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Modeling and Simulation

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https://www.readbyqxmd.com/read/29353335/leveraging-model-informed-approaches-for-drug-discovery-and-development-in-the-cardiovascular-space
#1
REVIEW
Marissa F Dockendorf, Ryan C Vargo, Ferdous Gheyas, Anne S Y Chain, Manash S Chatterjee, Larissa A Wenning
Cardiovascular disease remains a significant global health burden, and development of cardiovascular drugs in the current regulatory environment often demands large and expensive cardiovascular outcome trials. Thus, the use of quantitative pharmacometric approaches which can help enable early Go/No Go decision making, ensure appropriate dose selection, and increase the likelihood of successful clinical trials, have become increasingly important to help reduce the risk of failed cardiovascular outcomes studies...
January 20, 2018: Journal of Pharmacokinetics and Pharmacodynamics
https://www.readbyqxmd.com/read/29353199/applicability-of-kd-for-modelling-dissolved-137cs-concentrations-in-fukushima-river-water-case-study-of-the-upstream-ota-river
#2
Kazuyuki Sakuma, Hideki Tsuji, Seiji Hayashi, Hironori Funaki, Alex Malins, Kazuya Yoshimura, Hiroshi Kurikami, Akihiro Kitamura, Kazuki Iijima, Masaaki Hosomi
A study is presented on the applicability of the distribution coefficient (Kd) absorption/desorption model to simulate dissolved 137Cs concentrations in Fukushima river water. The upstream Ota River basin was simulated using GEneral-purpose Terrestrial Fluid-flow Simulator (GETFLOWS) for the period 1 January 2014 to 31 December 2015. Good agreement was obtained between the simulations and observations on water and suspended sediment fluxes, and on particulate bound 137Cs concentrations under both base and high flow conditions...
January 17, 2018: Journal of Environmental Radioactivity
https://www.readbyqxmd.com/read/29353192/monte-carlo-calculations-of-the-cellular-s-values-for-%C3%AE-particle-emitting-radionuclides-incorporated-into-the-nuclei-of-cancer-cells-of-the-mda-mb231-mcf7-and-pc3-lines
#3
E L Rojas-Calderón, O Ávila, G Ferro-Flores
S-values (dose per unit of cumulated activity) for alpha particle-emitting radionuclides and monoenergetic alpha sources placed in the nuclei of three cancer cell models (MCF7, MDA-MB231 breast cancer cells and PC3 prostate cancer cells) were obtained by Monte Carlo simulation. The MCNPX code was used to calculate the fraction of energy deposited in the subcellular compartments due to the alpha sources in order to obtain the S-values. A comparison with internationally accepted S-values reported by the MIRD Cellular Committee for alpha sources in three sizes of spherical cells was also performed leading to an agreement within 4% when an alpha extended source uniformly distributed in the nucleus is simulated...
January 10, 2018: Applied Radiation and Isotopes
https://www.readbyqxmd.com/read/29353081/hydrogels-based-on-poly-methyl-vinyl-ether-co-maleic-acid-and-tween-85-for-sustained-delivery-of-hydrophobic-drugs
#4
Eneko Larrañeta, Laura Barturen, Michael Ervine, Ryan F Donnelly
Hydrogels based on poly(methyl vinyl ether-co-maleic acid) and Tween 85 were prepared for hydrophobic drug delivery. The hydrogels were synthesized following a simple procedure carried out in solid state. The process did not require the use of any solvent and, as it is based on an esterification reaction, no toxic by-products were obtained. The resulting hydrogels contained Tween 85 inside the structure and due to the amphiphilic nature of this compound, hydrophobic domains within the hydrogel structure were formed...
January 15, 2018: International Journal of Pharmaceutics
https://www.readbyqxmd.com/read/29352935/development-of-ph-responsive-chitosan-based-hydrogel-modified-with-bone-ash-for-controlled-release-of-amoxicillin
#5
Didem Aycan, Neslihan Alemdar
In present study, bone ash-reinforced chitosan-based hydrogels were obtained by encapsulation of bone ash into the hydrogel structure which was fabricated by photopolymerization of chitosan-grafted-glycidyl methacrylate (CTS-g-GMA) and poly(ethylene glycol)diacrylate (PEGDA) under the UV light. Hydrogels were characterized by ATR-FTIR, SEM and XRD analyses. Mechanical performance of the hydrogels was determined by universal mechanical tester. Cytotoxicity tests for hydrogels were conducted with L929 cell lines to determine cellular compatibility...
March 15, 2018: Carbohydrate Polymers
https://www.readbyqxmd.com/read/29352843/tocilizumab-after-a-first-line-with-anti-tnf-in-rheumatoid-arthritis-a-cost-consequence-analysis-in-the-italian-setting
#6
Sergio Iannazzo, Maurizio Benucci, Ennio Giulio Favalli
OBJECTIVES: Switching to a different mechanism of action in rheumatoid arthritis (RA) patients after a first anti-TNF-α has proved to be effective. The objective of this study was a health economic assessment in Italy. METHODS: The study was conducted using a pharmacoeconomic model with a 3-year time horizon. Effectiveness was measured as days gained in low disease activity (LDA; DAS28-ESR <3.2) or in remission (DAS28-ESR <2.6). The model simulated the response to treatments, based on the Rotation Or Change (ROC) trial, the probability of discontinuation and switch to a 3rd-line biologic, and the transition to death...
January 15, 2018: Clinical and Experimental Rheumatology
https://www.readbyqxmd.com/read/29352800/efficient-reactive-brownian-dynamics
#7
Aleksandar Donev, Chiao-Yu Yang, Changho Kim
We develop a Split Reactive Brownian Dynamics (SRBD) algorithm for particle simulations of reaction-diffusion systems based on the Doi or volume reactivity model, in which pairs of particles react with a specified Poisson rate if they are closer than a chosen reactive distance. In our Doi model, we ensure that the microscopic reaction rules for various association and dissociation reactions are consistent with detailed balance (time reversibility) at thermodynamic equilibrium. The SRBD algorithm uses Strang splitting in time to separate reaction and diffusion and solves both the diffusion-only and reaction-only subproblems exactly, even at high packing densities...
January 21, 2018: Journal of Chemical Physics
https://www.readbyqxmd.com/read/29352797/physical-origins-of-temperature-continuity-at-an-interface-between-a-crystal-and-its-melt
#8
Truong Quoc Vo, BoHung Kim
We justify and discuss the physical origins for the assumption of temperature continuity at crystal/melt interfaces by performing atomistic simulations. We additionally answer why the crystal/melt interfaces differ from the typical solid/liquid interfaces, which usually exhibit dissimilarities and a resulting temperature drop. We present results for pure silver modeled using the embedded-atom method and Lennard-Jones potential function and contrast the results with each other. We find that the temperature continuity at an interface between a crystal and its melt originates from the perfect vibrational coupling, which is caused by the interfacial structural diffusivity...
January 21, 2018: Journal of Chemical Physics
https://www.readbyqxmd.com/read/29352789/hydrodynamic-relaxations-in-dissipative-particle-dynamics
#9
J S Hansen, Michael L Greenfield, Jeppe C Dyre
This paper studies the dynamics of relaxation phenomena in the standard dissipative particle dynamics (DPD) model [R. D. Groot and P. B. Warren, J. Chem. Phys. 107, 4423 (1997)]. Using fluctuating hydrodynamics as the framework of the investigation, we focus on the collective transverse and longitudinal dynamics. It is shown that classical hydrodynamic theory predicts the transverse dynamics at relatively low temperatures very well when compared to simulation data; however, the theory predictions are, on the same length scale, less accurate for higher temperatures...
January 21, 2018: Journal of Chemical Physics
https://www.readbyqxmd.com/read/29352785/markov-state-model-for-co2-binding-with-carbonic-anhydrase-under-confinement
#10
Gong Chen, Weina Xu, Diannan Lu, Jianzhong Wu, Zheng Liu
Enzyme immobilization with a nanostructure material can enhance its stability and facilitate reusability. However, the apparent activity is often compromised due to additional diffusion barriers and complex interactions with the substrates and solvent molecules. The present study elucidates the effects of the surface hydrophobicity of nano-confinement on CO2 diffusion to the active site of human carbonic anhydrase II (CA), an enzyme that is able to catalyze CO2 hydration at extremely high turnover rates. Using the Markov-state model in combination with coarse-grained molecular dynamics simulations, we demonstrate that a hydrophobic cage increases CO2 local density but hinders its diffusion towards the active site of CA under confinement...
January 21, 2018: Journal of Chemical Physics
https://www.readbyqxmd.com/read/29352784/calculation-of-a-solid-liquid-surface-tension-a-methodological-study
#11
T Dreher, C Lemarchand, L Soulard, E Bourasseau, P Malfreyt, N Pineau
The surface tension of a model solid/liquid interface constituted of a graphene sheet surrounded by liquid methane has been computed using molecular dynamics in the Kirkwood-Buff formalism. We show that contrary to the fluid/fluid case, the solid/liquid case can lead to different structurations of the first fluid layer, leading to significantly different values of surface tension. Therefore we present a statistical approach that consists in running a series of molecular simulations of similar systems with different initial conditions, leading to a distribution of surface tensions from which an average value and uncertainty can be extracted...
January 21, 2018: Journal of Chemical Physics
https://www.readbyqxmd.com/read/29352783/addressing-global-uncertainty-and-sensitivity-in-first-principles-based-microkinetic-models-by-an-adaptive-sparse-grid-approach
#12
Sandra Döpking, Craig P Plaisance, Daniel Strobusch, Karsten Reuter, Christoph Scheurer, Sebastian Matera
In the last decade, first-principles-based microkinetic modeling has been developed into an important tool for a mechanistic understanding of heterogeneous catalysis. A commonly known, but hitherto barely analyzed issue in this kind of modeling is the presence of sizable errors from the use of approximate Density Functional Theory (DFT). We here address the propagation of these errors to the catalytic turnover frequency (TOF) by global sensitivity and uncertainty analysis. Both analyses require the numerical quadrature of high-dimensional integrals...
January 21, 2018: Journal of Chemical Physics
https://www.readbyqxmd.com/read/29352779/hydrodynamically-coupled-brownian-dynamics-a-coarse-grain-particle-based-brownian-dynamics-technique-with-hydrodynamic-interactions-for-modeling-self-developing-flow-of-polymer-solutions
#13
V R Ahuja, J van der Gucht, W J Briels
We present a novel coarse-grain particle-based simulation technique for modeling self-developing flow of dilute and semi-dilute polymer solutions. The central idea in this paper is the two-way coupling between a mesoscopic polymer model and a phenomenological fluid model. As our polymer model, we choose Responsive Particle Dynamics (RaPiD), a Brownian dynamics method, which formulates the so-called "conservative" and "transient" pair-potentials through which the polymers interact besides experiencing random forces in accordance with the fluctuation dissipation theorem...
January 21, 2018: Journal of Chemical Physics
https://www.readbyqxmd.com/read/29352778/continuum-percolation-of-polydisperse-rods-in-quadrupole-fields-theory-and-simulations
#14
Shari P Finner, Mihail I Kotsev, Mark A Miller, Paul van der Schoot
We investigate percolation in mixtures of nanorods in the presence of external fields that align or disalign the particles with the field axis. Such conditions are found in the formulation and processing of nanocomposites, where the field may be electric, magnetic, or due to elongational flow. Our focus is on the effect of length polydispersity, which-in the absence of a field-is known to produce a percolation threshold that scales with the inverse weight average of the particle length. Using a model of non-interacting spherocylinders in conjunction with connectedness percolation theory, we show that a quadrupolar field always increases the percolation threshold and that the universal scaling with the inverse weight average no longer holds if the field couples to the particle length...
January 21, 2018: Journal of Chemical Physics
https://www.readbyqxmd.com/read/29352777/perspective-theory-of-quantum-transport-in-molecular-junctions
#15
Michael Thoss, Ferdinand Evers
Molecular junctions, where single molecules are bound to metal or semiconductor electrodes, represent a unique architecture to investigate molecules in a distinct nonequilibrium situation and, in a broader context, to study basic mechanisms of charge and energy transport in a many-body quantum system at the nanoscale. Experimental studies of molecular junctions have revealed a wealth of interesting transport phenomena, the understanding of which necessitates theoretical modeling. The accurate theoretical description of quantum transport in molecular junctions is challenging because it requires methods that are capable to describe the electronic structure and dynamics of molecules in a condensed phase environment out of equilibrium, in some cases with strong electron-electron and/or electronic-vibrational interaction...
January 21, 2018: Journal of Chemical Physics
https://www.readbyqxmd.com/read/29352630/surgical-damage-to-the-lymphatic-system-promotes-tumor-growth-via-impaired-adaptive-immune-response
#16
Yoshiyuki Nakamura, Yasuhiro Fujisawa, Naoko Okiyama, Rei Watanabe, Ryota Tanaka, Yosuke Ishitsuka, Hideaki Tahara, Manabu Fujimoto
BACKGROUND: Both lymph nodes (LNs) and lymphatic channels from primary sites to regional LNs are critical for initiation of adaptive immunity. However, as LNs are common metastatic sites in skin cancers, LN biopsies or dissections are frequently performed. In addition, reconstructive skin flaps after tumor resection may damage lymphatic flow from primary sites to regional LNs. OBJECTIVE: This study was designed to investigate the effect on tumor progression by such surgeries...
December 29, 2017: Journal of Dermatological Science
https://www.readbyqxmd.com/read/29352573/h%C3%A2-control-for-uncertain-linear-system-over-networks-with-bernoulli-data-dropout-and-actuator-saturation
#17
Jimin Yu, Chenchen Yang, Xiaoming Tang, Ping Wang
This paper investigates the H∞ control problems for uncertain linear system over networks with random communication data dropout and actuator saturation. The random data dropout process is modeled by a Bernoulli distributed white sequence with a known conditional probability distribution and the actuator saturation is confined in a convex hull by introducing a group of auxiliary matrices. By constructing a quadratic Lyapunov function, effective conditions for the state feedback-based H∞ controller and the observer-based H∞ controller are proposed in the form of non-convex matrix inequalities to take the random data dropout and actuator saturation into consideration simultaneously, and the problem of non-convex feasibility is solved by applying cone complementarity linearization (CCL) procedure...
January 15, 2018: ISA Transactions
https://www.readbyqxmd.com/read/29352322/qportal-a-platform-for-data-driven-biomedical-research
#18
Christopher Mohr, Andreas Friedrich, David Wojnar, Erhan Kenar, Aydin Can Polatkan, Marius Cosmin Codrea, Stefan Czemmel, Oliver Kohlbacher, Sven Nahnsen
Modern biomedical research aims at drawing biological conclusions from large, highly complex biological datasets. It has become common practice to make extensive use of high-throughput technologies that produce big amounts of heterogeneous data. In addition to the ever-improving accuracy, methods are getting faster and cheaper, resulting in a steadily increasing need for scalable data management and easily accessible means of analysis. We present qPortal, a platform providing users with an intuitive way to manage and analyze quantitative biological data...
2018: PloS One
https://www.readbyqxmd.com/read/29352228/dual-band-metamaterial-antenna-for-lte-bluetooth-wimax-system
#19
Md Mehedi Hasan, Mohammad Rashed Iqbal Faruque, Mohammad Tariqul Islam
A compact metamaterial inspired antenna operate at LTE, Bluetooth and WiMAX frequency band is introduced in this paper. For the lower band, the design utilizes an outer square metallic strip forcing the patch to radiate as an equivalent magnetic-current loop. For the upper band, another magnetic current loop is created by adding metamaterial structure near the feed line on the patch. The metamaterial inspired antenna dimension of 42 × 32 mm2 compatible to wireless devices. Finite integration technique based CST Microwave Studio simulator has been used to design and numerical investigation as well as lumped circuit model of the metamaterial antenna is explained with proper mathematical derivation...
January 19, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29352116/the-chemical-fluctuation-theorem-governing-gene-expression
#20
Seong Jun Park, Sanggeun Song, Gil-Suk Yang, Philip M Kim, Sangwoon Yoon, Ji-Hyun Kim, Jaeyoung Sung
Gene expression is a complex stochastic process composed of numerous enzymatic reactions with rates coupled to hidden cell-state variables. Despite advances in single-cell technologies, the lack of a theory accurately describing the gene expression process has restricted a robust, quantitative understanding of gene expression variability among cells. Here we present the Chemical Fluctuation Theorem (CFT), providing an accurate relationship between the environment-coupled chemical dynamics of gene expression and gene expression variability...
January 19, 2018: Nature Communications
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