MOLNs: A cloud platform for interactive, reproducible and scalable spatial stochastic computational experiments in systems biology using PyURDME

Computational experiments using spatial stochastic simulations have led to important new biological insights, but they require specialized tools, a complex software stack, as well as large and scalable compute and data analysis resources due to the large computational cost associated with Monte Carlo computational workflows. The complexity of setting up and managing a large-scale distributed computation environment to support productive and reproducible modeling can be prohibitive for practitioners in systems biology. This results in a barrier to the adoption of spatial stochastic simulation tools, effectively limiting the type of biological questions addressed by quantitative modeling. In this paper, we present PyURDME, a new, user-friendly spatial modeling and simulation package, and MOLNs, a cloud computing appliance for distributed simulation of stochastic reaction-diffusion models. MOLNs is based on IPython and provides an interactive programming platform for development of sharable and reproducible distributed parallel computational experiments

Parallel object-oriented algorithms for simulation of multiphysics : application to thermal systems

The present and the future expectation in parallel computing pose a new generational change in simulation and computing. Modern High Performance Computing (HPC) facilities have high computational power in terms of operations per second -today peta-FLOPS (10e15 FLOPS) and growing toward the exascale (10e18 FLOPS) which is expected in few years-. This opens the way for using simulation tools in a wide range of new engineering and scientific applications. For example, CFD&HT codes will be effectively used in the design phase of industrial devices, obtaining valuable information with reasonable time expenses. However, the use of the emerging computer architectures is subjected to enhancements and innovation in software design patterns. So far, powerful codes for individually studying heat and mass transfer phenomena at multiple levels of modeling are available. However, there is no way to combine them for resolving complex coupled problems. In the current context, this PhD thesis presents the development of parallel methodologies, and its implementation as an object-oriented software platform, for the simulation of multiphysics systems. By means of this new software platform, called NEST, the distinct codes can now be integrated into single simulation tools for specific applications of social and industrial interest. This is done in an intuitive and simple way so that the researchers do not have to bother either on the coexistence of several codes at the same time neither on how they interact to each other. The coupling of the involved components is controlled from a low level code layer, which is transparent to the users. This contributes with appealing benefits on software projects management first and on the flexibility and features of the simulations, later. In sum, the presented approaches pose a new paradigm in the production of physics simulation programs. Although the thesis pursues general purpose applications, special emphasis is placed on the simulation of thermal systems, in particular on buildings energy assessment and on hermetic reciprocating compressors.Las expectativas puestas en el uso de la computación en paralelo plantean un cambio generacional en simulación y computación. Las más modernas instalaciones computacionales de alto nivel -High Performance Computing (HPC)- alcanzan ya la capacidad de realizar gran cantidad de operaciones por segundo -hoy del orden de peta-FLOPS (1e15 FLOPS) y dirigiéndose hacia exaFlops (1e18 FLOPS)-. Esto abre la posibilidad de usar la simulación por ordenador en un amplio espectro de nuevas aplicaciones en ciencia e ingeniería. Por ejemplo, los códigos de CFD&HT van a poder usarse de una forma más efectiva en la fase de diseño de dispositivos industriales ya que se obtendrán resultados muy valiosos en tiempos de ejecución razonables. Por el momento, hay muchos códigos disponibles para el estudio individual de fenómenos de transferencia de calor i de masa con distintos niveles de modelización. Sin embargo, estos códigos no se pueden combinar entre sí para abordar problemas más complejos, en los cuales varios fenómenos físicos interactúan simultáneamente. Bajo este contexto, en esta tesis doctoral se presenta el desarrollo de una metodología de estrategia paralela, y su implementación en una plataforma informática, para la simulación de sistemas multi-físicos. De éste modo, ahora los distintos códigos pueden ser integrados para la creación de nuevas herramientas de simulación destinadas a aplicaciones específicas de interés tanto social como industrial. Esto se hace de una manera intuitiva y simple de manera que los investigadores no tienen que preocuparse ni por la coexistencia de varios códigos simultáneamente ni en cómo hacer que interactúen entre ellos. El acoplamiento entre los diferentes componentes involucrados en una simulación se realiza mediante un código más básico con el cual el usuario solamente interacciona a través de una interfase. Esto aporta interesantes beneficios tanto en la gestión de los proyectos de programario como en la flexibilidad y las características de las simulaciones. En resumen, la estrategia que se propone plantea un nuevo paradigma en la producción de programas de simulación de fenómenos físicos. Aunque la tesis persigue aplicaciones de propósito general se ha puesto especial atención en la simulación de sistemas térmicos, en particular en la evaluación energética de edificios y en compresores herméticos alternativos.Postprint (published version

Multiphysics simulation in buildings

Numerical simulation play an important role in the design, engineering, operation and management of buildings. It can help reducing energy consumption, improving indoor air quality and thermal comfort and provide quantitative data supporting decision making, e.g. choosing the best solution for designing, retrofitting or choosing the optimal HVAC system. Besides, buildings are composed more and more of different complex elements and systems which make the simulation of only thermal physics in buildings not enough to evaluate their whole performance. All the involved physical phenomena like moisture, airflow and pollutants should be considered and coupled in order to reproduce the reality with the highest possible level of details. In this context, this PhD thesis presents the models and the simulations of multi-physics inside buildings using an in-house developed modular and object oriented tool called NEST. All the physics of the coupled heat, moisture, airflow and pollutants transfer that take place inside buildings are considered and solved. In addition, the software allows the simulation of a building system as a collection of different numerical elements, like walls, rooms, HVAC systems, outdoor, etc., connected with each other and able to exchange boundary conditions. In this manner any building configuration can be set and simulated. The physical and mathematical formulations of the implemented elements are presented. Then, in order to assure the credibility of the developed software, the implemented models are validated and verified with different test cases from the literature. The list of test cases cover all the aspects of heat, moisture, airflow and pollutants transfer in the whole building and it can be used as a reference list for the validation of other buildings simulation tools. Special emphasis is placed on the simulation of buildings performance in real applications. First, the hygrothermal behaviour in different public buildings with different climates conditions are analysed before retrofitting them. Several weak points in the thermal and moisture resistance of the façades layers are identified and thermal and moisture loads before and after the expected retrofitting solutions are evaluated. Second, a residential building (semidetached house) in Netherlands is simulated and the airflow, heat and CO 2 transfer inside it is studied in order to optimize the energy consumption while maintaining acceptable levels of thermal comfort and indoor air quality.Postprint (published version

High-Performance Integrated Window and Façade Solutions for California

The researchers developed a new generation of high-performance façade systems and supporting design and management tools to support industry in meeting California’s greenhouse gas reduction targets, reduce energy consumption, and enable an adaptable response to minimize real-time demands on the electricity grid. The project resulted in five outcomes: (1) The research team developed an R-5, 1-inch thick, triplepane, insulating glass unit with a novel low-conductance aluminum frame. This technology can help significantly reduce residential cooling and heating loads, particularly during the evening. (2) The team developed a prototype of a windowintegrated local ventilation and energy recovery device that provides clean, dry fresh air through the façade with minimal energy requirements. (3) A daylight-redirecting louver system was prototyped to redirect sunlight 15–40 feet from the window. Simulations estimated that lighting energy use could be reduced by 35–54 percent without glare. (4) A control system incorporating physics-based equations and a mathematical solver was prototyped and field tested to demonstrate feasibility. Simulations estimated that total electricity costs could be reduced by 9-28 percent on sunny summer days through adaptive control of operable shading and daylighting components and the thermostat compared to state-of-the-art automatic façade controls in commercial building perimeter zones. (5) Supporting models and tools needed by industry for technology R&D and market transformation activities were validated. Attaining California’s clean energy goals require making a fundamental shift from today’s ad-hoc assemblages of static components to turnkey, intelligent, responsive, integrated building façade systems. These systems offered significant reductions in energy use, peak demand, and operating cost in California

INVESTIGATION OF ATMOSPHERIC EFFECTS ON VAPOR INTRUSION PROCESSES USING MODELLING APPROACHES

Most people in the United States (US) spend considerable amount of time indoors—about 90% of their time as compared to outdoors, which makes the US population vulnerable to adverse health effects of indoor air contaminants. Volatile organic compound (VOC) concentrations are well-known to be higher in indoor air than outdoor air. One source of VOC concentrations in indoor air that has gained considerable attention in public health and environmental regulatory communities is vapor intrusion. Vapor intrusion is the process by which subsurface vapors enter indoor spaces from contaminated soil and groundwater. It has been documented to cause indoor air contamination within hundreds of thousands of communities across the US. Vapor intrusion is well-known to be difficult to characterize because indoor air concentrations exhibit considerable temporal and spatial variability in homes throughout impacted communities. Unexplained variations in field data have not been systematically investigated using theoretical fate and transport processes. This study incorporates the use of numerical models to better understand processes that influence spatial and temporal variability in field data. The overall research hypothesis is that variability in indoor air VOC concentrations can be (partially) explained by variations in building air exchange rate (AER) and pressure differentials between indoor spaces and outdoor spaces. Neither AER nor pressure differentials are currently calculated by existing vapor intrusion numerical models. To date, most vapor intrusion models have focused on subsurface fate and transport processes; however, there is a need to understand the role of aboveground processes in the context of vapor intrusion exposure risks, which are commonly measured as indoor air VOC concentrations. Recent field studies identify these parameters as potentially important and their important role within the broader field of indoor air quality sciences has been well-documented, but more research is needed to investigate these parameters within the specific context of vapor intrusion. To test the overall hypothesis, the dissertation research developed a new vapor intrusion modeling technique that combines subsurface fate and transport modeling with building science approaches for modeling driving forces, such as wind and stack effects. The modeling results are compared with field data measurements from actual vapor intrusion sites and confirms that the research is relevant to not only academic researchers, but also policy decision makers

Transient Modeling of a Thermosiphon based Air Conditioner with Compact Thermal Storage: Modeling and Validation

The Roving Comforter (RoCo) is an innovative personal thermal management technology currently being developed at the University of Maryland as part of Advanced Research Projects Agency – Energy (ARPA-e) project. Among several system configurations of RoCo, the paper focuses on a miniature battery-powered vapor compression cycle (VCC) system fitted on an autonomous robotic platform. The heat rejected from the condenser during its operation is stored in a compact phase change material (PCM) based heat storage device. The PCM can store only a limited amount of heat until it melts completely. The PCM heat exchanger needs to be designed so that it captures the heat generated during the VCC operation and then gets frozen with minimal energy usage during the non-operation mode. A thermosiphon mechanism is envisioned for this recharging of PCM material during the non-operation mode. It operates through the same refrigerant circuit by bypassing certain components like the compressor. Thus the circuit operates as a VCC during the day and as thermosiphon during the night. The VCC needs to have a high coefficient of performance (COP) while the thermosiphon needs to reject heat at highest possible rate. Hence transient modeling of thermosiphon is desired. The prototype developed has a COP of 2.85 and needs roughly 8 hours to recharge the thermosiphon. These trends have been captured on a transient model for the VCC operation while the development of thermosiphon modeling is being carried out. Comparison of modeling results with the experimental data have been provided to estimate the error in the model. Several cases of RoCo thermosiphon are then simulated using the model for the optimum design fulfilling requirements for both VCC and thermosiphon

Theoretical and experimental development of a ZnO-based laterally excited thickness shear mode acoustic wave immunosensor for cancer biomarker detection

The object of this thesis research was to develop and characterize a new type of acoustic biosensor - a ZnO-based laterally excited thickness shear mode (TSM) resonator in a solidly mounted configuration. The first specific aim of the research was to develop the theoretical underpinnings of the acoustic wave propagation in ZnO. Theoretical calculations were carried out by solving the piezoelectrically stiffened Christoffel equation to elucidate the acoustic modes that are excited through lateral excitation of a ZnO stack. A finite element model was developed to confirm the calculations and investigate the electric field orientation and density for various electrode configurations. A proof of concept study was also carried out using a Quartz Crystal Microbalance device to investigate the application of thickness shear mode resonators to cancer biomarker detection in complex media. The results helped to provide a firm foundation for the design of new gravimetric sensors with enhanced capabilities. The second specific aim was to design and fabricate arrays of multiple laterally excited TSM devices and fully characterize their electrical properties. The solidly mounted resonator configuration was developed for the ZnO-based devices through theoretical calculations and experimentation. A functional mirror comprised of W and SiO2 was implemented in development of the TSM resonators. The devices were fabricated and tested for values of interest such as Q, and electromechanical coupling (K2) as well as their ability to operate in liquids. The third specific aim was to investigate the optimal surface chemistry scheme for linking the antibody layer to the ZnO device surface. Crosslinking schemes involving organosilane molecules and a phosphonic acid were compared for immobilizing antibodies to the surface of the ZnO. Results indicate that the thiol-terminated organosilane provides high antibody surface coverage and uniformity and is an excellent candidate for planar ZnO functionalization. The fourth and final specific aim was to investigate the sensitivity of the acoustic immunosensors to potential diagnostic biomarkers. Initial tests were performed in buffer spiked with varying concentrations of the purified target antigen to develop a dose-response curve for the detection of mesothelin-rFc. Subsequent tests were carried out in prostate cancer cell line conditioned medium for the detection of PSA. The results of the experiments establish the operation of the devices in complex media, and indicate that the acoustic sensors are sensitive enough for the detection of biomolecular targets at clinically relevant concentrations.Ph.D.Committee Chair: William D Hunt; Committee Member: Bruno Frazier; Committee Member: Dale Edmondson; Committee Member: Marie Csete; Committee Member: Peter Edmonson; Committee Member: Ruth O'Rega

Electrochemical-thermal Analysis of High Capacity Li-ion Pouch Cell for Automotive Applications

Latest regulatory trends implemented in order to limit emissions combined with research advances in alternative fuels have paved the road toward vehicle electrification. Major original equipment manufacturers (\acrshort{OEM}s) have already marketed electric vehicles in large scale but apart from business strategies and policies, the real engineering problems must be addressed. Lithium-ion batteries are a promising technology for energy storage; however, their low energy density and complex electro-chemical nature, compared to fossil fuels, presents additional challenges. Their complex nature and strong temperature dependence during operation must be studied with additional accuracy, capable to predict their behavior. In this research, a pseudo two dimensional (\acrshort{P2D}) electro-chemical model, coupled with a 3D thermal energy balance for a recent high capacity \acrshort{NMC} pouch cell for automotive applications is developed. The electrochemical model with its temperature dependent parameters is validated at different temperatures and various discharge C-rates to accurately replicate the battery cell operational conditions. The sources of heat are distinguished and characterized via advanced electrochemical-modelling approach, in various battery operations and different thermal boundary conditions. For example, it was determined that the temperature rise during discharge at high C-rates, under natural convection, could result in thermal runaway, if managed incorrectly. Ohmic heat generation of current collectors and cell tabs is investigated and included. Hence, the thermal analysis provides insights on the current and voltage profiles causing the minimum thermal stress on the cell and the location of heat generation spatially and temporally during the battery discharge. Different modelling approximation of the cell are studied starting from the cell fundamental unit. This provides effective design considerations for the battery thermal management system (\acrshort{BTMS}) to enhance performance, cycle life and safety of future electrified vehicle energy storage systems