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Theory of simulation

P Xenitidis, I Seimenis, S Kakolyris, A Adamopoulos
High-throughput technology like microarrays is widely used in the inference of gene regulatory networks (GRNs). We focused on time series data since we are interested in the dynamics of GRNs and the identification of dynamic networks. We evaluated the amount of information that exists in artificial time series microarray data and the ability of an inference process to produce accurate models based on them. We used dynamic artificial gene regulatory networks in order to create artificial microarray data. Key features that characterize microarray data such as the time separation of directly triggered genes, the percentage of directly triggered genes and the triggering function type were altered in order to reveal the limits that are imposed by the nature of microarray data on the inference process...
May 17, 2017: Journal of Theoretical Biology
Tao Zhao, Songyi Dian
This paper addresses a fuzzy dynamic output feedback H∞ control design problem for continuous-time nonlinear systems via T-S fuzzy model. The stability of the fuzzy closed-loop system which is formed by a T-S fuzzy model and a fuProd. Type: FTPzzy dynamic output feedback H∞ controller connected in a closed loop is investigated with Lyapunov stability theory. The proposed fuzzy controller does not share the same membership functions and number of rules with T-S fuzzy systems, which can enhance design flexibility...
May 17, 2017: ISA Transactions
Florian F Krause, Andreas Rosenauer, Dirk Van Dyck
A relatively simple yet accurate analytical model for the image formation in the imaging scanning TEM (ISTEM) imaging mode, which implements partial spatial incoherence using a combination of scanning illumination and conventional imaging, is presented. Based on an object function approximation the ISTEM intensity can be divided into a constant, a linear and a nonlinear term. Under certain conditions, which are discussed, the formation of both linear and nonlinear terms can be expressed by convolutions with point spread functions...
April 25, 2017: Ultramicroscopy
Benedict W J Irwin, David J Huggins
Evaluating solvation entropies directly and combining with direct energy calculations is one way of calculating free energies of solvation and is used by Inhomogeneous Fluid Solvation Theory (IFST). The configurational entropy of a fluid is a function of the interatomic correlations and can thus be expressed in terms of correlation functions. The entropies in this work are directly calculated from a truncated series of integrals over these correlation functions. Many studies truncate all terms higher than the solvent-solute correlations...
May 21, 2017: Journal of Chemical Physics
Manuel Athènes, Pierre Terrier
Markov chain Monte Carlo methods are primarily used for sampling from a given probability distribution and estimating multi-dimensional integrals based on the information contained in the generated samples. Whenever it is possible, more accurate estimates are obtained by combining Monte Carlo integration and integration by numerical quadrature along particular coordinates. We show that this variance reduction technique, referred to as conditioning in probability theory, can be advantageously implemented in expanded ensemble simulations...
May 21, 2017: Journal of Chemical Physics
Andrey Milchev, Sergei A Egorov, Arash Nikoubashman, Kurt Binder
Semiflexible polymers in lyotropic solution confined inside spherical nanoscopic "containers" with repulsive walls are studied by molecular dynamics simulations and density functional theory, as a first step to model confinement effects on stiff polymers inside of miniemulsions, vesicles, and cells. It is shown that the depletion effects caused by the monomer-wall repulsion depend distinctly on the radius R of the sphere. Further, nontrivial orientational effects occur when R, the persistence length ℓp, and the contour length L of the polymers are of similar magnitude...
May 21, 2017: Journal of Chemical Physics
Sai Duan, Guangjun Tian, Zhen Xie, Yi Luo
The use of a highly localized plasmonic field has enabled us to achieve sub-nanometer resolution of Raman images for single molecules. The inhomogeneous spatial distribution of plasmonic field has become an important factor that controls the interaction between the light and the molecule. We present here a gauge invariant interaction Hamiltonian (GIIH) to take into account the non-uniformity of the electromagnetic field distribution in the non-relativistic regime. The theory has been implemented for both resonant and nonresonant Raman processes within the sum-over-state framework...
May 21, 2017: Journal of Chemical Physics
Hiroaki Yoshida, Sophie Marbach, Lydéric Bocquet
In this paper, we explore osmotic transport by means of molecular dynamics (MD) simulations. We first consider osmosis through a membrane and investigate the reflection coefficient of an imperfectly semi-permeable membrane, in the dilute and high concentration regimes. We then explore the diffusio-osmotic flow of a solute-solvent fluid adjacent to a solid surface, driven by a chemical potential gradient parallel to the surface. We propose a novel non-equilibrium MD (NEMD) methodology to simulate diffusio-osmosis, by imposing an external force on every particle, which properly mimics the chemical potential gradient on the solute in spite of the periodic boundary conditions...
May 21, 2017: Journal of Chemical Physics
Jin Piao, Jing Ning, Christina D Chambers, Ronghui Xu
Evaluating and understanding the risk and safety of using medications for autoimmune disease in a woman during her pregnancy will help both clinicians and pregnant women to make better treatment decisions. However, utilizing spontaneous abortion (SAB) data collected in observational studies of pregnancy to derive valid inference poses two major challenges. First, the data from the observational cohort are not random samples of the target population due to the sampling mechanism. Pregnant women with early SAB are more likely to be excluded from the cohort, and there may be substantial differences between the observed SAB time and those in the target population...
May 18, 2017: Biostatistics
Tobias Setzer, Christian Lennartz, Andreas Dreuw
Recently, a successful Brønsted-acid mediated geometric isomerization of the meridional homoleptic carbenic iridium(iii) complexes tris-(N-phenyl,N-methyl-benzimidazol-2-yl)iridium(iii) (1) and tris-(N-phenyl,N-benzyl-benzimidazol-2-yl)iridium(iii) (2) into their facial form has been reported. In the present work the pronounced acid-dependency of this particular isomerization procedure is revisited and additional mechanistic pathways are taken into account. Moreover, the acid-induced material decomposition is addressed...
May 19, 2017: Dalton Transactions: An International Journal of Inorganic Chemistry
Wenjuan Fang, Baojiu Li, Gong-Bo Zhao
The morphological properties of the large scale structure of the Universe can be fully described by four Minkowski functionals (MFs), which provide important complementary information to other statistical observables such as the widely used 2-point statistics in configuration and Fourier spaces. In this work, for the first time, we present the differences in the morphology of the large scale structure caused by modifications to general relativity (to address the cosmic acceleration problem), by measuring the MFs from N-body simulations of modified gravity and general relativity...
May 5, 2017: Physical Review Letters
Jonathan D'Emidio, Ribhu K Kaul
We study fixed points of the easy-plane CP^{N-1} field theory by combining quantum Monte Carlo simulations of lattice models of easy-plane SU(N) superfluids with field theoretic renormalization group calculations, by using ideas of deconfined criticality. From our simulations, we present evidence that at small N our lattice model has a first-order phase transition which progressively weakens as N increases, eventually becoming continuous for large values of N. Renormalization group calculations in 4-ε dimensions provide an explanation of these results as arising due to the existence of an N_{ep} that separates the fate of the flows with easy-plane anisotropy...
May 5, 2017: Physical Review Letters
Jiří Kessler, Shigeki Yamamoto, Petr Bouř
Folding of proteins into insoluble amyloidal fibrils is implicated in a number of biological processes. Optical spectroscopy represents a convenient tool to monitor such structural variations. Recently, characteristic changes in Raman optical activity (ROA) spectra of insulin during a pre-fibrillar stage were reported but not supported by a theoretical model. In the present study, molecular dynamics and the density functional theory are used to simulate the spectra and understand the connection between the structure, and ROA and Raman spectral intensities...
May 19, 2017: Physical Chemistry Chemical Physics: PCCP
Stefan Landmann, Nicolas Preuss, Ulrich Behn
We consider self-tolerance and its failure -autoimmunity- in a minimal mathematical model of the idiotypic network. A node in the network represents a clone of B-lymphocytes and its antibodies of the same idiotype which is encoded by a bitstring. The links between nodes represent possible interactions between clones of almost complementary idiotype. A clone survives only if the number of populated neighbored nodes is neither too small nor too large. The dynamics is driven by the influx of lymphocytes with randomly generated idiotype from the bone marrow...
May 15, 2017: Journal of Theoretical Biology
Tao Han, Zhi-Hong Guan, Ming Chi, Bin Hu, Tao Li, Xian-He Zhang
This paper deals with the multi-formation control problem for nonlinear leader-following multi-agent systems. Both the fixed topology case and the switching topology case are considered. The neighbor-based multi-formation control protocols are proposed under the assumption that for one subgroup, the total information received from other subgroups is zero. Then, based on the Lyapunov stability theory combined with the algebraic graph theory, sufficient conditions are established to ensure that the leader-following multi-agent systems with nonlinear dynamics can reach and maintain the desired multi-formation control...
May 15, 2017: ISA Transactions
Li-Fei Ji, Jian-Xun Fan, Shou-Feng Zhang, Ai-Min Ren
A theoretical study was carried out to investigate the electronic structures and the charge transport properties of a series of naphthodithiophene diimide (NDTI) thiophene α-substituted derivatives NDTI-X using density functional theory and classical Marcus charge transfer theory. This study deeply revealed the structure-property relationships by analyzing the intermolecular interactions in crystal structures of C8-NDTI and C8-NDTI-Cl thoroughly by using the Hirshfeld surface, QTAIM theories and symmetry-adapted perturbation theory (SAPT)...
May 18, 2017: Physical Chemistry Chemical Physics: PCCP
Zijian Zhou, Rui Tian, Zhenyu Wang, Zhen Yang, Yijing Liu, Gang Liu, Ruifang Wang, Jinhao Gao, Jibin Song, Liming Nie, Xiaoyuan Chen
Clustering of magnetic nanoparticles (MNPs) is perhaps the most effective, yet intriguing strategy to enhance T2 relaxivity in magnetic resonance imaging (MRI). However, the underlying mechanism is still not fully understood and the attempts to generalize the classic outersphere theory from single particles to clusters have been found to be inadequate. Here we show that clustering of MNPs enhances local field inhomogeneity due to reduced field symmetry, which can be further elevated by artificially involving iron oxide NPs with heterogeneous geometries in terms of size and shape...
May 18, 2017: Nature Communications
Matthieu Authier, Lise M Aubry, Emmanuelle Cam
Understanding the processes behind change in reproductive state along life-history trajectories is a salient research program in evolutionary ecology. Two processes, state dependence and heterogeneity, can drive the dynamics of change among states. Both processes can operate simultaneously, begging the difficult question of how to tease them apart in practice. The Neutral Theory for Life Histories (NTLH) holds that the bulk of variations in life-history trajectories is due to state dependence and is hence neutral: Once previous (breeding) state is taken into account, variations are mostly random...
May 2017: Ecology and Evolution
Scott A Norris, Joy C Perkinson, Mahsa Mokhtarzadeh, Eitan Anzenberg, Michael J Aziz, Karl F Ludwig
In this work we analyze GISAXS measurements of the structure factor of Si surfaces evolving during 1 keV Ar+ ion bombardment. Using newly-developed methods sensitive to the full range of experimentally-available wavenumbers q, we extract the linear amplification rate R(q) governing surface stability over a range of wavenumbers 4-5 times larger than has previously been obtained. Comparing with theoretical models also retaining full wavenumber-dependence, we find an excellent fit of the experimental data over the full range of irradiation angles and wavenumbers...
May 17, 2017: Scientific Reports
Yoriko Murayama, Hiroshi Kori, Chiaki Oshima, Takao Kondo, Hideo Iwasaki, Hiroshi Ito
Cold temperatures lead to nullification of circadian rhythms in many organisms. Two typical scenarios explain the disappearance of rhythmicity: the first is oscillation death, which is the transition from self-sustained oscillation to damped oscillation that occurs at a critical temperature. The second scenario is oscillation arrest, in which oscillation terminates at a certain phase. In the field of nonlinear dynamics, these mechanisms are called the Hopf bifurcation and the saddle-node on an invariant circle bifurcation, respectively...
May 17, 2017: Proceedings of the National Academy of Sciences of the United States of America
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