2006 2005



















1.  Kurkcuoglu, O., Doruker, P. & Jernigan, R. L., “Loop Motions of Triosephosphate Isomerase Observed with Elastic Networks”, Biochemistry 45: 1173-1182, 2006.


2.  Doruker, P., Nilsson, L. & Kurkcuoglu, O., “Collective Dynamics of EcoRI-DNA Complex by Elastic Network Model and Molecular Dynamics Simulations”, Journal of Biomolecular Structure & Dynamics 24(1): 1-15, 2006.


3.  Ozer N., T. Haliloglu and C.A. Schiffer, "Substrate specificity in HIV-1 protease by a biased seqeunce search method", Proteins 64: 444-456, 2006.


4.  Kantarci N, Doruker P, Haliloglu T, “Cooperative fluctuations point to the dimerization interface of p53 core domain”, Biophysical Journal 91 (2): 421-432, 2006.


5.  Ertekin A, Nussinov R, Haliloglu T, “Association of putative protein binding sites with the fluctuation behavior of residues”, Protein Science 15(10): 2265-77, 2006.


6.  Konuklar, FAS, Aviyente, V, Haliloglu T, "Influence of Structural Fluctuations on Relationship between the Catalytic Activity and Deamidation Reaction in Triosephosphate Isomerase by Gaussian Network Model (GNM)", Proteins: Structure, Function and Bioinformatics, 62(3): 715-727, 2006.





1.  Kantarci N., Tamerler C., Sarikaya M., Haliloglu T., and Doruker P. “Molecular dynamics simulations on constraint metal binding peptides” Polymer 46: 4307-4313, 2005.


2.  Shental-Bechor, D, Kirca, S, Ben-Tal, N, Haliloglu, T, "Monte Carlo Studies of Folding, Dynamic and Stability in a-Helices", Biophysical Journal, 88 (4): 2391-2402, 2005.


3. Haliloglu, T, Keskin, O, Ma, B, Nussinov, R, "How similar are protein folding and protein binding nuclei? Examination of fluctuations of energy hot spots and conserved residues", Biophysical Journal 88 (3): 1552-1559, 2005.  


4. Kurkcuoglu, O., Jernigan, R.L., Doruker, P. “Collective dynamics of large proteins from mixed coarse-grained elastic network model” QSAR & Combinatorial Science 24: 443-448, 2005.


5. Alakent B., Camurdan M.C., Doruker P. “Hierarchical structure of the energy landscape of proteins revisited by time series analysis. I. Mimicking protein dynamics in different time scales” Journal of Chemical Physics 123, 144910, 2005.


6. Alakent B., Camurdan M.C., Doruker P. “Hierarchical structure of the energy landscape of proteins revisited by time series analysis. II. Investigation of explicit solvent effects” Journal of Chemical Physics 123, 144911, 2005.





1.  Z.T. Hamaudi, N. Nugay N, T. Nugay , “Anionic Polymerization of Methyl Methacrylate as Promoted by a N-butyl Lithium-pyridazine-polyether Alkoxide Based Complex Initiator System”, TURKISH JOURNAL OF CHEMISTRY, Vol. 28, 387-394, 2004.


2.  E. Kucukpinar, P. Doruker, “Effect of Absorbed Water on Oxygen Transport in EVOH Matrices. A Molecular Dynamics Study”,  POLYMER, Vol. 45, 3555-3564, 2004.


3.  O.G. Ersoy, N. Nugay, “A New Approach to Increase Weld Line Strength of Incompatible Polymer Blend Composites: Selective Filler Addition”, POLYMER, Vol. 45, 1243-1252, 2004.


4.  T. Eren, S.H. Kusefoglu, “Hydroxymethylation and Polymerization of Plant Oil Triglycerides”, JOURNAL OF APPLIED POLYMER SCIENCE, Vol. 91, 4037-4046, 2004.


5.  T. Eren, S.H. Kusefoglu, “One Step Hydroxybromination of Fatty Acid Derivatives”, EUROPEAN JOURNAL OF LIPID SCIENCE AND TECHNOLOGY, Vol. 106, 27-34, 2004.


6.  S. Kirca, S.B. Ozkan, T. Haliloglu, “Unfolding Events of Chymotrypsin Inhibitor 2 (CI2) Revealed by Monte Carlo (MC) Simulations and Their Consistency from Structure-based Analysis of Conformations”, POLYMER, Vol. 45, 581-595, 2004.


7.  O. Kurkcuoglu, R.L. Jernigan, P. Doruker, “Mixed Levels of Coarse-graining of Large Proteins Using Elastic Network Model Succeeds in Extracting the Slowest Motions”, POLYMER, Vol. 45, 649-657, 2004.


8.  T. Eren, S.H. Kusefoglu, “Synthesis and Polymerization of the Bromoacrylated Plant Oil Triglycerides to Rigid, Flame-retardant Polymers”, JOURNAL OF APPLIED POLYMER SCIENCE, Vol. 91, 2700-2710, 2004.


9.  B. Alakent, P. Doruker, M.C. Camurdan, “Time series analysis of collective motions in proteins”, JOURNAL OF CHEMICAL PHYSICS, Vol. 120, 1072-1088, 2004.


10. Yildirim Y., Doruker P. “Collective motions of RNA polymerases. Analysis of core enzyme, elongation complex and holoenzyme” Journal of Biomolecular structure & dynamics, 22: 267-280, 2004.


11. Alakent B., Doruker, P., Camurdan, M.C. “Application of time series analysis on molecular dynamics simulations of proteins. A study on different conformational spaces by principal component analysis” Journal of Chemical Physics 121: 4759-4769, 2004.





1.      S.B. Ozkan, K.A. Dill, I. Bahar, “Computing the Transition State Populations in Simple Protein Models”, BIOPOLYMERS, Vol. 68, 35-46, 2003.


2.    O.G. Ersoy, N. Nugay, “Effect of Inorganic Filler Phase on Mechanical and Morphological Properties of Binary Immiscible Polymer Blends”, POLYMER BULLETIN, Vol. 49, 465-472, 2003.


3.    N. Kurt, W.R.P. Scott, C.A. Schiffer, T. Haliloglu, “Cooperative Fluctuations of Unliganded and Substrate-bound HIV-1 Protease: A Structure-based Analysis on a Variety of Conformations from Crystallography and Molecular Dynamics Simulations”, PROTEINS-STRUCTURE FUNCTION AND GENETICS 2003, Vol. 51, 409-422, 2003.


4.    E. Kucukpinar, P. Doruker, “Molecular Simulations of Small Gas Diffusion and Solubility in Copolymers of Styrene”, POLYMER, Vol. 44, 3607-3620, 2003.


5.    N. Kurt, T. Haliloglu, C.A. Schiffer, “Structure-based prediction of potential binding and nonbinding peptides to HIV-1 protease”, BIOPHYSICAL JOURNAL, Vol. 85, 853-863, 2003.


6.    T. Eren, S.H. Kusefoglu, R. Wool, “Polymerization of Maleic Anhydride-modified Plant Oils with Polyols”, JOURNAL OF APPLIED POLYMER SCIENCE, Vol. 90, 197-202, 2003.


7.    H. Esen, S.H. Kusefoglu, “Photolytic and Free-radical Polymerization of Cinnamate Esters of Epoxidized Plant Oil Triglycerides”, JOURNAL OF APPLIED POLYMER SCIENCE, Vol. 89, 3882-3888, 2003.


8.    S. Sen, N. Nugay, T. Nugay, “Synthesis and Properties of Poly(4-vinylpyridine)/Montmorillonite Nanocomposites”, E-POLYMERS, art. No. 049, 2003. 


9.   A. Kessel, T. Haliloglu, N. Ben-Tal, “Interactions of the M2 Delta Segment of the Acetylcholine Receptor with Lipid Bilayers: A Continuum-solvent Model Study”, BIOPHYSICAL JOURNAL, Vol. 85, 3687-3695, 2003.


10. A. Kessel, D. Shental-Bechor, T. Haliloglu, N. Ben-Tal, “Interactions of Hydrophobic Peptides with Lipid Bilayers: Monte Carlo Simulations with M2 Delta”, BIOPHYSICAL JOURNAL, Vol. 85, 3431-3444, 2003.


11. T. Haliloglu, A. Kolinski, J. Skolnick, “Use of Residual Dipolar Couplings as Restraints in ab initio Protein Structure Prediction”, BIOPOLYMERS, Vol. 70, 548-562, 2003.


12. P. Doruker, R.L. Jernigan, “Functional Motions can be Extracted From on-lattice Construction of Protein Structures”, PROTEINS-STRUCTURE FUNCTION AND GENETICS, Vol. 53, 174-181, 2003.





1.       C. Baysal , A.R. Atilgan, "Relaxation Kinetics and the Glassiness of Proteins: The Case of Bovine Pancreatic Trypsin Inhibitor", Biophysics Journal, Vol 83, 699-705, 2002.


2.     T. Nugay, N. Nugay, R. Jerome, "Anionic polymerisation of methyl methacrylate with complex initiator system", Polymer Bulletin, Vol 48, 457-462, 2002.


3.     T. Kayhan, N. Nugay, T. Nugay, "Metallation of Metistylene by Organolithium Compounds in the Presence of Lithium Polyether Alkoxides", Turk J Chem , Vol 26, 965-971, 2002.


4.     P. Doruker, R. L. Jernigan,Isabelle Navizet, Rigoberto Hernandez, "Important Fluctuation Dynamics of Large Protein Structures Are Preserved Upon Coarse-Grained Renormalization", International J. of Quantum Chemistry, Vol 90, 822-837, 2002.


5.     N. Kurt, T. Haliloglu, "Distribution of cooperative interactions in barnase at different time windows by coarse-grained simulations", Polymer, Vol 43, 403-408, 2002.


6.     P. Doruker, "Simulation of polyethlene thin films composed of various chain lengths", Polymer, Vol 43, 425-430, 2002.


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


8.     P. Doruker, R. Jernigan, I. Bahar, "Dynamics of Large Proteins through Hierarchical Levels of Coarse- Grained Structures" J Comput Chem, Vol 23, 119-127, 2002.


9.     N. Nugay, S. Sen, "Swelling, Viscosity and Static-Mechanical Behaviour of Polyester Composites Based on Hybrid Filler System"  Makromol Symp, Vol 175, 421-428, 2002.


10.  B. Isin, P. Doruker, I. Bahar, "Functional Motions of Influenza Virus Hemagglutinin: A Structure-Based Analytical Approach" Biohysical Journal, Vol 82, 569-581, 2002.



1.       A.R. Atilgan, S.R. Durell, R.L. Jernigan, M.C. Demirel, O. Keskin, I. Bahar, "Anisotropy of Flutuation Dynamics of Proteins with an Elastic Network Model" Biophysical Journal, Vol 80, 505-515, 2001.


2.     C. Baysal, A.R. Atilgan, "Elucidating the Structural Mechanisms for Biological Activity of the Chemokine Family" Proteins, Vol 43, 150-160, 2001.


3.     P. Doruker, Y. Wang, W.L. Mattice, "Simulation of random scission of C-C bonds in the initial stage of the thermal degradation of polyethylene" Computational and Theoretical Polymer Science , Vol 11, 155-166, 2001.


4.     N. Kurt, T. Haliloglu, "Conformational Dynamics of Subtilisin-Chymotrypsin Inhibitor 2 Complex by Coarse-Grained Simulations" Journal of Biomolecular Structure & Dynamics, Vol 18, 713-731, 2001.


5.     M. Kahraman, N. Nugay, "Polydimethylsiloxane Composites Reinforced by Fumed Silica/Mica Hybrid Reinfocers" Intern J. Polymeric Mater,  Vol 00, 1-15, 2001.


6.     N. Nugay, B. Erman, "Hybrid Reinforcement in Nitrile Rubber Composites,Macromol Symp, Vol 169, 269-274, 2001.


7.     C. Baysal, A.R. Atilgan, "Coordination Topology and Stability for the Native and Binding Conformers of Chymotrypsin Inhibitor 2" Proteins,  Vol 45, 62-70, 2001.


8.     S. Banu Ozkan, I. Bahar, Ken A. Dill, "Transition states and the meaning of Phi values in protein folding kinetics" Nature Structural Biology,  Vol 8, 765-769, 2001.


9.     P. Doruker, Wayne L. Mattice, "Effect of Surface Rougheness on Structure and Dynamics in Thin Films", Macromol Theory Simul, Vol 10, 363-367, 2001.


10.  N. Nugay, B. Erman, "Propperty Optimization in Nitrile Rubber Composites via Hybrid Filler System" J. Applied Polymer Science, Vol 79, 366-374, 2001.


11.   L. Bokobza, N. Nugay, "Orientational Effect of Mica in Fumed Silica Reinforced Composites" J. Applied Polymer Science, Vol 80, 1-8, 2001.


12.  S. Sen, N. Nugay, "Tuning of final performances of unsaturated polyster composites with inorganic microsphere/platelet hybrid reinforcers" European Polymer Journal, 1-8, 2001.


13.  M. Sahin, N. Nugay, "Thixotropic Behavior of Nitrile rubber Composites Containing Waste Rubber Vulcanizates and Carbon Black" Polymer Preprints, Vol 42, 69, 2001.


14.  T. Nugay, Zahi Tim Hamoudi, "Anionic Polymerization of methyl Methacrylate By Using Self Ligated Initiators" Polymer Preprints, Vol 42, 421, 2001.


15.  Osman Ersoy, N. Nugay, "Weld Line Strength of Polypropylene/Polyarmide Blends" Polymeric Materials Science & Engrineering, Vol 85, 354, 2001.


16.  N. Nugay, T. Nugay, R. Jerome, "Lithiation of tolune by organolithium compounds activated by lithium polyether alkoxides", J of Molecular Catalysis A, Chemical, 3379, 1-6, 2001.


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


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


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


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


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


6.     N. Kurt, T. Haliloglu, "Conformational Dynamics of Chymotrypsin Inhibitor 2 in Free and Complex Forms" ACS Polymeric Materials Science and Engineering, Vol 83, 397-398, 2000.


7.     N. Nugay, T. Nugay, "Inter polymer complexes of poly(methyl methacrylate) block-poly(4- vinlypyridine)with polyacrylate)" Eurapean Polymer Journal, 36, 1027-1033, 2000.


8.     I. Bahar, "Dynamics of proteins and biomolecular complexes: Inferring functional motions from structure" Reviews in Chemical Engineering, Vol 15, 319-347, 2000.


9.     T. Haliloglu, W.L. Mattice, "Simulation of rotational isomeric state models for polypropylene melts on a high coordination lattice" Reviews in Chemical Engineering, Vol 15, 293-305, 2000.


10.  J.H. Jang, T. Haliloglu, E.D. vonMeerwall, W.L. Mattice, "Effect of vinyl content on self-diffusion in polybutadiene melts" Macromolecules, Vol 33, 4271-4277, 2000.


11.   P. Doriker, A.R. Atilgan, I. Bahar, "Dynamics of proteins predicted by molecular dynamics simulations and analytical approaches: Application to alpha-Amylase Inhibitor" Proteins, Vol 40, 512-524, 2000.


12.  L.S. Yilmaz, A.R. Atilgan, "Identifying the adaptive mechanism in globular proteins: Fluctuations in densely packed regions manipulate flexible parts" J of Chemical Physics, Vol 113, 4454-4464, 2000.


1.     I. Bahar, B. Erman, R. L. Jernigan, A. R. Atilgan, & D. Covell, "Collective dynamics of HIV-1 reverse transcriptase" J. Mol. Biol. 285, 1023-1037, 1999.


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


3.     T. Haliloglu, "Characterization of Internal Motions of Escherichia coli Ribonuclease H by Monte Carlo Simulation", Proteins: Structure, Function and Genetics, 34, 533-539, 1999.


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


5.     O. Keskin, I. Bahar, R. L. Jernigan & D. G. Covell, "Characterization of anticancer agents and their growth inhibitory potency. Relationship between potency and chemical structure" Biophys. J. 76, A386, 1999.


6.     R.L. Jernigan, M. C. Demirel & I. Bahar, "Relating structure to function through the dominant modes of motion of DNA topoisomerase II"  Int.J. Quantum Chem. 75, 301-302, 1999.


7.     I.Bahar & R. L. Jernigan, Subunit communication, processing and fluctuations in tryptophan synthase" Biophys. J. 76, A115, 1999.


8.     Haliloglu, T., "Coarse-grained simulations of conformational dynamics of proteins" Theoretical and Computational Polymer Science, 9/3-4, 255-260, 1999.


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


10.  T. Haliloglu & I. Bahar, "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, 1999.


11.   T. Haliloglu, W. L. Mattice, "Simulation of Rotational Isomeric State Models for Polypropylene Melts in a High Coordination Lattice",  Reviews in Chemical Engineering, 15, No:4, 1999.


12.  N. Kurt, T. Haliloglu, "Conformational Dynamics of Chymotrypsin Inhibitor 2 by Coarse-Grained Simulations", Proteins: Structure, Function and Genetics, 37, 454-464, 1999.


13.  T. Haliloglu, "Conformational Dynamics of Cytochrome c by Coarse-Grained Simulations", Polymer Preprints Am. Chem. S., 81, 155, 1999.


14.  T. Haliloglu, W. L. Mattice, "Detection of the onset of demixing in simulations of polypropylene melts in which the chains differ only in stereochemical composition",  J. Chem. Phys., 111(9), 4327-4333, 1999.


15.  P. Doruker, W. L. Mattice, "The effect of chain segregation on the mobility of thin films", Polymer Preprints Am. Chem. S., 81, 555-556, 1999.


16.  M. Kahraman, N. Nugay, "Hybrid reinforcement in polydimethyl siloxane composites", Abstracts of Papers of American Chemical Society", Vol.81, p157, 1999.


17.  M.C. Demirel, I. Bahar, A. R. Atilgan, "Predicting the Unsemble of Unfolding Pathways for Proteins: An Updated Incremental Lagrangian Model", Biophysical Journal., Vol. 76, No.1, p. A176, 1999.


18.  M. Sayar, and A. R. Atilgan, "A Sequence-Specific Low-Resolution Model of DNA", Tr. J. of Physics, Vol. 23, No.1, pp. 261-263, 1999.


19.  A. R. Atilgan, "Equilibrium Fluctuations in Attractors Embedded in Three-Dimensions", Tr. J. of Physics, Vol. 23, No.1, pp. 253-254, 1999.


20.  A. K. Alparslan, M. Sayar, A. R. Atilgan, "Local and Ensemble Forecasting of Chaotic Time Series", Tr. J. of Physics, Vol. 23, No.1, pp. 255-256, 1999.



1.      I. Bahar and R.L. Jernigan,  "Vibrational Dynamics of Transfer RNAs: Comparison of the Free and Synthetase-bound Forms", J. Mol. Biol. 281, 871-884 (1998)


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


3.     Haliloglu, T., Mattice, W. L., "Mapping of Rotational Isomeric State Chains with Asymmetric Torsional Potential Energy Functions on a High Coordination Lattice. Application to Polyproplylene", J. Chem. Phys.,108, 6989-6995 (1998)

4.     S. Erdal, I. Bahar and B. Erman, "Swelling of Sodium Chloride Filled Polybutadiene Networks in Aqueous Environment" Polymer 39, 2035-2041,(1998)


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


6.    Atilgan, A. R.,  "A Nonlinear Model for the Kinking Behavior of Unidirectional Polymer Matrix Composites," Zeitschrift fur Angewandte Mathematik und Mechanik (ZAMM), 78, 212-216, (1998)


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


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


9.     Atilgan, A. R., Haliloglu, T., Bahar, I., and Erman, B., "Correlated Fluctuations in Polymer Networks," Computational & Theoretical Polymer Science 8, 55-59, (1998)


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


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


12.  Lustig, B., Bahar, I. & Jernigan, R. L. "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, (1998)


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


14.  Bahar, I., Ptitsyn, O. B., Erman, B. & Jernigan, R. L. "Protein Dynamics for global motions" Biophys. J. 74, A276,(1998)


15.  Haliloglu, T., Bahar,I., "Investigation of Conformational Dynamics of Proteins by Coarse-Grained Simulations", Proteins: Structure, Function and Genetics 31, 271-281, (1998)


16.  Alparslan, K., Sayar, M., and Atilgan, A. R., "A State-Space Prediction Model for Chaotic Time Series," Physical Review E 58, 2640-2643, (1998)


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





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


2.   Burak Erman and James E. Mark, "Structures and properties of rubberlike networks", Oxford University Press, (1997)


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


4.  C. Baysal, B. Erman, I. Bahar, F. Laupretre, L. Monnerie,  "Local dynamics of bulk polybutadiene of various microstructures: comparison of theory with NMR measurements" Macromolecules 30, 2058-2066, (1997)


5.  S.Fakirov, Z. Sarac, T. Anbar, B. Boz, I. Bahar, M. Evstatiev, M., A. A. Apostolov J. E. Mark, A. Kloczkowski, "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, (1997)


6.  B.Erman, I.Bahar, R.L. Jernigan, "Equilibrium states of rigid bodies with multiple interaction sites: Application to protein helices" J.Chem. Phys. 107 (6), 2046-2059 (1997)


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


8.  I.Bahar, A. R. Atilgan, R. L. Jernigan and Erman, B. "Understanding the recognition of protein structural classes by amino acid composition" Proteins 9, 172-185, (1997)


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


10. B. Erman and L. Monnerie,  "Chains between two parallel walls: Distribution functions and force.deformation relations", Macromolecules, 30, 5075-5084, (1997)


11. B. Erman, "Significance of different modes in dynamics of chains in a dense medium", Macromol. Symp. 121, 163-173 (1997)


12. Demirel, M. C., Sayar, M., and Atilgan, A. R., "Statistical mechanics of Fermi-Pasta-Ulam chains with the canonical ensemble," Physical Review E, Vol. 55, No. 3( 1997) 3727 -3731.


13. Atilgan, A. R., "Analogy between dislocation mechanics and aerodynamics," Zeitschrift fŸr Angewandte Mathematik und Mechanik (ZAMM), Vol. 77, No. 8, 631 .634. (1997)


14. Sayar, M., Demirel, M. C., and Atilgan, A. R. "Dynamics of disordered structures: Effect of nonlinearity on the localization", Journal of Sound and Vibration, Vol. 205, No. 3, 372 -379 (1997)


15. Haliloglu, T. , Mattice, W. L., "Conformational transitions of end-adsorbed triblock copolymers in a non selective solvent", Macromoleculer Theory and Simulations, (1997)


16. T. Haliloglu, D. C. Stevenson, W. L. Mattice, W. L., "Monte Carlo Simulation of the adsorption from a nonselective solvent of symmetric triblock copolymers with sticky end blocks",  J. Chem. Phys., 106, 3365-3369 (1997)


17. P. Doruker, I. Bahar, "Role of water on unfolding kinetics of polypeptides studied by molecular dynamics simulations" Biophys. J. 7, 2445-2456, (1997)


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


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




1.  Haliloglu, T., Bahar, I., Erman, B., Kim E. G., Mattice, W. L., "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, (1996)


2.  W.V. Zhao, A. Kloczkowski, J. E. Mark, B. Erman and I. Bahar, "Oriented gelatin-a new source for high-performance materials", J. Macromol. Sci. Pure Appl. Chem. A33, 525-540(1996)


3.  R. L. Jernigan & I. Bahar, "Structure-derived potentials and protein simulations" Current Opinion in Structural Biology . 6, 195-209(1996)


4.  Baysal, C., Atilgan, A. R., Erman, B., Bahar, I., "Molecular dynamics analysis of coupling between librational motions and isomeric jumps in chain molecules", Macromolecules 29, 2510-2514, (1996)


5.  I. Bahar and B. Erman, "Segmental orientation in deformed rubbery networks", Oriented Polymer Materials, S. Fakirov (Ed.), HŸthig & Webf Verlag, Oxford, (1996) p467-481.


6.  Baysal, C., Erman, B., Bahar, I., Monnerie, L., "Kinematics of polymer chains in dense medium. 4. Effect of backbone geometry and application to polybutadiene" Macromolecules 29, 2980-2988, (1996)


7.  Haliloglu, T., Bahar, I., Erman, B., Mattice, W. L., "Mechanisms of the exchange of diblock copolymers between micelles at dynamic equilibrium", Macromolecules 29, 4764-4771( 1996)


8.  Zhao, W.V., Kloczkowski, A., Mark, J. E., Erman, B., Bahar, I. "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, (1996)



9.  Zhao, W. V., Kloczkowski, A., Mark, J. E., Erman, B., Bahar, I. "Main-chain lyotropic liquid-crystalline elastomers. 2. Orientation and mechanical properties of polyisocyanate films", Macromolecules 29, 2805-2812 (1996)


10. Haliloglu, T., Bahar, I., Erman, B. "The response of a single grafted chain to shear flow. A Brownian dynamics simulation study", J. Chemical Physics 105, 2919-2926 (1996)


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


12. P. Doruker, R. F. Rapold, W. L. Mattice "Rotational isomeric state models for polyoxyethylene and polythiaethylene on a high coordination lattice" Journal of Chemical Physics. 104(21) 8742-8749 (1996)


13. S. Fakirov, Z. Sarac , T. Anbar, B. Boz, I. Bahar, M. Evstatiev, A. A. Apostolov, J.E. Mark, A. Kloczkowski "Mechanical properties and transition temperatures of cross-linked oriented gelatin" Colloid Polym. Sci. 274. 334-341(1996)


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





1.  I. Bahar, B. Erman, L. Bokobza, and L. Monnerie, "Molecular Orientation in Deformed Bimodal Networks. 1. Theory" Macromolecules 28, 225.230, 1995.


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


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


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


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


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


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


8.  A. Kloczkowski, J. E. Mark and B. Erman "A Simple Derivation of the Exponent for Gaussian Chains with Excluded Volume" Macromol Theory Simul. 4, 245, 1995.


9.  A. Kloczkowski, J. E. Mark and B. Erman, "Diffused-Constraint Theory for the Elasticity of Amorphous Polymer Networks. 1. Fundamentals and Stress-Strain Isotherms in Elongations", Macromolecules, 28, 5089-5096, 1995.


10. A. Kloczkowski, J. E. Mark and B. Erman, "A Diffused-Constraint Theory for the Elasticity of Amorphous Polymer Networks. 2. Molecular Deformation Tensors and Strain Birefringence", Computational Polymer Science, 5, 37-45, 1995.


11. S. Fakirov, Z. Sarac, T. Anbar, B. Boz, M. Evstatiev, A.A. Apostolov, I. Bahar, J.E. Mark and A. Kloczkowski, "Mechanical Properties and Transition Temperatures of Crosslinked Oriented gelatin. II. Effect of Orientation and Water Content on transition temperatures" 1995.


12. S. Fakirov, Z. Sarac, T. Anbar, B. Boz and I. Bahar, "Mechanical Properties and Transition Temperatures of Cross-Linked Oriented Gelatin. I. Static and Dynamic Mechanical Properties of Cross-Linked gelatin" Polymer Science, 1995.


13.  W. Zhao, A. Kloczkowski and J. E. Mark, B. Erman and I. Bahar, "Oriented Gelatin-A New Source for High-Performance Materials" 1995.


14.  Y. Yang, A. Kloczkowski, J.E. Mark, B. Erman and I. Bahar, "Theoretical Analysis of the Elastomeric and Optical Properties of Networks of Semi-Rigid Chains in the Swollen State" 1995.


15.  T. Haliloglu, I. Bahar, B. Erman and E. Kim, W. L. Mattice, "A Dynamic Rotational Üsomeric State Approach for Extension of the Time Scale of the Local Dynamics Observed in Fully Atomistic Molecular Dynamics Simulations" 1995.


16.  W. Zhao, A. Kloczkowski, J. E. Mark, B. Erman, I. Bahar, "Main-Chain Lyotropic Liquid-Crystalline Elastomers. 1. Syntheses of Cross-Linked Polyisocyanate Gels Acquiring Liquid-Crystalline Behavior in the Swollen State" 1995.


17. W. Zhao, A. Kloczkowski, J. E. Mark, B. Erman and I. Bahar, "Main-Chain Lyotropic Liquid-Crystalline Elastomers. 2 Orientation, and Mechanical Properties of Polyisocyanate Films" 1995.


18. T. Haliloglu, I. Bahar and B. Erman, "Response of a Single Grafted Polyethylence Chain to Simple Shear Flow. A Brownian Dynamics Simulation Study " 1995.


19. Y.Yang, A. Kloczkowski, J.E. Mark, B. Erman and I. Bahar, "Experimental Studies of Elastomeric and Optical Properties, and Strain-Induced Liquid-Crystalline Phase Transitions, in Deformed Hydroxypropylcellulose Networks in the Swollen State" 1995.


20.  T. Haliloglu, I. Bahar, B. Erman, "Mechanisms of the Exchange of Diblock Copolymers between Micelles at Dynamic Equilibrium" 1995.





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


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


3.   Bahar. I, Jernigan. R, L. "Cooperative Structural Reorganizations Induced by Nonhomegeneus Intramolecular Interactions in Compact Globular Proteins" Biophsical Journal, 66, 467 (1994)


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


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


6.   Yang. Y, Kloczkowski. A, Mark. J, E, Erman. B and Bahar. I, "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" 272, 284 (1994)


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


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


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


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


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


12.  Wang. S, Mark. J. E, Erman. B, and Fakirov. S, "Mechanical Properties of Thermoplastic Elastomers of Polly (butylene terephthalate) and Poly (ethylene glycol) in a Bending Deformation" Journal of Applied Polymer Science, 51, 145-151 (1994)


13.  Erman. B, and Mark. J. E, "The Molecular Basis of Rubberlike Elasticity", Science and Technology of Rubber, Academic Press. (1994)





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


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


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


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


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


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


7.   Y. H. Hsu, J. E. Mark, B. Erman, "Moduli of Model Elastomeric Networks Prepared from Polymer Chains Having a High Plateau Modulus and Their Interpretation in Terms of the Constrained-Chain Model", J. Polym. Sci. : Part B: Polymer Physics, 31 , 481 (1993)


8.   "Mechanical Properties of Thermoplastic Elastomers of Poly(Butylene Terephtalate) and Poly(Ethylene Glycol) in a Bending Deformation. S. Wang J. E. Mark, B. Erman, S. Fakirov. submitted to J. Appl. Polym. Sci. , 31, 481 (1993)


9.   E. Yurtsever, B. Erman, "Configurational Properties of Polypyrrole Chains" Makromol Chem. Macromol. Symp. , 34, 3887 (1993)


10.  B. Erman, "Entanglements in Amorphous Polymer Networks" Macromol Chem. , Macromol. Symp . 76 , 53 (1993).


11. T. A. Vilgis, B. Erman, "Comparison of the Consrained Junction and the Slip-Link Models of Rubber Elasticity, Macromolecules, 26, 6657 (1993)


12.  A. Besbes, L. Bokobza, L. Monnerie, I. Bahar, B. Erman, "Segmental orientation in Model Networks of Poly(dimethyl siloxane). Fourier Transform Infrared dichroism Measurements and Theoretical Interpretation" ACS Abstracts, 205 , 144 (1993)


13.  I. Bahar, R. L. Jernigan, "Conformational Characteristics of Model Proteins with Homogeneous and Non Homogeneus Interactions" ACS Abstracts, 206, 79 (1993)


14.  Y. Yang, A. Kloczkowski, j. E. Mark, B. Erman, I. Bahar,"Elastic and Optical Properties of Deformed Swollen Networks of Semirigid Chains"  ACS Abstracts , 206, 295 (1993)


15.  Y. Yang , A. Kloczkowski, J. E. Mark, B. Erman, I. Bahar, "Orientation and Strain-Induced Liquid Crystalline Phase Transition of Networks of Semi-rigid Chains" ACS Abstracts , 205, 144 (1993)


16.  T. Haliloglu, W. L. Mattice, "Analysis of Orientation Autocorrelation and Cross-Correlation Functions for Polyethylene in the Inclusion Complex with Perhydrotriphenylene" Macromolecules, 26, 12 (1993)


17.  B. Erman, I. Bahar, "Local Chain Dynamics of Freely Rotating Polymer Chains in Dense polymer Systems. Prog Colloid Polym. Sci. , 91, 16 (1992)


18.  I. Bahar, B. Erman, F. Kremer, E. W. Fischer, "Dynamic Rotational Isomeric State Approach for Segmental Motions of cis-Polyisoprene in the Bulk State" Prog Colloid Polym. Sci. , 91, 1 (1992)





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


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


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


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


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


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


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


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


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


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


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


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


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


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


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


16. Erman, B. & Bahar, I. "Networks with Semiflexible Chains" ACS Abstracts, 203, 78, 1992.


17. Neuburger, N. A., Mattice, W. L. & Bahar, I. "Correlations of Nearest Neighbors Bonds in Certain Poly(dialkyl siloxanes)" ACS Abstracts 203, 35, 1992.


18.  J. E. Mark, B. Erman, "Elastomeric Polymer Networks" Prentice Hall, Polymer Science Series, 1992.


19. B. Erman, J. E. Mark. "Stress-Strain Isotherms for Elastomers Cross-Linked in Solution. 2. Interpretation in Terms of the Constrained-Chain model" Macromolecules. 25,1917, 1992.


20. Kloczkowski, A.; Mark, J. E.; Erman, B. "Correlations Among Chains Along a Cross-Linked Path in a Phantom Network and Their Characterization by SANS" Macromolecules. 25,2455, 1992.


21. B. Erman, L. Monnerie, "Correction to the Constrained Chain Model of Rubber Elasticity." Macromolecules. 25,4456, 1992.


22. M. A. Sharaf, A. Kloczkowski, J. E. Mark, B. Erman, "Networks Undergoing Strain-Induced Crystallization. Analysis in Terms of Constrained-Junction Model." Journal of Computational Polymer Science. 2, 84, 1992.


23. B. Erman, J. E. Mark. "Correction to Stress-Strain Isotherms for Elastomers Cross-Linked in Solution. 2. Interpretation in Terms of the Constrained-Chain model." Macromolecules. 25,6380, 1992.


24. M. A. Sharaf, A. Kloczkowski, J. E. Mark, B. Erman, "Theory of Strain-Induced Crystallization in Real Elastomeric Networks" Synthesis, Characterization, and Theory of Polymeric Networks and Gels, Ed. S. M. Aharoni, Plenum Press, New York, p. 227-242, 1992.





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


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


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


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


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


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


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



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


9. Kloczkowski, A.; Mark, J. E., Erman, B. & Bahar, I. "A Lattice Model for Segmental Orientation in Deformed Polymer Network, Characterization of Stress-Strain Relationships and Phase.Transition for Networks of Semirigid Chains" ACS Abstracts 202, 16, 1991.


10.  Erman, B. & Bahar, I. "Dynamics of Rotational Isomerization in Polymers in Solution and in the Bulk State" ACS Abstracts 202, 18, 1991.



11. Bahar, I., Lee, K. J. & Mattice, W. L. "Relaxation of Runs of Transrotational Isomers of Single Racemic Poly(vinyl chloride) Chains" ACS Abstracts 202, 69, 1991.


12. Erman, B., Bahar, I., Yang, Y., Kloczkowski, A. & Mark, J. E.  "Novel Orientation Techniques for the Preparation of High Performance Materials from Semi-flexible Polymers such as Cellulosics" ACS Abstracts 202, 15, 1991.


13.  H. Schweinler, B. Erman, J. E. Mark, A. Weinberg, "Eugene Guth", Physics Today, 44(6), 133, 1991.


14.  A. Kloczkowski, J. E. Mark, B. Erman, "Fluctuations, Correlations and Small Angle Neutron Scattering from Endlinked Gaussian Chains in Regular Bimodal Networks" Macromolecules. 24, 3266, 1991.


15.  A. Kloczkowski, J. E. Mark, B. Erman, B. E. Eichinger, "Comment on Statistical Mechanics of Rubber Elasticity", Journal of Chemical Physics, 94, 7015, 1991.





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


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


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


4.  Erman, B., Bahar, I., Kloczkowski, A. & Mark, J. E. "A Lattice Model for segmental orientation in Deformed Polymer Networks" ACS Abstracts, 200, 348, 1990.


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


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


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


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


9.   B. Erman, "Determination of Cross-Link Density in Amorphous Networks by Stress-Strain Swelling Experiments. in NATO ASI on Advanced Methods of Determination of Crosslinking and Scission in Polymers and their Effects on Mechanical Properties" Ed. O. Guven. Kluwer Academic Publishers, 292, 153, 1990.


10. A. Kloczkowski, J. E. Mark, B. Erman,"Neutron Scattering from Elastomeric Networks : II. An Alternative Phantom Network Model"  Macromolecules. 23, 1222, 1990.


11.  H. Ozkul, K. Onaran, B. Erman, "Stress Relaxation in Stretched Networks Immersed in Solvent" J. Polym. Sci. Polym. Phys. Ed. 28, 1781, 1990.


12.  B. Erman, L. Monnerie, "Segmental Orientation in Elastomers" Encyc. Matl. Sci. and Engn'g., Supp. Vol. 2. Ed. R. W. Cahn, p. 1246, 1990.



13.  A. Kloczkowski, J. E. Mark, B. Erman. "On the Flory-Ronca Theory of Systems of Rodlike Particles" Macromolecules. 23, 5035, 1990.