Modeling and optimization of populations subject to time-dependent mutation.

It has become clear that many organisms possess the ability to regulate their mutation rate in response to environmental conditions. So the question of finding an optimal mutation rate must be replaced by that of finding an optimal mutation schedule. We show that this task cannot be accomplished with standard population-dynamic models. We then develop a "hybrid" model for populations experiencing time-dependent mutation that treats population growth as deterministic but the time of first appearance of new variants as stochastic. We show that the hybrid model agrees well with a Monte Carlo simulation. From this model, we derive a deterministic approximation, a "threshold" model, that is similar to standard population dynamic models but differs in the initial rate of generation of new mutants. We use these techniques to model antibody affinity maturation by somatic hypermutation. We had previously shown that the optimal mutation schedule for the deterministic threshold model is phasic, with periods of mutation between intervals of mutation-free growth. To establish the validity of this schedule, we now show that the phasic schedule that optimizes the deterministic threshold model significantly improves upon the best constant-rate schedule for the hybrid and Monte Carlo models.

Gene cloning, molecular modeling, and phylogenetics of serine protease P32 and serine carboxypeptidase SCP1 from nematophagous fungi Pochonia rubescens and Pochonia chlamydosporia

The fungi Pochonia chlamydosporia and Pochonia rubescens are parasites of nematode eggs and thus are biocontrol agents of nematodes. Proteolytic enzymes such as the S8 proteases VCP1 and P32, secreted during the pathogenesis of nematode eggs, are major virulence factors in these fungi. Recently, expression of these enzymes and of SCP1, a new putative S10 carboxypeptidase, was detected during endophytic colonization of barley roots by these fungi. In our study, we cloned the genomic and mRNA sequences encoding P32 from P. rubescens and SCP1 from P. chlamydosporia. P32 showed a high homology with the serine proteases Pr1A from the entomopathogenic fungus Metarhizium anisopliae and VCP1 from P. chlamydosporia (86% and 76% identity, respectively). However, the catalytic pocket of P32 showed differences in the amino acids of the substrate-recognition sites compared with the catalytic pockets of Pr1A and VCP1 proteases. Phylogenetic analysis of P32 suggests a common ancestor with protease Pr1A. SCP1 displays the characteristic features of a member of the S10 family of serine proteases. Phylogenetic comparisons show that SCP1 and other carboxypeptidases from filamentous fungi have an origin different from that of yeast vacuolar serine carboxypeptidases. Understanding protease genes from nematophagous fungi is crucial for enhancing the biocontrol potential of these organisms.

Using multilevel modeling and mixed methods to make theoretical progress in microfoundations for strategy research

The microfoundations research agenda presents an expanded theoretical perspective because it considers individuals, their characteristics, and their interactions as relevant variables to help us understand firm-level strategic issues. However, microfoundations empirical research faces unique challenges because processes take place at different levels of analysis and these multilevel processes must be considered simultaneously. We describe multilevel modeling and mixed methods as methodological approaches whose use will allow for theoretical advancements. We describe key issues regarding the use of these two types of methods and, more importantly, discuss pressing substantive questions and topics that can be addressed with each of these methodological approaches with the goal of making theoretical advancements regarding the microfoundations research agenda and strategic management studies in general.

Logical Modeling and Dynamical Analysis of Cellular Networks

The logical (or logic) formalism is increasingly used to model regulatory and signaling networks. Complementing these applications, several groups contributed various methods and tools to support the definition and analysis of logical models. After an introduction to the logical modeling framework and to several of its variants, we review here a number of recent methodological advances to ease the analysis of large and intricate networks. In particular, we survey approaches to determine model attractors and their reachability properties, to assess the dynamical impact of variations of external signals, and to consistently reduce large models. To illustrate these developments, we further consider several published logical models for two important biological processes, namely the differentiation of T helper cells and the control of mammalian cell cycle.

Description and Prediction of Freezing of Gait in Parkinson's Disease from Wearable Inertial Measurements Units

Parkinson's disease (PD) is a neuro-degenerative disorder, the second most common after Alzheimer's disease. After diagnosis, treatments can help to relieve the symptoms, but there is no known cure for PD. PD is characterized by a combination of motor and no-motor dysfunctions. Among the motor symptoms there is the so called Freezing of Gait (FoG). The FoG is a phenomenon in PD patients in which the feet stock to the floor and is difficult for the patient to initiate movement. FoG is a severe problem, since it is associated with falls, anxiety, loss of mobility, accidents, mortality and it has substantial clinical and social consequences decreasing the quality of life in PD patients. Medicine can be very successful in controlling movements disorders and dealing with some of the PD symptoms. However, the relationship between medication and the development of FoG remains unclear. Several studies have demonstrated that visual or auditory rhythmical cuing allows PD patients to improve their motor abilities. Rhythmic auditory stimulation (RAS) was shown to be particularly effective at improving gait, specially with patients that manifest FoG. While RAS allows to reduce the time and the effects of FoGs occurrence in PD patients after the FoG is detected, it can not avoid the episode due to the latency of detection. An improvement of the system would be the prediction of the FoG. This thesis was developed following two main objectives: (1) the finding of specifics properties during pre FoG periods different from normal walking context and other walking events like turns and stops using the information provided by the inertial measurements units (IMUs) and (2) the formulation of a model for automatically detect the pre FoG patterns in order to completely avoid the upcoming freezing event in PD patients. The first part focuses on the analysis of different methods for feature extraction which might lead in the FoG occurrence.

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.

La digitalizzazione del processo costruttivo: la strategia Building Information Modeling and Management (BIMM) applicata ad un caso di studio di edilizia scolastica.

L’obiettivo della tesi è quello di fare una panoramica sulla strategia BIM e quindi sulla digitalizzazione del processo costruttivo. Grazie alla analisi di un caso di studio, altro obiettivo è quello di analizzare e valutare la metodologia BIM 4D/5D, ossia la gestione dei tempi e dei costi di realizzazione dell’opera. Nella prima fase si affronta il tema del BIM, con una analisi sull’evoluzione degli strumenti di elaborazione e rappresentazione digitale del progetto architettonico, su come questi strumenti si differenzino sia dal punto di vista operativo che concettuale rivoluzionando il flusso di lavoro odierno. Quindi, partendo da un’analisi che e ritrae l’estrema frammentazione del settore delle costruzioni, si va ad analizzare come il BIM aumenti e favorisca la collaborazione delle parti interessate, armonizzando l’intero processo costruttivo dell’opera. Si prosegue con l'esame della diffusione e del livello di maturità degli strumenti BIM, di come i privati e le amministrazioni pubbliche, a livello mondiale, stiano spingendo per favorire l’adozione della metodologia BIM. Inoltre si analizzano le dinamiche dell’interoperabilità, delle metodologie e protocolli di interscambio dati, che sono un elemento chiave per il successo del BIM per via dei numerosi strumenti, specializzati nelle varie discipline del settore edile. Nella terza parte, dedicata al Project Management di un caso di studio, si verifica la bontà delle metodologie teorizzate attraverso la realizzazione di un modello virtuale in Revit. Dal modello realizzato dal laureando sono estrapolate le informazioni necessarie alla gestione, e tramite il software STRVison CPM, si elaborano i principali documenti per la progettazione e gestione del cantiere: il CM, il CME, i tempi operativi, il cronoprogramma Gantt. Obbiettivo è constatare l’effettivo livello di maturità della strategia BIM 4D e 5D e la reale possibilità di un impiego capillare nel panorama italiano del settore delle costruzioni.

Modeling and analysis of a zipping elastomeric actuator

This thesis introduces and analyzes a dielectric elastomer actuator (DEA) working in zipping mode. Electrostatic zipping is a very familiar actuation principle used in silicon micro-electro-mechanical systems. With lower voltage supply, electrostatic zipping can provide great performance for forces and displacements of an elastic membrane. Applying this principle to dielectric elastomers, the softness of the material will provide better compliance compared to silicon materials. After the presentation of an analytical model, this thesis investigates how system geometry and elastomer pre-tensioning affect system response. Results highlight how a proper selection of system parameters makes it possible to improve system regulation and reduce operating voltage requirements. Potential applications of zipping DEAs are for microfluidic control and electro-forming.

Advanced filtering and prediction software for urban traffic control systems. Final report.

Transportation Department, Office of University Research, Washington, D.C.

Application of Monte Carlo techniques to insolation characterization and prediction : status report, October 1, 1978-June 1, 1979 /

"July 1979."

Modeling and participation: elements in education to reduce alcohol impaired driving. Final report.

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

Measurement and prediction of sediment yields in Wisconsin streams /

Prepared in cooperation with the cities of Madison, Middleton, Douglas County, University of Wisconsin-Extension, Geological and Natural History Survey, Army Corps of Engineers, Wisconsin Dept. of Natural Resources.

Rainfall-runoff modeling and preliminary regional flood characteristics of small rural watersheds in the Arkansas River basin in Colorado /

Mode of access: Internet.

Modeling and measurement techniques for evaluation of design alternatives in the implementation of database management software /

Thesis--University of Maryland.