Effects of Temperature and Grain Size on Diffusivity of Aluminium: Electromigration Experiment and Molecular Dynamic Simulation

Abstract Understanding the atomic diffusion features in metallic material is significant to explain the diffusion-controlled physical processes. In this paper, using electromigration experiments and molecular dynamic (MD) simulations, we investigate the effects of grain size and temperature on the self-diffusion of polycrystalline aluminum (Al). The mass transport due to electromigration are accelerated by increasing temperature and decreasing grain size. Magnitudes of effective diffusivity (Deff) and grain boundary diffusivity (DGBs) are experimentally determined, in which the Deff changes as a function of grain size and temperature, but DGBs is independent of the grain size, only affected by the temperature. Moreover, MD simulations of atomic diffusion in polycrystalline Al demonstrate those observations from experiments. Based on MD results, the Arrhenius equation of DGBs and empirical formula of the thickness of grain boundaries at various temperatures are obtained. In total, Deff and DGBs obtained in the present study agree with literature results, and a comprehensive result of diffusivities related to the grain size is presented.

Download Full-text

Creep Deformation of Ultrafine Grained Ni7 5B1 7Si8

MRS Proceedings ◽

10.1557/proc-58-421 ◽

1985 ◽

Vol 58 ◽

Cited By ~ 1

Author(s):

Gilles Nussbaum ◽

Dieter G. Ast

Keyword(s):

Activation Energy ◽

Grain Size ◽

Creep Deformation ◽

Stress Regime ◽

Fine Grained ◽

Self Diffusion ◽

Diffusion Controlled ◽

Superplastic Alloy ◽

Ultrafine Grained ◽

Applied Stresses

ABSTRACTThe creep behavior of the fine grained, intermetallic superplastic alloy of overall composition Ni7 5 B1 7Si8 prepared by crystallizing an amorphous precursor was studied in the temperature range between 500 and 615°C, the stress range between 36 and 800 MPa, and for grain sizes between 6.8 and 1.12*10−5 mm. The strain rates measured varied between 10−7 and 6*10−5 sec−1.Two different creep deformation mechanisms were observed. At low applied stresses, the material deformed in a diffusion controlled mode, with proportional to σ1. No dislocations developed in the grains, and the activation energy for creep was 4 eV. This value is higher than the self-diffusion of Ni in Ni (the principal constituent in the alloy) in agreement with observation in other Ni based alloy systems. At high applied stresses, a second mechanism became rate limiting. The activation energy of this process is about 0.6 eV and dislocations develop in the interior of grains when this mechanism operates.The transition between the two regimes is grain size and temperature dependent and occurs at about 400 MPa at a deformation temperature of 550°C and a grain size of 6.8 10−5 mm. An analysis of the grain size dependence of creep strain rate as well as its absolute value indicates that the low stress regime is Coble type creep.

Download Full-text

Spotting Differences in Molecular Dynamic Simulations of Influenza A M2 Protein-Ligand Complexes by Varying M2 construct, Lipid Bilayer and Force Field

10.26434/chemrxiv.11365943.v1 ◽

2019 ◽

Author(s):

Dimitrios Kolokouris ◽

Iris Kalenderoglou ◽

Panagiotis Lagarias ◽

Antonios Kolocouris

Keyword(s):

Molecular Dynamic ◽

Lipid Bilayer ◽

Influenza A ◽

Md Simulations ◽

Membrane Curvature ◽

Buffer Size ◽

M2 Protein ◽

Dynamic Simulations ◽

Amphipathic Helices ◽

Drug Protein Binding

We studied by molecular dynamic (MD) simulations systems including the inwardclosed state of influenza A M2 protein in complex with aminoadamantane drugs in membrane bilayers. We varied the M2 construct and performed MD simulations in M2TM or M2TM with amphipathic helices (M2AH). We also varied the lipid bilayer by changing either the lipid, DMPC or POPC, POPE or POPC/cholesterol (chol), or the lipids buffer size, 10x10 Å2 or 20x20 Å2. We aimed to suggest optimal system conditions for the computational description of this ion channel and related systems. Measures performed include quantities that are available experimentally and include: (a) the position of ligand, waters and chlorine anion inside the M2 pore, (b) the passage of waters from the outward Val27 gate of M2 S31N in complex with an aminoadamantane-aryl head blocker, (c) M2 orientation, (d) the AHs conformation and structure which is affected from interactions with lipids and chol and is important for membrane curvature and virus budding. In several cases we tested OPLS2005, which is routinely applied to describe drug-protein binding, and CHARMM36 which describes reliably protein conformation. We found that for the description of the ligands position inside the M2 pore, a 10x10 Å2 lipids buffer in DMPC is needed when M2TM is used but 20x20 Å2 lipids buffer of the softer POPC; when M2AH is used all 10x10 Å2 lipid buffers with any of the tested lipids can be used. For the passage of waters at least M2AH with a 10x10 Å2 lipid buffer is needed. The folding conformation of AHs which is defined from hydrogen bonding interactions with the bilayer and the complex with chol is described well with a 10x10 Å2 lipids buffer and CHARMM36.

Download Full-text

Water and Deuterium Oxide Permeability through Aquaporin 1: MD Predictions and Experimental Verification

The Journal of General Physiology ◽

10.1085/jgp.200709810 ◽

2007 ◽

Vol 130 (1) ◽

pp. 111-116 ◽

Cited By ~ 31

Author(s):

Artem B. Mamonov ◽

Rob D. Coalson ◽

Mark L. Zeidel ◽

John C. Mathai

Keyword(s):

Deuterium Oxide ◽

Diffusion Constant ◽

Structural Data ◽

Md Simulations ◽

Water Model ◽

Aquaporin 1 ◽

Self Diffusion ◽

Osmotic Permeability ◽

Protein Channels ◽

And Diffusion

Determining the mechanisms of flux through protein channels requires a combination of structural data, permeability measurement, and molecular dynamics (MD) simulations. To further clarify the mechanism of flux through aquaporin 1 (AQP1), osmotic pf (cm3/s/pore) and diffusion pd (cm3/s/pore) permeability coefficients per pore of H2O and D2O in AQP1 were calculated using MD simulations. We then compared the simulation results with experimental measurements of the osmotic AQP1 permeabilities of H2O and D2O. In this manner we evaluated the ability of MD simulations to predict actual flux results. For the MD simulations, the force field parameters of the D2O model were reparameterized from the TIP3P water model to reproduce the experimentally observed difference in the bulk self diffusion constants of H2O vs. D2O. Two MD systems (one for each solvent) were constructed, each containing explicit palmitoyl-oleoyl-phosphatidyl-ethanolamine (POPE) phospholipid molecules, solvent, and AQP1. It was found that the calculated value of pf for D2O is ∼15% smaller than for H2O. Bovine AQP1 was reconstituted into palmitoyl-oleoyl-phosphatidylcholine (POPC) liposomes, and it was found that the measured macroscopic osmotic permeability coefficient Pf (cm/s) of D2O is ∼21% lower than for H2O. The combined computational and experimental results suggest that deuterium oxide permeability through AQP1 is similar to that of water. The slightly lower observed osmotic permeability of D2O compared to H2O in AQP1 is most likely due to the lower self diffusion constant of D2O.

Download Full-text

Effects of viscosity and osmotic stress on the reaction of human butyrylcholinesterase with cresyl saligenin phosphate, a toxicant related to aerotoxic syndrome: kinetic and molecular dynamics studies

Biochemical Journal ◽

10.1042/bj20130389 ◽

2013 ◽

Vol 454 (3) ◽

pp. 387-399 ◽

Cited By ~ 34

Author(s):

Patrick Masson ◽

Sofya Lushchekina ◽

Lawrence M. Schopfer ◽

Oksana Lockridge

Keyword(s):

Osmotic Stress ◽

Osmotic Pressure ◽

Active Site ◽

Md Simulations ◽

Catalytic Triad ◽

Wild Type ◽

Irreversible Inhibitor ◽

Enzyme Active Site ◽

Diffusion Controlled ◽

Peripheral Site

CSP (cresyl saligenin phosphate) is an irreversible inhibitor of human BChE (butyrylcholinesterase) that has been involved in the aerotoxic syndrome. Inhibition under pseudo-first-order conditions is biphasic, reflecting a slow equilibrium between two enzyme states E and E′. The elementary constants for CSP inhibition of wild-type BChE and D70G mutant were determined by studying the dependence of inhibition kinetics on viscosity and osmotic pressure. Glycerol and sucrose were used as viscosogens. Phosphorylation by CSP is sensitive to viscosity and is thus strongly diffusion-controlled (kon≈108 M−1·min−1). Bimolecular rate constants (ki) are about equal to kon values, making CSP one of the fastest inhibitors of BChE. Sucrose caused osmotic stress because it is excluded from the active-site gorge. This depleted the active-site gorge of water. Osmotic activation volumes, determined from the dependence of ki on osmotic pressure, showed that water in the gorge of the D70G mutant is more easily depleted than that in wild-type BChE. This demonstrates the importance of the peripheral site residue Asp70 in controlling the active-site gorge hydration. MD simulations provided new evidence for differences in the motion of water within the gorge of wild-type and D70G enzymes. The effect of viscosogens/osmolytes provided information on the slow equilibrium E⇌E′, indicating that alteration in hydration of a key catalytic residue shifts the equilibrium towards E′. MD simulations showed that glycerol molecules that substitute for water molecules in the enzyme active-site gorge induce a conformational change in the catalytic triad residue His438, leading to the less reactive form E′.

Download Full-text

Atomic Diffusion and its Relation to Thermodynamic Forces in Al-Ni Melts

Defect and Diffusion Forum ◽

10.4028/www.scientific.net/ddf.289-292.705 ◽

2009 ◽

Vol 289-292 ◽

pp. 705-710 ◽

Cited By ~ 13

Author(s):

Axel Griesche ◽

Bo Zhang ◽

Jürgen Horbach ◽

Andreas Meyer

Keyword(s):

Chemical Diffusion ◽

Atomic Diffusion ◽

Dynamic Simulations ◽

X Ray ◽

Self Diffusion ◽

Ni Alloys ◽

Quasielastic Neutron ◽

Cross Correlations ◽

Quasielastic Neutron Scattering ◽

Thermodynamic Forces

We make use of a novel X-ray radiography method to measure chemical diffusion in capillaries in binary Al-Ni melts. Data are compared to self diffusion coefficients of Ni obtained by quasielastic neutron scattering as well as diffusion and thermodynamic data obtained by molecular dynamic simulations. Interdiffusion compared to self diffusion is enhanced with a maximum at Al40Ni60. We show that this enhancement is caused by thermodynamic forces as described by the Darken-Manning equation. In liquid Al-Ni alloys the Manning factor that is smaller than one can be attributed to collective cross correlations.

Download Full-text

Vacancy-Mediated Diffusion and Diffusion-Controlled Processes in Ordered Binary Intermetallics by Kinetic Monte Carlo Simulations

Diffusion Foundations ◽

10.4028/www.scientific.net/df.29.95 ◽

2021 ◽

Vol 29 ◽

pp. 95-115

Author(s):

Rafal Kozubski ◽

Graeme E. Murch ◽

Irina V. Belova

Keyword(s):

Monte Carlo ◽

Kinetic Monte Carlo ◽

Simulation Studies ◽

Self Diffusion ◽

Monte Carlo Techniques ◽

Diffusion Controlled ◽

Kinetic Monte Carlo Simulations ◽

Kinetic Effects ◽

Kinetics Of ◽

And Diffusion

We review the results of our Monte Carlo simulation studies carried out within the past two decades in the area of atomic-migration-controlled phenomena in intermetallic compounds. The review aims at showing the high potential of Monte Carlo methods in modelling both the equilibrium states of the systems and the kinetics of the running processes. We focus on three particular problems: (i) the atomistic origin of the complexity of the ‘order-order’ relaxations in γ’-Ni3Al; (ii) surface-induced ordering phenomena in γ-FePt and (iii) ‘order—order’ kinetics and self-diffusion in the ‘triple-defect’ β-NiAl. The latter investigation demonstrated how diverse Monte Carlo techniques may be used to model the phenomena where equilibrium thermodynamics interplays and competes with kinetic effects.

Download Full-text

Refinement of Size Distributions for Primary Crystallizations

MRS Proceedings ◽

10.1557/proc-481-213 ◽

1997 ◽

Vol 481 ◽

Author(s):

E. Pineda ◽

T. Pradell ◽

D. Crespo ◽

N. Clavaguera ◽

J. ZHU ◽

...

Keyword(s):

Grain Size ◽

Metastable Phase ◽

Primary Crystallization ◽

Controlled Growth ◽

Diffusion Controlled ◽

Average Grain Size ◽

Soft Impingement ◽

Single Grain ◽

Kinetics Of ◽

And Diffusion

ABSTRACTThe microstructure developed in primary crystallizations is studied under realistic conditions. The primary crystallization of an amorphous alloy is modeled by considering the thermodynamics of a metastable phase transition and the kinetics of nucleation and crystal growth under isothermal annealing. A realistic growth rate, including an interface controlled growth at the beginning of the growth of each single grain and diffusion controlled growth process with soft impingement afterwards is considered. The reduction in the nucleation rate due to the compositional change in the remaining amorphous matrix is also taken into account. The microstructures developed during the transformation are obtained by using the Populational KJMA method, from the above thermodynamic and kinetic factors. Experimental data of transformed fraction, grain density, average grain size, grain size distribution and other related parameters obtained from annealed metallic glasses are modeled.

Download Full-text