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| 1990 |
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1.
Kurkcuoglu, O., Doruker, P. &
Jernigan, R. L., “Loop Motions of Triosephosphate Isomerase Observed with
Elastic Networks”, Biochemistry 45: 1173-1182, 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.
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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.
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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.
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1.
S.B. Ozkan, K.A. Dill,
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:
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.
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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,
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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,
13.
M. Sahin,
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.
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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. |
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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
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 &
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,
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. |
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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,
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 &
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,
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,
15.
Haliloglu, T., Bahar,
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 &
|
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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,
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,
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,
7. Haliloglu, T., Bahar,
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,
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)
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1.
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.
5. Z. Sarac, B. Erman and
6. T. Haliloglu,
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
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.
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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
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)
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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
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.
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
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.
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,
18.
I. Bahar, B. Erman, F.
Kremer, E. W. Fischer,
"Dynamic
Rotational Isomeric State Approach for Segmental Motions of cis-Polyisoprene
in the
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1. Bahar,
2.
J. E. Mark & B. Erman,
"Stresss-Strain
and Segmental Orientation in Networks with Semirigid Chains" Erman, B.;
Bahar,
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,
5. Bahar,
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,
11.
Bahar,
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,
16. Erman, B. & Bahar,
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.
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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,
3.
Bahar,
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,
7. Erman, B., Bahar,
8. Bahar,
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. |