THE GRUEBELE GROUP

Former Members

Postdocs:

Jason Crane (Ph. D., UC Berkeley with C. Bradley Moore) 1998-2000.
(Director, Radiology Computational Core at UCSF)

Szabolcz Osvath (Ph.D., Medical U. Budapest) 2000-2001.
(Senior Researcher at Semmelweis University, Budapest; CEO of KinePict)

Dong-Xia Shi (Ph.D. Beijing Institute for Vacuum Technology), 2003-2004
(Professor, Chinese Academy of Science, Beijing)

Joshua Ballard (Ph.D. U. of Colorado, Beckman Fellow), 2003-2006

(Staff Scientist at NOAA, Boulder, Colorado; Senior Scientist at Zyvex)

Marcelo Nakaema (Ph.D. U. of Campinas, Brazil), 2005-2006
(Assistant Prof., U. of Rio Grande del Norte, Brazil)

Simon Ebbinghaus (Dr. rer. nat. Bochum U., Germany, von Humboldt Fellow), 2008-2010
(Junior Professor, U. Bochum, Germany; W3 Chair TU Braunschweig)

Björn Braunschweig (Dr. rer nat., von Humboldt Fellow joint with Dlott and Wieckowsi), 2009-2011
(Junior Professor, Uni Erlangen, Germany; WWU Münster)

Ionel Rata (PhD U. of Illinois) 2010-2011
(Staff Scientist Horia Hulubei National Institute for R&D in Physics and Nuclear Engineering, Bucharest)

Max Platkov (PhD Tel Aviv U.) 2011-2013
(Staff scientist Nuclear Research Centre, Negev)

Shahar Sukenik (PhD Weizmann Institute, Israel) 2014-2018
(Assistant Professor of Chemistry at UC Merced)

Lydia Kisley (PhD Rice U., joint with D. Leckband), 2015-2018
(Assistant Professor of Physics at Case Western Reserve)

Caitlin Davis (PhD Emory U., CPLC Postdoc), 2015-2019
(Assistant Professor of Chemistry at Yale U.)

PhD students:

Richard Ballew (B.S. U. of Virginia) Chemistry 1993-1996
(became senior scientist at Curagen Corporation, then at Celera Genomics)
Thesis: “Direct observation of fast protein folding: distinct nanosecond and microsecond events in the folding of apomyoglobin”

Robert Bigwood (B.S. IIT), Chemistry 1992-1998
(became senior engineer at Intel Portland)
Thesis: “Molecular vibrational energy redistribution: theory and experiment”

Jobiah Sabelko, (B.S. U. of Wisconsin) Chemistry 1994-2000
(became development scientist for Colgate-Palmolive pharmaceuticals)
Thesis: “The initial stages of protein folding: ms and sub-ms folding kinetics of horse apomyoglobin and yeast phosphoglycerate kinase”

Ryan Pearman (B.S. Harvey Mudd College) Chemistry 1995-2001
(went on to postdoc with George Flynn at Columbia, engineer at Intel Portland)
Thesis: “Toward the understanding of intramolecular energy transfer”
 
John Ervin (B.A. Cornell U.) Chemistry 1996-2001
(became staff scientist at UltraPhotonics)
Thesis: “Early events in the folding of the protein ubiquitin”

Vance Wong (B.S. UC San Diego), Chemistry1995-2001
(went on to postdoc with Mark Ratner at Northwestern University)
Thesis: “Computational and experimental studies of coherence and energy flow in microscopic and mesoscopic systems”


Brent Strickler (B.A. Haverford College) Chemistry 1997-2003
(went on to staff scientist position at MZA, Albuquerque)
Thesis: “Vibrational spectroscopy and potential energy surface analysis of the X and B states of thiophosgene”

Wei Yang (BS Taiwan NU) Biophysics 1997-2003
(went on to postdoc for Prof. S. Xie at Harvard; faculty at Academia Sinica, Taiwan)
Thesis: “Folding thermodynamic and kinetic characterization of small model proteins: l repressor, U1A, trpzip2 and PAO-12”

Houbi Nguyen (B.S. UCSD), Biophysics 1999-2004
(went on to postdoc with Steve Boxer at Stanford)
Thesis: “A survey of b-sheet folding: WW domains, zinc fingers, and membrane peptides“

Edgar Larios (UNAM, jointly with K. Schulten), Physics 1999-2005, IBM Fellow
(management consultant with McKinsey & Co, then SAP, then Salesforce)
Thesis: “A computational-experimental study of small globular proteins”

Hairong Ma, (M.S. U. Cincinnati, biophysics program) Biophysics 2001-2005
(postdoc with Ahmed Zewail, on the physics faculty at Drexel as of 2012)
Thesis: “Fast protein and RNA folding on a rough energy landscape“

Sandra Lee (B.S. U. Penn, Physical Chemistry) Chemistry 2000-2005
(staff scientist at Lam Research, Fremont, CA)
Thesis: “Global and local models for dilution factors: theory and stimulated emission pumping experiments“

Marja Engel,  (B.S. Harvey Mudd College) Chemistry 2001-2006
(management consultant with McKinsey Minneapolis office)
Thesis: “Development of a wavelet-based algorithm and fitness function for computational and experimental quantum control”

Seung Joong Kim (B.S. Seoul National University) Physics 2003-2008
(postdoc with Andrej Sali at UCSF, now professor at KAIST)
Thesis: “Studies of protein-protein and protein-water interactions by small angle X-ray scattering, Terahertz spectroscopy, and computer simulation”

Daniel Weidinger (U. Missouri) Physics 2002-2008
(postdoc with Jeff Owrutsky at NRL/Maryland)
Thesis: “Coherent control of molecules for quantum computation”

Erin Carmichael (now Kerwood) (B.S., University of Notre Dame) Chemistry 2003-2008
(Teaching faculty, Ivy Tech, Lafayette IN)
Thesis: “Optically –assisted scanning tunneling microscopy”

Feng Liu,  (Shangdong U.,  and U. Pittsburgh) Biophysics 2004-2009
(Assistant Professor, Peking University)
Thesis: “Exploring downhill protein folding free energy landscapes”

Sharlene Denos,  (UC Santa Cruz,) Biophysics 2003-2009, NSF GK12 Fellow
(outreach coordinator for CPLC, Science Teacher at Uni High, Outreach Director, CPLC)
Thesis: “Studies of protein folding on membranes and in crowded environments, and bridging the research-teaching gap in K-12 science”

Praveen Chowdary, (M.S. IIS Bangalore, 2004) Chemistry, 2005-2009
(postdoc with Bianxiao Cui at Stanford)
Thesis: “Molecular vibrational diagnostics: from quantum state stability to real-time histopathology”

Krishnarjun Sarkar, (M.S. IIT Bombay, 2004) Chemistry, 2004-2010
(postdoc at Johns Hopkins with Sarah Woodson)
Thesis: “Protein and RNA folding: from bulk towards high throughput single molecule experiments”

Apratim Dhar (M. S., IIT Kharagpur) Chemistry, 2006-2011
(Engineer, Intel Portland)
Thesis: “Protein folding in crowded environments and living cells”

Greg Scott (B.S. 2005, Davidson College) 2006-2011
(Assistant Professor at Cal. Poly State U., San Luis Obispo)
Thesis: “Single molecule optical absorption by STM and a new algorithm for solving dynamics on a free energy surface”

Sumit Ashtekar (M.S. IIT Kanpur) 2007-2012, Beckman Graduate Fellow
(Engineer, Intel)
Thesis: “Real-time atomic resolution dynamics of glass surfaces”

Eduardo Berrios (B.S. U. Santiago de Chile, 2007) Chemistry, 2008-2013
(Adjunct Professor, U. Santiago de Chile)
Thesis: “Dynamics of vibrational energy flow, quantum computing and laser assisted fusion”

Maxim Prighozin (B.S. Chemistry 2009 U. Toronto at Mississauga), Chemistry, 2009-2013, HHMI Fellow
(postdoc, Stanford University with Steven Chu, Assistant Professor, Harvard University)
Thesis: “Temperature- and pressure-induced protein dynamics from microseconds to minutes”

Minghao Guo (B.S. Physics 2008,  USTC), Physics, 2009-2013
(Staff scientist, Illumina)
Thesis: “Protein folding and diffusion: from in vitro to live cells”

Lea Nienhaus (B.S. Chemistry 2010, U. Ulm), Chemistry, 2010-2015
(Postdoc, Moungi Bawendi, MIT, then professor at FSU)
Thesis: “Single molecule optical absorption spectroscopy at room temperature detected by scanning tunneling microscopy”

Irisbel Guzman (B.S. Biochemistry 2009, U. Puerto Rico Humacao), Biochemistry, 2010-2015 NSF Fellow
(Presidential Management Fellow, US Department of Veterans’ Affairs)
Thesis: “Studies of the dynamics of protein-RNA interactions and protein folding”

Anna Jean Wirth (B.S. 2010 Chemistry, Coll. William and Mary), Chemistry, 2010-2015 NSF Fellow
(Analyst, RAND Corporation)
Thesis: “Protein folding in single cells and under pressure”

Hannah Gelman (B.S. Physics Dartmouth College , 2009) Physics, 2009-2015, CPLC Fellow
(Postdoc, David Baker, U. Washington)
Thesis: “Cellular influence on protein folding”

Kiran Girdhar (M.S. Materials Science TU Munich, joint with Yann Chemla) Biophysics, 2009-2015
(Postdoc, Pamela Sklar and Fromer Menachem groups, Mt. Sinai Medical School)
Thesis: “The behavioral space of zebrafish locomotion and its neural network analog”

Duc Nguyen (B.S. 2011 Hanoi U. Science) Chemistry, 2011-2016, Beckman Graduate Fellow
(Postdoc with Rick van Duyne, Northwestern; Intel)
Thesis: “Surface glassy dynamics and single-molecule absorption of quantum dots detected by scanning tunneling microscopy”

Shu-Han Chao (B.S. Physics, National Taiwan University, 2011; joint with Alek Aksimentiev) Physics, 2011-2016
(eBay, analytics)
Thesis: “Modification and regulation of biomolecules in vitro and in silico”

Kapil Dave (B.S. – M.S. Chemistry IISER Mohali, 2013) Biophysics, 2013-2017
(Intel, Senior Engineer)
Thesis: “In vitro and in vivo protein folding under stress”

Tatyana Perlova (B.S. and M.S. Physics, Moscow Inst. of Physics, 2011; joint with Yann Chemla) Physics, 2011-2017
(Data Scientist, Indigo AG, Vienna, Austria)
Thesis: “Shedding light on E. coli phototaxis”

Yi Zhang (B.S. Biochemistry, B.A. Mathematics U. Arizona, 2013; with Klaus Schulten) Biophysics, 2013-2017
(Statistical Quantitative Analyst and Vice President, Suntrust Bank, Atlanta, Georgia)
Thesis: “Frustration of protein folding from in vitro to in vivo”

Drishti Guin (B.S. + M.S. Chemistry, IIT Kharagpur, July 2013) Chemistry, 2013-2019
(Data Scientist, Synthego, Bay Area)
Thesis: “Protein interactions in vitro and in the cell”

Ruopei Feng (B.S. Renmin University 2013, joint with Yann Chema) Chemistry, 2013-2019
(SFL Scientific, Boston)
Thesis: “Behavior analysis and protein folding in zebrafish larvae”

Huy Nguyen (B.S. Chemistry, Cypress College CA 2015) Chemistry, 2015-2020
(Lam Research, CA)
Thesis: “Dynamic imaging of nanoparticles on femtoseconds to minutes time scale at atomic resolution”

Master Students

Michael McUne (B.S. U. New Mexico), M.S., 1993-1996
(became support engineer at Continuum Corp., then ABB, Cisco and Dynamic Database Design)
Thesis: “Creation and characterization of shaped laser pulses for coherent control of chemical reactions”

Brent Milam (B.A. U. Texas Austin), M.S., 1992-1997
(scientist at Emergent Information Technologies, CO; theory & composition instructor, Georgia State U.)
Thesis: “Mass spectrometry and spectroscopic studies of ammonia and thiophosgene”

Charles Dumont  (B.S. McGill University) Physics 2002-2008

Praveen Sundaradevan, (B. S. U. Texas at Arlington) 2007-2009
Thesis: “Fluorescence spectroscopy from highly excited states of SCCl2 and conformational energy of fluoroethanol”

Undergraduate students:

David Tampa, May – Aug. 1993 (gas phase spectroscopy)

Rebecca Davis, Sept. 1995 – May 1996 (protein folding)

Guinevere (Gwen) Murphy, Jan. – Dec. 1996 (protein folding) (PhD Boulder, medical writer)
B.S. Thesis: “Fast folding studies of cytochrome c using its cold denaturation properties”

Carmen Green, Jun. – Dec. 1997 (protein folding)

Gabriel Argao, Jun.- Aug. 1997 (protein folding; now science teacher at Leesville NC)

Nedda A. Beldawi, Jan 1999 – May 1999 (protein folding) (now lives in Georgia)

Jennifer Javier, Jun. – Aug. 1999 (group technician for protein work)

Sun Yun, May 1999 – May 2000 (Intel Phoenix, then Qualcomm; ketene spectroscopy)
B.S. Thesis: “Rotational and vibrational investigation of organic reactants”

Vladimir Petrovich, Jul.-Nov. 2001 (from Belgrade University; joined MIT Ph.D. program)

Milica Grkovic (Jul. 2001; from Belgrade University; protein folding)

Trent Schlesinger (May 2002-Dec. 2002; from 204)
B.S. Thesis: “Computation of survival probability for reaction control” (at Catalent Pharma)

Diana Tokat (June 2002-May 2003; protein folding)
B.S. Thesis: “Preparation of Pin1 and steady-state CD and FTIR measurements” (at Sterling Bay)

Milena Mladenovic (Jul. 2002-Oct. 2002; from Belgrade University; quantum dynamics)

Jason Lee (Sept. 2002-May 2003; went to Oxford PhD program; high P experiments)
B.S. Thesis: “Development of a pressure-jump instrument for protein folding studies”

Sravan Pappu (Sept. 2003-May 2005; STM and protein folding) (at Johnson Matthey)
B.S. Thesis: “Electric field effects on protein fluorescence and teaching modules for advanced physical chemistry”

Olivia Chandrawinata, (Jan. 2004-May 2005; from 204; protein IR spectroscopy)
B.S. Thesis: “FTIR library spectra of proteins“ Worked at Cooper Vision CA

Sahin Ates (visitor from Turkey, June 2004-August 2004; high pressure experiments)

Brittney Vorndick (Summer 2004, NSF-REU visiting student; BPT spectroscopy) Instructor at Durham Community College

Apratim Dhar (Summer 2005, visiting undergraduate from IIT, admitted to U of I Chemistry)

Eric Gotkowski (Fall 2006-May 2008; from 204; membrane peptides)
B.S. Thesis: “Evaluation of membrane-binding peptides” and publication in JPCB (MS Duke U., now Keyot)

Manish Kumar (May-July 2007, visiting undergraduate from IIT Kharagpur; single molecules)

Tripta Mishra Holtz (July 2007-August 2009; from 204; protein crowding project)
B.S. Thesis: “Protein expression for crowding and live cell experiments” (Sr. Fragrance Evaluator at l’Oréal)

Stevia Angesty (Fall 2007-Spring 2010 ; from 204; single molecules)
B.S. Thesis :” Deposition Techniques of Single-Walled Carbon Nanotubes and Quantum Dots For Scanning Probe Microscopy” (MS Stanford Materials Science, McKinsey Consulting)

Brandy Pappas (Spring 2007, co-op student from Rochester Inst. Technology) (NSF Fellow at Harvard)

Konrad Meister (Summer 2008 RNA folding dynamics, then PhD student at U. Bochum)
[publication in Biophys. J.]

Felipe Olivarez (Fall 2008-Summer 2010, from 204; ab initio calculations)
[publication in Chem. Phys. Lett.]

Stefan Elrington, Melisa Osborne (CPLC Summer School 2009)

Ho Yee Hui (2010-2011; from Chem 204; vibrational dynamics)

B.S. Thesis and publication in Chem. Phys. Lett.

Duc Nguyen (Summer 2009&2010, visiting student from Hanoi University of Science)
[Publication in RNA]

Lea Nienhaus (Spring 2010, visiting student from Ulm University)
B. S. Thesis: “Activity and Folding Dynamics of PGK in vitro and live cells” and publication in PNAS
[Publication in PNAS]

Digvijay Singh (Summer 2010, visiting student from IIT Kharagpur)
[Publication in Biophys. J.]

Steffen Büning (Summer 2010, visiting student from U. Bochum)

Aaron Cravens (Summer 2010; Central High; metal film surfaces) [BS Rochester, PhD Stanford]

Ila Sruti (2010-2011; from 204; protein transfection in mammalian cells)

Jay Goodman (Fall 2010-2013; biochemistry; mutant apomyoglobin folding)
Senior Thesis: “Redesigning the heme pocket in apomyoglobin” [1st au publication in J. Phys. Chem. B] [PhD student at Berkeley]

Matthew Kolaczkowski (Fall 2010-Spring 2011; chemistry, STM on metal films) [PhD UCB]

Alex Broyles (Spring 2011-Fall 2011; Chem 202, NIVI, STM)

Amartya Bose (Summer 2011; IIT Kanpur; PGK nanorods) (PhD at Illinois)

Susan Pratt (Summer 2011, Rochester U.; REU Physics, SCCl2 with Eduardo Berrios)
[Publication in J. Phys. Chem. A]

Nguyen Huu Huy (Summer 2011; HUS, folding in procaryotes)

Guannan Liu (Summer 2011; Chem 202, STM)

Krastyu Ugrinov (U. Notre Dame, CPLC Summer School 2011)

Yangfang “Harry” Xu (Summer 2011-Spring 2012; Chem 202; In-cell folding)
[Publication in PNAS]

Anmol Gulati (Fall 2011; Chem 202, crowding in vitro)

Jonathan Tai (Fall 2011-2014; Chem 202, in vivo folding with Irisbel Guzman)
[Publications in JMB and FEBS Lett (1st author)]

Prabhat Tripathi (Summer 2012; Indian School of Mines, SCCl2 with Eduardo Berrios)
[Publication in J. Phys. Chem. A]

Trung Nguyen (Summer 2012; VNU-HUS; STM lasers with Duc Nguyen)

Jens Holtermann (Copenhagen), Heike Gangel (Köln), Sourav Dev (Carnegie Mellon) and Michael Gramlich (UMass Amherst) (CPLC Summer School 2012)

Hanna Wirtz (Fall 2012, Bochum U. T-jump)

David Gnutt (Summer 2013, Bochum U. Live cell)

Maria Benitez-Jones (Summer 2013, U. New Mexico, fish behavior)

Rishabh Gupta (Summer 2013, Fall 2014, Indian School of Mines, glassy dynamics)

Phạm Thị Hà (Summer 2013, HUS K54 class, fish behavior)

David Jacobson (UCSB, Saleh lab), Joo Sang Lee (pd, NWU) (CPLC Summer School 2013)

Jan Schäfer (Jan-Mar 2014, U. Bochum, lambda PEGylation simulations
[Publication in JPC B, with Chu-Han Chao]

Sankalp Shukla (May-July 2014, IIT Kanpur, fish project)

Timothy Chen (May 2014-, Chem 202 2013 top of class; with Hannah Gelman)
[Publication in Febs Lett., Senior Thesis “Investigating the in vivo Folding Kinetics and Thermodynamics of Phosphoglycerate Kinase”

Meredith Rickard (May-July 2014, Chem REU Program; with Tanya Perlova)

DongYang Li, Suva Roy and Judith Warnau (CPLC Summer School 2014)

Sarah Wieghold (May 2014, winter 2014,  F. Esch group TUM, with Lea Nienhaus)
[Publication in J. Phys. Chem. C]

Vincent Hahn (July-September 2014, Uli Nienhaus group KIT; with Lea PGK kinetics and Irisbel organelles)
[Publication in FEBS Lett]

Rui “Anna” Ning (Fall 2014, from 2013 Chem 202 class, polyaniline membranes)

Basilio Cieza Huaman (Nov 2014-Jan 2015, U. Lima, Peru, PEG proteins)

Chu Thi Hien Thu (Thu, F) (Feb 15 2014-Apr 15 2015, VNU Chemistry K55, Kapil label effect)
[Publication in J. Phys. Chem. B]

Nguyen Thanh Nhan (Nhan, F) (Summer 2015, from VNU Chemistry K55, QD STM)
[Publication in ACS Nano]

Nguyen Van Kỳ (Ky, M) (Summer 2015, from VNU Chemistry, in vitro WW n-mer, Kapil)

Brian Pringle (Summer 2015-2017, UIUC, STM/AFM)
[Publication in PCCP]

Madeleine Daily (Summer 2015, Bowdoin, Physics REU 3-D fish with Yann)

Kori Sye (Summer 2015, North Central College, Chemistry REU, dodine with Drishti)
[Publication in Protein Science]

Mohammed Salam (Winter 2015-2017, UIUC from Chem 442, with Shahar)
[Publication in JACS]

Kimberly Park (Summer 2016, Physics REU, with Kapil)

Anisa Nuanes (Spring 2016, MatsSE, with Nikolai K.)

Andreas Arango (Summer 2016, incoming CBQB student, with Caitlin)

Kacper Lachowski (Spring 2016-Summer 2017, MatsSE, with Nikolai K.)

Zixuan (Lillo) Wei (Fall 2016-Fall 2017, Chemistry, with Ruopei Feng)

Pin Ren (2016-2017, Physics, with Shahar Sukenik)

Shashwat Kulkarni (Summer 2017, ICT Mumbai, with Caitlin Davis and Taras Pogorelov)

Ashwin Bhojwani (Summer 2017-Spring 2018, UIUC, with Nikolai K. on electro-membranes)

Can Liao (Summer 2017-2019 , UIUC, with Huy on SiO2 dynamics)
[Publication  J. Chem. Phys.]

Brian Bozymski (Summer 2018 Physics REU, with Drishti on dodine unfolding)
[Publication JPC Lett.]

Shardale Negre (Summer 2018, phYSics Young Scholar program 10th grader, with Alison and Huy)

Sylvia Xinyue Cui (2018, membrane electrochemistry with Nikolai)

Iain Carpenter (Fall 2018-Spring 2020, STM with Alison Wallum)

Shaili McNeely (Summer 2019, phYSics Young Scholar program, with Aniket)

Brahmmi Patel  (Summer 2019-2020 with Mayank Boob on PEG-proteins)

Brooke Ramsey (Summer 2019-2020 with Yuhan Wang on WIFI)

Ramone Randle (Fall 2019-Summer 2020 with Aniket Sravan on in vivo T-jump; now at DMC)

Al-Sadiq Rahmetulla (Fall 2020- with Aniket Sravan on in vivo T-jump)

Zetai Liu (Fall 2020 –Summer 2021 with Alison Wallum on STM)

Michael Zhang (Fall 2020-Summer 2021 , with Yuhan Wang on WIFI)

Allen Partin (Fall 2020- Summer 2021, with Gopika on U1A/HBV)

Oluwadara (Dara) Nafiu (Spring 2021, MD student with Zhaleh HBV simulations)

Szymon Kasperek (Spring 2021, MD student with Gopika HBV experiments)

Yousef Sakhini (Su 2021- undergrad with Mayank, extremophile PGKs)