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Publications 2014

CITATIONS

J236. Zomot E, Gur M, Bahar I (2014) Microseconds Simulations Reveal a New Sodium-Binding Site and the Mechanism of Sodium-Coupled Substrate Uptake by LeuT J of Biol Chem pii: jbc.M114.617555 PMID: 25381247

J235. Cheng MH, Bahar I (2014) Complete Mapping of Substrate Translocation Highlights the Role of LeuT N-terminal Segment in Regulating Transport Cycle PLoS Comput Biol 10: e1003879 PMID: 25299050

J234. Cobanoglu MC, Oltvai ZN, Taylor DL, Bahar I (2014) BalestraWeb: Efficient, online evaluation of drug-target interactions Bioinformatics PMID: 25192741 [Epub ahead of print]

J233. Liu B, Bhatt D, Oltvai ZN, Greenberger JS, Bahar I (2014) Significance of p53 dynamics in regulating apoptosis in response to ionizing radiation, and polypharmacological strategies Sci Rep 4: 6245 PMID: 25175563; PMC4150106

J232. Bahar I (2014) Coupling between Neurotransmitter Translocation and Protonation State of a Titratable Residue during Na(+)-Coupled Transport Biophys J 106: 2547-8 PMID: 24940770; PMC4070272

J231. Bakan A,* Dutta A,* Mao W, Liu Y, Chennubhotla C, Lezon TR, Bahar I (2014) Evol and ProDy for Bridging Protein Sequence Evolution and Structural Dynamics Bioinformatics PMID: 24849577; PMC4155247

J230. O'Reilly LP,* Long OS,* Cobanoglu MC,* Benson JA, Luke CJ, Miedel MT, Hale P, Perlmutter DH, Bahar I, Silverman GA, Pak SC (2014) A genome-wide RNAi screen identifies potential drug targets in a C. elegans model of α1-antitrypsin deficiency Hum Mol Genet PMID: 24838285; PMC4159156

J229. LaRusch J, Jung J, General I, Lewis MD, Woo Park H, Brand RE, Gelrud A, Anderson MA, Banks PA, Conwell D, Lawrence C, Romagnuolo J, Baillie J, Alkaade S, Cote' G, Gardner TB, Amann ST, Slivka A, Sandhu B, Aloe A, Kienholz ML, Yadav D, Barmada MM, Bahar I, Lee MG, Whitcomb DC, North American Pancreatitis Study Group (2014) Mechanisms of CFTR functional variants that impair regulated bicarbonate permeation and increase risk for pancreatitis but not for cystic fibrosis PLoS Genetics 10: e1004376 PMID: 25033378; PMC4102440

J228. General IJ, Liu Y, Blackburn M, Mao W, Gierasch L, Bahar I (2014) ATPase subdomain IA is a mediator of interdomain allostery in Hsp70 molecular chaperones PLoS Comp Bio 10: e1003624 PMID: 24831085; PMC4022485

J227. Korotchenko VN, Saydmohammed M, Vollmer LL, Bakan A, Sheetz K, Debiec KT, Greene KA, Agliori CS, Bahar I, Day BW, Vogt A, Tsang M (2014) In Vivo Structure-Activity Relationship Studies Support Allosteric Targeting of a Dual Specificity Phosphatase ChemBioChem 15: 1436-1445 PMID: 24909879; PMC4118675

J226. Das A, Gur M,* Cheng MH,* Jo S, Bahar I, Roux B (2014) Exploring the conformational transitions of biomolecular systems using a simple two-state anisotropic network model PLoS Comput Biol 10: e1003521 PMID: 24699246; PMC3974643

J225. Jiang J, Bakan A, Kapralov AA, Ishara Silva K, Huang Z, Amoscato AA, Peterson J, Krishna Garapati V, Saxena S, Bayir H, Atkinson J, Bahar I, Kagan VE (2014) Designing inhibitors of cytochrome c/cardiolipin peroxidase complexes: mitochondria-targeted imidazole-substituted fatty acids Free Radic Biol Med 71C: 221-230 PMID: 24631490

J224. Lui VW, Peyser ND, Ng PK, Hritz J, Zeng Y, Lu Y, Li H, Wang L, Gilbert BR, General IJ, Bahar I, Ju Z, Wang Z, Pendleton KP, Xiao X, Du Y, Vries JK, Hammerman PS, Garraway LA, Mills GB, Johnson DE, Grandis JR (2014) Frequent mutation of receptor protein tyrosine phosphatases provides a mechanism for STAT3 hyperactivation in head and neck cancer Proc Natl Acad Sci USA 111: 1114-9 PMID: 24395800; PMC3903220

Publications 2013

J223. Cobanoglu MC, Liu C, Hu F, Oltvai ZN, Bahar I (2013) Predicting drug-target interactions using probabilistic matrix factorization J Chem Inf Model 53: 3399-409 PMID: 24289468; PMC3871285

J222. Chu CT, Ji J, Dagda RK, Jiang JF, Tyurina YY, Kapralov AA, Tyurin VA, Yanamala N, Shrivastava IH, Mohammadyani D, Wang KZQ, Zhu J, Klein-Seetharaman J, Balasubramanian K, Amoscato AA, Borisenko G, Huang Z, Gusdon AM, Cheikhi A, Steer EK, Wang R, Baty C, Watkins S, Bahar I, Bayir H, Kagan VE (2013) Cardiolipin externalization to the outer mitochondrial membrane acts as an elimination signal for mitophagy in neuronal cells Nature Cell Biology 15: 1197-1205 PMID: 24036476; PMC3806088

J221. Gur M, Madura JD, Bahar I (2013) Global transitions of proteins explored by a multiscale hybrid methodology: Application to adenylate kinase Biophys J 105: 1643-1652 PMID: 24094405; PMC3791301

J220. Gur M, Zomot E, Bahar I (2013) Global motions exhibited by proteins in micro- to milliseconds simulations concur with anisotropic network model predictions J Chem Phys 139: 121912. PMID: 24089724; PMC3739829

J219. Cheng MH, Bahar I (2013) Coupled global and local changes direct substrate translocation by neurotransmitter-sodium symporter ortholog LeuT Biophys J 105: 630-639. PMID: 23931311; PMC3736663

J218. Zomot E, Bahar I (2013) Intracellular gating in an inward-facing state of aspartate transporter GltPh is regulated by the movements of the helical hairpin HP2 J Biol Chem 288: 8231-8237. PMID: 23386619; PMC3605641

Publications 2012

J217. Perez A, Yang Z, Bahar I, Dill KA, MacCallum JL (2012) FlexE: Using elastic network models to compare models of protein structure J Chem Theor Comp 8: 3985-3991.

J216. Kurkcuoglu Z, Bakan A, Kocaman D, Bahar I, Doruker P (2012) Coupling between catalytic loop motions and enzyme global dynamics PLoS Comput Biol 8: e1002705. PMID: 23028297; PMC3459879

J215. Bhatt D, Bahar I (2012) An adaptive weighted ensemble procedure for efficient computation of free energies and first passage rates J Chem Phys 137: 104101. PMID: 22979844; PMC3460967

J214. Dutta A, Shrivastava IH, Sukumaran M, Greger IH, Bahar I (2012) Comparative dynamics of NMDA- and AMPA-Glutamate receptor N-terminal domains Structure 20: 1838-49. PMID: 22959625; PMC3496038

J213. Isin B, Tirupula KC, Oltvai ZN, Klein-Seetharaman J, Bahar I (2012) Identification of motions in membrane proteins by elastic network models and their experimental validation Methods Mol Biol 914: 285-317. PMID: 22976035

J212. Zomot E, Bahar I (2012) A conformational switch in a partially unwound helix selectively determines the pathway for substrate release from the carnitine/-butyrobetaine antiporter CaiT J Biol Chem 287: 31823-32. PMID: 22843728; PMC3442516

J211. Bakan A, Nevins N, Lakdawala AS, Bahar I (2012) Druggability assessment of allosteric proteins by dynamics simulations in the presence of probe molecules J Chem Theory Comput 8: 2435-2447. PMID: 22798729; PMC3392909

J210. Liu Y, Bahar I (2012) Sequence evolution correlates with structural dynamics Mol Biol Evol 29: 2253-63.PMID: 22427707; PMC3424413

J209. Lezon TR, Bahar I (2012) Constraints imposed by the membrane selectively guide the alternating access dynamics of the glutamate transporter GltPh Biophys J 102: 1331-40. PMID: 22455916; PMC3309413

J208. Liberles DA, Teichmann SA, Bahar I, Bastolla U, Bloom J, Bornberg-Bauer E, Colwell LJ, de Koning AP, Dokholyan NV, Echave J, Elofsson A, Gerloff DL, Goldstein RA, Grahnen JA, Holder MT, Lakner C, Lartillot N, Lovell SC, Naylor G, Perica T, Pollock DD, Pupko T, Regan L, Roger A, Rubinstein N, Shakhnovich E, Sjölander K, Sunyaev S, Teufel AI, Thorne JL, Thornton JW, Weinreich DM, Whelan S (2012) The interface of protein structure, protein biophysics, and molecular evolution Protein Science 21: 769-85. PMID: 22528593; PMC3403413

J207. Liu L, Byeon IL, Bahar I, Gronenborn AM (2012) Domain swapping proceeds via complete unfolding: A 19F- and 1H- NMR study of the cyanovirin-N protein J Am Chem Soc 134: 4229-35. PMID: 22296296; PMC3326405

Publications 2011

J206. Liu L, Gronenborn AM, Bahar I (2011) Longer simulations sample larger subspaces of conformations while maintaining robust mechanisms of motion Proteins 80: 616-624. PMID: 22105881; PMC3290687

J205. Marcos E, Crehuet R, Bahar I (2011) Changes in dynamics upon oligomerization regulate substrate binding and allostery in amino acid kinase family members PLoS Comput Biol 9: e1002201. PMID: 21980279; PMC3182869

J204. Jiang J, Shrivastava IH, Watts SD, Bahar I, Amara SG (2011) Large collective motions regulate the functional properties of glutamate transporter trimers Proc Natl Acad Sci USA 108: 15141-6. PMID: 21876140; PMC3174670

J203. Meireles L, Gur M, Bakan A, Bahar I (2011) Pre-existing soft modes of motion uniquely defined by native contact topology facilitate ligand binding to proteins Protein Science 20: 1645-58. PMID: 21826755; PMC3218357

J202. Morel PA, Srinivas M, Turner MS, Fuschiotti P, Munshi R, Bahar I, Feili-Hariri M, Ahrens ET (2011) Gene expression analysis of dendritic cells that prevent diabetes in NOD mice: analysis of chemokines and costimulatory molecules J Leukoc Biol 90: 539-50. PMID: 21628331; PMC3157898

J201. Eyal E, Anindita D, Bahar I (2011) Cooperative dynamics of proteins unraveled by network models WIREs Computational Molecular Science 1: 426-439.

J200. Zomot E, Bahar I (2011) Protonation of glutamate-208 induces the release of agmatine in an outward-facing conformation of arginine/agmatine antiporter J Biol Chem 286: 19693-701. PMID: 21487006; PMC3103348

J199. Bakan A, Meireles LM, Bahar I (2011) ProDy: Protein dynamics inferred from theory and experiments Bioinformatics 27: 1575-1577. PMID: 21471012; PMC3102222

J198. Sukumaran M, Rossmann M, Shrivastava I, Dutta A, Bahar I, Gregor IH (2011) Dynamics and allosteric potential of the AMPA receptor N-terminal domain EMBO J 30: 972-82. PMID: 21317871; PMC3049213

J197. DeChancie J, Shrivastava IH, Bahar I (2011) Mechanism of substrate release by the aspartate transporter GltPh: Insights from simulations Mol. BioSyst 7:832-842. PMID: 21161089; PMC3227142

J196. Bakan A, Bahar I (2011) Computational generation inhibitor-bound conformers of p38 map kinase and comparison with experiments Pac Symp Biocomput 2011: 181-92. PMID: 21121046

J195. Mustata G, Li M, Zevola N, Bakan A, Zhang L, Epperly M, Greenberger JS, Yu J, Bahar I (2011) Development of small-molecule PUMA inhibitors for mitigating radiation-induced cell death Curr Top Med Chem 11: 281-90. PMID: 21320058; PMC3086011

Publications 2010

J194. Liu Y, Gierasch LM, Bahar I (2010) Role of Hsp70 ATPase domain intrinsic dynamics and sequence evolution in enabling its functional interactions with NEFs PLoS Comput Biol 6: e1000931. PMID: 20862304; PMC2940730

J193. Dutta A, Bahar I (2010) Metal-binding sites are designed to achieve optimal mechanical and signaling properties Structure 18: 1140-8. PMID: 20826340; PMC2937013

J192. Lezon TR, Bahar I (2010) Using entropy maximization to understand the determinants of structural dynamics beyond native contact topology PLoS Comput Biol 6: e:1000816. PMID: 20585542; PMC2887458

J191. Bahar I (2010) On the functional significance of soft modes predicted by coarse-grained models for membrane proteins J Gen Physiol 135: 563-73. PMID: 20513758; PMC2888054

J190. Zomot E, Bahar I (2010) The sodium/galactose symporter crystal structure is a dynamic, not so occluded state Mol Biosyst 6: 1040 -1046. PMID: 20358053; PMC2938171

J189. Marcos E, Crehuet R, Bahar I (2010) On the conservation of the slow conformational dynamics within the amino acid kinase family: NAGK the paradigm PLoS Comput Biol 6: e1000738. PMID: 20386738; PMC2851564

J188. Bahar I, Lezon TR, Yang LW, Eyal E (2010) Global Dynamics of Proteins: Bridging Between Structure and Function Annu Rev Biophys 39: 23-42. PMID: 20192781; PMC2938190

J187. Liu Y, Bahar I (2010) Toward understanding allosteric signaling mechanisms in the ATPase domain of molecular chaperones Pac Symp Biocomput 2010: 269-80. PMID: 1990837; PMC2938181

J186. Bahar I, Lezon T, Bakan A, Shrivastava I (2010) Normal mode analysis of biomolecular structures: functional mechanisms of membrane proteins Chem Rev 110: 1463-1497. PMID: 19785456; PMC2836427

Publications 2009

B15. Lezon TR, Shrivastava IH, Yang Z, Bahar I. in Handbook on Biological Networks. Edited by Boccaletti S, Latora V, Moreno Y (2009) Elastic network models for biomolecular dynamics: Theory and application to membrane proteins and viruses World Scientific

J185. Yang Z, Bahar I, Widom M (2009) Vibrational dynamics of icosahedrally symmetric biomolecular assemblies compared with predictions based on continuum elasticity Biophys J 96: 4438-48. PMID: 19486668; PMC2711457

J184. 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) Zebrafish chemical screening reveals an inhibitor of Dusp6 that expands cardiac cell lineages Nat Chem Biol 5: 680-7. PMID: 19578332; PMC2771339

J183. Liu L, Koharudin LM, Gronenborn AM, Bahar I (2009) A comparative analysis of the equilibrium dynamics of a designed protein inferred from NMR, X-ray, and computations Proteins 77: 927-939. PMID: 19688820; PMC2767477

J182. Lezon TR, Sali A, Bahar I (2009) Global Motions of the Nuclear Pore Complex: Insights from Elastic Network Models PLoS Comput Biol 9: e1000496. PMID: 19730674; PMC2725293

J181. Bakan A, Bahar I (2009) The intrinsic dynamics of enzymes plays a dominant role in determining the structural changes induced upon inhibitor bindingProc Natl Acad Sci USA 106: 14349-14354. PMID: 19706521; PMC2728110

J180. Yang Z, Májek P, Bahar I (2009) Allosteric Transitions of Supramolecular Systems Explored by Network Models: Application to Chaperonin GroEL  PLoS Comput Biol 5: e1000360. PMID: 19381265; PMC2664929

J179. Yang LW, Eyal E, Bahar I, Kitao A (2009) Principal component analysis of native ensembles of biomolecular structures (PCA_NEST): insights into functional dynamics  Bioinformatics 25: 606-614. PMID: 19147661; PMC2647834

J178. Mustata G, Follis AV, Hammoudeh DI, Metallo SJ, Wang H, Prochownik EV, Lazo JS, Bahar I (2009) Discovery of Novel Myc-Max Heterodimer Disruptors with a Three-Dimensional Pharmacophore Model J Med Chem 52: 1247-1250. PMID: 19215087; PMC2765518

J177. Gu Y, Shrivastava IH, Amara SG, Bahar I (2009) Molecular simulations elucidate the substrate translocation pathway in a glutamate transporter Proc Natl Acad Sci U S A 106: 2589-94. PMID: 19202063; PMC2637273

Publications 2008

J176. Bakan A, Lazo JS, Wipf P, Brummond KM, Bahar I (2008) Toward a molecular understanding of the interaction of dual specificity phosphatases with substrates: insights from structure-based modeling and high throughput screening
Curr Med Chem 15: 2536-44. PMID: 18855677; PMC2764859

J175. Shrivastava IH, Jiang J, Amara SG, Bahar I (2008) Time-resolved mechanism of extracellular gate opening and substrate binding in glutamate transporter  J Biol Chem 283: 28680-28690. PMID: 18678877; PMC2568915  (Supplementary Material)

J174. Engen JR, Wales TE, Hochrein JM, Meyn MA III, Ozkan SB, Bahar I, Smithgall TE (2008) Structure and dynamic regulation of Src-family kinases  Cell Mol Life Sci 65: 3058-73.

J173. Bagci EZ, Vodovotz Y, Billiar TR, Ermentrout B, Bahar I (2008) Computational Insights on the Competing Effects of Nitric Oxide in Regulating Apoptosis PLoS ONE 3: e2249. PMID: 18509469; PMC2386238

J172. Isin B, Schulten K, Tajkhorshid E, Bahar I (2008) Mechanism of Signal Propagation upon Retinal Isomerization: Insights from Molecular Dynamics Simulations of Rhodopsin Restrained by Normal Modes Biophysical J 95: 789-803.  PMID: 18390613; PMC2440475

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

J170. Chennubhotla C, Yang Z, Bahar I (2008) Coupling between global dynamics and signal transduction pathways: a mechanism of allostery for chaperonin GroEL Mol. BioSyst 4: 287-292. PMID: 18354781

J169. Eyal E, Bahar I (2008) Toward a molecular understanding of the anisotropic response of proteins to external forces: insights from elastic network models Biophys J 94: 3424-35. PMID: 18223005; PMC2292382

Publications 2007

J168. Bahar I, Chennubhotla C, Tobi D (2007) Intrinsic dynamics of enzymes in the unbound state and relation to allosteric regulation Curr Opin Struct Biol 17: 633-40. PMID: 18024008; PMC2197162

J167. Chennubhotla C, Bahar I (2007) Signal propagation in proteins and relation to equilibrium fluctuations PLoS Comput Biol 3, 17: 16-26. PMID: 17892319; PMC1988854

J166. Chennubhotla C, Bahar I (2007) Markov methods for hierarchical coarse-graining of large protein dynamics J Comput Biol 14: 765-76. PMID: 17691893

J165. Tobi D, Bahar I (2007) Recruitment of rare 3-grams at functional sites: Is this a mechanism for increasing enzyme specificity?   BMC Bioinformatics  8: 226. PMID: 17598909

J164. Eyal E, Chennubhotla C, Yang L-W, Bahar I (2007)Anisotropic Fluctuations of Amino Acids in Protein Structures: Insights from X-Ray Crystallography and Elastic Network Models Bioinformatics 23: i175-i184. PMID: 17646294 (Supplementary Materials)

J163.Eyal E, Pietrokovski S, Bahar I (2007) Rapid Assessment of Correlated Amino Acids from Pair-to-Pair (P2P) Substitution Matrices   Bioinformatics 23: 1837-1839. PMID: 17496318

J162. Yang L-W, Eyal E, Chennubhotla C, JunGoo J, Gronenborn AM, Bahar I (2007)Insights into Equilibrium Dynamics of Proteins from Comparison of NMR and X-ray Data with Computational Predictions   Structure 15: 741-749. PMID: 17562320; PMC2760440

J161. Lazo JS, Skoko JJ, Werner S, Mitasev B, Bakan A, Koizumi F, Yellow-Duke A, Bahar I, Brummond KM (2007) Structurally Unique Inhibitors of Human Mitogen-activated Protein Kinase Phosphatase-1 Identified in a Pyrrole Carboxamide Library J Pharmacol Exp Ther 322: 940-947. PMID: 17538006

J160. Vries JK, Liu X, Bahar I (2007) The relationship between N-gram patterns and protein secondary structure Proteins 68: 830-838. PMID: 17523186

J159. Iyer, AK, Tran KT, Borysenko CW, Cascio M, Camacho CJ, Blair HC, Bahar I, Wells AJ (2007)Tenascin cytotactin epidermal growth factor-like repeat binds epidermal growth factor receptor with low affinity J Cell Physiol  211: 748-58. PMID: 17311283

Publications 2006

J158. Eyal E, Yang LW, Bahar I (2006)Anisotropic network model: systematic evaluation and a new web interface Bioinformatics 22: 2619-27. PMID: 16928735

J157. Isin B, Rader AJ, Dhiman HK, Klein-Seetharaman J, Bahar I (2006) Predisposition of the dark state of rhodopsin to functional changes in structure Proteins 65: 970-83. PMID: 17009319

J156. Farkas IJ, Wu C, Chennubhotla C, Bahar I, Oltvai ZN (2006) Topological basis of signal integration in the transcriptional-regulatory network of the yeast, Saccharomyces cerevisiae BMC Bioinformatics 7: 478. PMID: 17069658; PMC1643839

J155. Chennubhotla C, Bahar I (2006) Markov propagation of allosteric effects in biomolecular systems: application to GroEL-GroES Mol Syst Biol 2: 36. PMID: 16820777; PMC1681507

J154. Yang LW, Rader AJ, X Liu, CJ Jursa, SC Chen, HA Karimi, Bahar I (2006) oGNM: online computation of structural dynamics using the Gaussian Network Model Nucleic Acids Res 34: W24-31. PMID: 16845002; 16845002

J153. Shrivastava IH, Bahar I (2006) Common Mechanism of Pore Opening Shared by Five Different Potassium Channels Biophys J 90: 3929-3940. PMID: 16533848; PMC1459499

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

J152. Munshi R, Coalson RD, Ermentrout GB, Madura JD, Meirovitch H, Stiles JR, Bahar I (2006) An Introduction to Simulation and Visualization of Biological Systems at Multiple Scales: A Summer Training Program for Interdisciplinary Research Biotechnology Progress 22: 179-185. PMID: 16454509

B13. Chennubhotla C, Bahar I (2006) Markov Methods for Hierarchical Coarse-Graining of Large Protein Dynamics Lect Notes in Comp Sci 3909: 379-393.

J151. Bagci EZ, Vodovotz Y, Billiar TR, Ermentrout GB, Bahar I (2006) Bistability in Apoptosis: Roles of Bax, Bcl-2, and Mitochondrial Permeability Transition Pores" Biophys J 90: 1546-1559.

J150. Tobi D, Bahar I (2006) Optimal Design of Protein Docking Potentials: Efficiency and Limitations Proteins: Structure, Function, and Bioinformatics 62: 970-981. PMID: 16385562


Publications 2005

J141. Rader AJ, Vlad D, Bahar I (2005) "Maturation Dynamics of Bacteriophage HK97 Capsid" RStructure  13: 413-21. PMID: 15766543

J142. Ramaswamy A, Bahar I, Ioshikhes I (2005) "Structural Dynamics of Nucleosome Core Particle: Comparison with Nucleosomes Containing Histone Variants" Proteins: Structure, Function and Bioinformatics 58: 683-696. PMID: 15624215

J143. Berberich J, Yang L-W, Bahar I, Russell AJ (2005)"Analysis of the impact of silver ions on creatine amidinohydrolase" ACTA Biomaterialia 1(2): 183-191. PMID: 16701795

J144. Berberich J, Yang L-W, Madura J, Bahar I, Russell AJ (2005) "A Stable Three Enzyme Creatinine Biosensor Impact of structure, function and environment on PEGylated and immobilized sarcosine oxidase" ACTA Biomaterialia 1(2): 173-181. PMID: 16701794

J145. Yang L-W, Bahar I (2005) Coupling between Catalytic Site and Collective Dynamics: A requirement for Mechanochemical Activity of Enzymes Structure 13: 893-904. PMID: 15939021; PMC1489920

J146. Yang L-W, Liu X, Jursa CJ, Holliman M, Rader AJ, Karimi H, Bahar I (2005) "iGNM: A Database of Protein Functional Motions Based on Gaussian Network Model" Bioinformatics 21: 2978 - 2987. PMID: 15860562; PMC1752228

J147. Bahar I, Rader AJ (2005) "Coarse-grained normal mode analysis in structural biology" Curr Opin Struct Biology 15: 1-7. PMID: 16143512; PMC1482533

J148. Tobi D, Bahar I (2005) "Structural Changes Involved in Protein Binding Correlate with intrinsic Motions of Proteins in the Unbound State" Proc Natl Acad Sci (USA) 102: 18908-18913. PMID: 16354836; PMC1323175

J149. Chennubhotla C, Rader AJ, Yang L-W, Bahar I (2005) "Elastic network models for understanding biomolecular machinery: from enzymes to supramolecular assemblies" CPhysical Biology 2: S173-S180. PMID: 16280623

Publications 2004

J130. Wang Y, Rader AJ, Bahar I, Jernigan RL (2004) "Global Ribosome Motions Revealed with Elastic Network Model" J Struct Biol 147: 302-314. PMID: 15450299

J132. Rader AJ, Anderson G, Isin B, Khorana HG, Bahar I, Klein-Seetharaman J (2004) "Identification of core amino acids stabilizing rhodopsin" Proc Natl Acad Sci USA 101: 7246-7251. PMID: 15123809; PMC409904

J132. Chen S-C, Bahar I (2004)"Mining frequent patterns in proteins: A study of serine proteinases" Bioinformatics 20: i77-i85. PMID: 15262784

J134. Temiz NA, Meirovitch E, Bahar I (2004) "E. coli Adenylate Kinase Dynamics: Comparison of Elastic Network Model Modes with Mode-Coupling 15N-NMR Relaxation Data" Proteins, Structure, Function and Bioinformatics 57: 468-480. PMID: 15382240; PMC1752299

J135. Sluis-Cremer N, Temiz NA, Bahar I (2004)"Conformational changes in HIV-1 reverse transcriptase induced by nonnucleoside reverse transcriptase inhibitor binding" Current HIV Research 2: 323-32. PMID: 15544453; PMC1298242

J136. Brisson M, Nguyen T, Vogt A, Yalowich J, Giorgianni A, Tobi D, Bahar I, Stephenson CRJ, Wipf P, Lazo JS (2004) "Discovery and characterization of novel small molecule inhibitors of human Cdc25B dual specificity phosphatase" Mol Pharmacology 66: 824-833. PMID: 15231869

J137. Vries JK, Munshi R, Tobi D, Klein-Seetharaman J, Benos PV, Bahar I (2004)"A Sequence Alignment-Independent Method For Protein Classification"   Applied Bioinformatics 3: 137-48. PMID: 15693739

J138. Seki M, Masutani C, Yang L-W, Schuffert A, Iwai S, Bahar I, Wood RD (2004) "High efficiency bypass of DNA damage by a single human DNA polymerase" EMBO J 10: 4484-94. PMID: 15496986; PMC526458

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

J139. Rader AJ, Bahar I (2004) "Folding Core Predictions from Network Models of Proteins" Polymer 45: 659-668.

J140. Vodovotz Y, Kim P, Bagci EZ, Ermentrout GB, Chow CC, Bahar I, Billiar TR (2004) "Inflammatory Modulation of Hepatocyte Apoptosis by Nitric Oxide: In Vivo, In Vitro, and In Silico Studies" Current Molecular Medicine 4: 753-762. PMID: 15579022

Publications 2003

J128. Ozkan SB, Dill KA, Bahar I (2003) "Computing the Transition State Populations in Simple Protein Models" Biopolymers 68: 35-46. PMID: 12579578

J129. Xu C, Tobi D, Bahar I (2003)"Allosteric Changes in Protein Structure Computed by a Simple Mechanical Model: Hemoglobin T --> R2 Transition"   J Mol Biol 333: 153-168.

J130. "Bagci Z, Kloczkowski A, Jernigan RL, Bahar I (2003) The Origin and Extent of Coarse-Grained Regularities in Protein Internal Packing"   Proteins: Structure, Function and Genetics 53: 56-67. PMID: 12945049

Publications 2002

J119. Doruker P, Jernigan RL, Bahar I (2002) "Dynamics of large proteins through hierarchical levels of coarse-grained structures" J Comp Chem 23: 119-12. PMID: 11913377

J120. Ozkan SB, Dill KA, Bahar I (2002) "Fast-folding protein kinetics, hidden intermediates and the sequential stabilization model" OProtein Science 11: 1958-1970. PMID: 12142450; PMC2373683

J121. Doruker P, Bahar I, Baysal C, Erman B (2002) "Collective deformations in proteins determined by a mode analysis of molecular dynamics trajectories" Polymer 43: 431-439.

J122. Isin B, Doruker P, Bahar I (2002) "Functional motions of influenza virus hemagglutinin: A structure-based analytical approach" Biophys J 82: 569-581. PMID: 11806902; PMC1301869

J123. Bagci Z, Jernigan RL, Bahar I (2002) "Residue coordination in proteins conforms to the closest packing of spheres" Polymer 43: 451-459.

J124. Keskin O, Bahar I, Flatow D, Covell DG, Jernigan RL (2002) "Molecular mechanisms of chaperonin GroEL/GroES function" Biochemistry 41: 491-501.

J125. Bagci Z, Jernigan RL, Bahar I (2002) "Residue packing in proteins: Uniform distribution on a coarse-grained scale " 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)

J126. Keskin O, Durell SR, Bahar I, Jernigan RL, Covell DG (2002) "Relating molecular flexibility to function: A case study of tubulin" Biophys J 83: 663-680. PMID: 12124255; PMC1302177

J127. Temiz NA, Bahar I (2002) "Inhibitor binding alters the directions of domain motions in HIV-1 reverse transcriptase" Proteins: Structure, Function and Genetics 49: 61-70.

Publications 2001

J116. Atilgan AR, Durrell SR, Jernigan RL, Demirel MC, Keskin O, Bahar I (2001) " Anisotropy of fluctuation dynamics of proteins with an elastic network model" Biophys J 80: 505-515.

J117. Konuklar FAS, Aviyente V, Sen TZ, Bahar I (2001)"Modeling the deamidation of asparagine residues via succinimide intermediates" J Mol Model 7: 147-160.

J118. Ozkan B, Bahar I, Dill KA (2001) "Transition states and the meaning of F-values in protein folding kinetics" Nature Struct Biol 8: 765-769.

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

Publications 2000

J110. Keskin O, Jernigan RL, Bahar I (2000) "Proteins with similar architecture exhibit similar large-scale dynamic behavior. Specificity resides in local differences" Biophysical Journal 78: 2093-2106.

J111. Keskin O, Bahar I, Jernigan RL, Myers TG, Beutler JA, Shoemaker RH, Sausville EA, Covell DG (2000) "Characterization of anticancer agents by their growth inhibitory activity and relationships to mechanism of action and structure" Anticancer Drug Design 15: 79-98. PMID: 10901296

J112. Haliloglu T, Bahar I, Jernigan RL (2000) "Collective dynamics of class I MHC/peptide complexes and binding to T cell receptors" Biophys J 78: 34A.

J113. Duman G, Keskin O, Bahar I, Robinson JR (2000) "Stabilization of the molten globule state of hen egg white lysozyme with solutions containing polyvinyl pyrrolidone" J Controlled Release 64: 331-333.

J114. Doruker P, Atilgan AR, Bahar I (2000) "Dynamics of proteins predicted by molecular dynamics simulations and analytical approaches: Application to a-amylase inhibitor" Proteins: Structure, Function & Genetics 40: 512-524.

J115. Jernigan RL, Bahar I, Covell DG, Atilgan AR, Erman B, Flatow D (2000) "Relating the structure of HIV-1 reverse transcriptase to its processing step" J Biomol Structure & Dynamics 1: 49-55.

Publications 1999

J104. Bahar I, Erman B, Jernigan RL, Atilgan AR, Covell D (1999) "Collective motions of HIV-1 reverse transcriptase. Examination of Flexibility and Enzyme Function" J Mol Biol 285: 1023-1037.

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

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

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

J108. Haliloglu T, Bahar I (1999) "Structure-based analysis of protein dynamics. Comparison of theoretical results for hen lysozyme with X-ray diffraction and NMR relaxation data" Proteins: Structure, Function & Genetics 37: 654-667.

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

J109. Bahar I (1999) "Dynamics of proteins and biomolecular complexes. Inferring functional motions from structure" Reviews in Chemical Engineering 15: 319-349.

Publications 1998

J92. Bahar I, Wallqvist A, Covell DG, Jernigan RL (1998) "Correlation between native state hydrogen exchange and cooperative residue fluctuations from a simple model" Biochemistry 37: 1067-1075.

B8. Jernigan RL, Bahar I Eds Schleyer P vR, Allinger NL, Clark T, Gasteiger J, Kollman PA, Schaefer III HF, Schreiner PR (1998) "Coarse Grained Searches over Protein Conformations" Encyclopedia of Computational Chemistry John Wiley & Sons: Chichester.

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

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

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

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

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

J98. Bahar I, Atilgan AR, Demirel MC, Erman B (1998)"Vibrational dynamics of proteins: Significance of slow and fast modes in relation to function and stability", Phys. Rev Lett 80: 2733-2736.

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

J100. Demirel MC, Atilgan AR, Jernigan RL, Erman B, Bahar I (1998) "Identification of kinetically hot residues in proteins" Protein Science 7: 2522-2532.

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

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

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

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

Publications 1997

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

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

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

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

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

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

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

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

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

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

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

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

Publications 1996

J68. Haliloglu T, Bahar I, Erman B, Kim EG, Mattice WL (1996) "A Dynamic Rotational Isomeric State Approach for Extension of the Time Scale of the Local Dynamics Observed in Fully Atomistic Molecular Dynamics Simulations" J Chem Phys 104: 4828-4834.

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

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

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

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

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

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

J74. Zhao WV, Kloczkowski A, Mark JE, Erman B, Bahar I (1996) "Main-Chain Lyotropic Liquid-Crystalline Elastomers. 1. Syntheses of Cross-Linked Polyisocyanate Gels Acquiring Liquid-Crystalline Behavior in the Swollen State" Macromolecules 29: 2796-2804.

J75. Zhao WV, Kloczkowski A, Mark JE, Erman B, Bahar I (1996) Main-Chain Lyotropic Liquid-Crystalline Elastomers. 2. Orientation and Mechanical Properties of Polyisocyanate Films, Macromolecules 29: 2805-2812.

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

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

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

J79. Zhao WY, Kloczkowski A, Mark JE, Erman B, Bahar I (1996) "Make tough plastic films from gelatin" Chemtech 26: 32-38.

Publications 1995

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

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

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

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

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

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

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

Publications 1994

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

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

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

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

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

J55. Yang Y, Kloczkowski A, Mark JE, Erman B, Bahar I (1994) "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", Colloid & Polym Sci272: 284.

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

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

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

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

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

Publications 1993

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

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

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

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

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

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

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

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

Publications 1992

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

B2. Erman B, Bahar I, Kloczkowski A, Mark JE Eds Mark JE, Erman B (1992) "Stresss-Strain and Segmental Orientation in Networks with Semirigid Chains" " Elastomeric Polymer Networks" Prentice Hall Polymer Science and Engineering Series Prentice Hall, Inc. New Jersey, p142.

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

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

J35. Bahar I, Neuburger N, Mattice WL (1992) "Mechanism of Local Conformational Transitions in Poly(dialkyl Siloxanes). Molecular Dynamics Simulation and Dynamic Rotational Isomeric State Approach" Macromolecules 25: 4619.

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

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

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

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

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

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

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

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

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

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

Publications 1991

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

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

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

J27. Bahar I, Zuniga I, Dodge R, Mattice WL (1991) " Conformational Statistics of Poly (dimethyl siloxane). I. Probability Distribution of Rotational Isomers from Molecular Dynamics Simulations " Macromolecules 24: 2986.

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

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

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

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

Publications 1990

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

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

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

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

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

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

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

Publications 1989

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

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

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

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

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

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

Publications 1988

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

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

J9. Bahar I, Erman B (1988)a href="publications/10.pdf" target="_blank">"Anisotropy of Static and Dynamic Orientational Correlations in n- Alkanes" J Chem Phys 88: 1228.

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

Publications 1987

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

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

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

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

Publications 1986

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

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

Publications 1985

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