T-cell epitope prediction and immune complex simulation using molecular dynamics:state of the art and persisting challenges

Atomistic Molecular Dynamics provides powerful and flexible tools for the prediction and analysis of molecular and macromolecular systems. Specifically, it provides a means by which we can measure theoretically that which cannot be measured experimentally: the dynamic time-evolution of complex systems comprising atoms and molecules. It is particularly suitable for the simulation and analysis of the otherwise inaccessible details of MHC-peptide interaction and, on a larger scale, the simulation of the immune synapse. Progress has been relatively tentative yet the emergence of truly high-performance computing and the development of coarse-grained simulation now offers us the hope of accurately predicting thermodynamic parameters and of simulating not merely a handful of proteins but larger, longer simulations comprising thousands of protein molecules and the cellular scale structures they form. We exemplify this within the context of immunoinformatics.

Humans:the missing link in manufacturing simulation?

Computer based discrete event simulation (DES) is one of the most commonly used aids for the design of automotive manufacturing systems. However, DES tools represent machines in extensive detail, while only representing workers as simple resources. This presents a problem when modelling systems with a highly manual work content, such as an assembly line. This paper describes research at Cranfield University, in collaboration with the Ford Motor Company, founded on the assumption that human variation is the cause of a large percentage of the disparity between simulation predictions and real world performance. The research aims to improve the accuracy and reliability of simulation prediction by including models of human factors.

Implications of Recent Trends in Telecommunications on Modeling and Simulation for the Telecommunication Industry

With this paper we would like to trigger a discussion on future needs of modeling and simulation techniques and tools for the telecommunication industry. We claim that the telecommunication market has undergone severe changes that affect the need for and type of simulations in industrial research. We suggest some approaches how to address these new challenges. We believe that there is need for intensive research in the area.

Networks of Evolutionary Processors: Java Implementation of a Threaded Processor

This paper is focused on a parallel JAVA implementation of a processor defined in a Network of Evolutionary Processors. Processor description is based on JDom, which provides a complete, Java-based solution for accessing, manipulating, and outputting XML data from Java code. Communication among different processor to obtain a fully functional simulation of a Network of Evolutionary Processors will be treated in future. A safe-thread model of processors performs all parallel operations such as rules and filters. A non-deterministic behavior of processors is achieved with a thread for each rule and for each filter (input and output). Different results of a processor evolution are shown.

Leveraging Existing Plasma Simulation Codes

This paper describes the process of wrapping existing scientific codes in the domain of plasma physics simulations through the use of the Sun’s Java Native Interface. We have created a Java front-end for a particular functionality, offered by legacy native libraries, in order to achieve reusability and interoperability without having to rewrite these libraries. The technique, introduced in this paper, includes two approaches – the one-to-one mapping for wrapping a number of native functions, and using peer classes for wrapping native data structures.

An agent-based model of team coordination and performance

This research is based on the premises that teams can be designed to optimize its performance, and appropriate team coordination is a significant factor to team outcome performance. Contingency theory argues that the effectiveness of a team depends on the right fit of the team design factors to the particular job at hand. Therefore, organizations need computational tools capable of predict the performance of different configurations of teams. This research created an agent-based model of teams called the Team Coordination Model (TCM). The TCM estimates the coordination load and performance of a team, based on its composition, coordination mechanisms, and job’s structural characteristics. The TCM can be used to determine the team’s design characteristics that most likely lead the team to achieve optimal performance. The TCM is implemented as an agent-based discrete-event simulation application built using JAVA and Cybele Pro agent architecture. The model implements the effect of individual team design factors on team processes, but the resulting performance emerges from the behavior of the agents. These team member agents use decision making, and explicit and implicit mechanisms to coordinate the job. The model validation included the comparison of the TCM’s results with statistics from a real team and with the results predicted by the team performance literature. An illustrative 26-1 fractional factorial experimental design demonstrates the application of the simulation model to the design of a team. The results from the ANOVA analysis have been used to recommend the combination of levels of the experimental factors that optimize the completion time for a team that runs sailboats races. This research main contribution to the team modeling literature is a model capable of simulating teams working on complex job environments. The TCM implements a stochastic job structure model capable of capturing some of the complexity not capture by current models. In a stochastic job structure, the tasks required to complete the job change during the team execution of the job. This research proposed three new types of dependencies between tasks required to model a job as a stochastic structure. These dependencies are conditional sequential, single-conditional sequential, and the merge dependencies.

Towards simulation and emulation of large-scale computer networks

Developing analytical models that can accurately describe behaviors of Internet-scale networks is difficult. This is due, in part, to the heterogeneous structure, immense size and rapidly changing properties of today's networks. The lack of analytical models makes large-scale network simulation an indispensable tool for studying immense networks. However, large-scale network simulation has not been commonly used to study networks of Internet-scale. This can be attributed to three factors: 1) current large-scale network simulators are geared towards simulation research and not network research, 2) the memory required to execute an Internet-scale model is exorbitant, and 3) large-scale network models are difficult to validate. This dissertation tackles each of these problems. ^ First, this work presents a method for automatically enabling real-time interaction, monitoring, and control of large-scale network models. Network researchers need tools that allow them to focus on creating realistic models and conducting experiments. However, this should not increase the complexity of developing a large-scale network simulator. This work presents a systematic approach to separating the concerns of running large-scale network models on parallel computers and the user facing concerns of configuring and interacting with large-scale network models. ^ Second, this work deals with reducing memory consumption of network models. As network models become larger, so does the amount of memory needed to simulate them. This work presents a comprehensive approach to exploiting structural duplications in network models to dramatically reduce the memory required to execute large-scale network experiments. ^ Lastly, this work addresses the issue of validating large-scale simulations by integrating real protocols and applications into the simulation. With an emulation extension, a network simulator operating in real-time can run together with real-world distributed applications and services. As such, real-time network simulation not only alleviates the burden of developing separate models for applications in simulation, but as real systems are included in the network model, it also increases the confidence level of network simulation. This work presents a scalable and flexible framework to integrate real-world applications with real-time simulation.^

Developing an enhanced model for combined heat and air infiltration energy simulation

The need for efficient, sustainable, and planned utilization of resources is ever more critical. In the U.S. alone, buildings consume 34.8 Quadrillion (1015) BTU of energy annually at a cost of $1.4 Trillion. Of this energy 58% is utilized for heating and air conditioning. ^ Several building energy analysis tools have been developed to assess energy demands and lifecycle energy costs in buildings. Such analyses are also essential for an efficient HVAC design that overcomes the pitfalls of an under/over-designed system. DOE-2 is among the most widely known full building energy analysis models. It also constitutes the simulation engine of other prominent software such as eQUEST, EnergyPro, PowerDOE. Therefore, it is essential that DOE-2 energy simulations be characterized by high accuracy. ^ Infiltration is an uncontrolled process through which outside air leaks into a building. Studies have estimated infiltration to account for up to 50% of a building's energy demand. This, considered alongside the annual cost of buildings energy consumption, reveals the costs of air infiltration. It also stresses the need that prominent building energy simulation engines accurately account for its impact. ^ In this research the relative accuracy of current air infiltration calculation methods is evaluated against an intricate Multiphysics Hygrothermal CFD building envelope analysis. The full-scale CFD analysis is based on a meticulous representation of cracking in building envelopes and on real-life conditions. The research found that even the most advanced current infiltration methods, including in DOE-2, are at up to 96.13% relative error versus CFD analysis. ^ An Enhanced Model for Combined Heat and Air Infiltration Simulation was developed. The model resulted in 91.6% improvement in relative accuracy over current models. It reduces error versus CFD analysis to less than 4.5% while requiring less than 1% of the time required for such a complex hygrothermal analysis. The algorithm used in our model was demonstrated to be easy to integrate into DOE-2 and other engines as a standalone method for evaluating infiltration heat loads. This will vastly increase the accuracy of such simulation engines while maintaining their speed and ease of use characteristics that make them very widely used in building design.^

A simulation-based decision support system for evaluating operating policies in an emergency room facility

Increased pressure to control costs and increased competition has prompted health care managers to look for tools to effectively operate their institutions. This research sought a framework for the development of a Simulation-Based Decision Support System (SB-DSS) to evaluate operating policies. A prototype of this SB-DSS was developed. It incorporates a simulation model that uses real or simulated data. ER decisions have been categorized and, for each one, an implementation plan has been devised. Several issues of integrating heterogeneous tools have been addressed. The prototype revealed that simulation can truly be used in this environment in a timely fashion because the simulation model has been complemented with a series of decision-making routines. These routines use a hierarchical approach to organize the various scenarios under which the model may run and to partially reconfigure the ARENA model at run time. Hence, the SB-DSS tailors its responses to each node in the hierarchy.

Logical simulation of communication subsystem for Universal Serial Bus (USB)

The primary purpose of this thesis was to design a logical simulation of a communication sub block to be used in the effective communication of digital data between the host and the peripheral devices. The module designed is a Serial interface engine in the Universal Serial Bus that effectively controls the flow of data for communication between the host and the peripheral devices with the emphasis on the study of timing and control signals, considering the practical aspects of them. In this study an attempt was made to realize data communication in the hardware using the Verilog Hardware Description language, which is supported by most popular logic synthesis tools. Various techniques like Cyclic Redundancy Checks, bit-stuffing and Non Return to Zero are implemented in the design to provide enhanced performance of the module.

Engineering tools

The aim of this report is to give an overview of the results of Work Package 5 “Engineering Tools”. In this workpackage numerical tools have been developed for all relevant CHCP systems in the PolySMART demonstration projects (WP3). First, existing simulation platforms have been described and specific characteristics have been identified. Several different simulation platforms are in principle appropriate for the needs in the PolySMART project. The result is an evaluation of available simulation and engineering tools for CHCP simulation, and an agreement upon a common simulation environment within the PolySMART project. Next, numerical models for components in the demonstration projects have been developed. These models are available to the PolySMART consortium. Of all modeled components an overall and detailed working principle is formulated, including a parameter list and (in some cases) a control strategy. Finally, for four CHCP systems in the PolySMART project, a system simulation model has been developed. For each system simulation a separate deliverable is available (D5.5b to D5.5e) These deliverables replace deliverable 5.4 ‘system models’. The numerical models for components and systems developed in the Polysmart project form a valuable basis for the component development and optimisation and for the system optimisation, both within and outside the project. Developers and researchers interested in more information about specific models can refer to the institutes and contact persons involved in the model development. 

A matlab-based toolbox for the simulation and design of L1 adaptive controllers

This thesis introduces the L1 Adaptive Control Toolbox, a set of tools implemented in Matlab that aid in the design process of an L1 adaptive controller and enable the user to construct simulations of the closed-loop system to verify its performance. Following a brief review of the existing theory on L1 adaptive controllers, the interface of the toolbox is presented, including a description of the functions accessible to the user. Two novel algorithms for determining the required sampling period of a piecewise constant adaptive law are presented and their implementation in the toolbox is discussed. The detailed description of the structure of the toolbox is provided as well as a discussion of the implementation of the creation of simulations. Finally, the graphical user interface is presented and described in detail, including the graphical design tools provided for the development of the filter C(s). The thesis closes with suggestions for further improvement of the toolbox.

Capacity analysis in CDMA systems using GIS based planning tools

We show a simulation model for capacity analysis in mobile systems using a geographic information system (GIS) based tool, used for coverage calculations and frequency assignment, and MATLAB. The model was developed initially for “narrowband” CDMA and TDMA, but was modified for WCDMA. We show also some results for a specific case in “narrowband” CDMA

Some parameters that affect CDMA capacity analysis. Results using GIS based simulation

In previous papers we describe a model for capacity analysis in CDMA systems using DC-Cell, a GIS based planning tool developed at Universidad Politecnica de Valencia, and MATLAB. We show some initial results of that model, and now, we are exploring different parameters like cell size, proximity between cells, number of cells in the system and “clustering” CDMA in order to improve the planning process for third generation systems. In this paper we show the results for variations of some of these parameters, specifically the cell size and number of cells. In CDMA systems is quite common to suppose only one carrier frequency for capacity estimation, and it is intuitive to think that for more base stations, mean more users. However the multiple access interference problem in CDMA systems could establish a limit for that supposition in a similar way that occurs in FDMA and TDMA systems.

Hydrometallurgical process modeling using advanced mathematical tools

Hydrometallurgical process modeling is the main objective of this Master’s thesis work. Three different leaching processes namely, high pressure pyrite oxidation, direct oxidation zinc concentrate (sphalerite) leaching and gold chloride leaching using rotating disc electrode (RDE) are modeled and simulated using gPROMS process simulation program in order to evaluate its model building capabilities. The leaching mechanism in each case is described in terms of a shrinking core model. The mathematical modeling carried out included process model development based on available literature, estimation of reaction kinetic parameters and assessment of the model reliability by checking the goodness fit and checking the cross correlation between the estimated parameters through the use of correlation matrices. The estimated parameter values in each case were compared with those obtained using the Modest simulation program. Further, based on the estimated reaction kinetic parameters, reactor simulation and modeling for direct oxidation zinc concentrate (sphalerite) leaching is carried out in Aspen Plus V8.6. The zinc leaching autoclave is based on Cominco reactor configuration and is modeled as a series of continuous stirred reactors (CSTRs). The sphalerite conversion is calculated and a sensitivity analysis is carried out so to determine the optimum reactor operation temperature and optimum oxygen mass flow rate. In this way, the implementation of reaction kinetic models into the process flowsheet simulation environment has been demonstrated.