion, however, is inherently isotropic, and therefore may yield incorrect results for anisotropic tissues, and the relevance of the VM stress to anisotropic materials is not clear. We explored the application of a well-studied anisotropic failure criterion, the Tsai-Hill (TH) theory, to the mechanically anisotropic porcine aorta. Uniaxial dogbones were cut at different angles and stretched to failure...
March 23, 2017: Journal of Biomechanical Engineering
https://www.readbyqxmd.com/read/28333960/effect-of-the-dilution-rate-on-microbial-competition-r-strategist-can-win-over-k-strategist-at-low-substrate-concentration
#3
Mari-K H Winkler, Pieter Boets, Birk Hahne, Peter Goethals, Eveline I P Volcke
The conditions present in both in vitro and in vivo ecosystems determine the microbial population harbouring it. One commonly accepted theory is that a species with a high substrate affinity and low growth rate (k-strategist) will win the competition against a second species with a lower substrate affinity and higher growth rate (r-strategist) if both species are subjected to low substrate concentrations. In this study two nitrite oxidizing bacteria (NOB), Nitrospira defluvii (k-strategist) and Nitrobacter vulgaris (r-strategist), were cultivated in a continuous reactor systems...
2017: PloS One
https://www.readbyqxmd.com/read/28333686/abnormal-nonlocal-scale-effect-on-the-static-bending-of-single-layer-mos2
#4
Ming-Lin Li, Haili Huang, Liping Tu, Weidong Wang, Peifeng Li, Yang Lu
The nonlocal scale parameter of the nonlocal Euler-Bernoulli beam theory is evaluated for the static bending of single layer molybdenum disulfide (SLMoS2) without the predetermined bending rigidity. The evaluation activity is performed by matching the fitted curve between the maximum deflection and the beam length obtained from molecular mechanics simulations. It was observed that the fitted curves have an abnormal sign in the second order term of the maximum deflection for SLMoS2, opposite to that for graphene and regardless of the used interatomic interaction potentials...
March 23, 2017: Nanotechnology
https://www.readbyqxmd.com/read/28330988/cell-size-distribution-in-epithelial-tissue-formation-and-homeostasis
#5
Alberto Puliafito, Luca Primo, Antonio Celani
How cell growth and proliferation are orchestrated in living tissues to achieve a given biological function is a central problem in biology. During development, tissue regeneration and homeostasis, cell proliferation must be coordinated by spatial cues in order for cells to attain the correct size and shape. Biological tissues also feature a notable homogeneity of cell size, which, in specific cases, represents a physiological need. Here, we study the temporal evolution of the cell-size distribution by applying the theory of kinetic fragmentation to tissue development and homeostasis...
March 2017: Journal of the Royal Society, Interface
https://www.readbyqxmd.com/read/28330614/a-predictive-3d-multi-scale-model-of-biliary-fluid-dynamics-in-the-liver-lobule
#6
Kirstin Meyer, Oleksandr Ostrenko, Georgios Bourantas, Hernan Morales-Navarrete, Natalie Porat-Shliom, Fabian Segovia-Miranda, Hidenori Nonaka, Ali Ghaemi, Jean-Marc Verbavatz, Lutz Brusch, Ivo Sbalzarini, Yannis Kalaidzidis, Roberto Weigert, Marino Zerial
Bile, the central metabolic product of the liver, is transported by the bile canaliculi network. The impairment of bile flow in cholestatic liver diseases has urged a demand for insights into its regulation. Here, we developed a predictive 3D multi-scale model that simulates fluid dynamic properties successively from the subcellular to the tissue level. The model integrates the structure of the bile canalicular network in the mouse liver lobule, as determined by high-resolution confocal and serial block-face scanning electron microscopy, with measurements of bile transport by intravital microscopy...
March 15, 2017: Cell Systems
https://www.readbyqxmd.com/read/28330413/molecular-dynamic-simulation-and-dft-study-on-the-drug-dna-interaction-crocetin-as-an-anticancer-and-dna-nanostructure-model
#7
Ebrahim Azarhazin, Mohammad Izadyar, Mohammad Reza Housaindokht
In this research, the interaction of Crocetin as an anticancer drug and a Dickerson DNA has been investigated. 25 ns molecular dynamic simulations of Crocetin and DNA composed of twelve base pairs and a sequence of d(CGCGAATTCGCG)2 were done in water. Three definite parts of the B-DNA were considered in analyzing the best interactive site from the thermodynamic point of view. Binding energy analysis showed that van der Waals interaction is the most important part related to the reciprocal O and H atoms of the Crocetin and DNA...
March 22, 2017: Journal of Biomolecular Structure & Dynamics
https://www.readbyqxmd.com/read/28330348/learning-molecular-energies-using-localized-graph-kernels
#8
Grégoire Ferré, Terry Haut, Kipton Barros
Recent machine learning methods make it possible to model potential energy of atomic configurations with chemical-level accuracy (as calculated from ab initio calculations) and at speeds suitable for molecular dynamics simulation. Best performance is achieved when the known physical constraints are encoded in the machine learning models. For example, the atomic energy is invariant under global translations and rotations; it is also invariant to permutations of same-species atoms. Although simple to state, these symmetries are complicated to encode into machine learning algorithms...
March 21, 2017: Journal of Chemical Physics
https://www.readbyqxmd.com/read/28330344/short-time-dynamics-and-decay-mechanism-of-2-1h-pyridinone-upon-excitation-to-the-light-absorbing-s4-2-1
#9
Teng-Shuo Zhang, Jia-Dan Xue, Xuming Zheng, Bin-Bin Xie, Wei-Hai Fang
The excited-state structural dynamics and the decay mechanism of 2(1H)-pyridinone (NHP) after excitation to the S4(2(1)ππ(*)) light-absorbing state were studied using resonance Raman spectroscopy and complete-active space self-consistent field (CASSCF) calculations. The B-band absorption cross-section and the corresponding absolute resonance Raman cross-sections were simulated using a simple model based on time-dependent wave-packet theory. The geometric structures of the singlet electronic excited states and their curve-crossing points were optimized at the CASSCF level of theory...
March 21, 2017: Journal of Chemical Physics
https://www.readbyqxmd.com/read/28328211/the-water-solvent-effect-on-theoretical-evaluation-of-1h-nmr-chemical-shifts-the-o-methyl-inositol-isomer
#10
Helio F Dos Santos, Marcelo Chagas, Leonardo De Souza, Willian Rocha, Mauro V De Almeida, Cleber P A Anconi, Wagner Batista De Almeida
In this paper, density functional theory calculations of nuclear magnetic resonance (NMR) chemical shifts for L-quebrachitol isomer, previously studied in our group (Mag. Res. Chem. 50 (2012) 608-614) are reported aiming to investigate in more details the water solvent effect on the prediction of 1H NMR spectra. In order to include explicit water molecules, twenty water-L-quebrachitol configurations obtained from Monte Carlo simulation were selected to perform geometry optimizations using the effective fragment potential method encompassing 60 water molecules around the solute...
March 22, 2017: Journal of Physical Chemistry. A
https://www.readbyqxmd.com/read/28327747/thermally-induced-breakup-of-metallic-nanowires-experiment-and-theory
#11
Martin Schnedlitz, Maximilian Lasserus, Daniel Knez, Andreas W Hauser, Ferdinand Hofer, Wolfgang E Ernst
We present time-resolved transmission electron microscopy studies of the degradation of Au, Ag, Cu and Ni nanowires deposited on a heated support. The wires are grown under fully inert conditions in superfluid helium droplets and deposited onto amorphous carbon. The inherent stability of these pristine metal nanowires with diameters below 10 nm is investigated in the absence of any stabilizers, templates or solvents. The phenomenon of Rayleigh-breakup, a consequence of diffusion processes along the wire surfaces, is analysed in situ via scans over time and support temperature...
March 22, 2017: Physical Chemistry Chemical Physics: PCCP
https://www.readbyqxmd.com/read/28327740/molecular-dynamics-simulations-elucidate-conformational-selection-and-induced-fit-mechanisms-in-the-binding-of-pd-1-and-pd-l1
#12
Wenping Liu, Bing Huang, Yashu Kuang, Guangjian Liu
Blockage of the interactions between immunologic checkpoint protein PD-1 and its ligand PD-L1 showed efficacy for cancer treatment. X-ray structures have captured static conformational snapshots of PD-1 and revealed that the CC' loop adopts an open conformation in the apo-protein but turns into a closed form and interacts with PD-L1 in the complex. This structural heterogeneity brings difficulties for structure-based drug discovery targeting PD-1. To gain insights into the role of the CC' loop in molecular recognition, we have undertaken a comparative study between the open and closed conformations in apo-PD-1 and the PD-1/PD-L1 complex using molecular dynamics simulations...
March 22, 2017: Molecular BioSystems
https://www.readbyqxmd.com/read/28327454/collective-variables-for-the-study-of-long-time-kinetics-from-molecular-trajectories-theory-and-methods
#13
REVIEW
Frank Noé, Cecilia Clementi
Collective variables are an important concept to study high-dimensional dynamical systems, such as molecular dynamics of macromolecules, liquids, or polymers, in particular to define relevant metastable states and state-transition or phase-transition. Over the past decade, a rigorous mathematical theory has been formulated to define optimal collective variables to characterize slow dynamical processes. Here we review recent developments, including a variational principle to find optimal approximations to slow collective variables from simulation data, and algorithms such as the time-lagged independent component analysis...
March 16, 2017: Current Opinion in Structural Biology
https://www.readbyqxmd.com/read/28326788/copolymerization-on-selective-substrates-experimental-test-and-computer-simulations
#14
Elena Yu Kozhunova, Alexey A Gavrilov, Mikhail Yur'Evich Zaremski, Alexander V Chertovich
We explore the influence of a selective substrate on the composition and sequence statistics during the free radical copolymerization. In particular, we study the radical copolymerization of styrene and acrylic acid in bulk and in silica pores of different sizes. We show that the substrate affects both polymer composition and sequence statistics. We use dissipative particle dynamics simulations to study the polymerization process in detail, trying to pinpoint the parameters responsible for the observed differences in the polymer chain composition and sequences...
March 22, 2017: Langmuir: the ACS Journal of Surfaces and Colloids
https://www.readbyqxmd.com/read/28326032/a-dynamic-circuit-hypothesis-for-the-pathogenesis-of-blepharospasm
#15
David A Peterson, Terrence J Sejnowski
Blepharospasm (sometimes called "benign essential blepharospasm," BEB) is one of the most common focal dystonias. It involves involuntary eyelid spasms, eye closure, and increased blinking. Despite the success of botulinum toxin injections and, in some cases, pharmacologic or surgical interventions, BEB treatments are not completely efficacious and only symptomatic. We could develop principled strategies for preventing and reversing the disease if we knew the pathogenesis of primary BEB. The objective of this study was to develop a conceptual framework and dynamic circuit hypothesis for the pathogenesis of BEB...
2017: Frontiers in Computational Neuroscience
https://www.readbyqxmd.com/read/28325911/theoretical-and-computational-validation-of-the-kuhn-barrier-friction-mechanism-in-unfolded-proteins
#16
Stanislav M Avdoshenko, Atanu Das, Rohit Satija, Garegin A Papoian, Dmitrii E Makarov
A long time ago, Kuhn predicted that long polymers should approach a limit where their global motion is controlled by solvent friction alone, with ruggedness of their energy landscapes having no consequences for their dynamics. In contrast, internal friction effects are important for polymers of modest length. Internal friction in proteins, in particular, affects how fast they fold or find their binding targets and, as such, has attracted much recent attention. Here we explore the molecular origins of internal friction in unfolded proteins using atomistic simulations, coarse-grained models and analytic theory...
March 21, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28325167/virtual-reality-in-the-assessment-understanding-and-treatment-of-mental-health-disorders
#17
D Freeman, S Reeve, A Robinson, A Ehlers, D Clark, B Spanlang, M Slater
Mental health problems are inseparable from the environment. With virtual reality (VR), computer-generated interactive environments, individuals can repeatedly experience their problematic situations and be taught, via evidence-based psychological treatments, how to overcome difficulties. VR is moving out of specialist laboratories. Our central aim was to describe the potential of VR in mental health, including a consideration of the first 20 years of applications. A systematic review of empirical studies was conducted...
March 22, 2017: Psychological Medicine
https://www.readbyqxmd.com/read/28325048/photoinduced-single-and-multiple-electron-dynamics-processes-enhanced-by-quantum-confinement-in-lead-halide-perovskite-quantum-dots
#18
Dayton Jon Vogel, Andrei Kryjevski, Talgat M Inerbaev, Dmitri S Kilin
Methyl-ammonium lead iodide perovskite (MAPbI3) is a promising material for photovoltaic devices. A modification of the MAPbI3 into confined nanostructures is expected to further increase efficiency of solar energy conversion. Photo-excited dynamic processes in a MAPbI3 quantum dot (QD) have been modeled by many-body perturbation theory and nonadiabatic dynamics. A photoexcitation is followed by either exciton cooling (EC), its radiative (RR) or non-radiative recombination (NRR), or multi-exciton generation (MEG) processes...
March 21, 2017: Journal of Physical Chemistry Letters
https://www.readbyqxmd.com/read/28325043/a-molecular-level-insight-of-the-effect-of-hofmeister-anions-on-the-interfacial-surface-tension-of-a-model-protein
#19
Soohaeng Yoo Willow, Sotiris S Xantheas
The effect of the Hofmeister anions on the precipitation of proteins is often discussed using liquid-vapor coexisting systems with the assumption that the liquid-vapor interface mimics the liquid-protein interface. Solvated proteins, however, have both hydrophobic and hydrophilic regions on their surfaces rather than just a pure hydrophobic one. Using a solvated parallel β-sheet layer consisting of both hydrophobic and positively charged hydrophilic surfaces, we investigated the adsorption of kosmotropic (SO4(2-)) and chaotropic (ClO4(-)) anions towards protein's hydrophobic and hydrophilic surfaces via Born-Oppenheimer molecular dynamics simulations using the BLYP density functional theory...
March 21, 2017: Journal of Physical Chemistry Letters
https://www.readbyqxmd.com/read/28324690/e-coli-interactions-adhesion-and-transport-in-alumino-silica-clays
#20
Houzhen Wei, Guang Yang, Boya Wang, Runwei Li, Gang Chen, Zhenze Li
Bacterial adhesion and transport in the geological formation are controlled by their mutual complex interactions, which have been quantified by the traditional and extended Derjaguin-Landau-Verwey-Overbeek (DLVO) theory as well as direct atomic force microscopy (AFM) measurements. In this research, the DLVO forces calculated based on the independently determined bacterial and porous media surface thermodynamic properties were compared with those of AFM measurements. Although differences in the order of several magnitudes existed, forces obtained from both ways could explain the observations of E...
March 8, 2017: Colloids and Surfaces. B, Biointerfaces
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