Study report on combining diagnostic and therapeutic considerations with subsystem and whole-body simulation

Current applications of simulation models for clinical research described included tilt model simulation of orthostatic intolerance with hemorrhage, and modeling long term circulatory circulation. Current capabilities include: (1) simulation of analogous pathological states and effects of abnormal environmental stressors by the manipulation of system variables and changing inputs in various sequences; (2) simulation of time courses of responses of controlled variables by the altered inputs and their relationships; (3) simulation of physiological responses of treatment such as isotonic saline transfusion; (4) simulation of the effectiveness of a treatment as well as the effects of complication superimposed on an existing pathological state; and (5) comparison of the effectiveness of various treatments/countermeasures for a given pathological state. The feasibility of applying simulation models to diagnostic and therapeutic research problems is assessed

Application of Electronic Analog Computer to Solution of Hydrologic and River Basin Planning Problems: Utah Simulation Model II

As demands upon available water supplies increase, there is an accompanying increase in the need to assess the downstream hydrologic system. At Utah State University this problem is being approached by electronic analog simulation of the hydrologic system. Modeling concepts are based upon the development of basic relationships which describe the various hydrologic processes. Within a system, these relationships are linked by the continuity -of-mass principle which requires a hydrologic balance at all points. Once established, the model is applied to any particular geographic unit by determining the appropriate constants of the hydrologic equations. The analog computer is ideally suited to the solution of the many time-dependent differential equations which are encountered in the hydrologic systems. The complexity of a hydrologic model depends to a large extent upon the magnitude of the time and spatial increments utilized in the model. In this study the mathematical development was based on the concepts of relatively small increments of space and large time increments. The model is, therefore, applicable to in-basin probelms involving a time increment of, for example, one month. To test individual equations and to verify the model, the Circle Valley subbasin of the Servier River system in Utah was simulated. Close agreement between computed and observed outflows was achieved on both a monthly and a total annual basis

KINETICS OF MOLTEN METAL CAPILLARY FLOW IN NON-REACTIVE AND REACTIVE SYSTEMS

Wetting and spreading of liquid systems on solid substrates under transient conditions, driven by surface tension and viscous forces along with the interface interactions (e.g., a substrate dissolution or diffusion and/or chemical reaction) is a complex problem, still waiting to be fully understood. In this study we have performed an extensive experimental investigation of liquid aluminum alloy spreading over aluminum substrate along with corroboration with theoretical modeling, performed in separate but coordinate study. Wetting and spreading to be considered take place during a transient formation of the free liquid surface in both sessile drop and wedge-tee mating surfaces’ configurations. The AA3003 is used as a substrate and a novel self-fluxing material called TrilliumTM is considered as the filler metal. In addition, benchmark, non-reactive cases of spreading of water and silicon oil over quartz glass are considered. The study is performed experimentally by a high temperature optical dynamic contact angle measuring system and a standard and high speed visible light camera, as well as with infra read imaging. Benchmark tests of non-reactive systems are conducted under ambient environment’s conditions. Molten metal experiment series featured aluminum and silicone alloys under controlled atmosphere at elevated temperatures. The chamber atmosphere is maintained by the ultra-high purity nitrogen gas purge process with the temperature monitored in real time in situ. Different configurations of the wedge-tee joints are designed to explore different parameters impacting the kinetics of the triple line movement process. Different power law relationships are identified, supporting subsequent theoretical analysis and simulation. Under ambient temperature conditions, the non-reactive liquid wetting and spreading experiments (water and oil systems) were studied to verify the equilibrium triple line location relationships. The kinetics relationship between the dynamic contact angle and the triple line location is identified. Additional simulation and theoretical analysis of the triple line movement is conducted using the commercial computer software platform Comsol in a collaboration with a team from Washington State University within the NSF sponsored Grant #1235759 and # 1234581. The experimental work conducted here has been complemented by a verification of the Comsol phase-field modeling. Both segments of work (experimental and numerical) are parts of the collaborative NSF sponsored project involving the University of Kentucky and Washington State University. The phase field modeling used in this work was developed at the Washington State University and data are corroborated with experimental results obtained within the scope of this Thesis

Hybrid Multiresolution Simulation & Model Checking: Network-On-Chip Systems

abstract: Designers employ a variety of modeling theories and methodologies to create functional models of discrete network systems. These dynamical models are evaluated using verification and validation techniques throughout incremental design stages. Models created for these systems should directly represent their growing complexity with respect to composition and heterogeneity. Similar to software engineering practices, incremental model design is required for complex system design. As a result, models at early increments are significantly simpler relative to real systems. While experimenting (verification or validation) on models at early increments are computationally less demanding, the results of these experiments are less trustworthy and less rewarding. At any increment of design, a set of tools and technique are required for controlling the complexity of models and experimentation. A complex system such as Network-on-Chip (NoC) may benefit from incremental design stages. Current design methods for NoC rely on multiple models developed using various modeling frameworks. It is useful to develop frameworks that can formalize the relationships among these models. Fine-grain models are derived using their coarse-grain counterparts. Moreover, validation and verification capability at various design stages enabled through disciplined model conversion is very beneficial. In this research, Multiresolution Modeling (MRM) is used for system level design of NoC. MRM aids in creating a family of models at different levels of scale and complexity with well-formed relationships. In addition, a variant of the Discrete Event System Specification (DEVS) formalism is proposed which supports model checking. Hierarchical models of Network-on-Chip components may be created at different resolutions while each model can be validated using discrete-event simulation and verified via state exploration. System property expressions are defined in the DEVS language and developed as Transducers which can be applied seamlessly for model checking and simulation purposes. Multiresolution Modeling with verification and validation capabilities of this framework complement one another. MRM manages the scale and complexity of models which in turn can reduces V&V time and effort and conversely the V&V helps ensure correctness of models at multiple resolutions. This framework is realized through extending the DEVS-Suite simulator and its applicability demonstrated for exemplar NoC models.Dissertation/ThesisDoctoral Dissertation Computer Science 201

Controlled vocabularies and semantics in systems biology

The use of computational modeling to describe and analyze biological systems is at the heart of systems biology. Model structures, simulation descriptions and numerical results can be encoded in structured formats, but there is an increasing need to provide an additional semantic layer. Semantic information adds meaning to components of structured descriptions to help identify and interpret them unambiguously. Ontologies are one of the tools frequently used for this purpose. We describe here three ontologies created specifically to address the needs of the systems biology community. The Systems Biology Ontology (SBO) provides semantic information about the model components. The Kinetic Simulation Algorithm Ontology (KiSAO) supplies information about existing algorithms available for the simulation of systems biology models, their characterization and interrelationships. The Terminology for the Description of Dynamics (TEDDY) categorizes dynamical features of the simulation results and general systems behavior. The provision of semantic information extends a model's longevity and facilitates its reuse. It provides useful insight into the biology of modeled processes, and may be used to make informed decisions on subsequent simulation experiments

Combination interventions for Hepatitis C and Cirrhosis reduction among people who inject drugs: An agent-based, networked population simulation experiment

Hepatitis C virus (HCV) infection is endemic in people who inject drugs (PWID), with prevalence estimates above 60 percent for PWID in the United States. Previous modeling studies suggest that direct acting antiviral (DAA) treatment can lower overall prevalence in this population, but treatment is often delayed until the onset of advanced liver disease (fibrosis stage 3 or later) due to cost. Lower cost interventions featuring syringe access (SA) and medically assisted treatment (MAT) for addiction are known to be less costly, but have shown mixed results in lowering HCV rates below current levels. Little is known about the potential synergistic effects of combining DAA and MAT treatment, and large-scale tests of combined interventions are rare. While simulation experiments can reveal likely long-term effects, most prior simulations have been performed on closed populations of model agents--a scenario quite different from the open, mobile populations known to most health agencies. This paper uses data from the Centers for Disease Control's National HIV Behavioral Surveillance project, IDU round 3, collected in New York City in 2012 by the New York City Department of Health and Mental Hygiene to parameterize simulations of open populations. Our results show that, in an open population, SA/MAT by itself has only small effects on HCV prevalence, while DAA treatment by itself can significantly lower both HCV and HCV-related advanced liver disease prevalence. More importantly, the simulation experiments suggest that cost effective synergistic combinations of the two strategies can dramatically reduce HCV incidence. We conclude that adopting SA/MAT implementations alongside DAA interventions can play a critical role in reducing the long-term consequences of ongoing infection