Publications 2009

J186 Normal Mode Analysis of Biomolecular Structures: Functional Mechanisms of Membrane Proteins. Bahar I, Lezon T, Bakan A, Shrivastava I. (2009) Chem. Rev. DOI: 10.1021/cr900095e

J185 Vibrational dynamics of icosahedrally symmetric biomolecular assemblies compared with predictions based on continuum elasticity. Yang Z, Bahar I, Widom M. (2009)Biophys J. 96: 4438-48.

J184 Zebrafish chemical screening reveals an inhibitor of Dusp6 that expands cardiac cell lineages. Molina G, Vogt A, Bakan A, Dai W, Queiroz de Oliveira P, Znosko W, Smithgall TE, Bahar I, Lazo JS, Day BW, Tsang M. (2009) Nat Chem Biol. 5:680-7

J183 A comparative analysis of the equilibrium dynamics of a designed protein inferred from NMR, X-ray, and computations. (2009) Liu L, Koharudin LM, Gronenborn AM, Bahar I. Proteins, in press.

J182 "Global Motions of the Nuclear Pore Complex: Insights from Elastic Network Models" Lezon TR, Sali A, Bahar I. (2009) PLoS Comput Biol. 9:e1000496

J181 "The intrinsic dynamics of enzymes plays a dominant role in determining the structural changes induced upon inhibitor binding" Ahmet Bakan, Ivet Bahar (2009) Proc Natl Acad Sci USA 106, 14349-14354

J180 "Allosteric Transitions of Supramolecular Systems Explored by Network Models: Application to Chaperonin GroEL" Zheng Yang , Peter Májek, Ivet Bahar (2009) PLoS Comput Biol 5(4): e1000360.

J179"Principal component analysis of native ensembles of biomolecular structures (PCA_NEST): insights into functional dynamics" Lee-Wei Yang, Eran Eyal, Ivet Bahar, Akio Kitao (2009) Bioinformatics 25: 606-614

J178 Discovery of Novel Myc-Max Heterodimer Disruptors with a Three-Dimensional Pharmacophore Model. Mustata G, Follis AV, Hammoudeh DI, Metallo SJ, Wang H, Prochownik EV, Lazo JS, Bahar I. (2009) J Med Chem 52: 1247-1250.

J177 Molecular simulations elucidate the substrate translocation pathway in a glutamate transporter. Gu Y, Shrivastava IH, Amara SG, Bahar I. (2009) Proc Natl Acad Sci U S A. 106:2589-94

Publications 2008

J176 Toward a molecular understanding of the interaction of dual specificity phosphatases with substrates: insights from structure-based modeling and high throughput screening.
Bakan A, Lazo JS, Wipf P, Brummond KM, Bahar I. (2007) Curr Med Chem. 15:2536-44

J175 "Time-resolved mechanism of extracellular gate opening and substrate binding in glutamate transporter"  Shrivastava IH, Jiang J, Amara SG and Bahar I (2008) J Biol. Chem. 2008; 283:28680-28690. PMID: 18678877. (Supplementary Material)

J174 "Structure and dynamic regulation of Src-family kinases"  Engen JR, Wales TE, Hochrein JM, Meyn MA III, Ozkan SB,  Bahar I and Smithgall TE (2008) Cell Mol Life Sci. PMID: 18563293.

J173 "Computational Insights on the Competing Effects of Nitric Oxide in Regulating Apoptosis" Bagci EZ, Vodovotz Y, Billiar TR, Ermentrout B and Bahar I. (2008) PLoS ONE 3, e2249.

J172 "Mechanism of Signal Propagation upon Retinal Isomerization: Insights from Molecular Dynamics Simulations of Rhodopsin Restrained by Normal Modes." Isin B, Schulten K, Tajkhorshid E, Bahar I (2008) Biophysical J 95, 789-803. PMID: 18390613

J171 "Analysis of correlated mutations in HIV-1 protease using spectral clustering." Liu Y, Eyal E, Bahar I (2008) Bioinformatics 24, 1243-50. PMID: 18375964

J170 "Coupling between global dynamics and signal transduction pathways: a mechanism of allostery for chaperonin GroEL." C. Chennubhotla, Z. Yang and Bahar I (2008) Mol. BioSyst. 4, 287-292.

J169 "Toward a molecular understanding of the anisotropic response of proteins to external forces: insights from elastic network models." Eyal E, Bahar I (2008) Biophys J. 94, 3424-35.

Publications 2007

J167 "Intrinsic dynamics of enzymes in the unbound state and relation to allosteric regulation." Bahar I, Chennubhotla C, Tobi D (2007) Curr Opin Struct Biol. 17, 633-40.

J166 "Signal propagation in proteins and relation to equilibrium fluctuations." Chennubhotla C, Bahar I (2007) PLoS Comput Biol 3, 1716-26.

J165 "Markov methods for hierarchical coarse-graining of large protein dynamics." Chennubhotla C, Bahar I (2007) J Comput Biol. 14, 765-76.

J164. "Recruitment of rare 3-grams at functional sites: Is this a mechanism for increasing enzyme specificity?" Dror Tobi, Ivet Bahar (2007)  BMC Bioinformatics  8:226.

J163. "Anisotropic Fluctuations of Amino Acids in Protein Structures: Insights from X-Ray Crystallography and Elastic Network Models" Eyal E, Chennubhotla C, Yang L-W, Bahar I (2007).Bioinformatics 23,  i175-184 (Supplementary Materials)

J162. "Rapid Assessment of Correlated Amino Acids from Pair-to-Pair (P2P) Substitution Matrices" Eyal E, Pietrokovski S and Bahar I. (2007)  Bioinformatics 23, 1837-1839.

J161. "Insights into Equilibrium Dynamics of Proteins from Comparison of NMR and X-ray Data with Computational Predictions" Yang L-W, Eyal E, Chennubhotla C, JunGoo J, Gronenborn AM and Bahar I. (2007)  Structure 15, 741-749.

J160. "Structurally Unique Inhibitors of Human Mitogen-activated Protein Kinase Phosphatase-1 Identified in a Pyrrole Carboxamide Library."Lazo JS, Skoko JJ, Werner S, Mitasev B, Bakan A, Koizumi F, Yellow-Duke A, Bahar I, Brummond KM. (2007) J Pharmacol Exp Ther 322, 940-947.

J159. "The relationship between N-gram patterns and protein secondary structure." Vries JK, Liu X, Bahar I (2007) Proteins 68, 830-838.

J158. "Tenascin cytotactin epidermal growth factor-like repeat binds epidermal growth factor receptor with low affinity." Iyer, AK, Tran KT, Borysenko CW, Cascio M, Camacho CJ, Blair HC, Bahar I, Wells AJ (2007) J. Cell Physiol  211, 748-58.

J157. "Anisotropic network model: systematic evaluation and a new web interface."Eyal E, Yang LW, Bahar I (2006) Bioinformatics  22, 2619-27.

J156. "Predisposition of the dark state of rhodopsin to functional changes in structure." Isin B, Rader AJ, Dhiman HK, Klein-Seetharaman J, Bahar I (2006) Proteins 65, 970-83.

J155. "Topological basis of signal integration in the transcriptional-regulatory network of the yeast, Saccharomyces cerevisiae." Farkas IJ, Wu C, Chennubhotla C, Bahar I, Oltvai ZN (2006) BMC Bioinformatics  7:478.

J154. "Markov propagation of allosteric effects in biomolecular systems: application to GroEL-GroES" Chakra Chennubhotla & Ivet Bahar (2006) Mol Syst Biol. 2:36

J153. "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 (2006) Nucleic Acids Res 34, W24-31

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

B14. "The Gaussian Network Model: Theory and Applications" by AJ Rader. C. Chennubhotla, L.-W. Yang, and I. Bahar, in "Normal Mode Analysis. Theory and Applications to Biological and Chemical Systems" Eds Q. Cui and I Bahar,  Math & Comp Biology Series, Chapman & Hall CRC Press, Taylor & Francis Group, 41-64, 2006.

J151. "An Introduction to Simulation and Visualization of Biological Systems at Multiple Scales: A Summer Training Program for Interdisciplinary Research". R. Munshi, R. D. Coalson, G. B. Ermentrout, J.D. Madura, H. Meirovitch, Joel R. Stiles & I. Bahar (2006) Biotechnology Progress 22, 179-185.

B13. "Markov Methods for Hierarchical Coarse-Graining of Large Protein Dynamics" Chakra Chennubhotla & Ivet Bahar (2006) Lect Notes in Comp Sci 3909, 379-393.

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 (2006) Biophys J 90, 1546-1559.

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

Publications 2005

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

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

J142. "Analysis of the impact of silver ions on creatine amidinohydrolase." Jason Berberich, Lee Wei Yang, Ivet Bahar & Alan J Russell. (2005)ACTA Biomaterialia 1(2), 183-191.

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(2005) ACTA Biomaterialia 1(2), 173-181.

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

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(2005) Bioinformatics 21: 2978 - 2987.

J146. "Coarse-grained normal mode analysis in structural biology." Ivet Bahar & AJ Rader(2005) Curr Opin Struct Biology 15:1-7.

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

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

Publications 2004

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

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

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

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 (2004) Proteins, Structure, Function and Bioinformatics 57: 468-480.

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

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 (2004) Mol Pharmacology 66: 824-833.

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 (2004)  Applied Bioinformatics 3:137-48.

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 (2004) EMBO J. 10, 4484-94.

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 (2004) Polymer 45: 659-668.

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 (2004) Current Molecular Medicine 4, 753-762.

Publications 2003

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

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

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

Publications 2002

J118. "Dynamics of large proteins through hierarchical levels of coarse-grained structures". Doruker P, Jernigan RL & Bahar I. (2002) J Comp Chem 23, 119-12.

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

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

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

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

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

J124. "Residue packing in proteins: Uniform distribution on a coarse-grained scale. " Bagci Z, Jernigan RL, Bahar I. (2002) J. Chem Physics 116, 2269-2276. (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. (2002) Biophys J. 83, 663-680.

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

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. (2001) Biophys. J. 80, 505-515.

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

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

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

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 (2000) Biophysical Journal 78, 2093-2106.

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 (2000) Anticancer Drug Design 15, 79-98.

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

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 (2000) J. Controlled Release 64, 331-333.

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

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 (2000) J. Biomol. Structure & Dynamics, 1, 49-55.

Publications 1999

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 (1999) J. Mol. Biol. 285, 1023-1037.

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 (1999) Macromolecules 32,3017-3024.

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

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

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 (1999) Proteins: Structure, Function, & Genetics 37, 654-667.

B10. "Geometric Regularities among bonded and nonbonded residues in proteins" R. L. Jernigan & I. Bahar. (1999) 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.

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

Publications 1998

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 (1998) Biochemistry 37, 1067-1075.

B8. "Coarse Grained Searches over Protein Conformations" R. L. Jernigan & I. Bahar, (1998) Encyclopedia of Computational Chemistry, by 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.

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

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

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

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

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

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, (1998) Phys. Rev. Lett. 80, 2733-2736.

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

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

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. (1998) Nucleic Acids Research 26, 5212-5217.

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

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 (1998) Protein Science 7, 2578-2586.

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

Publications 1997

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

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

J82. "Role of water on unfolding kinetics of polypeptides studied by molecular dynamics simulations" P. Doruker, I. Bahar (1997) Biophys. J. 72, 2445-2456. 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 (1997) Trends in Polymer Science 5, 155-160.

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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. (1997) Colloid. Polym. Sci. 275, 307-314.

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

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

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

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

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

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. (1997) Macromolecules 30, 2058-2066.

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

Publications 1996

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. (1996) J. Chem. Phys. 104, 4828-4834.

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

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

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. (1996) Macromolecules 29, 2510-2514.

B7. "Segmental Orientation in Deformed Rubbery Networks", I. Bahar and B. Erman (1996) Oriented Polymer Materials, S. Fakirov (Ed.), Huthig & Webf Verlag, Oxford, 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. (1996) Macromolecules 29, 2980-2988.

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

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. (1996) Macromolecules 29, 2796-2804.

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. (1996) Macromolecules 29, 2805-2812.

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

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

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

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

Publications 1995

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

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 (1995) Macromolecules 28, 231-235.

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, (1995) Polymer 36, 2371-2377.

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

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

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

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

Publications 1994

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

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

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

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

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

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 (1994) Colloid & Polym. Sci 272,284.

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, (1994) Polymer 35, 5247-5256.

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

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

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

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, (1994) Colloid & Polym. Sci 272, 393.

Publications 1993

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

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 (1993) Colloid Polym. Sci. 91, 1.

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, (1993) Polymer 34, 1179.

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

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, (1993) Polymer 34, 1858.

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. (1993) J. Chem. Phys. 99, 2235.

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

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

Publications 1992

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, (1992) Prentice Hall Polymer Science and Engineering Series, 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. (1992) Macromolecules 25, 1949.

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

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. (1992) Macromolecules 25, 4619.

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 (1992) J. Chem. Phys. 97, 4428.

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

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

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. (1992) J. Chem. Phys. 97, 5782.

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

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

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

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. (1992) in Polymer Solution, Blends and Interfaces, Eds. I. Noda & D. N. Rubingh, Elsevier Science Publishers B. V., p 209.

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

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

Publications 1991

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. (1991) Macromolecules 24, 901.

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

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., (1991) Comp. Polymer Science 1, 35, .

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. (1991) Macromolecules 24, 2986.

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

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

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

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

Publications 1990

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. (1990) J. Chem. Phys. 92, 4513.

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

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

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

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

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. (1990) Macromolecules 23, 5335.

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. (1990) Macromolecules 23, 5341.

Publications 1989

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

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

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

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. (1989) Macromolecules 22, 2396.

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. (1989) J. Chem. Phys. 90, 6775.

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. (1989) J. Chem Phys. 90, 6783.

Publications 1988

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

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

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

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. (1988) Polymer Commun. 29, 349.

Publications 1987

J3.“Investigation of Local Motions in Polymers by the Dynamic
Rotational Isomeric State Model” Bahar, I. & Erman, B. (1987) Macromolecules 20, 1368.

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. (1987) Macromolecules 20, 1353.

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

J6.“Activation Energies of Local Conformational Transitions in Polymer Chains” Bahar, I. & Erman, B. (1987) Macromolecules 20, 2310.

Publications 1986

J1. "Effect of Flow on Solutions of Rodlike Molecules" Bahar, I. & Erman, B. ( 1986) J. Polym. Sci. Polymer Phys.Ed.24, l36l,.

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

Publications 1985

B1."Thermodynamics of Compatibility in Binary Polymeric Mixtures", Bahar, I. (1985) in Polymer Blends and Mixtures, NATO ASI Series E: 89, Martinus Nijhoff Publishers, Dordrecht, p.349, .