IVET BAHAR |
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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
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
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-
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2000 European Molecular Biology Organization (EMBO), Elected Member |
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1998 Excellence in Research Award, Bogazici University |
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1997 Turkish Academy of Sciences (TUBA)(*), Elected Member |
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1995 TUBITAK-TWAS Science Prize |
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1991 Sedat Simavi Physical Sciences Prize (joint with B. Erman) |
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1990 Chemistry Award for Young Scientists from TUBITAK (Turkish National Scientific and Technological Research Council) |
(*) Member of ALLEA
(All European Academies)
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-
2006 | 2005 | 2004 | 2003 | 2002 | 2001 | ||
2000 | 1999 | 1998 | 1997 | 1996 | 1995 | 1994 | 1993 |
1992 | 1991 | 1990 | 1989 | 1988 | 1987 | 1986 | 1985 |
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)
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)
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)
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)
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.
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.
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.
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)
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.
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)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.
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)
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)