A simple tetrahedron model is used to study the effect of non-Gaussian chains on¯uctuations of ju... more A simple tetrahedron model is used to study the effect of non-Gaussian chains on¯uctuations of junctions in bimodal networks. The four chains are assumed to meet at a junction with their other ends being ®xed at the vertices of the tetrahedron. It is assumed that the angles between mean end-to-end vectors of all four chains connected at the junction are tetrahedral, but the lengths of edges of the tetrahedron may differ due to the difference in the lengths of the chains. The central junction is free to¯uctuate, subject to the constraints imposed by the pendant chains. The long chains are chosen to be Gaussian. The short chains are assumed to be non-Gaussian. Calculations show that the non-Gaussian nature of the short chains imposes severe restrictions on the¯uctuations of the central junction. The strength of these restrictions directs attention to the importance of anharmonic modes in networks. q
Background: An elastic network model is proposed for the interactions between closely (≤ 7.0 Å) l... more Background: An elastic network model is proposed for the interactions between closely (≤ 7.0 Å) located ␣-carbon pairs in folded proteins. A single-parameter harmonic potential is adopted for the fluctuations of residues about their mean positions in the crystal structure. The model is based on writing the Kirchhoff adjacency matrix for a protein defining the proximity of residues in space. The elements of the inverse of the Kirchhoff matrix give directly the auto-correlations or cross-correlations of atomic fluctuations.
The constrained junction model that represents the stressestrain relations of amorphous networks ... more The constrained junction model that represents the stressestrain relations of amorphous networks in equilibrium is modified to analyze stress relaxation. Deviation of stress from equilibrium when a network is stretched suddenly is represented by a time dependent constraint contribution that is of the same form as that of the equilibrium theory. The time dependent motions of the junctions are assumed to obey the Langevin equation. The only new term in the model is a time dependent k parameter that vanishes at long times. Results of the model are compared with uniaxial stress relaxation experiments on polyisoprene networks with different degrees of cross-linking. Experiments show that the time dependent k parameter obeys a stretched exponential form, kðtÞ ¼ k 0 exp½Àðt=tÞ b with b ¼ 0.4 and t ¼ 40 s, both of which are the same for all extensions and cross-link densities studied. The front factor k 0 depends on cross-link density in the same way as in the equilibrium case. Comparison with stress relaxation experiments shows satisfactory agreement at a wide range of extensions and for different degrees of cross-linking. The relatively low value of the stretched exponent parameter, b ¼ 0.4, is interpreted in terms of a molecular picture where entanglements contribute to relaxation at a wide spectrum of time scales.
Dynamic rotational isomeric state formalism is used to compute dipolar correlation functions for ... more Dynamic rotational isomeric state formalism is used to compute dipolar correlation functions for cis-polyisoprene in the bulk state. Transitions between rotational isomeric states take place through coupled motion of triplets of neighboring bonds in a given repeat unit, as follows from the study of intramolecular conformational energetics in the polymer. The intermolecular effect on local chain dynamics is included in
2010 5th International Symposium on Health Informatics and Bioinformatics, 2010
Abstract Histone proteins control many crucial cell regulatory processes post-translational modif... more Abstract Histone proteins control many crucial cell regulatory processes post-translational modifications. Among these modifications, methylation is recently shown to be reversible with the discovery of Lysine-specific Demethylase (LSD1) enzyme. As many studies have showed the relation of some cancer-type and other diseases with the abnormalities in the balance of methylation/demethylation, drug molecule design based on the information gained from reaction path analysis becomes very useful. In this paper, a chemically- ...
Proteins: Structure, Function, and Bioinformatics, 2014
Relevance of mode coupling to energy/information transfer during protein function, particularly i... more Relevance of mode coupling to energy/information transfer during protein function, particularly in the context of allosteric interactions is widely accepted. However, existing evidence in favor of this hypothesis comes essentially from model systems. We here report a novel formal analysis of the near-native dynamics of myosin II, which allows us to explore the impact of the interaction between possibly non-Gaussian vibrational modes on fluctutational dynamics. We show that, an informationtheoretic measure based on mode coupling alone yields a ranking of residues with a statistically significant bias favoring the functionally critical locations identified by experiments on myosin II.
This study reports that cis-1,4-polybutadiene can be converted into a semiconductor when doped wi... more This study reports that cis-1,4-polybutadiene can be converted into a semiconductor when doped with iodine. The conductivity achieved by iodine doping was about 10 y6 S/cm. The products were characterized by elemental analysis, FT-IR, differential scanning calorimetry (DSC) and thermal gravimetric analysis (TGA) techniques. Temperature dependence of electrical conductivity exhibits a semiconductor behavior.
... JL Fulton, DM Pfund, JB McClain, TJ Romack, EE Maury, JR Combes, ET Samulski, and JM DeSimone... more ... JL Fulton, DM Pfund, JB McClain, TJ Romack, EE Maury, JR Combes, ET Samulski, and JM DeSimone, Langmuir 11, 4241 (1995). RG Zielinski, ME Paulaitis, and EW Kaler, A sapphire cell for neutron scattering at elevated pressures, Rev. ... VP Saraf and E. Kiran, J. Supercrit. ...
Statistical averages and correlations for backbone torsion angles of chymotrypsin inhibitor 2 are... more Statistical averages and correlations for backbone torsion angles of chymotrypsin inhibitor 2 are calculated by using the Rotational Isomeric States model of chain statistics. Statistical weights of torsional states of pairs, needed for the statistics of the full chain, are obtained in two different ways: 1) by using knowledge-based pair-wise dependent energy maps from Protein Data Bank (PDB) and 2) by collecting torsion angle data from a large number of random coil configurations of an all-atom protein model with volume exclusion. Results obtained by using PDB data show strong correlations between adjacent torsion angle pairs belonging to both the same and different residues. These correlations favor the choice of the native-state torsion angles, and they are strongly context dependent, determined by the specific amino acid sequence of the protein. Excluded volume or steric clashes, only, do not introduce context-dependent correlations into the chain that would affect the choice of native-state torsional angles. Proteins 2004; 55:992–998.
The changes in the thermomechanical behaviour of a poly(ethylene terephthalate)/nylon-6 (PET/PA) ... more The changes in the thermomechanical behaviour of a poly(ethylene terephthalate)/nylon-6 (PET/PA) blend (l:l by weight) subjected to mechanical and thermal treatments are examined by means of dynamic mechanical measurements. It is established from previous studies that PET/PA blends are incompatible in the isotropic state, but form so-called microfibrillar-reinforced composites upon extrusion, drawing and suitable annealing. This study focuses mainly on the amorphous component of these blends and thus complements that recently performed (Polymer 1993, 34, 4669) in which the crystalline phases were analysed.
A segmented polyurethaneurea based on poly(tetramethylene oxide)glycol, a cycloaliphatic diisocya... more A segmented polyurethaneurea based on poly(tetramethylene oxide)glycol, a cycloaliphatic diisocyanate and an unsymmetrical diamine were prepared. Urea content of the copolymer was 35 wt%. Electrospinning behavior of this elastomeric polyurethaneurea copolymer in solution was studied. The effects of electrical ®eld, temperature, conductivity and viscosity of the solution on the electrospinning process and morphology and property of the ®bers obtained were investigated. Results of observations made by optical microscope, atomic force microscope and scanning electron microscope were interpreted and compared with literature data available on the electrospinning behavior of other polymeric systems. q
We develop a general framework for the analysis of residue fluctuations that simultaneously incor... more We develop a general framework for the analysis of residue fluctuations that simultaneously incorporates anharmonicity and mode-coupling in a unified formalism. We show that both deviations from the Gaussian model are important for modeling the multidimensional energy landscape of the protein Crambin (1EJG) in the vicinity of its native state. The effect of anharmonicity and mode-coupling on the fluctuational entropy is on the order of a few percent.
A simple tetrahedron model is used to study the effect of non-Gaussian chains on¯uctuations of ju... more A simple tetrahedron model is used to study the effect of non-Gaussian chains on¯uctuations of junctions in bimodal networks. The four chains are assumed to meet at a junction with their other ends being ®xed at the vertices of the tetrahedron. It is assumed that the angles between mean end-to-end vectors of all four chains connected at the junction are tetrahedral, but the lengths of edges of the tetrahedron may differ due to the difference in the lengths of the chains. The central junction is free to¯uctuate, subject to the constraints imposed by the pendant chains. The long chains are chosen to be Gaussian. The short chains are assumed to be non-Gaussian. Calculations show that the non-Gaussian nature of the short chains imposes severe restrictions on the¯uctuations of the central junction. The strength of these restrictions directs attention to the importance of anharmonic modes in networks. q
Background: An elastic network model is proposed for the interactions between closely (≤ 7.0 Å) l... more Background: An elastic network model is proposed for the interactions between closely (≤ 7.0 Å) located ␣-carbon pairs in folded proteins. A single-parameter harmonic potential is adopted for the fluctuations of residues about their mean positions in the crystal structure. The model is based on writing the Kirchhoff adjacency matrix for a protein defining the proximity of residues in space. The elements of the inverse of the Kirchhoff matrix give directly the auto-correlations or cross-correlations of atomic fluctuations.
The constrained junction model that represents the stressestrain relations of amorphous networks ... more The constrained junction model that represents the stressestrain relations of amorphous networks in equilibrium is modified to analyze stress relaxation. Deviation of stress from equilibrium when a network is stretched suddenly is represented by a time dependent constraint contribution that is of the same form as that of the equilibrium theory. The time dependent motions of the junctions are assumed to obey the Langevin equation. The only new term in the model is a time dependent k parameter that vanishes at long times. Results of the model are compared with uniaxial stress relaxation experiments on polyisoprene networks with different degrees of cross-linking. Experiments show that the time dependent k parameter obeys a stretched exponential form, kðtÞ ¼ k 0 exp½Àðt=tÞ b with b ¼ 0.4 and t ¼ 40 s, both of which are the same for all extensions and cross-link densities studied. The front factor k 0 depends on cross-link density in the same way as in the equilibrium case. Comparison with stress relaxation experiments shows satisfactory agreement at a wide range of extensions and for different degrees of cross-linking. The relatively low value of the stretched exponent parameter, b ¼ 0.4, is interpreted in terms of a molecular picture where entanglements contribute to relaxation at a wide spectrum of time scales.
Dynamic rotational isomeric state formalism is used to compute dipolar correlation functions for ... more Dynamic rotational isomeric state formalism is used to compute dipolar correlation functions for cis-polyisoprene in the bulk state. Transitions between rotational isomeric states take place through coupled motion of triplets of neighboring bonds in a given repeat unit, as follows from the study of intramolecular conformational energetics in the polymer. The intermolecular effect on local chain dynamics is included in
2010 5th International Symposium on Health Informatics and Bioinformatics, 2010
Abstract Histone proteins control many crucial cell regulatory processes post-translational modif... more Abstract Histone proteins control many crucial cell regulatory processes post-translational modifications. Among these modifications, methylation is recently shown to be reversible with the discovery of Lysine-specific Demethylase (LSD1) enzyme. As many studies have showed the relation of some cancer-type and other diseases with the abnormalities in the balance of methylation/demethylation, drug molecule design based on the information gained from reaction path analysis becomes very useful. In this paper, a chemically- ...
Proteins: Structure, Function, and Bioinformatics, 2014
Relevance of mode coupling to energy/information transfer during protein function, particularly i... more Relevance of mode coupling to energy/information transfer during protein function, particularly in the context of allosteric interactions is widely accepted. However, existing evidence in favor of this hypothesis comes essentially from model systems. We here report a novel formal analysis of the near-native dynamics of myosin II, which allows us to explore the impact of the interaction between possibly non-Gaussian vibrational modes on fluctutational dynamics. We show that, an informationtheoretic measure based on mode coupling alone yields a ranking of residues with a statistically significant bias favoring the functionally critical locations identified by experiments on myosin II.
This study reports that cis-1,4-polybutadiene can be converted into a semiconductor when doped wi... more This study reports that cis-1,4-polybutadiene can be converted into a semiconductor when doped with iodine. The conductivity achieved by iodine doping was about 10 y6 S/cm. The products were characterized by elemental analysis, FT-IR, differential scanning calorimetry (DSC) and thermal gravimetric analysis (TGA) techniques. Temperature dependence of electrical conductivity exhibits a semiconductor behavior.
... JL Fulton, DM Pfund, JB McClain, TJ Romack, EE Maury, JR Combes, ET Samulski, and JM DeSimone... more ... JL Fulton, DM Pfund, JB McClain, TJ Romack, EE Maury, JR Combes, ET Samulski, and JM DeSimone, Langmuir 11, 4241 (1995). RG Zielinski, ME Paulaitis, and EW Kaler, A sapphire cell for neutron scattering at elevated pressures, Rev. ... VP Saraf and E. Kiran, J. Supercrit. ...
Statistical averages and correlations for backbone torsion angles of chymotrypsin inhibitor 2 are... more Statistical averages and correlations for backbone torsion angles of chymotrypsin inhibitor 2 are calculated by using the Rotational Isomeric States model of chain statistics. Statistical weights of torsional states of pairs, needed for the statistics of the full chain, are obtained in two different ways: 1) by using knowledge-based pair-wise dependent energy maps from Protein Data Bank (PDB) and 2) by collecting torsion angle data from a large number of random coil configurations of an all-atom protein model with volume exclusion. Results obtained by using PDB data show strong correlations between adjacent torsion angle pairs belonging to both the same and different residues. These correlations favor the choice of the native-state torsion angles, and they are strongly context dependent, determined by the specific amino acid sequence of the protein. Excluded volume or steric clashes, only, do not introduce context-dependent correlations into the chain that would affect the choice of native-state torsional angles. Proteins 2004; 55:992–998.
The changes in the thermomechanical behaviour of a poly(ethylene terephthalate)/nylon-6 (PET/PA) ... more The changes in the thermomechanical behaviour of a poly(ethylene terephthalate)/nylon-6 (PET/PA) blend (l:l by weight) subjected to mechanical and thermal treatments are examined by means of dynamic mechanical measurements. It is established from previous studies that PET/PA blends are incompatible in the isotropic state, but form so-called microfibrillar-reinforced composites upon extrusion, drawing and suitable annealing. This study focuses mainly on the amorphous component of these blends and thus complements that recently performed (Polymer 1993, 34, 4669) in which the crystalline phases were analysed.
A segmented polyurethaneurea based on poly(tetramethylene oxide)glycol, a cycloaliphatic diisocya... more A segmented polyurethaneurea based on poly(tetramethylene oxide)glycol, a cycloaliphatic diisocyanate and an unsymmetrical diamine were prepared. Urea content of the copolymer was 35 wt%. Electrospinning behavior of this elastomeric polyurethaneurea copolymer in solution was studied. The effects of electrical ®eld, temperature, conductivity and viscosity of the solution on the electrospinning process and morphology and property of the ®bers obtained were investigated. Results of observations made by optical microscope, atomic force microscope and scanning electron microscope were interpreted and compared with literature data available on the electrospinning behavior of other polymeric systems. q
We develop a general framework for the analysis of residue fluctuations that simultaneously incor... more We develop a general framework for the analysis of residue fluctuations that simultaneously incorporates anharmonicity and mode-coupling in a unified formalism. We show that both deviations from the Gaussian model are important for modeling the multidimensional energy landscape of the protein Crambin (1EJG) in the vicinity of its native state. The effect of anharmonicity and mode-coupling on the fluctuational entropy is on the order of a few percent.
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Papers by B. Erman