scholarly journals Incorporating Nearest-Neighbor Site Dependence into Protein Evolution Models

2020 ◽  
Vol 27 (3) ◽  
pp. 361-375 ◽  
Author(s):  
Gary Larson ◽  
Jeffrey L. Thorne ◽  
Scott Schmidler
Keyword(s):  
Protein Evolution ◽  
Nearest Neighbor ◽  
Neighbor Site ◽  
Site Dependence

Oxygen vacancy migration in CSZ using density functional theory

2008 ◽  
Vol 1122 ◽  
Author(s):  
Byeong-Eon Lee ◽  
Dae-Hee Kim ◽  
Yeong-Cheol Kim
Keyword(s):  
Density Functional Theory ◽  
Oxygen Vacancy ◽  
Density Functional ◽  
Oxygen Vacancies ◽  
Nearest Neighbor ◽  
Functional Theory ◽  
The Third ◽  
Vacancy Migration ◽  
Neighbor Site ◽  
Formation Energies

AbstractWe studied oxygen migration in calcia-stabilized cubic zirconia (CSZ) using density functional theory. A Ca atom was substituted for a Zr atom in a 2×2×2 ZrO2 cubic supercell, and an oxygen vacancy was produced to satisfy the charge neutrality condition. We found that the formation energies of an oxygen vacancy, as a function of its location with respect to the Ca atom, were varied. The relative formation energies of the oxygen vacancies located at the first-, second-, third-, and fourth-nearest-neighbors were 0.0, −0.07, 0.19, and 0.19 eV, respectively. Therefore, the oxygen vacancy located at the second-nearest-neighbor site of the Ca atom was the most favorable, the oxygen vacancy located at the first-nearest-neighbor site was the second most favorable, and the oxygen vacancies at the third- and fourth-nearest-neighbor sites were the least favorable. We also calculated the energy barriers for the oxygen vacancy migration between oxygen sites. The energy barriers between the first and the second nearest sites, the second and third nearest sites, and the third and fourth nearest sites were 0.11, 0.46, and 0.23 eV, respectively. Therefore, the oxygen vacancies favored the first- and second-nearest-neighbor oxygen sites when they drifted under an electric field.

EFFECTS OF FINITE REACTION RATES ON THE KINETIC PHASE TRANSITIONS IN THE CATALYTIC OXIDATION OF CARBON MONOXIDE

2002 ◽  
Vol 09 (05n06) ◽  
pp. 1735-1739
Author(s):  
L. D. LÓPEZ-CARREÑO
Keyword(s):  
Carbon Monoxide ◽  
Phase Transitions ◽  
Steady State ◽  
Catalytic Oxidation ◽  
Active Sites ◽  
Nearest Neighbor ◽  
Reaction Rates ◽  
Neighbor Site ◽  
State Configuration ◽  
Oxidation Of Carbon Monoxide

Oxidation of carbon monoxide is one of the most extensively studied heterogeneous catalysis reactions, being important among other applications in automobile-emission control. Catalytic oxidation of carbon monoxide on platinum (111) surface was simulated by the Monte Carlo technique following an extended version of the model proposed by Ziff, Gulari and Barshad (ZGB). In the simulation, a simple square two-dimensional lattice of active sites replaces the surface of the catalyst. Finite reaction rates for (i) diffusion of the reactive species on the surface, (ii) reaction of a CO molecule with an oxygen atom in a nearest neighbor site, and (iii) desorption of unreacted CO molecules, have been taken into account. The produced CO 2 desorbs instantly. The average coverage of O, CO and the CO 2 production rate for a steady state configuration, as a function of the normalized CO partial pressure (P CO ), shows two kinetic phase transitions. In the ZGB model these transitions occur at P CO ≈ 0.39 and P CO ≈ 0.53. For 0.39 < P CO < 0.53 a reactive ( CO 2 production) steady state is found. Outside of the interval, the only steady state is a poisoned catalyst of pure CO or pure O. Our results show that finite reaction rates shift the values in which these phase transitions occur.

Comparison between the nearest and the next-nearest neighbor site–spin interactions in the Ising model

2002 ◽  
Vol 124 (9) ◽  
pp. 347-351 ◽  
Author(s):  
Baohua Teng ◽  
Yuanfu Chen ◽  
Hao Fu ◽  
Yongbai Tang ◽  
Mingling Tu ◽  
...  
Keyword(s):  
Ising Model ◽  
Nearest Neighbor ◽  
Neighbor Site ◽  
Spin Interactions

FROM NEXT NEAREST NEIGHBOR SITE PERCOLATION TO CONTINUUM PERCOLATION: APPLICATION TO HIGH-Tc SUPERCONDUCTORS

2004 ◽  
Vol 15 (02) ◽  
pp. 321-333 ◽  
Author(s):  
E. P. STOLL
Keyword(s):  
Nearest Neighbor ◽  
Translation Invariance ◽  
Continuum Percolation ◽  
Electric Conduction ◽  
Site Percolation ◽  
High Tc ◽  
Superconducting Cuprates ◽  
Neighbor Site ◽  
Excess Electrons ◽  
Dopant Atoms

In high-Tc superconductors dopant atoms supply holes or excess electrons, and electric conduction is established in the neighborhood of the dopant. We propose that percolation of these conducting areas leads to global electric conduction. To investigate these processes numerical procedures to simulate continuum percolation are developed. The relation between the concentration of connecting discs and the fraction of the area of the plane covered by all discs is computed in the whole range between next nearest neighbor site percolation and continuum percolation. This method is applied to investigate underdoped copper oxides where small hole or excess electron concentrations are insufficient to establish electric conduction. The results of this study are applied to the model of mobile charge carriers which consist of or are accompanied by diffusing d-electrons. Our investigations show that with increasing doping the Neel temperature of the antiferromagnetism vanishes and spin glass states appear in accordance with experiments. Furthermore, the peaks in the specific heat become very broad. This broadening due to randomness and loss of translation invariance has been observed in nuclear magnetic resonance peaks of doped superconducting cuprates.

The Korteweg-De Vries Equation of a New Lattice Model with a Consideration of the Next-Nearest-Neighbor Site and its Numerical Simulation

2013 ◽  
Vol 409-410 ◽  
pp. 1387-1391 ◽  
Author(s):  
Yang Xu ◽  
Zhen Zhou Yuan ◽  
Jun Fang Tian
Keyword(s):  
Nearest Neighbor ◽  
Vries Equation ◽  
Neutral Stability ◽  
Neutral Stability Curve ◽  
Lattice Hydrodynamic Model ◽  
Neighbor Interaction ◽  
Stability Curve ◽  
Traffic Jam ◽  
Neighbor Site ◽  
De Vries

Based on Nagatanis model, a new lattice hydrodynamic model of traffic flow with a consideration of the next-nearest-neighbor site is proposed. Using nonlinear analysis, we derive the Korteweg-de Vries (KdV, for short) equation near the neutral stability curve to describe the density waves. Numerical simulations are consonant with the analytical results and shows that the consideration of the next-nearest-neighbor interaction helps suppress traffic jam.

Observation of Superlattice Dislocations on Cube Planes in Ni3Al

1973 ◽  
Vol 31 ◽  
pp. 174-175 ◽  
Author(s):  
J. M. Oblak ◽  
W. H. Rand
Keyword(s):  
Nearest Neighbor ◽  
Antiphase Boundary ◽  
Nearest Neighbors ◽  
High Energy ◽  
Cross Slip ◽  
Octahedral Plane ◽  
Trapping Mechanism ◽  
Slip Traces

The energy of an a/2 <110> shear antiphase. boundary in the Ll2 expected to be at a minimum on {100} cube planes because here strue ture is there is no violation of nearest-neighbor order. The latter however does involve the disruption of second nearest neighbors. It has been suggested that cross slip of paired a/2 <110> dislocations from octahedral onto cube planes is an important dislocation trapping mechanism in Ni3Al; furthermore, slip traces consistent with cube slip are observed above 920°K.Due to the high energy of the {111} antiphase boundary (> 200 mJ/m2), paired a/2 <110> dislocations are tightly constricted on the octahedral plane and cannot be individually resolved.

Application of Lattice Imaging Techniques to Amorphous Films

1975 ◽  
Vol 33 ◽  
pp. 8-9
Author(s):  
S. R. Herd ◽  
P. Chaudhari
Keyword(s):  
Nearest Neighbor ◽  
Random Network ◽  
Imaging Techniques ◽  
Network Models ◽  
Accurate Method ◽  
Direct Transmission ◽  
Lattice Imaging ◽  
Transmission Electron ◽  
Lattice Planes ◽  
Nearest Neighbor Distances

Electron diffraction and direct transmission have been used extensively to study the local atomic arrangement in amorphous solids and in particular Ge. Nearest neighbor distances had been calculated from E.D. profiles and the results have been interpreted in terms of the microcrystalline or the random network models. Direct transmission electron microscopy appears the most direct and accurate method to resolve this issue since the spacial resolution of the better instruments are of the order of 3Å. In particular the tilted beam interference method is used regularly to show fringes corresponding to 1.5 to 3Å lattice planes in crystals as resolution tests.

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