People that still keep in touch:

  1. Dave Cerutti,, Worked on PME optimization, force field development, and crystal simulations. Now at Entos in Pasadena, CA.

  2. Premila Samuel,, Worked on simulations of heme proteins, including modeling of pathways for heme insertion and removal. Now a post-doc at the University of Illinois.

  3. Jonathon Gray,, graduate student, worked on solvent distributions around nucleic acids and computational aspects of crystallography. Now a post-doc at Butler University.

  4. George Giambasu,, post-doc (joint with Darrin York), worked on conformational transitions in small RNA molecules. Now at Merck in Boston.

  5. He Chen,, Chemistry graduate student, worked on electronic structure models for the water-oxidation site in Photosystem II. Now a software engineer at ByteDance.

  6. Hai Nguyen,, 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 in New York City.

  7. Jason Swails,, post-doc, worked on chemical shifts in RNA and general Amber development. Now Lead Software Engineer at Entos, Inc.

  8. Jason Deckman,, post-doc, worked on transition path analysis and on novel MD integrators. Now Head of Software Development at Abtech Systems in San Diego.

  9. Hung Nguyen,, 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 U.T. Austin.

  10. Jesse Johnson,, BioMaPS graduate student, worked on implicit solvent models and ligand-protein interactions. Now a Mathematical Computation Problem Solver in Somerset, NJ.

  11. Chunmei Liu,, 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.

  12. Pawel (Paul) Janowski,, graduate student, who worked on molecular dynamics simulations of biomolecular crystals. Now a senior data scientist at Recursion Pharmaceuticals.

  13. Iwen Fu,, BioMaPS graduate student, (now graduated!) worked on molecular dynamics simulations of collagen peptides. Now at New York University.

  14. Tyler Luchko,, post-doctoral fellow, worked on integral equation ("3D-RISM") simulations. Now on the faculty at California State University, Northridge.

  15. In-Suk Joung,, post-doctoral fellow, worked on force field parameterization and free energy calculations. Now on the faculty at the Sookmyung Women's University in Korea.

  16. Chris Lim, high school student, working on room-temperature ionic liquids and crystal simulations of collagen-related peptides. Chris was named as a semifinalist in the 2013 Intel Science talent search. Sadly, he was killed in a motor vehicle accident in November, 2020..

  17. Dan Roe,, post-doc, worked on drug design and Amber code development. Now at the Laboratory of Computational Biology at NIH.

  18. Qiantao Wang,, post-doc, worked on QM/MM models of active sites of metalloenzymes. Now on the faculty at Sichuan University in China.

  19. Sishi Tang,, BioMaPS graduate student, worked on the analysis of chemical shifts and chemical shift anisotropies in proteins, and on loop motions in proteins. Now working at Cruise Automation in the Bay Area.

  20. Junchao Xia,, post-doctoral fellow, who worked on force field and NMR analyses of carbohydrates. Now at the Princeton Research Software Engineering Group at Princeton University.

  21. Joachim Latzer,, post-doctoral fellow, worked on structural and thermodynamics aspects of phosphorylation. Now on the faculty at Southwestern College in Chula Vista, CA.

  22. Shruti Sharma,, high school senior, who worked on normal mode calculations of DNA and simulations of room-temperature ionic liquids. Now an undergrad at MIT.

  23. Thomas Gaillard,, post-doctoral fellow, worked on analysis of nucleic acid energetics, particularly for duplex DNA. Now at the Ecole Polytechnique in Paris.

  24. Thomas Steinbrecher,, post-doctoral fellow, worked on free energy methods and onQM/MM descriptions of radical cations in DNA. Now at Schrodinger in Mannheim, Germany.

  25. Susanna Monti,, visiting scholar from Pisa, worked on DNA Holliday junction models.

  26. Vance Wong,, post-doctoral fellow, worked on analysis of NMR relaxation behavior in proteins. Now at Biosite in San Diego.

  27. Tammy Dwyer,, 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.

  28. Yannick Bomble,, post-doctoral fellow who worked on multiscale models of nucleic acids. Now at the National Renewable Energy Laboratory in Golden, Colorado.

  29. Vladimir Pelmenschikov,, post-doctoral fellow who worked on quantum chemical studies of active sites of metalloproteins. Now at the University of Würzburg.

  30. Knut Teigen,, post-doctoral (now faculty) visitor from Bergen, Noway, studying cylic-AMP-dependent protein kinases.

  31. Mike Crowley,, 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.

  32. Wei Zhang,, 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.

  33. Qizhi Cui,, post-doc, working on comparing molecular dynamics simulations to NMR relaxation results, and on coarse-grained models of ribosome assembly. Now a senior data scientist at Microsoft.

  34. Devleena Shivakumar,, post-doc, who worked to integrate Amber implicit solvent models into evaluations of protein-ligand dockings. Now at Gilead in Foster City, CA.

  35. John Mongan,, 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.

  36. Seongho Moon,, post-doc, worked on computational aspects of biomolecular NMR, including QM/MM analyses of chemical shifts and anisotropies. Now at JSR Electronics Materials, Korea.

  37. Ross Walker,, post-doc, worked on making connections between fast optical dynamics, NMR and molecular dynamics simulations, and QM/MM implementation. Now at Glaxo-Smith-Kline in Upper Providence, Pennsylvania.

  38. Francois Dupradeau,, research associate and visitor from Universite de Picardie Jules Verne, in Amiens, studied electrostatic interactions in proteins and nucleic acids.

  39. Rhonda Torres,, post-doc, used using quantum chemistry and continuum solvation methods to study active sites of metallo-enzymes. Now at Merck & Co., New Jersey.

  40. Paramita Dasgupta,, post-doc, used using molecular dynamics simulations to study NMR relaxation in proteins. Now at the Mayo Clinic in Rochester, Minnesota.

  41. Dave Mathews,, 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.

  42. Alexey Onufriev,, post-doc who developed implicit solvation models. Now on the faculty at Virginia Tech.

  43. Holger Gohlke,, post-doc, looked at energetics of protein-protein and protein-ligand association. Now on the faculty at the University of Düsseldorf.

  44. Jens Carlsson,, graduate student from Sweden, who worked on pK calculations in proteins. Now on the faculty at Stockholm University.

  45. Tim Meyer,, graduate student in Biotechnology at the Université Louis Pasteur in Strasbourg, worked doing a research project on structure and dynamics of tRNA.

  46. Tiqing Liu,, post-doc, who explored quantum chemistry approaches to energetics and solvation effects in transition-metal complexes of biochemical interest. Now at Montana State University.

  47. Fahmi Himo,, 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.

  48. Xiaoping Xu,, 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.

  49. Georges Mer,, 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.

  50. Hongjun Liu,, 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.

  51. Tom Macke,, 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 retired from Kosmix in Mountain View.

  52. Vickie Tsui,, graduate student, who worked on molecular simulations and NMR-based refinements of nucleic acids and zinc-finger/nucleic acid complexes. Now at Gilead Sciences in Foster City, California.

  53. Matthias Ullmann,, 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.

  54. Vicki Feher,, post-doc who studied binding of small molecules to RNA. Now at Takeda San Diego.

  55. Will Briggs,, 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.

  56. Neill White,, 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

  57. Ru-jen Cheng,, sabbatical visitor from Taiwan, looked at electronic structure properties of metalloporphyrins and electrostatic interactions in heme proteins.

  58. 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.

  59. Jarrod Smith,, graduate student, who worked on NMR solution structures of DNA duplexes and drug-DNA complexes. Now a Research Associate Professor at Vanderbilt.

  60. Jayashree Srinivasan,, post-doc, used electrostatics analysis and other methods to investigate conformational energetics of DNA and RNA helices and hairpins.

  61. Annick Dejaegere,, collaborator from Strasbourg, works on theories of chemical shifts in nucleic acids.

  62. Doree Sitkoff,, post-doc, who worked on theories of chemical shifts in proteins and nucleic acids. Now at Bristol-Myers Squibb in Princeton, NJ.

  63. 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.

  64. Paul Beroza,, post-doc, studied the Bohr effect in hemoglobin using Poisson-Boltzmann electrostatic calculations. Now a Distinguished Scientist at Genentech.

  65. Ann Giammona,, graduate student, worked on force fields for metallo-porphyrins. Now at St. Jude Children's Hospital in Memphis.

  66. Kizhake Soman,, 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.

  67. Arie Aizman,, graduate student, worked on electronic structure calculations on iron-sulfur proteins. Now on the faculty at the Univ. Federico Santa Maria in Valparaiso, Chile.

  68. Ramiro Arratia-Perez,, graduate student, worked on relativistic quantum chemical calculations of heavy metal systems. Now on the faculty at the Universidad Andres Belo in Santiago, Chile.

  69. Steve Sontum,, post-doc, worked on electronic structures of metalloproteins. Now a Professor Emeritus at Middlebury College.

Updated on November 20, 2023. Comments to