Simulation Library Research Articles

SBMLSimulator: A Java Tool for Model Simulation and Parameter Estimation in Systems Biology.

The identification of suitable model parameters for biochemical reactions has been recognized as a quite difficult endeavor. Parameter values from literature or experiments can often not directly be combined in complex reaction systems. Nature-inspired optimization techniques can find appropriate sets of parameters that calibrate a model to experimentally obtained time series data. We present SBMLsimulator, a tool that combines the Systems Biology Simulation Core Library for dynamic simulation of biochemical models with the heuristic optimization framework EvA2. SBMLsimulator provides an intuitive graphical user interface with various options as well as a fully-featured command-line interface for large-scale and script-based model simulation and calibration. In a parameter estimation study based on a published model and artificial data we demonstrate the capability of SBMLsimulator to identify parameters. SBMLsimulator is useful for both, the interactive simulation and exploration of the parameter space and for the large-scale model calibration and estimation of uncertain parameter values.

Implementing a modeling software for animated protein-complex interactions using a physics simulation library.

To better understand the behaviors and structural dynamics of proteins within a cell, novel software tools are being developed that can create molecular animations based on the findings of structural biology. This study proposes our method developed based on our prototypes to detect collisions and examine the soft-body dynamics of molecular models. The code was implemented with a software development toolkit for rigid-body dynamics simulation and a three-dimensional graphics library. The essential functions of the target software system included the basic molecular modeling environment, collision detection in the molecular models, and physical simulations of the movement of the model. Taking advantage of recent software technologies such as physics simulation modules and interpreted scripting language, the functions required for accurate and meaningful molecular animation were implemented efficiently.

Developing a physical BIM library for building thermal energy simulation

Insufficient interoperability resulting from complex data exchange between architectural design and building energy simulation prevents the efficient use of energy performance analyses in the early design stage. This paper presents the development of a Modelica library for Building Information Modeling (BIM)-based building energy simulation (ModelicaBIM library) using an Object-Oriented Physical Modeling (OOPM) approach and Modelica, an equation-based OOPM language. By using the ModelicaBIM library, our project investigates system interfaces between BIM and energy simulation, which can perform semi-automatic translation from the building models in BIM to building energy modeling (BEM) using a BIM's authoring tool's Application Programming Interface (API). The ModelicaBIM library consists of OOPM-based BIM classes and OOPM-based BIM structure. OOPM-based BIM classes represent building component information. OOPM-based BIM structure consists of test case models that demonstrate (i) how building information in BIM can be transformed to OOPM and (ii) how design operations in BIM, such as changing a building geometry and editing building components, can be translated into BEM. A case study for simulation result comparisons has been conducted using (i) OOPM-based BIM models in the ModelicaBIM library and (ii) LBNL Modelica Buildings library (a Modelica-based building thermal simulation library developed by Lawrence Berkeley National Laboratory). Our implementation shows that the ModelicaBIM library enables (i) objects in BIM to be translated into the OOPM-based energy models and (ii) existing OOPM library to be utilized as a simulation solver for BIM-based energy simulation.

A C++ template library for efficient forward-time population genetic simulation of large populations.

fwdpp is a C++ library of routines intended to facilitate the development of forward-time simulations under arbitrary mutation and fitness models. The library design provides a combination of speed, low memory overhead, and modeling flexibility not currently available from other forward simulation tools. The library is particularly useful when the simulation of large populations is required, as programs implemented using the library are much more efficient than other available forward simulation programs.

A remanufacturing process library for environmental impact simulations

‘Closed loop’ end-of-life strategies such as remanufacturing must be applied to create eco-efficient products. Remanufacturing may be a key element in reducing the environmental impact of products, but this remains to be proved. The aim of this study is to help designers evaluate the environmental impacts of their remanufacturing process during the design phase. The first task is to identify, list and classify the various remanufacturing processes (disassembly, cleaning, sorting and controlling, reconditioning, reassembly) by the type of process and then estimate the environmental impact for each process. These processes are then formalized by characterization and organized in a database. Using a simulator, the different processes can be aggregated to assess the environmental impacts of a remanufacturing line. An example is presented in the last part of this paper to illustrate the proposal.

Deformation behavior of Zr65Cu17.5Ni10Al7.5 in superplastic forming with silicon mould: Simulation and application

We investigated the deformation behaviors of Zr65Cu17.5Ni10Al7.5 in superplastic forming in silicon mould via numerical modeling and experiments. The data needed for the constitutive formulation were obtained from compressive tests to establish a material library for finite-element simulation using a DEFORM 3D software. A constant speed forming process of a micro gear was modeled where the loading force, feature size and amount of deformation in the micro gear in silicon mould were analyzed in detail for the optimal requirements of micro gear forming and the protection of silicon mould. Guided by the modeling parameters, an amorphous metal micro gear was successfully obtained by our home-made superplastic forming system with the optimized parameters (temperature of 683 K, top speed of 0.003 mm/s until the load force reaching limiting value at 1960 N, and a gradually decelerating process for holding the force to the end). Our work gives a good example for optimization of superplastic forming and fabrication of BMGs in microparts.

Research of Case-Based Teaching of Electrical and Electronic Technology

Electrical and electronic technology is a foundation course in universities and colleges of technology. Some methods and suggestions of case-based teaching are presented in this paper with respect to the rational design of teaching content, effective design of assessment methods, construction of course website, teaching case library and simulation library.

Value network modelling and simulation for strategic analysis: a discrete event simulation approach

The survival of a company nowadays depends on answering to a customer-driven economy, and therefore relies on the performance of its entire network of partners. Competition is no longer among companies nor among supply chains, but rather between networks of companies which form a value network. Thus, the need has arisen to analyse the performance of a network of companies, and include the customer-perceived value in the strategic decision-making process. This paper proposes a framework and a tool to model, simulate and analyse a value network as a decision support system. The method extends the SimulValor approach and language. The discrete event simulation tool relies on a developed value network simulation library. This paper presents a case study in the shoemaking industry to validate the proposed approach.

Modeling and Simulation Library's Service for Net Generation: A System Dynamics Framework

The existence of a university library as an information center is required to provide services in accordance with the criteria and the needs of users being served. Users who utilize the services of university library are dominated by students who are classified as net generation. Today’s generation called “Net generation”, has different behavior pattern in seeking information compared to the previous generation. Understanding this will help librarians make innovations in library services that will ultimately improve number of the library visitors from this net generation. This study focused on modeling in the front office library service, designing the projection and analyzing the simulation results with cost benefit analysis. The system dynamics method allows writers to conduct comprehensive research to study the behavior and improve system performance. From the simulation results of pessimistic and optimistic projections, the total physical visitor of optimistic projection can achieve 23% higher than pessimistic projection. The increase in total website visitor on optimistic projection reached 169.701 visits at month 36. Meanwhile in the pessimistic projection, total website visitors reached 118.440 by the end of the 36th month. According to cost benefit analysis, the pessimistic projection provides a B/C ratio of 0.97, meanwhile the optimistic projection provides a B/C ratio of 1.38152. Optimistic projection has a better value than the pessimistic projection in terms of cost benefit analysis. Optimistic projection proposes the implementation of visual search, online acquisition, upgrading the server hardware, installation of Wi-Fi, improved comfort furniture, improved sanitation, additional opening hours, friendliness and expertise of library staffs in delivering services and a library exhibition.

Practical Benefits of Aspect-Oriented Programming Paradigm in Discrete Event Simulation

Aspect-oriented modeling and simulation is a new approach which uses the separation of concerns principle to enhance the quality of models and simulation tools. It adopts the separation of concerns (SOC) principle. Thus, crosscutting concerns such as processes synchronization, steady state detection, and graphical animation could be separated from simulation functional modules. The capture of crosscutting concerns in a modular way is carried out to cope with complexity and to achieve the required engineering quality factors such as robustness, modularity, adaptability, and reusability. This paper provides a summary of aspect-oriented paradigm with its usage in simulation by illustrating the main crosscutting concerns that may infect simulation systems. A practical example is given with the use of the Japrosim discrete event simulation library.

A new visual library for modeling and simulation of renewable energy desalination systems (REDS)

The recourse to renewable energy systems in general has become a reality. Thus, it has become very important for engineers to design and simulate such systems that serve the renewable desalination plants. A computer software package has been developed by the authors for design and simulation of renewable energy desalination systems (REDS). This was motivated by unavailability of such packages in the literature or on a commercial scale. Solar desalination systems, wind desalination systems, and geothermal desalination systems software libraries became affirmative parts of the main REDS software library. This library enables the user to construct different configurations by clicking the mouse over the required units (blocks). The interface aids designers, scientists, and operators to perform different analyses and calculations such as energy, exergy, cost, and thermoeconomics. Typical desalination processes such as a multi-stage flash, multi-effect distillation, and reverse osmosis are numerically modeled and embedded within the main library of the developed software. REDS shows a wide scope of validity, reliability, and capability to model and simulate renewable desalination systems.

GTKDynamo: a PyMOL plug-in for QC/MM hybrid potential simulations.

Hybrid quantum chemical/molecular mechanical (QCMM) potentials are very powerful tools for molecular simulation. They are especially useful for studying processes in condensed phase systems, such as chemical reactions that involve a relatively localized change in electronic structure and where the surrounding environment contributes to these changes but can be represented with more computationally efficient functional forms. Despite their utility, however, these potentials are not always straightforward to apply since the extent of significant electronic structure changes occurring in the condensed phase process may not be intuitively obvious. To facilitate their use, we have developed an open-source graphical plug-in, GTKDynamo that links the PyMOL visualization program and the pDynamo QC/MM simulation library. This article describes the implementation of GTKDynamo and its capabilities and illustrates its application to QC/MM simulations.

A Comparision Study of Common Routing Protocols Used In Wireless Ad-Hoc Networks

The aim of this study is to analyze and compare performance of both reactive and proactive Mobile Ad hoc Networks (MANETs) routing protocols using different environments. Wireless networks are divided into two types: infrastructure and ad hoc network. In wireless ad hoc networks each node can be a sender, router and receiver, so these types of network are less structure compared to infrastructure network. Therefore wireless ad hoc networks need special routing protocols to overcome the limitations of wireless ad hoc networks. Wireless ad hoc networks routing protocols can be categorized into two types: reactive (on demand) routing protocols and proactive routing protocols. In proactive routing protocols the nodes periodically send control messages across the network to build routing table. Different routing protocols have been simulated using GloMoSim (Global Mobile Information system simulation) library and PARSEC compiler. Five multi-hop wireless ad hoc network routing protocols have been simulated to cover a range of design choices: Wireless Routing Protocol (WRP), Fisheye State Routing (FSR), Dynamic Source Routing (DSR), Ad hoc On-demand Distance Vector (AODV) and Location Aided Routing (LAR). The protocols are evaluated in different environments to investigate performance metrics. Performance metric includes the following aspects: packets deliver ratio, end-to-end delay and end-to-end throughput.

Uncorrelated Power Supply Noise and Ground Bounce Consideration for Test Pattern Generation

Power supply noise and ground bounce can cause considerable path delay variations. Capturing the worst case power supply noise at a gate level is not a sufficient indicator for measuring the worst case path delay. Furthermore, path delay variations depend on multiple parameters such as input stimuli, cell placement, switching frequency, and available decoupling capacitors. All these variables obscure the rapport between supply noise and path delay and make the selection of stimuli for worst case path delay a difficult task during test pattern generation. In this paper, we utilize power supply noise and ground bounce distribution along with physical design data to generate test patterns for capturing worst case path delay. We propose accurate close-form mathematical models for capturing the effect of power supply noise and ground bounce on path delay. These models are based on modified nodal analysis formulation of power and ground networks, where current waveforms are obtained from levelized simulation and cell library characterization. The proposed test pattern generation flow is a simulated-annealing-based iterative process, which utilizes mathematical models for capturing the impact of supply noise on path delay for a given input pattern. We perform experiments on ITC'99 benchmarks and show that path delay variation can be considerable if test patterns are not properly selected.

Chaste: An Open Source C++ Library for Computational Physiology and Biology

Chaste — Cancer, Heart And Soft Tissue Environment — is an open source C++ library for the computational simulation of mathematical models developed for physiology and biology. Code development has been driven by two initial applications: cardiac electrophysiology and cancer development. A large number of cardiac electrophysiology studies have been enabled and performed, including high-performance computational investigations of defibrillation on realistic human cardiac geometries. New models for the initiation and growth of tumours have been developed. In particular, cell-based simulations have provided novel insight into the role of stem cells in the colorectal crypt. Chaste is constantly evolving and is now being applied to a far wider range of problems. The code provides modules for handling common scientific computing components, such as meshes and solvers for ordinary and partial differential equations (ODEs/PDEs). Re-use of these components avoids the need for researchers to ‘re-invent the wheel’ with each new project, accelerating the rate of progress in new applications. Chaste is developed using industrially-derived techniques, in particular test-driven development, to ensure code quality, re-use and reliability. In this article we provide examples that illustrate the types of problems Chaste can be used to solve, which can be run on a desktop computer. We highlight some scientific studies that have used or are using Chaste, and the insights they have provided. The source code, both for specific releases and the development version, is available to download under an open source Berkeley Software Distribution (BSD) licence at http://www.cs.ox.ac.uk/chaste, together with details of a mailing list and links to documentation and tutorials.

Pymote: High Level Python Library for Event-Based Simulation and Evaluation of Distributed Algorithms

In recent years we have witnessed strong development and widespread use of powerful wirelessly connected platforms, thus the set of the related problems that need to be solved by distributed algorithms is growing rapidly. Some of them present large obstacles in harnessing the full potential of this new technology, so there is an imminent need for a fast and easy evaluation of new ideas and approaches. Simulation is a fundamental part of distributed algorithm design and evaluation process. In this paper, we present a library for event-based simulation and evaluation of distributed algorithms. This library provides a set of simple but powerful tools with a goal to ease virtual setup of a complex system such as a distributed network of communicating entities and to define, simulate, and analyze its behavior. In order to reduce a huge problem space inherent in such systems, our library is using a high level of abstraction. This is made possible by a strict and complete definition of the distributed computing environment. The library is implemented in Python whose simple and expressive syntax provides a possibility of minimal implementations and a mild learning curve. In addition to executing automated simulations or larger experiments, the library fully supports interactive mode along with a step-by-step execution, which can be a very powerful combination.

Dynamic analysis of manufacturing cells: a dedicated simulation library and an empirical simulation study

The design of cellular manufacturing systems (CMS) is a complex decision process that, in general, has to be decomposed into several sub-problems. Analytical techniques have been used to tackle each of these sub-problems individually but its usage is limited when designing real-world CMS. Simulation tools enable the decision maker to capture the dynamic nature of CMS allowing the test of different designs and their evaluation through a wide set of performance measures. This research describes the structural modelling and implementation of a simulation template (simulation library) for the dynamic analysis of cellular manufacturing systems and illustrates its utilisation in the development of a real simulation study. The template was modelled using object-oriented concepts and some of its components were implemented in the simulation software ArenaÒ. The utilisation of the template in real CMS scenarios is allowing its validation and its continuous enhancement.

Vega: Non‐Linear FEM Deformable Object Simulator

AbstractThis practice and experience paper describes a robust C++ implementation of several non‐linear solid three‐dimensional deformable object strategies commonly employed in computer graphics, named the Vega finite element method (FEM) simulation library. Deformable models supported include co‐rotational linear FEM elasticity, Saint–Venant Kirchhoff FEM model, mass–spring system and invertible FEM models: neo‐Hookean, Saint–Venant Kirchhoff and Mooney–Rivlin. We provide several timestepping schemes, including implicit Newmark and backward Euler integrators, and explicit central differences. The implementation of material models is separated from integration, which makes it possible to employ our code not only for simulation, but also for deformable object control and shape modelling. We extensively compare the different material models and timestepping schemes. We provide practical experience and insight gained while using our code in several computer animation and simulation research projects.

INTERACTIVE 3D LANDSCAPES ON LINE

Abstract. The paper describes challenges identified while developing browser embedded 3D landscape rendering applications, our current approach and work-flow and how recent development in browser technologies could affect. All the data, even if processed by optimization and decimation tools, result in very huge databases that require paging, streaming and Level-of-Detail techniques to be implemented to allow remote web based real time fruition. Our approach has been to select an open source scene-graph based visual simulation library with sufficient performance and flexibility and adapt it to the web by providing a browser plug-in. Within the current Montegrotto VR Project, content produced with new pipelines has been integrated. The whole Montegrotto Town has been generated procedurally by CityEngine. We used this procedural approach, based on algorithms and procedures because it is particularly functional to create extensive and credible urban reconstructions. To create the archaeological sites we used optimized mesh acquired with laser scanning and photogrammetry techniques whereas to realize the 3D reconstructions of the main historical buildings we adopted computer-graphic software like blender and 3ds Max. At the final stage, semi-automatic tools have been developed and used up to prepare and clusterise 3D models and scene graph routes for web publishing. Vegetation generators have also been used with the goal of populating the virtual scene to enhance the user perceived realism during the navigation experience. After the description of 3D modelling and optimization techniques, the paper will focus and discuss its results and expectations.

Phantom-GRAPE: Numerical software library to accelerate collisionless N-body simulation with SIMD instruction set on x86 architecture

We have developed a numerical software library for collisionless N-body simulations named “Phantom-GRAPE” which highly accelerates force calculations among particles by use of a new SIMD instruction set extension to the x86 architecture, Advanced Vector eXtensions (AVX), an enhanced version of the Streaming SIMD Extensions (SSE). In our library, not only the Newton’s forces, but also central forces with an arbitrary shape f(r), which has a finite cutoff radius rcut (i.e. f(r)=0 at r>rcut), can be quickly computed. In computing such central forces with an arbitrary force shape f(r), we refer to a pre-calculated look-up table. We also present a new scheme to create the look-up table whose binning is optimal to keep good accuracy in computing forces and whose size is small enough to avoid cache misses. Using an Intel Core i7–2600 processor, we measure the performance of our library for both of the Newton’s forces and the arbitrarily shaped central forces. In the case of Newton’s forces, we achieve 2×109 interactions per second with one processor core (or 75 GFLOPS if we count 38 operations per interaction), which is 20 times higher than the performance of an implementation without any explicit use of SIMD instructions, and 2 times than that with the SSE instructions. With four processor cores, we obtain the performance of 8×109 interactions per second (or 300 GFLOPS). In the case of the arbitrarily shaped central forces, we can calculate 1×109 and 4×109 interactions per second with one and four processor cores, respectively. The performance with one processor core is 6 times and 2 times higher than those of the implementations without any use of SIMD instructions and with the SSE instructions. These performances depend only weakly on the number of particles, irrespective of the force shape. It is good contrast with the fact that the performance of force calculations accelerated by graphics processing units (GPUs) depends strongly on the number of particles. Substantially weak dependence of the performance on the number of particles is suitable to collisionless N-body simulations, since these simulations are usually performed with sophisticated N-body solvers such as Tree- and TreePM-methods combined with an individual timestep scheme. We conclude that collisionless N-body simulations accelerated with our library have significant advantage over those accelerated by GPUs, especially on massively parallel environments.