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Approximate simulation of cortical microtubule models using dynamical graph grammars

PHYSICAL BIOLOGY 2023年第5期20卷 055002-055002页

作者： Medwedeff, Eric Mjolsness, Eric San Diego State Univ Computat Sci Res Ctr 5500 Campanile Dr San Diego CA 92182 USA Univ Calif Irvine Dept Comp Sci Irvine CA 92697 USA Univ Calif Irvine Dept Math Irvine CA 92697 USA

Dynamical graph grammars (DGGs) are capable of modeling and simulating the dynamics of the cortical microtubule array (CMA) in plant cells by using an exact simulation algorithm derived from a master equation;however, the exact method is slow for large systems. We present preliminary work on an approximate simulation algorithm that is compatible with the DGG formalism. The approximate simulation algorithm uses a spatial decomposition of the domain at the level of the system's time-evolution operator, to gain efficiency at the cost of some reactions firing out of order, which may introduce errors. The decomposition is more coarsely partitioned by effective dimension (d = 0 to 2 or 0 to 3), to promote exact parallelism between different subdomains within a dimension, where most computing will happen, and to confine errors to the interactions between adjacent subdomains of different effective dimensions. To demonstrate these principles we implement a prototype simulator, and run three simple experiments using a DGG for testing the viability of simulating the CMA. We find evidence indicating the initial formulation of the approximate algorithm is substantially faster than the exact algorithm, and one experiment leads to network formation in the long-time behavior, whereas another leads to a long-time behavior of local alignment.

关键词： numerical computing dynamic graph grammars cortical microtubule array simulation algorithm cell complex local graph dynamics operator splitting

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iBrain: a simulation and visualization tool for activation of brain areas on a realistic 3D brain image

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BMC Neuroscience 2007年第2期8卷 1-2页

作者： Tohru Suzuki Kazuhisa Ichikawa Norio Fujimaki Department of Brain and Bioinformation Science Kanazawa Institute of Technology Hakusan Ishikawa Japan Biological ICT Group Kobe Advanced ICT Research Center National Institute of Information and Communications Technology Kobe Hyougo Japan

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Understanding competing risks: a simulation point of view

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BMC MEDICAL RESEARCH METHODOLOGY 2011年第1期11卷 86-86页

作者： Allignol, Arthur Schumacher, Martin Wanner, Christoph Drechsler, Christiane Beyersmann, Jan Univ Freiburg Freiburg Ctr Data Anal & Modeling D-7800 Freiburg Germany Univ Med Ctr Freiburg Inst Med Biometry & Med Informat Freiburg Germany Univ Wurzburg Dept Med 1 Div Nephrol D-97070 Wurzburg Germany

Background: Competing risks methodology allows for an event-specific analysis of the single components of composite time-to-event endpoints. A key feature of competing risks is that there are as many hazards as there are competing risks. This is not always well accounted for in the applied literature. Methods: We advocate a simulation point of view for understanding competing risks. The hazards are envisaged as momentary event forces. They jointly determine the event time. Their relative magnitude determines the event type. 'Empirical simulations' using data from a recent study on cardiovascular events in diabetes patients illustrate subsequent interpretation. The method avoids concerns on identifiability and plausibility known from the latent failure time approach. Results: The 'empirical simulations' served as a proof of concept. Additionally manipulating baseline hazards and treatment effects illustrated both scenarios that require greater care for interpretation and how the simulation point of view aids the interpretation. The simulation algorithm applied to real data also provides for a general tool for study planning. Conclusions: There are as many hazards as there are competing risks. All of them should be analysed. This includes estimation of baseline hazards. Study planning must equally account for these aspects.

关键词： simulation algorithm Baseline Hazard Empirical Power simulation Point Compete Risk Analysis

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Fast Time-Relaxation algorithm to Solve Plasma Fluid Equations

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IEEE TRANSACTIONS ON PLASMA SCIENCE 2010年第9期38卷 2312-2321页

作者： Gregorio, Jose Boisse-Laporte, Caroline Alves, Luis L. Inst Super Tecn Inst Plasmas & Fusao Nucl Lab Associado P-1049001 Lisbon Portugal Univ Paris 11 CNRS Phys Gaz & Plasmas Lab F-91405 Orsay France

This paper presents a fast time-relaxation quasi-implicit algorithm to solve plasma fluid-type equations for the transport of electron particles and mean energy, the transport of heavy species (ions and neutrals), the balance of the gas thermal energy, and the description of the fields (space-charge electrostatic and electromagnetic) affecting the plasma. The algorithm separately solves and converges the different model equations, within quasi-independent calculation modules, taking advantage of their characteristic relaxation times. In particular, the full solutions to the electron and ion transport equations are sequentially obtained, contrary to the procedure usually adopted in plasma fluid-type models. The algorithm is applied to the 1-D modeling of atmospheric-pressure microplasmas in argon, produced within the end gap of a microstrip-like transmission line by a continuous microwave excitation (at 2.45-GHz frequency). The runtimes are of 25-60 min on a 2.66-GHz CPU for the convergence criteria imposing global errors smaller than 10(-4)-10(-7).

关键词： Atmospheric-pressure plasma boundary-value problem fluid model microstrip resonator nonlinear differential equations simulation algorithm

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Planning Inland Container Shipping: A Stochastic Assignment Problem 1

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23rd International Conference on Analytical and Stochastic Modelling Techniques and Applications (ASMTA)

作者： Kooiman, Kees Phillipson, Frank Sangers, Alex TNO The Hague Netherlands Erasmus Univ Rotterdam Netherlands

ISBN: (数字)9783319439044

ISBN: (纸本)9783319439044;9783319439037

In this paper a case study is presented concerning the collection and delivery of containers between a container terminal and inland ports by barges making a round trip along these ports. The goal is to maximise the number containers arriving on time, transported by barge. To account for uncertain release times of the containers a simulation algorithm is used when making online decisions whether to assign a container to a barge or not. Using a realistic problem instance it is shown that the proposed simulation algorithm is the better performing one among several other benchmark solution methods.

关键词： Inland container shipping Stochastic assignment problem simulation algorithm Multimodal transportation planning Self-optimising

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A Geometry-based Method for Prediction of Shot-peening Coverage

A Geometry-based Method for Prediction of Shot-peening Cover...

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4th International Conference of Asian-Society-for-Precision-Engineering-and-Nanotechnology (ASPEN 2011)

作者： Kim, Hong Seok Lee, Yong-Sung Shin, Ki-Hoon Seoul Natl Univ Sci & Technol Dept Mech Engn 232 Gongneung Ro Seoul 139743 South Korea Seoul Natl Univ Sci & Technol Grad Sch NID Fus Technol Seoul 139743 South Korea

ISBN: (纸本)9783037854280

Shot-peening is the process of repeatedly hitting the work piece surface with small balls, making overlapping indentations on the surface. This process is extensively used on shafts, gears, springs, and jet engine parts because it imparts compressive residual stresses on the surface, thus improving the fatigue life of components. Under-peening does not give a sufficient fatigue life while over-peening induces cracking and reduces fatigue performance. Hence, determining optimal peening conditions such as peening time is very important. In general, optimal peening conditions are experimentally determined by measuring arc-height using Almen-strip or calculating coverage using microscope images. Shot-peening coverage is defined as the proportion of the exposed surface that has been impacted in a given time of shot-peening. To save the time and effort spent in repeating experimental measurement needed whenever the geometry of a work piece and peening conditions change, this paper presents a computer simulation algorithm for the prediction of shot-peening coverage, which is based on the geometry of a work piece. An example is presented to validate the proposed method.

关键词： shot-peening coverage fatigue life optimal peening condition simulation algorithm

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Marine Internal Combustion Engine Mathematical Model 5

Marine Internal Combustion Engine Mathematical Model

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5th IEEE International Conference on Methods and Systems of Navigation and Motion Control (MSNMC)

作者： Simanenkov, A. L. Rozhkov, S. A. Kherson State Maritime Acad Operat Ship Elect & Automat Equipment Dept Kherson Ukraine

ISBN: (纸本)9781538658703

A mathematical model of single-cylinder, two-stroke, low-speed marine internal combustion engine is presented. The simulation algorithm allows to perform diagnostics of the engine during a single cycle. The developed model is universal. The required number of cylinders is recruited by combining their mathematical models. The system makes it possible to evaluate the effect of fuel oil supply amount controlling on the engine operation.

关键词： mathematical model marine internal combustion engine simulation algorithm fuel oil

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Experiments With Single Core, Multi Core, and GPU-based Computation of Cellular Automata

Experiments With Single Core, Multi Core, and GPU-based Comp...

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1st International Conference on Advances in System simulation

作者： Rybacki, Stefan Himmelspach, Jan Uhrmacher, Adelinde M. Univ Rostock Inst Comp Sci D-18051 Rostock Germany

ISBN: (纸本)9781424448630

Cellular automata are a well-known modeling formalism exploited in a wide range of application areas. In many of those, the complexity of models hampers a thorough analysis of the system under study. Therefore, efficient simulation algorithms are required. We present here a comparison of seven different simulation algorithms for cellular automata: the classical "full" simulator, the classical "discrete event" simulator, a threaded (multi core) variant of each of these, an adaptable threaded variant, and a GPU based algorithm with and without readback of calculated states. The comparison is done based on the M&S framework JAMES II by using a set of well-known models.

关键词： Cellular automata GPU Multi Core simulation algorithm

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A Monte Carlo study of high-energy photon transport in matter: application for multiple scattering investigation in Compton spectroscopy

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JOURNAL OF SYNCHROTRON RADIATION 2016年第1期23卷 244-252页

作者： Brancewicz, Marek Itou, Masayoshi Sakurai, Yoshiharu Japan Synchrotron Radiat Res Inst JASRI Sayo Hyogo 6795198 Japan

The first results of multiple scattering simulations of polarized high-energy X-rays for Compton experiments using a new Monte Carlo program, MUSCAT, are presented. The program is developed to follow the restrictions of real experimental geometries. The new simulation algorithm uses not only well known photon splitting and interaction forcing methods but it is also upgraded with the new propagation separation method and highly vectorized. In this paper, a detailed description of the new simulation algorithm is given. The code is verified by comparison with the previous experimental and simulation results by the ESRF group and new restricted geometry experiments carried out at SPring-8.

关键词： photon transport multiple scattering Monte Carlo Compton spectroscopy simulation algorithm

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simulation of magnetostatic wave envelope soliton propagation in yttrium iron garnet films

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JAPANESE JOURNAL OF APPLIED PHYSICS PART 1-REGULAR PAPERS BRIEF COMMUNICATIONS & REVIEW PAPERS 1997年第5B期36卷 2966-2969页

作者： Koike, T Ito, T Hirao, T Taguchi, N Department of Electronic Engineering Tamagawa University Machida Tokyo 194 Japan

Although formation and propagation of magnetostatic soliton waves in YIG (yttrium iron garnet) films are attracting great attention, there has been no discussion about simulating soliton formation and propagation in YIG films from the viewpoint of circuit analysis and simulation. In this report, we propose anew algorithm to simulate the magnetostatic soliton wave output. We first describe the linear magnetostatic wave equivalent circuit model we have developed and then discuss the simulation algorithm, which combines the linear equivalent circuit model and the soliton wave solution of the nonlinear Schrodinger equation. The simulated results are in excellent agreement with reported experimental results. We also find that the proposed simulation is very effective to determine various physical parameters in the YIG film for given experimental conditions.

关键词： magnetostatic wave envelope soliton yttrium iron garnet films linear equivalent circuit model simulation algorithm

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