Join the group of Prof. Daniel M. Zuckerman, which is working to push the limits of statistical-mechanics-based computations for biomolecules and systems biology. Our work employs statistical physics to understand the behavior of proteins, molecular machines, and their interactions. The group has just moved to the Center for Spatial Systems Biomedicine and the Dept of Biomedical Engineering at the Oregon Health & Science University in Portland. OHSU recently raised one billion dollars to fund the establishment of a new cancer center.
The Zuckerman group works at a range of scales in cell and molecular biology and we are interested in a range of issues - binding and allostery, machine-like behavior of biomolecules, and drug design, as well as computational methods for studying these problems. We employ the atomistic models of molecular simulation and more coarse-grained descriptions including discrete-state kinetic models. In the atomistic regime, we pursue simulation methods for equilibrium and non-equilibrium sampling of proteins and other biomolecules, free-energy/binding-affinity estimation, and flexible docking. The group has a long history of developing new algorithms, software, and databases, including multi-trajectory parallel methods and multi-scale methodology for combining coarse and detailed models. The group also works at larger scales, on structure-based simulation approaches for virus capsid assembly, on discrete-state (chemical kinetics/master equation) models of molecular machines, and on cell signaling and the effects of cell geometry.
Two postdocs are being recruited:
(1) A postdoc is being recruited to work on one or more molecular simulation projects. Likely projects include development and application of the weighted ensemble (WE) and related methods for studying equilibrium and non-equilibrium behavior of biomolecules. Applications could include the study of protein (un)folding and (un)binding of small drug-like molecules to protein targets. Preliminary studies suggest WE could enable the massive speedup of protein folding and binding simulations. Data analysis will include the use of recently developed unbiased non-Markovian tools.
(2) A postdoc is being recruited for theoretical and computational investigation of molecular machines and cell-scale modeling. The primary projects will build on our recent article in PNAS, “Biophysical comparison of ATP synthesis mechanisms shows a kinetic advantage for the rotary process”. Projects will use discrete-state kinetic modeling to address mechanistic biophysical questions regarding rotary ATPases, which function as both pumps and ATP synthases under differing cellular conditions. For example, individual members of the V-ATPase family of pumps appear to exhibit variable proton:ATP “coupling ratios” depending on conditions. What types of biophysical kinetic models capture this behavior? A secondary focus of the position will be cell-scale modeling of cancer signaling processes, working in collaboration with OCSSB colleagues engaged in cutting-edge imaging research.
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Oregon Health & Science University values a diverse and culturally competent workforce. We are proud to be an equal opportunity, affirmative action organization. Individuals with diverse backgrounds and those who promote diversity and a culture of inclusion are encouraged to apply. Applicants with disabilities can request reasonable accommodation by contacting the Affirmative Action and Equal Opportunity Department at 503-494-5148.