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simulation model

Martín Romagnoli, Margarita Portapila, Alfredo Rigalli, Gisela Maydana, Martín Burgués, Carlos M García
Argentina has been among the world leaders in the production and export of agricultural products since the 1990s. The Carcarañá River Lower Basin (CRLB), a cropland of the Pampas region supplied by extensive rainfall, is located in an area with few streamgauging and other hydrologic/water-quality stations. Therefore, limited hydrologic data are available resulting in limited water-resources assessment. This work explores the application of Soil and Water Assessment Tool (SWAT) model to the CRLB in the Santa Fe province of the Pampas region...
April 25, 2017: Science of the Total Environment
Lorenzo Brilli, Luca Bechini, Marco Bindi, Marco Carozzi, Daniele Cavalli, Richard Conant, Cristopher D Dorich, Luca Doro, Fiona Ehrhardt, Roberta Farina, Roberto Ferrise, Nuala Fitton, Rosa Francaviglia, Peter Grace, Ileana Iocola, Katja Klumpp, Joël Léonard, Raphaël Martin, Raia Silvia Massad, Sylvie Recous, Giovanna Seddaiu, Joanna Sharp, Pete Smith, Ward N Smith, Jean-Francois Soussana, Gianni Bellocchi
Biogeochemical simulation models are important tools for describing and quantifying the contribution of agricultural systems to C sequestration and GHG source/sink status. The abundance of simulation tools developed over recent decades, however, creates a difficulty because predictions from different models show large variability. Discrepancies between the conclusions of different modelling studies are often ascribed to differences in the physical and biogeochemical processes incorporated in equations of C and N cycles and their interactions...
April 24, 2017: Science of the Total Environment
Ronen Berkovich, Jagannath Mondal, Inga Paster, Bruce J Berne
Single molecule force spectroscopy is a useful technique for investigating mechanically induced protein unfolding and refolding under reduced forces by monitoring the end-to-end distance of the protein, Ree. The data is often interpreted via a "two-state" model based on the assumption that Ree alone is a good reaction coordinate and the thermodynamic behavior is then ascribed to the free energy as a function of this one reaction coordinate. In this paper, we determined the free energy surface (PMF) of GB1 protein from atomistic simulations in explicit solvent under different applied forces as a function of two collective variables (Ree, and the fraction of native contacts ρ)...
April 28, 2017: Journal of Physical Chemistry. B
David R Hanson, Imanuel Bier, Baradan Panta, Coty N Jen, Peter H McMurry
Computational fluid dynamics simulations (CFD) of a flow reactor provided 3D spatial distributions of its temperature and flow profiles and abundances of sulfuric acid, nitrogeneous base and the acid-base clusters formed from them. Clusters were simulated via their kinetic formation and decomposition involving sulfuric acid and base molecules. Temperature and flow profiles and the base and sulfuric acid distributions are characterized and the latter is compared to mass spectrometer measurements. Concentrations of simulated clusters of sulfuric acid with either NH3 or dimethylamine were compared to experimentally measured particle concentrations...
April 28, 2017: Journal of Physical Chemistry. A
Michael Golden, Eduardo Garcia-Portugues, Michael Sørensen, Kanti V Mardia, Thomas Hamelryck, Jotun Hein
Recently described stochastic models of protein evolution have demonstrated that the inclusion of structural information in addition to amino acid sequences leads to a more reliable estimation of evolutionary parameters. We present a generative, evolutionary model of protein structure and sequence that is valid on a local length scale. The model concerns the local dependencies between sequence and structure evolution in a pair of homologous proteins. The evolutionary trajectory between the two structures in the protein pair is treated as a random walk in dihedral angle space, which is modeled using a novel angular diffusion process on the two-dimensional torus...
April 27, 2017: Molecular Biology and Evolution
Ivan Krukov, Bianca de Sanctis, A P Jason de Koning
Motivation: The simplifying assumptions that are used widely in theoretical population genetics may not always be appropriate for empirical population genetics. General computational approaches that do not require the assumptions of classical theory are therefore quite desirable. One such general approach is provided by the theory of absorbing Markov chains, which can be used to obtain exact results by directly analyzing population genetic Markov models, such as the classic bi-allelic Wright-Fisher model...
May 1, 2017: Bioinformatics
Richard H Adams, Drew R Schield, Daren C Card, Heath Blackmon, Todd A Castoe
Summary: We introduce GppFst, an open source R package that generates posterior predictive distributions of FST and dx under a neutral coalescent model to identify putative targets of selection from genomic data. Availability and Implementation: GppFst is available at ( ). Contact: Supplementary information: Supplementary data are available at Bioinformatics online...
May 1, 2017: Bioinformatics
Sean Maxwell, Mark R Chance, Mehmet Koyutürk
Motivation: In recent years, various network proximity measures have been proposed to facilitate the use of biomolecular interaction data in a broad range of applications. These applications include functional annotation, disease gene prioritization, comparative analysis of biological systems and prediction of new interactions. In such applications, a major task is the scoring or ranking of the nodes in the network in terms of their proximity to a given set of 'seed' nodes (e.g. a group of proteins that are identified to be associated with a disease, or are deferentially expressed in a certain condition)...
May 1, 2017: Bioinformatics
Mandi Yu, Jerome Phillip Reiter, Li Zhu, Benmei Liu, Kathleen A Cronin, Eric J Rocky Feuer
The National Cancer Institute's Surveillance, Epidemiology, and End Results Program releases research files of cancer registry data. These files include geography at the county level, but no finer. Access to finer geography, such as tract identifiers, would enable richer analyses, for example, examination of health disparities across neighborhoods. To date, tract identifiers are left off the research files because they could compromise the confidentiality of patients' identities. We present an approach to include tract identifiers based on multiply-imputed, synthetic data...
April 27, 2017: American Journal of Epidemiology
Eli Levy Karin, Dafna Shkedy, Haim Ashkenazy, Reed A Cartwright, Tal Pupko
The most common evolutionary events at the molecular level are single-base substitutions, and insertions and deletions of short DNA segments (indels). A large body of research has been devoted to develop probabilistic substitution models and to infer their parameters using likelihood and Bayesian approaches. In contrast, relatively little has been done to model indel dynamics, probably due to the difficulty in writing explicit likelihood functions. Here, we contribute to the effort of modeling indel dynamics by presenting SpartaABC, an approximate Bayesian computation (ABC) approach to infer indel parameters from sequence data (either aligned or unaligned)...
April 26, 2017: Genome Biology and Evolution
Patricia Therese Campbell, Jodie McVernon, Nicholas Geard
Rising pertussis incidence has prompted a number of countries to implement maternally-targeted vaccination to protect vulnerable infants, but questions remain about optimal design of such vaccination strategies. We simulated pertussis transmission within an individual based model parameterized to match Australian conditions, explicitly linking infants and their mothers to estimate the effectiveness of alternative maternally-targeted vaccination strategies (antenatal versus postnatal delivery) and the benefit of revaccination over multiple pregnancies...
April 27, 2017: American Journal of Epidemiology
Asmita S Kamble, Prayagraj M Fandilolu, Susmit B Sambhare, Kailas D Sonawane
Lack of naturally occurring modified nucleoside 5-taurinomethyluridine (τm5U) at the 'wobble' 34th position in tRNALeu causes mitochondrial myopathy, encephalopathy, lactic acidosis and stroke-like episodes (MELAS). The τm5U34 specifically recognizes UUG and UUA codons. Structural consequences of τm5U34 to read cognate codons have not been studied so far in detail at the atomic level. Hence, 50ns multiple molecular dynamics (MD) simulations of various anticodon stem loop (ASL) models of tRNALeu in presence and absence of τm5U34 along with UUG and UUA codons were performed to explore the dynamic behaviour of τm5U34 during codon recognition process...
2017: PloS One
Rose E Stafford, Christopher R Runyon, Jodi M Casabianca, Barbara G Dodd
This study examined the performance of four methods of handling missing data for discrete response options on a questionnaire: (1) ignoring the missingness (using only the observed items to estimate trait levels); (2) nearest-neighbor hot deck imputation; (3) multiple hot deck imputation; and (4) semi-parametric multiple imputation. A simulation study examining three questionnaire lengths (41-, 20-, and 10-item) crossed with three levels of missingness (10, 25, and 40 percent) was conducted to see which methods best recovered trait estimates when data were missing completely at random and the polytomous items were scored with Andrich's (1978) rating scale model...
2017: Journal of Applied Measurement
Tiago M Barbosa, Rui Ramos, António J Silva, Daniel A Marinho
The aim was to compare the passive drag-gliding underwater by a numerical simulation and an analytical procedure. An Olympic swimmer was scanned by computer tomography and modelled gliding at a 0.75-m depth in the streamlined position. Steady-state computer fluid dynamics (CFD) analyses were performed on Fluent. A set of analytical procedures was selected concurrently. Friction drag (Df), pressure drag (Dpr), total passive drag force (Df+pr) and drag coefficient (CD) were computed between 1.3 and 2.5 m · s(-1) by both techniques...
April 28, 2017: Journal of Sports Sciences
Franco Egidi, David B Williams-Young, Alberto Baiardi, Julien Bloino, Giovanni Scalmani, Michael J Frisch, Xiaosong Li, Vincenzo Barone
We present a reliable and cost-effective procedure for the inclusion of anharmonic effects in excited-state energies and spectroscopic intensities by means of second-order vibrational perturbation theory. This development is made possible thanks to a recent efficient implementation of excited-state analytic Hessians and properties within the time-dependent density functional theory framework. As illustrated in this work, by taking advantage of such algorithmic developments, it is possible to perform calculations of excited-state infrared spectra of medium-large isolated molecular systems, with anharmonicity effects included in both the energy and property surfaces...
April 28, 2017: Journal of Chemical Theory and Computation
Stavros Karakalos, Francisco Zaera
A Monte Carlo algorithm was developed and used to describe and explain previous experimental results associated with the kinetics of the uptake of chiral molecules on solid surfaces. The specific system simulated in this study is the adsorption of propylene oxide (PO) on Pt(111) surfaces. The surface was represented by a square lattice, and the time evolution of the adsorption, starting from a clean surface, was simulated via a number of sequential events chosen using a stochastic approach based on the so-called Master equation and derived from the formalism advanced by Gillespie...
April 28, 2017: Journal of Physical Chemistry. B
Noureldin Saleh, Passainte Ibrahim, Giorgio Saladino, Francesco Luigi Gervasio, Timothy Clark
A generally applicable metadynamics scheme for predicting the free-energy profile of ligand binding to G-protein coupled receptors (GPCRs) is described. A common collective variable (CV) can be defined because of the orientation of GPCRs in the cell membrane and because the relatively fixed residue Trp6.48 is highly conserved in GPCRs. Using this single CV together with well-tempered multiple-walker metadynamics with a funnel-like constraint allows an efficient exploration of the entire ligand-binding path from the extracellular medium to the orthosteric binding site, including vestibule and intermediate sites...
April 28, 2017: Journal of Chemical Information and Modeling
Rimjhim Agrawal, Sunil Vasu Kalmady, Ganesan Venkatasubramanian
Objective: Deficient brain-derived neurotrophic factor (BDNF) is one of the important mechanisms underlying the neuroplasticity abnormalities in schizophrenia. Aberration in BDNF signaling pathways directly or circuitously influences neurotransmitters like glutamate and gamma-aminobutyric acid (GABA). For the first time, this study attempts to construct and simulate the BDNF-neurotransmitter network in order to assess the effects of BDNF deficiency on glutamate and GABA. Methods: Using CellDesigner, we modeled BDNF interactions with calcium influx via N-methyl-D-aspartate receptor (NMDAR)- Calmodulin activation; synthesis of GABA via cell cycle regulators protein kinase B, glycogen synthase kinase and β-catenin; transportation of glutamate and GABA...
May 31, 2017: Clinical Psychopharmacology and Neuroscience: the Official Scientific Journal of the Korean College of Neuropsychopharmacology
Zhiguo Wang, Jiaxuan Chen, Guilian Wang, Qingshun Bai, Yingchun Liang
The anisotropy exhibited by single-crystal silicon in nanometric cutting is very significant. In order to profoundly understand the effect of crystal anisotropy on cutting behaviors, a large-scale molecular dynamics model was conducted to simulate the nanometric cutting of single-crystal silicon in the (100)[0-10], (100)[0-1-1], (110)[-110], (110)[00-1], (111)[-101], and (111)[-12-1] crystal directions in this study. The simulation results show the variations of different degrees in chip, subsurface damage, cutting force, and friction coefficient with changes in crystal plane and crystal direction...
December 2017: Nanoscale Research Letters
Tobias Lortzing, Vivien Firtzlaff, Duy Nguyen, Ivo Rieu, Sandra Stelzer, Martina Schad, Jim Kallarackal, Anke Steppuhn
Plants are attacked by diverse herbivores and respond with manifold defense responses. To study transcriptional and other early regulation events of these plant responses, herbivory is often simulated to standardize the temporal and spatial dynamics that vary tremendously for natural herbivory. Yet to what extent such simulations of herbivory are able to elicit the same plant response as real herbivory remains largely undetermined. We examined the transcriptional response of a wild model plant to herbivory by lepidopteran larvae and to a commonly used herbivory simulation by applying the larvae's oral secretions to standardized wounds...
April 27, 2017: Molecular Ecology Resources
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