IVET BAHAR      
          Research Lab and Topics

          Conference Schedule

          Bahar Lab Meeting Schedule

 

Correspondence

Department of Computational Biology
School of Medicine, University of Pittsburgh
3064 Biomedical Science Tower 3
3501 Fifth Avenue, Pittsburgh, PA 15213
http://www.ccbb.pitt.edu

Research Interests

Modeling and simulations of complex biomolecular systems and their dynamics; protein-DNA interactions, sequence-structure-function relationships; statistical mechanics of polymers; conformational dynamics of proteins; coarse-grained simulations; binding of biomolecules, receptor-ligand complexes, molecular aspects of biochemical and biophysical processes; statistical analyses based on database searches; screening of drug databases for computer-aided development of new drugs; computer modeling and engineering of enzyme-substrate, enzyme-drug binding and interactions

Current Position

John K. Vries Chair and Professor of Department of Computational Biology,
Professor, Department of Molecular Genetics & Biochemistry,
School of Medicine, Health Sciences, University of Pittsburgh,

Director,  Joint PhD Program in Computational Biology
Carnegie Mellon University and University of Pittsburgh

Education

Ph.D. in Chemistry, Istanbul Technical University, 1986.
M.S. in Chemical Engineering, Bogazici University, 1983.
B.S. in Chemical Engineering, Bogazici University, 1980.

Career/Employment

Chair, Department of Computational Biology, 2004 -
Director of Center for Computational Biology and Bioinformatics, 2001-2004
Professor, Department of Molecular Genetics & Biochemistry,
School of Medicine, Health Sciences, University of Pittsburgh, 2001-

Professor, Chemical Engineering Dept, Bogazici University, 1993-2001.
Director, Polymer Research Center, Bogazici University, 1992-2000.
Head, Adv Polymeric Materials Research Unit, TUBITAK, Bogazici University, 1998-2000.

Visiting Scientist, Laboratory of Experimental & Computational Biology, Molecular Structure Section, Division of Basic Sciences, NCI, NIH, Bethesda; summers of 1992-2000.
Visiting Scientist, NATO CRG and CNRS projects, Ecole Superieure de Physique & Chimie, Laboratoire de Physique et Chimie Structurale et Macromoleculaire, Paris; several short-term visits between 1989-1998.
Visiting Scholar, University of Akron, Institute of Polymer Science; summers of 1988-1991.

Associate Professor, Chemical Eng Dept, Bogazici U., 1987-1993.
UNESCO Fellow, University of Akron, Inst. Polymer Sci.; 1987 summer.
Assistant Professor, Chemical Eng Dept, Bogazici University, 1986-1987.
Research Assistant, Chemistry Dept, Istanbul Technical University, 1984-1986.

Awards

bullet 2000 European Molecular Biology Organization (EMBO), Elected Member
bullet 1998 Excellence in Research Award, Bogazici University
bullet 1997 Turkish Academy of Sciences (TUBA)(*), Elected Member
bullet 1995 TUBITAK-TWAS Science Prize
bullet 1991 Sedat Simavi Physical Sciences Prize (joint with B. Erman)
bullet 1990 Chemistry Award for Young Scientists from TUBITAK (Turkish National Scientific and Technological Research Council)

        (*) Member of ALLEA (All European Academies)

Memberships and Other Affiliations

Biophysical Society
Protein Society
American Association for the Advancement of Science
International Society for Computational Biology

Core Faculty, Pittsburgh Medical Informatics Training Program, University of Pittsburgh, 2001-
Faculty, Center for Uncertain Systems: Tools for Optimization and Management, Carnegie Mellon University, 2001-
Member Faculty, McGowan Institute for Regenerative Medicine, University of Pittsburgh, 2002-
Member, Molecular Medicine Institute, University of Pittsburgh, 2002-

Students/Theses

 

PUBLICATIONS
2006 2005 2004 2003 2002 2001
2000 1999 1998 1997 1996 1995 1994 1993
1992 1991 1990 1989 1988 1987 1986 1985

 

Publications'2006

J149. "Optimal Design of Protein Docking Potentials: Efficiency and Limitations" Dror Tobi & Ivet Bahar. Proteins: Structure, Function, and Bioinformatics,  62, 970-981, 2006 . Full Paper (.pdf)

J150. "Bistability in Apoptosis: Roles of Bax, Bcl-2, and Mitochondrial Permeability Transition Pores" E. Z. Bagci, Y. Vodovotz, T. R. Billiar, G. B. Ermentrout, and I. Bahar. Biophys J  90, 1546-1559, March 2006.  Full Paper (.pdf)

B13. "Markov Methods for Hierarchical Coarse-Graining of Large Protein Dynamics" Chakra Chennubhotla &  Ivet Bahar. RECOMB'06, accepted.   Lecture Notes in Computer Science 3909, 379-393 2006.  Full Paper (.pdf)

J151. "An Introduction to Simulation and Visualization of Biological Systems at Multiple Scales: A Summer Training Program for Interdisciplinary Research". Rajan Munshi, Rob D. Coalson, G. Bard Ermentrout, Jeffry D. Madura, Hagai Meirovitch, Joel R. Stiles & Ivet Bahar. Biotechnology Progress 22, 179-185, 2006. Full Paper (.pdf)

B14. "The Gaussian Network Model: Theory and Applications" by AJ Rader. Chakra Chennubhotla, Lee-Wei Yang, and Ivet Bahar, in "Normal Mode Analysis. Theory and Applications to Biological and Chemical Systems" Eds Qiang Cui and I Bahar, Chapman & Hall / CRC  Mathematical and Computational Biology Series, CRC Press, Taylor & Francis Group, 41-64, 2006.  Full Chapter (.pdf)

J152. "Common Mechanism of Pore Opening Shared by Five Different Potassium Channels" Indira H. Shrivastava & Ivet Bahar. Biophys J  90, 3929-3940, 2006.  Full Paper (.pdf)

B15. "oGNM: online computation of structural dynamics using the Gaussian Network Model" LeeWei Yang, AJ Rader, X Liu, CJ Jursa, SC Chen, HA Karimi, and Ivet Bahar. Nucleic Acids Res 34, W24-31, 2006.   Full Paper (.pdf)

J153. "Markov propagation of allosteric effects in biomolecular systems: application to GroEL-GroES"  Chakra Chennubhotla &  Ivet Bahar. Mol Syst Biol. 2:36, 2006.   Full Paper (.pdf)

Publications'2005

J140.  "Maturation Dynamics of Bacteriophage HK97 Capsid" AJ Rader, Daniel Vlad & Ivet Bahar.  Structure (Camb) 13:413-21, 2005 Full Paper (.pdf)

J141. "Structural Dynamics of Nucleosome Core Particle: Comparison with Nucleosomes Containing Histone Variants" Amutha Ramaswamy, Ivet Bahar & Ilya Ioshikhes. Proteins: Structure, Function and Bioinformatics 58:683-696, 2005. Full Paper (.pdf)

J142.  "Analysis of the impact of silver ions on creatine amidinohydrolase." Jason Berberich, Lee Wei Yang, Ivet Bahar &  Alan J Russell.  ACTA Biomaterialia 1(2) pg.183-191.  Full Paper (.pdf)

J143.  "A Stable Three Enzyme Creatinine Biosensor Impact of structure, function and environment on PEGylated and immobilized sarcosine oxidase." Jason Berberich, Lee Wei Yang, Jeff  Madura, Ivet Bahar &  Alan J Russell.  ACTA Biomaterialia 1(2) pg.173-181.  Full Paper (.pdf)

J144.  "Coupling between Catalytic Site and Collective Dynamics: A requirement for Mechanochemical Activity of Enzymes." Lee Wei Yang & Ivet Bahar.  Structure 13: 893-904 , 2005Full Paper (.pdf)

J145.  "iGNM: A Database of Protein Functional Motions Based on Gaussian Network Model." Lee Wei Yang, Xiong Liu, Christopher Jon Jursa, Mark Holliman, A.J. Rader, Hassan Karimi &  Ivet Bahar.  Bioinformatics 21: 2978 - 2987, 2005 Full Paper (.pdf)

J146.  "Coarse-grained normal mode analysis in structural biology." Ivet Bahar & AJ Rader. Current Opinion in Structural Biology 15:1-7, 2005. Full Paper (.pdf)

J147. "Structural Changes Involved in Protein Binding Correlate with intrinsic Motions of Proteins in the Unbound State" Dror Tobi &  Ivet Bahar. Proc Natl Acad Sci (USA) 102,  18908-18913, 2005.  Full Paper (.pdf)

J148. "Elastic network models for understanding biomolecular machinery: from enzymes to supramolecular assemblies" Chakra Chennubhotla, AJ Rader, Lee-Wei Yang &  Ivet Bahar. Physical Biology 2, S173-S180, 2005.  Full Paper (.pdf)

 

Publications'2004

J130. "Global Ribosome Motions Revealed with Elastic Network Model" Wang, Y. Rader, AJ, Bahar, I. & Jernigan, RL. , J. Struct Biol 147: 302-314, 2004. Full Paper (.pdf)

J131. "Identification of core amino acids stabilizing rhodopsin" Rader, AJ., G. Anderson, B. Isin, H. G. Khorana, I. Bahar, & J. Klein-Seetharaman. Proc. Natl. Acad Sci USA 101: 7246-7251, 2004. Full Paper (.pdf)

J132. "Mining frequent patterns in proteins: A study of serine proteinases" Chen, S.-C. & I. Bahar  Bioinformatics 20,  i77-i85, 2004. Full Paper (.pdf)

J133. "E. coli Adenylate Kinase Dynamics: Comparison of Elastic Network Model Modes with Mode-Coupling 15N-NMR Relaxation Data" NA Temiz, E Meirovitch &  I Bahar.  Proteins, Structure, Function and Bioinformatics  57: 468, 2004. Full Paper (.pdf)

J134. "Conformational changes in HIV-1 reverse transcriptase induced by nonnucleoside reverse transcriptase inhibitor binding." Nicolas Sluis-Cremer, N. Alpay Temiz & Ivet Bahar.  Current HIV Research 2: 323-32, 2004. Full Paper (.pdf)

J135. "Discovery and characterization of novel small molecule inhibitors of human Cdc25B dual specificity phosphatase" M. Brisson, T. Nguyen, A. Vogt, J. Yalowich, A. Giorgianni, D. Tobi, I. Bahar, Corey R. J. Stephenson, P. Wipf, and John S. Lazo.   Mol Pharmacology 66: 824-833, 2004. Full Paper (.pdf).

J136. "A Sequence Alignment-Independent Method For Protein Classification" John K. Vries  Rajan Munshi, Dror Tobi Judith Klein-Seetharaman, Panayiotis V. Benos and Ivet Bahar .  Applied Bioinformatics 3:137-48, 2004

J137. "High efficiency bypass of DNA damage by a single human DNA polymerase" Mineaki Seki, Chikahide Masutani, Lee Wei Yang, Anthony Schuffert, Shigenori Iwai, Ivet Bahar & Richard D. Wood. EMBO J. 10, :4484-94, 2004. Full Paper (.pdf)

B11.  "Protein Functional Motion Query and Visualization" Liu, X., Karimi, H., Yang, L-.W. and Bahar, I.  IEEE Proceedings, 28th Annual International Computer Software and Applications Conference - (COMPSAC'04), 2004.

J138. "Folding Core Predictions from Network Models of Proteins" AJ Rader & Ivet Bahar, Polymer 45: 659-668, 2004. Full Paper (.pdf).

J139. "Inflammatory Modulation of Hepatocyte Apoptosis by Nitric Oxide: In Vivo, In Vitro, and In Silico Studies." Yoram Vodovotz, Peter Kim, E. Zerrin Bagci, G. Bard Ermentrout, Carson C. Chow, Ivet Bahar, Timothy R. Billiar. Current Molecular Medicine 4, 753-762, 2004. Full Paper (.pdf)

 

Publications'2003

J127. "Computing the Transition State Populations in Simple Protein Models" Ozkan SB, Dill KA, Bahar I. Biopolymers  68:  35-46, 2003.  Full Paper (.pdf)

J128. "Allosteric Changes in Protein Structure Computed by a Simple Mechanical Model: Hemoglobin T --> R2 Transition" Chunyan Xu, Dror Tobi and Ivet Bahar, J. Mol. Biol. 333, 153-168, 2003. Full Paper(.pdf)

J129.  "The Origin and Extent of Coarse-Grained Regularities in Protein Internal Packing" Zerrin Bagci, Andrzej Kloczkowski, Robert L. Jernigan & Ivet Bahar , Proteins: Structure, Function and Genetics 53: 56-67, 2003. Full Paper(.pdf)

 

Publications'2002

J118.  "Dynamics of large proteins through hierarchical levels of coarse-grained structures". Doruker P, Jernigan RL &  Bahar I. J Comp Chem 23:119-127, 2002.  Full paper (.pdf)

J119. "Fast-folding protein kinetics, hidden intermediates and the sequential stabilization model" Ozkan SB, Dill KA &  Bahar I.  Protein Science 11, 1958-1970, 2002.  Full Paper (.pdf)

J120. "Collective deformations in proteins determined by a mode analysis of molecular dynamics trajectories"  Doruker P, Bahar I, Baysal C & Erman, B. Polymer 43: 431-439, 2002.  Full paper (.pdf)

J121. "Functional motions of influenza virus hemagglutinin: A structure-based analytical approach" Isin B, Doruker P, Bahar I.  Biophys J. 82:569-581, 2002.  Full paper (.pdf)

J122. "Residue coordination in proteins conforms to the closest packing of spheres" Bagci, Z. Jernigan, R.L. & I. Bahar.   Polymer 43: 451-459, 2002.  Full paper (.pdf)

J123. "Molecular mechanisms of chaperonin GroEL/GroES function" Keskin O, Bahar I, Flatow D, Covell DG, Jernigan RL. Biochemistry 41:491-501, 2002. Full paper (.pdf)

J124. "Residue packing in proteins: Uniform distribution on a coarse-grained scale. " Bagci Z, Jernigan RL, Bahar I. J. Chem Physics 116, 2269-2276, 2002.  (selected for the February 1, 2002 issue of the Virtual Journal of Biological Physics Research in http://www.vjbio.org) Full Paper (.pdf)

J125. "Relating molecular flexibility to function: A case study of tubulin" Keskin O, Durell SR, Bahar I, Jernigan RL, Covell, DG.  Biophys J. 83, 663-680, 2002.  Full paper (.pdf)

J126. "Inhibitor binding alters the directions of domain motions in HIV-1 reverse transcriptase" Temiz NA &  Bahar I, Proteins: Structure, Function and Genetics 49, 61-70, 2002.  Full paper (.pdf)

 

Publications'2001

J115. " Anisotropy of fluctuation dynamics of proteins with an elastic network model" Atilgan, AR, Durrell, SR, Jernigan, RL, Demirel, MC, Keskin, O. & Bahar, I. Biophys. J. 80, 505-515, 2001. Full Paper (.pdf)

J116. "Modeling the deamidation of asparagine residues via succinimide intermediates" Konuklar, F.A.S., Aviyente, V. Sen, T.Z., Bahar, I., J. Mol. Model. 7, 147-160, 2001.  Full paper (.pdf)

J117. "Transition states and the meaning of F-values in protein folding kinetics" B. Ozkan, I. Bahar, & K. A. Dill, Nature Struct. Biol. 8, 765-769, 2001.  Full Paper (.pdf)

P1 (Patent1). High Performance of Biodegradable Materials from Oriented Starch Derivatives,  B. Erman, J. E. Mark, B.Z. Paterson,  I.Bahar, A. Kloczkowski.  US Patent #6,218,532 B1 (2001).

 

Publications'2000

J109. "Proteins with similar architecture exhibit similar large-scale dynamic behavior. Specificity resides in local differences" O. Keskin, R. L. Jernigan & I. Bahar, Biophysical Journal 78, 2093-2106, 2000. Full paper (Acrobat)

J110. "Characterization of anticancer agents by their growth inhibitory activity and relationships to mechanism of action and structure" O. Keskin, I. Bahar, R.L.Jernigan, T.G.Myers, J.A.Beutler, R.H.Shoemaker, E.A.Sausville, D.G.Covell Anticancer Drug Design 15, 79-98, 2000.  Full paper (.pdf)

J111. "Collective dynamics of class I MHC/peptide complexes and binding to T cell receptors" T. Haliloglu, I. Bahar & R.L. Jernigan Biophys. J. 78, 34A, 2000.

J112. "Stabilization of the molten globule state of hen egg white lysozyme with solutions containing polyvinyl pyrrolidone" G. Duman, O. Keskin, I. Bahar & J. R. Robinson J. Controlled Release 64, 331-333, 2000.

J113. "Dynamics of proteins predicted by molecular dynamics simulations and analytical approaches: Application to a-amylase inhibitor" P. Doruker, A. R. Atilgan & I. Bahar, Proteins: Structure, Function & Genetics 40, 512-524, 2000.  Full paper (.pdf)

J114. "Relating the structure of HIV-1 reverse transcriptase to its processing step" R.L.Jernigan, I. Bahar, D.G.Covell, A.R.Atilgan, B. Erman & D. Flatow, J. Biomol. Structure & Dynamics, 1, 49-55, 2000. Full Paper (.pdf)

 

Publications'99

J104. "Collective motions of HIV-1 reverse transcriptase. Examination of Flexibility and Enzyme Function" I. Bahar, B. Erman, R. L. Jernigan, A. R. Atilgan, & D. Covell J. Mol. Biol. 285, 1023-1037, 1999. Full paper (.pdf)

J105. "Local dynamics of cis-polybutadiene and cis-polyisoprene. A comparative study based on cooperative kinematics theory and NMR experiments" T. Z. Sen, I. Bahar, B. Erman, F. Laupretre & L. Monnerie Macromolecules 32,3017-3024, 1999.  Full paper (.pdf)

J106. "Cooperative fluctuations and subunit communication in tryptophan synthase" I. Bahar & R.L. Jernigan Biochemistry 38, 3478-3490, 1999. Full paper (.pdf)

J107. "Relating structure to function through the dominant slow modes of motion of DNA topoisomerase II" R.L. Jernigan, M. C. Demirel & I. Bahar Int.J. Quantum Chem. 75, 301-312, 1999. Full paper (.pdf)

J107. "Structure-based analysis of protein dynamics. Comparison of theoretical results for hen lysozyme with X-ray diffraction and NMR relaxation data" T. Haliloglu & I. Bahar, Proteins: Structure, Function, & Genetics 37, 654-667, 1999.  Full paper (.pdf)

B10. "Geometric Regularities among bonded and nonbonded residues in proteins" R. L. Jernigan & I. Bahar. In Perspectives in Structural Biology (GN Ramachandran Volume) M. Vijayan, N. Yathindra and A.S. Kolaskar Eds., Indian Academy of Sciences, Universities Press, Hyderabad, pp 209-225, 1999.

J108. "Dynamics of proteins and biomolecular complexes. Inferring functional motions from structure" I. Bahar, Reviews in Chemical Engineering 15, 319-349, 1999.

 

Publications'98

J92."Correlation between native state hydrogen exchange and cooperative residue fluctuations from a simple model" I. Bahar, A. Wallqvist, D. G. Covell, & R.L. Jernigan Biochemistry 37, 1067-1075, 1998. Full Paper (.pdf)

B8. "Coarse Grained Searches over Protein Conformations" R. L. Jernigan & I. Bahar, Encyclopedia of Computational Chemistry Schleyer, P. v.R.; Allinger, N. L.; Clark, T.; Gasteiger, J.; Kollman, P. A.; Schaefer III, H. F.; Schreiner, P. R. (Eds.) John Wiley & Sons: Chichester, 1998.

J93. " Coarse-grained simulations of conformational dynamics of proteins. Application to apomyoglobin" T. Haliloglu & I. Bahar, Proteins: Structure, Function and Genetics 3, 271-281, 1998.  Full Paper (.pdf)

J94. Recognition of native structure from complete enumeration of low resolution models with constraints. B. Ozkan & I. Bahar Proteins: Structure, Function and Genetics 32, 211-222, 1998. Full Paper (.pdf)

J95. Vibrational dynamics of transfer RNAs. Comparison of the free and enzyme-bound forms. I. Bahar & R. L. Jernigan J. Mol. Biol. 281, 871-884, 1998. Full Paper (.pdf)

J96. " Correlated fluctuations in polymer networks" Atilgan, A. R., Haliloglu, T., Bahar, I. & Erman, B. Comput. Theor. Polym. Sci. 8, 55-59, 1998. Full Paper (.pdf)

J97. "Swelling of sodium chloride filled polybutadiene networks in aqueous environment" S. Erdal, I. Bahar & B. Erman, Polymer 39, 2035-2041, 1998.

J98. "Vibrational dynamics of proteins: Significance of slow and fast modes in relation to function and stability", I. Bahar, A. R. Atilgan, M. C. Demirel, & B. Erman, Phys. Rev. Lett. 80, 2733-2736, 1998. Full Paper (.pdf)

J99. "Packing of sidechains in low resolution models for proteins" Keskin, O. & Bahar, I. Folding & Design 3, 469-479, 1998. Full Paper (.pdf)

J100."Identification of kinetically hot residues in proteins" M. C. Demirel, A. R. Atilgan, R. L. Jernigan, B. Erman & I. Bahar Protein Science 7, 2522-2532, 1998. Full Paper (.pdf)

J101. "RNA bulge entropies are correlated with peptide binding strengths for HIV-1 and BIV TAR RNA because of improved conformational access" Lustig, B., Bahar, I. & Jernigan, R. L. Nucleic Acids Research 26, 5212-5217, 1998. Full paper (.pdf)

J102. "Local chain dynamics and glass transition" B. Erman & I. Bahar Makromolekulare Chem. Makromol. Symp. 133, 33-46, 1998.

J103. "Empirical solvent-mediated potentials hold for both intramolecular and inter-molecular inter-residue interactions" O. Keskin, I. Bahar, A. Badredtinov, O. Ptitsyn & R. L. Jernigan Protein Science 7, 2578-2586, 1998. Full Paper (.pdf)

B9. "Simulation of polymeric systems" B. Erman & I. Bahar, in Continuum Models and Discrete Systems E. Inan & K. Z. Markov (Editors), pp 297-303, World Scientific Publishing, 1998.

 

Publications'97

J80. "Inter-residue potentials in globular proteins and the dominance of highly specific hydrophilic interactions at close separations" I. Bahar & R. L. Jernigan, J. Mol. Biol. 266, 195-214, 1997. Full Paper (.pdf)

J81. "Direct evaluation of thermal fluctuations in protein using a single parameter harmonic potential" I. Bahar, A. R. Atilgan, and B. Erman Folding & Design 2, 173-181, 1997. Full Paper (.pdf)

J82. "Role of water on unfolding kinetics of polypeptides studied by molecular dynamics simulations" P. Doruker, I. Bahar Biophys. J. 72, 2445-2456, 1997. Abstract

J83. "Three approaches that permit more efficient simulation of the dynamics of atomistic models of polymers" I. Bahar, J. Cho. P. Doruker, B. Erman, T. Haliloglu, E. -G. Kim, W. L. Mattice, L. Monnerie and R. F. Rapold Trends in Polymer Science 5, 155-160, 1997.

J84. "Mechanical properties and transition temperatures of crosslinked-oriented gelatin. II.Effect of orientation and water content on transition temperatures. Fakirov, S. Sarac, Z. Anbar, T., Boz, B. Bahar, I., Evstatiev, M., Apostolov, A. A., Mark, J. E., Kloczkowski, A., Colloid. Polym. Sci. 275, 307-314, 1997.

J85. "Equilibrium states of rigid bodies with multiple interaction sites. Application to protein helices" B. Erman, I. Bahar and R. L. Jernigan J. Chem. Phys. 107, 2046-2059, 1997. Full Paper (.pdf)

J86. "Understanding the recognition of protein structural classes by amino acid composition" I. Bahar, A. R. Atilgan, R. L. Jernigan and B. Erman Proteins 29, 172-185, 1997.  Full Paper (.pdf)

J87. "Short-range conformational energies, secondary structure propensities, and recognition of correct sequence-structure matches" I. Bahar, M. Kaplan, & R. L. Jernigan Proteins 29, 292-308, 1997. Full Paper (.pdf)

J88. "Local relaxation in dense media: cooperative kinematics theory and applications." I. Bahar Macromol. Theory & Simulations 6, 881-906, 1997.

J89. "Gaussian dynamics of folded proteins" Haliloglu, T. Bahar, I. & Erman, B.Phys. Rev. Lett. 79, 3090-3093, 1997. Full Paper (.pdf)

J90. "Local dynamics of bulk polybutadiene of various microstructures: Comparison of Theory with NMR Measurements" Baysal, C., Erman, B.; Bahar, I., Laupretre, L., Monnerie, L. Macromolecules 30, 2058-2066, 1997. Full Paper (.pdf)

J91. "Efficient characterization of collective motions and interresidue correlations in proteins by low-resolution simulations" Bahar, I., Erman, B. Haliloglu, T. & Jernigan, R. L. Biochemistry 36, 13512-13523, 1997. Full Paper (.pdf)
 

Publications'96

J68. "A Dynamic Rotational Isomeric State Approach for Extension of the Time Scale of the Local Dynamics Observed in Fully Atomistic Molecular Dynamics Simulations", Haliloglu, T., Bahar, I., Erman, B., Kim E. G. & Mattice, W. L., J. Chem. Phys. 104, 4828-4834, 1996. Full Paper (.pdf)

J69. "Oriented Gelatin- A New Source for High-Performance Materials", W.V. Zhao, A. Kloczkowski, J. E. Mark, B. Erman & I. Bahar J. Macromol. Sci. Pure Appl. Chem. A33, 525-540, 1996.

J70. "Structure-Derived Potentials and Protein Simulations" R. L. Jernigan & I. Bahar Current Opinion in Structural Biology 6, 195-209, 1996. Abstract, Full Paper (.pdf)

J71. "A Molecular Dynamics Analysis of Coupling between Librational Motions and Isomeric Jumps in Chain Molecules" Baysal, C., Atilgan, A. R., Erman, B. & Bahar, I. Macromolecules 29, 2510-2514, 1996. Full Paper (.pdf)

B7. "Segmental Orientation in Deformed Rubbery Networks", I. Bahar and B. Erman, Oriented Polymer Materials, S. Fakirov (Ed.), Huthig & Webf Verlag, Oxford, 1996, p467-481.

J72. "Kinematics of Polymer Chains in Dense Medium. 4. Effect of Backbone Geometry and Application to Polybutadiene" Baysal, C., Erman, B., Bahar, I.& Monnerie, L. Macromolecules 29, 2980-2988, 1996. Full Paper (.pdf)

J73. "Mechanisms of the Exchange of Diblock Copolymers between Micelles at Dynamic Equilibrium" Haliloglu, T., Bahar, I., Erman, B. & Mattice, W. L. Macromolecules 29, 4764-4771, 1996. Full Paper (.pdf)

J74. "Main-Chain Lyotropic Liquid-Crystalline Elastomers. 1. Syntheses of Cross-Linked Polyisocyanate Gels Acquiring Liquid-Crystalline Behavior in the Swollen State", Zhao, W.V., Kloczkowski, A., Mark, J. E., Erman, B.& Bahar, I. Macromolecules 29, 2796-2804, 1996. Full Paper (.pdf)

J75. "Main-Chain Lyotropic Liquid-Crystalline Elastomers. 2. Orientation and Mechanical Properties of Polyisocyanate Films", Zhao, W. V., Kloczkowski, A., Mark, J. E., Erman, B. & Bahar, I. Macromolecules 29, 2805-2812, 1996.

J76. "The Response of a Single Grafted Chain to Shear Flow. A Brownian Dynamics Simulation Study", Haliloglu, T., Bahar, I. & Erman, B. J. Chemical Physics 105, 2919-2926, 1996. Full Paper (.pdf)

J77. "Coordination geometry of non-bonded residues in globular proteins. Bahar I. & Jernigan, R. L. Folding & Design 1, 357-370, 1996. Full Paper (.pdf)

J78 "Relative contributions of coupled rotations and small amplitude torsions to conformational relaxation in polymers" T. Haliloglu, I. Bahar, B. Erman & W. L. Mattice Macromolecules 29, 8942-8947, 1996. Full Paper (.pdf)

J79. "Make tough plastic films from gelatin" W. Y. Zhao, A. Kloczkowski, J.E. Mark, B. Erman & I. Bahar Chemtech 26, 32-38, 1996.

 

Publications'95

J61."Molecular Orientation in Deformed Bimodal Networks. 1. Theory" I. Bahar, B. Erman, L. Bokobza, and L. Monnerie, Macromolecules 28, 225- 230, 1995. Full Paper (.pdf)

J62. "Molecular Orientation in Deformed Bimodal Networks. 2. Fourier Transform Infrared Measurements on PDMS Networks and Comparison with Theory" by S. Besbes, L. Bokobza, L. Monnerie, I. Bahar, and B. Erman, Macromolecules 28, 231-235, 1995. Full Paper (.pdf)

J63. "Dynamic-Mechanical Study of Amorphous Phases in Poly(ethylene terephtalate)/Nylon-6 Blends" T. Serhatkulu, B. Erman, I. Bahar and S. Fakirov, M. Evstatiev and D. Sapundjieva, Polymer 36, 2371-2377, 1995. Full Paper (.pdf)

J64. "Kinematics of Polymer Chains in Dense Medium. 3. Influence of Intramolecular Conformational Potentials" I. Bahar, N. Baysal B. Erman and L. Monnerie, Macromolecules 28, 1038-1048, 1995. Full Paper (.pdf)

J65. "Segmental Orientation in Deformed Networks. 2. Molecular Theory of Biaxial Deformation" Z. Sarac, B. Erman and I. Bahar, Macromolecules 28, 582-588, 1995. Full Paper (.pdf)

J66. " Dependence of Segmental Orientation on Polymer Conformational Characteristics" T. Haliloglu, I. Bahar and B. Erman, Polymer 36, 4131-4134, 1995. Full Paper (.pdf)

J67. "Coupling Between Different Modes in Local Chain Dynamics: A Modal Correlation Analysis" C. Baysal, A. R. Atilgan, B. Erman and I. Bahar J. Chem. Soc. Faraday Trans. 91, 2483-2490, 1995.
 

Publications'94

J50. " Stabilization of Intermediate Density States in Globular Proteins by Homogeneous Intramolecular Attractive Interactions" I. Bahar and R. L. Jernigan, Biophysical Journal 66, 454, 1994. Abstract

J51. " Cooperative Structural Reorganizations Induced by Nonhomogeneous Intramolecular Interactions in Compact Globular Proteins " I. Bahar and R. L. Jernigan, Biophysical Journal 66, 467, 1994. Abstract

J52. "Computer Simulation of Two-Dimensional Trifunctional Bimodal Networks" G. Sakrak; I. Bahar; B. Erman Macromol. Theory Simul. 3, 151, 1994.

J53. "Effect of Molecular Structures on Local Chain Dynamics: Analytical Approaches and Computational Methods" Bahar, I.; Erman, B.; Monnerie, L. Adv. Polymer Sciences 116, 145-206, Springer-Verlag Berlin Heidelberg 1994.

J54. "Role of Structural Heterogeneities on Segmental Orientation in Deformed Chains: Application to Alternating Copolymers" I. Bahar, T. HaliloÛlu and B. Erman, Macromolecules 27, 1703, 1994. Full Paper (.pdf)

J55. "A Novel Orientation Technique for Semi-Rigid Polymers. 1. Preparation of Cross-linked Cellulose Acetate and Hydroxypropylcellulose Films Having Permanent Anisotropy in the Swollen State", Y. Yang, A. Kloczkowski, J. E. Mark, B. Erman and I. Bahar, Colloid & Polym. Sci 272,284, 1994.

J56. "Structural and Mechanical Studies of a Blend of Poly(butylene terephtalate) and Poly(ether ester) Based on Poly(butylene terephtalate) and Poly(ethylene glycol)" A. A. Apostolov, S. Fakirov, B. Sezen, I. Bahar and A. Kloczkowski, Polymer 35, 5247-5256, 1994.

J57. " Characterization of Interactions and Metal Ion Binding Sites in Proteins" R. L. Jernigan, G. Raghunathan and I. Bahar, Current Opinion in Structural Biology 4, 256-263, 1994.

J58. "Contribution of Bond Rotational Interdependence to Local Chain Dynamics: A Brownian Dynamics Study" C. Baysal, B. Erman and I. Bahar, Macromolecules 27, 3650-2657, 1994.

J59. " Intramolecular Contributions to Stretched Exponential Relaxation Behavior in Polymers" I. Bahar, B. Erman, G. Fytas and W Steffen, Macromolecules 27, 5200-5205, 1994. Full Paper (.pdf)

J60. "A Novel Orientation Technique for Semi-rigid Polymers. 2. Mechanical Properties of the Cellulose Acetate and Hydroxypropyl cellulose Films", J. E. Mark, Y. Yang, A. Kloczkowski, B. Erman and I. Bahar, Colloid & Polym. Sci 272, 393, 1994.

 

Publications'93

J42 "Local Dynamics of Freely Rotating Chains in Dense Systems". B. Erman & I. Bahar Prog. Colloid Polym. Sci. 91, 16, 1993.

J43."Dynamic Rotational Isomeric State Approach for Segmental Motions of cis-Polyisoprene in the Bulk State" I. Bahar, B. Erman, F. Kremer, & E. W. Fischer Prog Colloid Polym. Sci. 91, 1, 1993.

J44. " An Infrared Dichroism Investigation of Segmental Orientation in Dry and Swollen Poly(dimethyl siloxane) Networks " S. Besbes, L. Bokobza, L. Monnerie, I. Bahar & B. Erman, Polymer 34, 1179, 1993.

J45" Orientational Mobility of Uniaxially Deformed Polymer Chains: A Brownian Dynamics Simulation Study" T. Haliloglu, B. Erman & I. Bahar, Polymer Communications 34, 440, 1993.

J46. " Interpretation of Segmental Orientation in Deformed Networks in Terms of Constrained Junction Model of Rubber Elasticity" B. Erman, I. Bahar, S. Besbes, L. Bokobza & L. Monnerie, Polymer 34, 1858, 1993.

J47. " Solvent Effect on Translational Diffusivity and Segmental Orientational Mobility of Polymers in Dilute Solution: A Molecular Dynamics Study" Bahar, I. and Badur, B., Doruker, P. J. Chem. Phys. 99, 2235, 1993. Full Paper (.pdf)

J48. "Effect of Intrachain Constraints and Polymer-Solvent Interactions on Chain Statistics and Dynamics" P. Doruker & I. Bahar, Comp. Polymer Science 3, 87, 1993.

J49. " Stress-Strain-Molecular Orientation in Highly Cross-Linked cis- Polyisoprene Networks" , C. Kanberoglu; I. Bahar & B. Erman, Polymer 34, 4997, 1993.
 

Publications'92

J32. " Segmental Motions of cis-Polyisoprene in the Bulk State: Interpretation of Dielectric Relaxation Data" Bahar, I.; Erman, B.; Kremer, F. & Fischer, E. W., Macromolecules 25, 816, 1992.

B2. " Stresss-Strain and Segmental Orientation in Networks with Semirigid Chains" Erman, B.; Bahar, I.; Kloczkowski, A. & Mark, J. E. in " Elastomeric Polymer Networks" Ed. J. E. Mark & B. Erman, Prentice Hall Polymer Science and Engineering Series, 1992, Prentice Hall, Inc. New Jersey, p142.

J33. "Segmental Orientation in Model Networks of Poly(dimethyl siloxane): Fourier Transform Infrared Dichroism Measurements and Theoretical Interpretation" Besbes, S.; Cermelli, I.; Bokobza, L.; Monnerie, L.; Bahar, I.; Erman, B. & Herz, J. Macromolecules 25, 1949, 1992. Full Paper (.pdf)

J34." Molecular Dynamics Simulations of Poly (dialkylsiloxanes). Equilibrium Statistics and Unperturbed Chain Dimensions" Neuburger, N.; Bahar, I. & Mattice, W. L. Macromolecules 25, 2447, 1992. Full Paper (.pdf)

J35. " Mechanism of Local Conformational Transitions in Poly(dialkyl Siloxanes). Molecular Dynamics Simulation and Dynamic Rotational Isomeric State Approach" Bahar, I.; Neuburger, N. & Mattice, W. L. Macromolecules 25, 4619, 1992. Full Paper (.pdf)

J36."Orientational and Conformational Correlations in Deformed Polymer Chains with Fixed End-to-End Separation: A Brownian Dynamics Simulation Study" by T. Haliloglu, I. Bahar & B. Erman, J. Chem. Phys. 97, 4428, 1992. Full Paper (.pdf)

J37. "Time-Dependent Probability Distribution Functions for Orientational Motions of Segments in Polymer Chains" by T. Haliloglu, B. Erman & I. Bahar, J. Chem. Phys. 97, 4438, 1992. Full Paper (.pdf)

J38. "Nonlinear Kinetics of Spinodal Decomposition and Dissolution of Inhomogeneities formed by Spinodal Decomposition in Polymer Blends" Akcasu, A. Z.; Erman, B. & Bahar, I. Makromolekulare Chemie Makromol. Symp. 62, 43, 1992.

J39. " Theoretical and Experimental Study of Dissolution of Inhomogeneities Formed During Spinodal Decomposition in Polymer Mixtures" Akcasu, A. Z.; Bahar, I.; Erman, B.; Feng, Y. & Han, C. C. J. Chem. Phys. 97, 5782, 1992.

J40. " Kinematics of Polymer Chains with Freely Rotating Bonds in Restrictive Environment. 1. Theory" Bahar, I.; Erman, B. & Monnerie, L. Macromolecules 25, 6309, 1992. Full Paper (.pdf)

J41. " Kinematics of Polymer Chains with Freely Rotating Bonds in Restrictive Environment. 2. Conformational and Orientational Correlations" Bahar, I.; Erman, B. & Monnerie, L. Macromolecules 25, 6315, 1992. Full Paper (.pdf)

B3. " Local Dynamics of Polymers in Restrictive Environment" Erman, B. and Bahar, I. in Polymer Solution, Blends and Interfaces, Eds. I. Noda and D. N. Rubingh, Elsevier Science Publishers B. V., p 197, 1992.

B4. " Novel Orientation Techniques for the Preparation of High- Performance Materials from Semi-Flexible Polymers such as Cellulosics" Erman, B., Bahar, I., Yang, Y., Kloczkowski, A. & Mark, J. E. in Polymer Solution, Blends and Interfaces, Eds. I. Noda & D. N. Rubingh, Elsevier Science Publishers B. V., p 209, 1992.

B5. "Isotropic-Nematic Phase Transitions in Polymer Networks Deformed in the Dry and Swollen States" A. Kloczkowski, J. E. Mark, B. Erman & I. Bahar in Polymer Solution, Blends and Interfaces, Eds. I. Noda & D. N. Rubingh, Elsevier Science Publishers B. V., p 221, 1992.

B6."Networks with Semi-Flexible Chains", B. Erman, I. Bahar, A. Kloczkowski & J. E. Mark, in "Synthesis, Characterization, and Theory of Polymeric Networks and Gels", Ed. S. M. Aharoni, Plenum Press, New York, p.113-126, (1992).
 

Publications'91

J24. "Segmental Orientation in Uniaxially Deformed Networks: A Higher Order Approximation for Finite Chains at Large Deformations " Erman, B., Haliloglu, T., Bahar, I. & Mark, J. E. Macromolecules 24, 901, 1991.

J25." Bimodal Distribution of Relaxational Modes for the Helix-Coil Transition in Poly(oxymethylene) " Bahar, I. & Mattice, W. L. Macromolecules, 24, 877, 1991. Full Paper (.pdf)

J26. " Use of Molecular Dynamics Trajectories for the Formulation of Statistical Weight Matrices for Chains with Symmetric Threefold Rotation Potentials" Mattice, W. L., Zuniga, I., Dodge, R., & Bahar, I., Comp. Polymer Science 1, 35, 1991.

J27. " Conformational Statistics of Poly (dimethyl siloxane). I. Probability Distribution of Rotational Isomers from Molecular Dynamics Simulations " Bahar, I.; Zuniga, I. ; Dodge, R. & Mattice, W. L. Macromolecules 24, 2986, 1991. Full Paper (.pdf)

J28. " Configurational Statistics of Poly(dimethyl siloxane). II. A New Rotational Isomeric State Approach " Bahar, I.; Dodge, R.; Zuniga, I. & Mattice, W. L. Macromolecules 24, 2993, 1991. Full Paper (.pdf)

J29. " A Stochastic Treatment of Conformational Transitions of Polymer Chains in the Sub-Rouse Regime" Bahar, I ., Erman, B. & Monnerie, L. Macromolecules 24, 3618, 1991. Full Paper (.pdf)

J30. "Segmental Orientation in Poly(oxyethylene) Networks" HaliloÛlu, T.; Bahar, I. & Erman, B. Comp. Polymer Science 1, 151, 1991.

J31. " Molecular Dynamics Analysis of Transitions Between Rotational Isomers in Polymethylene with Discrete Hydrogen Atoms " Zuniga, I.; Bahar, I. ; Dodge, R. & Mattice, W. L., J. Chem. Phys. 95, 5348, 1991. Full Paper (.pdf)
 

Publications'90

J17. "A Closed Form Solution for the Internal Dynamics of Polymer Chains: I. Bonds with Independent Rotational Potentials " Kloczkowski, A., Mark, J. E., Bahar, I. & Erman, B. J. Chem. Phys. 92, 4513, 1990. Full Paper (.pdf)

J18. "Local Orientational Motions in Flexible Polymeric Chains " Bahar, I., Erman, B. & Monnerie, L. Macromolecules 23, 1174, 1990. Full Paper (.pdf)

J19. "Efficient Calculation of the Intramolecular Contribution to Orientational Autocorrelation Functions Using Dynamic Rotational Isomeric State Theory " Bahar, I. & Mattice, W. L. Macromolecules 23, 2719, 1990. Full Paper (.pdf)

J20. "Effect of Surrounding Medium on Intramolecular Conformational Changes in Probe Molecules " Bahar, I ., Erman, B. & Monnerie, L. Macromolecules 23, 3805, 1990. Full Paper (.pdf)

J21. "Conformational Characteristics of Poly(ethyl methacrylate). Dipole Moment Measurements and Calculations " Kuntman, A., Baysal, B. & Bahar, I. Macromolecules 23, 4959, 1990. Full Paper (.pdf)

J22. "A Lattice Model for Segmental Orientation in Deformed Polymeric Networks.1. Contribution of Intermolecular Correlations " Erman, B., Bahar, I., Kloczkowski, A. & Mark, J. E. Macromolecules 23, 5335, 1990.

J23. "A Lattice Model for Segmental Orientation in Deformed Polymeric Networks.2. Effect of Chain Stiffness and Thermotropic Interactions " Bahar, I., Erman, B., Kloczkowski, A. & Mark, J. E. Macromolecules 23, 5341, 1990.
 

Publications'89

J11. "Comparison of Dynamic Rotational Isomeric State Results with Previous Expressions for Local Chain Motion " Bahar, I., Erman, B. & Monnerie, L. Macromolecules 22, 431, 1989. Full Paper (.pdf)

J12. "Stochastics of Rotational Isomeric Transitions in Polymer Chains " Bahar, I. J. Chem. Phys. 91, 6525, 1989. Full Paper (.pdf)

J13. "Rheology of Solutions of Rodlike Polymers: Theory and Comparison with Experiments " Erman, B., Bahar, I. & Navard, P. Macromolecules 22, 358, 1989. Full Paper (.pdf)

J14. "Application of the Dynamic Isomeric States Model to Poly(ethylene oxide) and Comparison with Nuclear Magnetic Relaxation Data " Bahar, I. Erman,B. & Monnerie, L. Macromolecules 22, 2396, 1989. Full Paper (.pdf)

J15. "Dynamics of Conformational Transitions to Isomeric States Favoring Intramolecular Excimer Formation in Polymeric Chains: Application to Dimer Models of Polystyrene" Bahar, I. & Mattice, W. L. J. Chem. Phys. 90, 6775, 1989. Full Paper (.pdf)

J16. "Dynamics of Conformational Transitions to Isomeric States Favoring Intramolecular Excimer Formation in Aromatic Polyesters with Methylene or Oxyethylene Spacers " Bahar, I. & Mattice, W. L. J. Chem Phys. 90, 6783, 1989. Full Paper (.pdf)

 

Publications'88

J7 "Effects of Chain Structure and Network Constitution on Segmental Orientation in Deformed Amorphous Polymeric Networks " Erman, B. & Bahar, I. Macromolecules 2l, 452, 1988. Full Paper (.pdf)

J8. "The Configurational Contribution to the Segmental Orientation in Network Chains Subject to Excluded Volume Effect " Bahar, I. & Mattice, W.L. J. Chem. Phys. 89, 1153, 1988. Full Paper (.pdf)

J9. "Anisotropy of Static and Dynamic Orientational Correlations in n- Alkanes" Bahar, I. & Erman, B. J. Chem. Phys. 88, 1228, 1988. Full Paper (.pdf)

J10. "A New Approach to the Relationship Between Chemical Structure and Local Dynamics Nuclear Magnetic Resonance Measurements in Dilute Polymer Solutions " Bahar, I., Erman, B. & Monnerie, L. Polymer Commun. 29, 349, 1988.

 

Publications'87

J3. " Investigation of Local Conformational Transitions in Polymer Chains" Bahar, I. & Erman, B. Macromolecules 20, 1368, 1987.Full Paper (.pdf)

J4. "Determination of Polymer-Solvent Interaction Parameter from Swelling of Networks: The System Poly (2-hydroxy ethyl methacrylate)-Diethylene Glycol" Bahar, I., Erbil, H. Y., Baysal, B. & Erman, B. Macromolecules 20, 1353, 1987. Full Paper (.pdf)

J5. "Osmotic Compressibility and Mechanical Moduli of Swollen Polymer Networks" Bahar, I. & Erman, B. Macromolecules 20, 1696, 1987. Full Paper (.pdf)

J6. "Activation Energies of Local Motions in Polymers by the Dynamic Rotational Isomeric State Model " Bahar, I. & Erman, B. Macromolecules 20, 2310, 1987. Full Paper (.pdf)

 

Publications'86

J1. "Effect of Flow on Solutions of Rodlike Molecules" Bahar, I. & Erman, B. J. Polym. Sci. Polymer Phys.Ed.24, l36l, l986.

J2. "Local Solvent Effects on the Configurational Characteristics of Polymer Chains: Poly (p-chlorostyrene) in Benzene" Bahar, I., Baysal, B. & Erman, B. Macromolecules 19, 1703, 1986. Full Paper (.pdf)
Publications'85

B1."Thermodynamics of Compatibility in Binary Polymeric Mixtures", Bahar, I. in Polymer Blends and Mixtures, NATO ASI Series E: 89, Martinus Nijhoff Publishers, Dordrecht, p.349, l985.
 


Last Updated: March 2006