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Chemical Biology

Michael E. Colvin

The past century has seen tremendous progress in determining the biochemical and biophysical processes that constitute life. One exciting consequence of this understanding is the possibility of developing mathematical models of biological function that are accurate and even predictive.
Professor Colvin's research uses a wide range of simulation methods to model biological systems at different levels. Much of his research uses molecular modeling to study biochemical problems, with a particular emphasis on modeling the activity of DNA-binding food mutagens and anticancer drugs. These methods involve computing the structures and energetics of biomolecules using either quantum or classical mechanics, and often require the use of supercomputers.
Other molecular modeling projects include studying:

  • Synthetic analogs to nucleic acids and exotic nucleic acid structures
  • The function of DNA-processing multiprotein complexes
  • The mechanism of cytochrome P450 and other enzymes

More recently, his research interests have expanded to include simulations of biophysical and cellular processes using equations that describe the system as continuous (and sometime stochastic) dynamical systems. These projects include:

  • Simulating the formation mutagenic compounds during cooking
  • The operation of the nuclear pore complex
  • Cell fate decisions

These projects offer a wide range of research projects for students interested in the application of mathematics and computers to understand the living world.
(209) 228-4364
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Patricia LiWang
  • Biochemistry and biophysics
  • Structural biology of chemokines
  • Applications to HIV and inflammatory diseases
(209) 228-4568
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Matthew Meyer
Associate Professor

Professor Meyer's research is directed toward developing techniques to aid in drug discovery. Students in his lab have the opportunity to become proficient in:

  • Organic synthesis
  • Protein expression and purification
  • Modern NMR techniques
  • Computational chemistry

Drugs are often small molecules that inhibit enzymes or receptors in the body. The inhibitors that are important for use as therapeutic agents are usually molecules that preferentially compete for the binding site(s) on an enzyme or receptor.

Currently, Professor Meyer is working on developing a technique that quantitatively probes the binding interactions of lipoxygenases with their natural substrates along the reaction pathway from reactants to products. Human lipoxygenases are important because they have been implicated in asthma, heart disease, various cancers, and a host of other diseases. Developing techniques to measure how strongly these enzymes interact with their substrates along the reaction pathway may lead to information that is crucial to designing drugs to treat these diseases -  specifically those that utilize many of the structural features of the natural substrate. This is important because it could allow for the efficient design of therapeutic lead structures that would not be as likely to produce unforeseen side effects.  A development of this nature could significantly reduce the costs associated with drug development in the pharmaceutical industry.
(209) 228-2982
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Aleksandr Noy
Associate Adjunct Professor
  • Bionanoelectronics
  • Molecular self-assembly in systems with reduced dimensionality
  • Inorganic nanowires and carbon nanotubes
  • Biophysics and measurement of biological forces using scanning probe microscopy
  • Nanofluidics, and molecular transport at nanoscale
  • Nanotechnology
(925) 424-6203
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Andy LiWang

The rising and setting of the sun causes dramatic oscillations in light and temperature each day. Most life forms involuntarily coordinate their lifestyles to these cyclic variations by means of an endogenous clock called the circadian clock. These circadian clocks have been identified in diverse organisms from cyanobacteria to humans, and studies suggest that the circadian clock has adaptive value.

Professor LiWang's laboratory is resolving the structural and biochemical basis of rhythmicity of the cyanobacterial circadian clock. The central oscillator of this clock is composed of only three proteins, which by themselves in a test tube with ATP generate a self-sustained circadian rhythm for several days. Their objective is to develop a comprehensive understanding of how a simple mixture of three proteins keeps time.
(209) 777-6341
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