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Computer simulation of void growth dynamics under the action of electromigration and capillary forces in narrow thin interconnects (2001)

Ogurtani, Tarik Omer ; Oren, Ersin Emre

[S.l.] : American Institute of Physics (AIP)

Journal of Applied Physics 90 (2001), S. 1564-1572

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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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Simulation of dislocation damping spectra associated with the collective motion of point defects and kink chain subjected to bulk segregation (2002)

Ogurtani, Tarik O. ; Güngör, Mehmet R. ; Oren, Ersin Emre

[S.l.] : American Institute of Physics (AIP)

Journal of Applied Physics 91 (2002), S. 1860-1870

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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

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Dynamics of hierarchical folding on energy landscapes of hexapeptides (2001)

Levy, Yaakov ; Jortner, Joshua ; Becker, Oren M.

College Park, Md. : American Institute of Physics (AIP)

The Journal of Chemical Physics 115 (2001), S. 10533-10547

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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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4

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Energy landscapes of conformationally constrained peptides (2001)

Levy, Yaakov ; Becker, Oren M.

College Park, Md. : American Institute of Physics (AIP)

The Journal of Chemical Physics 114 (2001), S. 993-1009

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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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5

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Relationship between plant hydraulic and biochemical properties derived from a steady-state coupled water and carbon transport model (2003)

KATUL, G. ; LEUNING, R. ; OREN, R.

Oxford, UK : Blackwell Science, Ltd

Plant, cell & environment 26 (2003), S. 0

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ISSN: 1365-3040

Source: Blackwell Publishing Journal Backfiles 1879-2005

Topics: Biology

Notes: There is growing evidence that plant stomata have evolved physiological controls to satisfy the demand for CO2 by photosynthesis while regulating water losses by leaves in a manner that does not cause cavitation in the soil–root–xylem hydraulic system. Whether the hydraulic and biochemical properties of plants evolve independently or whether they are linked at a time scale relevant to plant stand development remains uncertain. To address this question, a steady-state analytical model was developed in which supply of CO2 via the stomata and biochemical demand for CO2 are constrained by the balance between loss of water vapour from the leaf to the atmosphere and supply of water from the soil to the leaf. The model predicts the intercellular CO2 concentration (Ci) for which the maximum demand for CO2 is in equilibrium with the maximum hydraulically permissible supply of water through the soil–root–xylem system. The model was then tested at two forest stands in which simultaneous hydraulic, ecophysiological, and long-term carbon isotope discrimination measurements were available. The model formulation reproduces analytically recent findings on the sensitivity of bulk stomatal conductance (gs) to vapour pressure deficit (D); namely, gs = gref(1 − m × lnD), where m is a sensitivity parameter and gref is a reference conductance defined at D = 1 kPa. An immediate outcome of the model is an explicit relationship between maximum carboxylation capacity (Vcmax) and soil–plant hydraulic properties. It is shown that this relationship is consistent with measurements reported for conifer and rain forest angiosperm species. The analytical model predicts a decline in Vcmax as the hydraulic capacity of the soil–root–xylem decreases with stand development or age.

Type of Medium: Electronic Resource

URL: http://dx.doi.org/10.1046/j.1365-3040.2003.00965.x

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6

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Increased anthocyanin accumulation in aster flowers at elevated temperatures due to magnesium treatment (2002)

Shaked-Sachray, Liat ; Weiss, David ; Reuveni, Moshe ; [et al.]

Oxford, UK : Blackwell Science, Ltd

Physiologia plantarum 114 (2002), S. 0

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ISSN: 1399-3054

Source: Blackwell Publishing Journal Backfiles 1879-2005

Topics: Biology

Notes: Temperature is one of the main external factors affecting anthocyanin accumulation in plant tissues: low temperatures cause an increase and elevated temperatures cause a decrease in anthocyanin concentration. Several metals have been shown to increase the half-life time of anthocyanins, by forming complexes with them. We studied the combined effect of elevated temperatures and increased metal concentrations on the accumulation of anthocyanins in aster ‘Sungal’ flowers. It has been found that magnesium treatment of aster plants or detached flower buds, partially prevents colour fading at elevated temperatures. Anthocyanin concentration of aster ‘Sungal’ flowers grown at 29°C/21°C day/night, respectively, was about half that of flowers grown at 17°C/9°C. The activity of phenylalanine ammonia-lyase (PAL) and chalcone isomerase (CHI) decreased as the temperature increased. Treatment of both whole plants and detached flower buds grown at elevated temperatures in the presence of magnesium salts, increased flower anthocyanin concentration by up to 80%. Measurement of magnesium following these treatments revealed an increased level of the metal in the petals, suggesting a direct effect. Magnesium treatment does not seem to cause increased synthesis of anthocyanin through a stress-related reaction, since the activities of both PAL and CHI did not increase due to this treatment. The results of this study show that increasing magnesium levels in aster petals prevents the deleterious effect of elevated temperatures on anthocyanin accumulation, thus enhancing flower colour.

Type of Medium: Electronic Resource

URL: http://dx.doi.org/10.1034/j.1399-3054.2002.1140408.x

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Estimating maximum mean canopy stomatal conductance for use in models (2001)

Ewers, B E ; Oren, R ; Johnsen, K H ; [et al.]

Canadian Science Publishing

In: Canadian Journal of Forest Research. 2001; 31(2): 198-207. Published 2001 Feb 01. doi: 10.1139/x00-159.

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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