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Date: Thu Oct 6 15:10:39 2016
Subject: 16.10.05 Postdoc in Biophysical Molecular Simulation - Zuckerman Group - Portland, Oregon
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 is interested in 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.  We are attacking 
key technical problems in the field: 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.  


A postdoc is being recruited to work on one or more projects.  Likely 
projects include development and application of the weighted ensemble 
(WE) method 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 

Candidates must hold a PhD in Physics, Theoretical Chemistry, 
Chemical Engineering, Biophysics or related field.  Candidates 
should have experience with programming (e.g., C, Python), 
scripting and software packages for molecular simulation 
(e.g., Amber, NAMD) and analysis (e.g., Matlab, Mathematica).

Salary: $43,692.00 - 50,000.00 per year.  Salary will 
depend on experience

To begin the application process, please send your CV with a cover 
letter explaining your suitability for the position.  Email these to 
zuckermd :

About OHSU - Oregon Health & Science University
Oregon Health & Science University is a renowned medical and research 
institution in Portland. Perhaps best known for recently raising one 
billion dollars for its new cancer center, OHSU has great strength in 
many areas, ranging from structural biology to super-resolution 
imaging and analysis. The city of Portland is famous for its great 
food, coffee, bike-friendliness, and proximity to all the natural 
beauty of the Pacific Northwest.

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.

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