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Theory of simulation

Zhaohui Zhou, Jin Liu, Run Long, Linqiu Li, Liejin Guo, Oleg V Prezhdo
Ultrafast charge recombination in hematite (α-Fe2O3) severely limits its applications in solar energy conversion and utilization, for instance, in photo-electrochemical water splitting. We report the first time-domain ab initio study of charge relaxation dynamics in α-Fe2O3 with and without the oxygen vacancy (Ov) defect, using non-adiabatic molecular dynamics implemented within time-dependent density functional theory. The simulations show that the hole trapping is the rate-limiting step in the electron-hole recombination process for both neutral and ionized Ov systems...
April 26, 2017: Journal of the American Chemical Society
A D Squires, R A Lewis, Adam J Zaczek, Timothy M Korter
Through a combined experimental and theoretical investigation we determine that the fundamental modes of three quinacridones fall in the terahertz spectral range (1-10 THz, ∼30-300 cm(-1)). In each spectrum the terahertz resonances correspond to wagging, rocking, or twisting of the quinacridone rings, with the most intense absorption being an in-plane rocking vibration of the carbonyl oxygens. In spite of these spectral similarities, we demonstrate that terahertz measurements readily differentiate β-quinacridone, γ-quinacridone, and 2,9-dimethylquinacridone...
April 26, 2017: Journal of Physical Chemistry. A
Keiichiro Inagaki, Yutaka Hirata
The vestibulo-ocular reflex (VOR) can be viewed as an adaptive control system that maintains compensatory eye movements during head motion. As the cerebellar flocculus is intimately involved in this adaptive motor control of the VOR, the VOR has been a popular model system for investigating cerebellar motor learning. Long-term depression (LTD) and long-term potentiation (LTP) at the parallel fiber-Purkinje cell synapses are considered to play major roles in cerebellar motor learning. A recent study using mutant mice demonstrated cerebellar motor learning with hampered LTD; the study concluded that the parallel fiber-Purkinje cell LTD is not essential...
April 25, 2017: Cerebellum
Katherine M McKendy, Yusuke Watanabe, Elif Bilgic, Ghada Enani, Amani Munshi, Lawrence Lee, Liane S Feldman, Gerald M Fried, Melina C Vassiliou
BACKGROUND: Time and accuracy are commonly used metrics to assess laparoscopic skills in a simulated environment. However, they do not provide trainees with meaningful information about how to improve their skills. The objective of this study was to provide preliminary validity evidence for the creation a formative feedback tool (FFT) for advanced laparoscopic suturing skills. METHODS: Videotapes of senior surgical residents (PGY3-5; SRs) and minimally invasive surgeons (MIS) performing 3 advanced laparoscopic suturing tasks were analyzed: needle handling (NH), suturing under tension (UT), and continuous suturing (CS)...
April 25, 2017: Surgical Endoscopy
Scott Morris, Mike Bass, Mirinae Lee, Richard E Neapolitan
Objective: : The Patient Reported Outcomes Measurement Information System (PROMIS) initiative developed an array of patient reported outcome (PRO) measures. To reduce the number of questions administered, PROMIS utilizes unidimensional item response theory and unidimensional computer adaptive testing (UCAT), which means a separate set of questions is administered for each measured trait. Multidimensional item response theory (MIRT) and multidimensional computer adaptive testing (MCAT) simultaneously assess correlated traits...
March 11, 2017: Journal of the American Medical Informatics Association: JAMIA
Masoud Darvish Ganji, Razieh Dodangeh
Membranes have attracted much attention for the efficient separation of gas mixtures, due to their specific structural and unique properties. In this work, density functional theory (DFT) and molecular dynamic (MD) simulations have been employed to evaluate the performance of nanoporous hexagonal boron nitride (h-BN) monolayers for hydrogen purification. Various porous membranes were designed, and full structural relaxation was carried out by using DFT calculations and then MD simulations to investigate the H2 purification performance of the nanoporous h-BN membranes...
April 26, 2017: Physical Chemistry Chemical Physics: PCCP
Alberto Roldan, Nora H de Leeuw
The interaction of water with catalyst surfaces is a common process which requires investigation. Here, we have employed density functional theory calculations to investigate the adsorption of up to ten water molecules on the {001} surface of greigite (Fe3S4), which owing to its redox properties, is of increasing interest as a catalyst, e.g. in electro-catalysis. We have systematically analyzed and characterized the modes of water adsorption on the surface, where we have considered both molecular and dissociative adsorption processes...
April 26, 2017: Physical Chemistry Chemical Physics: PCCP
Elise F D Sabattié, Jos Tasche, Mark R Wilson, Maximilian W A Skoda, Arwel Hughes, Torsten Lindner, Richard L Thompson
Compatibility between oligomers and polymers was systematically assessed using differential scanning calorimetry (DSC) and was correlated with similarity in saturation and solubility parameter. These measurements enabled validation of detailed volume of mixing calculations using Statistical Association Fluid Theory (SAFT-γ Mie) and molecular dynamics (MD) simulations, which can be used to predict behaviour beyond the experimentally accessible conditions. These simulations confirmed that squalane is somewhat more compatible with poly(isoprene), "PI" than poly(butadiene), "PB", and further enabled prediction of the temperature dependence of compatibility...
April 26, 2017: Soft Matter
Yanzhen Gan, Ling Yue, Xugeng Guo, Chaoyuan Zhu, Zexing Cao
An on-the-fly trajectory surface hopping dynamic simulation has been performed for revealing the multi-state nonadiabatic deactivation mechanism of coumarin. The mechanism involves three adiabatic excited states, S3(ππ*Lb), S2(nπ*, ππ*La) and S1(ππ*La, nπ*), and the ground state S0 at the four state-averaged complete active space self-consistent field, SA4-CASSCF(12,10)/6-31G* level of theory. Upon photoexcitation to the third excited state S3(ππ*Lb) in the Franck-Condon region, 80% sampling trajectories decay to the dark S2(nπ*) state within an average of 5 fs via the conical intersection S3(ππ*Lb)/S2(nπ*), while 20% decay to the S2(ππ*La) state within an average of 11 fs via the conical intersection S3(ππ*Lb)/S2(ππ*La)...
April 26, 2017: Physical Chemistry Chemical Physics: PCCP
Salman S Seyedi, Morteza M M Waskasi, Dmitry V Matyushov
Extensive simulations of cytochrome c in solution are performed to address the apparent contradiction between large reorganization energies of protein electron transfer typically reported by atomistic simulations and much smaller values produced by protein electrochemistry. The two sets of data are reconciled by deriving the activation barrier for electrochemical reaction in terms of an effective reorganization energy composed of half the Stokes shift (characterizing the medium polarization in response to electron transfer) and the variance reorganization energy (characterizing the breadth of electrostatic fluctuations)...
April 26, 2017: Journal of Physical Chemistry. B
Magdalena Perchacz, Ricardo Keitel Donato, Leandro Seixas, Alexander Zhigunov, Rafal Konefal, Magdalena Serkis-Rodzeń, Hynek Benes
This work describes the solvent-free sol-gel synthesis of epoxy-functionalized silica-based precursors, in the presence of 1-butyl-3-methylimidazolium-based ionic liquids (ILs) containing different anions - chloride (Cl(-)) and methanesulfonate (MeSO3(-)). The IL-driven sol-gel mechanisms were investigated in details using experimental characterizations ((29)Si NMR and ATR FTIR spectroscopy) and a theoretical computational method based on density functional theory (DFT). We observed a complex IL's influence on both hydrolysis and condensation steps, involving especially H-bonding and Coulomb coupling stabilization of the process intermediates...
April 26, 2017: ACS Applied Materials & Interfaces
N V Brilliantov, Yu A Budkov, C Seidel
We analyze, theoretically and by means of molecular dynamics (MD) simulations, the generation of mechanical force by a polyelectrolyte (PE) chain grafted to a plane and exposed to an external electric field; the free end of the chain is linked to a deformable target body. Varying the field, one can alter the length of the non-adsorbed (bulk) part of the chain and hence the deformation of the target body and the arising force. We focus on the impact of added salt on the magnitude of the generated force, which is especially important for applications...
April 25, 2017: Faraday Discussions
Jinfeng Liu, Xiao He, John Z H Zhang
The nature of the dynamical hydrogen-bond network of liquid water under ambient conditions has challenged both experimental and theoretical researchers for decades and remains a topic of intense debate. In this work, we addressed the structural issue of the hydrogen-bond network of liquid water based on an accurate ab initio molecular dynamics simulation. The present work showed clearly that liquid water is neither accurately described by a static picture of mostly tetrahedral water molecules nor dominated by "ring-and-chain" like structures...
April 25, 2017: Physical Chemistry Chemical Physics: PCCP
James M Goodman, Sliman J Bensmaia
For decades, the dominant theory of roughness coding in the somatosensory nerves posited that perceived roughness was determined by the spatial pattern of activation in one population of tactile nerve fibers, namely slowly adapting type 1 (SA1) afferents. Indeed, the perceived roughness of coarsely textured surfaces tracks the spatial variation in SA1 responses - the degree to which response strength varies across SA1 afferents. However, in a later study, the roughness of a different set of dot patterns was found to be a monotonic function of dot spacing, a result interpreted as evidence that roughness was determined by the strength of SA1 responses - the population firing rate - rather than their spatial layout...
April 25, 2017: Scientific Reports
Jauwairia Nasir, Yong-Ho Yoo, Deok-Hwa Kim, Jong-Hwan Kim
Memory modeling has been a popular topic of research for improving the performance of autonomous agents in cognition related problems. Apart from learning distinct experiences correctly, significant or recurring experiences are expected to be learned better and be retrieved easier. In order to achieve this objective, this paper proposes a user preference-based dual-memory adaptive resonance theory network model, which makes use of a user preference to encode memories with various strengths and to learn and forget at various rates...
April 24, 2017: IEEE Transactions on Neural Networks and Learning Systems
Jacob Herrmann, Eric A Hoffman, David W Kaczka
We seek to use computed tomography (CT) to characterize regional lung parenchymal deformation during highfrequency and multi-frequency oscillatory ventilation. Periodic motion of thoracic structures results in artifacts of CT images obtained by standard reconstruction algorithms, especially for frequencies exceeding that of the X-ray source rotation. In this study, we propose an acquisition and reconstruction technique for high resolution imaging of the thorax during periodic motion. Our technique relies on phase-binning projections according to the frequency of subject motion relative to the scanner rotation, prior to volumetric reconstruction...
April 18, 2017: IEEE Transactions on Medical Imaging
Vincent Pohl, Gunter Hermann, Jean Christophe Tremblay
The aim of the present contribution is to provide a framework for analyzing and visualizing the correlated many-electron dynamics of molecular systems, where an explicitly time-dependent electronic wave packet is represented as a linear combination of N-electron wave functions. The central quantity of interest is the electronic flux density, which contains all information about the transient electronic density, the associated phase, and their temporal evolution. It is computed from the associated one-electron operator by reducing the multideterminantal, many-electron wave packet using the Slater-Condon rules...
April 24, 2017: Journal of Computational Chemistry
Asif Rahman, Belen Lafon, Lucas C Parra, Marom Bikson
KEY POINTS: Direct current stimulation (DCS) polarity specifically modulates synaptic efficacy during a continuous train of presynaptic inputs, despite synaptic depression. DCS polarizes afferent axons and postsynaptic neurons, boosting cooperativity between synaptic inputs. Polarization of afferent neurons in upstream brain regions may modulate activity in the target brain region during transcranial DCS (tDCS). A statistical theory of coincident activity predicts that the diffuse and weak profile of current flow can be advantageous in enhancing connectivity between co-active brain regions...
April 23, 2017: Journal of Physiology
Udo Schnupf, John W Brady
Many important biological solutes possess not only polar and hydrogen bonding functionalities, but also weakly-hydrating, or hydrophobic, surfaces. Theories of the hydration of such surfaces predict that their solvent interactions will change from a wetting type interaction to a dewetting regime as a function of the solute size, with a gradual transition in behavior taking place around characteristic lengths of ∼1 nm. Aggregations of non-polar species over this size range will undergo a transition from being dominated by entropy to being dominated by enthalpy...
April 24, 2017: Physical Chemistry Chemical Physics: PCCP
Kohei Shimamura, Fuyuki Shimojo, Aiichiro Nakano, Shigenori Tanaka
A recent series of shock experiments by Nakazawa et al. starting in 2005 (e.g. [Nakazawa et al., Earth Planet. Sci. Lett., 2005, 235, 356]) suggested that meteorite impacts on ancient oceans would have yielded a considerable amount of NH3 to the early Earth from atmospheric N2 and oceanic H2O through reduction by meteoritic iron. To clarify the mechanisms, we imitated the impact events by performing multi-scale shock technique-based ab initio molecular dynamics in the framework of density functional theory in combination with multi-scale shock technique (MSST) simulations...
April 24, 2017: Physical Chemistry Chemical Physics: PCCP
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