- Hai Nguyen, email@example.com,
post-doc, worked on properties of modified DNA and RNA, and author of pytraj
and other python-based MD and MD-analysis tools. Now at Schrodinger.
- Jason Swails, firstname.lastname@example.org,
post-doc, worked on chemical shifts in RNA and general Amber development.
Now at Luton Corp. in Easton, PA.
- Jason Deckman, email@example.com,
post-doc, worked on transition path analysis and on novel MD integrators.
Now Head of Software Development at Abtech Systems in San Diego.
- Hung Nguyen, firstname.lastname@example.org,
BioMaPS graduate student, worked on some aspects of small-angle X-ray
scattering, and on ion properties near surfactant micelles. Now a post-doc at
- Jesse Johnson, email@example.com,
BioMaPS graduate student, worked on implicit solvent models and
ligand-protein interactions. Now working at Valve, in Seattle.
- Chunmei Liu, firstname.lastname@example.org,
visiting graduate student from Zhengzhou University, Henan province, China,
worked on intercalation complexes in nucleic acids and biomolecular crystal
simulations. She is now teaching at Zhengzhou University.
- Pawel (Paul) Janowski, email@example.com,
graduate student, who worked on molecular dynamics
simulations of biomolecular crystals. Now at Microsoft in Seattle.
- Iwen Fu, firstname.lastname@example.org, BioMaPS graduate
student, (now graduated!) worked on molecular dynamics simulations of
collagen peptides. Now at New York University.
- Tyler Luchko, email@example.com,
post-doctoral fellow, worked on integral equation ("3D-RISM") simulations.
Now on the faculty at California State University, Northridge.
- In-Suk Joung, firstname.lastname@example.org,
post-doctoral fellow, worked on force field parameterization and free energy
calculations. Now at the Korea Institute for Advanced Studies.
- Chris Lim, high school student, working on room-temperature ionic liquids and
crystal simulations of collagen-related peptides. Chris
is now an undergrad at Harvard. He was recently
named as a semifinalist in the 2013 Intel Science talent
- Dan Roe, email@example.com,
post-doc, worked on drug design and Amber code development. Now at the
Laboratory of Computational Biology at NIH.
- Qiantao Wang, firstname.lastname@example.org,
post-doc, worked on QM/MM models of active sites of metalloenzymes. Now on
the faculty at Sichuan University in China.
- Sishi Tang, email@example.com,
BioMaPS graduate student,
worked on the analysis of chemical shifts and chemical shift anisotropies in
proteins, and on loop motions in proteins. Now at Goldman-Sachs.
- Junchao Xia, firstname.lastname@example.org,
post-doctoral fellow, who worked on force field and NMR analyses of
carbohydrates. Now an Assistant Research Professor at Temple University.
- Joachim Latzer, email@example.com, post-doctoral
fellow, worked on structural and thermodynamics aspects of phosphorylation.
Now on the faculty at Southwestern College in Chula Vista, CA.
- Shruti Sharma, firstname.lastname@example.org,
high school senior, who worked on normal mode calculations of DNA and
simulations of room-temperature ionic liquids. Now an undergrad at MIT.
- Thomas Gaillard, email@example.com,
post-doctoral fellow, worked on analysis of nucleic acid energetics,
particularly for duplex DNA. Now at the Ecole Polytechnique in Paris.
- Thomas Steinbrecher, firstname.lastname@example.org, post-doctoral
fellow, worked on free energy methods and onQM/MM descriptions of radical
cations in DNA. Now at Schrodinger in Mannheim, Germany.
- Susanna Monti, email@example.com,
visiting scholar from Pisa, worked on DNA Holliday junction models.
- Vance Wong, firstname.lastname@example.org, post-doctoral
fellow, worked on analysis of NMR relaxation behavior in proteins. Now at
Biosite in San Diego.
- Tammy Dwyer, email@example.com,
visiting investigator from the University of San Diego, who worked on aspects
of nucleic acid conformation analysis, with particular attention to
minor-groove binding drugs.
- Yannick Bomble, Yannick_Bomble@nrel.gov,
post-doctoral fellow who worked on multiscale models of nucleic acids. Now
at the National Renewable Energy Laboratory in Golden, Colorado.
- Vladimir Pelmenschikov, firstname.lastname@example.org,
post-doctoral fellow who worked on quantum chemical studies of active
sites of metalloproteins. Now at the University of Würzburg.
- Knut Teigen, email@example.com, post-doctoral
(now faculty) visitor from Bergen, Noway, studying cylic-AMP-dependent protein kinases.
- Mike Crowley, Michael_Crowley@nrel.gov,
staff scientist, worked on Amber and CHARMM development, and a variety of
other scientific programming tasks. Now at the National Renewable Energy Lab
in Golden, Colorado.
- Wei Zhang, firstname.lastname@example.org,
post-doc who worked on path-integral molecular dynamics, and on a new
front-end to the Amber simulation programs. Now at the University of
Texas--Houston Medical School.
- Qizhi Cui, Qizhi.Cui@bri.nrc.ca,
post-doc, working on comparing molecular dynamics simulations to NMR
relaxation results, and on coarse-grained models of ribosome assembly.
Now at the National Research Council of Canada.
- Devleena Shivakumar, Devleena.Shivakumar@gilead.com, post-doc,
who worked to integrate Amber implicit solvent models into evaluations of
protein-ligand dockings. Now at Gilead in Foster City, CA.
- John Mongan, email@example.com, M.D./Ph.D.
student from UCSD, who worked on implicit solvent simulations and novel ways
to model pH-dependent behavior in macromolecules. Now a faculty member
in the Radiology Department at UCSF.
- Seongho Moon, firstname.lastname@example.org,
post-doc, worked on computational aspects of biomolecular NMR, including
QM/MM analyses of chemical shifts and anisotropies. Now at Samsung Research
- Ross Walker, email@example.com,
post-doc, worked on making connections between fast optical dynamics, NMR
and molecular dynamics simulations, and QM/MM implementation. Now on the
faculty at UCSD.
- Francois Dupradeau, firstname.lastname@example.org,
research associate and visitor from Universite de Picardie Jules Verne,
in Amiens, studied electrostatic interactions in proteins and nucleic
- Rhonda Torres, email@example.com,
post-doc, used using quantum chemistry and continuum solvation methods to
study active sites of metallo-enzymes. Now at Merck & Co., New Jersey.
- Paramita Dasgupta, Dasgupta.Paramita@mayo.edu, post-doc,
used using molecular dynamics simulations to study NMR relaxation in proteins.
Now at the Mayo Clinic in Rochester, Minnesota.
- Dave Mathews, David_Mathews@urmc.rochester.edu, studied
conformational transitions in RNA, and aspects of RNA secondary structure
prediction. Dave has implemented the nudged elastic band model into Amber,
and developed some new partition-function-based algorithms for RNA secondary
structure analysis. Now on the faculty at the University of Rochester.
- Alexey Onufriev, firstname.lastname@example.org,
post-doc who developed implicit solvation models. Now on the faculty
at Virginia Tech.
- Holger Gohlke, email@example.com,
looked at energetics of protein-protein and protein-ligand association.
Now on the faculty at the University of Düsseldorf.
- Jens Carlsson, firstname.lastname@example.org, graduate
student from Sweden, who worked on pK calculations in proteins. Now on the
faculty at Stockholm University.
- Tim Meyer, email@example.com,
graduate student in Biotechnology at the Université Louis Pasteur
in Strasbourg, worked doing a research project on structure and dynamics of
- Tiqing Liu, firstname.lastname@example.org, post-doc,
explored quantum chemistry approaches to energetics and solvation effects
in transition-metal complexes of biochemical interest. Now at Montana State
- Fahmi Himo, email@example.com,
post-doc, who worked on
quantum chemistry approaches to energetics and solvation effects
in radical-containing complexes of biochemical interest. Now on the faculty
at Stockholm University.
- Xiaoping Xu, firstname.lastname@example.org,
post-doc, used quantum chemistry calculations to obtain insights into
chemical shift behavior in proteins and nucleic acids. Now at the Burnham
Institute in La Jolla.
- Georges Mer, email@example.com,
post-doc, who prepared isotopically-labeled DNA and RNA samples, and
carryied out NMR relaxation and structural studies on oligonucleotide
systems. Now a faculty memeber at the Mayo Clinic in Rochester, Minnesota.
- Hongjun Liu, firstname.lastname@example.org,
post-doc, who worked on fitting atomic models to densities derived from
cryo-electron microscopy and low-resolution X-ray diffraction. Now at the
Burnham Institute in La Jolla.
- Tom Macke, email@example.com,
graduate student and post-doc. Tom developed
the nucleic-acid builder (NAB) molecular modelling package,
the rnamotif program to find RNA sequence motifs, and other
bioinformatics-related software. Now at Kosmix in Mountain View.
- Vickie Tsui,
graduate student, who worked on molecular simulations and NMR-based
refinements of nucleic acids and zinc-finger/nucleic acid complexes.
Now at Genentech, South San Francisco.
- Matthias Ullmann, Matthias.Ullmann@iwr.uni-heidelberg.de,
post-doc, who used quantum chemistry and continuum solvation methods to
study electron and proton transport in cytochrome bc1 and related
systems; although worked on fundamental theories of titration behavior in
macromolecules. Now on the faculty at Bayreuth University.
- Vicki Feher, Victoria.Feher@takedasd.com,
post-doc who studied binding of small molecules to RNA.
Now at Takeda San Diego.
- Will Briggs,firstname.lastname@example.org,
visiting undergraduate from the University of Vermont, is converting our AVS
molecular graphics modules to Data Explorer (openDX). The openDX link at
the left points to Will's work.
- Neill White, email@example.com,
graduate student at San Diego State University, worked on the
development of distance geometry and low-resolution nucleic acid models
in the NAB program environment. Now at Isis Pharmaceuticals in Carlsbad.
His Java-based molecular modeling program "B" is available at
- Ru-jen Cheng,firstname.lastname@example.org,
sabbatical visitor from Taiwan, looked at electronic structure
properties of metalloporphyrins and electrostatic interactions in heme
- Jian Li,
post-doc, worked on quantum chemistry calculations on iron-sulfur and
molybdenum-iron-sulfur clusters in metalloenzymes. Recently moved from
Johnson & Johnson to Peking University.
- Jarrod Smith,
graduate student, who worked on NMR solution structures
of DNA duplexes and drug-DNA complexes. Now a Research Associate Professor
- Jayashree Srinivasan, email@example.com,
post-doc, used electrostatics analysis
and other methods to investigate conformational energetics of DNA and RNA
helices and hairpins.
- Annick Dejaegere, firstname.lastname@example.org,
collaborator from Strasbourg, works on theories of chemical shifts in
- Doree Sitkoff, email@example.com,
post-doc, who worked on theories of chemical shifts in proteins
and nucleic acids. Now at Bristol-Myers Squibb in Princeton, NJ.
- Garry Gippert
graduate student who developed
a variety of programs for determiation of solution structures of proteins by
NMR, including routines to carry out systematic conformation searches.
More information on the GAP (Geometric Analysis Programs) Garry wrote
can be found by following the link in the menu bar at the left.
Now at Novozymes in Copenhagen.
- Paul Beroza, firstname.lastname@example.org,
post-doc, studied the Bohr
effect in hemoglobin using Poisson-Boltzmann electrostatic calculations.
His web site
contains information on PEP (Paul's Electrostatics Program) to compute
numerical solutions to the Poisson-Boltzmann equation, and to peptide analysis
programs. Now at Elan Pharmaceuticals in South San Francisco.
- Ann Giammona, email@example.com,
graduate student, worked on force fields for metallo-porphyrins. Now at St.
Jude Children's Hospital in Memphis.
- Kizhake Soman, firstname.lastname@example.org,
post-doc who worked on structure determination from
NMR data (Zn finger) and all atom MD simulations of helical peptides in water.
Currently at the University of Texas Medical Branch in Galveston.
- Arie Aizman, email@example.com,
graduate student, worked on electronic structure calculations on iron-sulfur
proteins. Now on the faculty at the Univ. Federico Santa Maria in Valparaiso,
- Ramiro Arratia-Perez, firstname.lastname@example.org,
graduate student, worked on relativistic quantum chemical calculations of
heavy metal systems. Now on the faculty at the Universidad Andres Belo in
- Steve Sontum, email@example.com,
post-doc, worked on electronic structures of metalloproteins. Now a Professor
Emeritus at Middlebury College.
Updated on February 14, 2018. Comments to firstname.lastname@example.org