Browsing FAS Theses and Dissertations by FAS Department "Biophysics"
Now showing items 1-20 of 25
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Bistable dynamics in microbial ecology and systems biology
(2016-05-04)Bistability, in which a system has two stable states, is a common property of many dynamic systems. This thesis explores the properties of such systems across a range of length scales, from gene circuits to ecosystems. ... -
Competition and Coexistence in Yeast Experimental Evolution
(2016-05-19)Natural selection gives rise to biodiversity by purging the less-fit among variants that are too similar (a principle known as character displacement), but to predict how fit or different an organism needs to be to survive ... -
Comprehensive Approaches to Identifying the Targets of Natural and Synthetic Antibodies Using Microarray DNA Synthesis and High-Throughput Sequencing
(2015-09-24)The incredible flexibility and specificity of the humoral immune response is dependent on the highly diverse repertoire of naïve and affinity-matured antibodies. Utilizing and understanding the power of this response ... -
Constrained Bayesian Optimization and Applications
(2015-05-17)Bayesian optimization is an approach for globally optimizing black-box functions that are expensive to evaluate, non-convex, and possibly noisy. Recently, Bayesian optimization has been used with great effectiveness for ... -
DNA Polymerase Exchange and Lesion Bypass in Escherichia Coli
(2015-11-13)Translesion synthesis (TLS) alleviates replication stalling at DNA lesions. Bypass of lesions by specialized translesion DNA polymerases involves exchange with high-fidelity replicative polymerases. As a consequence of ... -
Engineered Biofilms for Materials Production and Patterning
(2016-04-22)Natural materials, such as bone, integrate living cells composed of organic molecules together with inorganic components. This enables combinations of functionalities, such as mechanical strength and the ability to regenerate ... -
High-Throughput Image-Based Screening of Pooled Genetic Variant Libraries
(2018-05-13)Image-based, high-throughput screening of pooled libraries of genetic perturbations will greatly advance our understanding of biological systems and facilitate many biotechnology applications. Here we report a high-throughput ... -
Improved PET Data Quantification in Simultaneous PET/MR Neuroimaging
(2015-05-16)Recently, systems that integrate positron emission tomography and magnetic resonance imaging (PET/MR) have become available for clinical use. This new technology, which combines the high spatial resolution and superior ... -
An Investigation of the Interaction Between Graphene and Hydrated Ions
(2016-05-17)The ability of graphene and carbon nanotubes to generate an electric potential from flowing fluids has attracted much interest. The effect is thought to occur because certain ionic and molecular species bind to the surface ... -
Machine-guided design and evolution of biological systems: from the protein to the genome scale
(2018-05-11)Evolution has shown that mutation and selection over billions of years can produce complex molecules and organisms that thrive in a diverse range of environments. As biological engineers, we would like to systematize the ... -
Microscopic Image Guidance: Real-Time Thermal Therapy Monitoring for Epithelial Lesions
(2017-04-12)Conventional image guidance is typically based on macroscopic clinical imaging modalities, such as magnetic resonance imaging, computed tomography and ultrasound imaging, which are limited in their ability to guide therapeutic ... -
Molecular Mechanisms of the Formation and Maintenance of the Tubular Endoplasmic Reticulum Network
(2018-05-13)Membrane-bound organelles, a defining feature of eukaryotic cells, display a diverse set of characteristic shapes that range from highly spherical, to flattened sheets, and even thin tubules. Therefore, how the characteristic ... -
Monte Carlo Simulation Approaches to Protein Stability and Aggregation Prediction
(2017-05-10)A protein’s sequence and set of covalent modifications determine its stability and aggregation propensity in a given environment. Given a change in sequence or covalent structure, we would like to be able to predict the ... -
Nanoscale Organization and Optical Observation of Biomolecules With DNA Nanotechnology
(2016-05-19)Understanding biomolecular information at the single-molecule level requires tools for manipulating and observing individual biomolecules at the nanoscale. Programmable DNA nanotechnology provides an ideal interface to ... -
Predicting the Effects of Missense Variation on Protein Structure, Function, and Evolution
(2015-05-08)Estimating the effects of missense mutations is a problem with many important applications in a variety of fields, including medical genetics, evolutionary theory, population genetics, and protein structure and design. ... -
Prediction as a Rule for Unsupervised Learning in Deep Neural Networks
(2017-08-10)While machine learning systems have recently achieved impressive, (super)human-level performance in several tasks, they have often relied on unnatural amounts of supervision - e.g. large numbers of labeled images or ... -
Probing the Spatio-Temporal Organizations and Dynamics of Gene Expression and DNA Replication in the Mammalian Cell Nucleus
(2015-05-15)The nucleus is an organelle of central importance to the mammalian cell. However, our understanding of the organizations and dynamics of many nuclear structures and processes remains inadequate, largely due to the difficulty ... -
Role of Recurrent Computations in Object Completion
(2016-01-11)Existing models of visual object recognition posit that recognition is orchestrated by a hierarchy of processing layers. In these models, neural computation proceeds in a largely feed-forward path up this hierarchy, without ... -
Simultaneous Inference of Cell Types, Lineage Trees, and Regulatory Genes From Gene Expression Data
(2016-05-13)Important goals of developmental biology include identifying cell types, understanding the sequence of lineage choices made by multipotent cells and unconvering the molecular networks controlling these decisions. Achieving ... -
Single Molecule FRET Studies of Reverse Transcription and Chromatin Remodeling
(2015-08-21)The measurement of Förster resonance energy transfer (FRET) at the single-molecule level provides a powerful method for monitoring the structural dynamics of biomolecular systems in real time. These single-molecule FRET ...