Accelerated Stochastic Simulation of Large Chemical Systems

Fine-Grained Parallel and Distributed Spatial Stochastic Simulation of Biological Reactions

Large and complex systems from the EMC point of view are objects that contain different structures requiring individually composed methods for modeling as well as calculation. Automobiles, aircraft, or PCBs with devices are large and complex systems. The paper describes activities that were done to handle automotive EMC problems with computer simulations. A set of methods was compiled to allow, in a first stage, a fast calculation model generation, and, to apply in a second stage with minimum user interaction, accurate and fast multi step hybrid methods. The paper focuses less on the methods themselves, but more on the completeness of the process chain that is required to do successful simulations of automobiles or other large systems.

Current simulation tools for multibody dynamics are not problem dependent, they use the same modeling process to all cases regardless of their characteristics. In addition, real-time simulation of small multibody systems is achievable by existing simulation tools, however, real-time simulation of large and complex systems is not possible with existing methods. This is a challenge that needs to be addressed before further advances in mechanical simulation with hardware-in-the-loop and man-in-the-loop, as well as virtual prototyping are made possible. This paper addresses the issue of how the modeling process-dependent versus independent coordinates, and descriptor form versus state-space form of the equations of motion-affects the dynamic simulation of multibody systems and how it may be taken into account and added to the concept of intelligent simulation. With this new concept all the factors involved in the simulation process — modeling, equations, solution, etc. — are chosen and combined depending upon the characteristics of the system to be simulated. It is envisioned that this concept will lead to faster and more robust real-time simulators.

This paper documents a practical numerical method of evaluating damping of slow oscillations in computer simulations of large power systems. This technique has been tested and improved over the last two years. The damping coefficients can assist in evaluation of acceptable transfer limitations. The proposed method also provides a means to evaluate the sensitivity of various transfer path loadings and transmission and generation facility contingencies on system damping.

This study examines the performance of integration methods for hybrid simulation of large and complex structural systems in the context of structural collapse due to seismic excitations. The target application is not necessarily for real-time testing, but rather for models that involve large-scale physical sub-structures and highly nonlinear numerical models. Four case studies are presented and discussed. In the first case study, the accuracy of integration schemes including two widely used methods, namely, modified version of the implicit Newmark with fixed-number of iteration (iterative) and the operator-splitting (non-iterative) is examined through pure numerical simulations. The second case study presents the results of 10 hybrid simulations repeated with the two aforementioned integration methods considering various time steps and fixed-number of iterations for the iterative integration method. The physical sub-structure in these tests consists of a single-degree-of-freedom (SDOF) cantilever column with replaceable steel coupons that provides repeatable highlynonlinear behavior including fracture-type strength and stiffness degradations. In case study three, the implicit Newmark with fixed-number of iterations is applied for hybrid simulations of a 1:2 scale steel moment frame that includes a relatively complex nonlinear numerical substructure. Lastly, a more complex numerical substructure is considered by constructing a nonlinear computational model of a moment frame coupled to a hybrid model of a 1:2 scale steel gravity frame. The last two case studies are conducted on the same porotype structure and the selection of time steps and fixed number of iterations are closely examined in pre-test simulations. The generated unbalance forces is used as an index to track the equilibrium error and predict the accuracy and stability of the simulations.

This paper documents a practical numerical method of evaluating damping of slow oscillations in computer simulations of large power systems. This technique has been tested and improved over the last two years. The damping coefficients can assist in evaluation of acceptable transfer limitations. The proposed method also provides a means to evaluate the sensitivity of various transfer path loadings and transmission and generation facility contingencies on system damping.

Agent-based simulation of large multicellular biological systems has become a viable option owing to affordable parallel computers, such as Beowulf-style clusters. We describe a scalable modular software platform that (i) provides for an easy integration of different solvers computing internal dynamics of the cells, and (ii) dynamically adapts to the changing loads on the cluster nodes using a load balancing algorithm. Simulations of systems of about 100,000 bacterial cells have been shown to be feasible using the platform.KeywordsBiological CellNode PerformanceSignal Transduction NetworkBrownian Motion ModelList Schedule AlgorithmThese keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.

The scalability of massively parallel algorithms is a fundamental question in computer science. We study the scalability and the efficiency of a conservative massively parallel algorithm for discrete-event simulations where the discrete events are Poisson arrivals. The parallel algorithm is applicable to a wide range of problems, including dynamic Monte Carlo simulations for large asynchronous systems with short-range interactions. The evolution of the simulated time horizon is analogous to a growing and fluctuating surface, and the efficiency of the algorithm corresponds to the density of local minima of this surface. In one dimension we find that the steady state of the macroscopic landscape is governed by the Edwards-Wilkinson Hamiltonian, which implies that the algorithm is scalable. Preliminary results for higher-dimensional logical topologies are discussed.

Interactions between lipids and membrane proteins play a key role in determining the nanoscale dynamic and structural properties of biological membranes. Molecular dynamics (MD) simulations provide a valuable tool for studying membrane models, complementing experimental approaches. It is now possible to simulate large membrane systems, such as simplified models of bacterial and viral envelope membranes. Consequently, there is a pressing need to develop tools to visualize and quantify the dynamics of these immense systems, which typically comprise millions of particles. To tackle this issue, we have developed visual and quantitative analyses of molecular positions and their velocity field using path line, vector field and streamline techniques. This allows us to highlight large, transient flow-like movements of lipids and to better understand crowding within the lipid bilayer. The current study focuses on visualization and analysis of lipid dynamics. However, the methods are flexible and can be readily applied to e.g. proteins and nanoparticles within large complex membranes. The protocols developed here are readily accessible both as a plugin for the molecular visualization program VMD and as a module for the MDAnalysis library.

The research is aimed at solving the problem of faster than real time distributed interactive simulation for large scale systems based on personal computer networks or workstation networks. The HLA services are integrated with the reflective memory networks and the sector minimization method are used in the study. An approach is proposed to solve the problem of faster than real time data transfer, ensuring the general speed of simulation and the speed of instantaneous synchronization for the large scale system simulation. A platform based on this approach provides interface services of which the call methods are the same as HLA. Using the platform, the existing HLA simulation systems can be conveniently migrated and new simulation systems can be developed and run in faster than real time.

A parallel implementation of the Stokesian Dynamics method applied to the simulation of colloidal suspensions

In the context of a research project with the aim of investigating the influence of human-machine interfaces on the error-proneness of situation assessment in technical systems by humans, extensive user experiments have been conducted. The paper reports influences of a pattern oriented display (the mass data display) as well as time oriented displays (trend graphs) on the classification of process states. All interfaces that have been investigated were based on P&I (piping and instrumentation) diagrams, a threshold oriented visualisation form, which is commonly used in simulation and control (S&C) of large technical systems. Comparing the different displays with each other a strategy of adding and removing was applied. Primarily, the features of investigated displays are introduced and discussed. Based on the features of displays the assumed performance of each display is shown. Finally, the assumed and measured performances are compared with each other. The results are discussed as well in a taxonomy context.

Multi-scale methods such as wavelet and multigrid schemes are efficient algorithms for the numerical solution of large classes of partial differential equations (PDEs). In this chapter we illustrate the basic ideas behind iterative methods for the solution of large linear systems which arise from the discretisation of PDEs. Besides describing the concepts of wavelet preconditioning, we summarise the main ingredients of multigrid methods. Examples from computational geosciences will show the importance of multi-scale methods for the simulation of large and complex systems.

A new QM/MM molecular dynamics approach that can deal with the dynamics of large real systems involving several simultaneous active zones is presented. Multiple, unconnected but interacting quantum regions are treated independently in an ordinary QM/MM approach but in a manner which converges to a unique simulation. The multiple active zones in the hybrid QM/MM molecular dynamics methodology (maz-QM/MM MD) involve molecular dynamics that is driving the whole simulation with several parallel executions of energy gradients within the QM/MM approach that merge into each MD step. The Ewald-summation method is used to incorporate long-range electrostatic interactions among the active zones in conjunction with periodic boundary conditions. To illustrate and ascertain capabilities and limitations, we present several benchmark calculations using this approach. Our results show that the maz-QM/MM MD method is able to provide simultaneous treatment of several active zones of very large proteins such as the Cu-4His-ΔC* cage, a self-assembly of a 24-mer cage-like protein ferritin.

This review attempts to bring together basic and systematic information which has been gathered on cellulose structure, types, principally that of native cellulose, over the last few decades. Even though advances have been made in the field of crystallography, powder crystallography cannot yield a definitive cellulose structure and single crystal diffraction is not possible due to the lack of suitable crystals. Knowledge obtained on the biosynthesis of native cellulose and on the polymorphy of cellulose and its derivatives help our understanding of ultrastructure. Many inconsistencies between early crystallographic studies of native cellulose have been clarified by the discovery that two polymorphs (á and â) of cellulose I exist. Models of the possible ultrastructural arrangements within native cellulose have been put forward over the decades; with advancement in technology, computer simulations of small and large systems are being created to test the viability of these ultrastructural models. It is hoped that this review will aid in the understanding of the complexity and uncertainties that still exist in this subject.