Theory Simulation and Modeling

Special Seminar: Erol Akçay, Princeton

Mon, 2013-02-04 10:00
Speaker: 
Dr. Erol Akçay
Princeton University

New frontiers in social evolution theory

Host: Josh Plotkin (Biology)
Location: 

Lynch Lecture Hall

 

Cooperation between organisms is a major driving force of biological organization at all levels, from single cells to whole ecosystems. Understanding the evolutionary dynamics of cooperation and other social traits therefore is a central goal of evolutionary theory. I will talk about my recent work that aims to advance the frontiers of social evolution theory in two directions.

 

Special Seminar: Emilia Huerta-Sanchez, University of California, Berkeley

Mon, 2013-01-28 10:00
Speaker: 

Dr. Emilia Huerta-Sanchez

University of California, Berkeley

 

Detecting and characterizing natural selection from next generation sequencing data

 

Host: Charles Epstein (Math)

Location: 

Lynch Lecture Hall

 

Special Seminar: Sharon Aviran, University of California, Berkeley

Thu, 2013-01-24 10:00
Speaker: 

Dr. Sharon Aviran

University of California, Berkeley

 

High-throughput RNA structure analysis from chemical footprinting experiments

 

Host: Randy Kamien (Physics)

Location: 

Lynch Lecture Hall

 

New regulatory roles continue to emerge for both natural and engineered RNAs, many of which have specific structures essential to their function. This highlights a growing need to develop technologies that enable rapid and accurate characterization of structural features within complex RNA populations. Yet, available techniques that are reliable are also vastly limited by technological constraints, while the accuracy of popular computational methods is generally poor. These limitations thus pose a major barrier to comprehensive determination of structure from sequence.

Special Seminar: Kirill Korolev, MIT

Tue, 2013-01-22 10:00
Speaker: 

Dr. Kirill Korolev

Massachusetts Institute of Chemistry

 

The interplay between ecology and evolution in cancerous tumors and expanding populations

 

Host: Andrea Liu

Location: 

Lynch Lecture Hall

 

Special Seminar: Eleni Katifori, MPI-Goettingen

Thu, 2013-01-17 10:00
Speaker: 

Dr. Eleni Katifori

Max Planck Institute - Goettingen

 

The evolution of leaf vasculature: deciphering the design of optimal loopy architectures

 

Host: Douglas Jerolmack (Earth and Environmental Sciences)

Location: 

Lynch Lecture Hall

 

Hirschmann Visiting Professor Lecture 1 - James Skinner, Univ. Wisconsin

Tue, 2013-02-19 16:00
Speaker: 

James L. Skinner, University of Wisconsin, Madison

 


Lecture 1

The mystery of water and its phases
Tuesday, February 19, 2013
4:00 PM
Reception to follow in Nobel Hall

Location: 

Carolyn Lynch Lecture Hall

Joseph Subotnik

Photo: 
First Name: 
Joseph
Last Name: 
Subotnik
Official Title: 
Professor of Chemistry

Physical and Theoretical Chemistry

Contact Information
Office Location: 
268 Cret wing
Email: 
subotnik@sas.upenn.edu
Phone: 
215-746-7078
Admin Support: 
Education: 

B.A. Harvard University, 2000

Physics and Math (summa cum laude)


Ph.D.  UC Berkeley, 2006  Biophysics

 

NSF International Research Fellow (2007 -2009), Tel-Aviv

Postdoctoral Fellow, Northwestern University (2009-2010)

Research Interests: 

Research in the Subotnik group focuses on the intersection of static quantum chemistry methods (especially for excited states) with nonadiabatic dynamics methods (specifically surface hopping). The focus is quantifying electron transfer, energy transfer, and electronic relaxation. Applications are to almost all photo-induced processes!

Jeffery G. Saven

Photo: 
First Name: 
Jeffery G.
Last Name: 
Saven
Official Title: 
Professor of Chemistry

Biological and Theoretical Physical Chemistry

Contact Information
Office Location: 
266 Cret, Lab 261 Cret
Email: 
saven@sas.upenn.edu
Phone: 
215-573-6062
Fax: 
215-573-2112
Admin Support: 
Education: 
  • BA, New College of Florida
  • PhD, Columbia University & University of Wisconsin
  • NSF Postdoctoral Fellow in Chemistry, University of Illinois, Urbana-Champaign, 1993-1995. Postdoctoral Research Associate, University of Illinois, Urbana-Champaign, 1995-1997
Research Interests: 

Computationally designed protein complex containing a nonbiological cofactor, designed and studied in collaboration with the DeGrado and Therien groups in the Department of Chemistry. On the left is the computationally designed protein scaffold (magenta) and two abiotic porphyrin cofactors (yellow). On the right is a model of the computationally designed sequence and structure.

 

Our research interests involve theoretical chemistry, particularly as it applies to biopolymers, macromolecules, condensed phases, and disordered systems. We are developing computational methods for understanding and designing molecular sytems having many physical and chemical degrees of freedom. Molecular simulation techniques are used both to study molecular systems in detail and to test and illustrate our theories. 

 

A current thrust of the group involves developing computational tools for understanding the properties of protein sequences consistent with a chosen three-dimensional structure. The group works closely with experimental groups at Penn and at other universities; some group members are involved in joint theoretical/experimental projects. Recent projects involve the design of soluble and membrane bound proteins, discerning the origins of conservation in naturally occurring proteins, biomolecular simulation, and the design of nonbiological folding molecules.

Andrew M. Rappe

Photo: 
First Name: 
Andrew M.
Last Name: 
Rappe
Official Title: 
Blanchard Professor of Chemistry

Physical and Theoretical Chemistry

Additional Titles: 
Professor of Materials Science and Engineering
Co-Director, Pennergy
Contact Information
Office Location: 
264 Cret, Lab: 263, 265, 267, 268 Cret
Email: 
rappe@sas.upenn.edu
Phone: 
(215) 898-8313
Fax: 
(215) 573-2112
Admin Support: 
Education: 
  • B.A. Chemistry and Physics, Summa Cum Laude, Harvard University (1986)
  • ONR Graduate Fellow, Massachusetts Institute of Technology (1986-1989)
  • JSEP Graduate Fellow, Massachusetts Institute of Technology (1990-1992)
  • Ph. D. Physics and Chemistry, Massachusetts Institute of Technology (1992)
  • IBM Postdoctoral Fellow, University of California at Berkeley (1992-1994)
  • Assistant Professor of Chemistry, University of Pennsylvania (1994-2000)
  • Associate Professor of Chemistry, University of Pennsylvania (2000-2006)
  • Professor of Chemistry, University of Pennsylvania (2006-present)
  • NSF CAREER Award (1997-2001)
  • Alfred P. Sloan Foundation Fellow (1998-2000)
  • Dreyfus Teacher-Scholar Award (1999-2004)
Research Interests: 

 

My research group creates and uses new theoretical and computational approaches to study complex systems in materials science, condensed-matter physics, and physical chemistry.

 

We look for new phenomena that occur when different components are brought together. For example, we examine molecules adsorbing on metal surfaces, in order to understand the effect of surface composition and structure on preferred adsorption sites, dissociation pathways, and vibrational dynamics. We also study how the compositions of oxide solid solutions lead to Angstrom-scale chemical structure, nanometer scale structural disorder, and long-range ferroelectric and piezoelectric properties. These studies find real-world applications in catalysis, corrosion, SONAR, fuel cells and other important technologies. Whenever possible, we model systems analytically, in order to extract general principles and simple pictures from complex systems. We recently derived general expressions for the vibrational lifetimes of molecules on surfaces, revealing the dependence of lifetime on molecular coverage and arrangement. Our recent exploration of quantum stress fields has helped to link chemical and mechanical effects in materials.

 

We are constantly developing methods for computing new properties, and for making quantum-mechanical calculations more accurate and more efficient. We tailor computational algorithms to maximize performance on modern computing platforms such as Beowulf clusters. Wherever possible, we also model systems analytically, in order to extract general principles and simple pictures from complex systems. This combination of theoretical and computational tools enables us to identify new phenomena in complex systems, like multicenter bonds between methyl radicals and the rhodium surface. ( See figure below )

Converting the 5d wavefunction of gold to a smoother pseudowavefunction results in a dramatic reduction in the required basis set size for converged calculations.

Department of Chemistry

231 S. 34 Street, Philadelphia, PA 19104-6323

215.898.8317 voice | 215.573.2112 fax | web@chem.upenn.edu

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