Background: Stochastic simulation can be used to illustrate the development of biological systems over time and the stochastic nature of these processes. Currently available programs for stochastic simulation, however...
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Background: Stochastic simulation can be used to illustrate the development of biological systems over time and the stochastic nature of these processes. Currently available programs for stochastic simulation, however, are limited in that they either a) do not provide the most efficient simulation algorithms and are difficult to extend, b) cannot be easily integrated into other applications or c) do not allow to monitor and intervene during the simulation process in an easy and intuitive way. Thus, in order to use stochastic simulation in innovative high-level modeling and analysis approaches more flexible tools are necessary. Results: In this article, we present FERN (Framework for Evaluation of Reaction Networks), a Java framework for the efficient simulation of chemical reaction networks. FERN is subdivided into three layers for network representation, simulation and visualization of the simulation results each of which can be easily extended. It provides efficient and accurate state-of-the-art stochastic simulation algorithms for well-mixed chemical systems and a powerful observer system, which makes it possible to track and control the simulation progress on every level. To illustrate how FERN can be easily integrated into other systems biology applications, plugins to Cytoscape and CellDesigner are included. These plugins make it possible to run simulations and to observe the simulation progress in a reaction network in real-time from within the Cytoscape or CellDesigner environment. Conclusion: FERN addresses shortcomings of currently available stochastic simulation programs in several ways. First, it provides a broad range of efficient and accurate algorithms both for exact and approximate stochastic simulation and a simple interface for extending to new algorithms. FERN's implementations are considerably faster than the C implementations of gillespie2 or the Java implementations of ISBJava. Second, it can be used in a straightforward way both as a stand-alo
Gas-solid heat transfer during dilute phase pneumatic conveying is numerically studied by formulating and solving a two-dimensional, two-fluid model. The model is arrived after neglecting minority terms in the governi...
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Gas-solid heat transfer during dilute phase pneumatic conveying is numerically studied by formulating and solving a two-dimensional, two-fluid model. The model is arrived after neglecting minority terms in the governing equations. A new algorithm for solution of governing equations is proposed, that is non-iterative and computationally less intensive. The performance of simulation algorithm is verified in comparison with the literature data. Heat transfer simulations have been carried out for particles of different sizes at a constant solid to gas mass flow ratio. Various aspects of profiles of phase velocities and temperatures and the effect of particle size on these profiles have been discussed. (c) 2006 Elsevier Ltd. All rights reserved.
A new technique for modelling multiple- order Compton scatter which uses the absolute probabilities relating the image space to the projection space in 3D whole body PET is presented. The details considered in this wo...
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A new technique for modelling multiple- order Compton scatter which uses the absolute probabilities relating the image space to the projection space in 3D whole body PET is presented. The details considered in this work give a valuable insight into the scatter problem, particularly for multiple scatter. Such modelling is advantageous for large attenuating media where scatter is a dominant component of the measured data, and where multiple scatter may dominate the total scatter depending on the energy threshold and object size. The model offers distinct features setting it apart from previous research: ( 1) specification of the scatter distribution for each voxel based on the transmission data, the physics of Compton scattering and the specification of a given PET system;( 2) independence from the true activity distribution;( 3) in principle no scaling or iterative process is required to find the distribution;( 4) explicit multiple scatter modelling;( 5) no scatter subtraction or addition to the forward model when included in the system matrix used with statistical image reconstruction methods;( 6) adaptability to many different scatter compensation methods from simple and fast to more sophisticated and therefore slower methods;( 7) accuracy equivalent to that of a Monte Carlo model. The scatter model has been validated using Monte Carlo simulation (SimSET).
Automatic design of electronic logic circuits has become a new research focus with the cooperation of FPGA technology and intelligent algorithms in recent twenty years. However, as the size of logic circuits became la...
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ISBN:
(纸本)9783540746256
Automatic design of electronic logic circuits has become a new research focus with the cooperation of FPGA technology and intelligent algorithms in recent twenty years. However, as the size of logic circuits became larger and more complex, it has become difficult for the automatic design method to obtain valid and optimized circuits. Based on a divide-and-conquer approach, a two-layer encoding scheme was devised for design of electronic logic circuits. In the process of evolvement, each layer was evolved parallel and they contacted each other at the same time. Moreover, in order to simulate and evaluate evolved electronic logic circuits, a two-step simulation algorithm was proposed to reduce pp computation complexity of simulating circuits and to improve the simulation efficiency. At last, a random number generator was automatically designed with this encoding scheme and the proposed simulation algorithm, and the result showed this method was efficient.
This paper studies the simulation problem of meshes with separable buses (MSB) by meshes with multiple partitioned buses (MMPB). The M S B and the M M P B are the mesh-connected computers with row/column broadcasting ...
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This paper studies the simulation problem of meshes with separable buses (MSB) by meshes with multiple partitioned buses (MMPB). The M S B and the M M P B are the mesh-connected computers with row/column broadcasting buses. The broadcasting buses of the M S B can be dynamically sectioned into smaller bus segments by program control, while those of the MMPB are statically partitioned in advance. In the M S B, each row/column has only one separable bus, while in the M M P B, each row/column has L partitioned buses (L >= 1, L is a fixed constant). Two results are shown: (1) the n x n MMPB can simulate any step of the n x n MSB time-optimally in O(n(1/(2L+1))) steps, and (2) the m x in MMPB with L = 1 can simulate any step of the n x n MSB in O(n(2)/m(2) + n(1/3)) steps (m <= n). The latter implies that the MMPB with L = 1 can solve the scaling-simulation problem of the MSB time-optimally when m = O(n(5/6)) holds. (C) 2006 Elsevier Inc. All rights reserved.
Several stochastic simulation tools have been developed recently for cell signaling. A comparative evaluation of the stochastic simulation tools is needed to highlight the current state of the development. In our stud...
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ISBN:
(纸本)9781424400324
Several stochastic simulation tools have been developed recently for cell signaling. A comparative evaluation of the stochastic simulation tools is needed to highlight the current state of the development. In our study, we have chosen to evaluate three stochastic simulation tools: Dizzy, Systems Biology Toolbox, and Copasi, using our own MATLAB (R) implementation as a benchmark. The Gillespie stochastic simulation algorithm is used in all tests. With all the tools, we are able to simulate stochastically the behavior of the selected test case and to produce similar results as our own MATLAB (R) implementation. However, it is not possible to use time-dependent inputs in stochastic simulations in Systems Biology Toolbox and Copasi. The present study is one of the first evaluations of stochastic simulation tools for realistic signal transduction pathways.
Based on the Dormand-Prince (DP) formula, a fast and effective method is proposed, which can implement automatic step-size adjustment to solve the model equations of fiber Raman amplifiers and erbium-doped fiber ampli...
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Based on the Dormand-Prince (DP) formula, a fast and effective method is proposed, which can implement automatic step-size adjustment to solve the model equations of fiber Raman amplifiers and erbium-doped fiber amplifiers (EDFAs). Numerical results show that (1) the CPU time of the proposed method is about 4.2 times smaller than that of the DIP method when the Raman amplifier propagation equations are solved;(2) our method reduces the running time by more than two orders of magnitude in comparison with the classical fourth-order Runge-Kutta method;(3) in comparison with the DP method, the proposed method can increase the computational speed by about 2.5 times in solving the model equations of EDFAs. (c) 2005 Society of Photo-Optical Instrumentation Engineers.
The design of user friendly and expressive virtual brush systems for interactive digital painting and calligraphy has attracted a lot of attention and effort in both computer graphics and human-computer interaction ci...
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The design of user friendly and expressive virtual brush systems for interactive digital painting and calligraphy has attracted a lot of attention and effort in both computer graphics and human-computer interaction circles for a long time. Providing a digital environment for paper-less artwork creation is not only challenging in terms of algorithmic design, but also promising for its potential market values. This paper proposes a novel algorithmic framework for interactive digital painting and calligraphy based a novel virtual hairy brush model. The algorithms in the kernel of our simulation framework are built upon solid modeling techniques. Implementing the algorithms, we have developed a virtual hairy brush prototype system with which end users can interactively produce high-quality digital paintings and calligraphic artwork. (The latest progress of our virtual brush project is reported at the website “http://***/~songhua/e-brush/”.)
Recent technological and theoretical advances are only now allowing the simulation of detailed kinetic models of biological systems that reflect the stochastic movement and reactivity of individual molecules within ce...
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Recent technological and theoretical advances are only now allowing the simulation of detailed kinetic models of biological systems that reflect the stochastic movement and reactivity of individual molecules within cellular compartments. The behavior of many systems could not be properly understood without this level of resolution, opening up new perspectives of using computer simulations to accelerate biological research. We review the modeling methodology applied to stochastic spatial models, also to the attention of non-expert potential users. Modeling choices, current limitations and perspectives of improvement of current general-purpose modeling/simulation platforms for biological systems are discussed. (c) 2005 Federation of European Biochemical Societies. Published by Elsevier B.V. All rights reserved.
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