Research Topics - All Ongoing Projects
The scope of the research efforts of the Theoretical and Computational Biophysics Group includes a variety of fields of inquiry - quantum biology, nanoengineering, bioenergetic proteins, membrane biophysics, steered/interactive molecular dynamics, and other topics - across many levels of organization, from the molecular to the cellular level, with an emphasis on modeling large macromolecular systems in realistic environments. Under this category are descriptions of the ongoing research efforts by group members.
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The ear is a sensitive and robust device, able to perceive the faint sound of flowing water and the thunderous blast of an air plane. Like a microphone, the ear transforms a complex, mechanical stimulus (sound), into an electrical signal, a voltage change in a nerve cell, that can be understood by our brain. This transformation is called "mechanotransduction" and is accomplished by a series of amazingly minute devices that each connect a soft spring to an ion channel, both located in specialized sensory cells, the hair cells of the inner ear. The springs, through their vibrations agitated by particular sound frequencies, control ion currents passing through the channels, thereby, modifying the hair cell internal electrical potential. This leads to neural signaling to the acoustic cortex of the brain. Recently reported molecular dynamics simulations using NAMD, some of the most extensive simulations accomplished to date both in size and duration, showed that the mechanical characteristics of hair cell signaling can be traced to a single protein, ankyrin, that acts as a helical spring. Imagine a soft spring that is extended several inches by the weight of a feather! Ankyrin is such a spring, but a billion times finer.
Papers
Research Projects
- Structure, Dynamics, and Function of Aquaporins
- HDL and Nanodiscs
- Multiscale Modeling of Gene Repression
- Mechanical Strength of the Titin/Telethonin Complex
- Molecular Basis of Hearing
- Fibronectin and Integrin
- Nanotube
- Organization of Energy Transfer Networks in Photosynthesis
- ATP Hydrolysis in F1-ATPase
- Biological Photoreceptors
- Conformational Change of Holliday Junction
- The Nuclear Pore Complex
- Gas Transport Inside Hydrogenase




