CV_Feb_2018

Curriculum Vitae

Qiang Cui

Department of Chemistry

Boston University

590 Commonwealth Avenue, Boston, MA 02215

E-mail: [email protected]

Personal

Date and place of birth: 1975, Beijing, P. R. China

Employment

Boston University

Professor of Chemistry, Jan. 2018-

University of Wisconsin, Madison

Professor of Chemistry, Jul. 2010-Dec. 2017; Associate Professor of Chemistry, Jul.

2007-Jun. 2010; Assistant Professor of Chemistry, Aug. 2001-Jun. 2007

Education

Postdoctoral fellow, Oct. 1997- Jul. 2001

Harvard University, Boston, MA Advisor: Martin Karplus

Ph.D. Physical Chemistry, Sept. 1997

Emory University, Atlanta, GA Advisor: Keiji Morokuma

Thesis: Theoretical studies of molecular processes

B. S. Chemical Physics, Jul. 1993

University of Science and Technology of China (USTC), Hefei, Anhui, P. R. China

Awards, Honors and Service

• Kellet Mid-Career Award, UW-Madison (2016-2021)

• Secretary and Treasurer, Physical Chemistry Division (2018-present) Chair, Biophysics

subdivision, Physical Chemistry Division, American Chemical Society (2015-2017)

• Vilas Associate, UW-Madison (2014-2016)

• CAPA (Chinese-American Chemistry & Chemical Biology Professors Association)

Distinguished Faculty Award, 2010

• H. Romnes Fellow, UW-Madison, 2010-2015

• Member, Faculty of 1000, 2008-present

• Editorial Board Member, Journal of Theoretical and Computational Chemistry, 2007-2014;

Chemical Physics Lett.; 2016-present; Interdisciplinary Sciences – Computational Life

Sciences, 2008-present; Journal of Physical Chemistry, B, 2012-2015; 2018-present;

Specialist Editor, Comp. Phys. Comm. 2013-present

• Alfred P. Sloan Research Fellowship, 2004.

• CAREER Award, National Science Foundation, 2004-2009.

• Research Innovation Award, Research Corporation, 2003-2005.

• Graduate student fellowship, Phillips Petroleum Co. 1994 — 1997.

• Lester Award, Department of Chemistry, Emory University, 1996.

• Osborn R. Quayle Award, Department of Chemistry, Emory University, 1995.

• Outstanding student scholarship, USTC, 1989, 1992.

Professional Affiliations

American Physical Society, American Chemical Society, Biophysics Society, American

Association for the Advancement of Science, Alpha Phi Simga

Invited University/Institute seminars and Conference presentations (2002-present)

2018 (17)

Dec. Computational and Mathematical Approaches for Bioinformatics and Biophysics

Sanya, China

Nov. QM/MM workshop Wako, Japan

Oct. CECAM Workshop on Allostery Lugao, Switzerland

Oct. PKU/BU/UW-Madison theoretical chemistry symposium Beijing, China

Sept. CECAM Workshop on structural transitions of proteins Paris, France

Jul. Telluride workshop on Coarse-graining Telluride, CO

Jul. ISRIUM conference Ascona, Switzerland

Jul. CECAM Workshop on Metalloenzymes Lugano, Switzerland

Jul. Telluride workshop on proton transfers Telluride, CO

Jun. Protein Electrostatics Belgrade, Serbia

Jun. Worldwide Chinese Computational Biology & Molecular Simulation Conference

Apr. Southern Methodist University Dallas, TX

Apr. Brandies University Waltham, MA

Apr. Harvard/MIT/BU seminar Boston, MA

Mar. Japanese Chemical Society Annual Meeting Funabashi, Japan

Mar. ACS National Meeting New Orleans, LA

Feb. Sanibel Symposium St. Simons, GA

2017 (10)

Nov. Castle Reisensburg Electrochemistry workshop Ulm, Germany

Sept. MGM meeting Manchester, UK

Aug. WATOC2017 Munich, Germany

Aug. ACS National Meeting Washington DC

Jul. ACTC2017 Boston, MA

Jun. Telluride workshop on Protein Electrostatics (cancelled) Telluride, CO

Jun. CECAM workshop on Nano/Bio interface Bremen, Germany

Apr. ACS National Meeting (cancelled) San Francesco, CA

Mar. Department of Chemistry, Boston University Boston, MA

Feb. CECAM workshop on multi-scale simulations (cancelled) Vienna, Austria

2016 (14)

Dec. Theoretical Chemistry Conference (cancelled) India

Nov. DFTB Developer Meeting (cancelled) Beijing

Oct. Bilaterial Conference on Theoretical Chemistry (cancelled) Changsha, China

Aug. ACS National Meeting Philadelphia, PA

Jul. GRC in Comp. Chem. Girona, Spain

Jul. Protein Electrostatics Berlin, Germany

Jul. Telluride workshop on proton transfers Telluride, CO

May Functional motions in biomolecular machines Hong Kong

May Mathematical & Computational Methods in Quantum Chemistry, New Heaven, CT

Apr. Lund University Lund, Sweden

Apr. Uppsala University Uppsala, Sweden

Apr. Laufer Center of Quantitative Biology, SUNY-Stony Brooks Stony Brooks, NY

Apr. Department of Biophysics, Johns Hopkins Baltimore, MD

Mar. ACS National Meeting San Diego, CA

Jan. Asia-Pacific Conference of Theoretical and Computational Chemistry, Taiwan

2015 (17)

Dec. Pacifichem, Metal ions in proteins Hawaii

Nov. MRS Meeting, Simulations and Theory-Driven Design of Soft Materials, Boston, MA

Nov. ACS Meeting Memphis, TN

Oct. Univ. of Minnesota Duluth, MN

Oct. CECAM workshop on next generation of DFTB Bremen, Germany

Oct. MBI Workshop on Electrostatics Columbus, Ohio

Sept. Protonation Dynamics in Redox Proteins Berlin, Germany

Aug. NYU-ECNU Workshop on Computational Chemistry Shanghai, China

Aug. Zing Conference on Computational Chemical Biology Cairns, Australia

Jul. CECAM workshop on QM based dynamics Bremen, Germany

Jun. Telluride workshop on protein electrostatics Telluride, CO

Jun. Canadian Society for Chemistry Conference Ottawa, Canada

Jun. Satellite meeting of ICQC on biomolecular simulations Changchun, China

Apr. Chemistry, Michigan State Lansing, MI

Mar. ACS National Meeting (3) Denver, CO

Mar. Telluride workshop on membrane biophysics Telluride, CO

Jan. Chemistry, UCSD San Diego, CA

2014 (16)

Dec. International workshop on Computational Science & Engineering (IWCSE 2014)

Hong Kong

Dec. Dept. of Chem., HKUST Hong Kong

Sept. Biophysics Society Meeting of Japan Hokkaido, Japan

Aug. ACS National Meeting San Francisco, CA

Aug. Coarse-grained modeling of biological systems Telluride, CO

July Large-scale DFT workshop Aberdeen, MD

July Protein electrostatics workshop Lisbon, Portugal

Jun. Proton Transfer in Biology Telluride, CO

Jun. Molecular simulation summer school Calgary, Canada

Jun. Dept. of Chem. Univ. of Basal Basal, Switzerland

Jun. DFTB developers’ workshop Karlsruhe, Germany

Jun. Uppsala Univ. Uppsala, Sweden

May Workshop on potential function developments for materials Madison, WI

May ACS FAME Tampa, FL

Feb. Biophysical Society Meeting San Francisco, CA

Jan. CRC-EC International symposium Atlanta, GA

2013 (17)

Dec. Dept. of Chem., Hong Kong Univ. of Sci. & Tech. Hong Kong

Dec. Workshop on Complex systems Hong Kong

Nov. Univ. of Iowa Iowa City

Oct. Computational Materials Science Initiative Nagoya, Japan

Sept. ACS National Meeting Indianapolis

Aug. ISTCP-VIII Budapest, Hungary

Aug. Beijing University Beijing, PRCHINA

Jul. Dept. of Chem. Kwangwoon University Seoul, Korea

Jul. Snowmass workshop on free energy simulations Snowmass, CO

May University of Washington Seattle, WA

Apr. 1

International Symposium on Transformative Biomolecules

Nagoya, Japan

Apr. Fukui Institute Kyoto, Japan

Apr. Science on the Edge seminar, MSU East Lansing, MI

Apr. Univ. North. Illinois DeKalb, IL

Mar. APS National Meeting Baltimore, MD

Mar. Telluride workshop on Membrane biophysics Telluride, CO

Feb. University of Minnesota, Chemistry Minneapolis, MN

2012 (14)

Dec. University of Calgary Calgary, Canada

Nov. CECAM workshop on protein dynamics Lugano, Switzerland

Sept. TACC Italy

Aug. MPI Frankfurt Frankfurt, Germany

Aug. ACS National meeting (2) Philadelphia, PA

Aug. Comp Biol 2012 Dalian, PRCHINA

Jul. Telluride workshop on proton transports Telluride, CO

Jun. High-performance computing in Chemistry Nanjing, PRCHINA

Apr. Dept. of Chem. Univ. of Maryland College Park, MD

Mar. Dept. of Chem. Univ. of Montana Missoula, MT

Feb. GRC on Protons and Membrane Reactions Ventura, CA

Feb. Multiscale Methods and Validations in Medicine/Biology San Francisco, CA

Feb. Dept. of Chem. Wayne State Detroit, MI

2011 (18)

Nov. UW-Eau Claire Eau Claire, WI

Aug. Dalian Institute of Chemical Physics Dalian, PRCHINA

Aug. Telluride workshop on Molecular machines Telluride, CO

Jul. IUPAC 2011 Puerto Rico

Jul. WATOC2011 Spain

Jun. Dept. of Chem. Fudan Univ. Shanghai, PRCHINA

Jun. CAPA meeting 2011 Guiyang, PRCHINA

Jun. QM/MM workshop Beijing, PRCHINA

Jun. Materia Medica, Chinese Academy of Sciences Shanghai, PRCHINA

Jun. ACS Regional Meeting Indianapolis, IN

May DOE workshop Denver, CO

May Dept. of Chem. Marquett Milwaukee, WI

Apr. Dept. of Chem., Univ. Colorado-Denver Denver, CO

Apr. Dept. of Biochem. Iowa State Ames, IA

Mar. A*Research Institute Singapore

Mar. Dept. of Chemistry, NUS Singapore

Mar. Dept. of Chemistry, NTU Singapore

Mar. Dept. of Material Science, NTU Singapore

2010 (16)

Dec. Hamilton College Clinton, NY

Nov. University of Delaware Delaware, DE

Nov. University of Missouri Columbia, MO

Oct. International workshop on DFTB methods Thailand

Sept. CECAM workshop on DFTB Breman, Germany

Sept. Gordon Conference on Computational Chemistry Switzerland

Aug. ACS National Meeting Boston, MA

Aug. 4

Shanghai International Conference on Biophycis Shanghai, PRC

Aug. Telluride workshop on proton transfers Telluride, CO

Jul. Telluride workshop on coarse-grained models Telluride, CO

Jun. Telluride workshop on energy landscape Telluride, CO

Jun. Telluride workshop on phosphoryl transfers (organizer) Telluride, CO

Jun. From Computational Biophysics to Systems Biology Traverse City, MI

Jun. German-American Conference on Frontier of Science Berlin, Germany

Mar. Telluride workshop on Membrane Biophysics (organizer) Telluride, CO

Feb. Workshop on proton mobility in Chemistry and Biology Israel

2009 (22)

Dec. 6

Xiamen Workshop on Surface Science Xiamen, PRChina

Dec. 5

WCTCC Xiamen, PRChina

Dec. CAS-MPG Partner Institute of Computational Biology Shanghai, PRC

Dec. Workshop on “Theoretical Methods Developments” Hongkong

Nov. Dept. of Physics, SUNY-Buffalo Buffalo, NY

Sept. Dept. of Biophysics, Univ. of Bochum Bochum, Germany

Sept. MPI workshop on “Future of Computational Biology” Berlin, Germany

Sept. University of Tokyo Tokyo, Japan

Sept. Riken Institute Toyko, Japan

Sept. Workshop on Biomolecular Motors Kyoto, Japan

Aug. ACS National Meeting Washington, DC

Jul. China KITPC program on protein function & dynamics Beijing, PRC

Jul. Morokuma birthday symposium Kyoto, Japan

Jul. Telluride workshop on pKa prediction Telluride, CO

Apr. Dept. of Chem., MIT Boston, MA

Apr. Dept. of Chem., Arizona State Univ. Tempe, AZ

Apr. Dept. of Physiol., UW-Madison Madison, WI

Mar. Dept. of Chem. West Michigan Univ. Kalamazoo, MI

Mar. Dept. of Chem., Cornell Ithaca, NY

Mar. Sanibel Symposium Georgia

Feb. Proton Transfer Gordon Conference Ventura, CA

Jan. Mesilla Workshop on Multi-scale modeling in Biology Mesilla, NM

2008 (17)

Dec. Dept. of Bioeng., Univ. Texas, Austin Austin, TX

Sept. TCAA 2008 Shanghai, China

Sept. Dept. of Chem., Xiamen Univ. Xiamen, China

Aug. ACS National Meeting Philadelphia, PA

Jul. ISTCP-VI Vancouver, Canada

Jul. ACTC 2008 Evanston, IL

Jul. Telluride Workshop Telluride, CO

Jun. ISQBP 2008 Ascona, Switzerland

May National Conference on Quantum Chemistry Nanjing, China

May Enzyme Dynamics & Function New York

Apr. Dept. of Chem. Univ. of Miami Miami, FL

Apr. Dept. of Chem. Univ. of Nebraska Lincoln, NE

Apr. Dept. of Chem. Ohio State University Columbus, OH

Mar. Telluride Workshop Telluride, CO

Mar. Basel Computational Biology Conference Basael, Switzerland

Feb. Ibaraki Univ. Japan

2007 (15)

Nov. Dept. of Chem. East Carolina Univ.

Nov. BioGen, Inc. Boston, MA

Oct. Center of Bioinformatics, Kansas State

Sept. Multi-scale simulations in Biology Imperial College, London

Sept. Quantum Systems in Chemistry and Physics University of London

Aug. QM/MM Workshop Phildelphia, PA

Aug. ACS National Meeting Boston, MA

Jul. Telluride Workshop in “Proton Transfer” Telluride, CO

May Dept. of Chem. NYU New York, NY

Apr. Center of Bioinformatics and Biostatics, Iowa State Ames, IA

Apr. Dept. of Chem. Purdue Univ. Lafayette, IN

Mar. ACS National Meeting Chicago, IL

Mar. Biophysical Society National Meeting Baltimore, MD

Feb. Dept. of Biochemistry, Univ. of Minnesota Minneapolis, MN

Feb. Quantitative Computations in Biophysics Tallahassee, FL

2006 (20)

Nov. Dept. of Chem. Univ. of Notre Dame Notre Dame, IN

Nov. Beckeman Institute, UIUC Urbana, IL

Nov. Dept. of Mechanical Eng., Johns Hopkins Baltimore, MD

Oct. Dept. of Chem., Univ. of Chicago Chicago, IL

Oct. Center of Theoretical Biophysics, UCSD San Diego, CA

Oct. Dept. of Mol. Biol., Scripps San Diego, CA

Sept. ACS National Meeting San Francisco, CA

Aug. Dept. of Biochem., Univ. of Iowa Iowa City, IW

Aug. 4

World Wide Chinese Theoretical and Computational Chemistry Conference

Kunming, China

Jun. Cross-strait biophysics conference BITS 5, Sun-Moon-Lake, Taiwan

Jun. International symposium “Biomolecules: Proteins, DNA/RNA, and Their Interactions”,

Taipei, Taiwan

Jun. Midwest Theoretical Chemistry Conference Columbus, OH

Jun. Trends in Enzymology Como, Italy

Jun. Mitsubishi Chemical Tokyo, Japan

May Dept. of Informatics, Kobe Univ. Kobe, Japan

May Satellite meeting for International Congress of Quantum Chemistry

Kyoto, Japan

Apr. Dept. of Chem., Florida State Univ. Tallahassee, FL

Apr. Dept. of Chem., Univ. Pittsburgh Pittsburgh, PA

Mar. APS National Meeting Baltimore, MD

Mar. Gordon Research Conference “Protons & Membrane Reactions”,

poster selected for talk, Harbortown, CA

2005 (13)

Dec. M2CELL: Modeling from Macromolecules to Cells Paris, France

Oct. International workshop “Multi-scale simulation of biological systems”

Snowbird, Utah

Sept. Dept. of Chem., Univ. of Detroit Mercy Detroit, MI

Aug. ACS National Meeting Washington, D.C.

Aug. Telluride Workshop on “Vibrational Dynamics” Telluride, CO

Jul. International symposium “Protein folding, dynamics and function”

Beijing, China

May Workshop on “Enzyme dynamics”, Mathematical Bioscience Institute,

Ohio-State University Columbus, OH

Apr. Dept. of Biochem. & Mol. Biophys., Washington Univ. St. Louise, MO

Apr. Dept. of Chem., Jackson State Univ. Jackson, MS

Mar. Dept. of Chem., Univ. of Penn. Philadelphia, PA

Mar. Dept. of Biochem., Michigan State Univ. East Lansing, MI

Jan. WATOC 2005 Cape Town, South Africa

Jan. International symposium “Theoretical and computational chemistry of complex systems”

Hongkong

2004 (11)

Nov. Triangle symposium Chapel Hill, NC

Oct. NSF Workshop on “Molecular basis of life processes” Oakridge, TN

Sept. Worshop on “Towards Accurate calculation of biomolecular recognition and reactivity”

Manchester, UK

Sept. CIBM Program seminar series, Univ. of Wisc. Madison Madison, WI

Aug. ACS National Meeting Philadelphia, PA

Aug. 4th Conference for Worldwide Chinese Young Chemists Chengdu, China

Jul. German-American Symposium on Frontiers of Chemistry Seeon, Germany

Jul. DKFZ Heidelberg, Germany

May UCLA-IPAM Proteomics Workshop: Molecular Machine Los Angles, CA

May Dept. of Chem., SUNY, Stony Brook Stony brook, NY

Mar. Dept. of Chem., Penn. State Univ. University Park, PA

2003 (10)

Dec. Dept. of Chem. Univ. of Michigan Ann Arbor, MI

Nov. Dept. of Chem. Univ. of Nevada-Reno Reno, NV

Nov. Center for Comput. Biol., Univ. of Pittsburgh Pittsburgh, PA

Sept. Dept. of Chem. Univ. of Wisc. Madison Madison, WI

Aug. Workshop on “Grand challenges in modeling the assembly and properties of

nanomaterials” Argonne, IL

Aug. Workshop on “Excited state processes in electronic and bio nano-materials”

Las Alamos, NM

Aug. Satellite meeting for International Congress of Quantum Chemistry

Mulheim, Germany

Aug. CECAM workshop Lyon, France

Mar. ACS National Meeting New Orleans, LA

Feb. Sanibel Symposium Augusta, FL

2002 (9)

Oct. Dept. of Mathematics, Univ. of Wisc. Madison Madison, WI

Oct. Dept. of Chem., College of Staten Island, CUNY Staten Island, NY

Oct. Dept. of Chem., Univ. New Mexico Albuquerque, NM

Sept. 2

Worldwide Chinese Theoretical and Computational Chemistry Conference

Taipei, Taiwan

Aug. 2

German American Symposium on the frontier of Chemistry, Durham, NH

Jul. Gordon Research Conference in Comput. Chem. Durham, NH

Jun. Great-Lake regional ACS meeting Minneapolis, MN

Apr. Dept. of Chem., Eng. Univ. of Wisc. Madison Madison, WI

Apr. Dept. of Chem., Univ. of Iowa Iowa City, IW

Departmental/University Service [UW-Madison]

• Member, Finance Committee of Chemistry Department [2016-2017]

• Graduate Program of Biophysics; Chair, graduate program admission committee [2011-

present]; Steering committee [2006-2017]

• Member, Computer Committee of Chemistry Department [2007-2017]

• Member, Graduate Student Faculty Liaison Committee [2006-2010]

• Member, Graduate Recruiting Committee (responsible for international recruiting for

physical chemistry division) [2001-2017]

• Organizer, Theoretical Chemistry Institute Seminar Series [2001-2017]

• Member, Library Committee of Chemistry Department [2002-2006]

• Member, University Appeal Committee [2007-2009]

• Alternate member of UW Faculty Senate [2006-2007, 2010-2017]

• Member, Committee for Cluster Hire in “Materials by Design” [2006-2007]

• Thesis committee members for students in Chemistry, Biophysics, Biochemistry, Materials

Science, Neuroscience.

• Member of training grants in: CIBM (Computations and Informatics in Biology and

Medicine), Molecular Biophysics, Chemical Biology

Professional Activities

2018 Co-organizer (with D. M. York, G. H. Li and M. Elstner), Telluride Workshop on Multi-

scale computations, Telluride, CO

2017 Co-organizer (with R. J. Hamers, J. A. Pedersen and T. Fraunheim), CECAM workshop

on “Tackling complexity of the Nano/Bio interface”, Bremen, Germany

2016 Co-organizer (with X. Huang and H. Yang), HKUST-IAS workshop on “Functional

Dynamics of Biomolecular Machines”

2015 Organizer (with M. Meuwly, Y. Q. Gao, T. Allen), Pacifichem symposium on “Metal ions

and protein function”

2014 Editor (with M. Meuwly, P. Ren), Monograph on “Many-Body Effects and Electrostatics

in Biomolecules”

2014 Organizer (with B. Garcia-Moreno), Telluride Workshop on “Proton transfers in

biology”

2014 Co-chair (with S. Hammes-Schiffer), symposium in Biophysical Society Meeting on

“Application of Quantum Mechanics to Biophysical Problems”

2012 Organizer (with M. Meuwly, M. Elstner), CECAM Workshop on “Protein Dynamics”

2011 Organizer (with H. Yang, S. Sun), Telluride Workshop on “Rise of the Machines”

2010 Organizer (with D. York and D. Herschlag), Telluride Workshop on “Phosphoryl

transfers”

2008, 2010, 2013 Organizer (with A. Yethiraj), Telluride Workshop on “Frontiers of Molecular

Simulations”

2006 Co-Organizer (with G. Phillips, J. Mitchell, R. Jernigan), 32

Steenbock symposium on

“Dynamics of proteins and macromolecular assemblies”

2005 Organizer (with J. M. Bowman, Emory Univ.), Telluride Workshop on “Vibrational

Dynamics of Biomolecules”

2004 Editor (with I. Bahar, Univ. of Pittsburgh), Monograph on “Normal Mode Analysis:

Theory and Applications to Biological and Chemical Systems”

2003 Organizer, ACS National Meeting, “Physical Chemistry of Biomolecular Motors”

Current Postdoctoral Fellows

Dr. Mesele Oluwaseun (8/17-), Dr. M. Huynh (9/17-), Dr. Shingo Ito (03/18-)

Dr. Mandal Taraknath (4/18-), Dr. Rui Lai (6/18-)

Current Graduate Students

Mr. Darren Demapan (Chemistry, 2014-present)

Ms. Gladys Vazquez (Biophysics, 2014-present, joint with Prof. A. Senes)

Mr. Dongyue Liang (Chemistry, 2015-present)

Mr. Tanmoy Pal (Chemistry, 2016-present)

Undergraduate Students

Mr. M. Wolfsen (2004-2006) Graduate student, MIT

Mr. N. Schaefer (2008) PhD, UCSD

Ms. Jane (Yi-Chen) Lin (2014)

Mr. S. Slattery (2012-2016)

Ms. Lixue Cheng (2014-2017, joint with Prof. M. T. Record, Jr. ) Graduate student, Cal Tech

Mr. Rishi Ragsdale (2014-2016); Mr. Stephen Pan (2015-2017)

Former Graduate Students

Ms. Megan Hyland (Chemistry) (2002-2004), M. S. PPD, Inc., WI

Ms. Patricia Schaefer (Chemistry) (2002-2005), M. S. High-school teacher, WI

Dr. Mark S. Formaneck (Chemistry) (2001-2005), Ph.D. 02/06 Epic Systems, WI

Dr. Demian Riccardi (Chemistry) (2001-2006), Ph.D. 12/06 NIST

Dr. Adam Van Wynsberghe (Biophysics, 2001-2006), Ph.D. 12/06 Hamilton (Asso. Prof.)

Ms. Junjun Yu (Chemistry, 2005-2009), M.S. 08/09

Dr. Nilanjan Ghosh (Chemistry) (2003-2009), Ph.D., 01/09 Intel

Dr. Yang Yang (Chemistry, 2004-2008), Ph.D. 12/08 Haverford Coll. (Visit. Prof.)

Dr. Liang Ma (Biophysics, 2004-2009), Ph.D. 08/09 S. Carolina (Asst. Prof.)

Dr. Xiao Zhu (Chemistry, joint with Prof. A. Yethiraj, 2004-2009)

Ph.D. 01/10 Computer Center, Purdue

Dr. Jejoong Yoo (Biophysics, 2005-2010), Ph. D. 06/10 IBS Fellow, Korea

Dr. Guanhua Hou (Chemistry, 2007-2012), Ph. D. 06/12 Micron

Dr. Zhe Wu (Chemistry, 2007-2012, joint with Prof. A. Yethiraj)

Ph.D. 08/12 Merck Co.

Mr. Shuo Yang (Chemistry, 2006-2013) Huawei Inc.

Dr. Puja Goyal (Chemistry, 2008-2013), Ph. D. 08/13 SUNY-Binghamton (Asst.

Prof.)

Dr. Xueqin Pang (Visiting student, DICP, 2011-2013) UW-Madison, Pharmacy

Ms. Fang He (Visiting student from National University of Singapore, 2012-2013)

Dr. Leili Zhang (Chemistry, 2010-2015, joint with Prof. A. Yethiraj)

Ph. D. 09/15 IBM

Dr. Elif Nihal Korkmaz (Biophysics, 2010-2016), Ph. D. 05/16 U. Washington

Dr. Xiya Lu (Chemistry, 2010-2016), Ph.D. 06/17 LinkedIn Co.

Mr. Runze Liu (DICP visiting graduate student, 2014-2016) DICP

Mr. Haiyun Jin (Chemistry, 2013-2017), M.S. 06/17 Amazon, Seattle

Mr. Jiewei Hong (Chemistry, 2014-2017), M. S. 08/17 UW-Madison, CS

Mr. Ruochen Lin (Chemistry, 2016-2017) UW-Madison, CS

Mr. Mingren Shen (Biophysics, 2016-2017) UW-Madison, Biophysics

Dr. Changyun Son (Chemistry, 2012-2017, joint with Prof. A. Yethiraj) Cal Tech

Dr. Yuqing Zheng (Biophysics, 2012-2017) Schneider, Inc.

Former Postdoctoral Fellows

Dr. Xiaodong Zhang (2001-2002) UC-Santa Barbara, CA

Dr. Guohui Li (2001-2003) Dalian Inst. Of Chem. Phys.

(Principal Investigator)

Dr. Demitry Khoroshun (2002-05/2004) MPI-Mulheim, Germany

Dr. Xavier Prat-Resina (2005-2006) Univ. Minnesota-Rochester

(Asso. Prof.)

Dr. Justin Hoerter (joint with Prof. S. Stahl, 11/2004-05/2007) Dupont

Dr. Peter König (BACTER postdoctoral fellow, 01/2006-06/2007) P & G

Dr. Haibo Yu (01/2005-09/2007) Wollongong (Asst. Prof.)

Dr. Dmitry Kondrashov (CIBM postdoctoral fellow) Univ. of Chicago (Lecturer)

Dr. Demian Riccardi (06/10-12/10) NIST

Dr. Michael Daily (CIBM fellow, 07/08-06/11) Monsanto

Dr. Jan Zienau (05/10-08/12) Frankfurt

Dr. M. Gauss (11/11-03/13) SAP, Germany

Dr. T. Mori (10/12-11/13) IMS, Japan (Asst. Prof.)

Dr. C. Mahajan (11/13-07/14) Deceased

Dr. A. S. Christensen (9/14-9/16) Basel, Switzerland

Dr. D. Fang (10/14-9/16) Jingtai Inc., China

Dr. D. Roston (9/13-12/17) UW-Madison

Research Funding and Support (PI: Q. Cui unless otherwise stated)

Current:

Project: Phase II Center for Chemical Innovation, A Molecular Basis for Sustainable

Nanotechnology

Source: National Science Foundation (PI: Hamers)

Total Award: $20,000,000 Period: 9/1/15-8/31/20

Location: UW-Madison

Commitment to Project: 0.5 SM

Project: Multi-scale simulation methods for energy transduction and macromolecular

assembly

Source: National Science Foundation Period: 8/1/17-7/31/20

Total Award: $450,000

Location: UW-Madison

Commitment to Project: 0.5 SM

Project: Collaborative Research: Multi-scale models of membrane fission catalyzed by

the ESCRT complexes

Source: NSF (PIs: Cui, Audhya, Spagnolie)

Total Award: $1,200,000 Period: 07/1/17-6/30/21

Location: UW-Madison

Commitment to Project: 0.8 SM

Project: Development and application of QM/MM methods for metalloenzymes

Source: NIH

Total Award: $290,736 per year Period: 09/1/13-7/31/21

Location: UW-Madison

Commitment to Project: 1.0 SM

Pending Grants

Project: Toward a biomolecular force field based on many-body expansion models

PI: F. Paesani (UCSD), Co-PI: Q. Cui

Source: NIH

Total Award: $275,000 direct cost Period: 07/1/18-6/31/20

Location: UW-Madison

Commitment to Project: 0.5 SM

Completed Grants

1. ACS-PRF-G: Probing conformational dynamics and luminescent reactions in

photoproteins with novel QM/MM methods

$35,000 direct cost, 09/01/02-08/31/04

2. Research Corporation: Understanding allosteric transition in biomolecules with novel

molecular simulation methods

$35,000 direct cost, 06/01/03-11/18/06

3. NSF-MCB: Collaborative research of proton transfers in enzymes: A synergestic theory-

experiment approach

PI: Q. Cui, Co-PIs: H. Guo (Univ. of New Mexico), R. Viola (University of Toledo)

$174, 235 total cost to Cui, 09/01/03-08/31/06

4. Alfred P. Sloan Foundation: Sloan research fellowship

$40,000 direct cost, 09/01/2004-08/31/2008

5. NSF-CHEM-CAREER: Theoretical analysis of oxygen chemistry in biological systems

$510,000 total cost, 03/01/04-08/31/09

6. Graduate school funding: continuum mechanics models of proteins

Supporting one graduate student, 07/01/08-06/30/09

7. NIH-R01: Coupling between conformation and chemistry in enzymes

$976,423 total cost, 03/01/05-08/31/10

8. NSF-CRC: Catalytic manipulation of amide-based molecules and materials

PI: S. Gellman, Co-PIs: S. Stahl, Q. Cui, A. Yethiraj, A. E. Barron (Northwestern)

$2,325,000 total cost, 09/01/04-08/31/10

9. DOE-BACTER: Bringing Advanced Computational Techniques to Environmental

Research

PI: J. Mitchell; Co-PI: Cui and 7 others

$4,200,000 total cost, 08/01/08-03/31/12

10. NIH-ARRA: QM/MM analysis of redox driven proton pumping

PI: Q. Cui, Co-PI: M. Gunner (CUNY)

$549,556 total cost, 09/30/09-08/31/12

11. NIH: Conformational duality of the human chemokine lymphotactin

PI: B. Volkman, Co-PI: Q. Cui

$57,592 total cost, 08/01/11-06/30/12

12. I. H. Romnes Fellowship, UW-Madison, $50,000, 07/01/10-06/30/15

13. Graduate school funding: QM/MM models for DNA repair enzymes

Supporting one graduate student, 07/01/11-06/30/12

14. NSF: New methods for treating electrostatics and adaptive partitioning in QM/MM

simulations

PI: Q. Cui

$410,001 total cost, 01/15/10-08/31/13

15. NSF: UW NSEC

$60,000 to Cui research, 09/01/13-08/31/14

16. NSF-CHE: Development of multi-scale models for enzyme catalysis in complex

environments

$405,000 total cost, 08/1/13-7/31/17

17. NSF: UW CEMRI on Structured Interfaces

PI: Abbott & 28 co-PIs), $18,000,000 ($53,153 to Cui research annually), 01/01/13-08/31/17

18. NSF-DMS: FRG: Collaborative Research: Variational multiscale approaches to

biomolecular structure, dynamics and transport

PI: J Mitchell, co-PI: Q Cui, $321,054 total 09/15/12-08/31/17

Publication List

Qiang Cui

Department of Chemistry

Boston University

590 Commonwealth Avenue, Boston, MA 02215

February 16, 2018

Boston University (01/2018-present); Univ. of Wisconsin-M ad is on (08/2001 - 12/2017),

* indicates corresponding author)

Google Scholar Proﬁle: http://scholar.google.com/citations?hl=en&user=4x1QeogAAAAJ

h-index: 66 (Google Scholar); 57 (Web of Science)

237. Speciﬁc Substates of Ras to Interact with GAPs and E↵ectors: Revealed by Theoretical

Simulations and FTIR Experiments, Y. Li, Y. W. Zhang, F. Groer¨uschkamp, S. Stephan, Q. Cui,

C. K¨ottig, F . Xia and K. Gerwert, J. Phys. Chem. Lett. Submitted (2017)

236. N

-methyldeoxyadenosine directs nucleosome positioning in eukaryotic DNA, G. Z. Luo, Z.

Y. Hao, M. R. Shen, D. Sparvoli, Y. Q. Zheng, Z. J. Zhang, X. C. Weng, K. Chen, Q. Cui, A.

Turkewitz and C. He

⇤

, eLife, Submitted (2017)

235. Gating and Inactivation of Mechanosensitive Channels of Small Conductance: A Continuum

Mechanics Study, L. L. Zhu, Q. Cui, H. Xiao, X. B. Liao and X. Chen

⇤

, Submit te d (2017)

234. Proposed exit pathway for protons to the P-side of Cytochrome c Oxidase, X. H. Cai, K.

Haider, J. X. Lu, S. Radik, C. Y. Son, Q. Cui and M. Gunner

⇤

, Proc. Natl. Acad. Sci. USA

Submitted (2017)

233. Speciﬁcity Landscapes unmask di↵erential sequence preferences of homologous t r an scr i pt i on

factors, D. Bhimsaria, J. A. Rodriguez-Martinez, J. K. Pan, D. Rost on, E. N. Korkmaz, Q. Cui, P.

Ramanathan, and A. Z. Ansari

⇤

, Proc. Natl. Acad. Sci. USA Submi t t ed (2017)

232. Contact Ion Pairing Drives Lipid Corona Formation from Nanoparticle Interactions with

Bilayer Membranes, L. L. Olenick, J . M. Troiano, A. Vartanian, E. S. Melby, A. Mensch, L. L.

Zhang, T. Qiu, S . Lohse, X. Zhang, T. R. Kuech, A. Millevolte, I. Gunsolus, A. C. McGeachy, M.

Dogang¨un, D. H. Hu, S. R. Walter, S. Lovern, H. Owen, M. D. Torelli, Z. V. Feng, K. R. Hurley,

J. Dalluge, G. Chong, C. L. Haynes, R. J. Hamers , J. A. Pedersen, Q. Cui, R. Hernandez, G. Orr,

C. J. Murphy, and F. M. Ge ige r

⇤

, Nat. Comm. Submitted (2017)

231. Essence of Small Molecule-Mediated Control of Hydroxyapatite Growth: Free Energy Calcu-

lations of amino acid side chain analogs, Z. J. Xu

⇤

, Q. C. Wei, W. L. Zhao, Q. Cui and N. Sahai

⇤

J. Phys. Chem. C, In press (2018) [DOI: 10.1021/acs.jpcc.7b12142]

230. Inspiring Molecular Quantum Chemist, Obituary for Professor K ei ji Morokuma, Angew Chim.

Intl. Ed. 57, 2-4 (2018)

229. Mul t i p le Pathways and Timescales for Conformational Transit i on s in apo-Adenylate Kinase,

Y. Q. Zheng and Q. Cui

⇤

, J. Chem. Theory Comput. In press (2018) [DOI: 10.1021/acs.jctc.7b01064]

228. Dynamics and number of trans-SNARE complexes determine nascent fusion pore properties,

H. Bao, D . Das, N. A. Courtney, Y. H. Jiang, J. Briguglio, X. C. Lou, D. Roston, Q. Cui, B.

Chanda and E. R. Chapman

⇤

, Nature, 554, 260-263 (2018)

227. Iron starvat i on inhibits late stages of b act er i al cytokinesis, T. M. A. Santos, M. G. Lammers,

M. Q. Zhou, I. L. Spark s, M. Rajendran, D. Fang, C. L. Y. De J es us , G. F. R. Carneiro, Q. Cui

and D. B. Weibel

⇤

, ACS Chem. Bio, 13, 235-246 (2018)

226. Structural and f u nc ti on al analysis of the FtsLB tetrameric complex of the bacterial divisome,

D. A. Mahbuba, S. G. F. Condon, C. R. Armstrong, G. Diaz-Vazquez, S. J. Craven, L. M. LaPointe,

A. S. Khadria, R. Chadda, J. A. Crooks, N. Rangarajan, D. B. Weibel, A. A. Hoskins, J. L.

Robertson, Q. Cui, A. Senes

⇤

, J. Biol. Chem., 293, 1623-1641 (2018)

225. Analysis of Conformational Properties of Amine Ligands at the Gold/Water Interface with

QM, MM and QM/MM simulations, D. Y. Liang, J. W. Hong, F. Dong, J. W. Bennett, S. E.

Mason, R. J. Hamers and Q. Cui

⇤

, Phys. Chem. Chem. Phys., 20, 3349-3362 (2018)

224. Cavity Hydration Dynamics in Cytochrome c Oxidase and Functional Implications, C. Y.

Son, A. Yethiraj and Q. Cui

⇤

, Proc. Natl. Acad. Sci. USA 114, E8830-E8836 (2017)

223. Benchmarking Density Functional Ti ght Binding Models for Barrier Heights and Reaction

Energetics of Organic Molecules, M. Gruden

⇤

, L. Andjelkovic, J. A. Kuriappan, S. Step anovic, M.

Zlatar, Q. Cui*, M. El st n er

⇤

, J. Comput. Chem., 38, 2171-2185 (2017)

222. Intermolecular Interactions in t h e Con de ns ed P h ase: Evaluation of Semi-empirical Quantum

Mechanical Methods, A. S. Christensen, J. C. Kromann, J. H. Jensen and Q. Cui

⇤

, J. Chem. Phys.,

Special Issue on “From Quantum Mechanics to Force Fields”, 147, 161704 (2017)

221. Quantifying the Electrostatics of Polycation-Lipid Bilayer Interactions, J. M. Troiano, A. C.

McGeachy, L. L. Olenick, D. Fang, D. Y. Liang, J. W. Hong, T. R. Kuech, J. A. Pedersen, Q. Cui

and F. M. Geiger

⇤

, J. Am. Chem. Soc., 139, 5808-5816 (2017)

220. Regulation and Plasticity of Catalysis in Enzymes: Insights from Analysis of Mechanochemical

Coupling in Myosin, X. Lu, V. Ovchinnikov, D. R. Roston, D. Demapan an d Q. Cui

⇤

, Biochem.,

56, 1482-1497 (2017)

219. A Hybrid Molecular Dynamics/Multi Conformer Continuum Electrostatics (MD/MCCE)

Approach for the Determination of Surface Charge of Nanomaterials, J. W. Hong, R. J. Hamers,

J. A. Pedersen and Q. Cui

⇤

, J. Phys. Chem. C, 121, 3584- 3596 (2017)

218. Microscopic Mechanisms that Govern the Titration Response and pK

Values of Burie d

Residues in Staphylococcal Nuclease Mutants, Y. Q. Zheng and Q. Cui

⇤

, Proteins: Struct., Funct.

&Bioinform., 85, 268-281 (2017) Cover

217. Structure and dynamics underlying elementary ligand binding events in pacemaking channels,

M. P. Goldschen-Ohm, V. A. Klenchin, D. S. White, J. B. Cowgill, Q. Cui, R. H. Goldsmith, B.

Chanda

⇤

, eLife, 5, e20797 (2016)

216. Perspective: Quantum Mechanical Methods in Biochemistry and Biophysics, Q. Cui

⇤

, J.

Chem. Phys., 145, 140901 (2016) Invited Perspective, Cover

215. Substrate and Transition St at e Binding in Alkaline Phosphatase Analyzed by Computat i on

of Oxygen Isotope E↵ects, D. Roston

⇤

,Q.Cui

⇤

, J. Am. Chem. Soc., 138, 11946-11957 (2016)

214. Multiple gas-phase conformations of proline-containing peptides: Is it always cis/trans iso-

merization? C. B. Lietz, Z. Chen, C. Y. Son, Q. Cui and L. Li

⇤

, Analyst, 141, 4863-4869 (2016)

213. Sustainable Nanotechnology: Opportunities and Challe nge s for Theoretical/Computational

Studies, Q. Cui

⇤

, R. Hernandez

⇤

, S. E. Mason

⇤

, T. Frauenh ei m, J. A. Pedersen, F. M. Gei ge r, J.

Phys. Chem., B., 120, 7297-7306 (2016) Invited Review, Cover

212. Predicting the St r uc t ur e- act i v ity Relationship of Hyd r oxyapatite-binding Peptides by Enhanced-

sampling Molecular Simulation, W. L. Zhao, Z. J. Xu, Q. Cui and N. Sahai

⇤

, Langmuir, 32, 7009-

7022 (2016)

211. Leaving Group Ability Observably A↵ects Tr ans it i on State Structure for Phosphoryl Transfer

in a Single Enz ym e Active Site, D. Roston, D. Demapan and Q. Cui

⇤

, J. Am. Chem. Soc., 138,

7386-7394 (2016)

210. QM/MM Analysis of Transition States and Transition State Analogues in Metalloenzymes, D.

Roston

⇤

and Q. Cui

⇤

,inMethods in Enzymology, Issue on “Computational Approaches for Studying

Enzyme Mechanism”, Ed. G. A. Voth, Vol. 577, 213-250 (2016) Invited contribution

209. Ionic Hydrogen Bonds and Lipid Packing Defects Determine the Binding Orientation and

Insertion Depth of RecA on Mu lt i -c omponent Lipid Bilayers, L. L. Zhang, M. Rajendram, D. B.

Weibel, A. Yethiraj and Q . Cui

⇤

, J. Phys. Chem., B Andy McCammon Festschrift, 120,

8424-8437 (2016)

208. Towards a Barrier Height Benchmark Set for Biologically Relevant Sy st e ms, J. C. Kromann,

A. S. Christensen, Q. Cui and J. H. Jensen

⇤

, Peer J., e1994 ( 2016)

207. Gating Mechanism of Mechanosensitive Channel of Large Conductance: A Coupled Contin-

uum Mechanical-Continuum Solvation Approach, L. Zhu, J. Wu, Y. Liu , Y. Yan, Q . Cui an d X.

Chen

⇤

, Biomechan.& Modeling in Mechanobi o., 15, 1557-1576 (2016)

206. First Principles United Atom Force Field for the Ionic Liquid [BMIM

][BF



] : An Alternative

to Charge Scaling, C. Y. Son , J. McDaniel, J. R. Schmidt, Q. Cui and A. Yethiraj

⇤

, J. Phys. Chem.

B, 120, 3560-3568 (2016)

205. Semi-empirical Quantum Mechanical Methods for Non-covalent Interactions for Chemical and

Biochemical Applications, A. S. Chr i st en se n, T. Kubar, Q. Cui

⇤

and M. Elstner

⇤

, Chem. Rev., 116,

5301-5337 (2016)

204. A Computational Investigation on the Substrate Pr ef er en ce of TET2, J. Y. Lu, L. L. Hu, J.

D. Cheng, D. Fang, C. Wang, K. Q. Yu, H. L. Jiang, Q. Cui, Y. H. Xu

⇤

and C. Luo

⇤

, Phys. Chem.

Chem. Phys., 18, 4728-4738 (2016)

203. D i ↵e re nt States of Synaptotagmin Regulate Evoked versus Spontaneous Release, B. Hua, R.

H. Xue, H. Bao, L. Zhang, A. Yethiraj, Q. Cui and E. R. Chapman

⇤

, Nat. Comm., 7, 10971 (2016)

202. QM/MM Free Energy Simulations: Recent Progress and Challenges, X. Lu, D. Fang, S. Ito, Y.

Okamoto, V. Ovchinnikov and Q. Cui

⇤

, Mol. Simul. Special Issu e on “Free Energy Simul ati ons ”,

42, 1056-1078 (2016) Invited review

201. Copper Oxidation/Reduction in Water and Protein: Studies with DFTB3/MM and VAL-

BOND Molecular Dynamics Simulations, H. Jin, P. Goyal, A. Kumar Das, M. Gaus, M. Meuwly

⇤

and Q. Cui

⇤

, J. Phys. Chem. B Bruce Garrett Festschrift, 120, 1894-1910 (2016)

200. Comparison of Native and Non-native Ubiquitin Oligomers Reveals Analogous Structures

and Reactivities, G. H. Pham, A. S. J.B. Rana, E. N. Korkmaz, V. H. Trang, Q. Cui, and E. R.

Strieter

⇤

, Prot. Sci., 25, 456-471 (2016)

199. A Composite Approach to a Complete Model of the Myosin Rod, E. H. Korkmaz, K. C.

Taylor, M. P. Anreas, G. Ajay, N. T. Heinz, Q. Cui

⇤

and I. Rayment

⇤

, Proteins, 84, 172-189 (2016)

198. Structural Insight into Substrate Preference for T ET- med i at ed Oxidation, L. L. Hu, J. Y. Lu,

J. D. Cheng, Q. H. Rao, Z. Li, H. F. Hou, Z. Y. Lou, L. Zhang, W. Li, W. Gong, M. J. Liu, C.

Sun, X. T. Yin, J. Li, X. S. Tan, P. C. Wang, Y. S. Wang, D. Fang, Q. Cui, P. Y. Yang, C. He, H.

L. Jiang, C. Luo

⇤

and Y. H. Xu

⇤

, Nature, 527, 118-122 (2015)

197. Electronic Polarization E↵ects in Cation Interactions with First and Second Coordination

Shell Ligands in Metalloproteins, V. Ngo, M. C. da Si l va, M. Ku bi l l us , M. Elstner, H. Li, B. Roux,

Q. Cui

⇤

, D. R. Salahub

⇤

and S. Noskov

⇤

, J. Chem. Theory Comp. 11, 4992-5001 (2015)

196. Anionic Phospholipids Interact with RecA and Stabiliz e Nucleoprotein Filam ents in Es-

cherichia coli, M. Rajendram, L. Zhang, H. H. Tuson, B. J. Reynolds, K. N. Ngo, M. M. Cox, A.

Yethiraj, Q. Cui and D. B. Weibel

⇤

, Mol. Cell, 60, 374-384 (2015)

195. Improving Intermolecular Interactions in DFTB3 Using Extended Polarization from Chemical-

potential Equ al i zat i on, A. S. Christensen, M. Elstner and Q. Cui

⇤

, J. Chem. Phys. 143, 084123

(2015)

194. DFTB3 Parametrization for Copper: the Importance of Orbital Angular Momentum Depen-

dence of Hubbard Parameters, M. Gaus, H. Jin, D. Demapan, A. S. Chris t en sen , P. Goyal, M.

Elstner an d Q. Cui

⇤

, J. Chem. Theory Comp. 11, 4205-4219 (2015)

193. Interplay of Electrostatics and Hydrophobic E↵ects i n the Metamorphic Protein Human

Lymphotactin, N. Korkmaz, B. Volkman and Q . Cui

⇤

, J. Phys. Chem. B 119, 9547-9558 (2015)

192. Skip Residues M odulate the Structural Properties of the Myosin Rod and Guide Thick Fil-

ament Assembly, K. C. Taylor, M. Buvoli, N. Korkmaz, A. Buvoli, Y. Q. Zhen g, N. T. Heinz, Q .

Cui

⇤

, L. A. Leinwand

⇤

, and I. Rayment

⇤

, Proc. Natl. Acad. Sci. USA E3806-E3815 (2015)

191. Biological Responses to En gi ne er ed Nanomaterials: Needs for the Next Decade, C. J. Murphy

⇤

A. M. Vartanian, FM. Geiger, R. J. Hamers, J. Pederson, Q. Cu i , C. L. Haynes, E. E. Carlson, R.

Hernandez, R . D. Klaper, G. Orr and Z. Rosenzweig, ACS Cen tral, 1, 117-123 (2015)

190. Electrostatics and Many-body E↵ects in Biomolecular Simulations,Eds. Q.Cui,M.Meuwly

and P. Ren, Pan Stanford Publishing (2015)

189. Histone H3 N-terminal Tail: a Computational Analysis of Free Energy Landscape and Kinetics,

Y. Zheng and Q. Cui

⇤

, Phys. Chem. Chem. Phys., 17, 13689 - 13698 (2015)

188. Elastic Models of Biomolecules, Q. Cui

⇤

, in “Coarse-grained Modeling of Biomolecules”, Ed.

G. Papoian, CRC Press. In press (2015) Invited Book Chapter

187. Parameterization of DFTB3/3OB for Magnesium and Zinc for Chemical and Biological Appli-

cations, X. Lu, M. Gau s, M. Elstner and Q. Cui

⇤

, J. Phys. Chem. B, Bill Jorgensen Festschrift,

119, 1062-82 (2015)

186. Molecular Mechanisms for Intraﬁbrillar Collagen Mineralization in S keletal Tissues, Z. Xu, Y.

Yang, W. Zhao, Z. Wang, W. J. Landis, Q. Cui and N. Sahai

⇤

, Biomater ial s , 39, 59-66 (2015)

185. Microscopic Basis for Kinetic Gating in Cytochrome c Oxidase: Insights from QM/MM

Analysis, P. Goyal, S. Yang and Q. Cui

⇤

, Chem. Sci., 6, 826-841 (2015)

184. UO

Uptake by Proteins: Understanding the Binding Features of the Super Uranyl-Binding

Protein (SUP) and Design of a Protein with Higher Aﬃnity, S. O. Odoh, G. C. Bondarevsky, J.

Karpus, Q . Cui, C. He, R. Spezia, L. Gagliardi

⇤

, J. Am. Chem. Soc., 136, 17484-17494 (2014)

183. Infrared spectral marker bands characterizing a transient water wire inside a hydrophobic

membrane protein, S. Wolf, E. Freier, Q. Cui and K. Gerwert

⇤

, J. Chem. Phys . , “Special Issue on

Biological Water”, 141, 22D524 (2014)

182. Molecular simulation of water and hydration e↵ects in di↵erent environments: challenges and

developments for DFTB based models, P. Goyal, H-J. Qian, S. Irle, X. Lu, D. Roston, T. Mori, M.

Elstner an d Q. Cui

⇤

, J. Phys. Chem. B Featured Articles, 118, 11007-11027 (2014)

181. Editorial : Making Biomolecular Simulations Accessibl e in t h e post-Nobel prize era. Q. Cui

⇤

and R. Nussinov

⇤

, PLoS Comp. Biol. 10, e1003786 (2014)

180. Structural analysis and modeling reveals new mechanisms governing ESCRT-III spiral ﬁlament

assembly, Q. T. Shen, A. L. Schuh, Y. Q. Zheng, K. Quinney, L. Wang, M. Hanna, J. C. Mitchell,

M. S. Otegui, P. Ahlquist, Q. Cu i, and A. Audhya

⇤

, J. Cell Biol., 206, 763-777 (2014)

179. Free energy calculations for the peripheral binding of proteins/peptides to an anionic mem-

brane. I. Implicit membrane models, L. Zhang, A. Yethiraj and Q. Cui

⇤

, J. Chem. Theo. Comp.,

Special issue on “Free ene rgy calculations: three decades of adventure in chemistry

and biophysics”, 10, 2845-2859 (2014)

178. Den si ty Functional Tight Binding: values of semi-empirical methods in an ab initio era, Q.

Cui

⇤

,M.Elstner

⇤

, PCCP, Invited perspective in the thematic issue on “Density Functional

Theory and Its Applications”, 16, 14368-14377 (2014)

177. Integrated Hamiltonian Sampling: a simple and versatile method for free energy simulations

and conformational sampl i n g, T. Mori, R. J. Hamers, J. A. Pederson and Q. Cui

⇤

, J. Phys. Chem.

B Special Issue: Jim Skinner Festschr ift, 118, 8210-8220 (2014)

176. Parameterization of DFTB3/3O B for Sulfur and Phosphorus for chemical and bi ol ogic al

applications, M. Gaus, X. Lu, M. Elstner

⇤

and Q. Cui

⇤

, J. Chem. Theo. Comp., 10, 1518-1537

(2014)

175. Quantum Mechanical/Molecular Mechanical Studies of Zinc Hydrolases, D. G. Xu

⇤

,Q.Cui

and Hua Guo

⇤

, Int. Rev. Phys. Chem., 33, 1-41 (2014)

174. Gas-phase Fragment Ion Isomer Analysis Reveals the Mechanism of Peptide Sequence Scram-

bling, C. Jia, Z. Wu, C. B. Lietz, Z. Liang, Q. Cui and L. Li

⇤

, Anal. Chem. 86, 2917-2924 (2014)

Cover

173. Small Molecule-Mediated Control of Hydroxyapatite Growth: Free Energy Calculations

Benchmarked to Density Functional Theory, Z. J. Xu, Y. Yang, Z. Q. Wang, D . Mkhonto, C.

Shang, Z. P. Liu, Q. Cui and N. Sahai

⇤

, J. Comp. Chem. 35, 70-81 (2014)

172. Density Functional Tight Binding (D F TB) : Application to organic and biological molecules,

M. Gaus, Q. Cui and M. Elstner, W I REs Comput. Mol. Sci., 4, 49-61 (2014)

171. Tethered spectroscopic probes esti mat e dynamic distances with s ub -n anom et er resolution in

voltage-dependent potassium channels, B. W. Jarecki, S. Q. Zheng, L. L. Zhang, X. C. Li, X. Zhou,

Q. Cui, W. P. Tang and B. Chanda

⇤

, Biophys . J. 105, 2724-2732 (2013)

170. Changing hydration level in an internal cavity modulates t h e proton aﬃnity of a key glutamate

in Cytochrome c Oxidase , P. Goyal, J . Lu, S. Yang, M. R. Gunner

⇤

and Q. Cui

⇤

, Proc. Natl . Acad.

Sci. USA, 110, 18886-18891 (2013)

169. An explicit consid er at i on of de sol vation is critical to binding free energy calculations of charged

molecules at ionic surfaces, T. Mori, R. J. Hamers, J. A. Pedersen and Q. Cui

⇤

, J. Chem. Theo.

Comp., 9, 5059-5069 (2013)

168. Why do Arginine and Lysine organize lipids di↵ e re ntly? Insights from coarse-grained and

atomistic s i mulations, Z. Wu, Q. Cui

⇤

, A. Yethiraj

⇤

, J. Phys. Chem. B 117, 12145-12156 (2013)

167. Generation and sensing of membrane curvature: where materials science and b i ophysics meet,

Q. Cui

⇤

, L. Zhan g, Z. Wu and A. Yethiraj

⇤

, Curr. Opin. Solid State Mater. Sci. 17, 164-174

(2013) Invited Review

166. Contribution of Electrostatics to the Binding of Pancreatic-Type Ribonucleases to Membranes,

N. K. Sundlass, C. H. Eller, Q. Cu i and R. T. Raines

⇤

, Biochem. 52, 6304-6312 (2013)

165. Stabilization of Di↵erent Types of Transition States in a Single Enzyme Active Site: QM /M M

Analysis of Enzymes in the Alkaline Phosphatase Superfamily, G. Hou, Q. Cui

⇤

, J. Am. Chem.

Soc. 135, 10457-10469 (2013)

164. A simple but e↵ective modeling strategy for structural properties of non-heme Fe(II) sites in

proteins: test of force ﬁeld models and application to proteins in the AlkB family, X. Pang, K . Han

and Q. Cui, J. Comp. Chem. 34, 1620-1635 (2013) Cover

163. Molecular Simulation of Biominer al Nucleation and Crystal Growth: Mode rn Computational

Challenges and Approaches, Y. Yang, Z. J. Xu, Q. Cui and N. Sahai, Characterization of Biomin-

erals and Biomimetic Materials, Eds. L. Gower, E. DiMasi, Taylor & Francis, In press (2013)

Invited Review

162. Toward quantitative analysis of metalloenzyme function us i ng MM and hybrid QM/MM

methods: challenges, methods and recent applications, M. Gaus, P. Goyal, G. Hou, X. Lu, X. Pang,

J. Zienau, X. Xu, M. Elstner and Q. Cui

⇤

,“Molecular Modeling at the Atomic Scale: Methods and

Applications in Quantitative Biology”, Ed. Ruhong Zhou, In press (2013) Invited Review

161. FTO-Mediated Formation of N6-Hydroxymethyladenosine and N6-Formyladenosine in Mam-

malian RNA, Y. Fu, G. Jia, X. Pang, R. Wang, X. Wang, C. Li, Q. Dai, K. Han, Q. Cui , C. He

⇤

Nat. Comm., 4, 1798 (2013)

160. Conformational Disor de r Enhances Electron Transfer Through Alkyl Monolayers: Ferrocene

on Conductive Diamond, R. E. Ruther, Q. Cui and R. J. Hamers

⇤

, J. Am. Chem. Soc., 135,

5751-5761 (2013)

159. Charging free energy calculations using the Generalized Solvent Boundary Potential (G SB P)

and periodic boundary condit i on : a comparative analysis using ion solvation and reduct ion potential

in protei ns , X. Lu and Q. Cui

⇤

, J. Phys. Chem. B 117, 2005-2018 (2013)

158. A Comparison of Coarse-Grained and Continuum Models for Membrane Bending in Lipid

Bilayer Fusion Pores, J. Yoo, M. Jackson and Q. Cui

⇤

, Biophys. J., 104, 841-852 (2013)

157. Membrane-mediated protein-protein interactions and connection to elastic models: a coarse-

grained simulation analysis of gram i ci di n A association, J. Yoo and Q. Cui

⇤

Biophys. J., 104,

128-138 (2013) Cover

156. Three-dimensional stress ﬁeld around a membrane protein: atomistic and coarse-grained

simulation analysis of gramicidin A, J. Yoo and Q. Cui

⇤

, Biophys . J., 104, 117-127 (2013)

155. Allosteric activation transitions in enzymes an d biomolecular motors: insights from atomistic

and coarse-grained simulations, M. Daily, H. Yu, G. N. Phillips, Jr. and Q. Cui

⇤

, Special Issue

of Topics in Current Chemistry, “Macromolecular Dynamics in B i ol ogical Catalysis”,Eds. S.

Hammes-Schi↵er and J. Klinman, 337, 139-164 (2013) Invited Review

154. Detailed structure of the H



-GDP intermediate in Ras-GAP decoded from FTIR experi-

ments by biomolecular simulations, F. Xia, T. Rudack, Q. Cui, C. K¨otting and K. Gerwert, J. Am.

Chem. Soc. 134, 20041-20044 (2012)

153. Implementation of the Solvent Macromolecule Boundar y Potential and Application to Model

and Realistic Enzyme Syste ms, J. Zienau and Q. Cui

⇤

, J. Phys. Chem. B 116, 12522-12534 (2012)

152. A modiﬁed QM/MM Hamiltonian with the Self-Consistent-Charge Density-Func t ion al -Ti ght-

Binding Theory for highly charged QM regions, G. Hou, X. Zhu, M. Elstner and Q. Cui

⇤

, J. Chem.

Theo. Comp. 8, 4293-4304 (2012)

151. Identiﬁcation of the Ah-receptor stru ct u r al determinants for ligand preferences, Y. N. Xing

⇤

M. Nukaya, K. Satyshur, L. Jiang, V. Stanevich, E. N. Korkmaz, L. Burd et t e , G. Kennedy, Q. Cui,

C. A. Bradﬁeld, Toxicol. Sci., 129, 86-97 (2012)

150. Large-scale motions in the adenylate kinase solution ensemble: coarse-grained simulations and

comparison with solution X-ray scattering, M. Daily, L. Makowski, G. N. Phillips, Jr. and Q. Cui,

Special Issue on “Functional dynamics of proteins”, Chem. Phys. 396, 84-91 (2012)

149. Protein Functional Dynamics: From Femtoseconds to Milliseconds, M. Meuwly and Q. Cui,

Editorial, Special Issue on “Functional dynamics of proteins”, Chem. Phys., 396, 1-2 (2012)

148. Catalysis induced by molecular self-assembly: insights from computer simulation, J. Mondal,

X. Zhu, Q. Cui and A. Yethiraj

⇤

, J. Phys. Chem. B 116, 491-495 (2012)

147. QM/MM analysis suggests that Alkaline Phosphatase (AP) and Nucleotide pyrophosphatase

phosphodiesterase s l ightly tighten the transition state f or phosphate diester hydrolysis relative to

solution: implication for cat aly t i c promiscuity i n the AP superfamily, G. Hou and Q. Cui

⇤

, J. Am.

Chem. Soc. 134, 229-246 (2012)

146. Toward molecular models of proton pumping: challenges, methods and rele vant applications,

D. Riccard i , X. Zhu, P. Goyal, S. Yang, G. Hou and Q. Cui

⇤

, “Special Topic: The Frontiers of

Chemical Biology and Synthesis ” , Science China, Chemistry, 55, 3-18 (2012) Invited Review

145. A new coarse-grained for ce ﬁeld for membrane-peptide simulations, Z. Wu, Q. Cui

⇤

and A.

Yethira j

⇤

, J. Chem. Theo. Comp. 11, 3793-3802 (2011)

144. Permeation of styryl dyes through nanometer-scale pores in membranes, Y. Wu, L. Ma, S.

Cheley, H. P. Bayley, Q. Cui and E. Chapman

⇤

, Biochem. 50, 7493-7502 (2011)

143. Proton storage site in bacteriorhodopsin: new insights from QM/MM simulations of mi-

croscopic pK

and infrared spectra, P. Goyal, N. Ghosh, P. Phat ak, M. Clemens, M. Gauss , M.

Elstner

⇤

and Q. Cui

⇤

, J. Am. Chem. Soc. 133, 14981-14997 (2011)

142. The drivin g force for the association of hydrophobic peptides: The importance of electrostatic

interactions in coarse-gr ain ed water models, Z. Wu, Q. Cui

⇤

and A. Yethiraj

⇤

, J. Phys. Chem.

Lett. 2, 1794-1798 (2011)

141. Interconversion of Functional Motions between M es oph i li c and Thermophilic Adenylate Ki-

nases, M. Daily, G. N. Phillips, Jr., Q. Cui

⇤

, PLoS Comp. Biol. 7, e1002103 (2011)

140. Glu286 rotation and water wire reorientation are unlikely the gating elements f or proton

pumping in Cytochrome c oxidase, S. Yang and Q. Cui

⇤

, Biophys. J., 101, 61-69 (2011)

139. Application of the SCC-DFTB method to neutral and protonated water clusters and bulk

water, P. Goyal, M. Elstn er and Q. Cui

⇤

, J. Phys. Chem. B 115, 6790-6805 (2011)

138. Role of Arg82 in the early steps of the bacteriorh odopsin proton-pumping cycle, M. Clemens,

P. Phatak, Q. Cui, A. N. Bondar, M. Elstner

⇤

, J. Phys. Chem. B 115, 7129-7135 (2011)

137. DFTB-3

: Extension of the self-consistent-charge density-functional tight-binding method

SCC-DFTB, M . Gaus, Q. Cui and M. Elst n er

⇤

, J. Chem. Theo. Comp., 7, 931-948 (2011)

136. Theoretical Study of Bone Sialoprotein in Bone Biomineralization, Y. Yang, Q. Cui and N.

Sahai

⇤

, Cells, Tissues, Organs, 194, 182-187 (2011)

135. Disruption and formation of surface salt bridges are coupled to DNA binding in integration host

factor (IHF): a computational analysis, L. Ma, N. Sundlass, R. T. Raines and Q. Cui

⇤

, Biochem.,

50, 266-275 (2011)

134. Computational Studies of Enzyme Motions, Q. Cui

⇤

, Encyclopedia of Biophysics, Springer

(2010) p353-360 Invited Review [published in 2013]

133. Chemical v s. mechanical perturbations on the protonation state of Arginine in com ple x lipid

membranes: insights from microscopic pK

calculations, J. Yoo and Q. Cui

⇤

, Biophys. J. 99,

1529-1538 (2010)

132. Electronic properties and desolvation penalties of metal ions plus protein electrostatics di ct at e

the metal binding aﬃnity and selectivity in the Cop per e✏ux Regulator, L. Rao, Q. Cui

⇤

and X.

⇤

, J. Am. Chem. Soc. 132, 18092-18102 (2010)

131. Self-assembly of -peptides: insight from the pair and many-body free energy of association,

J. Mondal, X. Zhu, Q. Cui and A. Yethiraj

⇤

, J. Phys. Chem. C, 114, 13551- 13556 (2010)

130. Iron-Catalyzed Oxidation Intermediates Captured in A DNA Repair Monooxygenase, C. Yi,

G. Jia, G. Hou, Q. Dai, G. Zheng, X. Jian, C. G. Yang, Q. Cui, and C. He

⇤

, Nature, 468, 330-333

(2010)

129. An imp l ic i t solvent model for SCC-DFTB with Charge-Dependent Radii, G. Hou, X. Zhu and

Q. Cui

⇤

, J. Chem. Theo. Comp., 6, 2303-2314 (2010)

128. Evaluating Elastic Network Models of Crystalline Biological Molecules with Temperature

Factors, Correlated Motions, and Di↵use X-Ray Scattering, D. Riccardi

⇤

, Q. Cui and G. N. Phillips,

Jr.

⇤

Biophys. J., 99, 2616-2625 (2010)

127. Sequence-dependent interaction of -peptides with membranes, J. Mondal, X. Zhu, Q. Cui

and A. Yethiraj

⇤

, J. Phys. Chem. B, 14, 13585-13592 (2010)

126. QM/MM Alchemical free ene r gy simulations: Challenges and Recent Developments, W.

Yang

⇤

, Q. Cui, D. Min and H. Li, Annual Reports in Comput. Chem. 6, 51-62 Invited Review

(2010)

125. A new coarse-grained model for water: The importance of electrostatic interactions, Z. Wu,

Q. Cui

⇤

and A. Yethiraj

⇤

, J. Phys. Chem. B 114, 10524-10529 (2010)

124. How does bone sialoprotein promote the nucleation of hydroxyapatite? A molecular dynamics

study using model peptides of di↵erent conformations, Y. Yang, Q. Cui, and N. Sahai

⇤

, Langmuir,

26, 9848-9859 (2010)

123. Many low-barrier l ocal motions coop e rat e to produce the adenylate kinase conformational

transition, M. Daily, G. N. Phillips, Jr. and Q. Cui

⇤

, J. Mol. Biol., 400, 618-631 (2010)

122. Conservation and Variation of Structu r al Flexibility in Protein Families, A. W. Van Wynsberghe

⇤

Q. Cui

⇤

, Structure, 18, 281-283 (2010) Invited Commentary

121. Preferential interactions between small solutes and the protein backbone: A computational

analysis, L. Ma, L. Pegram, M. T. Record, Jr., Q. Cui

⇤

, Biochem., 49, 1954-1962 (2010)

120. Establishing e↵ective simulation protocols for - and ↵/-peptides. III. Molecular Mechanical

(MM) model for a n on -cy cl i c -residue, X. Zhu, P. K¨onig, M . Ho↵man, A. Yethiraj

⇤

and Q. Cui

⇤

J. Comp. Chem., 31, 2063-2077 (2010)

119. Proton Transfer Fun ct i on of Carbonic Anhydrase: Insights from QM/MM simulations, D.

Riccardi, S. Yang and Q. Cui

⇤

, BBA-Prot. & Proteomics, Invited special issue on “Carbonic

Anhydrase and Superoxide Dismutase”, 1804, 342-351 (2010)

118. Curvature Generation and Pressure Proﬁle in Membrane with lysolipids: In si ghts from coarse-

grained simulations, J. Yoo and Q. Cu i

⇤

, Biophys . J. 97, 2267-2276 (2009)

117. The hydrolysis activity of Adenosine trip hos ph at e in myosin: a theoretical analysis of anomeric

e↵ects and the nature of transi t i on state, Y. Yang

⇤

and Q. Cui

⇤

, J. Phys. Chem. A (R. M. Pitzer

Festschrift), 113, 12439-12446 (2009)

116. CHARMM: The biomolecular simulation program, B. R. Brooks, et al., Q. Cui, et al., M.

Karplus, J. Comp. Chem. 30, 1545-1614 (2009)

115. Multi-scale methods for the description of chemical events in biological systems, M. Elstner

⇤

and Q. Cui

⇤

, NIC (John von Neu man n Institut f¨ur Computing) series (2009) Invited Rev i ew

114. Does water relayed proton transfer play a role in phosphoryl transfer reactions? A theoretical

analysis of uridi ne 3’-m-nitrobenzyl phosphate isomerization in water and tert-butanol, Y. Yang

and Q. Cui

⇤

, J. Phys. Chem. B 113, 4930-4939 (2009)

113. Microscopic pK

analysis of Glu 286 in Cyto chrome c Oxidase (Rhodobacter sphaeroids):

towards a consiste nt molecular model, N. Ghosh, X. Prat-Resina, M. Gunner and Q. Cui

⇤

, Biochem.,

48, 2468-2485 (2009)

112. A combined continuum mechanics and continuum electrostatics (CM/CE) computational

framework for macromolecules: application to the salt concentration dependence of DNA bendabil-

ity, L. Ma, Y. Tang, A. Yethiraj, X. Chen

⇤

and Q. Cui

⇤

, Biophys . J. 96, 3543-3554 (2009)

111. Application of elastic network models to proteins in the crystalline state, D. Riccardi, Q. Cui

and G. Phillips, Jr.

⇤

Biophys. J. 96, 464-475 (2009)

110. Mechano chemical cou pl i ng in molecular motors: insights from molecular simulations of the

myosin motor domain, H. Yu, Y. Yang, L. Ma and Q. Cui

⇤

, Book Chapt er in “Proteins: Energy,

Heat and Signal Flow”, Eds. D. Lei t ne r and J. E. Straub, CRC Press (2009), p p23-46 Invited

Book Chapter

109. Description of phos ph at e hydrolysis reactions with the Self-Consistent-Charge Density-Functional-

Tight-Binding (SCC-DFTB ) theory. 1. Parameterization, Y. Yang, H. Yu, D. York, M. Elstn er

⇤

and Q. Cui

⇤

, J. Chem. Theo. Comp., 4, 2067-2084 (2008)

108. Computational Molecular Biomechanics: A Hierarchical Multiscale Framework with Applica-

tions to Gating of Mechanosensitive Channels of Large Conductance, X. Chen

⇤

&Q.Cui

⇤

,inTrends

in Computational NanoMechanics, Ed. T. Dumitrica, Springer Series: Challenges and Advances

in Computational Chemistry and Physics, (2008) Invited Book Chap ter

107. Mechanosensitive Channels: Insights from Continuum-Based Simulations, Y. Tang, J. Yoo,

A. Yethiraj, Q. Cui

⇤

and X. Chen

⇤

, Cell Biochem. & Biophys., 52, 1-18 (2008) Invited Review

106. Amino acids with an intermolecular proton bond as the proton storage site in bacteri-

orhodopsin, P. Phatak

‡

, N. Ghosh

‡

, H. Yu, Q. Cui

⇤

and M. Elstner

⇤

, Proc. Natl. Acad. Sci.

USA, 105, 19672-19677 (2008) [

‡

These author s contributed equally]

105. Extensive con format i on al changes are required to turn on ATP hydrolysis in myosin, Y. Yang,

H. Yu and Q. Cui

⇤

, J. Mol. Biol., 381, 1407-1420 (2008)

104. pK

of residue 66 in Staphylococal nuclease: insights from QM /MM simulations with conven-

tional sampl i n g, N. Ghosh, Q. Cui

⇤

, J. Phys. Chem. B, 112, 8387-8397 (2008) Cover

103. Gating Mechanisms of Mechanosensitive Channels of Large Conductance Part II: Systematic

Study of Conformation al Transitions , Y. Tang, J . Yoo, A. Yethiraj, Q. Cui and X. Chen

⇤

, Biophys.

J., 95, 581-596 (2008) Cover

102. G at in g Mechanisms of Mechanosensitive Channels of Large Conductance Part I: A Continuum

Mechanics-Based Hierarchical Framework, X. Chen

⇤

, Q. Cui, Y. Tang, J. Yoo and A. Yethiraj,

Biophys. J., 95, 563-580 (2008)

101. QM/MM and multi-scale methods for the simulation of bio chemical processes in complex

environments, Q. Cui

⇤

and M. Elstner

⇤

,inSolvation e↵ects on molecules and biomolecules: Com-

putational methods and applications, Ed. S. Canuto, Springer Series: Challenges and Advances in

Computational Chemistry and Physi cs , (2008) Invited Book Chapter

100. “Multi-scale” QM/MM methods with the Self-Consistent-Charge Density-Functional-Tight-

Binding (SCC-DFTB) Method, Q. Cui

⇤

and M. Elstner

⇤

,inMulti-scale Quantum Models for Bio-

catalysis, Eds. D. York, T. Lee (2008) Invited Book Chapter

99. Does Arg remain protonate d in the lipid membrane? Insights from microscopic pK

calcula-

tions, J. Yoo and Q. Cui

⇤

, Biophys . J. Lett, L61-L63 (2008)

98. Establishing e↵ective si mulation protocols for - and ↵/-peptides. II. Molecular Mechanical

(MM) model for a Cyclic -residue, X. Zhu, P. K¨onig, S. Gellman, A. Yethiraj

⇤

and Q. Cui

⇤

, J.

Phys. Chem. B, 112, 5439-5448 (2008)

97. Allostery and Cooperativity Rev i si t ed , Q. Cui

⇤

, M. Karplus

⇤

, Protein Sci., 17, 1295-1307 (2008)

96. Functional Motions in Biomolecules: Insights from Computational Studies at Multiple Scales,

A. W. van Wynsberghe, L. Ma, X. Chen and Q. Cui

⇤

,inComputational Structural Biology,Eds.

T. Schwede, M . Peitsch, pp253-298 World Scientifc (2008) Invited Book Chapter

95. Proton tran sf er in Carbonic Anhydrase is controlled by electrostatics rather than the or ie ntation

of the acceptor, D. Ricc ard i , P. K¨onig, H. Guo and Q. Cui

⇤

, Biochem., 47, 2369-2378 (2008)

94. Discovery and mechanistic study of Al

III

-catalyzed transamidation of tertiary amides, J. M.

Hoerter, K. M. Otte, S. H. Gellman

⇤

,Q.Cui

⇤

and S. S. Stahl

⇤

, J. Am. Chem. Soc., 130, 647-654

(2008)

93. The vibrational spectra of protonated water clusters: A benchmark for SCC-DFTB, H. Yu and

Q. Cui

⇤

, J. Chem. Phys., 127, 234504 (2007)

92. Improving t he Self-Consistent-Charge Tight-Binding-Density-Function al method for proton

aﬃnities and hydrogen bonding interactions, Y. Yang, H. Yu, D. York, Q. Cui

⇤

,M.Elstner

⇤

, J.

Phys. Chem. A, 111, 10861-10873 (2007)

91. Antibiotic Deactivation by a Dizinc beta-Lactamase: Mechanistic Insights from QM/MM and

DFT Stud ie s, D. Xu, H. Guo

⇤

and Q. Cui, J. Am. Chem. Soc., 129, 10814-10822 (2007)

90. The activation mechanism of a signaling protein at atomi c resolution from advanced computa-

tions, L. Ma, Q. Cui

⇤

, J. Am. Chem. Soc., 129, 10261-10268 (2007)

89. Numerical simulations of patch clamp and nanoindentation experiments on mechanosensitive

channels of large conductance, Y. Tang, X. Chen

⇤

, J. Yoo and A. Yethiraj, Q. Cui, J. Exp. Mech.

49, 35-46 (2009) [Published onl i ne : 3 Jul 2007]

88. Application of the computati onall y eﬃcient self-consistent-charge density-functional-tight-

binding method to Magne si um -containing molecules, Z. Cai, P. Lopez, J. R. Reimers, Q. Cui

and M. Elstner, J. Phys. Chem. A (DFTB Sympos i um issue) 111, 5743-5750 (2007)

87. pK

analysis for the zinc-bound water in Human Carbonic Anhydrase II: benchmark for “multi-

scale” QM/MM simulations and mechanistic implications, D. Riccardi, Q. Cui,

⇤

J. Phys. Chem.

A (DFTB Symposium Issue) 111, 5703-5711 (2007)

86. Antibiotic binding to metallo-be t a-l act amas e L1 from Stenotrophomonas maltophilia: SCC-

DFTB/CHARMM and DFT studies, D. Xu, H. Guo

⇤

and Q. Cui, J. Phys. Chem. A (DFTB

Symposium Issue), 111, 5630-5636 (2007)

85. Establishing e↵ective simulation p rot ocols for  and mixed ↵/ peptides, 1. QM and QM/MM

models, X. Zhu, A. Yethiraj

⇤

and Q. Cui

⇤

, J. Chem. Theo. Comp., 3, 1538-1549 (2007)

84. Interactions between Phosphate and Water in Solu t i on: A Natural Bond Orbital Based Analysis

in a QM/MM Framework, Y. Yang, Q. Cui

⇤

, J. Phys. Chem. B, 111, 3999-4002 (2007)

83. A speciﬁc reaction parameterization for the AM1/d Hamilt on i an for t r ans ph osp hor y l at ion

reactions, K. Nam, Q. Cu i, J. Gao, D. M. York

⇤

, J. Theo. Comp. Chem., 3, 486-504 ( 2007)

82. Mechanochemical coupling in myosin motor domain, II. Analysis of critical residues, H. Yu, L.

Ma, Y. Yang and Q. Cui

⇤

, PLoS Comput. Biol., 3, 0214 (2007)

81. Mechanochemical coupling in myosin motor domain, I . Equilibrium active site simulations, H.

Yu, L. Ma, Y. Yang and Q. Cu i

⇤

, PLoS Comput. Biol., 3, 0199 (2007)

80. Ti

-mediated reactions between primary amines and secondary carboxamides: Ami di n e for-

mation versus transamidation, D. A. Kissounko, J. M. Hoerter, I. A. Guzei, Q. Cui

⇤

, S. H. Gellman

⇤

S. S. Stahl,

⇤

J. Am. Chem. Soc., 129, 1776-1783 (2007)

79. Protein structural variation in computational models and crystallographic data, D. A. Kon-

drashov, A. W. Van Wynsberghe, R. M. Bannen, Q. Cui, G. N. Ph i l li p s, Jr.

⇤

, Structure, 15, 169-177

(2007)

78. “Proton holes” in long-range proton transfer reactions in solution and enzymes: A theoretical

analysis, D. Riccardi, P. K¨onig, X. Prat-Resina, H. Yu, M. Elstner, T. Frauenheim, Q. Cui

⇤

, J.

Am. Chem. Soc., 128, 16302-16311 (2006)

77. Temperature de pendenc e of local salt accumulation is sequence speciﬁc, L. Ma, Q. Cui

⇤

Biochem., 45, 14466-14472 (2006)

76. Interpretating correlated motions using normal mode analy s is , A. Van Wyn sberghe, Q. Cui,

⇤

Structure, 14, 1647-1653 (2006)

75. Optimization and eval uat ion of a coarse-grained model of p rot e in motion using X-ray crystal

data, D. A. Kondrashov, G. N. Phillips, Jr.

⇤

,Q.Cui,Biophys. J., 91, 2760-2767 (2006)

74. A ﬁnite element framework for studying mechanical response of macromolecules: Applicati on to

the gating of the mechanosensitive channel, MscL, Y. Tang, G. Cao, X. Chen

⇤

, J. Yoo, A. Yethiraj,

Q. Cui

⇤

, Biophys. J., 91, 1248-1263 (2006) Cover

73. E↵ects of Temperature and Salt Concentration on the Structural Stabil i ty of Human Ly mph o-

tactin: Ins ights from Molec ul ar Simulations, M. Formaneck, L. Ma, Q. Cui*, J. Am. Chem . Soc.,

128, 9506-9517 (2006)

72. The use of a generalized Born model for the analysi s of protein conformational transitions. A

comparative study with expli c it solvent simulations for chemotaxis Y Protein (CheY), M. Forma-

neck, Q. Cui*, J. Comput. Chem., 27, 1923-1943 (2006)

71. Development of e↵ective quantum mechanical/molecular mechanical (QM/MM) methods for

complex biological processes, D. Riccardi, P. Schaefer, Y. Yang, H. Yu, N. Ghosh, X. Prat-Resina,

P. Konig, G. Li, D. Xu, H. Guo, M. Elstner, an d Q. Cui*, J. Phys. Chem. B Feature Article, 110,

6458-6469 (2006) Cover

70. Reconciling the “old” an d “new” views of allosteric c onf orm at ion al transition in proteins. A

molecular simulation study of the chemotaxis protein Y (CheY), M. For man eck, L. Ma, Q. Cui*,

Protei ns : Structure, Genetics & Bioinform., 63, 846-867 (2006)

69. Theoretical analysis of mechanochemical coupling in myosin, Q. Cui*, Special Issue on “WA-

TOC2005: Modelling Molecular Structure and Reactivity in Biological Systems”, Royal Society

Chemistry, p66-75 (2006) Invited Conference Special Is s u e

68. Theoretical and computational studies of vectorial processes in biomolecules, Q. Cui*, Special

Issue on “New Perspectives in Theoretical Chemistry”, Theoretical Chemistry Accounts, 116, 51-59

(2006) Invited Perspective

67. Towards theore ti c al analysis of long-range proton transfer kinetics in biomolecul ar pumps, P.

Koenig, N. Ghosh, M . Ho↵man, M. Elstner, E. Tajkh or sh i d, Th. Frauenheim*, Q. Cui*, J. Phys.

Chem. A, D. G. Truhlar Festschrift, 110, 548-563 (2006)

66. Hydrogenation of Imines by Hydroxycyclopentadienyl Ruthenium Hydride: Intramolecular

Trapping Evidence for Hydride and Proton Transfer Outside the Coordination Sphere of the Metal ,

C. P. Casey*, G. A. Bikzhanova, Q. Cui, and I. A. Guze i , J. Am. Chem. Soc., 127, 14072-14071

(2005)

65. Comparisons of mode analyses at di↵erent resolutions applied to nucleic acid syst em s, A. Van

Wynsberghe, Q. Cui*, Biophys. J. , 89, 2939-2949 (2005) Cover

64. Direct determination of reaction path and saddle points on the potential of mean force surface,

G. Li, Q. Cui*, J. Mol. Graphics & Modelli ng, Special Issue for Prof. I. Hillier, 24, 82-93 (2005)

63. pK

Calculations in Solution and Proteins with QM/MM Free Energy Perturbation Simula-

tions: A quantitative test of Q M /M M protocol s, D. Riccardi, P. Schaefer, Q. Cui*, J. Phys. Chem.

B, 109, 17715-17733 (2005) Cover

62. Benchmark calculations of proton aﬃnities and gas phase basicities of molecules important in

the study of bi ologi c al phosphoryl transfer, K. Range, D. Riccardi, Q. C ui, M. Elstner and D. M.

York*, PhysChemChemPhys, 7, 3070-3079 (2005)

61. Reliable treatment of long-range electrostatics in combined QM/MM si mulation of macro-

molecules, P. Schaefer, D. Riccardi, Q. Cui*, J. Chem. Phys. 123, 014905 (2005)

60. A critical evaluation of di↵erent QM/MM frontier treatments using SCC-DFTB as the QM

method, P. Koenig, M. Ho↵man, Th. Frauenheim, Q. Cui*, J. Phys. Chem. B 109, 9082-9095

(2005)

59. Normal mode analysis of macromolecul es : from enzyme active site to molecular machines, G.

Li, A. van Wynsberghe, O. N. A. Demerdash, Q. Cui*, In Normal Mode Analysis: Theory and

Applications to Biological and Chemical Systems, Eds. Q. Cui, I. Bahar, CRC Press (2005)

58. Hydrogen elimination from a hydroxycyclopentadienyl Ruthenium (II) hydride: study of hydro-

gen activation in a ligand-metal bifunction al hydrogenation catalyst, C. P. Casey*, J. B. Johnson,

S. W. Singer and Q. Cui

⇤

, J. Am. Chem. Soc. 127, 3100-3109 (2005)

57. QM/MM Studies of Enzyme Catalyzed Dechlorination of 4-Chlorobenzoyl-CoA and Their

Implications to Kinetic M odel, D. Xu, Y. Wei, J. Wu, D. Du naway-Mariano and H. Guo*, Q. Cui,

J. Gao, J. Am. Ch em. Soc. 126, 13649-13658 (2004)

56. Normal mode analysis suggests protein ﬂex ib i l ity modulation throughout RNA polymerase’s

Functional cycle, A. van Wynsberghe, G. Li, Q. Cui*, Biochem . 43, 13083-13096 (2004)

55. Th e importance of van der Waals interactions in QM/MM simulations, D. Riccardi, G. Li, Q.

Cui*, J. Phys. Chem. B 108, 6467-6478 (2004)

54. A normal mode an aly s is of structural plasticity in the biomolecular motor F

-ATPase, Q. Cui *,

G. Li, J. Ma, M. Karplus, J. Mol. Biol., 340, 345-372 (2004)

53. Formation of the Meisenheimer complex in a nucleophilic aromatic substitution reaction cat-

alyzed by 4-chlorobenzoyl-CoA dehalogenase, A QM/MM study, D. Xu , H. Guo*, J. Gao and Q.

Cui, Chem. Comm. 7, 892-893 (2004)

52. Mechanochemical coupling i n myosin. A theoretical analysis of ATP hydrolysis with molecular

dynamics and combined QM/MM reaction path calcu l at i ons , G. Li, Q. Cui*, J. Phys. Chem. B ,

108, 3342-3357 (2004)

51. Analysis of the functional motions in “Brownian molecular machines” with an eﬃcient block

normal mode approach, G. Li, Q. Cui*, B io phys . J. 86, 743-763 (2004)

50. pK

calculations with QM/MM free energy perturbations, G. Li, Q. Cui*, J. Phys. Chem. B,

107, 14521-14528 (2003)

49. What i s so special about Arg 55 in the catalysis of cyclophilin A? Insights from hybrid QM/MM

simulations, G. Li, Q. Cui*, J. Am. Chem. Soc. 125, 15028-15038 (2003)

48. Free energy perturbation calculations with combined QM/MM potentials - com pl i cat i on s,

simpliﬁcations and applications to redox potential calculations, G. Li, X. Zhang, Q. Cui*, J. Phys .

Chem. B 107, 8643-8653 (2003)

47. Catalysis and speciﬁcity in enzymes: A study of triosephosphate isomerase (TIM) and com-

parison with methylglyoxal synthase (MGS), Q. Cui *, M. Karplu s*, Adv. Prot. C hem . 66, 315-372

(2003) Invited Review

46. The missing link between thermodynamics and structures in F

-ATPase, W. Yang, Y. Gao, Q.

Cui, J. Ma, and M. Karplus*, Proc. Na tl. Acad. Sci. USA, 100, 874 (2003)

45. Kinetic is ot ope e↵ec t s for concerted multiple proton transfe r: A direct dynamics s t ud y of an

active-site model of carbonic anhydrase, Z. Smedarchina*, W. Siebrand, A. Fernandez-Ramos, Q.

Cui*, J. Am. Chem. Soc., 125, 243-251 (2003)

44. The functional speciﬁcities of Methylglyoxal Synthase (MGS) and Triosephosphate Is omer ase

(TIM): A combined QM/MM analysis, X. Zhang, D. H. T. Harrison, Q. Cui*, J. Am. Chem. Soc.

124, 14871-14878 (2002)

43. Combining implicit solvation models with hybrid quantum mechanical/molecular mechanical

methods: A cri t i cal test with glycine, Q. Cui*, J. Chem. Phys., 117, 4720-4728 (2002)

42. A coarse-grained normal mode approach for macromolecules: An eﬃcient implementation and

application to Ca

-ATPase, G. Li, Q. Cui*, Biophys. J. 83, 2457-2474 (2002)

41. Calculat in g accurat e r ed ox potentials in enzymes with a combined QM/MM free en er gy per-

turbation approach, M. S. Formaneck, G. Li , X. Zhang, Q. Cui*, J. Theo. Comput. Chem. 1,

53-68 (2002)

Postdoctoral, Harvard (1998-2001)

40. Underst and i ng the role of acti ve-site r e si du es i n chorismate mutase cataly si s fr om molec ul ar -

dynamics simulations, H. Guo, Q. Cui, W. N. Lipscomb, M. Karplus, Angew. Chim. Intl. Ed. 42,

1508-1511 (2003)

39. Molecular dynamics simulations of yeast chorismate mutase: substrate conformational transi-

tions and enzymatic c at al ys i s, H. Guo, W. N. Lipscomb, Q. Cui and M. Karplus, NATO Sci. Ser.

I 364, 63-74 (2005)

38. Modeling zinc in biomolecules with the Self Consistent Charge Density Functi on al Tight Binding

(SCC-DFTB) method: appli cat i ons to stru ct u ral and energe ti c al analy si s , M. Elstner, Q. Cui, P.

Munih, E . Kaxiras, T. Frauenheim, M. Karplus, J. Compt. Chem. 24, 565-581 (2003)

37. Is proton-wire concerted or step-wise? A model stud y of proton transfe r in carbonic anhydrase,

Q. Cui, M. Karplus, J. Phys. Chem. B, 107, 1071-1078 (2003)

36. Combining ab i n i t io and density functional theory with semi-empirical methods, Q. Cu i , H.

Guo, M. Karplus, J. Chem. Phys., 117, 5617-5631 (2002)

35. Promoting m odes and demoting modes in enzyme catalyzed proton tr ans fe r reactions: A study

of models and realistic system s, Q. Cui, M. Karplus, J. Phys. Chem. B, 106, 7929-7947 (2002)

34. A dynamic analysis of the rotation mechanism for conformational change i n F

-ATPase, J. Ma,

T. C. Flynn, Q. Cui, A. Leslie, J . E. Walker, and M. K arp l us , Structure, 10, 921-931 ( 2002)

33. A theoretical analysis of the proton and hydride transfer in Liver Alcohol Dehydrogenase

(LADH), Q. Cui, M. El st n er , M. Karplus, J. Phys. Chem. B 106, 2721-2740 (2002)

32. QM/MM Studies of the Triosephosphate isomerase (TIM) Catalyzed Reactions: The e↵e ct of

geometry and tunneling on proton transfer rate c ons t ants, Q. Cui, M . Karplus, J. Am. Chem. Soc.

124, 3093-3124 (2002)

31. QM/MM Studies of the Triosephosphat e Isomerase ( TIM ) Catalyzed Reactions: Veriﬁcation

of Methodology and Analysis of the Reaction Mechanisms, Q. Cui, M. Karplus, J. Phys . Chem. B

106, 1768-1798 (2002)

30. Substrate conformational transitions in the active site of chorismate mutase: Their role in the

catalytic mechanism? H. Guo, Q. Cui , W. N. Lipscomb and M. Karplus, Proc. Natl. Acad. Sci.

USA 98, 9032-9037 (2001)

29. A QM/MM implementation of the Self-Consist ent-Charge Density Functional Tight Binding

(SCC-DFTB) method, Q. Cui, M. Elstner, E. Kaxiras, T. Frauenheim and M. Karplus, J. Phys.

Chem. B 105, 569-585 (2001)

28. Triosephosphate isomerase (TIM) : A theoret ic al comparison of al t e rn at i ve pathways, Q. Cui,

M. Karplu s, J. Am. Chem. Soc. 122, 2284-2290 (2001)

27. Molecular Properties from combined QM/MM methods. II. Chemic al shifts in large molecules,

Q. Cui, M. Karplus, J. Phys. Chem. B 104, 3721-3743 (2000)

26. Molecular Properties from combined QM/MM methods. I. Analytical second derivative and

vibrational calculations, Q. Cui, M. Karplus, J. Chem. Phys. 112, 1133-1149 (2000)

Graduate School, Emory (1993-1997)

25. Ab initi o th eor et i cal s t ud i es on phot odissociation of HNCO upon S

(

A)!S

(

A) excitation:

The role of internal conversion and intersystem crossing, A. Klaiden, Q. Cui, M. C. Heaven, K.

Morokuma, J. Chem. Phys. 111, 5004-5016 (1999)

24. The spin -f or bi dde n reacti on CH(

⇧)+N

revisited. II. Non-adiabatic transition state theory

and application, Q. Cui, K. Morokuma and J. M. B owman, S. J. Klippenstein, J. Chem. Phys.

110, 9469-9482 (1999)

23. The spin-forbidden react i on CH(

⇧)+N

revisited. I. Ab initi o studies, Q. Cui and K. Mo-

rokuma, Theor. Chem . Acct. (Fuku i Issue), 102, 127-133 (1999)

22. Theoretical studies of the N

Cleavage by Three-Coordinated Group VI complexes ML

,D.G.

Musaev, Q. Cui, M. Svensson and K. Morokuma, ACS Symposium Series, 721, 198-207 (1998)

21. Potential energy surfaces and their dynamic al implications Non- adi ab ati c transition state

theory and ion-molecule reactions, K. Morokuma, Q. Cui and Z. Liu, Faraday Discussion, 110,

71-89 (1998)

20. Molecular orbital study of H

and CH

activation on small metal cluste r s. II. Pt

and Pd

,Q.

Cui, D. G. Musaev, K . Morokuma, J. Phys. Chem. 102, 6373-6384 (1998)

19. Theoretical stu dy on the mechanism of CH

reaction: Mode enhancement e↵ect, Q.

Cui, Z. Liu, K. Morokum a, J. Chem. Phys. 109, 56-62 (1998)

18. Molecular orbital study of H

and CH

activation on small metal clusters. I. Pt, Pd, Pt

and

, Q. Cui, D. G. Musaev, K. Morok um a, J. Chem. Phys. 108, 8418-8428 (1998)

17. Density functional study on the mechanisms of palladium(0)-catalyzed thioboration reaction of

alkynes : di↵erenc es betwee n Pd(0) and Pt(0) catalysts and between thiob orat i on and diborat ion ,

Q. Cui, D. G. Musaev , K. Morokuma, Organometallics, 17, 1383-1392 (1998)

16. Ab initio studies on the electronic excited states and photodissociation of O



,Q.Cui,K.

Morokuma, J. Chem. Phys. 108, 7684-7694 (1998)

15. Ab initio calc ul at i on s on the reaction of C

cation and NH

. Eﬃcient Charge Transfer

and P rot on transfer processes competing wi t h stable complex formation, Q. Cui, K . Morokuma, J.

Chem. Phys. 108, 4021-4030 (1998)

14. Ab initio calculation on the excited states of Cl

. A. Klaiden, W. Lawrence, M. Heaven and

Q. Cui, J. Stevens, K. Morokuma. J. Chem. Phys. 108, 2771-2783 (1998)

13. Theoretical study of the spin-allowed and spin-forb i dd en processes in the reaction of C

I+O(

P).

J. Stevens, Q. Cui, K. Morokuma, J. Chem. Phys. 108, 1544-1551 (1998)

12. Th eor et i cal study of the mechanism of HNCO photodissociation S

state, J. Stevens, Q. Cui,

K. Morokum a, J. Chem. Phys. 108, 1452-1458 (1998)

11. Ab initio molecular orbital studies on the structure, energies, and photodissociation of the

electronic excited states of C

H. Q. Cui, K. Morokuma , J. Chem. Phys. 108, 626-636 (1998)

10. Why Do Pt(PR

)

complexes catalyze the alkyne diboration reaction, but its Pd(0) analog

does not ? A density functional study, Q. Cui, D. G. Mu sae v , K. Morokuma, O rganometallics, 17,

742-751 (1998)

9. Ab initio study of non-adiabatic interactions in the photodissociation of ketene, Q. Cui, K.

Morokuma, J. Chem. Phys. 107, 4951-4959 (1997)

8. Ab initio MO studies on the photodissociation of C

from the S

(

) state II. Mechanism

involving triplet states, Q. Cui, K. Morokuma, Chem. Phys. Lett. 272, 319-327 (1997)

7. Molecu l ar orbital study of the mechanism of Platinum(0)-catalyzed alkene and al k y ne diboration

reaction, Q. Cui, D. G. Musaev, K. Morokuma, Organometallics , 16, 1355-1364 (1997)

6. Ab initio MO studies on the photodissociation of methoxy family CX

Y (X=H, F; Y=O, S)

from the

state, Q. Cui, K. Mor ok um a, Chem. Phys. Lett. 263, 54-62 (1996)

5. Ab initio MO studies on the photodissociation of C

.from the S

(

) state: Non-adiabatic

e↵ects and S-T interaction, Q. Cui, K. Morokuma, J. F. Stanton, Chem. Phys. Lett. 263, 46-53

(1996)

4. Infrared S pectros cop i c Characterization of Cyanmocuprates, H. Huang, K. Alvarez, Q. Cui, T.

M. Barnhart, J. P. Snyder, and J. E. Penner-Hahn, J. Am. Chem. Soc. 118, 8808-8816 (1996)

[Correction: 118, 12252 (1996)]

3. Ab init i o molecular orbital study of the mechanism of photodissociation of trans-azomethane,

R. Liu, Q. Cui, K. Morokuma, J. Chem. Phys. 105, 2333-2345 (1996)

2. Analytical second derivatives for E↵e ct i ve Core Potential. Application to the stu d y of Cp

(µ-

, and mechanism of the reaction Cu+CH

, Q. Cui, D. G. Musaev, M. Svensson, K. Morokuma,

J. Phys. Chem. 100, 10936-10944 (1996)

1. N

cleavage by three-c oordinate group 6 complexes: W(III) complexes would be better than

Mo(III) complexes, Q. Cui, D. G. Musaev, M. Svensson and K. Morokuma, J. Am. Chem. Soc.

Comm. 117, 12366-12367 (1995)