Solutions of alkyl methanoates and alkanes: Simultaneous modeling of phase equilibria and mixing properties. Estimation of behavior by UNIFAC with recalculation of parameters.

[EN]Isobaric vapor–liquid equilibria at p = 101.32 kPa (iso-p VLE) and the mixing properties, hE and vE, are determined for a set of twelve binary solutions: HCOOCuH2u+1(1)+CnH2n+2(2) with u = (1–4) and n = (7– 9). The (iso-p VLE) present deviations from the ideal behavior, which augment as u diminishes and n increases. Systems with [u = 2,3 n = 7] and [u =4 , n = 7,8] present a minimum-boiling azeotrope. The nonideality is also reflected in high endothermic values, hE > 0, and expansive effects, vE > 0, for all the binaries, which increase regularly with n

Modeling and simulation of a synthetic genetic circuit that implements a multicelled behavior in a growing microcolony of E. coli

Synthetic Biology is a relatively new discipline, born at the beginning of the New Millennium, that brings the typical engineering approach (abstraction, modularity and standardization) to biotechnology. These principles aim to tame the extreme complexity of the various components and aid the construction of artificial biological systems with specific functions, usually by means of synthetic genetic circuits implemented in bacteria or simple eukaryotes like yeast. The cell becomes a programmable machine and its low-level programming language is made of strings of DNA. This work was performed in collaboration with researchers of the Department of Electrical Engineering of the University of Washington in Seattle and also with a student of the Corso di Laurea Magistrale in Ingegneria Biomedica at the University of Bologna: Marilisa Cortesi. During the collaboration I contributed to a Synthetic Biology project already started in the Klavins Laboratory. In particular, I modeled and subsequently simulated a synthetic genetic circuit that was ideated for the implementation of a multicelled behavior in a growing bacterial microcolony. In the first chapter the foundations of molecular biology are introduced: structure of the nucleic acids, transcription, translation and methods to regulate gene expression. An introduction to Synthetic Biology completes the section. In the second chapter is described the synthetic genetic circuit that was conceived to make spontaneously emerge, from an isogenic microcolony of bacteria, two different groups of cells, termed leaders and followers. The circuit exploits the intrinsic stochasticity of gene expression and intercellular communication via small molecules to break the symmetry in the phenotype of the microcolony. The four modules of the circuit (coin flipper, sender, receiver and follower) and their interactions are then illustrated. In the third chapter is derived the mathematical representation of the various components of the circuit and the several simplifying assumptions are made explicit. Transcription and translation are modeled as a single step and gene expression is function of the intracellular concentration of the various transcription factors that act on the different promoters of the circuit. A list of the various parameters and a justification for their value closes the chapter. In the fourth chapter are described the main characteristics of the gro simulation environment, developed by the Self Organizing Systems Laboratory of the University of Washington. Then, a sensitivity analysis performed to pinpoint the desirable characteristics of the various genetic components is detailed. The sensitivity analysis makes use of a cost function that is based on the fraction of cells in each one of the different possible states at the end of the simulation and the wanted outcome. Thanks to a particular kind of scatter plot, the parameters are ranked. Starting from an initial condition in which all the parameters assume their nominal value, the ranking suggest which parameter to tune in order to reach the goal. Obtaining a microcolony in which almost all the cells are in the follower state and only a few in the leader state seems to be the most difficult task. A small number of leader cells struggle to produce enough signal to turn the rest of the microcolony in the follower state. It is possible to obtain a microcolony in which the majority of cells are followers by increasing as much as possible the production of signal. Reaching the goal of a microcolony that is split in half between leaders and followers is comparatively easy. The best strategy seems to be increasing slightly the production of the enzyme. To end up with a majority of leaders, instead, it is advisable to increase the basal expression of the coin flipper module. At the end of the chapter, a possible future application of the leader election circuit, the spontaneous formation of spatial patterns in a microcolony, is modeled with the finite state machine formalism. The gro simulations provide insights into the genetic components that are needed to implement the behavior. In particular, since both the examples of pattern formation rely on a local version of Leader Election, a short-range communication system is essential. Moreover, new synthetic components that allow to reliably downregulate the growth rate in specific cells without side effects need to be developed. In the appendix are listed the gro code utilized to simulate the model of the circuit, a script in the Python programming language that was used to split the simulations on a Linux cluster and the Matlab code developed to analyze the data.

Modeling and simulation of fibrinogen and its adsorption behavior

In this thesis different approaches for the modeling and simulation of the blood protein fibrinogen are presented. The approaches are meant to systematically connect the multiple time and length scales involved in the dynamics of fibrinogen in solution and at inorganic surfaces. The first part of the thesis will cover simulations of fibrinogen on an all atom level. Simulations of the fibrinogen protomer and dimer are performed in explicit solvent to characterize the dynamics of fibrinogen in solution. These simulations reveal an unexpectedly large and fast bending motion that is facilitated by molecular hinges located in the coiled-coil region of fibrinogen. This behavior is characterized by a bending and a dihedral angle and the distribution of these angles is measured. As a consequence of the atomistic detail of the simulations it is possible to illuminate small scale behavior in the binding pockets of fibrinogen that hints at a previously unknown allosteric effect. In a second step atomistic simulations of the fibrinogen protomer are performed at graphite and mica surfaces to investigate initial adsorption stages. These simulations highlight the different adsorption mechanisms at the hydrophobic graphite surface and the charged, hydrophilic mica surface. It is found that the initial adsorption happens in a preferred orientation on mica. Many effects of practical interest involve aggregates of many fibrinogen molecules. To investigate such systems, time and length scales need to be simulated that are not attainable in atomistic simulations. It is therefore necessary to develop lower resolution models of fibrinogen. This is done in the second part of the thesis. First a systematically coarse grained model is derived and parametrized based on the atomistic simulations of the first part. In this model the fibrinogen molecule is represented by 45 beads instead of nearly 31,000 atoms. The intra-molecular interactions of the beads are modeled as a heterogeneous elastic network while inter-molecular interactions are assumed to be a combination of electrostatic and van der Waals interaction. A method is presented that determines the charges assigned to beads by matching the electrostatic potential in the atomistic simulation. Lastly a phenomenological model is developed that represents fibrinogen by five beads connected by rigid rods with two hinges. This model only captures the large scale dynamics in the atomistic simulations but can shed light on experimental observations of fibrinogen conformations at inorganic surfaces.

Modeling contaminant behavior in Lake Superior : a comparison of PCBs, PBDEs, and mercury

A mass‐balance model for Lake Superior was applied to polychlorinated biphenyls (PCBs), polybrominated diphenyl ethers (PBDEs), and mercury to determine the major routes of entry and the major mechanisms of loss from this ecosystem as well as the time required for each contaminant class to approach steady state. A two‐box model (water column, surface sediments) incorporating seasonally adjusted environmental parameters was used. Both numerical (forward Euler) and analytical solutions were employed and compared. For validation, the model was compared with current and historical concentrations and fluxes in the lake and sediments. Results for PCBs were similar to prior work showing that air‐water exchange is the most rapid input and loss process. The model indicates that mercury behaves similarly to a moderately‐chlorinated PCB, with air‐water exchange being a relatively rapid input and loss process. Modeled accumulation fluxes of PBDEs in sediments agreed with measured values reported in the literature. Wet deposition rates were about three times greater than dry particulate deposition rates for PBDEs. Gas deposition was an important process for tri‐ and tetra‐BDEs (BDEs 28 and 47), but not for higher‐brominated BDEs. Sediment burial was the dominant loss mechanism for most of the PBDE congeners while volatilization was still significant for tri‐ and tetra‐BDEs. Because volatilization is a relatively rapid loss process for both mercury and the most abundant PCBs (tri‐ through penta‐), the model predicts that similar times (from 2 ‐ 10 yr) are required for the compounds to approach steady state in the lake. The model predicts that if inputs of Hg(II) to the lake decrease in the future then concentrations of mercury in the lake will decrease at a rate similar to the historical decline in PCB concentrations following the ban on production and most uses in the U.S. In contrast, PBDEs are likely to respond more slowly if atmospheric concentrations are reduced in the future because loss by volatilization is a much slower process for PBDEs, leading to lesser overall loss rates for PBDEs in comparison to PCBs and mercury. Uncertainties in the chemical degradation rates and partitioning constants of PBDEs are the largest source of uncertainty in the modeled times to steady‐state for this class of chemicals. The modeled organic PBT loading rates are sensitive to uncertainties in scavenging efficiencies by rain and snow, dry deposition velocity, watershed runoff concentrations, and uncertainties in air‐water exchange such as the effect of atmospheric stability.

The Texas driver responsibility program: A preliminary analysis of the impact on impaired driving and trauma system funding

Objective. In 2003, the State of Texas instituted the Driver Responsibility Program (TDRP), a program consisting of a driving infraction point system coupled with a series of graded fines and annual surcharges for specific traffic violations such as driving while intoxicated (DWI). Approximately half of the revenues generated are earmarked to be disbursed to the state's trauma system to cover uncompensated trauma care costs. This study examined initial program implementation, the impact of trauma system funding, and initial impact on impaired driving knowledge, attitudes and behaviors. A model for targeted media campaigns to improve the program's deterrence effects was developed. ^ Methods. Data from two independent driver survey samples (conducted in 1999 and 2005), department of public safety records, state health department data and a state auditor's report were used to evaluate the program's initial implementation, impact and outcome with respect to drivers' impaired driving knowledge, attitudes and behavior (based on constructs of social cognitive theory) and hospital uncompensated trauma care funding. Survey results were used to develop a regression model of high risk drivers who should be targeted to improve program outcome with respect to deterring impaired driving. ^ Results. Low driver compliance with fee payment (28%) and program implementation problems were associated with lower surcharge revenues in the first two years ($59.5 million versus $525 million predicted). Program revenue distribution to trauma hospitals was associated with a 16% increase in designated trauma centers. Survey data demonstrated that only 28% of drivers are aware of the TDRP and that there has been no initial impact on impaired driving behavior. Logistical regression modeling suggested that target media campaigns highlighting the likelihood of DWI detection by law enforcement and the increased surcharges associated with the TDRP are required to deter impaired driving. ^ Conclusions. Although the TDRP raised nearly $60 million in surcharge revenue for the Texas trauma system over the first two years, this study did not find evidence of a change in impaired driving knowledge, attitudes or behaviors from 1999 to 2005. Further research is required to measure whether the program is associated with decreased alcohol-related traffic fatalities. ^

On the analytical approach for modeling photovoltaic systems behavior

The 1-diode/2-resistors electric circuit equivalent to a photovoltaic system is analyzed. The equations at particular points of the I–V curve are studied considering the maximum number of terms. The maximum power point as a boundary condition is given special attention. A new analytical method is developed based on a reduced amount of information, consisting in the normal manufacturer data. Results indicate that this new method is faster than numerical methods and has similar (or better) accuracy than other existing methods, numerical or analytical.

Microstructure-based numerical modeling of the mechanical behavior of Mg alloys

Dentro de los materiales estructurales, el magnesio y sus aleaciones están siendo el foco de una de profunda investigación. Esta investigación está dirigida a comprender la relación existente entre la microestructura de las aleaciones de Mg y su comportamiento mecánico. El objetivo es optimizar las aleaciones actuales de magnesio a partir de su microestructura y diseñar nuevas aleaciones. Sin embargo, el efecto de los factores microestructurales (como la forma, el tamaño, la orientación de los precipitados y la morfología de los granos) en el comportamiento mecánico de estas aleaciones está todavía por descubrir. Para conocer mejor de la relación entre la microestructura y el comportamiento mecánico, es necesaria la combinación de técnicas avanzadas de caracterización experimental como de simulación numérica, a diferentes longitudes de escala. En lo que respecta a las técnicas de simulación numérica, la homogeneización policristalina es una herramienta muy útil para predecir la respuesta macroscópica a partir de la microestructura de un policristal (caracterizada por el tamaño, la forma y la distribución de orientaciones de los granos) y el comportamiento del monocristal. La descripción de la microestructura se lleva a cabo mediante modernas técnicas de caracterización (difracción de rayos X, difracción de electrones retrodispersados, así como con microscopia óptica y electrónica). Sin embargo, el comportamiento del cristal sigue siendo difícil de medir, especialmente en aleaciones de Mg, donde es muy complicado conocer el valor de los parámetros que controlan el comportamiento mecánico de los diferentes modos de deslizamiento y maclado. En la presente tesis se ha desarrollado una estrategia de homogeneización computacional para predecir el comportamiento de aleaciones de magnesio. El comportamiento de los policristales ha sido obtenido mediante la simulación por elementos finitos de un volumen representativo (RVE) de la microestructura, considerando la distribución real de formas y orientaciones de los granos. El comportamiento del cristal se ha simulado mediante un modelo de plasticidad cristalina que tiene en cuenta los diferentes mecanismos físicos de deformación, como el deslizamiento y el maclado. Finalmente, la obtención de los parámetros que controlan el comportamiento del cristal (tensiones críticas resueltas (CRSS) así como las tasas de endurecimiento para todos los modos de maclado y deslizamiento) se ha resuelto mediante la implementación de una metodología de optimización inversa, una de las principales aportaciones originales de este trabajo. La metodología inversa pretende, por medio del algoritmo de optimización de Levenberg-Marquardt, obtener el conjunto de parámetros que definen el comportamiento del monocristal y que mejor ajustan a un conjunto de ensayos macroscópicos independientes. Además de la implementación de la técnica, se han estudiado tanto la objetividad del metodología como la unicidad de la solución en función de la información experimental. La estrategia de optimización inversa se usó inicialmente para obtener el comportamiento cristalino de la aleación AZ31 de Mg, obtenida por laminado. Esta aleación tiene una marcada textura basal y una gran anisotropía plástica. El comportamiento de cada grano incluyó cuatro mecanismos de deformación diferentes: deslizamiento en los planos basal, prismático, piramidal hc+ai, junto con el maclado en tracción. La validez de los parámetros resultantes se validó mediante la capacidad del modelo policristalino para predecir ensayos macroscópicos independientes en diferentes direcciones. En segundo lugar se estudió mediante la misma estrategia, la influencia del contenido de Neodimio (Nd) en las propiedades de una aleación de Mg-Mn-Nd, obtenida por extrusión. Se encontró que la adición de Nd produce una progresiva isotropización del comportamiento macroscópico. El modelo mostró que este incremento de la isotropía macroscópica era debido tanto a la aleatoriedad de la textura inicial como al incremento de la isotropía del comportamiento del cristal, con valores similares de las CRSSs de los diferentes modos de deformación. Finalmente, el modelo se empleó para analizar el efecto de la temperatura en el comportamiento del cristal de la aleación de Mg-Mn-Nd. La introducción en el modelo de los efectos non-Schmid sobre el modo de deslizamiento piramidal hc+ai permitió capturar el comportamiento mecánico a temperaturas superiores a 150_C. Esta es la primera vez, de acuerdo con el conocimiento del autor, que los efectos non-Schmid han sido observados en una aleación de Magnesio. The study of Magnesium and its alloys is a hot research topic in structural materials. In particular, special attention is being paid in understanding the relationship between microstructure and mechanical behavior in order to optimize the current alloy microstructures and guide the design of new alloys. However, the particular effect of several microstructural factors (precipitate shape, size and orientation, grain morphology distribution, etc.) in the mechanical performance of a Mg alloy is still under study. The combination of advanced characterization techniques and modeling at several length scales is necessary to improve the understanding of the relation microstructure and mechanical behavior. Respect to the simulation techniques, polycrystalline homogenization is a very useful tool to predict the macroscopic response from polycrystalline microstructure (grain size, shape and orientation distributions) and crystal behavior. The microstructure description is fully covered with modern characterization techniques (X-ray diffraction, EBSD, optical and electronic microscopy). However, the mechanical behaviour of single crystals is not well-known, especially in Mg alloys where the correct parameterization of the mechanical behavior of the different slip/twin modes is a very difficult task. A computational homogenization framework for predicting the behavior of Magnesium alloys has been developed in this thesis. The polycrystalline behavior was obtained by means of the finite element simulation of a representative volume element (RVE) of the microstructure including the actual grain shape and orientation distributions. The crystal behavior for the grains was accounted for a crystal plasticity model which took into account the physical deformation mechanisms, e.g. slip and twinning. Finally, the problem of the parametrization of the crystal behavior (critical resolved shear stresses (CRSS) and strain hardening rates of all the slip and twinning modes) was obtained by the development of an inverse optimization methodology, one of the main original contributions of this thesis. The inverse methodology aims at finding, by means of the Levenberg-Marquardt optimization algorithm, the set of parameters defining crystal behavior that best fit a set of independent macroscopic tests. The objectivity of the method and the uniqueness of solution as function of the input information has been numerically studied. The inverse optimization strategy was first used to obtain the crystal behavior of a rolled polycrystalline AZ31 Mg alloy that showed a marked basal texture and a strong plastic anisotropy. Four different deformation mechanisms: basal, prismatic and pyramidal hc+ai slip, together with tensile twinning were included to characterize the single crystal behavior. The validity of the resulting parameters was proved by the ability of the polycrystalline model to predict independent macroscopic tests on different directions. Secondly, the influence of Neodymium (Nd) content on an extruded polycrystalline Mg-Mn-Nd alloy was studied using the same homogenization and optimization framework. The effect of Nd addition was a progressive isotropization of the macroscopic behavior. The model showed that this increase in the macroscopic isotropy was due to a randomization of the initial texture and also to an increase of the crystal behavior isotropy (similar values of the CRSSs of the different modes). Finally, the model was used to analyze the effect of temperature on the crystal behaviour of a Mg-Mn-Nd alloy. The introduction in the model of non-Schmid effects on the pyramidal hc+ai slip allowed to capture the inverse strength differential that appeared, between the tension and compression, above 150_C. This is the first time, to the author's knowledge, that non-Schmid effects have been reported for Mg alloys.

Modeling and validation of the thermal behavior of buildings for the development of demand response methods

The representation of the thermal behaviour of the building is achieved through a relatively simple dynamic model that takes into account the effects due to the thermal mass of the building components. The model of a intra-floor apartment has been built in the Matlab-Simulink environment and considers the heat transmission through the external envelope, wall and windows, the internal thermal masses, (i.e. furniture, internal wall and floor slabs) and the sun gain due to opaque and see-through surfaces of the external envelope. The simulations results for the entire year have been compared and the model validated, with the one obtained with the dynamic building simulation software Energyplus.

The effects of alcohol on the driver's decision-making behavior. Volume I: executive summary and technical report. Final report.

National Highway Traffic Safety Administration, Washington, D.C.

The effects of alcohol on the driver's decision-making behavior. Volume II: appendices. Final report.

National Highway Traffic Safety Administration, Washington, D.C.

Analytical modeling of driver response in crash avoidance maneuvering. Volume I: technical background. Final report.

National Highway Traffic Safety Administration, Washington, D.C.

Analytical modeling of driver response in crash avoidance maneuvering. Volume II: an interactive tire model for driver/vehicle simulation. Final report.

National Highway Traffic Safety Administration, Washington, D.C.