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Contact
| Oliver Ruebenacker | Phone: (617) 547-4562 |
| 11 Peabody Terrace, Ap 1904 | E-Mail: curoli@gmail.com |
| Cambridge, MA 02138 | WWW: http://www.oliver.curiousworld.org |
Education
| Year | Degree | Institution |
|---|---|---|
| 2005 | PhD (Physics) | University of Massachusetts, Amherst |
| 2001 | MS (Physics) | University of Massachusetts, Amherst |
| 2000 | Diplom (Physics) | University of Karlsruhe (TH), Germany |
Publications
-
Complexity and Modularity of Intracellular Networks -
A Systematic Approach for Modeling and Simulation
Michael L Blinov, Oliver Ruebenacker, Ion I Moraru
To appear in IET Systems Biology -
Kinetic Modeling Using BioPAX Ontology
Oliver Ruebenacker, Ion I Moraru, James C Schaff, Michael L Blinov
IEEE International Conference on Bioinformatics and Biomedicine, 2007, Proceedings, pages 339-348. -
Weakly interacting Bose gases in the fluctuation region
Oliver Ruebenacker
PhD thesis at the University of Massachusetts at Amherst, MA, US (2006) Thesis advisor: Nikolay Prokof'ev -
"Weakly interacting Bose gas in the vicinity of the critical
point"
Nikolay Prokof`ev, Oliver Ruebenacker, Boris Svistunov
Phys. Rev. A 69 , 053625 (2004) -
"Critical Point of a Weakly Interacting Two-Dimensional Bose
Gas"
Nikolay Prokof`ev, Oliver Ruebenacker, Boris Svistunov
Phys. Rev. Lett. 87 , 160601 (2001) -
"Hole Dynamics in a two-dimensional quantum anti-ferromagnet"
Oliver Ruebenacker
Diplom thesis at University of Karlsruhe, Germany, 2000
Thesis advisors: Peter Woelfle and Nikolay Prokof`ev
Presentations
-
Towards unifying systems biology - using pathway
data in BioPAX format for SBML simulators
Oliver Ruebenacker, Michael L Blinov, Ion I Moraru
Accepted to Second Annual q-bio Conference on Cellular Information Processing (2008)
Submitted to International Conference on Computational Methods in Systems Biology (2008) -
Modeling Complex Networks: Integrating Rules (BioNetGen)
and Data Mining (BioPAX ontology) into the Virtual Cell Framework
Ion I Moraru, Oliver Ruebenacker, James C Schaff, Leslie M Loew Michael L Blinov
The Eighth International Conference on Systems Biology, 2007 -
Kinetic Modeling Using BioPAX Ontology
Oliver Ruebenacker, Ion I Moraru, James C Schaff, Michael L Blinov
IEEE International Conference on Bioinformatics and Biomedicine, 2007- Membrane Nano-Structures: The Three Tether Junction
Oliver Ruebenacker, Greg Huber American Physical Society, March Meeting 2006- Three-Dimensional Weakly Interacting Bose Gas in the Vicinity of the Critical Point
Nikolay Prokof`ev, Oliver Ruebenacker, Boris Svistunov
American Physical Society, March Meeting 2004- Worm Algorithm simulations of the hole dynamics in the t-J model
Nikolay Prokof`ev, Oliver Ruebenacker
American Physical Society, March Meeting 2001 - Membrane Nano-Structures: The Three Tether Junction
Experience
- Post-doc (February 2007 to August 2008)
- Part of Virtual Cell team, software development for simulation of cellular reaction networks; integration of SBML and BioPAX using Semantic Web methods.
- Post-doc (February 2005 to February 2007)
- Research in biological physics at University of Connecticut Health Center
-
Instructor (June 2004 to July 2004)
- Physics 131: Introductory Physics I
-
Graduate Teaching Assistant (September 2003 to August 2004)
- In charge of department resource room, offering help to students with questions regarding all undergrad physics classes and the online homework system OWL.
- Taught general physics labs, including grading
-
Graduate Research Assistant (September 1999 to August 2003)
- Did research as PhD candidate in condensed matter theory involving analytical and numerical methods applied to statistical physics, such as holes in a two-dimensional quantum antiferromagnet and Bose and psi-4 gases in two and three dimensions.
- Administered research computer systems, including setup and maintainance of two Redhat Linux Beowulf clusters (15 and 12 nodes).
Skills
- Programming Languages
- Java, C++, C, Perl, Fortran 95, ML, PostScript, Pascal, Logo, Oberon
- Software Development
- Semantic Web, XML, RDF, OWL, SPARQL, Reasoning, Swing, Jena, Eclipse, SVN, BioPAX, SBML, libSBML
- Analytical
- Critical phenomena, universality considerations, mean field theory, dimensional analysis, differential geometry
- Numerical
- Worm Algorithm, diagrammatic methods, Monte Carlo for highly constrained configurations with local updates only, world line algorithms, classical and quantum simulations, simulating mechanics of surfaces by level set and triangulation
- Document Processing
- LaTeX/TeX and relatives, PostScript, MS Word, MS Excel, MS PowerPoint, HTML
- System Administration
- Redhat Linux, including building and administrating a Beowulf cluster, network, security, backup, hardware maintainance, Apple G5 servers, Mac OSX
- Languages
- German (mothertongue), English (fluent), Turkish (some)
- Awards
- Won prizes at German national and State of Baden-Wuerttemberg math competitions.
Activities
- Physics Graduate Student Association
- President (2001-2003), Chair of Academic and Research Committee (2003-2004)
- Graduate Employee Organization/UAW Local 2322
- Steering committee (2001), Physics Department steward (2000-2003), chair of constitutional committee (2001-2002)
- GRIPS (math and science student club)
- Chair, Vice-Chair
- Schachfreunde Kraichtal (Local Chess Club)
- Treasurer, Captain of first team, Youth Leader