Chemistry is the called the central science because it not only impacts virtually all fields of science and technology but also because it is a central contributor to the modern life that society enjoys. The PhD Program in Chemistry at the City University of New York (CUNY) provides students with a strong foundation in all areas of chemistry: analytical, biological, inorganic, materials, nano, organic, polymer, and physical.

Chemistry

Research Areas

• Analytical Chemistry • Inorganic Chemistry • Organometallic Chemistry • Biochemistry • Materials Chemistry • Polymer Chemistry • Biophysics • Medicinal Chemistry • Photochemistry • Chemical Biology • Nanoscience • Physical Chemistry • Computational Chemistry • Organic Chemistry • Radiochemistry

CUNY  Chemistry        •  Diverse  faculty        •  100+  faculty  mentors        •  250  papers  per  year    Interdisciplinary  efforts        •  Molecular  biophysics        •  Radiochemistry        •  Nanotechnology        •  Photonics        •  Medicinal  chemistry  

CUNY prides itself on the diversity of its faculty and students. Each student choses a research mentor from over 100 members of the CUNY doctoral faculty in Chemistry. These mentors are distributed among seven CUNY campuses and the CUNY Advanced Science Research Center that fosters interdisciplinary interactions. A flexible curriculum allows each student to personalize the coursework to their specific needs. Additional training in professionalism, safety, pedagogy, and career opportunities are provided to ensure your career success.

All students admitted to the PhD Program in Chemistry are awarded a CUNY Science Scholarship. This five-year award allows our student to concentrate on their research. CUNY Science Scholars spend the first year at the CUNY Graduate Center taking courses and learning about the research opportunities available to them. There is no teaching in year one. Students select a mentor and move to their mentors campus by the end of year one.

CUNY Science Scholars

Student comments The   chemistry   Ph.D  program  at   CUNY  has   allowed  me   to   pursue  my   interest.   I   have   greatly  benefited  from  my  experience  with  my  mentor,  professors  and  fellow  students.  

     Zhantong Mao (PhD 2015)   CUNY   is   dense   with   fantasLc   faculty,   administrators   and   fellow   students   that   collecLvely  engender  a  strong  likelihood  of  success.  

       Douglas Achan (PhD 2015)

CUNY Science Scholarship • five year support package • competitive stipend • low-cost health insurance • tuition remission

Years 2-5 are spent at a CUNY campus focused on their dissertation research and perhaps teaching.

CUNY offers s tudents the opportunity to do cutting-edge chemical research in a supportive program that has the feel of a small college while living in one of the world’s most dynamic cities. The PhD Program in Chemistry is unique amongst its peers in that it is a consor t ium of seven campuses throughout New York City. While all student receive their degree from the CUNY Graduate Center, they do their research at one of the CUNY colleges or the Advanced Science Research Center. The size of CUNY offers the resources to do world-class science while working at a campus with a small college feel.

World-Class Science + Intimate Setting

Research Centers The   jewel   in  the  crown  of  CUNY’s  mulL-­‐billion  dollar   investment   in   interdisciplinary  scienLfic  research   is   the   CUNY   Advanced   Science   Research   Center   (hTp://asrc.cuny.edu).     Brimming  with   state-­‐of-­‐the-­‐art   instrumentaLon   and   experLse   in   nanoscience,   structural   biology,  photonics,   environmental   science,   and   neuroscience,   it   is   open   to   all   CUNY   students   and  faculty.     This   collaboraLve   resource   augments   the   resources   and   instrumentaLon   found   on  each   of   the   CUNY   campuses.     In   addiLon,   students   further   their   research   efforts   using   the  CUNY  High  Performance  CompuLng  Center  (hTp://www.csi.cuny.edu/cunyhpc/).

Participating Colleges • Brooklyn College • City College of New York • College of Staten Island • Hunter College • Lehman College • Queens College • York College

Publications A.  Glantz,   S.T.,   Carpenter,   E.J.Melkonian,  

M.,  Gardner,  K.H.,  Boyden,  E.S.,  Wong,  G.   K-­‐S.,   Chow,   B.Y.   Proceedings   of   the  NaLonal   Academy   of   Sciences,   USA,  2016,    113,  E1442-­‐E1451.  

B.  ChaTerjee,  S.,  Matas,  A.J.,   Isaacson,  T.,  Kehlet,  C.,  Rose,  J.K.C.,  Stark,  R.E.  Solid-­‐state   13C   NMR   del ineates   the  architectural   design   of   biopolymers   in  naLve   and   geneLcally   altered   tomato  fruit  cuLcles  Biomacromolecules,  2016,    17,  pp.  215-­‐224  

C.  Perea,  W.,  Schroeder,  K.T.,  Bryant,  A.N.,  Greenbaum,   N.L.   InteracLon   between  the  Spliceosomal  Pre-­‐mRNA  Branch  Site  a n d   U 2   s n R N P   P r o t e i n   p 1 4  Biochemistry,   2016,   55   (4),   pp.  629-­‐632.  

Research Areas • Biophysical mechanisms of ligand binding • Protein NMR • Structural Biology • Computational biophysical chemistry • Neutron scattering • Enzymology • X-ray Crystallography • Biotechnology

Molecular Biophysics seeks to understand essential biological processes in terms of physical chemistry. CUNY has over 30 faculty working in this area. Research interests include the mechanisms of signal transduction in cells, protein dynamics by neutron scattering and NMR, experimental and computational analysis of membrane protein structure and dynamics, and protein design. Students are encouraged to contact an individual faculty member to explore different research opportunities.

Molecular Biophysics Prof. Ruth Stark, Subdiscipline Chair rstark@ccny.cuny.edu  

Zimei Bu Associate Professor The City College of New York 160 Convent Avenue New York, NY 10031 zbu@ccny.cuny.edu http://www.sci.ccny.cuny.edu/~zbu/

Publications Phosphatidylinositol 4,5-Bisphosphate Clusters the Cell Adhesion Molecule CD44 and Assembles a Specific CD44-Ezrin Heterocomplex, as Revealed by Small Angle Neutron Scattering., Chen X, Ali Khajeh J, Ju JH, Gupta YK, Stanley CB, Do C, Heller WT, Aggarwal AK, Callaway DJ, Bu Z, J Biol Chem. 2015; 290(10):6639-52. Molecular conformation of the full-length tumor suppressor NF2/Merlin - a small angle neutron scattering study. Ali Khajeh, J., Ju, J., Atchiba, M., Allaire,M., Stanley, C., Heller, W.T., Callaway, D.J., Bu, Z., J Mol Biol. 2014 Jul 29;426(15):2755-68. Ligand-induced dynamic changes in extended PDZ domains from NHERF1., Bhattacharya S, Ju JH, Orlova N, Khajeh JA, Cowburn D, Bu Z., J Mol Biol. 2013 Jul 24;425(14):2509-28. Open Con fo rma t i on o f Ez r i n Bound to Phosphatidylinositol 4,5-Bisphosphate and to F-actin Revealed by Neutron Scattering, Jayasundar JJ, Ju JH, He L, Liu D, Meilleur F, Zhao J, Callaway DJ, Bu Z., J. Bio. Chem. 287:37119-33, 2012 Activation of nanoscale allosteric protein domain motion revealed by neutron spin echo spectroscopy. Farago, B., Li, J., Cornilescu, G., Callaway, D.J.E., Bu, Z., Biophys J. 99:3473-82, 2010 Research Interests

Keywords: Cell signaling, cell adhesion, intracellular trafficking of membrane receptors, neutron scattering, protein dynamics Research Projects include: 1.  Structure, dynamics, and assembly of transmembrane cell adhesion molecules and receptors; 2.  Protein-lipid interactions; 3.  How intracellular adapter proteins influence the trafficking, assembly and function of transmembrane

receptors; 4.  Small angle X-ray and neutron scattering; 5.  Quasielastic neutron scattering, neutron spin echo spectroscopy.

is a molecular biophysicist at City College

Dr. Zimei Bu

Emilio Gallicchio Assistant Professor Department of Chemistry, Brooklyn College 2900 Bedford Avenue Brooklyn, NY egallicchio@brooklyn.cuny.edu sites.google.com/site/emiliogallicchiolab

Publications Emilio Gallicchio, et al. BEDAM Binding Free Energy Predictions for the SAMPL4 Octa-Acid Host Challenge. J. Comp. Aided Mol. Des.  29, 315-325 (2015). Emilio Gallicchio, et al. Virtual Screening of Integrase Inhibitors by Large Scale Binding Free Energy Calculations: the SAMPL4 Challenge. J Comp Aided Mol Design, 28, 475-490 (2014). Guohua Yi, Mauro Lapelosa, Emilio Gallicchio, Gail Ferstandig Arnold et al. Chimeric Rhinoviruses Displaying MPER Epitopes Elicit Anti-HIV Neutralizing Responses. PLoS ONE 8(9), e72205 (2013). Gallicchio E. Role of Ligand Reorganization and Conformational Restraints on the Binding Free Energies of DAPY Non-Nucleoside Inhibitors to HIV Reverse Transcriptase. Computational Molecular Bioscience, 2, 7-22 (2012).

Research Interests - Thermodynamics of protein-protein and protein-ligand binding - Virtual drug screening -  Protein conformational equilibria - Statistical thermodynamics of protein folding and misfolding - Thermodynamics of solvation of biological macromolecules - Force field development and high resolution protein modeling - Design of high performance computational chemistry algorithms - Parallel and distributed computing

Emilio Gallicchio’s research is in the area of computational molecular biophysics. He uses advanced computational models to investigate the dynamics and thermodynamics of biological systems.

2013- current Asst. Professor, Dept. Chemistry, Brooklyn College 2012-2013 Research Professor, Dept. Chemistry, Rutgers University 2001-2012 Associate Director, BioMaPS Institute, Rutgers University 1997-2000 Postdoctoral, Rutgers University 1991-1996 PhD Columbia University, Chemical Physics

Dr. Emilio Gallicchio

Kevin H. Gardner Director, Structural Biology Initiative CUNY Advanced Science Center, Room 3.322 85 St. Nicholas Terrace New York, NY 10031 Kevin.Gardner@asrc.cuny.edu structbio.asrc.cuny.edu • kglab.org

Publications Y. Guo et al., Coiled-coil coactivators play a structural role mediating interactions in hypoxia inducible factor heterodimerization. J. Biol. Chem., 2015, online now. V. Ocasio et al., Ligand-induced folding of a two component signal ing receiver domain. Biochemistry, 54, 1353-1363. G. Rivera-Cancel et al., Full-length structure of a monomeric histidine kinase reveals basis for sensory regulation, Proc. Natl. Acad. Sci USA, 2014, 111, 17839-17844. L.B. Motta-Mena et al., An optogenetic gene expression system with rapid activation and deactivation kinetics. Nat. Chem. Biol., 2014, 10, 196-202. T.H. Scheuermann et al., Allosteric inhibition of Hypoxia Inducible Factor 2 with small molecules. Nat. Chem. Biol., 9, 271-276.

Research Interests Keywords: environmental sensing • protein/protein interactions • ligand binding • allostery • NMR spectroscopy • X-ray diffraction • biochemistry • photosensors • cancer • protein engineering

The Gardner lab studies how cells perceive and respond to changes in the environment around them. Such information provides insights into fundamental p r i n c i p l e s o f p r o t e i n structure and signaling, guides the engineering of new protein-based tools, and lays the foundation for new therapeutic strategies.

2014- current Director, Structural Biology Initiative, CUNY Advanced Science Research Center Einstein Professor of Chemistry, City College of New York

1998-2014 Professor of Biophysics and Biochemistry, UT Southwestern Medical Center 1995-1998 Postdoc – Biomolecular NMR methods development, University of Toronto (w/ Dr. Lewis E.

Kay) 1989-1995 Ph.D. – Molecular Biophysics & Biochemistry, Yale University (w/ Dr. Joseph E. Coleman)

Dr. Kevin H. Gardner

Publications Assignargues, C. et al. “Structure and Function of a Bacterial Microcompartment Shell Protein Engineered to Bind a [4Fe-4S] Cluster”,IJ. Am. Chem. Soc. . 2016, 138, 5262-5270. Reddi A.R. et al. “Evaluation of the Intrinsic Zn(II) Affinity of a Cys3His1 Site in the Absence of Protein Folding Effects”, Inorg. Chem. 2015, 54, 5942-5948. Chan, K.L. et al. Characterization of the Zn(II) Binding Properties of the Wilms’ Tumor Suppressor Protein C-Terminal Zinc Finger Peptide”, Inorg. Chem. 2014, 53, 6309-6320. Gibney, B.R. Heme, Encylcopedia of Biophysics, Gordon Roberts, Ed. Springer, 2013. Gibney, B.R. Metallopeptides as Tools to Understand Metalloprotein Folding and Stability in Protein Folding and Metal Ions – Mechanisms, Biology and Disease, Gomes, C and Wittung-Stafshede, P. Eds. 2011, 227-245. Deng, B. et al. Unique Heme Pocket in Human Ncb5or and Structural Basis for Intra-Domain Electron Transfer. J. Biol. Chem. 2010, 285, 30181-30191.

Research Interests Keywords: De novo metalloprotein design, inorganic coordination chemistry, biophysics, bioenergetics, electrochemistry Our research focuses on the role of metal ions in biological systems from both an inorganic coordination chemistry and biophysical perspective. We are currently investigating the role of zinc in controlling gene expressions in human cancer, and the role of heme proteins in cardiovascular disease.

The Gibney Lab uses metalloprotein design to investigate the fundamental engineering of biological systems. These studies provide insight into metal-induced protein folding, heme electrochemistry, and the role of chemically modified hemes in biology.

2018- current Associate Professor Brooklyn College 2005-2008 Associate Professor Columbia University 2000-2005 Assistant Professor Columbia University 1995-2000 NIH Postdoc University of Pennsylvania 1990-1995 PhD University of Michigan 1986-1990 BS (ACS Certified) Florida State University

Dr. Brian R. Gibney

Brian R. Gibney Associate Professor Brooklyn College 2900 Bedford Avenue Brooklyn, NY 11210 bgibney@broklyn.cuny.edu http://www.biochemistry.nyc

Dr. Dixie Goss Hunter College Chemistry Dept. 695 Park Ave New York, NY 10065 dgoss@hunter.cuny.edu http://www.hunter.cuny.edu/chemistry/faculty/Dixie/goss-group-1/resume

Publications  Recruitment of 40S Ribosome to the 3' Untranslated Region (UTR) of a Viral mRNA, via the eIF4F Complex, Facilitates Cap-independent Translation. Das Sharma S, Kraft JJ, Miller WA, Goss DJ. J Biol Chem. 2015 Mar 19. Pokeweed antiviral protein, a ribosome inactivating protein: activity, inhibition and prospects. Domashevskiy AV, Goss DJ. Toxins (Basel). 2015 Jan 28;7(2):274-98. Rapid kinetics of iron responsive element (IRE) RNA/iron regulatory protein 1 and IRE-RNA/eIF4F complexes respond differently to metal ions. Khan MA, Ma J, Walden WE, Merrick WC, Theil EC, Goss DJ. Nucleic Acids Res. 2014 Jun;42(10):6567-77. Eukaryotic initiation factor (eIF) 4F binding to barley yellow dwarf virus (BYDV) 3'-untranslated region correlates with translation efficiency. Banerjee B, Goss DJ. J Biol Chem. 2014 Feb 14;289(7):4286-94. Poly(A) binding proteins: are they all created equal? Goss DJ, Kleiman FE. Wiley Interdiscip Rev RNA. 2013 Mar-Apr;4(2):167-79.

Research Interests Keywords: protein synthesis, virus, protein-nucleic acid interactions We use biophysical approaches to understand how non-coding regions of mRNA regulate function. Miss regulation of protein synthesis in responsible for many diseases including cancer. We are interested in how unique structures in viral RNA allow viruses to take over host cell protein synthesis.

Prof. Goss is a professor of Chemistry and Biochemistry and Elion Endowed Scholar

1990- current Professor of Chemistry 1989-1990 Associate Professor of Chemistry 1984-1989 Assistant Professor

Post-Doc. U. of Nebraska and U. of Georgia

1975 Ph.D U. of Nebraska

Dr. Dixie J. Goss

Michael E Green Professor City College of New York Dept. of Chemistry 160 Convent Ave New York NY 10031 green@sci.ccny.cuny.edu http://forum.sci.ccny.cuny.edu/people/science-division-directory/b009

Publications A. M. Kariev and M. E. Green, "Caution is required in interpretation of mutations in the voltage sensing domain of voltage gated channels as evidence for gating mechanisms.," Int'l J. Molec. Sci. (2015) 16, 1627-1643. A. M. Kariev and M. E. Green, "Quantum Effects in a Simple Ring with Hydrogen Bonds " J. Phys. Chem. B (2015)119,5962-5969 A. M. Kariev, P. Njau, and M. E. Green, "The Open Gate of the Kv1.2 Channel: Quantum Calculations Show The Key Role Of Hydration," Biophys J. (2014). 106, 548-555 A. M. Kariev and M. E. Green, "Voltage Gated Ion Channel Function: Gating, Conduction, and the Role of Water and Protons," Int'l J. Molec. Sci. (2012) 13, 1680-1709

S. Liao and M. E. Green, "Quantum calculations on salt bridges with water: Potentials, structure, and properties," Comput. Theo. Chem. (2011) 963, 207-214.

Research Interests Keywords: Description of research activities and strategy.

Dr. Green is a computational chemist, with a principal in terest in b iophysical problems, especially related to a class of proteins, ion channels, responsible for the nerve impulse, among other things.

Dr. Green has been a faculty member in Chemistry at CCNY since Sept 1966.

Research Interests    Keywords: Quantum calculations, proteins, water structure, hydrogen bonds, salt bridges, membranes, water transport through membranes Research Strategy: Primarily we carry out quantum calculations on overlapping sections of proteins, such as voltage sensing domains of ion channels, to determine structure, bonding, energetics, and transitions of protein, water, hydrogen bonds, and salt bridges, leading to mechanisms, for example, of sensing voltage.

Dr. Michael Green

Professor Hunter College of CUNY Dept. of Chemistry & Biochemistry 695 Park Avenue New York NY 10065 ngreenba.hunter@cuny.edu www.cuny.edu/chemistry/faculty/nancy/greenbaum

Publications Riskowski, R.A., Armstrong, R.E., Greenbaum, N.L, and Strouse, G.F. (2016) Triangulating Nucleic Acid Conformations Using Multicolor Surface Energy Transfer (McSET) ACS Nano 10:1926-1938. Zhao, C, Devany, M, Greenbaum, NL (2014) Measurement of Chemical Exchange between RNA Conformers by 19F NMR. Biochem. Biophys. Res. Comm. 453,692-695. Popović, M, Greenbaum, NL (2014) Role of helical constraints of the EBS1-IBS1 duplex of a group II intron on demarcation of the 5′ splice site. RNA 20, 24-35. Zhao, C*, Bachu, R*, Popović, M, Devany, M, Brenowitz, M, Schlatterer, JC, Greenbaum, NL (2013) Conformational heterogeneity of the protein-free human spliceosomal U2-U6 snRNA complex. RNA 19, 561-573. *these authors contributed equally to the work. Popović, M, Nelson, JD, Schroeder, KT, Greenbaum, NL (2012) Impact of base pair identity 5ʹ′ to the spliceosomal branch site adenosine on branch site conformation. RNA 18, 2093-2103. Research Interests

Keywords: RNA, spliceosome, NMR We  aTempt  to  answer  quesLons  about  how  RNA  molecules  fold  and  interact  with  other  RNA,  metal  ions,  and  proteins  in  order  to  carry  out  the  complex  acLvity  of  precursor  messenger  (pre-­‐m)RNA  splicing.  This  process,  by  which  noncoding  intron  sequences  of  pre-­‐mRNA  molecules  are  excised  and  flanking  coding  exons  are  ligated  together,  is  an  essenLal  step  in  preparaLon  of  mRNA  transcripts  prior  to  translaLon  of  their  message  into  protein  sequences.    Pre-­‐mRNA  splicing  in  eukaryoLc  cells  is  performed  by  the  spliceosome,  a  dynamic  nuclear  supramolecular  assembly  that  comprises  five  recyclable  small  nuclear  (sn)RNA  molecules  and  many  proteins.  SimilariLes  between  spliceosomal  snRNAs  of  and  funcLonally  analogous  regions  of  Group  II  introns,  which  excise  themselves  even  in  the  absence  of  proteins,  suggests  shared  evoluLonary  ancestry  and  the  likelihood  that  the  spliceosomal  reacLon  is  also  catalyzed  by  its  RNA  components.  Using  a  combinaLon  of  biochemistry,  biophysical,  and  spectroscopy  techniques,  we  characterize  the  molecular  basis  of  recogniLon  and  conformaLonal  dynamic  leading  RNA  splicing  in  the  two  systems.

Prof. Greenbaum is a structural biologist whose research addresses the role of biomolecular structure and funct ion in biochemical activity of noncoding RNA molecules. We incorporate solution NMR, fluorescence techniques, and biochemical approaches in our studies.

2007- current Professor, Hunter College 2004-2007 Associate Professor, Florida State Univ. 1997-2004 Assistant Professor, Florida State Univ. 1992-1996 Postdoc, Columbia University 1985-1989 Postdoc, Rockefeller University 1981-1984 PhD, University of Pennsylvania

Dr. Nancy Greenbaum

Reza Khayat Assistant Professor City College of New York Center for Discovery and Innovation 85 Saint Nicholas Terrace; 12316 New York, NY 10031 rkhayat@ccny.cuny.edu www.khayatlab.org

Publications Veesler D, Khayat R, Architecture of a dsDNA viral capsid in complex with its maturation protease. Structure 2014 Feb 4 (22): 1-8 Khayat R, Lee JH, Structural characterization of cleaved, soluble human immunodeficiency virus type-1 envelope glycoprotein trimers. J. Virology, 2013 Sep;87(17):9865-72 Pejchal R, Khayat R, A potent and broad neutralizing antibody recognizes and penetrates the HIV glycan shield, Science 2011 Nov. 25:334(6059):1097-103 Khayat R, Brunn N, The 2.3-angstrom structure of porcine circovirus 2, 2011 J. Virology Aug; 85(15):7856-62 Khayat R, Lander GC, An automated procedure for detecting protein folds from sub-nanometer resolution electron density, 2010 J. Struct. Bio. Jun; 170(3); 513-21

Research Interests Keywords: cryo-electron microscopy, X-ray crystallography, biophysics, biochemistry, cellular biology We seek to understand the structural and chemical mechanism by which pathogens hijack the cellular machinery of their host for infection and replication. We use a combination of techniques to understand this mechanism at the atomic resolution to relate how chemistry drives biology, and a number of techniques to understand how biology feeds back into chemistry for new pathways to be exploited by the pathogen for infection and replication. We are also interested in developing computational methods to further combine X-ray crystallography with cryo-electron microscopy.

Khayat group studies the structure and function of proteins encoded for and utilized by pathogens to infect and replicate. We use a combination of X-ray c r ys ta l l og raphy, c r yo -e l e c t r o n m i c r o s c o p y, biophysics, biochemistry, and cellular biology to complete these studies.

2012- current Current position 2008-2012 Sr. Research Associate, TSRI 2003-2008 Research Associate, The Scripps

Research Institute 1998-2003 PhD, Columbia University

Dr. Reza Khayat

Themis Lazaridis Professor City College of New York Dept of Chemistry and Biochemistry 160 Convent Ave New York NY tlazaridis@ccny.cuny.edu http://www.sci.ccny.cuny.edu/~themis/

Publications Brice A., Lazaridis T. "Structure and Dynamics of a Fusion Peptide Helical Hairpin on the Membrane Surface: Comparison of Molecular Simulations and NMR", J. Phys. Chem. B, 118:4461-70 (2014) Lazaridis T., Versace R. "The treatment of solvent in multiscale biophysical modeling", Isr. J. Chem., 54:1074-83 (2014) Lazaridis T., Leveritt JM, PeBenito L. "Implicit membrane treatment of buried charged groups. Application to peptide translocation across lipid bilayers", BBA Biomembranes, 1838:2149-59 (2014) Prieto L., He Y., Lazaridis T. "Protein arcs may form stable pores in membranes", Biophys J, 106:154-161 (2014) Rahaman A., Lazaridis, T. "A thermodynamic approach to alamethicin pore formation", BBA Biomembranes 1838:98 (2014)

Research Interests My research is in the area of Theoretical and Computational Biophysical Chemistry, which aims to understand how biological systems work in terms of the fundamental laws of Physics and Chemistry. Biomolecules, such as proteins and nucleic acids, have well defined conformations which often change in the course of their function. Our goal is to understand the forces that operate within and between biomolecules and develop quantitative mathematical models for their energy as a function of conformation. Such models are useful in many ways, such as predicting the three-dimensional structure from sequence, characterizing conformational changes involved in biological function, or predicting the binding affinity between two biomolecules.

The Lazaridis lab works in the area of theoretical and computational Biophysics. In the past few years we have worked on the interaction of proteins with biological m e m b r a n e s . W e a r e especially interested in the process of pore formation by antimicrobial peptides and other toxins.

1998- City College 1992-1998 Postdoc, Harvard University 1987-1992 PhD, University of Delaware

Dr Themis Lazaridis

Hiroshi Matsui Professor Hunter College 695 Park Avenue, New York, NY 10065 lmassa@hunter.cuny.edu http://www.hunter.cuny.edu/chemistry/faculty/Lou/Lou

Publications Dielectric Response of High Explosives at THz Frequencies Calculated by Density Functional Theory, Lulu Huang, Andrew Shabaev, Sam Lambrakos, Noam Bernstein, Vern Jacobs, Dan Finkenstadt, Lou Massa, Journal of Materials Engineering and Performance (2012) 21(7), 1120-1132.

The Kernel Energy Method: Application to Graphene and Extended Aromatics, Lulu Huang, Hugo Bohorquez, Cherif F. Matta and Lou Massa, IJQC, Vol. 111, 15, 4150-4157 (2011) The Kernel Energy Method: Construction of 3 & 4 tuple Kernels from a List of Double Kernel Interactions, Lulu Huang, Lou Massa, Journal of Molecular Structure: THEOCHEM, Vol. 962, issue 1-3, 72-79 (2010) Calculation of Strong and Weak Interactions in TDA1 and RangDP52 by Kernel Energy Method, Huang, L.; Massa, L.; Karle, I.; Karle, J. Proceedings of the National Academy of Sciences, Vol. 106, No. 10, 3664-3669 (2009) The Kernel Energy Method of Quantum Mechanical Approximation carried to Fourth Order Terms, Huang, L.; Massa, L.; and Karle, J. PNAS, Vol. 105, No. 6, 1849-1854 (2008)

Research Interests Keywords: differential equations, density matrices, density functional theory, Xray crystallography, kernel energy method, information theory, Applications of Quantum Mechanics to the electronic structure of atoms, molecules, and solids.

Postdoc: Brookhaven National Laboratory PhD: Theoretical Molecular Physics, Georgetown University

Dr. Louis Massa

Sébastien Poget Assistant Professor College of Staten Island, CUNY Department of Chemistry 2800 Victory Blvd. Staten Island, NY 10314 sebastien.poget@csi.cuny.edu www.csi.cuny.edu/faculty/POGET_SEBASTIEN.html

Publications P. Anand, A. Grigoryan, M. H. Bhuiyan, B. Ueberheide, V. Russell, J. Quinoñez, P. Moy, B. T. Chait, S. F. Poget, M. Holford: Sample limited characterization of a novel disulfide-rich venom peptide toxin from terebrid marine snail Terebra variegata. PLoS ONE 2014, 9, e94122. S. F. Poget, M. E. Girvin: Solution NMR of membrane proteins in bilayer mimics: Small is beautiful, but sometimes bigger is better. Biochim. Biophys. Acta 2007, 1768, 3098-106. S. F. Poget, S. M. Cahill, M. E. Girvin: Isotropic bicelles stabilize the functional form of a small multidrug-resistance pump for NMR structural studies. J. Am. Chem. Soc. 2007, 129 2432-2433.

Research Interests Keywords: Solution-state NMR, membrane protein structural biology, ion channels, toxins, electrophysiology, biophysics The Poget lab is interested in the structural and functional study of membrane proteins through solution-state NMR and other biophysical methods. Our studies focus on better understanding the interactions of animal peptide toxins with their target ion channel domains as tools for an improved understanding of ion channel function and starting point for drug development. To carry out these studies at the cutting edge of structural biology, we are also involved in the development of new and improved methods for membrane protein studies, including development of more powerful membrane mimetics such as bicelles and optimized NMR methods.

Dr. Poget is interested in membrane protein structure a n d f u n c t i o n , w i t h a particular emphasis on the interactions between ion channe l domains and animal peptide toxins.

2009- current Assistant Professor, College of Staten Island, CUNY

2003-2009 Postdoc, Albert Einstein College of Medicine, NY

2001-2003 Postdoc, Rockefeller University, NY 1997-2001 PhD, University of Cambridge, UK

Dr. Sébastien Poget

Adam A. Profit, Ph.D. Associate Professor York College 94-20 Guy R. Brewer Blvd Jamaica, NY 11451 Email.aprofit@york.cuny.edu www.york.cuny.edu/portal_college/aprofit

Publications Profit, A. A., Vedad, J. Saleh, M., and Desamero, R.Z.B. “Aromaticity and Amyloid Formation: Effect of π-Electron Distribution and Aryl Substituent Geometry on the Self-Assembly of Peptides Derived from hIAPP22-29” Arch Biochem Biophys 2015, 567, 46-58. Profit, A. A., Felsen, V., Chinwong, J., Mojica, E-R., and Desamero, R.Z.B. “Evidence of π-stacking Interactions in the Self-assembly of hIAPP22-29” PROTEINS: Structure, Function and Bioinformatics 2013, 81, 690-703.

Research Interests Keywords: Amyloid, protein kinases, peptides, peptoids, enzymology, solid phase synthesis The abnormal formation of protein aggregates, or amyloid deposits, is the hallmark of Alzheimer’s disease as well as type 2 diabetes. My laboratory is investigating the molecular interactions that occur between key proteins that contribute to the formation of amyloid in these diseases. Through a more detailed understanding of how these proteins self-assembly to form aggregates, we hope to design and develop small molecule and peptide mimetic inhibitors which may serve as potential therapeutic agents.

We are also developing compounds that inhibit the activity of key enzymes (kinases) which can cause tissues to grow out of control and develop into tumors. To accomplish this we are synthesizing molecules that exploit the unique molecular recognition motifs found in these enzymes to more effectively deliver inhibitory species to the active site.

Protein-ligand interactions is the unifying theme of my research in terests . In part icular, the design, synthesis and application of biologically relevant probe molecules to study and elucidate protein-protein and protein-ligand interactions involved in amyloid diseases and cancer.

2014- current Associate Professor of Chemistry 2004-2014 Assistant Professor of Chemistry 2000-2004 Merck Research Laboratories 1997-2000 Postdoc - Albert Einstein College of Medicine 1997 PhD - Stony Brook University

Dr. Adam A. Profit

Susan A. Rotenberg Position: Professor Affiliation: Queens College Department of Chemistry & Biochemistry 65-30 Kissena Boulevard Flushing, NY 11367 Susan.Rotenberg@qc.cuny.edu http://rotenberglab.com/ (website under construction)

Publications X. Zhao, and S.A. Rotenberg. “Phosphorylation of Cdc42 effector protein-4 (CEP4) by protein kinase C promotes motility of human breast cells.” J. Biol. Chem. 2014, 289:25844-25854. S. De, A. Tsimounis, X. Chen, and S.A. Rotenberg. "Phosphorylation of α-tubulin by protein kinase C stimulates microtubule dynamics in human breast cells." Cytoskeleton 2014, 71: 257-272. X. Chen, X. Zhao, T. P. Abeyweera, and S. A. Rotenberg. “Analysis of substrates of protein kinase C isoforms in human breast cells by the traceable kinase method.” Biochemistry 2012, 51: 7087-7097. X. Chen and S.A. Rotenberg. “Phospho-MARCKS drives motility of mouse melanoma cells.” Cell. Signal. 2010, 22: 1097-1103. T.P. Abeyweera, X. Chen, and S. A. Rotenberg. “Phosphorylation of α6-tubulin by protein kinase Cα activates motility of human breast cells.” J. Biol. Chem. 2009, 284: 17648-17656.

Research Interests Keywords: Enzyme inhibitors; protein structure and function relationships; cell signaling pathways

Prof. Rotenberg

1990 - current Professor 1985 - 1990 Postdoctoral - Rockefeller University,

Columbia University 1980 - 1985 Ph.D. – Brown University

Dr. Susan A. Rotenberg

Chwen-Yang Shew Professor College of Staten Island Department of Chemistry 2800 Victory Boulevard Staten Island, NY 10314 ChwenYang.Shew@csi.cuny.edu www.csi.cuny.edu/faculty/SHEW_CHWEN_YANG.html

Publications S.   Oda,   Y.   Kubo,   C.-­‐Y.   Shew,   K.   Yoshikawa,  FluctuaLons  induced  transiLon  of  localizaLon  of  granular  objects  caused  by  degrees  of  crowding,  Physica  D  (2016)  in  press.    C.-­‐Y.  Shew,  and  K.  Yoshikawa,  “A  toy  model  for  nucleus-­‐sized   crowding   confinement   “J.   Phys.:  Condens.  Ma3er  27  064118  (2015)      E.   Sánchez-­‐Díaz,   C.-­‐Y.   Shew,   X.   Li,   B.  Wu,  G.   S.  Smith  and  W.-­‐R.  Chen,  “Phase  Behavior  Under  a  Noncentrosymmetric   InteracLon:   Shioed-­‐Charge   Colloids   InvesLgated   by   Monte   Carlo  SimulaLon,” J.   Phys.   Chem.  B,  118,   6963–6971  (2014)    C.-­‐Y.  Shew,  K.  Kondo  and  K.  Yoshikawa,  “Rigidity  of   a   spherical   capsule   switches   the   localizaLon  of   encapsulated   parLcles   between   inner   and  peripheral   regions   under   crowding   condiLon:  Simple  model  on  cellular  architecture,” J.  Chem.  Phys.  140,  024907  (2014).    C.-­‐Y.   Shew   and   K.   Yoshikawa,   “AbstracLng   the  essence  of  the  confinement  effect  on  crowding  microspheres:  Mean-­‐field  theory  and  numerical  simulaLon,” Chem.   Phys.   Le3.   590,   196-­‐200  (2013).      

Research Interests Keywords: Statistical Mechanics, Thermodynamics, Liquid State Theory and Computer Simulation Our   group   develops   model,   theory   and   simulaLon   to   elucidate   the   structure   of   colloids,  polymeric  materials,  confined  and  crowded  cells,  and  self-­‐assembled  nanoparLcles.

Research Area: Theoretical Physical Chemistry in Structure of Condensed Matters, Macromolecules, and Biological Cells

2011- current Professor, CSI 2005-2010 Associate Professor, CSI 1999-2004 Assistant Professor, CSI 1995-1998 Postdoc. UW-Madison 2000-2005 PhD, CUNY

Dr Chwen-Yang Shew

Ruth E. Stark Distinguished Professor City College Dept. of Chemistry and Biochemistry CUNY Institute for Macromolecular Assemblies CCNY CDI 1S-11302, 85 St. Nicholas Terrace New York, NY 10031 Email.rstark@ccny.cuny.edu http://www.sci.ccny.cuny.edu/resgroup

Publications W. S. Lagakos, X. Guan, S.-Y. Ho, L. R. Sawicki, B. Corsico, K. Murota, R. E. Stark, J. Storch, Liver Fatty Acid-binding Protein Binds Monoacylglycerol in vitro and in Mouse Liver Cytosol, J. Biol. Chem., 2013, 288, 19805-15. T.H. Yeats, W. Huang, S. Chatterjee, H. M-F. Viart, M.H. Clausen, R. E. Stark, J.K.C. Rose, Biochemical characterization of CD1 and Putative Orthologs Reveals an Ancient Family of Cutin Synthase-like Proteins that are Conserved Among Land Plants, 2014, Plant J., 77, 667-675. O. Serra,* S. Chatterjee,* M. Figueras, M. Molinas, R.E. Stark, Deconstructing a plant m a c r o m o l e c u l a r a s s e m b l y : c h e m i c a l architecture, molecular flexibility, and mechanical performance of natural and engineered potato suberins, Biomacromolecules, 2014,15, 799-811. K. Dastmalchi, Q. Cai, K. Zhou, W. Huang, O. Serra, R.E. Stark, Completing the Jigsaw Puzzle of Wound-Healing Potato Cultivars: Metabolite Profiling and Antioxidant Activity, J. Agric. Food Chem., 2014, 62, 7963-7975. S. Chatterjee, R. Prados-Rosales, B. Itin, A. Casadevall, R.E. Stark, Solid-state NMR Reveals the Carbon-based Molecu lar Architecture of Melanized Cryptococcus neoformans Fungal Cells, J. Biol. Chem., 2015, 290, 13779-13790. Research Interests

Keywords: molecular biophysics, biopolymers, bioanalytical chemistry, solid- and solution-state NMR The Stark Laboratory uses structural biology approaches to study plant protective polymers, lipid metabolism, and potentially pathogenic melanized fungal cells. Study of the molecular and mesoscopic architectures underlying the integrity of cuticles in natural and engineered tomatoes and potatoes is undertaken using solid- and solution-state nuclear magnetic resonance (NMR), mass spectrometry, and atomic force microscopy. Ligand recognition and peroxisome proliferator-activated receptor interactions of fatty acid-binding proteins are under investigation by solution-state NMR and isothermal titration calorimetry. The molecular structure and development of melanin pigments within fungal cells are probed using (bio)chemical synthesis and solid-state NMR.

Dr. Stark’s biophysics research program focuses on the molecular structure a n d i n t e r - a c t i o n s o f p r o t e c t i v e p l a n t biopolymers, nutri-tionally important fatty acid-binding prote ins, and melanin pigments associated with human fungal infections.

2007 - current CUNY Dist. Prof., CCNY 1985 - 2007 Assoc.-Dist. Prof., Coll. of Staten Island 1979 - 1985 Asst. Prof., Amherst College 1977 - 1979 Postdoctoral Fellow, M.I.T. 1977 PhD, Physical Chemistry, UC San

Diego

Dr. Ruth E. Stark