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  • Wiley  (45)
  • American Institute of Physics (AIP)  (7)
  • American Geophysical Union  (6)
  • Canadian Science Publishing
  • 2000-2004  (38)
  • 1995-1999  (22)
  • 1
    Electronic Resource
    Electronic Resource
    Computer simulation of void growth dynamics under the action of electromigration and capillary forces in narrow thin interconnects (2001)
    [S.l.] : American Institute of Physics (AIP)
    Journal of Applied Physics 90 (2001), S. 1564-1572 
    Details
    ISSN: 1089-7550
    Source: AIP Digital Archive
    Topics: Physics
    Notes: A comprehensive picture of void dynamics in connection with the critical morphological evolution has been developed in order to understand the conditions under which premature failure of metallic thin interconnects occurs. Our mathematical model on the mass flow and accumulation on void surfaces, under the action of applied electrostatic and elastostatic force fields, and capillary effects, follows an irreversible but discrete thermodynamic formulation of interphases and surfaces. This formalism also takes into account in a natural way the mass transfer process (the void growth), between bulk phase and the void region in multi-component systems, in terms of the normalized local values of Gibbs free energy of transformation with respect to the specific surface Gibbs free energy, in addition to the contribution due to local curvature of the advancing reaction front, rather rigorously. © 2001 American Institute of Physics.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1063/1.1382835
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  • 2
    Electronic Resource
    Electronic Resource
    Simulation of dislocation damping spectra associated with the collective motion of point defects and kink chain subjected to bulk segregation (2002)
    [S.l.] : American Institute of Physics (AIP)
    Journal of Applied Physics 91 (2002), S. 1860-1870 
    Details
    ISSN: 1089-7550
    Source: AIP Digital Archive
    Topics: Physics
    Notes: A theory of interactive and completely coupled systems of dislocations and mobile point defects is presented. The computer simulations yield an accurate prediction of experimental spectral data in terms of dislocation induced Cottrell relaxation and its gradual conversion into a Cottrell–Koster relaxation peak at high concentrations of spherical point defect. The bulk segregation of point defects to the kinked-dislocation line is also accounted for. Excellent results are obtained in computer simulations of aging, peaking, and finally the stabilization behavior of transient dislocation damping peaks. © 2002 American Institute of Physics.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1063/1.1429769
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  • 3
    Electronic Resource
    Electronic Resource
    Temperature quench echoes in proteins (1995)
    College Park, Md. : American Institute of Physics (AIP)
    The Journal of Chemical Physics 103 (1995), S. 3112-3123 
    Details
    ISSN: 1089-7690
    Source: AIP Digital Archive
    Topics: Physics , Chemistry and Pharmacology
    Notes: Temperature quench echoes are analyzed in terms of the temperature–temperature correlation function in the harmonic approximation, and the resulting expressions are compared with molecular dynamics simulations. The relationship between the time dependence of the echo depth and the density of states is demonstrated for harmonic systems. For a protein, which has significant anharmonicity, the time dependence is dominated by relaxation effects that originate from dephasing of the periodic motions. A simple relaxation model is shown to provide a good description of the results observed in the simulations. © 1995 American Institute of Physics.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1063/1.470270
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  • 4
    Electronic Resource
    Electronic Resource
    The topology of multidimensional potential energy surfaces: Theory and application to peptide structure and kinetics (1997)
    College Park, Md. : American Institute of Physics (AIP)
    The Journal of Chemical Physics 106 (1997), S. 1495-1517 
    Details
    ISSN: 1089-7690
    Source: AIP Digital Archive
    Topics: Physics , Chemistry and Pharmacology
    Notes: Topological characteristics of multidimensional potential energy surfaces are explored and the full conformation space is mapped on the set of local minima. This map partitions conformation space into energy-dependent or temperature-dependent "attraction basins'' and generates a "disconnectivity'' graph that reflects the basin connectivity and characterizes the shape of the multidimensional surface. The partitioning of the conformation space is used to express the temporal behavior of the system in terms of basin-to-basin kinetics instead of the usual state-to-state transitions. For this purpose the transition matrix of the system is expressed in terms of basin-to-basin transitions and the corresponding master equation is solved. As an example, the approach is applied to the tetrapeptide, isobutyryl-(ala)3-NH-methyl (IAN), which is the shortest peptide that can form a full helical turn. A nearly complete list of minima and barriers is available for this system from the work of Czerminiski and Elber. The multidimensional potential energy surface of the peptide is shown to exhibit an overall "funnel'' shape. The relation between connectivity and spatial proximity in dihedral angle space is examined. It is found that, although the two are similar, closeness in one does not always imply closeness in the other. The basin to basin kinetics is examined using a master equation and the results are interpreted in terms of kinetic connectivity. The conformation space of the peptide is divided up in terms of the surface topography to model its "folding'' behavior. Even in this very simple system, the kinetics exhibit a "trapping'' state which appears as a "kinetic intermediate,'' as in the folding of proteins. The approach described here can be used more generally to classify multidimensional potential energy surfaces and the time development of complex systems. © 1997 American Institute of Physics.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1063/1.473299
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  • 5
    Electronic Resource
    Electronic Resource
    Melittin at a membrane/water interface: Effects on water orientation and water penetration (1999)
    College Park, Md. : American Institute of Physics (AIP)
    The Journal of Chemical Physics 111 (1999), S. 8672-8685 
    Details
    ISSN: 1089-7690
    Source: AIP Digital Archive
    Topics: Physics , Chemistry and Pharmacology
    Notes: Melittin, a small peptide found in bee venom, is known to induce membrane lysis. A molecular dynamics simulation of melittin embedded in a hydrated dipalmitoylphosphatidylcholine bilayer is analyzed in order to study the peptide's effect on water molecules at the membrane/water interface. The peptide, with a protonated N-terminus, was embedded in a trans-bilayer orientation. The simulation highlights the microscopic mechanism by which melittin induces the formation of transmembrane water "pores," leading to membrane lysis. It was found that melittin has a profound effect on the behavior of the water molecules at the membrane/water interface. It modifies the orientation of the water dipoles and induces water penetration into the bilayer. In fact, melittin's residue Lys-7 and its protonated N-terminus facilitate the formation of transmembrane water pores by steering water penetration from both sides of the bilayer. The initial step towards pore formation takes about 200 ps, and the process relays on melittin's bent conformation and tilted orientation. A large body of experimental observations supports the simulation results and the suggested microscopic mechanism. © 1999 American Institute of Physics.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1063/1.480207
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  • 6
    Electronic Resource
    Electronic Resource
    Dynamics of hierarchical folding on energy landscapes of hexapeptides (2001)
    College Park, Md. : American Institute of Physics (AIP)
    The Journal of Chemical Physics 115 (2001), S. 10533-10547 
    Details
    ISSN: 1089-7690
    Source: AIP Digital Archive
    Topics: Physics , Chemistry and Pharmacology
    Notes: In this paper we apply the master equation approach to study the effects of the energy landscape topology and topography on the kinetics of folding, and on kinetic transitions of three alanine-hexapeptides analogs which involve polypeptides with neutral and charged groups and a cyclized polypeptide. We rely on the potential-energy landscapes of these molecular systems, which have been constructed using both a topological mapping analysis and a principal component analysis. It was found that the different topology and topography of the energy landscapes result in different "folding" time scales and that the systems with geometrical constraints (cyclization and opposite charges at the termini) "fold" more slowly than the unconstrained peptide. In addition, for each of the three polypeptide systems, the kinetics is nonexponential at the temperature range 400–600 K. The relaxation kinetics is characterized by logarithmic oscillations, which indicate hierarchical dynamics characterized by multiple time scales of fast (few ps) and slow (few μs) events. At higher temperatures, successive relaxation channels with similar characteristic time scales collapse into a single relaxation channel. While the kinetics of the unconstrained peptide at 600 K can be reasonably well described by a single exponential time scale, the kinetics of the constrained hexapeptides are inherently hierarchical and featured by multiple time scales even at high temperatures. © 2001 American Institute of Physics.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1063/1.1415444
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  • 7
    Electronic Resource
    Electronic Resource
    Energy landscapes of conformationally constrained peptides (2001)
    College Park, Md. : American Institute of Physics (AIP)
    The Journal of Chemical Physics 114 (2001), S. 993-1009 
    Details
    ISSN: 1089-7690
    Source: AIP Digital Archive
    Topics: Physics , Chemistry and Pharmacology
    Notes: Conformation constraints are known to affect the flexibility and bioactivity of peptides. In this study we analyzed the effect of conformation constraints on the topography of the energy landscapes of three analogous hexapeptides. The three analogs vary in the degree of constraint imposed on their conformational motion: linear alanine hexapeptide with neutral terminals (Ala6), linear alanine hexapeptide with charged terminals (chrg-Ala6), and cyclic alanine hexapeptide (cyc-Ala6). It was found that significantly different energy landscapes characterize each of the three peptides, leading to different folding behaviors. Since all three analogs would be encoded by the same gene, these results suggest that nongenomic post-translational modifications may play an important role in determining the properties of proteins as well as of their folding pathways. In addition, the present study indicates that the complexity of those energy landscapes that are dominated by funnel topography can be captured by one or two reaction coordinates, such as conformational similarity to the native state. However, for more complex landscapes characterized by multiple basins such a description is insufficient. This study also shows that similar views of the landscape topography were obtained by principal component analysis (based only on local minima) and by topological mapping analysis (based on minima and barrier information). Both methods were able to resolve the complex landscape topographies for all three peptides. © 2001 American Institute of Physics.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1063/1.1329646
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  • 8
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    Estimating maximum mean canopy stomatal conductance for use in models (2001)
    Canadian Science Publishing
    Details
    Publication Date: 2001-02-01
    Description: Fertilized (F) and irrigated and fertilized (IF) stands of Pinus taeda L. produced twice the leaf area index of irrigated (I) and control (C) stands. Based on sap flux-scaled mean stomatal conductance (GS), we found that stomatal conductance in F was half that in other treatments. During the growing season, GS was related to vapor pressure deficit (D) and soil moisture. During the cooler season, soil moisture was high and light accompanied D in controlling GS. Under all conditions and treatments, the rate of decrease in GS with D was proportional to GS at low D (= 1 kPa). We evaluated whether GS can be used as an input to growth models and used a simple growth model (3-PG), which also predicts stand transpiration (EC), to compare with direct EC measurements in the four stands. Model predictions of monthly EC based on Penman-Montieth equation parameterized with maximum GS (GSmax) estimated under highest "native" soil moisture (0.07 m3·m3) produced long-term values within 10% of measured EC. When the model was parameterized with GSmax estimated under experimentally raised soil moisture, or with porometrically measured conductance, EC values were consistently overpredicted from 12 to 33%. Thus, sap-flux scaled mean canopy stomatal conductance obtained under non limiting light conditions, low D, and highest native soil moisture, is the most appropriate parameter value for certain single-leaf type of models.
    Print ISSN: 0045-5067
    Electronic ISSN: 1208-6037
    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition
    Published by Canadian Science Publishing
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  • 9
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    Estimating ma×imum mean canopy stomatal conductance for use in models (2001)
    Canadian Science Publishing
    Details
    Publication Date: 2001-01-01
    Print ISSN: 0045-5067
    Electronic ISSN: 1208-6037
    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition
    Published by Canadian Science Publishing
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  • 10
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    Baculovirus-mediated expression of a scorpion depressant toxin improves the insecticidal efficacy achieved with excitatory toxins (1998)
    Wiley
    Details
    Publication Date: 1998-01-30
    Print ISSN: 0014-5793
    Electronic ISSN: 1873-3468
    Topics: Biology , Chemistry and Pharmacology
    Published by Wiley on behalf of Federation of European Biochemical Societies.
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