Multi-scale Simulation of BAR Domain Coupling to Membrane Curvature
The goal of this project is to understand the mechanisms of BAR domain mechanisms of BAR domain membrane remodeling and curvature sensing. To obtain this goal, both local and global mechanisms must be studied. Locally, the atomistic mechanisms of BAR domain coupling to local membrane curvature will be studied.
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Multi-scale Modeling of the Spectrin Tetramer
Understanding the rest shape and the associated large reversible deformation of the red blood cell has long been a common goal for cell biologists and physicists. It has been found that the red blood cell's unique shape and elastic properties are related to the structure of the underlying cytoskeleton. Although the specific proteins that comprise the cytoskeleton have been identified, the exact mechanisms by which the red blood cell deforms and maintiains its shape are still a topic of debate. The cytoskeleton of th red blood cell is a mesh network of mostly spectrin protein tetramers. The elasticity of the cell is thought to originate from spectrin's ability to deform easily. The have been various approaches to understanding this system, ranging from a continuum free energy formulation for the whole membrane, to computer simulations of various two-dimensional tethered network systems. What is lacking in all such studies is an accurate description of the elasticity of the spectrin tetramer described in the form of a force-extension profile and an understanding of the source of this elasticity from an atomistic level. Our study defines the first effort to map the elasticity of the spectrin tetramer starting from the atomistic level.
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Particle-based Modeling of the Bacterial Flagellum
A bacterial cell lives in an aqueous environment and is able to respond to changes in its environment, such as changes in temperature, light intensity, or chemical composition. The response of the organism to chemical stimuli, referred to as chemotaxis, is carried out by swimming in the squeous medium towards regimes with an increasing chemical gradient. This is accomplished by executing a series of runs and tumbles cause by the bundling and unbundling of external organelles of locomotion known as flagella. These long helical filaments are tubular structures comprisesd of eleven photofilaments of plymerized flagellin proteins. They are driven by a reversible rotary motor composed of proteins located at the flagellum's anchor point embedded in the cell wall. This motor can run in both clockwise and counterclockwise directions generating a torque that rotates the rigid, helical filament attached to it via a short proximal hook. Understanding the motile behavior of such a complex system in a low Reynolds number hydrodynamic environment; however, most of these efforts focus on treating the elastic nature of the filament and then approximating the hydrodynamics, or vice versa. Our study makes an effort to bring together both of these components of bacterial motility that are responsible for the propulsive dynamics.
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