Browsing Faculty of Arts and Sciences by Keyword "Biophysics, General"
Now showing items 1-20 of 42
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Active dynamics of microtubule and motor protein networks
(2017-05-04)Cellular components have the remarkable ability to self-organize in space and time into higher order structures necessary to carry out biological functions. One example of such a structure is the spindle apparatus, a ... -
Assembly and Regulation of the Inflammasome Governed by a Unified Polymerization Mechanism
(2016-05-13)The innate immune system employs a diverse set of pattern recognition receptors to detect intrinsic and extrinsic danger signals for host protection. Inflammasomes represent an important class of receptors that elicit ... -
The Biophysics of Vertebrate Hearing: A Single-Molecule Approach
(2015-05-22)Inner-ear mechanotransduction relies on tip links, fine protein filaments made of cadherin-23 and protocadherin-15 that convey tension to mechanosensitive channels at the tips of hair-cell stereocilia. The tip-link cadherins ... -
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 ... -
Development of New Tools for Single-Molecule Force Spectroscopy & The Application of these Tools to Mapping the Role of Force Directionality in the Actin Mechanome
(2015-09-28)Actin filaments serve as a hub of focal adhesion-based mechanotransduction network in a wide variety of cell types. In this role filaments and networks of filaments are exposed to forces in a range of directions and ... -
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 ... -
Dynamics of protein evolution within complex biophysical constraints
(2017-03-03)Proteins evolve within complex biophysical constraints. Natural selection promotes the survival of the fittest organisms. Therefore, protein variants that decrease organismal fitness are likely to go extinct along with the ... -
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 ... -
Evolution of the Amphibian Head and Neck: Fate and Patterning of Cranial Mesoderm in the Axolotl (Ambystoma Mexicanum)
(2016-02-19)The vertebrate head is a complex structure derived from all three embryonic germ layers. Cranial mesoderm forms most of the neurocranium, cardiovascular tissues and voluntary muscles required for intake of food and oxygenated ... -
Exploring Biomolecular Interactions Through Single-Molecule Force Spectroscopy and Computational Simulation
(2016-04-11)Molecular interactions between cellular components such as proteins and nucleic acids govern the fundamental processes of living systems. Technological advancements in the past decade have allowed the characterization of ... -
Genetic Draft and Linked Selection in Rapidly Adapting Populations
(2017-01-18)Evolution proceeds by the stochastic emergence and fixation of mutations over time. The dynamics of this process are well understood if beneficial mutations are sufficiently rare or the population is sufficiently small. ... -
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 ... -
Holographic Microscopy for Soft Matter and Biophysics
(2016-09-14)I discuss a series of advancements I have made towards making digital holographic microscopy into a useful tool for experimental scientists in soft-matter physics and biophysics. Digital holograms can be recorded with ... -
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 ... -
Mechanisms of Bacterial Envelope Stress From Within and Without
(2017-01-25)The bacterial cell envelope is the frontline protective barrier between the cell and the environment. It is a complex multilayered structure essential for maintaining cellular integrity and plays a crucial defensive role ... -
The Mechanistic Basis of Dynein Microtubule Binding and Its Regulation
(2015-01-22)Eukaryotic cells use a diverse toolbox of cytoskeletal motors to transport and position cellular materials in space and time. Two microtubule-based motors—kinesin and dynein—transport organelles, RNA and protein cargos ... -
Mechanistic Studies of the Microtubule-Based Motors Dynein and Kinesin-8
(2015-05-20)The precise delivery and organization of intracellular factors in space and time relies on a set of molecules that move along and regulate the dynamics of cytoskeletal filaments. The two families of microtubule-based ... -
Molecular Evolution in Rapidly Evolving Populations
(2016-05-17)Advances in DNA sequencing are creating new opportunities for studying the process of evolution. These measurements can be particularly useful for rapidly evolving microbial organisms, whose small size and fast generation ... -
Molecular Mechanism of Secretory Protein Translocation by the SecA ATPase
(2015-05-06)In bacteria, most secretory proteins are translocated across the plasma membrane by the interplay of the SecA ATPase and the SecY channel. How SecA moves a broad range of polypeptide substrates is only poorly understood. ...