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Theory of simulation

Quefeng Li, Menggang Yu, Sijian Wang
In the era of big data, integrative analyses that pool data from different sources are now extensively conducted in order to improve performance. Among many interesting applications, genomics research is an area where integrative methods become popular tools to identify prognostic biomarkers for various diseases. In this paper, we propose such a framework for pathway and gene identification. Our method employs a hierarchical decomposition on genes' effects followed by a proper regularization to identify important pathways and genes across multiple studies...
April 2017: Journal of Multivariate Analysis
Xiaoling Wang, Shuo Meng, Jingshi Han
The Bacterial flagellar filament can undergo a polymorphic phase transition in response to both mechanical and chemical variations in vitro and in vivo environments. Under mechanical stimuli, such as viscous flow or forces induced by motor rotation, the filament changes its phase from left-handed normal (N) to right-handed semi-coiled (SC) via phase nucleation and growth. Our detailed mechanical analysis of existing experiments shows that both torque and bending moment contribute to the filament phase transition...
September 14, 2017: Journal of Biomechanics
Samira Mchinda, Gopal Varma, Valentin H Prevost, Arnaud Le Troter, Stanislas Rapacchi, Maxime Guye, Jean Pelletier, Jean-Philippe Ranjeva, David C Alsop, Guillaume Duhamel, Olivier M Girard
PURPOSE: To implement, characterize, and optimize an interleaved inhomogeneous magnetization transfer (ihMT) gradient echo sequence allowing for whole-brain imaging within a clinically compatible scan time. THEORY AND METHODS: A general framework for ihMT modelling was developed based on the Provotorov theory of radiofrequency saturation, which accounts for the dipolar order underpinning the ihMT effect. Experimental studies and numerical simulations were performed to characterize and optimize the ihMT-gradient echo dependency with sequence timings, saturation power, and offset frequency...
September 23, 2017: Magnetic Resonance in Medicine: Official Journal of the Society of Magnetic Resonance in Medicine
Sergey A Akimov, Pavel E Volynsky, Timur R Galimzyanov, Peter I Kuzmin, Konstantin V Pavlov, Oleg V Batishchev
Lipid membranes serve as effective barriers allowing cells to maintain internal composition differing from that of extracellular medium. Membrane permeation, both natural and artificial, can take place via appearance of transversal pores. The rearrangements of lipids leading to pore formation in the intact membrane are not yet understood in details. We applied continuum elasticity theory to obtain continuous trajectory of pore formation and closure, and analyzed molecular dynamics trajectories of pre-formed pore reseal...
September 22, 2017: Scientific Reports
Jamshed Anwar, Dirk Zahn
Transformations in the solid state are of considerable interest, both for fundamental reasons and because they underpin important technological applications. The interest spans a wide spectrum of disciplines and application domains. For pharmaceuticals, a common issue is unexpected polymorphic transformation of the drug or excipient during processing or on storage, which can result in product failure. A more ambitious goal is that of exploiting the advantages of metastable polymorphs (e.g. higher solubility and dissolution rate) while ensuring their stability with respect to solid state transformation...
September 19, 2017: Advanced Drug Delivery Reviews
Baicheng Mei, Zhenhua Wang, Yuyuan Lu, Hongfei Li, Lijia An
Our recent molecular dynamics simulation results of binary particle glass-former systems demonstrated that the non-monotonic temperature T-dependence of the point-to-set dynamic length scale ξc(dyn) in harmonic (HM) systems is not an intrinsic property of bulk liquids but originates from wall effects. We would expect our results to apply equally to other simple models, such as Lennard-Jones (LJ) systems. However, Hocky et al. presented a monotonic T-dependent ξc(dyn) in a LJ system. Therefore, the present work employs molecular dynamics simulations to investigate the T-dependent behavior of ξc(dyn) in the LJ system employed by Hocky et al...
September 21, 2017: Journal of Chemical Physics
Vinicius B Tergolina, Alexandre P Dos Santos
In this paper we perform molecular dynamics simulations of a spherical polyelectrolyte brush and counterions in a salt-free medium. The dielectric discontinuity on the grafted nanoparticle surface is taken into account by the method of image charges. Properties of the polyelectrolyte brush are obtained for different parameters, including valency of the counterions, radius of the nanoparticle, and the brush total charge. The monovalent counterions density profiles are obtained and compared with a simple mean-field theoretical approach...
September 21, 2017: Journal of Chemical Physics
Emilia A Lubecka, Adam Liwo
Based on the theory of the construction of coarse-grained force fields for polymer chains described in our recent work [A. K. Sieradzan et al., J. Chem. Phys. 146, 124106 (2017)], in this work effective coarse-grained potentials, to be used in the SUGRES-1P model of polysaccharides that is being developed in our laboratory, have been determined for the O⋯O⋯O virtual-bond angles (θ) and for the dihedral angles for rotation about the O⋯O virtual bonds (γ) of 1 → 4-linked glucosyl polysaccharides, for all possible combinations of [α,β]-[d,l]-glucose...
September 21, 2017: Journal of Chemical Physics
A P Tyutnev, S V Novikov, V S Saenko, E D Pozhidaev
We have performed Monte-Carlo simulations of the charge carrier transport in a model molecularly doped polymer using three most popular hopping theories (the dipolar glass model, the Gaussian disorder model, and an intermediate between them) in a wide range of applied electric fields and temperatures. Time of flight transients have been computed and analyzed in logarithmic coordinates to study the Poole-Frenkel field dependence, the non-Arrhenius mobility temperature dependence, and the nondispersive versus dispersive current shapes...
September 21, 2017: Journal of Chemical Physics
Hiroki Matsubara, Gota Kikugawa, Mamoru Ishikiriyama, Seiji Yamashita, Taku Ohara
Thermal conductivity of a material can be comprehended as being composed of microscopic building blocks relevant to the energy transfer due to a specific microscopic process or structure. The building block is called the partial thermal conductivity (PTC). The concept of PTC is essential to evaluate the contributions of various molecular mechanisms to heat conduction and has been providing detailed knowledge of the contribution. The PTC can be evaluated by equilibrium molecular dynamics (EMD) and non-equilibrium molecular dynamics (NEMD) in different manners: the EMD evaluation utilizes the autocorrelation of spontaneous heat fluxes in an equilibrium state whereas the NEMD one is based on stationary heat fluxes in a non-equilibrium state...
September 21, 2017: Journal of Chemical Physics
Stefanie Winkelmann, Christof Schütte
Well-mixed stochastic chemical kinetics are properly modeled by the chemical master equation (CME) and associated Markov jump processes in molecule number space. If the reactants are present in large amounts, however, corresponding simulations of the stochastic dynamics become computationally expensive and model reductions are demanded. The classical model reduction approach uniformly rescales the overall dynamics to obtain deterministic systems characterized by ordinary differential equations, the well-known mass action reaction rate equations...
September 21, 2017: Journal of Chemical Physics
Hongguan Wu, Yu Li, Damir Kadirov, Shuangliang Zhao, Xiaohua Lu, Honglai Liu
The solvent-mediated interaction, or equivalently the depletion force, play a pivotal role in the processes, by which two objects in solution such as lock and key particles, antibody and antigen, macromolecule and substrate, are attracted to each other. The quantification of this interaction is important yet challenging since it depends on the microscopic solvent structure in the surrounding. Here, we report an efficient molecular approach for predicting the solvent-mediated interaction by combining the classical density functional theory with a reversible solvation thermodynamic circle...
September 22, 2017: Langmuir: the ACS Journal of Surfaces and Colloids
Wei Hu, Lin Lin, Chao Yang
The commutator direct inversion of the iterative subspace (commutator DIIS or C-DIIS) method developed by Pulay is an efficient and the most widely used scheme in quantum chemistry to accelerate the convergence of self consistent field (SCF) iterations in Hartree-Fock theory and Kohn-Sham density functional theory. The C-DIIS method requires the explicit storage of the density matrix, the Fock matrix and the commutator matrix. Hence the method can only be used for systems with a relatively small basis set, such as the Gaussian basis set...
September 22, 2017: Journal of Chemical Theory and Computation
Jose Julio Gutierrez Moreno, Michael Nolan
Titanium nitride (TiN) is widely used in industry as a protective coating due to its hardness and resistance to corrosion and can spontaneously form a thin oxide layer when it is exposed to air, which could modify the properties of the coating. With limited understanding of the TiO2 - TiN interfacial system at present, this work aims to describe the structural and electronic properties of oxidized TiN based on a density functional theory (DFT) study of the rutile TiO2 (110) - TiN (100) interface model system, also including Hubbard +U correction on Ti 3d states...
September 22, 2017: ACS Applied Materials & Interfaces
Te Hsun Lin, Yin Kuang Yang, Chien-Chung Fu
The periodic structure of laser interference lithography (LIL) fabrication is superior to other lithography technologies. In contrast to traditional lithography, LIL has the advantages of being a simple optical system with no mask requirements, low cost, high depth of focus, and large patterning area in a single exposure. Generally, a simulation pattern for the periodic structure is obtained through optical interference prior to its fabrication through LIL. However, the LIL process is complex and combines the fields of optical and polymer materials; thus, a single simulation theory cannot reflect the real situation...
September 22, 2017: Nanotechnology
L Mehrvar, M Sadeghipari, S H Tavassoli, S Mohajerzadeh, M Fathipour
Surface enhanced Raman scattering (SERS) systems with large number of active sites exhibit superior capability in detection of low concentration analytes. In this paper, we present theoretical as well as experimental studies on the optical properties of a unique hybrid nanostructure, Ag NPs decorated silicon double nanocones (Si-DNCs) array, which provide high density of hot spots. The Si-DNC array is fabricated by employing electron beam lithography together with plasma etching process. Multipole analysis of the scattering spectra, based on the multipole expansion theory, confirms that the toroidal dipole moment dominates over other electric and magnetic multipole moments in the Si-DNCs array...
September 21, 2017: Scientific Reports
Renata Vezzoli, Gianfausto Salvadori, Carlo De Michele
One of the ultimate goals of climate studies is to provide projections of future scenarios: for this purpose, sophisticated models are conceived, involving lots of parameters calibrated via observed data. The outputs of such models are used to investigate the impacts on related phenomena such as floods, droughts, etc. To evaluate the performance of such models, statistics like moments/quantiles are used, and comparisons with historical data are carried out. However, this may not be enough: correct estimates of some moments/quantiles do not imply that the probability distributions of observed and simulated data match...
September 21, 2017: Scientific Reports
Tianbo Xu, Ashwani Jha, Parashkev Nachev
Lesion-deficit mapping remains the most powerful method for localising function in the human brain. As the highest court of appeal where competing theories of cerebral function conflict, it ought to be held to the most stringent inferential standards. Though at first sight elegantly transferable, the mass-univariate statistical framework popularized by functional imaging is demonstrably ill-suited to the task, both theoretically and empirically. The critical difficulty lies with the handling of the data's intrinsically high dimensionality...
September 18, 2017: Neuropsychologia
Seong Won Kim, Allison J Taggart, Claire Heintzelman, Kamil J Cygan, Caitlin G Hull, Jing Wang, Barsha Shrestha, William G Fairbrother
Research into the problem of splice site selection has followed a reductionist approach focused on how individual splice sites are recognized. Early applications of information theory uncovered an inconsistency. Human splice signals do not contain enough information to explain the observed fidelity of splicing. Here, we conclude that introns do not necessarily contain 'missing' information but rather may require definition from neighboring processing events. For example, there are known cases where an intronic mutation disrupts the splicing of not only the local intron but also adjacent introns...
September 19, 2017: Nucleic Acids Research
Meiting Wang, Pengfei Li, Xiangyu Jia, Wei Liu, Yihan Shao, Wenxin Hu, Jun Zheng, Bernard R Brooks, Ye Mei
The partitioning of solute molecules between immiscible solvents with significantly different polarities is of great importance. The polarization between the solute and solvent molecules plays an essential role in determining the solubility of the solute, which makes computational studies utilizing molecular mechanics (MM) rather difficult. In contrast, quantum mechanics (QM) can provide more reliable predictions. In this work, the partition coefficients of the side chain analogs of some amino acids between water and chloroform were computed...
September 21, 2017: Journal of Chemical Information and Modeling
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