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# Theory of simulation

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#1
Michael Fischer
Zeolites and structurally related materials (zeotypes) have received considerable attention as potential adsorbents for selective carbon dioxide adsorption. Within this group, zeotypes with aluminophosphate composition (AlPOs) could be an interesting alternative to the more frequently studied aluminosilicate zeolites. So far, however, only a few AlPOs have been characterised experimentally in terms of their CO2 adsorption properties. In this study, force-field based grand-canonical Monte Carlo (GCMC) simulations were used to evaluate the potential of AlPOs for CO2/N2 separation, a binary mixture that constitutes a suitable model system for the removal of carbon dioxide from flue gases...
August 16, 2017: Physical Chemistry Chemical Physics: PCCP
#2
Xing-Feng Zhu, Qi Wei, Ying Cheng, Da-Jian Wu, Xiao-Jun Liu
A rapidly modulated stratified medium with a large mass density modulation depth (LMMD) is proposed to achieve non-diffraction propagation (NDP) of acoustic waves. It is found that the NDP in LMMD medium is independent of the incident angle and can be operated in a broad-band manner. Such an NDP is robust and is unhampered by medium losses. An effective medium theory (EMT) is developed for acoustic waves propagating in the LMMD medium based on the first-principles method. The LMMD EMT is verified by using the transfer-matrix method (TMM) for both propagating and evanescent waves...
August 15, 2017: Scientific Reports
#3
Xiao-Dan Tang
By Means of Marcus electron transfer theory, the charge transport properties of tetraazapentacene (4N-PEN) derivatives were systematically explored. The reorganization energies were studied by both adiabatic potential-energy surfaces and normal mode analysis. The charge diffusion constants were evaluated from the random walk simulation. From the perspective of homology modeling, a selected 4N-PEN derivative without experimental crystal structure was built into three kinds of possible packing modes with reference to its relative analogues and then fully optimized...
June 23, 2017: Journal of Molecular Graphics & Modelling
#4
Thomas P Fay, Alan M Lewis, David E Manolopoulos
We have used an efficient new quantum mechanical method for radical pair recombination reactions to study the spin-dependent charge recombination along PTZ(•+)-Phn-PDI(•-) molecular wires. By comparing our results with the experimental data of Weiss et al. [J. Am. Chem. Soc. 126, 5577 (2004)], we are able to extract the spin-dependent (singlet and triplet) charge recombination rate constants for wires with n = 2-5. These spin-dependent rate constants have not been extracted previously from the experimental data because they require fitting its magnetic field-dependence to the results of quantum spin dynamics simulations...
August 14, 2017: Journal of Chemical Physics
#5
Yen-Ching Ho, Yi-Siang Wang, Sheng D Chao
Modeling fluid cycloalkanes with molecular dynamics simulations has proven to be a very challenging task partly because of lacking a reliable force field based on quantum chemistry calculations. In this paper, we construct an ab initio force field for fluid cyclopropane using the second-order Møller-Plesset perturbation theory. We consider 15 conformers of the cyclopropane dimer for the orientation sampling. Single-point energies at important geometries are calibrated by the coupled cluster with single, double, and perturbative triple excitation method...
August 14, 2017: Journal of Chemical Physics
#6
Kyle S Gustafson, Guoxi Xu, Karl F Freed, Jian Qin
The multiple-scattering theory for the electrostatics of many-body systems of monopolar spherical particles, embedded in a dielectric medium, is generalized to describe the electrostatics of these particles with embedded dipoles and multipoles. The Neumann image line construction for the electrostatic polarization produced by one particle is generalized to compute the energy, forces, and torques for the many-body system as functions of the positions of the particles. The approach is validated by comparison with direct numerical calculation, and the convergence rate is analyzed and expressed in terms of the discontinuity in dielectric contrast and particle density...
August 14, 2017: Journal of Chemical Physics
#7
Can Wang, Dongmei Niu, Haipeng Xie, Baoxing Liu, Shitan Wang, Menglong Zhu, Yongli Gao
The electronic structure at the organic-inorganic semiconductor interface of π-conjugated copper phthalocyanine (CuPc) on a black phosphorus (BP) crystal surface is studied with photoemission spectroscopy and density functional theory calculations. From the photoemission spectra, we observe a shift of about 0.7 eV for the highest occupied molecular orbital, which originates from the transition of phase in the organic molecular thin film (from the interface phase to the bulk phase). On the other hand, we find 0...
August 14, 2017: Journal of Chemical Physics
#8
Hsiu-Yu Yu, Zahera Jabeen, David M Eckmann, Portonovo S Ayyaswamy, Ravi Radhakrishnan
We have studied the microstructure of a flow-driven hardsphere suspension inside a cylinder using dynamical density functional theory and Monte Carlo simulations. In order to be representative of various physical conditions that may prevail in experiments, we investigate the problem using both the grand canonical ($\mu VT$) ensemble and the canonical ($NVT$) ensemble. In both ensembles, the hydrodynamic effect on the suspension mediated by the presence of the confining wall is implemented in a mean-field fashion by incorporating the thermodynamic work done by the inertial lift force on the particle given the average flow field...
August 15, 2017: Langmuir: the ACS Journal of Surfaces and Colloids
#9
Matthias Wohlgemuth, Mitsuhiko Miyazaki, Kohei Tsukada, Martin Weiler, Otto Dopfer, Masaaki Fujii, Roland Mitrić
Most proteins work in aqueous solution and the interaction with water strongly affects their structure and function. However, experimentally the motion of a specific single water molecule is difficult to trace by conventional methods, because they average over the heterogeneous solvation structure of bulk water surrounding the protein. Here, we provide a detailed atomistic picture of the water rearrangement dynamics around the -CONH- peptide linkage in the two model systems formanilide and acetanilide, which simply differ by the presence of a methyl group at the peptide linkage...
August 15, 2017: Physical Chemistry Chemical Physics: PCCP
#10
Manuel Graf, Herbert Looser, Lukas Emmenegger, Béla Tuzson
We present computational and experimental investigations of the beam folding properties and fringe suppression capabilities in monolithic toroidal multipass cells (MPCs) when combined with absorption masks. Coherent field simulations based on the Fresnel-Huygens theory were performed to understand the effect of multiple field truncations in such an optically semi-unstable mirror arrangement. The explicit numerical calculation of the radiation field at each reflection allows detailed optimization and performance analysis...
August 15, 2017: Optics Letters
#11
Richard N Collins, Kevin M Rosso
Molecular-level pathways in the aqueous redox transformation of uranium by iron remain unclear, despite the importance of this knowledge for predicting uranium transport and distribution in natural and engineered environments. As the relative importance of homogeneous versus heterogeneous pathways is difficult to probe experimentally, here we apply computational molecular simulation to isolate rates of key one electron transfer reactions in the homogenous pathway. By comparison to experimental observations the role of the heterogeneous pathway also becomes clear...
August 15, 2017: Journal of Physical Chemistry. A
#12
Yong Dang, Wenyue Guo, Lianming Zhao, Houyu Zhu
Graphdiyne family has attracted a high degree of concern, because of its intriguing and promising properties. However, graphdiyne materials reported to date represent only a tiny fraction of the possible combinations. In this work, we demonstrate a computational approach to generate a series of conceivable graphdiyne-based frameworks (GDY-Rs and Li@GDY-Rs) by introducing a variety of functional groups (R = -NH2, -OH, -COOH, and -F) and doping metal (Li) in the molecular building blocks of graphdiyne without restriction of experimental conditions and rapidly screen the best candidates for the application of CO2 capture and sequestration (CCS)...
August 15, 2017: ACS Applied Materials & Interfaces
#13
Fan Zuo, Priyadarshini Panda, Michele Kotiuga, Jiarui Li, Mingu Kang, Claudio Mazzoli, Hua Zhou, Andi Barbour, Stuart Wilkins, Badri Narayanan, Mathew Cherukara, Zhen Zhang, Subramanian K R S Sankaranarayanan, Riccardo Comin, Karin M Rabe, Kaushik Roy, Shriram Ramanathan
A central characteristic of living beings is the ability to learn from and respond to their environment leading to habit formation and decision making. This behavior, known as habituation, is universal among all forms of life with a central nervous system, and is also observed in single-cell organisms that do not possess a brain. Here, we report the discovery of habituation-based plasticity utilizing a perovskite quantum system by dynamical modulation of electron localization. Microscopic mechanisms and pathways that enable this organismic collective charge-lattice interaction are elucidated by first-principles theory, synchrotron investigations, ab initio molecular dynamics simulations, and in situ environmental breathing studies...
August 14, 2017: Nature Communications
#14
Andrew C Trautz, Tissa H Illangasekare, Ignacio Rodriguez-Iturbe
Plant performance (i.e., fecundity, growth, survival) depends on an individual's access to space and resources. At the community level, plant performance is reflected in observable vegetation patterning (i.e., spacing distance, density) often controlled by limiting resources. Resource availability is, in turn, strongly dependent on plant patterning mediated by competitive and facilitative plant-plant interactions. Co-occurring competition and facilitation has never been specifically investigated from a hydrodynamic perspective...
August 14, 2017: Proceedings of the National Academy of Sciences of the United States of America
#15
Jennifer M Macleod, Josh Lipton-Duffin, Chaoying Fu, Tyler Taerum, Dmitrii F Perepichka, Federico Rosei
Two-dimensional (2D) molecular self-assembly allows for the formation of well-defined supramolecular layers with tailored geometrical, compositional and chemical properties. To date, random intermixing and entropic effects in these systems have largely been associated with crystalline disorder and glassy phases. Here we describe a 2D crystalline self-assembled molecular system that exhibits random incorporation of substitutional molecules. The lattice is formed from a mixture of trimesic acid (TMA) and terthienobenzenetricarboxylic acid (TTBTA), C3-symmetric hydrogen-bonding units of very different sizes (0...
August 14, 2017: ACS Nano
#16
H A Mulder, H Rashidi
Response to infection in animals has 2 main mechanisms: resistance (ability to control pathogen burden) and tolerance (ability to maintain performance given the pathogen burden). Selection on disease resistance and tolerance to infections seems a promising avenue to increase productivity of animals in the presence of disease infections, but it is hampered by a lack of records of pathogen burden of infected animals. Selection on resilience (ability to maintain performance regardless of pathogen burden) may, therefore, be an alternative pragmatic approach, because it does not need records of pathogen burden...
August 2017: Journal of Animal Science
#17
Ramin Ekhteiari Salmas, Yusuf Serhat Is, Serdar Durdagi, Matthias Stein, Mine Yurtsever
The dopamine D2 Receptor (D2R) is a member of the G-Protein Coupled Receptor (GPCR) family and plays a critical role in neurotransmission activities in the human brain. Dysfunction in dopamine receptor signaling may lead to mental health illnesses such as schizophrenia and Parkinson's disease. D2R is the target protein of the commonly used anti-psychotic drugs such as risperidone, clozapine, aripiprazole, olanzapine, ziprasidone and quetiapine. Due to their significant side effects and nonselective profiles, the discovery of novel drugs has become a challenge for researchers working in this field...
August 14, 2017: Journal of Biomolecular Structure & Dynamics
#18
C A Martínez, K Khare, S Rahman, M A Elzo
Several statistical models used in genome-wide prediction assume uncorrelated marker allele substitution effects, but it is known that these effects may be correlated. In statistics, graphical models have been identified as a useful tool for covariance estimation in high-dimensional problems and it is an area that has recently experienced a great expansion. In Gaussian covariance graph models (GCovGM), the joint distribution of a set of random variables is assumed to be Gaussian and the pattern of zeros of the covariance matrix is encoded in terms of an undirected graph G...
August 13, 2017: Journal of Animal Breeding and Genetics, Zeitschrift Für Tierzüchtung und Züchtungsbiologie
#19
Mark H C Lai, Jiaqi Zhang
In conventional structural equation modeling (SEM), with the presence of even a tiny amount of data contamination due to outliers or influential observations, normal-theory maximum likelihood (ML-Normal) is not efficient and can be severely biased. The multivariate-t-based SEM, which recently got implemented in Mplus as an approach for mixture modeling, represents a robust estimation alternative to downweigh the impact of outliers and influential observations. To our knowledge, the use of maximum likelihood estimation with a multivariate-t model (ML-t) to handle outliers has not been shown in SEM literature...
2017: Frontiers in Psychology
#20
Walter Talamonti, Louis Tijerina, Mike Blommer, Radhakrishnan Swaminathan, Reates Curry, R Darin Ellis
This paper describes a new method, a 'mirage scenario,' to support formative evaluation of driver alerting or warning displays for manual and automated driving. This method provides driving contexts (e.g., various Times-To-Collision (TTCs) to a lead vehicle) briefly presented and then removed. In the present study, during each mirage event, a haptic steering display was evaluated. This haptic display indicated a steering response may be initiated to drive around an obstacle ahead. A motion-base simulator was used in a 32-participant study to present vehicle motion cues similar to the actual application...
November 2017: Applied Ergonomics
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