The O’Brien lab is opening in January 2014 at the Department of Chemistry at Pennsylvania State University, University Park and is aiming to hire three post-doctoral scholars. We’re putting together a team of researchers from a diverse range of educational backgrounds who are interested in addressing questions at the cutting-edge of molecular and cellular biology by developing and utilizing tools rooted firmly in the fields of Chemistry, Physics and Computer Science. These tools include mathematical modelling [1,2], coarse-grained molecular simulations [3-5] and bioinformatic/systems methods 6. A primary focus of the lab is to develop a framework to understand, model and predict the influence of translation on the behavior of newly synthesized proteins and its implications for down-stream cellular processes. Theoretical and computational investigations have the opportunity to significantly advance this field because there are many unanswered questions that can be addressed with our techniques. This research will have implications for the basic, biomedical and applied sciences. There will be numerous opportunities to develop new methods, theories and approaches that can be tested against published experimental data and unpublished data from experimental collaborators.
As part of this research effort we are looking to fill three postdoctoral positions in the areas of (1) analytic theory and mathematical modeling of cellular processes; (2) coarse-grained model development for the simulation of biomolecular complexes using molecular dynamics; and (3) bioinformatic and systems methods applied to the nascent proteome. Creative, tenacious researchers with the relevant skills from the fields of chemistry, physics, engineering, bioinformatics, systems biology and related fields are encouraged to apply.
The start date for these positions is very flexible: any time between now and January, 2015 is possible. Graduate students who will be finishing their Ph.D. within the next year are recommended to apply now and arrange for a later start date in the O’Brien lab.
Position 1. Analytic theory and mathematical modeling of cellular processes. A postdoctoral scholar hired to this position will have strong mathematical skills and experience applying them to the modeling of biological systems. This researchers’ efforts in the O’Brien lab will be focused on developing models that connect the rates of translation-related processes to the behavior of nascent proteins in terms of their folding 1, misfolding, aggregation, degradation and translocation. This will involve modeling reaction networks and estimating the relevant parameters from experimental data sets. Predictions will be tested in a number of ways, including experimental data from collaborators as well as against the results from molecular dynamics simulations. Several years of funding are available for this position.
Position 2. Coarse-grained model development and the simulation of biomolecular complexes. A postdoctoral scholar hired to this position will have strong computational skills, including scripting and data analysis of molecular simulations, experience in developing coarse-grained force-fields for biomolecules, and extensive experience in simulating biomolecules in high-performance computing environments. Experience with the program CHARMM is a plus, but is not required. This researchers’ efforts in the O’Brien lab will be focused on developing models for the cellular environment a nascent protein is exposed to3-5 and applying them to important biological questions. This work will naturally complement the theoretical modeling of other members of the O’Brien lab, and vice versa. Several years of funding are available for this position.
Position 3. Computational Biology and systems methods. A postdoctoral scholar hired to this position will have strong bioinformatic skills, including handing large data sets, extracting relevant biological data from disparate databases, and the ability to integrate such data into predictive models. This researchers’ efforts in the O’Brien lab will be focused on extracting important information from high-throughput data sets to estimate relevant parameters for our models and to make predictions about proteome-wide nascent protein behavior in cells6. Several years of funding are available for this position.
Some additional information on the O’Brien Labs publications can be found on ResearchGate or Google Scholars.
(1) O’Brien, E. P.; Vendruscolo, M.; Dobson, C. M. Nature Communications 2012, 3, 868.
(2) O’Brien, E. P.; Ziv, G.; Haran, G.; Brooks, B. R.; Thirumalai, D. P Natl Acad Sci USA 2008, 105, 13403.
(3) O’Brien, E. P.; Christodoulou, J.; Vendruscolo, M.; Dobson, C. M. J Am Chem Soc 2011, 133, 513.
(4) O’Brien, E. P.; Hsu, S. T. D.; Christodoulou, J.; Vendruscolo, M.; Dobson, C. M. J Am Chem Soc 2010, 132, 16928.
(5) O’Brien, E. P.; Christodoulou, J.; Vendruscolo, M.; Dobson, C. M. J Am Chem Soc 2012, 134, 10920.
(6) Ciryam, P.; Morimoto, R. I.; Vendruscolo, M.; Dobson, C. M.; O’Brien, E. P. P Natl Acad Sci USA 2013, 110, E132.
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