Józef Adam Liwo CURRICULUM VITAE

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1 Józef Adam Liwo CURRICULUM VITAE Current positions: Full Professor and Head of Laboratory of Molecular Modeling, Faculty of Chemistry, University of Gdańsk, Gdańsk, Poland. KIAS Scholar, Korea Institute for Advanced Study, Seoul, Rep. of Korea. Primary office address: Room B325, Faculty of Chemistry, University of Gdańsk, Poland, phone: , fax: , Citizenship: Poland Languages: Polish (mother tongue), English (fluent), German (good), Russian (good), Spanish (good), Mandarin Chinese (good), Korean (basic), French (basic), Latin (basic). Education, scientific degrees and titles: Training: 2001: Professor of Chemical Sciences (title received from the President of the Republic of Poland after approval by the Central Committee for Scientific Degrees and Titles). 1997: DSc (habilitation) (Physical and Theoretical Chemistry) Faculty of Chemistry, University of Gdańsk, Poland. 1989: PhD (Physical and Theoretical Chemistry) Faculty of Mathematics, Physics, and Chemistry Chemistry, University of Gdańsk, Poland. 1983: MSc (Chemistry, with honors) Faculty of Mathematics, Physics, and Chemistry, University of Gdańsk, Poland. The curriculum included extended program in math , 1994, Postdoctoral Associate, Department of Chemistry and Chemical Biology, Cornell University (supervisor: H.A. Scheraga). Employment: 1983-present Faculty of Chemistry, University of Gdańsk; tenured full professor since 2001; member of the Faculty Council since 1997; director of the Laboratory of Molecular Modeling since present: Korea Institute for Advanced Study (KIAS), Seoul, Republic of Korea; KIAS Scholar Senior Research Associate, Dep. of Chemistry and Chemical Biology, Cornell University (H.A. Scheraga group) Vice-Director for Scientific Affairs, Academic Computer Center in Gdańsk, TASK. Short-term employment: 09/2015 Department of Physics, Beijing Institute of Technology, Beijing, P.R. China, Visiting Professor. 1

2 05/2012 and 07/2012 Department of Physics and Astronomy, Uppsala University, Uppsala, Sweden, Visiting Scientist (A. Niemi group) month employment as a Visiting Scientists, Cornell University, U.S.A. (Scheraga group) /1995 Mt. Sinai School of Medicine, New York, N.Y., U.S.A., Visiting Scientist (S. Rackovsky group) /1994 SUNY Upstate Medical University, Visiting Scientist (M. Pincus group). Organizational activity: 1998-present Member of the Interdisciplinary Team of Mathematical Modeling at the Academic Computer Center in Gdańsk, TASK Co-organizer of the 1 st Polish-Korean Conference on Protein Folding: Theoretical and Experimental Approaches, Korea Institute for Advanced Study, Seoul, Republic of Korea (with J. Lee and C. Czaplewski) Co-organizer of the 2014 Workshop: From Computational Biophysics to System Biology (CBSB 14) in Gdańsk, Poland (with U.H.E. Hansmann and C. Czaplewski) Organizer of the Summer School on Parallel Computing in Biomolecular Simulations and Summer School of Parallel Programming at the Technical University of Gdańsk, Poland Co-organizer of the International Conference on Conformation of Peptides, Proteins and Nucleic Acids, Debrzyno 2000, Debrzyno near Gdańsk, Poland (with J. Ciarkowski and S. Ołdziej) President of the Scientific Council of the Academic Computer Center in Gdańsk, TASK. Professional Memberships: 2008-present: Member of the American Chemical Society present: Member of the Biophysical Society present: Member of the Polish Chemical Society present: Member of the Scienfitic Society of Gdańsk prsent: Member of the Polish Society of Computer Simulation Member of the Committee of Biochemistry and Biophysics of the Polish Academy of Sciences. Honors and Awards: 2015 Travel Award from Biophysical Society (presented on 59 th National Biophysical Societ Meeting in Baltimore) 2013 Mistrz (Master) subsidy for distinguished professors from the Foundation from Polish Science. 2013, 2006, 1999, award from the Rector of the University of Gdansk for distinguished research Elected a member of the Committee of Biochemistry and Biophysics of the Polish Academy of Sciences. 2

3 Publications: 2001, 1995, Award as a team member from the Polish Minister of Education; 1998 individual award from the Polish Minister of Education. 221 original papers and 10 review articles (38 in the last five years) in ISI journals. 6 original papers and 2 review articles in non-isi journals. 9 book chapters. Editor of 1 book. Number of citations excluding self-citations: 3,727. H-index: 37. Three representative publications are the following: 1. Y. He, M. Maciejczyk, S. Ołdziej, H.A. Scheraga, A. Liwo, Mean-field Interactions between nucleic-acid-base dipoles can drive the formation of a double helix, Phys. Rev. Lett., 2013, 110, (corresponding author; paper cited 20 times). 2. E. Gołaś, G.G. Maisuradze, P. Senet, S. Ołdziej, C. Czaplewski, H.A. Scheraga, A. Liwo. Simulation of the opening and closing of Hsp70 chaperones by coarse-grained molecular dynamics, J. Chem.Theory Comput., 2012, 8, (corresponding author; paper cited 15 times). 3. A. Liwo, M. Khalili, H.A. Scheraga. Ab initio simulations of protein-folding pathways by molecular dynamics with the united-residue model of polypeptide chains. Proc. Natl. Acad. Sci. U.S.A., 2005, 102, (cited 169 times). Current research: The goal of my research is to understand how intra- and inter-molecular interactions make a given biomolecular system attain its unique structure and perform a given biological action. I use the coarse-graining approach for this purpose, in which interactions are treated at the sitesite rather than detailed atomistic level. I developed a theory, which is based on the clustercumulant expansion of the potential of mean force of a given system, which enables us to construct a physics-based simplified effective energy function (as opposed to most of other successful coarse-grained force fields which are based on statistical data from proteinstructure databases). For proteins, the theory resulted in the development of the UNRES force field for the simulation of protein structure and dynamics; this approach performs very well in the CASP experiments of blind prediction of protein structure. The UNRES approach provides a tremendous increase in the time- and size-scale of simulated systems; for example, a the functionally-important motions of a 600-residue Hsp70 chaperone has been simulated in a week of wall-clock time with 2048 processors of IBM BlueGene/P. Very recently, I extended the approach with success to construct similar coarse-grained force fields for nucleic acids (NARES-2P) and polysaccharides (SUGRES-1P). All three models are now being merged into the Unified Coarse Grained Model of biological macromolecules. Current research support (with role as PI): Polish National Science Center (NCN): (i) UMO-2012/06/A/ST4/ /15/13-03/14/18, A unified coarse-grained model of biological macromolecules based on mean-field multipole-multipole interactions, total budget: 1,071,480 PLN (appr. $325,000). 3

4 (ii) UMO-2013/10/M/ST4/ /24/ /23/2017, An integrated approach to the prediction of the structures of proteins and protein complexes with the use of the coarse-grained UNRES force field and utilizing the information from structural data bases, total budget: 694,678 PLN (appr. $211,000). Foundation for Polish Science, Mistrz7./2013 (a subsidy for distinguished professors), A unified coarse-grained model of biological macromolecules based on mean-field multipole-multipole interactions with extension to multiscale treatment, total budget: 300,000 PLN (appr. $91,000). Collaborators: Harold A. Scheraga (Cornell University, U.S.A.), Jooyoung Lee (Korea Institute for Advanced Study, Seoul, Rep. of Korea), Stan Ołdziej (Univ. of Gdańsk and Medical Univ. of Gdańsk, Poland). Silvia Crivelli (NIH, U.S.A.), Michela Taufer (Delaware Univ., U.S.A), Andrzej Kloczkowski (Nationwide Childrens Hospital, Columbus, U.S.A.), Antti J. Niemi (Uppsala University, Sweden, University of Tours, France, and Beijing Institute of Technology, P.R. China), Yi Xiao (Huazhong University of Science and Technology, Wuhan, P.R. China), U.H.E. Hansmann (University of Oklahoma, U.S.A.), Maciej Kozak (Adam Mickiewicz University, Poznan, Poland). Teaching: Courses taught at present (Faculty of Chemistry, University of Gdansk): Theoretical Chemistry Level 2 (lectures and recitation classes; course director). This course includes the basics of analysis of the energy hypersurfaces of molecular systems, molecular mechanics and dynamics, basic concepts of force fields, normalmode analysis, statistical mechanics, including the calculation of thermodynamic functions of systems of non-interacting polyatomic molecules and calculation equilibrium constants of gas-phase reactions from the first principles. Numerical Methods and Data Analysis in Chemistry (lab classes, a course for advanced students). This course includes interpolation, numerical differentiation, numerical integration, numerical algorithms of linear algebra, solving nonlinear equations and systems of nonlinear equations, local and global optimization, and numerical solution of differential equations. Protein Structure and Energetics (lectures; a course for graduate students and advanced undergraduate students, also taught in September 2015 at Beijing Institute of Technology, P.R. China; course director). The scope of this course includes the description of protein structure at various levels, protein energy landscapes, principles of foldability, and basics of force fields and simulation methods. Molecular Simulations in Chemistry (lectures; a course for graduate students and advanced undergraduate students; course director). The scope of this course includes Monte Carlo and molecular dynamics techniques and their extensions including replica-exchange and multicanonical sampling, computing structural, mechanical, and thermodynamic quantities from simulation results, and all-atom and coarse-grained force fields developed to treat biological macromolecules. 4

5 Programming with Ansi C and FORTRAN (lab classes, a course for advanced students). This is a two-level course in which the students are taught the basics of programming languages and programming in ansi C and, subsequently, programming in FORTRAN 77 and higher versions of FORTRAN. The course is designed for future developers of computational chemistry and chemoinformatics software, where FORTRAN still remains a programming language of considerable use. Courses taught in the past (Faculty of Chemistry, University of Gdansk): Basic Chemistry (recitation and lab classes), Inorganic Chemistry (recitation and lab classes), Physical Chemistry (recitation classes), Molecular Modeling (lectures and lab classes; course director), Data Analysis in Chemistry (lectures and recitation classes; course director), Informatics and Chemistry (lectures and lab classes; course director). Mentoring: Currently: 2 postdocs, 3 graduate students, 2 undergraduate students. Previously: 1 postdoc (completed the assignment in September, 2015), 10 graduate students who successfully completed their curriculum and received Ph.D. degrees, and 10 undergraduate students. 5