Electronic structure and relative stability of the coherent and semi-coherent HfO2/III-V interfaces

NASA Astrophysics Data System (ADS)

Lahti, A.; Levämäki, H.; Mäkelä, J.; Tuominen, M.; Yasir, M.; Dahl, J.; Kuzmin, M.; Laukkanen, P.; Kokko, K.; Punkkinen, M. P. J.

2018-01-01

III-V semiconductors are prominent alternatives to silicon in metal oxide semiconductor devices. Hafnium dioxide (HfO2) is a promising oxide with a high dielectric constant to replace silicon dioxide (SiO2). The potentiality of the oxide/III-V semiconductor interfaces is diminished due to high density of defects leading to the Fermi level pinning. The character of the harmful defects has been intensively debated. It is very important to understand thermodynamics and atomic structures of the interfaces to interpret experiments and design methods to reduce the defect density. Various realistic gap defect state free models for the HfO2/III-V(100) interfaces are presented. Relative energies of several coherent and semi-coherent oxide/III-V semiconductor interfaces are determined for the first time. The coherent and semi-coherent interfaces represent the main interface types, based on the Ga-O bridges and As (P) dimers, respectively.

Thermodynamic and Information Entropy in Electroconvection

NASA Astrophysics Data System (ADS)

Cressman, John; Daum, Marcus; Patrick, David; Cerbus, Rory; Goldburg, Walter

Transitions in driven systems often produce wild fluctuations that can be both detrimental and beneficial. Our fundamental understanding of these transients is inadequate to permit optimal interactions with systems ranging from biology, to energy generation, to finance. Here we report on experiments performed in electroconvecting liquid crystals where we abruptly change the electrical forcing across the sample from a state below defect turbulence into a state of defect turbulence. We simultaneously measure the electrical power flow through the liquid crystal as well as image the structure in the sample. These measurements enable us to simultaneously track the evolution of the thermodynamic and information entropies. Our experiments demonstrate that there are strong correlations between the fluctuations in these two entropic measures however they are not exact. We will discuss these discrepancies as well as the relevance of large transient fluctuations in non-equilibrium transitions in general.

Ab initio thermodynamic model for magnesium carbonates and hydrates.

PubMed

Chaka, Anne M; Felmy, Andrew R

2014-09-04

An ab initio thermodynamic framework for predicting properties of hydrated magnesium carbonate minerals has been developed using density-functional theory linked to macroscopic thermodynamics through the experimental chemical potentials for MgO, water, and CO2. Including semiempirical dispersion via the Grimme method and small corrections to the generalized gradient approximation of Perdew, Burke, and Ernzerhof for the heat of formation yields a model with quantitative agreement for the benchmark minerals brucite, magnesite, nesquehonite, and hydromagnesite. The model shows how small differences in experimental conditions determine whether nesquehonite, hydromagnesite, or magnesite is the result of laboratory synthesis from carbonation of brucite, and what transformations are expected to occur on geological time scales. Because of the reliance on parameter-free first-principles methods, the model is reliably extensible to experimental conditions not readily accessible to experiment and to any mineral composition for which the structure is known or can be hypothesized, including structures containing defects, substitutions, or transitional structures during solid state transformations induced by temperature changes or processes such as water, CO2, or O2 diffusion. Demonstrated applications of the ab initio thermodynamic framework include an independent means to evaluate differences in thermodynamic data for lansfordite, predicting the properties of Mg analogues of Ca-based hydrated carbonates monohydrocalcite and ikaite, which have not been observed in nature, and an estimation of the thermodynamics of barringtonite from the stoichiometry and a single experimental observation.

First-Principles Analysis of Defect Thermodynamics and Ion Transport in Inorganic SEI Compounds: LiF and NaF

DOE Office of Scientific and Technical Information (OSTI.GOV)

Yildirim, Handan; Kinaci, Alper; Chan, Maria K. Y.

The formation mechanism and composition of the solid electrolyte interphase (SEI) in lithium ion batteries has been widely explored. However, relatively little is known about the function of the SEI as a transport medium. Such critical information is directly relevant to battery rate performance, power loss, and capacity fading. To partially bridge this gap in the case of inorganic SEI compounds, we report herein the results of first-principles calculations on the defect thermodynamics, the dominant diffusion carriers, and the diffusion pathways associated with crystalline LiF and NaF, which are stable components of the SEI in Li-ion and Na-ion batteries, respectively.more » The thermodynamics of common point defects are computed, and the dominant diffusion carriers are determined over a voltage range of 0-4 V, corresponding to conditions relevant to both anode and cathode SEI's. Our analyses reveal that for both compounds, vacancy defects are energetically more favorable, therefore form more readily than interstitials, due to the close-packed nature of the crystal structures. However, the vacancy concentrations are very small for the diffusion processes facilitated by defects. Ionic conductivities are calculated as a function of voltage, considering the diffusion carrier concentration and the diffusion barriers as determined by nudged elastic band calculations. These conductivities are more than ten orders of magnitude smaller in NaF than in LiF. As compared to the diffusivity of Li in other common inorganic SEI compounds, such as Li2CO3 and Li2O,the cation diffusivity in LiF and NaF is quite low, with at least three orders of magnitude lower ionic conductivities. The results quantify the extent to which fluorides pose rate limitations in Li and Na batteries.« less

Density functional theory study of defects in unalloyed δ-Pu

DOE PAGES

Hernandez, S. C.; Freibert, F. J.; Wills, J. M.

2017-03-19

Using density functional theory, we explore in this paper various classical point and complex defects within the face-centered cubic unalloyed δ-plutonium matrix that are potentially induced from self-irradiation. For plutonium only defects, the most energetically stable defect is a distorted split-interstitial. Gallium, the δ-phase stabilizer, is thermodynamically stable as a substitutional defect, but becomes unstable when participating in a complex defect configuration. Finally, complex uranium defects may thermodynamically exist as uranium substitutional with neighboring plutonium interstitial and stabilization of uranium within the lattice is shown via partial density of states and charge density difference plots to be 5f hybridization betweenmore » uranium and plutonium.« less

Density functional theory study of defects in unalloyed δ-Pu

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hernandez, S. C.; Freibert, F. J.; Wills, J. M.

Using density functional theory, we explore in this paper various classical point and complex defects within the face-centered cubic unalloyed δ-plutonium matrix that are potentially induced from self-irradiation. For plutonium only defects, the most energetically stable defect is a distorted split-interstitial. Gallium, the δ-phase stabilizer, is thermodynamically stable as a substitutional defect, but becomes unstable when participating in a complex defect configuration. Finally, complex uranium defects may thermodynamically exist as uranium substitutional with neighboring plutonium interstitial and stabilization of uranium within the lattice is shown via partial density of states and charge density difference plots to be 5f hybridization betweenmore » uranium and plutonium.« less

Interface-Driven Phenomena in Solids: Thermodynamics, Kinetics and Chemistry

DOE PAGES

Abdeljawad, Fadi; Foiles, Stephen M.

2016-05-04

The study of materials interfaces dates back over a century. In solid systems and from an engineering perspective, free surfaces and internal (grain and/or phase) boundaries influence a wide range of properties, such as thermal, electrical and optical transport, and mechanical ones. The properties and the role of interfaces has been discussed extensively in various reviews such as by Sutton and Balluffi. As the characteristic feature size of a materials system (i.e., grain size) is decreased to the nanometer scale, interface-driven physics is expected to dominate due to the increased density of such planar defects. Moreover, interfacial attributes, thermodynamics, andmore » mobility play a key role in phase transformations, such as solidification dynamics and structural transitions in solids, and in homogenization and microstructural evolution processes, such as grain growth, coarsening, and recrystallization. In summary, the set of articles published in this special topic titled: “Interface-Driven Phenomena in Solids: Thermodynamics, Kinetics and Chemistry” covers topics related to microstructure evolution, segregation/adsorption phenomena and interface interactions with other materials defects.« less

Interface-Driven Phenomena in Solids: Thermodynamics, Kinetics and Chemistry

DOE Office of Scientific and Technical Information (OSTI.GOV)

Abdeljawad, Fadi; Foiles, Stephen M.

The study of materials interfaces dates back over a century. In solid systems and from an engineering perspective, free surfaces and internal (grain and/or phase) boundaries influence a wide range of properties, such as thermal, electrical and optical transport, and mechanical ones. The properties and the role of interfaces has been discussed extensively in various reviews such as by Sutton and Balluffi. As the characteristic feature size of a materials system (i.e., grain size) is decreased to the nanometer scale, interface-driven physics is expected to dominate due to the increased density of such planar defects. Moreover, interfacial attributes, thermodynamics, andmore » mobility play a key role in phase transformations, such as solidification dynamics and structural transitions in solids, and in homogenization and microstructural evolution processes, such as grain growth, coarsening, and recrystallization. In summary, the set of articles published in this special topic titled: “Interface-Driven Phenomena in Solids: Thermodynamics, Kinetics and Chemistry” covers topics related to microstructure evolution, segregation/adsorption phenomena and interface interactions with other materials defects.« less

First-principles thermodynamics and defect kinetics guidelines for engineering a tailored RRAM device

DOE Office of Scientific and Technical Information (OSTI.GOV)

Clima, Sergiu, E-mail: clima@imec.be; Chen, Yang Yin; Goux, Ludovic

Resistive Random Access Memories are among the most promising candidates for the next generation of non-volatile memory. Transition metal oxides such as HfOx and TaOx attracted a lot of attention due to their CMOS compatibility. Furthermore, these materials do not require the inclusion of extrinsic conducting defects since their operation is based on intrinsic ones (oxygen vacancies). Using Density Functional Theory, we evaluated the thermodynamics of the defects formation and the kinetics of diffusion of the conducting species active in transition metal oxide RRAM materials. The gained insights based on the thermodynamics in the Top Electrode, Insulating Matrix and Bottommore » Electrode and at the interfaces are used to design a proper defect reservoir, which is needed for a low-energy reliable switching device. The defect reservoir has also a direct impact on the retention of the Low Resistance State due to the resulting thermodynamic driving forces. The kinetics of the diffusing conducting defects in the Insulating Matrix determine the switching dynamics and resistance retention. The interface at the Bottom Electrode has a significant impact on the low-current operation and long endurance of the memory cell. Our first-principles findings are confirmed by experimental measurements on fabricated RRAM devices.« less

Study on the intrinsic defects in tin oxide with first-principles method

NASA Astrophysics Data System (ADS)

Sun, Yu; Liu, Tingyu; Chang, Qiuxiang; Ma, Changmin

2018-04-01

First-principles and thermodynamic methods are used to study the contribution of vibrational entropy to defect formation energy and the stability of the intrinsic point defects in SnO2 crystal. According to thermodynamic calculation results, the contribution of vibrational entropy to defect formation energy is significant and should not be neglected, especially at high temperatures. The calculated results indicate that the oxygen vacancy is the major point defect in undoped SnO2 crystal, which has a higher concentration than that of the other point defect. The property of negative-U is put forward in SnO2 crystal. In order to determine the most stable defects much clearer under different conditions, the most stable intrinsic defect as a function of Fermi level, oxygen partial pressure and temperature are described in the three-dimensional defect formation enthalpy diagrams. The diagram visually provides the most stable point defects under different conditions.

First-principles investigation of thermodynamic and kinetic properties in titanium-hydrogen system and B2-nickel-alminum compound: Phase stability, point defect complexes and diffusion

NASA Astrophysics Data System (ADS)

Xu, Qingchuan

The purpose of this thesis is to show the technique of predicting thermodynamic and kinetic properties from first-principles using density functional theory (DFT) calculations, cluster expansion methods and Monte Carlo simulations instead of experiments. Two material systems are selected as examples: one is an interstitial system (Ti-H system) and another is a substitutional compound (B2-NiAl alloy). For Ti-H system, this thesis investigated hydride stability, exploring the role of configurational degrees of freedom, zero-point vibrational energy and coherency strains. The tetragonal gamma-TiH phase was predicted to be unstable relative to hcp alpha-Ti and fcc based delta-TiH2. Zero point vibrational energy makes the gamma phase even less stable. The coherency strains between hydride precipitates and alpha-Ti matrix stabilize gamma-TiH relative to alpha-Ti and delta-TiH2. We also found that hydrogen prefers octahedral sites at low hydrogen concentration and tetrahedral sites at high concentration. For B2-NiAl, this thesis investigated the point defects and various diffusion mechanisms. A low barrier collective hop was discovered that could mediate Al diffusion through the anti-structural-bridge (ASB) mechanism. We also found an alternative hop sequence for the migration of a triple defect and a six-jump-cycle than that proposed previously. Going beyond the mean field approximation, we found that the inclusion of interactions among point defects is crucial to predict the concentration of defect complexes. Accounting for interactions among defects and incorporating all diffusion mechanisms proposed for B2-NiAl in Monte Carlo simulation, we calculated tracer diffusion coefficients. For the first time, the relative importance of various diffusion mechanisms is revealed. The ASB hop is the dominant mechanism for Ni in Ni-rich alloy and for Al diffusion in Al-rich alloys. Other mechanisms also play a role to various extents. We also calculated the self and interdiffusion coefficients for B2-NiAl. We found in Al-rich alloys that the thermodynamic factor of Al is much greater than that of Ni while in Ni-rich alloys they are very similar. This difference in thermodynamic factors results in a much higher self-diffusion coefficient of Al compared to that of Ni in Al-rich alloys and also causes two different interdiffusion coefficients.

Characterization of point defects in monolayer arsenene

NASA Astrophysics Data System (ADS)

Liang, Xiongyi; Ng, Siu-Pang; Ding, Ning; Wu, Chi-Man Lawrence

2018-06-01

Topological defects that are inevitably found in 2D materials can dramatically affect their properties. Using density functional theory (DFT) calculations and ab initio molecular dynamics (AIMD) method, the structural, thermodynamic, electronic and magnetic properties of six types of typical point defects in arsenene, i.e. the Stone-Wales defect, single and double vacancies and adatoms, were systemically studied. It was found that these defects were all more easily generated in arsenene with lower formation energies than those with graphene and silicene. Stone-Wales defects can be transformed from pristine arsenene by overcoming a barrier of 2.19 eV and single vacancy defects tend to coalesce into double vacancy defects by diffusion. However, a type of adatom defect does not exhibit kinetic stability at room temperature. In addition, SV defects and another type of adatom defect can remarkably affect the electronic and magnetic properties of arsenene, e.g. they can introduce localized states near the Fermi level, as well as a strongly local magnetic moment due to dangling bond and unpaired electron. Furthermore, the simulated scanning tunneling microscopy (STM) and Raman spectroscopy were computed and the types of point defects can be fully characterized by correlating the STM images and Raman spectra to the defective atomistic structures. The results provide significant insights to the effect of defects in arsenene for potential applications, as well as identifications of two helpful tools (STM and Raman spectroscopy) to distinguish the type of defects in arsenene for future experiments.

Thermodynamic stability and structure of cuprous chloride surfaces: a DFT investigation.

PubMed

Suleiman, Ibrahim A; Radny, Marian W; Gladys, Michael J; Smith, Phillip V; Mackie, John C; Kennedy, Eric M; Dlugogorski, Bogdan Z

2015-03-14

Density functional theory together with ab initio atomistic thermodynamics has been utilized to study the structures and stabilities of the low index CuCl surfaces. It is shown that the Cl-terminated structures are more stable than the Cu-terminated configurations, and that the defective CuCl(110)-Cu structure is more stable than the stoichiometric CuCl(110) surface. The equilibrium shape of a cuprous chloride nanostructure terminated by low-index CuCl surfaces has also been predicted using a Wulff construction. It was found that the (110) facets dominate at low chlorine concentration. As the chlorine concentration is increased, however, the contributions of the (100) and (111) facets to the Wulff construction also increase giving the crystal a semi-prism shape. At high chlorine concentration, and close to the rich limit, the (111) facets were found to be the only contributors to the Wulff construction, resulting in prismatic nanocrystals.

Defect formation in LaGa(Mg,Ni)O3-δ : A statistical thermodynamic analysis validated by mixed conductivity and magnetic susceptibility measurements

NASA Astrophysics Data System (ADS)

Naumovich, E. N.; Kharton, V. V.; Yaremchenko, A. A.; Patrakeev, M. V.; Kellerman, D. G.; Logvinovich, D. I.; Kozhevnikov, V. L.

2006-08-01

A statistical thermodynamic approach to analyze defect thermodynamics in strongly nonideal solid solutions was proposed and validated by a case study focused on the oxygen intercalation processes in mixed-conducting LaGa0.65Mg0.15Ni0.20O3-δ perovskite. The oxygen nonstoichiometry of Ni-doped lanthanum gallate, measured by coulometric titration and thermogravimetric analysis at 923-1223K in the oxygen partial pressure range 5×10-5to0.9atm , indicates the coexistence of Ni2+ , Ni3+ , and Ni4+ oxidation states. The formation of tetravalent nickel was also confirmed by the magnetic susceptibility data at 77-600K , and by the analysis of p -type electronic conductivity and Seebeck coefficient as function of the oxygen pressure at 1023-1223K . The oxygen thermodynamics and the partial ionic and hole conductivities are strongly affected by the point-defect interactions, primarily the Coulombic repulsion between oxygen vacancies and/or electron holes and the vacancy association with Mg2+ cations. These factors can be analyzed by introducing the defect interaction energy in the concentration-dependent part of defect chemical potentials expressed by the discrete Fermi-Dirac distribution, and taking into account the probabilities of local configurations calculated via binomial distributions.

The self-healing of defects induced by the hydriding phase transformation in palladium nanoparticles

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ulvestad, A.; Yau, A.

Nanosizing can dramatically alter material properties by enhancing surface thermodynamic contributions, shortening diffusion lengths, and increasing the number of catalytically active sites per unit volume. These mechanisms have been used to explain the improved properties of catalysts, battery materials, plasmonic materials, etc. Here we show that Pd nanoparticles also have the ability to self-heal defects in their crystal structures. Using Bragg coherent diffractive imaging, we image dislocations nucleated deep in a Pd nanoparticle during the forward hydriding phase transformation that heal during the reverse transformation, despite the region surrounding the dislocations remaining in the hydrogen-poor phase. We show that defectivemore » Pd nanoparticles exhibit sloped isotherms, indicating that defects act as additional barriers to the phase transformation. Our results resolve the formation and healing of structural defects during phase transformations at the single nanoparticle level and offer an additional perspective as to how and why nanoparticles differ from their bulk counterparts.« less

Defect Clustering and Nano-Phase Structure Characterization of Multi-Component Rare Earth Oxide Doped Zirconia-Yttria Thermal Barrier Coatings

NASA Technical Reports Server (NTRS)

Zhu, Dongming; Chen, Yuan L.; Miller, Robert A.

2003-01-01

Advanced oxide thermal barrier coatings have been developed by incorporating multi-component rare earth oxide dopants into zirconia-yttria to effectively promote the creation of the thermodynamically stable, immobile oxide defect clusters and/or nano-scale phases within the coating systems. The presence of these nano-sized defect clusters has found to significantly reduce the coating intrinsic thermal conductivity, improve sintering resistance, and maintain long-term high temperature stability. In this paper, the defect clusters and nano-structured phases, which were created by the addition of multi-component rare earth dopants to the plasma-sprayed and electron-beam physical vapor deposited thermal barrier coatings, were characterized by high-resolution transmission electron microscopy (TEM). The defect cluster size, distribution, crystallographic and compositional information were investigated using high-resolution TEM lattice imaging, selected area diffraction (SAD), electron energy-loss spectroscopy (EELS) and energy dispersive spectroscopy (EDS) analysis techniques. The results showed that substantial defect clusters were formed in the advanced multi-component rare earth oxide doped zirconia- yttria systems. The size of the oxide defect clusters and the cluster dopant segregation was typically ranging from 5 to 50 nm. These multi-component dopant induced defect clusters are an important factor for the coating long-term high temperature stability and excellent performance.

Defect Clustering and Nano-Phase Structure Characterization of Multi-Component Rare Earth Oxide Doped Zirconia-Yttria Thermal Barrier Coatings

NASA Technical Reports Server (NTRS)

Zhu, Dongming; Chen, Yuan L.; Miller, Robert A.

1990-01-01

Advanced oxide thermal barrier coatings have been developed by incorporating multi- component rare earth oxide dopants into zirconia-yttria to effectively promote the creation of the thermodynamically stable, immobile oxide defect clusters and/or nano-scale phases within the coating systems. The presence of these nano-sized defect clusters has found to significantly reduce the coating intrinsic thermal conductivity, improve sintering resistance, and maintain long-term high temperature stability. In this paper, the defect clusters and nano-structured phases, which were created by the addition of multi-component rare earth dopants to the plasma- sprayed and electron-beam physical vapor deposited thermal barrier coatings, were characterized by high-resolution transmission electron microscopy (TEM). The defect cluster size, distribution, crystallographic and compositional information were investigated using high-resolution TEM lattice imaging, selected area diffraction (SAD), and energy dispersive spectroscopy (EDS) analysis techniques. The results showed that substantial defect clusters were formed in the advanced multi-component rare earth oxide doped zirconia-yttria systems. The size of the oxide defect clusters and the cluster dopant segregation was typically ranging fiom 5 to 50 nm. These multi-component dopant induced defect clusters are an important factor for the coating long-term high temperature stability and excellent performance.

Theoretical studies of aluminum and aluminide alloys using CALPHAD and first-principles approach

NASA Astrophysics Data System (ADS)

Jiang, Chao

Heat-treatable aluminum alloys have been widely used in the automobile and aerospace industries as structural materials due to their light weight and high strength. To study the age-hardening process in heat-treatable aluminum alloys, the Gibbs energies of the strengthening metastable phases, e.g. theta ' and theta″, are critical. However, those data are not included in the existing thermodynamic databases for aluminum alloys due to the semi-empirical nature of the CALPHAD approach. In the present study, the thermodynamics of the Al-Cu system, the pivotal age-hardening system, is remodeled using a combined CALPHAD and first-principles approach. The formation enthalpies and vibrational formation entropies of the stable and metastable phases in the Al-Cu system are provided by first-principles calculations. Special Quasirandom Structures (SQS's) are applied to model the substitutionally random fee and bee alloys. SQS's for binary bee alloys are developed and tested in the present study. Finally, a self-consistent thermodynamic description of the Al-Cu system including the two metastable theta″ and theta' phases is obtained. During welding of heat-treatable aluminum alloys, a detrimental phenomenon called constitutional liquation, i.e. the local eutectic melting of second-phase particles in a matrix at temperatures above the eutectic temperature but below the solidus of the alloy, may occur in the heat-affected zone (HAZ). In the present study, diffusion code DICTRA coupled with realistic thermodynamic and kinetic databases is used to simulate the constitutional liquation in the model Al-Cu system. The simulated results are in quantitative agreement with experiments. The critical heating rate to avoid constitutional liquation is also determined through computer simulations. Besides the heat-treatable aluminum alloys, intermetallic compounds based on transition metal aluminides, e.g. NiAl and FeAl, are also promising candidates for the next-generation of high-temperature structural materials for aerospace applications due to their high melting temperature and good oxidation resistance. Many important properties of B2 aluminides are governed by the existences of point defects. In the present study, Special Quasirandom Structures (SQS's) are developed to model non-stoichiometric B2 compounds containing large concentrations of constitutional point defects. The SQS's are then applied to study B2 NiAl. The first-principles SQS results provide formation enthalpies, equilibrium lattice parameters and elastic constants of B2 NiAl which agree satisfactorily with the existing experimental data in the literature. It is unambiguously shown that, at T = 0K and zero pressure, Ni vacancies and antisite Ni atoms are the energetically favorable point defects in Al-rich and Ni-rich B2 NiAl, respectively. Remarkably, it is predicted that high defect concentrations can lead to structural instability of B2 NiAl, which explains well the martensitic transformation observed in this compound at high Ni concentrations.

Hydrogen Diffusion and Trapping in α -Iron: The Role of Quantum and Anharmonic Fluctuations

NASA Astrophysics Data System (ADS)

Cheng, Bingqing; Paxton, Anthony T.; Ceriotti, Michele

2018-06-01

We investigate the thermodynamics and kinetics of a hydrogen interstitial in magnetic α -iron, taking account of the quantum fluctuations of the proton as well as the anharmonicities of lattice vibrations and hydrogen hopping. We show that the diffusivity of hydrogen in the lattice of bcc iron deviates strongly from an Arrhenius behavior at and below room temperature. We compare a quantum transition state theory to explicit ring polymer molecular dynamics in the calculation of diffusivity. We then address the trapping of hydrogen by a vacancy as a prototype lattice defect. By a sequence of steps in a thought experiment, each involving a thermodynamic integration, we are able to separate out the binding free energy of a proton to a defect into harmonic and anharmonic, and classical and quantum contributions. We find that about 30% of a typical binding free energy of hydrogen to a lattice defect in iron is accounted for by finite temperature effects, and about half of these arise from quantum proton fluctuations. This has huge implications for the comparison between thermal desorption and permeation experiments and standard electronic structure theory. The implications are even greater for the interpretation of muon spin resonance experiments.

Proceedings of the Seventh Annual Mechanics of Composites Review, held 28-30 October 1981, Dayton, Ohio.

DTIC Science & Technology

1982-04-01

structural components. 289 AFWtAL-TR-82-400 7 CONTRACTS INCREMENTAL ANALYSIS OF IMPACT DAMAGE NASI -15888 79 August 3 - 82 November 30 Project...THERMODYNAMICS TO COMPOSITE MATERIALS NASi -16301 80 August 18 - 82 January 03 Project Engineer: Dr. Norman J. Johnston Mail Stop 226 NASA Langley...that the system responds by the formation of dissipative rather than equi- librium structures or defects. GRAPHITE FIBER SURFACE TREATMENT NASI -15869

Computing the absolute Gibbs free energy in atomistic simulations: Applications to defects in solids

NASA Astrophysics Data System (ADS)

Cheng, Bingqing; Ceriotti, Michele

2018-02-01

The Gibbs free energy is the fundamental thermodynamic potential underlying the relative stability of different states of matter under constant-pressure conditions. However, computing this quantity from atomic-scale simulations is far from trivial, so the potential energy of a system is often used as a proxy. In this paper, we use a combination of thermodynamic integration methods to accurately evaluate the Gibbs free energies associated with defects in crystals, including the vacancy formation energy in bcc iron, and the stacking fault energy in fcc nickel, iron, and cobalt. We quantify the importance of entropic and anharmonic effects in determining the free energies of defects at high temperatures, and show that the potential energy approximation as well as the harmonic approximation may produce inaccurate or even qualitatively wrong results. Our calculations manifest the necessity to employ accurate free energy methods such as thermodynamic integration to estimate the stability of crystallographic defects at high temperatures.

Chemical Interactions and Their Role in the Microphase Separation of Block Copolymer Thin Films

PubMed Central

Farrell, Richard A.; Fitzgerald, Thomas G.; Borah, Dipu; Holmes, Justin D.; Morris, Michael A.

2009-01-01

The thermodynamics of self-assembling systems are discussed in terms of the chemical interactions and the intermolecular forces between species. It is clear that there are both theoretical and practical limitations on the dimensions and the structural regularity of these systems. These considerations are made with reference to the microphase separation that occurs in block copolymer (BCP) systems. BCP systems self-assemble via a thermodynamic driven process where chemical dis-affinity between the blocks driving them part is balanced by a restorative force deriving from the chemical bond between the blocks. These systems are attracting much interest because of their possible role in nanoelectronic fabrication. This form of self-assembly can obtain highly regular nanopatterns in certain circumstances where the orientation and alignment of chemically distinct blocks can be guided through molecular interactions between the polymer and the surrounding interfaces. However, for this to be possible, great care must be taken to properly engineer the interactions between the surfaces and the polymer blocks. The optimum methods of structure directing are chemical pre-patterning (defining regions on the substrate of different chemistry) and graphoepitaxy (topographical alignment) but both centre on generating alignment through favourable chemical interactions. As in all self-assembling systems, the problems of defect formation must be considered and the origin of defects in these systems is explored. It is argued that in these nanostructures equilibrium defects are relatively few and largely originate from kinetic effects arising during film growth. Many defects also arise from the confinement of the systems when they are ‘directed’ by topography. The potential applications of these materials in electronics are discussed. PMID:19865513

Temperature dependent structural properties and bending rigidity of pristine and defective hexagonal boron nitride

NASA Astrophysics Data System (ADS)

Thomas, Siby; Ajith, K. M.; Chandra, Sharat; Valsakumar, M. C.

2015-08-01

Structural and thermodynamical properties of monolayer pristine and defective boron nitride sheets (h-BN) have been investigated in a wide temperature range by carrying out atomistic simulations using a tuned Tersoff-type inter-atomic empirical potential. The temperature dependence of lattice parameter, radial distribution function, specific heat at constant volume, linear thermal expansion coefficient and the height correlation function of the thermally excited ripples on pristine as well as defective h-BN sheet have been investigated. Specific heat shows considerable increase beyond the Dulong-Petit limit at high temperatures, which is interpreted as a signature of strong anharmonicity present in h-BN. Analysis of the height fluctuations, < {{h}2}> , shows that the bending rigidity and variance of height fluctuations are strongly temperature dependent and this is explained using the continuum theory of membranes. A detailed study of the height-height correlation function shows deviation from the prediction of harmonic theory of membranes as a consequence of the strong anharmonicity in h-BN. It is also seen that the variance of the height fluctuations increases with defect concentration.

Evolutions of lamellar structure during melting and solidification of Fe9577 nanoparticle from molecular dynamics simulations

NASA Astrophysics Data System (ADS)

Wu, Yongquan; Shen, Tong; Lu, Xionggang

2013-03-01

A structural evolution during solidification and melting processes of nanoparticle Fe9577 was investigated from MD simulations. A perfect lamellar structure, consisting alternately of fcc and hcp layers, was obtained from solidification process. A structural heredity of early embryo is proposed to explain the structural preference of solidification. Defects were found inside the solid core and play the same role as surface premelting on melting. hcp was found more stable than fcc in high temperature. The difference between melting and solidification points can be deduced coming fully from the overcoming of thermodynamic energy barrier, instead of kinetic delay of structural relaxation.

High-pressure phase transition and phase diagram of gallium arsenide

NASA Astrophysics Data System (ADS)

Besson, J. M.; Itié, J. P.; Polian, A.; Weill, G.; Mansot, J. L.; Gonzalez, J.

1991-09-01

Under hydrostatic pressure, cubic GaAs-I undergoes phase transitions to at least two orthorhombic structures. The initial phase transition to GaAs-II has been investigated by optical-transmittance measurements, Raman scattering, and x-ray absorption. The structure of pressurized samples, which are retrieved at ambient, has been studied by x-ray diffraction and high-resolution diffraction microscopy. Various criteria that define the domain of stability of GaAs-I are examined, such as the occurrence of crystalline defects, the local variation in atomic coordination number, or the actual change in crystal structure. These are shown not to occur at the same pressure at 300 K, the latter being observable only several GPa above the actual thermodynamic instability pressure of GaAs-I. Comparison of the evolution of these parameters on increasing and decreasing pressure locates the thermodynamic transition region GaAs-I-->GaAs-II at 12+/-1.5 GPa and at 300 K that is lower than generally reported. The use of thermodynamic relations around the triple point, and of regularities in the properties of isoelectronic and isostructural III-V compounds, yields a phase diagram for GaAs which is consistent with this value.

Ambient Carbon Dioxide Capture Using Boron-Rich Porous Boron Nitride: A Theoretical Study.

PubMed

Li, Lanlan; Liu, Yan; Yang, Xiaojing; Yu, Xiaofei; Fang, Yi; Li, Qiaoling; Jin, Peng; Tang, Chengchun

2017-05-10

The development of highly efficient sorbent materials for CO 2 capture under ambient conditions is of great importance for reducing the impact of CO 2 on the environment and climate change. In this account, strong CO 2 adsorption on a boron antisite (B N ) in boron-rich porous boron nitrides (p-BN) was developed and studied. The results indicated that the material achieved larger adsorption energies of 2.09 eV (201.66 kJ/mol, PBE-D). The electronic structure calculations suggested that the introduction of B N in p-BN induced defect electronic states in the energy gap region, which strongly impacted the adsorption properties of the material. The bonding between the B N defect and the CO 2 molecule was clarified, and it was found that the electron donation first occurred from CO 2 to the B N double-acceptor state then, followed by electron back-donation from B N to CO 2 accompanied by the formation of a B N -C bond. The thermodynamic properties indicated that the adsorption of CO 2 on the B N defect to form anionic CO 2 δ- species was spontaneous at temperatures below 350 K. Both the large adsorption energies and the thermodynamic properties ensured that p-BN with a B N defect could effectively capture CO 2 under ambient conditions. Finally, to evaluate the energetic stability, the defect formation energies were estimated. The formation energy of the B N defects was found to strongly depend on the chemical environment, and the selection of different reactants (B or N sources) would achieve the goal of reducing the formation energy. These findings provided a useful guidance for the design and fabrication of a porous BN sorbent for CO 2 capture.

Interactions of Organic Solvents at Graphene/α-Al 2 O 3 and Graphene Oxide/α-Al 2 O 3 Interfaces Studied by Sum Frequency Generation

DOE Office of Scientific and Technical Information (OSTI.GOV)

Achtyl, Jennifer L.; Vlassiouk, Ivan V.; Dai, Sheng

2014-07-17

The adsorption of 1-hexanol from cyclohexane-d12 at single-layer graphene/α-Al2O3 interfaces was probed at mole percent values as low as 0.05 in the C–H stretching region using vibrational sum frequency generation (SFG). The SFG spectra are indiscernible from those obtained in the absence of graphene, and from those obtained in the presence of graphene oxide films prepared via oxygen plasma treatment of pristine single-layer graphene. A Langmuir adsorption model yields observed free adsorption energies of -19.9(5) to -20.9(3) kJ/mol for the three interfaces. The results indicate that the molecular structure of the hexanol alkyl chain is subject to the same orientationmore » distribution when graphene, oxidized or not, is present or absent at the α-Al2O3/cyclohexane-d12 interface. Moreover, it appears that the adsorption of 1-hexanol in this binary mixture is driven by hexanol interactions with the underlying oxide support, and that a single layer of graphene does not influence the extent of this interaction, even when defects are introduced to it. Finally, our structural and quantitative thermodynamic data provide important benchmarks for theoretical calculations and atomistic simulations of liquid/graphene interfaces. We hypothesize that defects emerging in graphene during operation of any device application that relies on layered solvent/graphene/oxide interfaces have little impact on the interfacial structure or thermodynamics, at least for the binary mixture and over the range of defect densities probed in our studies.« less

Thermodynamics of surface defects at the aspirin/water interface

NASA Astrophysics Data System (ADS)

Schneider, Julian; Zheng, Chen; Reuter, Karsten

2014-09-01

We present a simulation scheme to calculate defect formation free energies at a molecular crystal/water interface based on force-field molecular dynamics simulations. To this end, we adopt and modify existing approaches to calculate binding free energies of biological ligand/receptor complexes to be applicable to common surface defects, such as step edges and kink sites. We obtain statistically accurate and reliable free energy values for the aspirin/water interface, which can be applied to estimate the distribution of defects using well-established thermodynamic relations. As a show case we calculate the free energy upon dissolving molecules from kink sites at the interface. This free energy can be related to the solubility concentration and we obtain solubility values in excellent agreement with experimental results.

Thermodynamic assessment of oxygen diffusion in non-stoichiometric UO2±x from experimental data and Frenkel pair modeling

NASA Astrophysics Data System (ADS)

Berthinier, C.; Rado, C.; Chatillon, C.; Hodaj, F.

2013-02-01

The self and chemical diffusion of oxygen in the non-stoichiometric domain of the UO2 compound is analyzed from the point of view of experimental determinations and modeling from Frenkel pair defects. The correlation between the self-diffusion and the chemical diffusion coefficients is analyzed using the Darken coefficient calculated from a thermodynamic description of the UO2±x phase. This description was obtained from an optimization of thermodynamic and phase diagram data and modeling with different point defects, including the Frenkel pair point defects. The proposed diffusion coefficients correspond to the 300-2300 K temperature range and to the full composition range of the non stoichiometric UO2 compound. These values will be used for the simulation of the oxidation and ignition of the uranium carbide in different oxygen atmospheres that starts at temperatures as low as 400 K.

Surface structure and structural point defects of liquid and amorphous aluminosilicate nanoparticles.

PubMed

Linh, Nguyen Ngoc; Hoang, Vo Van

2008-07-02

The surface structure of liquid and amorphous aluminosilicate nanoparticles of composition Al(2)O(3)·2SiO(2) has been investigated in a model of different sizes ranging from 2.0 to 5.0 nm with the Born-Mayer type pair potential under non-periodic boundary conditions. Models have been obtained by cooling from the melts at a constant density of 2.6 g cm(-3) via molecular dynamics (MD) simulation. The surface structure has been investigated via the coordination number, bond-angle distributions and structural point defects. Calculations show that surface effects on surface static and thermodynamic properties of models are significant according to the change in the number of Al atoms in the surface layers. Evolution of the local environment of oxygen in the surface shell of nanoparticles upon cooling from the melt toward the glassy state was also found and discussed. In addition, the nanosize dependence of the glass transition temperature was presented.

Surface structure and structural point defects of liquid and amorphous aluminosilicate nanoparticles

NASA Astrophysics Data System (ADS)

Linh, Nguyen Ngoc; Van Hoang, Vo

2008-07-01

The surface structure of liquid and amorphous aluminosilicate nanoparticles of composition Al2O3·2SiO2 has been investigated in a model of different sizes ranging from 2.0 to 5.0 nm with the Born-Mayer type pair potential under non-periodic boundary conditions. Models have been obtained by cooling from the melts at a constant density of 2.6 g cm-3 via molecular dynamics (MD) simulation. The surface structure has been investigated via the coordination number, bond-angle distributions and structural point defects. Calculations show that surface effects on surface static and thermodynamic properties of models are significant according to the change in the number of Al atoms in the surface layers. Evolution of the local environment of oxygen in the surface shell of nanoparticles upon cooling from the melt toward the glassy state was also found and discussed. In addition, the nanosize dependence of the glass transition temperature was presented.

Thermodynamic and kinetic modelling of fuel oxidation behaviour in operating defective fuel

NASA Astrophysics Data System (ADS)

Lewis, operating defective fuel B. J.; Thompson, W. T.; Akbari, F.; Thompson, D. M.; Thurgood, C.; Higgs, J.

2004-07-01

A theoretical treatment has been developed to predict the fuel oxidation behaviour in operating defective nuclear fuel elements. The equilibrium stoichiometry deviation in the hyper-stoichiometric fuel has been derived from thermodynamic considerations using a self-consistent set of thermodynamic properties for the U-O system, which emphasizes replication of solubilities and three-phase invariant conditions displayed in the U-O binary phase diagram. The kinetics model accounts for multi-phase transport including interstitial oxygen diffusion in the solid and gas-phase transport of hydrogen and steam in the fuel cracks. The fuel oxidation model is further coupled to a heat conduction model to account for the feedback effect of a reduced thermal conductivity in the hyper-stoichiometric fuel. A numerical solution has been developed using a finite-element technique with the FEMLAB software package. The model has been compared to available data from several in-reactor X-2 loop experiments with defective fuel conducted at the Chalk River Laboratories. The model has also been benchmarked against an O/U profile measurement for a spent defective fuel element discharged from a commercial reactor.

Embedded-atom-method study of structural, thermodynamic, and atomic-transport properties of liquid Ni-Al alloys

NASA Astrophysics Data System (ADS)

Asta, Mark; Morgan, Dane; Hoyt, J. J.; Sadigh, Babak; Althoff, J. D.; de Fontaine, D.; Foiles, S. M.

1999-06-01

Structural, thermodynamic, and atomic-transport properties of liquid Ni-Al alloys have been studied by Monte Carlo and molecular-dynamics simulations based upon three different embedded-atom method (EAM) interatomic potentials, namely those due to Foiles and Daw (FD) [J. Mater. Res. 2, 5 (1987)], Voter and Chen (VC) [in Characterization of Defects in Materials, edited by R. W. Siegel et al. MRS Symposia Proceedings. No. 82 (Materials Research Society, Pittsburgh, 1987), p.175] and Ludwig and Gumbsch (LG) [Model. Simul. Mater. Sci. Eng. 3, 533 (1995)]. We present detailed comparisons between calculated results and experimental data for structure factors, atomic volumes, enthalpies of mixing, activities, and viscosities. Calculated partial structure factors are found to be in semiquantitative agreement with published neutron scattering measurements for Ni20Al80 alloys, indicating that short-range order in the liquid phase is qualitatively well described. Calculated thermodynamic properties of mixing are found to agree very well with experimental data for Ni compositions greater than 75 atomic %, while for alloys richer in Al the magnitudes of the enthalpies and entropies of mixing are significantly underestimated. The VC and LG potentials give atomic densities and viscosities in good agreement with experiment for Ni-rich compositions, while FD potentials consistently underestimate both properties at all concentrations. The results of this study demonstrate that VC and LG potentials provide a realistic description of the thermodynamic and atomic transport properties for NixAl1-x liquid alloys with x>=0.75, and point to the limitations of EAM potentials for alloys richer in Al.

Thermodynamic Stability of Low- and High-Index Spinel LiMn 2 O 4 Surface Terminations

DOE Office of Scientific and Technical Information (OSTI.GOV)

Warburton, Robert E.; Iddir, Hakim; Curtiss, Larry A.

2016-05-04

Density functional theory calculations are performed within the generalized gradient approximation (GGA+U) to determine stable terminations of both low- and high-index spinel LiMn2O4 (LMO) surfaces. A grand canonical thermodynamic approach is employed, permitting a direct comparison of offstoichiometric surfaces with previously reported stoichiometric surface terminations at various environmental conditions. Within this formalism, we have identified trends in the structure of the low-index surfaces as a function of the Li and O chemical potentials. The results suggest that, under a range of chemical potentials for which bulk LMO is stable, Li/O and Li-rich (111) surface terminations are favored, neither of whichmore » adopts an inverse spinel structure in the subsurface region. This thermodynamic analysis is extended to identify stable structures for certain high-index surfaces, including (311), (331), (511), and (531), which constitute simple models for steps or defects that may be present on real LMO particles. The low- and high-index results are combined to determine the relative stability of each surface facet under a range of environmental conditions. The relative surface energies are further employed to predict LMO particle shapes through a Wulff construction approach, which suggests that LMO particles will adopt either an octahedron or a truncated octahedron shape at conditions in which LMO is thermodynamically stable. These results are in agreement with the experimental observations of LMO particle shapes.« less

Unraveling the formation mechanism of graphitic nitrogen-doping in thermally treated graphene with ammonia

NASA Astrophysics Data System (ADS)

Li, Xiao-Fei; Lian, Ke-Yan; Liu, Lingling; Wu, Yingchao; Qiu, Qi; Jiang, Jun; Deng, Mingsen; Luo, Yi

2016-03-01

Nitrogen-doped graphene (N-graphene) has attractive properties that has been widely studied over the years. However, its possible formation process still remains unclear. Here, we propose a highly feasible formation mechanism of the graphitic-N doing in thermally treated graphene with ammonia by performing ab initio molecular dynamic simulations at experimental conditions. Results show that among the commonly native point defects in graphene, only the single vacancy 5-9 and divacancy 555-777 have the desirable electronic structures to trap N-containing groups and to mediate the subsequent dehydrogenation processes. The local structure of the defective graphene in combining with the thermodynamic and kinetic effect plays a crucial role in dominating the complex atomic rearrangement to form graphitic-N which heals the corresponding defect perfectly. The importance of the symmetry, the localized force field, the interaction of multiple trapped N-containing groups, as well as the catalytic effect of the temporarily formed bridge-N are emphasized, and the predicted doping configuration agrees well with the experimental observation. Hence, the revealed mechanism will be helpful for realizing the targeted synthesis of N-graphene with reduced defects and desired properties.

Discrete elastic model for two-dimensional melting.

PubMed

Lansac, Yves; Glaser, Matthew A; Clark, Noel A

2006-04-01

We present a network model for the study of melting and liquid structure in two dimensions, the first in which the presence and energy of topological defects (dislocations and disclinations) and of geometrical defects (elemental voids) can be independently controlled. Interparticle interaction is via harmonic springs and control is achieved by Monte Carlo moves which springs can either be orientationally "flipped" between particles to generate topological defects, or can be "popped" in force-free shape, to generate geometrical defects. With the geometrical defects suppressed the transition to the liquid phase occurs via disclination unbinding, as described by the Kosterlitz-Thouless-Halperin-Nelson-Young model and found in soft potential two-dimensional (2D) systems, such as the dipole-dipole potential [H. H. von Grünberg, Phys. Rev. Lett. 93, 255703 (2004)]. By contrast, with topological defects suppressed, a disordering transition, the Glaser-Clark condensation of geometrical defects [M. A. Glaser and N. A. Clark, Adv. Chem. Phys. 83, 543 (1993); M. A. Glaser, (Springer-Verlag, Berlin, 1990), Vol. 52, p. 141], produces a state that accurately characterizes the local liquid structure and first-order melting observed in hard-potential 2D systems, such as hard disk and the Weeks-Chandler-Andersen (WCA) potentials (M. A. Glaser and co-workers, see above). Thus both the geometrical and topological defect systems play a role in melting. The present work introduces a system in which the relative roles of topological and geometrical defects and their interactions can be explored. We perform Monte Carlo simulations of this model in the isobaric-isothermal ensemble, and present the phase diagram as well as various thermodynamic, statistical, and structural quantities as a function of the relative populations of geometrical and topological defects. The model exhibits a rich phase behavior including hexagonal and square crystals, expanded crystal, dodecagonal quasicrystal, and isotropic liquid phases. In this system the geometrical defects effectively control the melting, reducing the solid-liquid transition temperature by a factor of relative to the topological-only case. The local structure of the dense liquid has been investigated and the results are compared to that from simulations of WCA systems.

Molecular dynamical simulations of melting Al nanoparticles using a reaxff reactive force field

NASA Astrophysics Data System (ADS)

Liu, Junpeng; Wang, Mengjun; Liu, Pingan

2018-06-01

Molecular dynamics simulations were performed to study thermal properties and melting points of Al nanoparticles by using a reactive force field under canonical (NVT) ensembles. Al nanoparticles (particle size 2–4 nm) were considered in simulations. A combination of structural and thermodynamic parameters such as the Lindemann index, heat capacities, potential energy and radial-distribution functions was employed to decide melting points. We used annealing technique to obtain the initial Al nanoparticle model. Comparison was made between ReaxFF results and other simulation results. We found that ReaxFF force field is reasonable to describe Al cluster melting behavior. The linear relationship between particle size and melting points was found. After validating the ReaxFF force field, more attention was paid on thermal properties of Al nanoparticles with different defect concentrations. 4 nm Al nanoparticles with different defect concentrations (5%–20%) were considered in this paper. Our results revealed that: the melting points are irrelevant with defect concentration at a certain particle size. The extra storage energy of Al nanoparticles is proportional to nanoparticles’ defect concentration, when defect concentration is 5%–15%. While the particle with 20% defect concentration is similar to the cluster with 10% defect concentration. After melting, the extra energy of all nanoparticles decreases sharply, and the extra storage energy is nearly zero at 600 K. The centro-symmetry parameter analysis shows structure evolution of different models during melting processes.

Defect Clustering and Nano-phase Structure Characterization of Multicomponent Rare Earth-Oxide-Doped Zirconia-Yttria Thermal Barrier Coatings

NASA Technical Reports Server (NTRS)

Zhu, Dongming; Chen, Yuan L.; Miller, Robert A.

2004-01-01

Advanced thermal barrier coatings (TBCs) have been developed by incorporating multicomponent rare earth oxide dopants into zirconia-based thermal barrier coatings to promote the creation of the thermodynamically stable, immobile oxide defect clusters and/or nanophases within the coating systems. In this paper, the defect clusters, induced by Nd, Gd, and Yb rare earth dopants in the zirconia-yttria thermal barrier coatings, were characterized by high-resolution transmission electron microscopy (TEM). The TEM lattice imaging, selected area diffraction (SAD), and electron energy-loss spectroscopy (EELS) analyses demonstrated that the extensive nanoscale rare earth dopant segregation exists in the plasma-sprayed and electron-physical-vapor-deposited (EB PVD) thermal barrier coatings. The nanoscale concentration heterogeneity and the resulting large lattice distortion promoted the formation of parallel and rotational defective lattice clusters in the coating systems. The presence of the 5-to 100-nm-sized defect clusters and nanophases is believed to be responsible for the significant reduction of thermal conductivity, improved sintering resistance, and long-term high temperature stability of the advanced thermal barrier coating systems.

Formation mechanism of Ruddlesden-Popper-type antiphase boundaries during the kinetically limited growth of Sr rich SrTiO3 thin films

PubMed Central

Xu, Chencheng; Du, Hongchu; van der Torren, Alexander J. H.; Aarts, Jan; Jia, Chun-Lin; Dittmann, Regina

2016-01-01

We elucidated the formation process for Ruddlesden-Popper-type defects during pulsed laser deposition of Sr rich SrTiO3 thin films by a combined analysis of in-situ atomic force microscopy, low energy electron diffraction and high resolution scanning transmission electron microscopy. At the early growth stage of 1.5 unit cells, the excess Sr results in the formation of SrO on the surface, resulting in a local termination change from TiO2 to SrO, thereby forming a Sr rich (2 × 2) surface reconstruction. With progressive SrTiO3 growth, islands with thermodynamically stable SrO rock-salt structure are formed, coexisting with TiO2 terminated islands. During the overgrowth of these thermodynamically stable islands, both lateral as well as vertical Ruddlesden-Popper-type anti-phase boundaries are formed, accommodating the Sr excess of the SrTiO3 film. We suggest the formation of thermodynamically stable SrO rock-salt structures as origin for the formation of Ruddlesden-Popper-type antiphase boundaries, which are as a result of kinetic limitations confined to certain regions on the surface. PMID:27922069

Formation mechanism of Ruddlesden-Popper-type antiphase boundaries during the kinetically limited growth of Sr rich SrTiO3 thin films

NASA Astrophysics Data System (ADS)

Xu, Chencheng; Du, Hongchu; van der Torren, Alexander J. H.; Aarts, Jan; Jia, Chun-Lin; Dittmann, Regina

2016-12-01

We elucidated the formation process for Ruddlesden-Popper-type defects during pulsed laser deposition of Sr rich SrTiO3 thin films by a combined analysis of in-situ atomic force microscopy, low energy electron diffraction and high resolution scanning transmission electron microscopy. At the early growth stage of 1.5 unit cells, the excess Sr results in the formation of SrO on the surface, resulting in a local termination change from TiO2 to SrO, thereby forming a Sr rich (2 × 2) surface reconstruction. With progressive SrTiO3 growth, islands with thermodynamically stable SrO rock-salt structure are formed, coexisting with TiO2 terminated islands. During the overgrowth of these thermodynamically stable islands, both lateral as well as vertical Ruddlesden-Popper-type anti-phase boundaries are formed, accommodating the Sr excess of the SrTiO3 film. We suggest the formation of thermodynamically stable SrO rock-salt structures as origin for the formation of Ruddlesden-Popper-type antiphase boundaries, which are as a result of kinetic limitations confined to certain regions on the surface.

The shape of strings to come: How topological defects twist, bend, and wrinkle filament bundles

NASA Astrophysics Data System (ADS)

Bruss, Isaac; Grason, Gregory

2015-03-01

Topological defects are crucial to the thermodynamics and structure of condensed matter systems. For instance, when incorporated into crystalline membranes like graphene, 5- and 7-fold disclinations produce conical- and saddle-like geometries respectively. A recently discovered mapping between the inter-filament spacing within a deformed bundle and the metric properties of curved surfaces, suggests previously unexplored parallels between the two, specifically in regards to how 2D patterning promotes 3D shape transitions. This discovery is poised to describe the structure of a host of filamentous materials-both biological and microfabricated-that exhibit distinctive shapes and packings. Motivated by the filamentous analogs to the conical and saddles shapes found in thin membranes, we investigate for the first time the interplay between defects in the cross section of a bundle and its global structure, using a combination of continuum elasticity theory and numerical simulation of cohesive bundles with a fixed packing topology. Focusing primarily on the instability response to disclinations, we predict a host of new equilibria structures, some of which are without direct parallel to the analogous membrane, including torsional wrinkling, radial kinking, and helical winding. Center for Hierarchical Manufacturing-CMMI 10-25020, NSF CAREER Award-DMR 09-55760, & UMass MRSEC.

Defect kinetics and resistance to amorphization in zirconium carbide

NASA Astrophysics Data System (ADS)

Zheng, Ming-Jie; Szlufarska, Izabela; Morgan, Dane

2015-02-01

To better understand the radiation response of zirconium carbide (ZrC), and in particular its excellent resistance to amorphization, we have used density functional theory methods to study the kinetics of point defects in ZrC. The migration barriers and recombination barriers of the simple point defects are calculated using the ab initio molecular dynamics simulation and the nudged elastic band method. These barriers are used to estimate C and Zr interstitial and vacancy diffusion and Frenkel pair recombination rates. A significant barrier for C Frenkel pair recombination is found but it is shown that a large concentration of C vacancies reduces this barrier dramatically, allowing facile healing of radiation damage. The mechanisms underlying high resistance to amorphization of ZrC were analyzed from the perspectives of structural, thermodynamic, chemical and kinetic properties. This study provides insights into the amorphization resistance of ZrC as well as a foundation for understanding general radiation damage in this material.

Native point defects in MoS2 and their influences on optical properties by first principles calculations

NASA Astrophysics Data System (ADS)

Saha, Ashim Kumar; Yoshiya, Masato

2018-03-01

Stability of native point defect species and optical properties are quantitatively examined through first principles calculations in order to identify possible native point defect species in MoS2 and its influences on electronic structures and resultant optical properties. Possible native point defect species are identified as functions of thermodynamic environment and location of Fermi-level in MoS2. It is found that sulphur vacancies can be introduced more easily than other point defect species which will create impurity levels both in bandgap and in valence band. Additionally, antisite Mo and/or Mo vacancies can be created depending on chemical potential of sulphur, both of which will create impurity levels in bandgap and in valence band. Those impurity levels result in pronounced photon absorption in visible light region, though each of these point defects alone has limited impact on the optical properties unless their concentration remained low. Thus, attention must be paid when intentional impurity doping is made to MoS2 to avoid unwanted modification of optical properties of MoS2. Those impurity may enable further exploitation of photovoltaic energy conversion at longer wavelength.

Layer-by-layer epitaxial growth of defect-engineered strontium cobaltites

DOE PAGES

Andersen, Tassie K.; Cook, Seyoung; Wan, Gang; ...

2018-01-18

Here, control over structure and composition of (ABO 3) perovskite oxides offers exciting opportunities since these materials possess unique, tunable properties. Perovskite oxides with cobalt B-site cations are particularly promising, as the range of the cation’s stable oxidation states leads to many possible structural frameworks. Here, we report growth of strontium cobalt oxide thin films by molecular beam epitaxy, and conditions necessary to stabilize different defect concentration phases. In situ X-ray scattering is used to monitor structural evolution during growth, while in situ X-ray absorption near-edge spectroscopy is used to probe oxidation state and measure changes to oxygen vacancy concentrationmore » as a function of film thickness. Experimental results are compared to kinetically-limited thermodynamic predictions, in particular, solute trapping, with semi-quantitative agreement. Agreement between observations of dependence of cobaltite phase on oxidation activity and deposition rate, and predictions indicates that a combined experimental/theoretical approach is key to understanding phase behavior in the strontium cobalt oxide system.« less

Layer-by-layer epitaxial growth of defect-engineered strontium cobaltites

DOE Office of Scientific and Technical Information (OSTI.GOV)

Andersen, Tassie K.; Cook, Seyoung; Wan, Gang

Here, control over structure and composition of (ABO 3) perovskite oxides offers exciting opportunities since these materials possess unique, tunable properties. Perovskite oxides with cobalt B-site cations are particularly promising, as the range of the cation’s stable oxidation states leads to many possible structural frameworks. Here, we report growth of strontium cobalt oxide thin films by molecular beam epitaxy, and conditions necessary to stabilize different defect concentration phases. In situ X-ray scattering is used to monitor structural evolution during growth, while in situ X-ray absorption near-edge spectroscopy is used to probe oxidation state and measure changes to oxygen vacancy concentrationmore » as a function of film thickness. Experimental results are compared to kinetically-limited thermodynamic predictions, in particular, solute trapping, with semi-quantitative agreement. Agreement between observations of dependence of cobaltite phase on oxidation activity and deposition rate, and predictions indicates that a combined experimental/theoretical approach is key to understanding phase behavior in the strontium cobalt oxide system.« less

Layer-by-Layer Epitaxial Growth of Defect-Engineered Strontium Cobaltites

DOE Office of Scientific and Technical Information (OSTI.GOV)

Andersen, Tassie K.; Cook, Seyoung; Wan, Gang

Control over structure and composition of (ABO(3)) perovskite oxides offers exciting opportunities since these materials possess unique, tunable properties. Perovskite oxides with cobalt B-site cations are particularly promising, as the range of the cations stable oxidation states leads to many possible structural frameworks. Here, we report growth of strontium cobalt oxide thin films by molecular beam epitaxy, and conditions necessary to stabilize different defect concentration phases. In situ X-ray scattering is used to monitor structural evolution during growth, while in situ X-ray absorption near-edge spectroscopy is used to probe oxidation state and measure changes to oxygen vacancy concentration as amore » function of film thickness. Experimental results are compared to kinetically limited thermodynamic predictions, in particular, solute trapping, with semiquantitative agreement. Agreement between observations of dependence of cobaltite phase on oxidation activity and deposition rate, and predictions indicates that a combined experimental/theoretical approach is key to understanding phase behavior in the strontium cobalt oxide system.« less

Limits on passivating defects in semiconductors: the case of Si edge dislocations.

PubMed

Chan, Tzu-Liang; West, D; Zhang, S B

2011-07-15

By minimizing the free energy while constraining dopant density, we derive a universal curve that relates the formation energy (E(form)) of doping and the efficiency of defect passivation in terms of segregation of dopants at defect sites. The universal curve takes the simple form of a Fermi-Dirac distribution. Our imposed constraint defines a chemical potential that assumes the role of "Fermi energy," which sets the thermodynamic limit on the E(form) required to overcome the effect of entropy such that dopant segregation at defects in semiconductors can occur. Using Si edge dislocation as an example, we show by first-principles calculations how to map the experimentally measurable passivation efficiency to our calculated E(form) by using the universal curve for typical n- and p-type substitutional dopants. We show that n-type dopants are ineffective. Among p-type dopants, B can satisfy the thermodynamic limit while improving electronic properties.

Application of constrained equilibrium thermodynamics to irradiated alloy systems

NASA Astrophysics Data System (ADS)

Holloway, James Paul; Stubbins, James F.

1984-05-01

Equilibrium thermodynamics are applied to systems with an excess of point defects to calculate the relative stability of phases. It is possible to model systems with supersaturation levels of vacancies and interstitials, such as those found under irradiation. The calculations reveal the extent to which phase compositional boundaries could shift when one phase or both in a two phase system contain an excess of point defects. Phase boundary shifts in the Ni-Si, Fe-Ni, Ni-Cr, and Fe-Cr systems are examined as a function of the number of excess defects in each phase. It is also found that the critical temperature of the sigma phase in the Fe-Cr system and the fcc-bcc transition in the Fe-Ni are sensitive to excess defect concentrations. These results may apply to local irradiation-induced phase transformations in the presence of solute segregation.

Interpreting equilibrium-conductivity and conductivity-relaxation measurements to establish thermodynamic and transport properties for multiple charged defect conducting ceramics.

PubMed

Zhu, Huayang; Ricote, Sandrine; Coors, W Grover; Kee, Robert J

2015-01-01

A model-based interpretation of measured equilibrium conductivity and conductivity relaxation is developed to establish thermodynamic, transport, and kinetics parameters for multiple charged defect conducting (MCDC) ceramic materials. The present study focuses on 10% yttrium-doped barium zirconate (BZY10). In principle, using the Nernst-Einstein relationship, equilibrium conductivity measurements are sufficient to establish thermodynamic and transport properties. However, in practice it is difficult to establish unique sets of properties using equilibrium conductivity alone. Combining equilibrium and conductivity-relaxation measurements serves to significantly improve the quantitative fidelity of the derived material properties. The models are developed using a Nernst-Planck-Poisson (NPP) formulation, which enables the quantitative representation of conductivity relaxations caused by very large changes in oxygen partial pressure.

Equilibrium defects and solute site preferences in intermetallics: I. thermodynamics

NASA Astrophysics Data System (ADS)

Collins, Gary S.; Zacate, Matthew O.

2001-03-01

A model was developed to describe equilibrium defects and site preferences of dilute solute atoms in compounds having the CsCl and Ni_2Al3 structures. Equilibrium defects considered were combinations of elementary point defects that preserve the composition. Equilibria among possible defect combinations were combined with appropriate equations of constraint to obtain defect concentrations as a function of temperature and possible deviation from the stoichiometric composition. As an application, site-energies of defects and solutes in AB and A_2B_3) systems were estimated using Miedema's empirical model, with A=(Ni, Pd, Pt) and B= (Al, Ga, In). Dominant equilibrium defects in the respective systems were found to be the "triple defect" (2V_A+ A_B) and "octal defect" (5V_A+ 3A_B). Site preferences were found to depend on concentrations of intrinsic defects as well as on site-energy differences, and results reveal how preferences generally depend on temperature and composition. Consider solute S which, based on site energies, prefers to replace atom B. It is found that S always occupies B-sites in B-deficient alloys. In B-rich alloys, however, S may or may not occupy B-sites, depending on site-energy differences and the formation energies of equilibrium defects. For a solute that prefers to replace atom A, analogous results are obtained but with A replacing B in the three preceding sentences. This work was supported in part by the NSF under grant DMR 96-12306.

Defect related electrical and optical properties of AlN bulk crystals grown by physical vapor transport

NASA Astrophysics Data System (ADS)

Irmscher, Klaus

AlN crystallizes thermodynamically stable in the wurtzite structure and possesses a direct band gap of about 6 eV. It is the ideal substrate for the epitaxial growth of Al-rich AlxGa1-xN films that enable deep ultraviolet (UV) emitters. Appropriate AlN bulk crystals can be grown by physical vapor transport (PVT). Besides high structural perfection, such substrate crystals should be highly UV transparent and ideally, electrically conductive. It is well known that point defects like impurities and intrinsic defects may introduce electronic energy levels within the bandgap, which lead to additional optical absorption or electrical compensation. Among the impurities, which may be incorporated into the AlN crystals during PVT growth at well above 2000 ° C, oxygen, carbon, and silicon play the major role. Based on our own experimental data as well as on experimental and theoretical results reported in literature, we discuss energy levels, charge states and possible negative-U behavior of these impurities and of vacancy-type defects. In particular, we develop a model that explains the absorption behavior of the crystals in dependence on the Fermi level that can be controlled by the growth conditions, including intentional doping. Further, we pay attention on spectroscopic investigations giving direct evidence for the chemical nature and atomic arrangement of the involved point defects. As examples local vibrational mode (LVM) spectroscopy of carbon related defects and recent reports of electron paramagnetic resonance (EPR) spectroscopy are discussed.

Investigation of oxygen self-diffusion in PuO 2 by combining molecular dynamics with thermodynamic calculations

DOE PAGES

Saltas, V.; Chroneos, A.; Cooper, Michael William D.; ...

2016-01-01

In the present work, the defect properties of oxygen self-diffusion in PuO 2 are investigated over a wide temperature (300–1900 K) and pressure (0–10 GPa) range, by combining molecular dynamics simulations and thermodynamic calculations. Based on the well-established cBΩ thermodynamic model which connects the activation Gibbs free energy of diffusion with the bulk elastic and expansion properties, various point defect parameters such as activation enthalpy, activation entropy, and activation volume were calculated as a function of T and P. Molecular dynamics calculations provided the necessary bulk properties for the proper implementation of the thermodynamic model, in the lack of anymore » relevant experimental data. The estimated compressibility and the thermal expansion coefficient of activation volume are found to be more than one order of magnitude greater than the corresponding values of the bulk plutonia. As a result, the diffusion mechanism is discussed in the context of the temperature and pressure dependence of the activation volume.« less

Structure and stability of pyrophyllite edge surfaces: Effect of temperature and water chemical potential

NASA Astrophysics Data System (ADS)

Kwon, Kideok D.; Newton, Aric G.

2016-10-01

The surfaces of clay minerals, which are abundant in atmospheric mineral dust, serve as an important medium to catalyze ice nucleation. The lateral edge surface of 2:1 clay minerals is postulated to be a potential site for ice nucleation. However, experimental investigations of the edge surface structure itself have been limited compared to the basal planes of clay minerals. Density functional theory (DFT) computational studies have provided insights into the pyrophyllite edge surface. Pyrophyllite is an ideal surrogate mineral for the edge surfaces of 2:1 clay minerals as it possesses no or little structural charge. Of the two most-common hydrated edge surfaces, the AC edge, (1 1 0) surface in the monoclinic polytype notation, is predicted to be more stable than the B edge, (0 1 0) surface. These stabilities, however, were determined based on the total energies calculated at 0 K and did not consider environmental effects such as temperature and humidity. In this study, atomistic thermodynamics based on periodic DFT electronic calculations was applied to examine the effects of environmental variables on the structure and thermodynamic stability of the common edge surfaces in equilibrium with bulk pyrophyllite and water vapor. We demonstrate that the temperature-dependent vibrational energy of sorbed water molecules at the edge surface is a significant component of the surface free energy and cannot be neglected when determining the surface stability of pyrophyllite. The surface free energies were calculated as a function of temperature from 240 to 600 K and water chemical potential corresponding to conditions from ultrahigh vacuum to the saturation vapor pressure of water. We show that at lower water chemical potentials (dry conditions), the AC and B edge surfaces possessed similar stabilities; at higher chemical potentials (humid conditions) the AC edge surface was more stable than the B edge surface. At high temperatures, both surfaces showed similar stabilities regardless of the water chemical potential. The equilibrium morphology of pyrophyllite crystals is also expected to be dependent on these two environmental variables. Surface defects may impact the surface reactivity. We discuss the thermodynamic stability of a possible Si cation vacancy defect which provides additional hydroxyl group on the surface.

Why don't we find more polymorphs?

PubMed

Price, Sarah L

2013-08-01

Crystal structure prediction (CSP) studies are not limited to being a search for the most thermodynamically stable crystal structure, but play a valuable role in understanding polymorphism, as shown by interdisciplinary studies where the crystal energy landscape has been explored experimentally and computationally. CSP usually produces more thermodynamically plausible crystal structures than known polymorphs. This article illustrates some reasons why: because (i) of approximations in the calculations, particularly the neglect of thermal effects (see §1.1); (ii) of the molecular rearrangement during nucleation and growth (see §1.2); (iii) the solid-state structures observed show dynamic or static disorder, stacking faults, other defects or are not crystalline and so represent more than one calculated structure (see §1.3); (iv) the structures are metastable relative to other molecular compositions (see §1.4); (v) the right crystallization experiment has not yet been performed (see §1.5) or (vi) cannot be performed (see §1.6) and the possibility (vii) that the polymorphs are not detected or structurally characterized (see §1.7). Thus, we can only aspire to a general predictive theory for polymorphism, as this appears to require a quantitative understanding of the kinetic factors involved in all possible multi-component crystallizations. For a specific molecule, analysis of the crystal energy landscape shows the potential complexity of its crystallization behaviour.

Effects of Vacancy Cluster Defects on Electrical and Thermodynamic Properties of Silicon Crystals

PubMed Central

Huang, Pei-Hsing; Lu, Chi-Ming

2014-01-01

A first-principle plane-wave pseudopotential method based on the density function theory (DFT) was employed to investigate the effects of vacancy cluster (VC) defects on the band structure and thermoelectric properties of silicon (Si) crystals. Simulation results showed that various VC defects changed the energy band and localized electron density distribution of Si crystals and caused the band gap to decrease with increasing VC size. The results can be ascribed to the formation of a defect level produced by the dangling bonds, floating bonds, or high-strain atoms surrounding the VC defects. The appearance of imaginary frequencies in the phonon spectrum of defective Si crystals indicates that the defect-region structure is dynamically unstable and demonstrates phase changes. The phonon dispersion relation and phonon density of state were also investigated using density functional perturbation theory. The obtained Debye temperature (θ D) for a perfect Si crystal had a minimum value of 448 K at T = 42 K and a maximum value of 671 K at the high-temperature limit, which is consistent with the experimental results reported by Flubacher. Moreover, the Debye temperature decreased with increases in the VC size. VC defects had minimal effects on the heat capacity (C v) value when temperatures were below 150 K. As the temperature was higher than 150 K, the heat capacity gradually increased with increasing temperature until it achieved a constant value of 11.8 cal/cell·K. The heat capacity significantly decreased as the VC size increased. For a 2 × 2 × 2 superlattice Si crystal containing a hexagonal ring VC (HRVC10), the heat capacity decreased by approximately 17%. PMID:24526923

Coarse Grained Modeling of Block Copolymer Lithography: The Effects of Pattern Design on the Thermodynamics and Kinetics of the Directed Self Assembly of Block Copolymers

NASA Astrophysics Data System (ADS)

Garner, Grant Parker

The directed self assembly of block copolymers is an exciting complimentary technique for the fabrication of nanoscale structures for lithographic applications. Typically a directed self assembly process is driven through substrates with chemical (chemoepitaxy) or topographical (graphoepitaxy) guiding features. These patterning strategies have led to the ability to assemble structures with a high degree of perfection over large areas. However, a guiding pattern has not been created which assembles the desired features with a defect density that is commensurate with industrial standards of 1 defect/100cm 2. This work focuses on using molecular simulations on the Theoretically Informed Coarse Grained model to provide design rules for substrate patterns which drive the assembly of desired, device-oriented morphologies. Prior to the work presented in Chapter 2, the TICG model has been used in conjunction with a chemical pattern that is approximated as a hard-impenetrable surface. As many experimental systems use polymer brushes to help guide the polymer melt deposited on the substrate, this work analyzes the consequences of such an assumption by comparing a model where the polymer brush is explicitly implemented to the hard-wall substrate used in the past. Then, a methodology which utilizes a evolutionary optimization method is used to map the parameters of the more detailed model to the hard-surface model. This provides a qualitative understanding of how to interpret the model parameters used in previous works in the context of real experimental pattern designs. Chapter 3 discuss the concept of competitive assemblies in regards to defining a thermodynamic processing window in design space for assembling lines-and-spaces. The most competitive assembly to the desired orientation of the lamella is defined as a rotation of assembled lamella to the underlying pattern. Thermodynamic integration is used to calculate the free-energy difference between these assemblies over chemical patterns with varied design parameters. Local maximums in the free-energy difference are observed over pattern designs that are in qualitatively agreement with the pattern designs which produce the most perfect assemblies in experiments. The analysis is extended to study how choice of chemistry impacts this thermodynamic selection for the desired morphology. Finally, Chapter 4 provides insight into the kinetics of patterned directed self-assembly by investigating cylinder forming block copolymers within cylindrical confinements. Through the use of the string method, the minimum free-energy path between a defective state and the desired assembled morphology is calculated and clear transition states are highlighted. The effects of key parameters of the confinement design on the calculated minimum free energy path are calculated to identify design rules which should lead to a better understanding of optimal connement design for eliminating defects. In addition, a specific modification to existing cylindrical confinements is discussed as a possibility for tackling the problem of placement accuracy for a cylinder that is assembled within the confinement.

High-pressure phases of Mg2Si from first principles

NASA Astrophysics Data System (ADS)

Huan, Tran Doan; Tuoc, Vu Ngoc; Le, Nam Ba; Minh, Nguyen Viet; Woods, Lilia M.

2016-03-01

First-principles calculations are presented to resolve the possible pressure-dependent phases of Mg2Si . Although previous reports show that Mg2Si is characterized by the cubic antifluorite F m 3 ¯m structure at low pressures, the situation at higher pressures is less clear with many contradicting results. Here we utilize several methods to examine the stability, electron, phonon, and transport properties of this material as a function of pressure and temperature. We find that Mg2Si is thermodynamically stable at low and high pressures. Between 6 and 24 GPa, Mg2Si can transform into Mg9Si5 , a defected compound, and vice versa, without energy cost. Perhaps this result is related to the aforementioned inconsistency in the structures reported for Mg2Si within this pressure range. Focusing solely on Mg2Si , we find a new monoclinic C 2 /m structure of Mg2Si , which is stable at high pressures within thermodynamical considerations. The calculated electrical conductivity and Seebeck coefficient taking into account results from the electronic structure calculations help us understand better how transport can be affected in this material by modulating pressure and temperature.

Branching points in the low-temperature dipolar hard sphere fluid

NASA Astrophysics Data System (ADS)

Rovigatti, Lorenzo; Kantorovich, Sofia; Ivanov, Alexey O.; Tavares, José Maria; Sciortino, Francesco

2013-10-01

In this contribution, we investigate the low-temperature, low-density behaviour of dipolar hard-sphere (DHS) particles, i.e., hard spheres with dipoles embedded in their centre. We aim at describing the DHS fluid in terms of a network of chains and rings (the fundamental clusters) held together by branching points (defects) of different nature. We first introduce a systematic way of classifying inter-cluster connections according to their topology, and then employ this classification to analyse the geometric and thermodynamic properties of each class of defects, as extracted from state-of-the-art equilibrium Monte Carlo simulations. By computing the average density and energetic cost of each defect class, we find that the relevant contribution to inter-cluster interactions is indeed provided by (rare) three-way junctions and by four-way junctions arising from parallel or anti-parallel locally linear aggregates. All other (numerous) defects are either intra-cluster or associated to low cluster-cluster interaction energies, suggesting that these defects do not play a significant part in the thermodynamic description of the self-assembly processes of dipolar hard spheres.

Effect of substrate orientation on CdS homoepitaxy by molecular dynamics

DOE PAGES

Almeida, S.; Chavez, J. J.; Zhou, X. W.; ...

2016-02-10

CdS homoepitaxy growth was performed by molecular dynamics using different substrate orientations and structures in order to analyze the CdS crystallinity. As anticipated from thermodynamics of homoepitaxy, highly crystalline films with only point defects were obtained on substrates with rectangular surface geometries, including View the MathML source[112¯] zinc blende (ZB), [101¯0] wurtzite (WZ), [112¯0] WZ, [110][110] ZB, [010][010] ZB, and View the MathML source[1101110] ZB. In contrast, films grown on substrates with hexagonal surface geometries, corresponding to the [0001][0001] WZ and [111][111] ZB growth directions, showed structures with a large number of defects including; anti-sites, vacancies, stacking faults, twinning, andmore » polytypism. WZ and ZB transitions and grain boundaries are identified using a lattice identification algorithm and represented graphically in a structural map. A dislocation analysis was performed to detect, identify, and quantify linear defects within the atomistic data. Systematic simulations using different temperatures, deposition rates, and substrate polarities were perform to analyze the trends of dislocation densities on [0001][0001] WZ direction and showed persistent polytypism. As a result, the polytypism observed in the films grown on the substrates with hexagonal surface geometry is attributed to the similar formation energies of the WZ and ZB phases.« less

Selective Improvement of NO2 Gas Sensing Behavior in SnO2 Nanowires by Ion-Beam Irradiation.

PubMed

Kwon, Yong Jung; Kang, Sung Yong; Wu, Ping; Peng, Yuan; Kim, Sang Sub; Kim, Hyoun Woo

2016-06-01

We irradiated SnO2 nanowires with He ions (45 MeV) with different ion fluences. Structure and morphology of the SnO2 nanowires did not undergo noticeable changes upon ion-beam irradiation. Chemical equilibrium in SnO2/gas systems was calculated from thermodynamic principles, which were used to study the sensing selectivity of the tested gases, demonstrating the selective sensitivity of the SnO2 surface to NO2 gas. Being different from other gases, including H2, ethanol, acetone, SO2, and NH3, the sensor response to NO2 gas significantly increases as the ion fluence increases, showing a maximum under an ion fluence of 1 × 10(16) ions/cm(2). Photoluminescence analysis shows that the relative intensity of the peak at 2.1 eV to the peak at 2.5 eV increases upon ion-beam irradiation, suggesting that structural defects and/or tin interstitials have been generated. X-ray photoelectron spectroscopy indicated that the ionic ratio of Sn(2+/)Sn(4+) increases by the ion-beam irradiation, supporting the formation of surface Sn interstitials. Using thermodynamic calculations, we explained the observed selective sensing behavior. A molecular level model was also established for the adsorption of NO2 on ion-irradiated SnO2 (110) surfaces. We propose that the adsorption of NO2-related species is considerably enhanced by the generation of surface defects that are comprised of Sn interstitials.

Thermodynamic approach to the stability of multi-phase systems. Application to the Y 2O 3–Fe system

DOE PAGES

Samolyuk, German D.; Osetskiy, Yury N.

2015-07-07

Oxide-metal systems (OMSs) are important in many practical applications, and therefore, are under extensive studies using a wide range of techniques. The most accurate theoretical approaches are based on density functional theory (DFT), which are limited to ~10 2 atoms. Multi-scale approaches, e.g., DFT+Monte Carlo, are often used to model OMSs at the atomic level. These approaches can describe qualitatively the kinetics of some processes but not the overall stability of OMSs. In this paper, we propose a thermodynamic approach to study equilibrium in multiphase systems, which can be sequentially enhanced by considering different defects and microstructures. We estimate themore » thermodynamic equilibrium by minimization the free energy of the whole multiphase system using a limited set of defects and microstructural objects for which the properties are calculated by DFT. As an example, we consider Y 2O 3+bcc Fe with vacancies in both the Y 2O 3 and bcc Fe phases, Y substitutions and O interstitials in Fe, Fe impurities and antisite defects in Y 2O 3. The output of these calculations is the thermal equilibrium concentration of all the defects for a particular temperature and composition. The results obtained confirmed the high temperature stability of yttria in iron. As a result, model development towards more accurate calculations is discussed.« less

Role of Sink Density in Nonequilibrium Chemical Redistribution in Alloys

DOE PAGES

Martinez, Enrique Saez; Senninger, Oriane; Caro, Alfredo; ...

2018-03-08

Nonequilibrium chemical redistribution in open systems submitted to external forces, such as particle irradiation, leads to changes in the structural properties of the material, potentially driving the system to failure. Such redistribution is controlled by the complex interplay between the production of point defects, atomic transport rates, and the sink character of the microstructure. In this work, we analyze this interplay by means of a kinetic Monte Carlo (KMC) framework with an underlying atomistic model for the Fe-Cr model alloy to study the effect of ideal defect sinks on Cr concentration profiles, with a particular focus on the role ofmore » interface density. We observe that the amount of segregation decreases linearly with decreasing interface spacing. Within the framework of the thermodynamics of irreversible processes, a general analytical model is derived and assessed against the KMC simulations to elucidate the structure-property relationship of this system. Interestingly, in the kinetic regime where elimination of point defects at sinks is dominant over bulk recombination, the solute segregation does not directly depend on the dose rate but only on the density of sinks. Furthermore, this model provides new insight into the design of microstructures that mitigate chemical redistribution and improve radiation tolerance.« less

Role of Sink Density in Nonequilibrium Chemical Redistribution in Alloys

DOE Office of Scientific and Technical Information (OSTI.GOV)

Martinez, Enrique Saez; Senninger, Oriane; Caro, Alfredo

Nonequilibrium chemical redistribution in open systems submitted to external forces, such as particle irradiation, leads to changes in the structural properties of the material, potentially driving the system to failure. Such redistribution is controlled by the complex interplay between the production of point defects, atomic transport rates, and the sink character of the microstructure. In this work, we analyze this interplay by means of a kinetic Monte Carlo (KMC) framework with an underlying atomistic model for the Fe-Cr model alloy to study the effect of ideal defect sinks on Cr concentration profiles, with a particular focus on the role ofmore » interface density. We observe that the amount of segregation decreases linearly with decreasing interface spacing. Within the framework of the thermodynamics of irreversible processes, a general analytical model is derived and assessed against the KMC simulations to elucidate the structure-property relationship of this system. Interestingly, in the kinetic regime where elimination of point defects at sinks is dominant over bulk recombination, the solute segregation does not directly depend on the dose rate but only on the density of sinks. Furthermore, this model provides new insight into the design of microstructures that mitigate chemical redistribution and improve radiation tolerance.« less

Role of Sink Density in Nonequilibrium Chemical Redistribution in Alloys

NASA Astrophysics Data System (ADS)

Martínez, Enrique; Senninger, Oriane; Caro, Alfredo; Soisson, Frédéric; Nastar, Maylise; Uberuaga, Blas P.

2018-03-01

Nonequilibrium chemical redistribution in open systems submitted to external forces, such as particle irradiation, leads to changes in the structural properties of the material, potentially driving the system to failure. Such redistribution is controlled by the complex interplay between the production of point defects, atomic transport rates, and the sink character of the microstructure. In this work, we analyze this interplay by means of a kinetic Monte Carlo (KMC) framework with an underlying atomistic model for the Fe-Cr model alloy to study the effect of ideal defect sinks on Cr concentration profiles, with a particular focus on the role of interface density. We observe that the amount of segregation decreases linearly with decreasing interface spacing. Within the framework of the thermodynamics of irreversible processes, a general analytical model is derived and assessed against the KMC simulations to elucidate the structure-property relationship of this system. Interestingly, in the kinetic regime where elimination of point defects at sinks is dominant over bulk recombination, the solute segregation does not directly depend on the dose rate but only on the density of sinks. This model provides new insight into the design of microstructures that mitigate chemical redistribution and improve radiation tolerance.

A first principles calculation and statistical mechanics modeling of defects in Al-H system

NASA Astrophysics Data System (ADS)

Ji, Min; Wang, Cai-Zhuang; Ho, Kai-Ming

2007-03-01

The behavior of defects and hydrogen in Al was investigated by first principles calculations and statistical mechanics modeling. The formation energy of different defects in Al+H system such as Al vacancy, H in institution and multiple H in Al vacancy were calculated by first principles method. Defect concentration in thermodynamical equilibrium was studied by total free energy calculation including configuration entropy and defect-defect interaction from low concentration limit to hydride limit. In our grand canonical ensemble model, hydrogen chemical potential under different environment plays an important role in determing the defect concentration and properties in Al-H system.

Point-Defect Nature of the Ultraviolet Absorption Band in AlN

NASA Astrophysics Data System (ADS)

Alden, D.; Harris, J. S.; Bryan, Z.; Baker, J. N.; Reddy, P.; Mita, S.; Callsen, G.; Hoffmann, A.; Irving, D. L.; Collazo, R.; Sitar, Z.

2018-05-01

We present an approach where point defects and defect complexes are identified using power-dependent photoluminescence excitation spectroscopy, impurity data from SIMS, and density-functional-theory (DFT)-based calculations accounting for the total charge balance in the crystal. Employing the capabilities of such an experimental computational approach, in this work, the ultraviolet-C absorption band at 4.7 eV, as well as the 2.7- and 3.9-eV luminescence bands in AlN single crystals grown via physical vapor transport (PVT) are studied in detail. Photoluminescence excitation spectroscopy measurements demonstrate the relationship between the defect luminescent bands centered at 3.9 and 2.7 eV to the commonly observed absorption band centered at 4.7 eV. Accordingly, the thermodynamic transition energy for the absorption band at 4.7 eV and the luminescence band at 3.9 eV is estimated at 4.2 eV, in agreement with the thermodynamic transition energy for the CN- point defect. Finally, the 2.7-eV PL band is the result of a donor-acceptor pair transition between the VN and CN point defects since nitrogen vacancies are predicted to be present in the crystal in concentrations similar to carbon-employing charge-balance-constrained DFT calculations. Power-dependent photoluminescence measurements reveal the presence of the deep donor state with a thermodynamic transition energy of 5.0 eV, which we hypothesize to be nitrogen vacancies in agreement with predictions based on theory. The charge state, concentration, and type of impurities in the crystal are calculated considering a fixed amount of impurities and using a DFT-based defect solver, which considers their respective formation energies and the total charge balance in the crystal. The presented results show that nitrogen vacancies are the most likely candidate for the deep donor state involved in the donor-acceptor pair transition with peak emission at 2.7 eV for the conditions relevant to PVT growth.

Theoretical study of superionic phase transition in Li2S.

PubMed

Jand, Sara Panahian; Zhang, Qian; Kaghazchi, Payam

2017-07-19

We have studied temperature-induced superionic phase transition in Li 2 S, which is one of the most promising Li-S battery cathode material. Concentration of ionic carriers at low and high temperature was evaluated from thermodynamics of defects (using density functional theory) and detailed balance condition (using ab initio molecular dynamics (AIMD)), respectively. Diffusion coefficients were also obtained using AIMD simulations. Calculated ionic conductivity shows that superionic phase transition occurs at T = 900 K, which is in agreement with reported experimental values. The superionic behavior of Li 2 S is found to be due to thermodynamic reason (i.e. a large concentration of disordered defects).

Real-time monitoring of thermodynamic microenvironment in a pan coater.

PubMed

Pandey, Preetanshu; Bindra, Dilbir S

2013-02-01

The current study demonstrates the use of tablet-size data logging devices (PyroButtons) to quantify the microenvironment experienced by tablets during pan coating process. PyroButtons were fixed at the inlet and exhaust plenums, and were also placed to freely move with the tablets. The effects of process parameters (spray rate and inlet-air humidity) on the thermodynamic conditions inside the pan coater were studied. It was shown that the same exhaust temperature (a parameter most commonly monitored and controlled during film coating) can be attained with very different tablet-bed conditions. The tablet-bed conditions were found to be more sensitive to the changes in spray rate as compared with the inlet-air humidity. Both spray rate and inlet-air humidity were shown to have an effect on the number of tablet defects (loss of logo definition), and a good correlation between number of tablet defects and tablet-bed humidity was observed. The ability to quantify the thermodynamic microenvironment experienced by the tablets during coating and be able to correlate that to macroscopic tablet defects can be an invaluable tool that can help to establish a process design space during product development. Copyright © 2012 Wiley Periodicals, Inc.

Phase-field Model for Interstitial Loop Growth Kinetics and Thermodynamic and Kinetic Models of Irradiated Fe-Cr Alloys

DOE Office of Scientific and Technical Information (OSTI.GOV)

Li, Yulan; Hu, Shenyang Y.; Sun, Xin

2011-06-15

Microstructure evolution kinetics in irradiated materials has strongly spatial correlation. For example, void and second phases prefer to nucleate and grow at pre-existing defects such as dislocations, grain boundaries, and cracks. Inhomogeneous microstructure evolution results in inhomogeneity of microstructure and thermo-mechanical properties. Therefore, the simulation capability for predicting three dimensional (3-D) microstructure evolution kinetics and its subsequent impact on material properties and performance is crucial for scientific design of advanced nuclear materials and optimal operation conditions in order to reduce uncertainty in operational and safety margins. Very recently the meso-scale phase-field (PF) method has been used to predict gas bubblemore » evolution, void swelling, void lattice formation and void migration in irradiated materials,. Although most results of phase-field simulations are qualitative due to the lake of accurate thermodynamic and kinetic properties of defects, possible missing of important kinetic properties and processes, and the capability of current codes and computers for large time and length scale modeling, the simulations demonstrate that PF method is a promising simulation tool for predicting 3-D heterogeneous microstructure and property evolution, and providing microstructure evolution kinetics for higher scale level simulations of microstructure and property evolution such as mean field methods. This report consists of two parts. In part I, we will present a new phase-field model for predicting interstitial loop growth kinetics in irradiated materials. The effect of defect (vacancy/interstitial) generation, diffusion and recombination, sink strength, long-range elastic interaction, inhomogeneous and anisotropic mobility on microstructure evolution kinetics is taken into account in the model. The model is used to study the effect of elastic interaction on interstitial loop growth kinetics, the interstitial flux, and sink strength of interstitial loop for interstitials. In part II, we present a generic phase field model and discuss the thermodynamic and kinetic properties in phase-field models including the reaction kinetics of radiation defects and local free energy of irradiated materials. In particular, a two-sublattice thermodynamic model is suggested to describe the local free energy of alloys with irradiated defects. Fe-Cr alloy is taken as an example to explain the required thermodynamic and kinetic properties for quantitative phase-field modeling. Finally the great challenges in phase-field modeling will be discussed.« less

Achieving DFT accuracy with a machine-learning interatomic potential: Thermomechanics and defects in bcc ferromagnetic iron

NASA Astrophysics Data System (ADS)

Dragoni, Daniele; Daff, Thomas D.; Csányi, Gábor; Marzari, Nicola

2018-01-01

We show that the Gaussian Approximation Potential (GAP) machine-learning framework can describe complex magnetic potential energy surfaces, taking ferromagnetic iron as a paradigmatic challenging case. The training database includes total energies, forces, and stresses obtained from density-functional theory in the generalized-gradient approximation, and comprises approximately 150,000 local atomic environments, ranging from pristine and defected bulk configurations to surfaces and generalized stacking faults with different crystallographic orientations. We find the structural, vibrational, and thermodynamic properties of the GAP model to be in excellent agreement with those obtained directly from first-principles electronic-structure calculations. There is good transferability to quantities, such as Peierls energy barriers, which are determined to a large extent by atomic configurations that were not part of the training set. We observe the benefit and the need of using highly converged electronic-structure calculations to sample a target potential energy surface. The end result is a systematically improvable potential that can achieve the same accuracy of density-functional theory calculations, but at a fraction of the computational cost.

Tunable magnetism in metal adsorbed fluorinated nanoporous graphene

DOE PAGES

Kumar, Pankaj; Sharma, Vinit; Reboredo, Fernando A.; ...

2016-08-24

Developing nanostructures with tunable magnetic states is crucial for designing novel data storage and quantum information devices. Using density functional theory, we study the thermodynamic stability and magnetic properties of tungsten adsorbed tri-vacancy fluorinated (TVF) graphene. We demonstrate a strong structure-property relationship and its response to external stimuli via defect engineering in graphene-based materials. Complex interplay between defect states and the chemisorbed atom results in a large magnetic moment of 7 μ B along with high in-plane magneto-crystalline anisotropy energy (MAE) of 17 meV. Under the influence of electric field, spin crossover effect accompanied by a change in the MAEmore » is observed. The ascribed change in spin-configuration is caused by the modification of exchange coupling between defect states and a change in the occupation of d-orbitals of the metal complex. In conclusion, our predictions open a promising way towards controlling the magnetic properties in graphene based spintronic and non-volatile memory devices.« less

ReaxFF Reactive Force-Field Study of Molybdenum Disulfide (MoS2).

PubMed

Ostadhossein, Alireza; Rahnamoun, Ali; Wang, Yuanxi; Zhao, Peng; Zhang, Sulin; Crespi, Vincent H; van Duin, Adri C T

2017-02-02

Two-dimensional layers of molybdenum disulfide, MoS 2 , have been recognized as promising materials for nanoelectronics due to their exceptional electronic and optical properties. Here we develop a new ReaxFF reactive potential that can accurately describe the thermodynamic and structural properties of MoS 2 sheets, guided by extensive density functional theory simulations. This potential is then applied to the formation energies of five different types of vacancies, various vacancy migration barriers, and the transition barrier between the semiconducting 2H and metallic 1T phases. The energetics of ripplocations, a recently observed defect in van der Waals layers, is examined, and the interplay between these defects and sulfur vacancies is studied. As strain engineering of MoS 2 sheets is an effective way to manipulate the sheets' electronic and optical properties, the new ReaxFF description can provide valuable insights into morphological changes that occur under various loading conditions and defect distributions, thus allowing one to tailor the electronic properties of these 2D crystals.

Thermodynamic Stability and Defect Chemistry of Bismuth-Based Lead-Free Double Perovskites.

PubMed

Xiao, Zewen; Meng, Weiwei; Wang, Jianbo; Yan, Yanfa

2016-09-22

Bismuth- or antimony-based lead-free double perovskites represented by Cs 2 AgBiBr 6 have recently been considered promising alternatives to the emerging lead-based perovskites for solar cell applications. These new perovskites belong to the Fm3‾ m space group and consist of two types of octahedra alternating in a rock-salt face-centered cubic structure. We show, by density functional theory calculations, that the stable chemical potential region for pure Cs 2 AgBiBr 6 is narrow. Ag vacancies are a shallow accepters and can easily form, leading to intrinsic p-type conductivity. Bi vacancies and Ag Bi antisites are deep acceptors and should be the dominant defects under the Br-rich growth conditions. Our results suggest that the growth of Cs 2 AgBiBr 6 under Br-poor/Bi-rich conditions is preferred for suppressing the formation of the deep defects, which is beneficial for maximizing the photovoltaic performance. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Theoretical prediction of the energy stability of graphene nanoblisters

NASA Astrophysics Data System (ADS)

Glukhova, O. E.; Slepchenkov, M. M.; Barkov, P. V.

2018-04-01

The paper presents the results of a theoretical prediction of the energy stability of graphene nanoblisters with various geometrical parameters. As a criterion for the evaluation of the stability of investigated carbon objects we propose to consider the value of local stress of the nanoblister atomic grid. Numerical evaluation of stresses experienced by atoms of the graphene blister framework was carried out by means of an original method for calculation of local stresses that is based on energy approach. Atomistic models of graphene nanoblisters corresponding to the natural experiment data were built for the first time in this work. New physical regularities of the influence of topology on the thermodynamic stability of nanoblisters were established as a result of the analysis of the numerical experiment data. We built the distribution of local stresses for graphene blister structures, whose atomic grid contains a variety of structural defects. We have shown how the concentration and location of defects affect the picture of the distribution of the maximum stresses experienced by the atoms of the nanoblisters.

First-Principles Thermodynamics Study of Spinel MgAl 2 O 4 Surface Stability

DOE Office of Scientific and Technical Information (OSTI.GOV)

Cai, Qiuxia; Wang, Jian-guo; Wang, Yong

The surface stability of all possible terminations for three low-index (111, 110, 100) structures of the spinel MgAl2O4 has been studied using first-principles based thermodynamic approach. The surface Gibbs free energy results indicate that the 100_AlO2 termination is the most stable surface structure under ultra-high vacuum at T=1100 K regardless of Al-poor or Al-rich environment. With increasing oxygen pressure, the 111_O2(Al) termination becomes the most stable surface in the Al-rich environment. The oxygen vacancy formation is thermodynamically favorable over the 100_AlO2, 111_O2(Al) and the (111) structure with Mg/O connected terminations. On the basis of surface Gibbs free energies for bothmore » perfect and defective surface terminations, the 100_AlO2 and 111_O2(Al) are the most dominant surfaces in Al-rich environment under atmospheric condition. This is also consistent with our previously reported experimental observation. This work was supported by a Laboratory Directed Research and Development (LDRD) project of the Pacific Northwest National Laboratory (PNNL). The computing time was granted by the National Energy Research Scientific Computing Center (NERSC). Part of computing time was also granted by a scientific theme user proposal in the William R. Wiley Environmental Molecular Sciences Laboratory (EMSL), which is a U.S. Department of Energy national scientific user facility located at PNNL in Richland, Washington.« less

DOE Office of Scientific and Technical Information (OSTI.GOV)

Varanasi, S. R., E-mail: s.raovaranasi@uq.edu.au, E-mail: guskova@ipfdd.de; John, A.; Guskova, O. A., E-mail: s.raovaranasi@uq.edu.au, E-mail: guskova@ipfdd.de

Fullerene C{sub 60} sub-colloidal particle with diameter ∼1 nm represents a boundary case between small and large hydrophobic solutes on the length scale of hydrophobic hydration. In the present paper, a molecular dynamics simulation is performed to investigate this complex phenomenon for bare C{sub 60} fullerene and its amphiphilic/charged derivatives, so called shape amphiphiles. Since most of the unique properties of water originate from the pattern of hydrogen bond network and its dynamics, spatial, and orientational aspects of water in solvation shells around the solute surface having hydrophilic and hydrophobic regions are analyzed. Dynamical properties such as translational-rotational mobility, reorientationalmore » correlation and occupation time correlation functions of water molecules, and diffusion coefficients are also calculated. Slower dynamics of solvent molecules—water retardation—in the vicinity of the solutes is observed. Both the topological properties of hydrogen bond pattern and the “dangling” –OH groups that represent surface defects in water network are monitored. The fraction of such defect structures is increased near the hydrophobic cap of fullerenes. Some “dry” regions of C{sub 60} are observed which can be considered as signatures of surface dewetting. In an effort to provide molecular level insight into the thermodynamics of hydration, the free energy of solvation is determined for a family of fullerene particles using thermodynamic integration technique.« less

Direct Probing of the Dielectric Scavenging-Layer Interface in Oxide Filamentary-Based Valence Change Memory.

PubMed

Celano, Umberto; Op de Beeck, Jonathan; Clima, Sergiu; Luebben, Michael; Koenraad, Paul M; Goux, Ludovic; Valov, Ilia; Vandervorst, Wilfried

2017-03-29

A great improvement in valence change memory performance has been recently achieved by adding another metallic layer to the simple metal-insulator-metal (MIM) structure. This metal layer is often referred to as oxygen exchange layer (OEL) and is introduced between one of the electrodes and the oxide. The OEL is believed to induce a distributed reservoir of defects at the metal-insulator interface thus providing an unlimited availability of building blocks for the conductive filament (CF). However, its role remains elusive and controversial owing to the difficulties to probe the interface between the OEL and the CF. Here, using Scalpel SPM we probe multiple functions of the OEL which have not yet been directly measured, for two popular VCMs material systems: Hf/HfO 2 and Ta/Ta 2 O 5 . We locate and characterize in three-dimensions the volume containing the oxygen exchange layer and the CF with nanometer lateral resolution. We demonstrate that the OEL induces a thermodynamic barrier for the CF and estimate the minimum thickness of the OEL/oxide interface to guarantee the proper switching operations is ca. 3 nm. Our experimental observations are combined to first-principles thermodynamics and defect kinetics to elucidate the role of the OEL for device optimization.

Activation of CO and CO2 on homonuclear boron bonds of fullerene-like BN cages: first principles study

NASA Astrophysics Data System (ADS)

Sinthika, S.; Kumar, E. Mathan; Surya, V. J.; Kawazoe, Y.; Park, Noejung; Iyakutti, K.; Thapa, Ranjit

2015-12-01

Using density functional theory we investigate the electronic and atomic structure of fullerene-like boron nitride cage structures. The pentagonal ring leads to the formation of homonuclear bonds. The homonuclear bonds are also found in other BN structures having pentagon line defect. The calculated thermodynamics and vibrational spectra indicated that, among various stable configurations of BN-60 cages, the higher number of homonuclear N-N bonds and lower B:N ratio can result in the more stable structure. The homonuclear bonds bestow the system with salient catalytic properties that can be tuned by modifying the B atom bonding environment. We show that homonuclear B-B (B2) bonds can anchor both oxygen and CO molecules making the cage to be potential candidates as catalyst for CO oxidation via Langmuir-Hinshelwood (LH) mechanism. Moreover, the B-B-B (B3) bonds are reactive enough to capture, activate and hydrogenate CO2 molecules to formic acid. The observed trend in reactivity, viz B3 > B2 > B1 is explained in terms of the position of the boron defect state relative to the Fermi level.

Activation of CO and CO2 on homonuclear boron bonds of fullerene-like BN cages: first principles study

PubMed Central

Sinthika, S.; Kumar, E. Mathan; Surya, V. J.; Kawazoe, Y.; Park, Noejung; Iyakutti, K.; Thapa, Ranjit

2015-01-01

Using density functional theory we investigate the electronic and atomic structure of fullerene-like boron nitride cage structures. The pentagonal ring leads to the formation of homonuclear bonds. The homonuclear bonds are also found in other BN structures having pentagon line defect. The calculated thermodynamics and vibrational spectra indicated that, among various stable configurations of BN-60 cages, the higher number of homonuclear N-N bonds and lower B:N ratio can result in the more stable structure. The homonuclear bonds bestow the system with salient catalytic properties that can be tuned by modifying the B atom bonding environment. We show that homonuclear B-B (B2) bonds can anchor both oxygen and CO molecules making the cage to be potential candidates as catalyst for CO oxidation via Langmuir–Hinshelwood (LH) mechanism. Moreover, the B-B-B (B3) bonds are reactive enough to capture, activate and hydrogenate CO2 molecules to formic acid. The observed trend in reactivity, viz B3 > B2 > B1 is explained in terms of the position of the boron defect state relative to the Fermi level. PMID:26626147

Activation of CO and CO2 on homonuclear boron bonds of fullerene-like BN cages: first principles study.

PubMed

Sinthika, S; Kumar, E Mathan; Surya, V J; Kawazoe, Y; Park, Noejung; Iyakutti, K; Thapa, Ranjit

2015-12-02

Using density functional theory we investigate the electronic and atomic structure of fullerene-like boron nitride cage structures. The pentagonal ring leads to the formation of homonuclear bonds. The homonuclear bonds are also found in other BN structures having pentagon line defect. The calculated thermodynamics and vibrational spectra indicated that, among various stable configurations of BN-60 cages, the higher number of homonuclear N-N bonds and lower B:N ratio can result in the more stable structure. The homonuclear bonds bestow the system with salient catalytic properties that can be tuned by modifying the B atom bonding environment. We show that homonuclear B-B (B2) bonds can anchor both oxygen and CO molecules making the cage to be potential candidates as catalyst for CO oxidation via Langmuir-Hinshelwood (LH) mechanism. Moreover, the B-B-B (B3) bonds are reactive enough to capture, activate and hydrogenate CO2 molecules to formic acid. The observed trend in reactivity, viz B3 > B2 > B1 is explained in terms of the position of the boron defect state relative to the Fermi level.

Molecular basis for increased risk for late-onset Alzheimer disease due to the naturally occurring L28P mutation in apolipoprotein E4.

PubMed

Argyri, Letta; Dafnis, Ioannis; Theodossiou, Theodossis A; Gantz, Donald; Stratikos, Efstratios; Chroni, Angeliki

2014-05-02

The apolipoprotein (apo) E4 isoform has consistently emerged as a susceptibility factor for late-onset Alzheimer disease (AD), although the exact mechanism is not clear. A rare apoE4 mutant, apoE4[L28P] Pittsburgh, burdens carriers with an added risk for late-onset AD and may be a useful tool for gaining insights into the role of apoE4 in disease pathogenesis. Toward this end, we evaluated the effect of the L28P mutation on the structural and functional properties of apoE4. ApoE4[L28P] was found to have significantly perturbed thermodynamic properties, to have reduced helical content, and to expose a larger portion of the hydrophobic surface to the solvent. Furthermore, this mutant is thermodynamically destabilized and more prone to proteolysis. When interacting with lipids, apoE4[L28P] formed populations of lipoprotein particles with structural defects. The structural perturbations brought about by the mutation were accompanied by aberrant functions associated with the pathogenesis of AD. Specifically, apoE4[L28P] promoted the cellular uptake of extracellular amyloid β peptide 42 (Aβ42) by human neuroblastoma SK-N-SH cells as well as by primary mouse neuronal cells and led to increased formation of intracellular reactive oxygen species that persisted for at least 24 h. Furthermore, lipoprotein particles containing apoE4[L28P] induced intracellular reactive oxygen species formation and reduced SK-N-SH cell viability. Overall, our findings suggest that the L28P mutation leads to significant structural and conformational perturbations in apoE4 and can induce functional defects associated with neuronal Aβ42 accumulation and oxidative stress. We propose that these structural and functional changes underlie the observed added risk for AD development in carriers of apoE4[L28P].

Phase transformations at interfaces: Observations from atomistic modeling

DOE PAGES

Frolov, T.; Asta, M.; Mishin, Y.

2016-10-01

Here, we review the recent progress in theoretical understanding and atomistic computer simulations of phase transformations in materials interfaces, focusing on grain boundaries (GBs) in metallic systems. Recently developed simulation approaches enable the search and structural characterization of GB phases in single-component metals and binary alloys, calculation of thermodynamic properties of individual GB phases, and modeling of the effect of the GB phase transformations on GB kinetics. Atomistic simulations demonstrate that the GB transformations can be induced by varying the temperature, loading the GB with point defects, or varying the amount of solute segregation. The atomic-level understanding obtained from suchmore » simulations can provide input for further development of thermodynamics theories and continuous models of interface phase transformations while simultaneously serving as a testing ground for validation of theories and models. They can also help interpret and guide experimental work in this field.« less

Physical and Mechanical Metallurgy of Zirconium Alloys for Nuclear Applications: A Multi-Scale Computational Study

NASA Astrophysics Data System (ADS)

Glazoff, Michael Vasily

In the post-Fukushima world, thermal and structural stability of materials under extreme conditions is an important issue for the safety of nuclear reactors. Because the nuclear industry will continue using zirconium (Zr) cladding for the foreseeable future, it becomes critical to gain a fundamental understanding of several interconnected problems. First, what are the thermodynamic and kinetic factors affecting oxidation and hydrogen pick-up by these materials at normal, off-normal conditions, and in long-term storage? Secondly, what protective coatings could be used in order to gain valuable time at off-normal conditions (temperature exceeds ~1200°C (2200°F)? Thirdly, the kinetics of the coating's oxidation must be understood. Lastly, one needs automated inspection algorithms allowing identifying cladding's defects. This work attempts to explore the problem from a computational perspective, utilizing first principles atomistic simulations, computational thermodynamics, plasticity theory, and morphological algorithms of image processing for defect identification. It consists of the four parts dealing with these four problem areas preceded by the introduction. In the 1st part, computational thermodynamics and ab initio calculations were used to shed light upon the different stages of zircaloy oxidation and hydrogen pickup, and microstructure optimization to increase thermal stability. The 2 nd part describes the kinetic theory of oxidation of the several materials considered to be perspective coatings for Zr alloys: SiC and ZrSiO4. The 3rd part deals with understanding the respective roles of the two different plasticity mechanisms in Zr nuclear alloys: twinning (at low T) and crystallographic slip (higher T's). For that goal, an advanced plasticity model was proposed. In the 4th part projectional algorithms for defect identification in zircaloy coatings are described. Conclusions and recommendations are presented in the 5th part. This integrative approach's value is in developing multi-faceted understanding of complex processes taking place in nuclear fuel rods. It helped identify several problems pertaining to the safe operations with nuclear fuel: limits of temperature that should be strictly obeyed in storage to retard zircaloy hydriding; understanding the benefits and limitations of coatings; developing in-depth understanding of Zr plasticity; developing original algorithms for defect identification in SiC-braided zircaloy. The obtained results will be useful for the nuclear industry.

Impact of hydrogen and oxygen defects on the lattice parameter of chemical vapor deposited zinc sulfide

DOE Office of Scientific and Technical Information (OSTI.GOV)

McCloy, John S.; Wolf, Walter; Wimmer, Erich

2013-01-09

The lattice parameter of cubic chemical vapor deposited (CVD) ZnS with measured oxygen concentrations < 0.6 at.% and hydrogen impurities of < 0.015 at.% have been measured and found to vary between -0.10% and +0.09% relative to the reference lattice parameter (5.4093 Å) of oxygen-free cubic ZnS as reported in the literature. Defects other than substitutional O must be invoked to explain these observed volume changes. The structure and thermodynamic stability of a wide range of native and impurity induced defects in ZnS have been determined by Ab initio calculations. Lattice contraction is caused by S-vacancies, substitutional O on Smore » sites, Zn vacancies, H in S vacancies, peroxy defects, and dissociated water in S-vacancies. The lattice is expanded by interstitial H, H in Zn vacancies, dihydroxy defects, interstitial oxygen, Zn and [ZnHn] complexes (n=1,…,4), interstitial Zn, and S2 dumbbells. Oxygen, though present, likely forms substitutional defects for sulfur resulting in lattice contraction rather than as interstitial oxygen resulting in lattice expansion. It is concluded based on measurement and calculations that excess zinc atoms either at anti-sites (i.e. Zn atoms on S-sites) or possibly as interstitial Zn are responsible for the relative increase of the lattice parameter of commercially produced CVD ZnS.« less

Thermodynamics of Oxygen Ordering in Yttrium BARIUM(2) COPPER(3) OXYGEN(6+X)

NASA Astrophysics Data System (ADS)

Schieger, Paul Richard

An apparatus has been built to study and manipulate the oxygen in high temperature superconductors. It uses the principle of cryogenically assisted volumetric titration to precisely set changes in the oxygen content of high -T_{c} samples. The apparatus has been used to study the thermodynamics of oxygen in YBa_2Cu_3O _{6 + x} in order to help determine the correct model for oxygen thermodynamics as well as to provide standard curves for materials preparation by other methods. In particular, extensive measurements have been made on the oxygen pressure isotherms as a function of x for temperatures between 450^circ C and 650^circC. The measurement technique also allows one to extract the thermodynamic response function, (partial x/ partialmu)_{T}, ( mu is the chemical potential), which is sensitive to the oxygen configuration and which can be calculated by any candidate theory of the oxygen thermodynamics. Several existing theoretical models for the oxygen ordering thermodynamics are presented and compared to the experimental results. The models considered are classed into two basic approaches: lattice gas models and defect chemical models. It is found that the lattice gas models which assume static effective pair interactions between oxygen atoms, do not fit the experimental data very well, especially in the orthorhombic phase. The defect chemical models, which incorporate additional degrees of freedom (spin and charge) due to the creation of electronic defects, fit significantly better, but make crude assumptions for the configurational entropy of oxygen atoms. Using a commonly accepted picture for the creation of mobile electron holes and unpaired spins on the copper sites, it is possible to relate these quantities in terms of short range cluster probabilities defined in mean field approximations to the 2D lattice gas models. Based upon this connection, a thermodynamical model is developed, which takes into account interactions between oxygen atoms and the additional spin and charge degrees of freedom, assuming a narrow band, high temperature limit for the motion of the charge carriers. The model, containing the nearest-neighbour oxygen interaction (0.241eV) and the single site oxygen binding energy (-0.82eV - D/2; D is the dissociation energy of an oxygen molecule) as the only adjustable parameters, is compared to experimental results for the chemical potential, kT(partial x/partialmu)_{T}, fractional site occupancies, structural phase diagram, the number of monovalent coppers, and the total number of mobile electron holes. Qualitative agreement is found for all compared quantities, and quantitative agreement is found for the chemical potential, fractional site occupancies and kT(partial x/partialmu)_ {T} in the orthorhombic phase. Improvements to the model are outlined which should result in a quantitative fit to all results, in particular the valence and hole count vs. x. In addition to illuminating what is lacking in the commonly used two dimensional lattice gas models, the theory may form the basis for accurately predicting the electron hole count of the CuO_2 plane of YBa_2Cu_3 O_{6 + x} as a function of the sample preparation conditions.

Influence of columnar defects on the thermodynamic properties of BSCCO

NASA Astrophysics Data System (ADS)

van der Beek, C. J.; Indenbom, M. V.; Berseth, V.; Konczykowski, M.; Li, T. W.; Kes, P. H.; Benoit, W.

1996-03-01

Amorphous columnar defects strongly affect the reversible magnetization of Bi2Sr2CaCu2O8+δ single crystals both in the vortex solid, where the change reflects the change in vortex energy due to pinning, and in the vortex liquid, where the randomly positioned columns disrupt the interaction between superconducting fluctuations.

Defect engineering of complex semiconductor alloys: Cu2-2xMxO1-yXy

NASA Astrophysics Data System (ADS)

Lany, Stephan; Stevanovic, Vladan

2013-03-01

The electrical properties of semiconductors are generally controlled via doping, i.e., the incorporation of dilute concentrations of aliovalent impurity atoms, whereas the band structure properties (gap, effective masses, optical properties) are manipulated by alloying, i.e., the incorporation of much larger amounts of isovalent elements. Theoretical approaches usually address either doping or alloying, but rarely both problems at the same time. By combining defect supercell calculations, GW quasi-particle energy calculation, and thermodynamic modeling, we study the range of electrical and band structure properties accessible by alloying aliovalent cations (M = Mg, Zn, Cd) and isovalent anions (X = S, Se) in Cu2O. In order to extend dilute defect models to higher concentrations, we take into account the association/dissociation of defect pairs and complexes, as well as the composition dependence of the band gap and the band edge energies. Considering a composition window for the Cu2-2xMxO1-yXy alloys of 0 <= (x,y) <= 0.2, we predict a wide range of possible band gaps from 1.7 to 2.6 eV, and net doping concentrations between p = 1019 cm-3 and n = 1017cm-3, notably achieving type conversion from p- to n-type at Zn or Cd compositions around x = 0.1. This work is supported as part of the SunShot initiative by the U. S. Department of Energy, Office of Energy Efficiency and Renewable Energy under Contract No. DE-AC36-08GO28308 to NREL.

Strain control of oxygen kinetics in the Ruddlesden-Popper oxide La 1.85Sr 0.15CuO 4

DOE Office of Scientific and Technical Information (OSTI.GOV)

Meyer, Tricia L.; Jacobs, Ryan; Lee, Dongkyu

Oxygen defect control has long been considered an important route to functionalizing complex oxide films. However, the nature of oxygen defects in thin films is often not investigated beyond basic redox chemistry. One of the model examples for oxygen-defect studies is the layered Ruddlesden–Popper phase La 2-xSr x CuO 4-δ (LSCO), in which the superconducting transition temperature is highly sensitive to epitaxial strain. However, previous observations of strain-superconductivity coupling in LSCO thin films were mainly understood in terms of elastic contributions to mechanical buckling, with minimal consideration of kinetic or thermodynamic factors. Here, we report that the oxygen nonstoichiometry commonlymore » reported for strained cuprates is mediated by the strain-modified surface exchange kinetics, rather than reduced thermodynamic oxygen formation energies. Remarkably, tensile-strained LSCO shows nearly an order of magnitude faster oxygen exchange rate than a compressively strained film, providing a strategy for developing high-performance energy materials.« less

Strain control of oxygen kinetics in the Ruddlesden-Popper oxide La 1.85Sr 0.15CuO 4

DOE PAGES

Meyer, Tricia L.; Jacobs, Ryan; Lee, Dongkyu; ...

2018-01-08

Oxygen defect control has long been considered an important route to functionalizing complex oxide films. However, the nature of oxygen defects in thin films is often not investigated beyond basic redox chemistry. One of the model examples for oxygen-defect studies is the layered Ruddlesden–Popper phase La 2-xSr x CuO 4-δ (LSCO), in which the superconducting transition temperature is highly sensitive to epitaxial strain. However, previous observations of strain-superconductivity coupling in LSCO thin films were mainly understood in terms of elastic contributions to mechanical buckling, with minimal consideration of kinetic or thermodynamic factors. Here, we report that the oxygen nonstoichiometry commonlymore » reported for strained cuprates is mediated by the strain-modified surface exchange kinetics, rather than reduced thermodynamic oxygen formation energies. Remarkably, tensile-strained LSCO shows nearly an order of magnitude faster oxygen exchange rate than a compressively strained film, providing a strategy for developing high-performance energy materials.« less

Relationship Between Solidification Microstructure and Hot Cracking Susceptibility for Continuous Casting of Low-Carbon and High-Strength Low-Alloyed Steels: A Phase-Field Study

NASA Astrophysics Data System (ADS)

Böttger, B.; Apel, M.; Santillana, B.; Eskin, D. G.

2013-08-01

Hot cracking is one of the major defects in continuous casting of steels, frequently limiting the productivity. To understand the factors leading to this defect, microstructure formation is simulated for a low-carbon and two high-strength low-alloyed steels. 2D simulation of the initial stage of solidification is performed in a moving slice of the slab using proprietary multiphase-field software and taking into account all elements which are expected to have a relevant effect on the mechanical properties and structure formation during solidification. To account for the correct thermodynamic and kinetic properties of the multicomponent alloy grades, the simulation software is online coupled to commercial thermodynamic and mobility databases. A moving-frame boundary condition allows traveling through the entire solidification history starting from the slab surface, and tracking the morphology changes during growth of the shell. From the simulation results, significant microstructure differences between the steel grades are quantitatively evaluated and correlated with their hot cracking behavior according to the Rappaz-Drezet-Gremaud (RDG) hot cracking criterion. The possible role of the microalloying elements in hot cracking, in particular of traces of Ti, is analyzed. With the assumption that TiN precipitates trigger coalescence of the primary dendrites, quantitative evaluation of the critical strain rates leads to a full agreement with the observed hot cracking behavior.

Semantic modeling of the structural and process entities during plastic deformation of crystals and rocks

NASA Astrophysics Data System (ADS)

Babaie, Hassan; Davarpanah, Armita

2016-04-01

We are semantically modeling the structural and dynamic process components of the plastic deformation of minerals and rocks in the Plastic Deformation Ontology (PDO). Applying the Ontology of Physics in Biology, the PDO classifies the spatial entities that participate in the diverse processes of plastic deformation into the Physical_Plastic_Deformation_Entity and Nonphysical_Plastic_Deformation_Entity classes. The Material_Physical_Plastic_Deformation_Entity class includes things such as microstructures, lattice defects, atoms, liquid, and grain boundaries, and the Immaterial_Physical_Plastic_Deformation_Entity class includes vacancies in crystals and voids along mineral grain boundaries. The objects under the many subclasses of these classes (e.g., crystal, lattice defect, layering) have spatial parts that are related to each other through taxonomic (e.g., Line_Defect isA Lattice_Defect), structural (mereological, e.g., Twin_Plane partOf Twin), spatial-topological (e.g., Vacancy adjacentTo Atom, Fluid locatedAlong Grain_Boundary), and domain specific (e.g., displaces, Fluid crystallizes Dissolved_Ion, Void existsAlong Grain_Boundary) relationships. The dynamic aspect of the plastic deformation is modeled under the dynamical Process_Entity class that subsumes classes such as Recrystallization and Pressure_Solution that define the flow of energy amongst the physical entities. The values of the dynamical state properties of the physical entities (e.g., Chemical_Potential, Temperature, Particle_Velocity) change while they take part in the deformational processes such as Diffusion and Dislocation_Glide. The process entities have temporal parts (phases) that are related to each other through temporal relations such as precedes, isSubprocessOf, and overlaps. The properties of the physical entities, defined under the Physical_Property class, change as they participate in the plastic deformational processes. The properties are categorized into dynamical, constitutive, spatial, temporal, statistical, and thermodynamical. The dynamical properties, categorized under the Dynamical_Rate_Property and Dynamical_State_Property classes, subsume different classes of properties (e.g., Fluid_Flow_Rate, Temperature, Chemical_Potential, Displacement, Electrical_Charge) based on the physical domain (e.g., fluid, heat, chemical, solid, electrical). The properties are related to the objects under the Physical_Entity class through diverse object type (e.g., physicalPropertyOf) and data type (e.g., Fluid_Pressure unit 'MPa') properties. The changes of the dynamical properties of the physical entities, described by the empirical laws (equations) modeled by experimental structural geologists, are modeled through the Physical_Property_Dependency class that subsumes the more specialized constitutive, kinetic, and thermodynamic expressions of the relationships among the dynamic properties. Annotation based on the PDO will make it possible to integrate and reuse experimental plastic deformation data, knowledge, and simulation models, and conduct semantic-based search of the source data originating from different rock testing laboratories.

Electron and hole stability in GaN and ZnO.

PubMed

Walsh, Aron; Catlow, C Richard A; Miskufova, Martina; Sokol, Alexey A

2011-08-24

We assess the thermodynamic doping limits of GaN and ZnO on the basis of point defect calculations performed using the embedded cluster approach and employing a hybrid non-local density functional for the quantum mechanical region. Within this approach we have calculated a staggered (type-II) valence band alignment between the two materials, with the N 2p states contributing to the lower ionization potential of GaN. With respect to the stability of free electron and hole carriers, redox reactions resulting in charge compensation by ionic defects are found to be largely endothermic (unfavourable) for electrons and exothermic (favourable) for holes, which is consistent with the efficacy of electron conduction in these materials. Approaches for overcoming these fundamental thermodynamic limits are discussed. © 2011 IOP Publishing Ltd

A simplified approach to the band gap correction of defect formation energies: Al, Ga, and In-doped ZnO

NASA Astrophysics Data System (ADS)

Saniz, R.; Xu, Y.; Matsubara, M.; Amini, M. N.; Dixit, H.; Lamoen, D.; Partoens, B.

2013-01-01

The calculation of defect levels in semiconductors within a density functional theory approach suffers greatly from the band gap problem. We propose a band gap correction scheme that is based on the separation of energy differences in electron addition and relaxation energies. We show that it can predict defect levels with a reasonable accuracy, particularly in the case of defects with conduction band character, and yet is simple and computationally economical. We apply this method to ZnO doped with group III elements (Al, Ga, In). As expected from experiment, the results indicate that Zn substitutional doping is preferred over interstitial doping in Al, Ga, and In-doped ZnO, under both zinc-rich and oxygen-rich conditions. Further, all three dopants act as shallow donors, with the +1 charge state having the most advantageous formation energy. Also, doping effects on the electronic structure of ZnO are sufficiently mild so as to affect little the fundamental band gap and lowest conduction bands dispersion, which secures their n-type transparent conducting behavior. A comparison with the extrapolation method based on LDA+U calculations and with the Heyd-Scuseria-Ernzerhof hybrid functional (HSE) shows the reliability of the proposed scheme in predicting the thermodynamic transition levels in shallow donor systems.

Oxygen nonstoichiometry and thermodynamic quantities in solid solution SrFe1-xSnxO3-δ

NASA Astrophysics Data System (ADS)

Merkulov, O. V.; Markov, A. A.; Leonidov, I. A.; Patrakeev, M. V.; Kozhevnikov, V. L.

2018-06-01

The oxygen content (3-δ) variations in tin substituted derivatives SrFe1-xSnxO3-δ, where x = 0.05, 0.1, 0.17 and 0.25, of perovskite-like strontium ferrite, have been studied by coulometric titration measurements within oxygen partial pressure (pO2) range 10-19-10-2 atm at 800-950 °С. The obtained dependencies of (3-δ) from pO2 and temperature are used for calculations of partial molar thermodynamic functions of oxygen in the oxide structure. It is found that a satisfactory explanation of the experimental results can be attained within frameworks of the ideal solution model with ion and electron defects appearing in the result of oxidation and disproportionation of iron cations. The increase of the oxidation reaction enthalpy with tin content is consistent with the increase of the unit cell parameter, i.e., the stretch and relaxation of Fe-O chemical bonds.

Molecular pathways for defect annihilation in directed self-assembly

PubMed Central

Hur, Su-Mi; Thapar, Vikram; Ramírez-Hernández, Abelardo; Khaira, Gurdaman; Segal-Peretz, Tamar; Rincon-Delgadillo, Paulina A.; Li, Weihua; Müller, Marcus; Nealey, Paul F.; de Pablo, Juan J.

2015-01-01

Over the last few years, the directed self-assembly of block copolymers by surface patterns has transitioned from academic curiosity to viable contender for commercial fabrication of next-generation nanocircuits by lithography. Recently, it has become apparent that kinetics, and not only thermodynamics, plays a key role for the ability of a polymeric material to self-assemble into a perfect, defect-free ordered state. Perfection, in this context, implies not more than one defect, with characteristic dimensions on the order of 5 nm, over a sample area as large as 100 cm2. In this work, we identify the key pathways and the corresponding free energy barriers for eliminating defects, and we demonstrate that an extraordinarily large thermodynamic driving force is not necessarily sufficient for their removal. By adopting a concerted computational and experimental approach, we explain the molecular origins of these barriers and how they depend on material characteristics, and we propose strategies designed to overcome them. The validity of our conclusions for industrially relevant patterning processes is established by relying on instruments and assembly lines that are only available at state-of-the-art fabrication facilities, and, through this confluence of fundamental and applied research, we are able to discern the evolution of morphology at the smallest relevant length scales—a handful of nanometers—and present a view of defect annihilation in directed self-assembly at an unprecedented level of detail. PMID:26515095

Molecular pathways for defect annihilation in directed self-assembly.

DOE PAGES

Hur, Su-Mi; Thapar, Vikram; Ramirez-Hernandez, Abelardo; ...

2015-11-17

Over the last few years, the directed self-assembly of block copolymers by surface patterns has transitioned from academic curiosity to viable contender for commercial fabrication of next-generation nanocircuits by lithography. Recently, it has become apparent that kinetics, and not only thermodynamics, plays a key role for the ability of a polymeric material to self-assemble into a perfect, defect-free ordered state. Perfection, in this context, implies not more than one defect, with characteristic dimensions on the order of 5 nm, over a sample area as large as 100 cm2. In this work, we identify the key pathways and the corresponding free-energymore » barriers for eliminating defects, and we demonstrate that an extraordinarily large thermodynamic driving force is not necessarily sufficient for their removal. By adopting a concerted computational and experimental approach, we explain the molecular origins of these barriers, how they depend on material characteristics, and we propose strategies designed to over-come them. The validity of our conclusions for industrially-relevant patterning processes is established by relying on instruments and assembly lines that are only available at state-of-the-art fabrication facilities and, through this confluence of fundamental and applied research, we are able to discern the evolution of morphology at the smallest relevant length scales - a handful of nanometers -, and present a view of defect annihilation in directed self-assembly at an unprecedented level of detail.« less

Thermodynamics and defect chemistry of substitutional and interstitial cation doping in layered α-V2O5.

PubMed

McColl, Kit; Johnson, Ian; Corà, Furio

2018-05-25

A systematic study of the location and energetics of cation dopants in α-V2O5 has been conducted using pair-potential methods, supplemented by first-principles calculations. The consequences of doping on intrinsic defect equilibria have been discussed and the effects of selected dopants on Li+ and Mg2+ diffusion energy barriers have been investigated.

Carrier providers or killers: The case of Cu defects in CdTe

DOE PAGES

Yang, Ji -Hui; Metzger, Wyatt K.; Wei, Su -Huai

2017-07-24

Defects play important roles in semiconductors for optoelectronic applications. Common intuition is that defects with shallow levels act as carrier providers and defects with deep levels are carrier killers. Here, taking the Cu defects in CdTe as an example, we show that relatively shallow defects can play both roles. Using first-principles calculation methods combined with thermodynamic simulations, we study the dialectic effects of Cu-related defects on hole density and lifetime in bulk CdTe. Because CuCd can form a relatively shallow acceptor, we find that increased Cu incorporation into CdTe indeed can help achieve high hole density; however, too much Cumore » can cause significant non-radiative recombination. We discuss strategies to balance the contradictory effects of Cu defects based on the calculated impact of Cd chemical potential, copper defect concentrations, and annealing temperature on lifetime and hole density. Lastly, these findings advance the understanding of the potential complex defect behaviors of relatively shallow defect states in semiconductors.« less

Carrier providers or killers: The case of Cu defects in CdTe

DOE Office of Scientific and Technical Information (OSTI.GOV)

Yang, Ji -Hui; Metzger, Wyatt K.; Wei, Su -Huai

Defects play important roles in semiconductors for optoelectronic applications. Common intuition is that defects with shallow levels act as carrier providers and defects with deep levels are carrier killers. Here, taking the Cu defects in CdTe as an example, we show that relatively shallow defects can play both roles. Using first-principles calculation methods combined with thermodynamic simulations, we study the dialectic effects of Cu-related defects on hole density and lifetime in bulk CdTe. Because CuCd can form a relatively shallow acceptor, we find that increased Cu incorporation into CdTe indeed can help achieve high hole density; however, too much Cumore » can cause significant non-radiative recombination. We discuss strategies to balance the contradictory effects of Cu defects based on the calculated impact of Cd chemical potential, copper defect concentrations, and annealing temperature on lifetime and hole density. Lastly, these findings advance the understanding of the potential complex defect behaviors of relatively shallow defect states in semiconductors.« less

Protein control of true, gated, and coupled electron transfer reactions.

PubMed

Davidson, Victor L

2008-06-01

Electron transfer (ET) through and between proteins is a fundamental biological process. The rates of ET depend upon the thermodynamic driving force, the reorganization energy, and the degree of electronic coupling between the reactant and product states. The analysis of protein ET reactions is complicated by the fact that non-ET processes might influence the observed ET rate in kinetically complex biological systems. This Account describes studies of the methylamine dehydrogenase-amicyanin-cytochrome c-551i protein ET complex that have revealed the influence of several features of the protein structure on the magnitudes of the physical parameters for true ET reactions and how they dictate the kinetic mechanisms of non-ET processes that sometimes influence protein ET reactions. Kinetic and thermodynamic studies, coupled with structural information and biochemical data, are necessary to fully describe the ET reactions of proteins. Site-directed mutagenesis can be used to elucidate specific structure-function relationships. When mutations selectively alter the electronic coupling, reorganization energy, or driving force for the ET reaction, it becomes possible to use the parameters of the ET process to determine how specific amino acid residues and other features of the protein structure influence the ET rates. When mutations alter the kinetic mechanism for ET, one can determine the mechanisms by which non-ET processes, such as protein conformational changes or proton transfers, control the rates of ET reactions and how specific amino acid residues and certain features of the protein structure influence these non-ET reactions. A complete description of the mechanism of regulation of biological ET reactions enhances our understanding of metabolism, respiration, and photosynthesis at the molecular level. Such information has important medical relevance. Defective protein ET leads to production of the reactive oxygen species and free radicals that are associated with aging and many disease states. Defective ET within the respiratory chain also causes certain mitochondrial myopathies. An understanding of the mechanisms of regulation of protein ET is also of practical value because it provides a logical basis for the design of applications utilizing redox enzymes, such as enzyme-based electrode sensors and fuel cells.

Defect character at grain boundary facet junctions: Analysis of an asymmetric Σ = 5 grain boundary in Fe

DOE Office of Scientific and Technical Information (OSTI.GOV)

Medlin, D. L.; Hattar, K.; Zimmerman, J. A.

Grain boundaries often develop faceted morphologies in systems for which the interfacial free energy depends on the boundary inclination. Although the mesoscale thermodynamic basis for such morphological evolution has been extensively studied, the influence of line defects, such as secondary grain boundary dislocations, on the facet configurations has not been thoroughly explored. In this paper, through a combination of atomistic simulations and electron microscopic observations, we examine in detail the structure of an asymmetric Σ = 5 [001] grain boundary in well-annealed, body-centered cubic (BCC) Fe. The observed boundary forms with a hill-and-valley morphology composed of nanoscale {310} and {210}more » facets. Our analysis clarifies the atomic structure of the {310}/{210} facet junctions and identifies the presence of an array of secondary grain boundary dislocations that are localized to these junctions. Analysis of the Burgers vectors of the grain boundary dislocations, which are of type (1/5)<310> and (1/5)<120>, shows that the defect density is consistent with that required to accommodate a small observed angular deviation from the exact Σ = 5 orientation relationship. As a result, these observations and analysis suggest a crucial role for secondary grain boundary dislocations in dictating the length-scale of grain boundary facets, a consideration which has not been included in prior analyses of facet evolution and equilibrium facet length.« less

Defect character at grain boundary facet junctions: Analysis of an asymmetric Σ = 5 grain boundary in Fe

DOE PAGES

Medlin, D. L.; Hattar, K.; Zimmerman, J. A.; ...

2016-11-16

Grain boundaries often develop faceted morphologies in systems for which the interfacial free energy depends on the boundary inclination. Although the mesoscale thermodynamic basis for such morphological evolution has been extensively studied, the influence of line defects, such as secondary grain boundary dislocations, on the facet configurations has not been thoroughly explored. In this paper, through a combination of atomistic simulations and electron microscopic observations, we examine in detail the structure of an asymmetric Σ = 5 [001] grain boundary in well-annealed, body-centered cubic (BCC) Fe. The observed boundary forms with a hill-and-valley morphology composed of nanoscale {310} and {210}more » facets. Our analysis clarifies the atomic structure of the {310}/{210} facet junctions and identifies the presence of an array of secondary grain boundary dislocations that are localized to these junctions. Analysis of the Burgers vectors of the grain boundary dislocations, which are of type (1/5)<310> and (1/5)<120>, shows that the defect density is consistent with that required to accommodate a small observed angular deviation from the exact Σ = 5 orientation relationship. As a result, these observations and analysis suggest a crucial role for secondary grain boundary dislocations in dictating the length-scale of grain boundary facets, a consideration which has not been included in prior analyses of facet evolution and equilibrium facet length.« less

First-principles engineering of charged defects for two-dimensional quantum technologies

NASA Astrophysics Data System (ADS)

Wu, Feng; Galatas, Andrew; Sundararaman, Ravishankar; Rocca, Dario; Ping, Yuan

2017-12-01

Charged defects in two-dimensional (2D) materials have emerging applications in quantum technologies such as quantum emitters and quantum computation. The advancement of these technologies requires a rational design of ideal defect centers, demanding reliable computation methods for the quantitatively accurate prediction of defect properties. We present an accurate, parameter-free, and efficient procedure to evaluate the quasiparticle defect states and thermodynamic charge transition levels of defects in 2D materials. Importantly, we solve critical issues that stem from the strongly anisotropic screening in 2D materials, that have so far precluded the accurate prediction of charge transition levels in these materials. Using this procedure, we investigate various defects in monolayer hexagonal boron nitride (h -BN ) for their charge transition levels, stable spin states, and optical excitations. We identify CBVN (nitrogen vacancy adjacent to carbon substitution of boron) to be the most promising defect candidate for scalable quantum bit and emitter applications.

Crystalline, Glassy and Polymeric Electrolytes:. Similarities and Differences in Ionic Transport Mechanisms

NASA Astrophysics Data System (ADS)

Souquet, Jean Louis

2006-06-01

Ionocovalent crystals or glasses as well as molten salts or salt polymer complexes are currently studied as electrolytes for high energy density batteries. Their large Red/Ox stability range results from their thermodynamic or kinetic characteristics. For all these electrolytes, charge carriers are the consequence of local deviations from electroneutrality, identified as point defects for ionic crystals or partial dissociation in disordered structures. The charge carriers formation derives from a similar activated process. The main difference comes from the migration process, which depends on the dynamic properties of the surrounding medium. When the structural relaxation time is large, an activated process, mainly enthalpic, prevails for charge carriers migration. It is the usual case for ionic crystals or glasses. In the liquid or overcooled liquid states, the structural relaxation time of the medium is shorter that the time required for the activated migration process to occur and a local reorganization of the medium vanishes the energy barrier and provides the free volume necessary to ionic migration. In that case, the migration is mainly an entropic process. The configurational entropy necessary to this process decreases with temperature and vanishes at the so called ideal glass transition temperature which can be estimated by extrapolation of the transport properties or of the thermodynamic characteristics of the medium. However, at the experiment time scale, this configurational entropy disappears at a somewhat higher temperature, the glass transition temperature at which the structural relaxation time corresponds to the measurement time. Some glass forming ionic melts studied in a large temperature scale, over and below the glass transition temperature, evidence the two, enthalpic and entropic, migration mechanisms, allowing the determination of the thermodynamic characteristics of the charge carriers formation and migration. Some recent results indicate that entropic process, associated to long scale deformations, may also exist in crystalline structures.

Phases, phase equilibria, and phase rules in low-dimensional systems

DOE Office of Scientific and Technical Information (OSTI.GOV)

Frolov, T., E-mail: timfrol@berkeley.edu; Mishin, Y., E-mail: ymishin@gmu.edu

2015-07-28

We present a unified approach to thermodynamic description of one, two, and three dimensional phases and phase transformations among them. The approach is based on a rigorous definition of a phase applicable to thermodynamic systems of any dimensionality. Within this approach, the same thermodynamic formalism can be applied for the description of phase transformations in bulk systems, interfaces, and line defects separating interface phases. For both lines and interfaces, we rigorously derive an adsorption equation, the phase coexistence equations, and other thermodynamic relations expressed in terms of generalized line and interface excess quantities. As a generalization of the Gibbs phasemore » rule for bulk phases, we derive phase rules for lines and interfaces and predict the maximum number of phases than may coexist in systems of the respective dimensionality.« less

Anion Exchange in II-VI Semiconducting Nanostructures via Atomic Templating.

PubMed

Agarwal, Rahul; Krook, Nadia M; Ren, Ming-Liang; Tan, Liang Z; Liu, Wenjing; Rappe, Andrew M; Agarwal, Ritesh

2018-03-14

Controlled chemical transformation of nanostructures is a promising technique to obtain precisely designed novel materials, which are difficult to synthesize otherwise. We report high-temperature vapor-phase anion-exchange reactions to chemically transform II-VI semiconductor nanostructures (100-300 nm length scale) while retaining the single crystallinity, crystal structure, morphology, and even defect distribution of the parent material via atomic templating. The concept of atomic templating is employed to obtain kinetically controlled, thermodynamically metastable structural phases such as zincblende CdSe and CdS from zincblende CdTe upon complete chemical replacement of Te with Se or S. The underlying transformation mechanisms are explained through first-principles density functional theory calculations. Atomic templating is a unique path to independently tune materials' phase and composition at the nanoscale, allowing the synthesis of novel materials.

Towards understanding the mechanism of rhenium and osmium precipitation in tungsten and its implication for tungsten-based alloys

NASA Astrophysics Data System (ADS)

Li, Yu-Hao; Zhou, Hong-Bo; Deng, Huiqiu; Lu, Gang; Lu, Guang-Hong

2018-07-01

Using a first-principles method in combination with thermodynamic models, we investigate the interaction between rhenium/osmium (Re/Os) and defects to explore the mechanism of radiation-induced Re/Os precipitation in tungsten (W). We demonstrate that radiation-induced defects play a key role in the solute precipitation in W, especially for self-interstitial atoms (SIAs). The presence of SIAs can significantly reduce the total nucleation free energy change of Re/Os, and thus facilitate the nucleation of Re/Os in W. Further, SIA is shown to be easily trapped by Re/Os once overcoming a low energy barrier, forming a W-Re/Os mixed dumbbell. Such W-Re/Os dumbbell forms a high stable Re/Os-Re/Os dumbbell structure with the substitutional Re/Os atoms, which can serve as a trapping centre for subsequent interstitial-Re/Os, leading to the growth of Re/Os-rich clusters. Consequently, an interstitial-mediated migration and aggregation mechanism for Re/Os precipitation in W has been proposed. Our results reveale that the alloying elements-defects interaction has significantly effect on their behaviors under irradiation, which should be considered in the design of W-based alloys for future fusion devices.

Revealing the properties of defects formed by CH3NH2 molecules in organic-inorganic hybrid perovskite MAPbBr3

NASA Astrophysics Data System (ADS)

Wang, Ji; Zhang, Ao; Yan, Jun; Li, Dan; Chen, Yunlin

2017-03-01

The properties of defects in organic-inorganic hybrid perovskite are widely studied from the first-principles calculation. However, the defects of methylamine (methylamine = CH3NH2), which would be easily formed during the preparation of the organic-inorganic hybrid perovskite, are rarely investigated. Thermodynamic properties as well as defect states of methylamine embedded MAPbX3 (MA = methyl-ammonium = CH3NH3, X = Br, I) are studied based on first-principles calculations of density functional theory. It was found that there is a shallow defect level near the highest occupied molecular orbital, which induced by the interstitial methylamine defect in MAPbBr3, will lead to an increase of photoluminescence. The calculation results showed that interstitial defect states of methylamine may move deeper due to the interaction between methylamine molecules and methyl-ammonium cations. It was also showed that the interstitial methylamine defect is stable at room temperature, and the defect can be removed easily by annealing.

Impact of medium-range order on the glass transition in liquid Ni-Si alloys

NASA Astrophysics Data System (ADS)

Lü, Y. J.; Entel, P.

2011-09-01

We study the thermophysical properties and structure of liquid Ni-Si alloys using molecular dynamics simulations. The liquid Ni-5% and 10%Si alloys crystallize to form the face-centered cubic (Ni) at 900 and 850 K, respectively, and the glass transitions take place in Ni-20% and 25%Si alloys at about 700 K. The temperature-dependent self-diffusion coefficients and viscosities exhibit more pronounced non-Arrhenius behavior with the increase of Si content before phase transitions, indicating the enhanced glass-forming ability. These appearances of thermodynamic properties and phase transitions are found to closely relate to the medium-range order clusters with the defective face-centered cubic structure characterized by both local translational and orientational order. This locally ordered structure tends to be destroyed by the addition of more Si atoms, resulting in a delay of nucleation and even glass transition instead.

Ternary semiconductors NiZrSn and CoZrBi with half-Heusler structure: A first-principles study

NASA Astrophysics Data System (ADS)

Fiedler, Gregor; Kratzer, Peter

2016-08-01

The ternary semiconductors NiZrSn and CoZrBi with C 1b crystal structure are introduced by calculating their basic structural, electronic, and phononic properties using density functional theory. Both the gradient-corrected PBE functional and the hybrid functional HSE06 are employed. While NiZrSn is found to be a small-band-gap semiconductor (Eg=0.46 eV in PBE and 0.60 eV in HSE06), CoZrBi has a band gap of 1.01 eV in PBE (1.34 eV in HSE06). Moreover, effective masses and deformation potentials are reported. In both materials A B C , the intrinsic point defects introduced by species A (Ni or Co) are calculated. The Co-induced defects in CoZrBi are found to have a higher formation energy compared to Ni-induced defects in NiZrSn. The interstitial Ni atom (Nii) as well as the VNiNii complex introduce defect states in the band gap, whereas the Ni vacancy (VNi) only reduces the size of the band gap. While Nii is electrically active and may act as a donor, the other two types of defects may compensate extrinsic doping. In CoZrBi, only the VCoCoi complex introduces a defect state in the band gap. Motivated by the reported use of NiZrSn for thermoelectric applications, the Seebeck coefficient of both materials, both in the p -type and the n -type regimes, is calculated. We find that CoZrBi displays a rather large thermopower of up to 500 μ V /K when p doped, whereas NiZrSn possesses its maximum thermopower in the n -type regime. The reported difficulties in achieving p -type doping in NiZrSn could be rationalized by the unintended formation of Nii2 + in conjunction with extrinsic acceptors, resulting in their compensation. Moreover, it is found that all types of defects considered, when present in concentrations as large as 3%, tend to reduce the thermopower compared to ideal bulk crystals at T =600 K. For NiZrSn, the calculated thermodynamic data suggest that additional Ni impurities could be removed by annealing, leading to precipitation of a metallic Ni2ZrSn phase.

Phase separation and defect formation in stable, metastable, and unstable GaInAsSb alloys for infrared applications

NASA Astrophysics Data System (ADS)

Yildirim, Asli

GaInAsSb is a promising material for mid-infrared devices such as lasers and detectors because it is a direct band gap material with large radiative coefficient and a cut-off wavelength that can be varied across the mid-infrared (from 1.7 to 4.9 mum) while remaining lattice matched to GaSb. On the other hand, the potential of the alloy is hampered by predicted ranges of concentration where the constituents of the alloy become immiscible when the crystal is grown near thermodynamic equilibrium at typical growth temperatures. There have been efforts to extend the wavelength of GaInAsSb alloys through such techniques as digital alloy growth and non-equilibrium growth, but most of the compositional range has for a long time been inaccessible due to immiscibility challenges. Theoretical studies also supported the existence of thermodynamic immiscibility gaps for non-equilibrium growth conditions. Lower growth temperatures lead to shorther adatom diffusion length. While a shorter adatom diffusion length suppresses phase separation, too short an adatom length is associated with increased defect formation and eventually loss of crystallinity. On the other hand, hotter growth temperatures move epitaxial growth closer to thermodynamic equilib- rium conditions, and will eventually cause phase separation to occur. In this study thick 2 um; bulk GaInAsSb layers lattice-matched to GaSb substrates were grown across the entire (lattice-matched) compositional range at low growth temperatures (450° C), including the immiscibility region, when grown under non-equilibrium conditions with MBE. High quality epitaxial layers were grown for all compositions, as evidenced by smooth morphology (atomic force microscopy), high structural quality (X-ray diffraction), low alloy fluctuactions (electron dispersive spectroscopy in cross sectioned samples), and bright room temperature photoluminescence. Because initial theoretical efforts have suggessted that lattice strain can influence layer stability, we have studied effects of strain on alloy stability. Unstable and metastable alloys were grown hot enough for the onset of phase separation, then progressively strained and characterized. We show that strain is effective in suppressing phase separation. Finally, we performed time-resolved carrier lifetime measurements for InAsSb alloy with low concentrations of Ga to investigate the role of Ga in influencing nonradiative carrier recombination. There have been studies on non-Ga containing antimonide structures (InAsSb, InAs/InAsSb) that show long carrier lifetimes, which suggest that Ga plays a role in reducing carrier lifetime, because Ga-containing structures such as InAs/GaSb superlattices have much shorter carrier lifetimes. Ga may reduce carrier lifetime through native defects that increase background carrier concentration, or that create mid-gap electronic states. Here, a series of GaInAsSb alloys were grown with low to zero Ga concentration. No difference in carrier lifetime was observed between Ga and Ga-free structures, and minority carrier lifetimes > 600 ns were observed. Additional work remains to be done to obtain background carrier densities in the samples with Hall measurements.

Physical concepts in the development of constitutive equations

NASA Technical Reports Server (NTRS)

Cassenti, B. N.

1985-01-01

Proposed viscoplastic material models include in their formulation observed material response but do not generally incorporate principles from thermodynamics, statistical mechanics, and quantum mechanics. Numerous hypotheses were made for material response based on first principles. Many of these hypotheses were tested experimentally. The proposed viscoplastic theories and the experimental basis of these hypotheses must be checked against the hypotheses. The physics of thermodynamics, statistical mechanics and quantum mechanics, and the effects of defects, are reviewed for their application to the development of constitutive laws.

Energetics of Intermediate Temperature Solid Oxide Fuel Cell Electrolytes: Singly and Doubly doped Ceria Systems

NASA Astrophysics Data System (ADS)

Buyukkilic, Salih

Solid oxide fuel cells (SOFCs) have potential to convert chemical energy directly to electrical energy with high efficiency, with only water vapor as a by-product. However, the requirement of extremely high operating temperatures (~1000 °C) limits the use of SOFCs to only in large scale stationary applications. In order to make SOFCs a viable energy solution, enormous effort has been focused on lowering the operating temperatures below 700 °C. A low temperature operation would reduce manufacturing costs by slowing component degradation, lessening thermal mismatch problems, and sharply reducing costs of operation. In order to optimize SOFC applications, it is critical to understand the thermodynamic stabilities of electrolytes since they directly influence device stability, sustainability and performance. Rare-earth doped ceria electrolytes have emerged as promising materials for SOFC applications due to their high ionic conductivity at the intermediate temperatures (500--700 °C). However there is a fundamental lack of understanding regarding their structure, thermodynamic stability and properties. Therefore, the enthalpies of formation from constituent oxides and ionic conductivities were determined to investigate a relationship between the stability, composition, structural defects and ionic conductivity in rare earth doped ceria systems. For singly doped ceria electrolytes, we investigated the solid solution phase of bulk Ce1-xLnxO2-0.5x where Ln = Sm and Nd (0 ≤ x ≤ 0.30) and analyzed their enthalpies of formation, mixing and association, and bulk ionic conductivities while considering cation size mismatch and defect associations. It was shown that for ambient temperatures in the dilute dopant region, the positive heat of formation reaches a maximum as the system becomes increasingly less stable due to size mismatch. In concentrated region, stabilization to a certain solubility limit was observed probably due to the defect association of trivalent cations with charge-balancing oxygen vacancies. At higher temperatures near 700 °C, maximum enthalpy of formation shifts toward higher dopant concentrations, as a result of defect disordering. This concentration coincides with that of maximum ionic conductivity, extending the correlation seen previously near room temperature. It is also possible to co-dope these systems with Sm and Nd to further enhance ionic conductivity. For doubly doped ceria electrolytes, the solid solution phase of Ce1-xSm0.5xNd0.5xO2-0.5x (0 ≤ x ≤ 0.30) was investigated. It has been shown that for doubly doped ceria, the maximum enthalpy of formation occurs towards higher dopant concentration than that of singly doped counterparts, with less exothermic association enthalpies. These studies provide insight into the structure-composition-property-stability relations and aid in the rational design of the future SOFCs electrolytes.

Hybrid Functional Study of Sodium and Potassium Incorporation in Cu2ZnSnS4

NASA Astrophysics Data System (ADS)

Tse, Kin Fai; Wong, Manhoi; Zhang, Yiou; Zhang, Jingzhao; Zhu, Junyi

The thermodynamics of Na and K incorporation and its effects in Cu2ZnSnS4 (CZTS) is studied using density functional theory with hybrid functional. The allowed chemical potential of Na/K in CZTS is established. Formation energy calculations shows that Na can be significantly incorporated as both substitutional defects and interstitial defects, and incorporation of K related defects are generally less favorable. Transition energy calculations is performed showing that both Na and K exhibit benign defect properties and act as a p-type dopant. The qualitative disagreement between GGA with rigid band edge shifting and HSE calculations, formation of defect complexes, and implications in experiment will also be discussed. The understandings on the defect properties of Na and K provides an essential knowledge to further understand the surfactant effects of Na and K observed in experiments. This work is supported by General Research Fund Ref. No: 14319416.

Thermodynamic study of the native and phosphorylated regulatory domain of the CFTR

DOE Office of Scientific and Technical Information (OSTI.GOV)

Marasini, Carlotta, E-mail: marasini@ge.ibf.cnr.it; Galeno, Lauretta; Moran, Oscar

2012-07-06

Highlights: Black-Right-Pointing-Pointer CFTR mutations produce cystic fibrosis. Black-Right-Pointing-Pointer Chloride transport depends on the regulatory domain phosphorylation. Black-Right-Pointing-Pointer Regulatory domain is intrinsically disordered. Black-Right-Pointing-Pointer Secondary structure and protein stability change upon phosphorylation. -- Abstract: The regulatory domain (RD) of the cystic fibrosis transmembrane conductance regulator (CFTR), the defective protein in cystic fibrosis, is the region of the channel that regulates the CFTR activity with multiple phosphorylation sites. This domain is an intrinsically disordered protein, characterized by lack of stable or unique tertiary structure. The disordered character of a protein is directly correlated with its function. The flexibility of RD may bemore » important for its regulatory role: the continuous conformational change may be necessary for the progressive phosphorylation, and thus activation, of the channel. However, the lack of a defined and stable structure results in a considerable limitation when trying to in build a unique molecular model for the RD. Moreover, several evidences indicate significant structural differences between the native, non-phosphorylated state, and the multiple phosphorylated state of the protein. The aim of our work is to provide data to describe the conformations and the thermodynamic properties in these two functional states of RD. We have done the circular dichroism (CD) spectra in samples with a different degree of phosphorylation, from the non-phosphorylated state to a bona fide completely phosphorylated state. Analysis of CD spectra showed that the random coil and {beta}-sheets secondary structure decreased with the polypeptide phosphorylation, at expenses of an increase of {alpha}-helix. This observation lead to interpret phosphorylation as a mechanism favoring a more structured state. We also studied the thermal denaturation curves of the protein in the two conditions, monitoring the changes of the mean residue ellipticity measured at 222 nm as a function of temperature, between 20 and 95 Degree-Sign C. The thermodynamic analysis of the denaturation curves shows that phosphorylation of the protein induces a state of lower stability of R domain, characterized by a lower transition temperature, and by a smaller Gibbs free energy difference between the native and the unfolded states.« less

Liquid metal-organic frameworks

NASA Astrophysics Data System (ADS)

Gaillac, Romain; Pullumbi, Pluton; Beyer, Kevin A.; Chapman, Karena W.; Keen, David A.; Bennett, Thomas D.; Coudert, François-Xavier

2017-11-01

Metal-organic frameworks (MOFs) are a family of chemically diverse materials, with applications in a wide range of fields, covering engineering, physics, chemistry, biology and medicine. Until recently, research has focused almost entirely on crystalline structures, yet now a clear trend is emerging, shifting the emphasis onto disordered states, including `defective by design’ crystals, as well as amorphous phases such as glasses and gels. Here we introduce a strongly associated MOF liquid, obtained by melting a zeolitic imidazolate framework. We combine in situ variable temperature X-ray, ex situ neutron pair distribution function experiments, and first-principles molecular dynamics simulations to study the melting phenomenon and the nature of the liquid obtained. We demonstrate from structural, dynamical, and thermodynamical information that the chemical configuration, coordinative bonding, and porosity of the parent crystalline framework survive upon formation of the MOF liquid.

Liquid metal-organic frameworks.

PubMed

Gaillac, Romain; Pullumbi, Pluton; Beyer, Kevin A; Chapman, Karena W; Keen, David A; Bennett, Thomas D; Coudert, François-Xavier

2017-11-01

Metal-organic frameworks (MOFs) are a family of chemically diverse materials, with applications in a wide range of fields, covering engineering, physics, chemistry, biology and medicine. Until recently, research has focused almost entirely on crystalline structures, yet now a clear trend is emerging, shifting the emphasis onto disordered states, including 'defective by design' crystals, as well as amorphous phases such as glasses and gels. Here we introduce a strongly associated MOF liquid, obtained by melting a zeolitic imidazolate framework. We combine in situ variable temperature X-ray, ex situ neutron pair distribution function experiments, and first-principles molecular dynamics simulations to study the melting phenomenon and the nature of the liquid obtained. We demonstrate from structural, dynamical, and thermodynamical information that the chemical configuration, coordinative bonding, and porosity of the parent crystalline framework survive upon formation of the MOF liquid.

Liquid metal–organic frameworks

DOE Office of Scientific and Technical Information (OSTI.GOV)

Gaillac, Romain; Pullumbi, Pluton; Beyer, Kevin A.

Metal–organic frameworks (MOFs) are a family of chemically diverse materials, with applications in a wide range of fields, covering engineering, physics, chemistry, biology and medicine. Until recently, research has focused almost entirely on crystalline structures, yet now a clear trend is emerging, shifting the emphasis onto disordered states, including ‘defective by design’ crystals, as well as amorphous phases such as glasses and gels. Here we introduce a strongly associated MOF liquid, obtained by melting a zeolitic imidazolate framework. We combine in situ variable temperature X-ray, ex situ neutron pair distribution function experiments, and first-principles molecular dynamics simulations to study themore » melting phenomenon and the nature of the liquid obtained. We demonstrate from structural, dynamical, and thermodynamical information that the chemical configuration, coordinative bonding, and porosity of the parent crystalline framework survive upon formation of the MOF liquid.« less

Arrhenius thermodynamics and birth defects: chemical teratogen synergy. Untested, testable, and projected relevance.

PubMed

Miller, Morton W; Church, Charles C

2013-03-01

This article addresses the issue of hyperthermia-induced birth defects with an accompanying additional teratogen, be it a chemical or a physical agent (i.e., a simultaneous "combinational" exposure to two teratogens, one of which is hyperthermia). Hyperthermia per se is a recognized human and animal teratogen. An excellent example of such combinational exposures is an epileptic woman who becomes pregnant while taking valproic acid (VPA) to control seizures. VPA is a recognized chemical teratogen, and fever (hyperthermia) is not an uncommon event during pregnancy. While VPA also may occasionally induce fever as a side effect, we are concerned here with fevers arising from other, unrelated causes. There is a small but internally consistent literature on these combinational-teratogen exposures involving hyperthermia plus a chemical teratogen; in each instance, the effect level has been observed to be synergistically elevated above levels induced by the separate teratogenic components. The data were empirical. The observed synergy is, however, consistent with Arrhenius thermodynamics, a well-known chemical rate equation. The need for information about combinational teratogen exposures is acute; fever is a common occurrence during pregnancy; and there are many instances whereby there is also the simultaneous presence of some other teratogen(s). Given that the rate of autism spectrum disorders in the United States was recently presented as 1 in 88 births, it seems reasonable to suspect that such combinational regimens are much more prevalent than previously thought. Our hypothesis is that synergistic birth defect levels from combinational regimens are consistent with Arrhenius thermodynamics. Copyright © 2013 Wiley Periodicals, Inc.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Aron-Dine, S.; Pomrehn, G. S.; Pribram-Jones, A.

Two quaternary Heusler alloys, equiatomic CuNiMnAl and CuNiMnSn, are studied using density functional theory to understand their tendency for atomic disorder on the lattice and the magnetic effects of disorder. Disordered structures with antisite defects of atoms of the same and different sublattices are considered, with the level of atomic disorder ranging from 3% to 25%. Formation energies and magnetic moments are calculated relative to the ordered ground state and combined with a simple thermodynamical model to estimate temperature effects. We predict the relative levels of disordering in the two equiatomic alloys with good correlation to experimental x-ray diffraction results.more » In conclusion, the effect of swaps involving Mn is also discussed.« less

In vacancies in InN grown by plasma-assisted molecular beam epitaxy

NASA Astrophysics Data System (ADS)

Reurings, Floris; Tuomisto, Filip; Gallinat, Chad S.; Koblmüller, Gregor; Speck, James S.

2010-12-01

The authors have applied positron annihilation spectroscopy to study the effect of different growth conditions on vacancy formation in In- and N-polar InN grown by plasma-assisted molecular beam epitaxy. The results suggest that the structural quality of the material and limited diffusion of surface adatoms during growth dictate the In vacancy formation in low electron-density undoped epitaxial InN, while growth conditions and thermodynamics have a less important role, contrary to what is observed in, e.g., GaN. Furthermore, the results imply that in high quality InN, the electron mobility is likely limited not by ionized point defect scattering, but rather by threading dislocations.

Optical Metrology for Directed Self-assembly Patterning Using Mueller Matrix Spectroscopic Ellipsometry Based Scatterometry

NASA Astrophysics Data System (ADS)

Dixit, Dhairya J.

The semiconductor industry continues to drive patterning solutions that enable devices with higher memory storage capacity, faster computing performance, lower cost per transistors, and higher transistor density. These developments in the field of semiconductor manufacturing along with the overall minimization of the size of transistors require cutting-edge metrology tools for characterization. Directed self-assembly (DSA) patterning process can be used to fabricate nanoscale line-space patterns and contact holes via thermodynamically driven micro-phase separation of block copolymer (BCP) films with boundary constraints from guiding templates. Its main advantages are high pattern resolution (~10 nm), high throughput, no requirement of a high-resolution mask, and compatibility with standard fab-equipment and processes. Although research into DSA patterning has demonstrated a high potential as a nanoscale patterning process, there are critical challenges that must be overcome before transferring DSA into high volume manufacturing, including achievement of low defect density and high process stability. For this, advances in critical dimension (CD) and overlay measurement as well as rapid defect characterization are required. Both scatterometry and critical dimension-scanning electron microscopy (CD-SEM) are routinely used for inline dimensional metrology. CD-SEM inspection is limited, as it does not easily provide detailed line-shape information, whereas scatterometry has the capability of measuring important feature dimensions including: line-width, line-shape, sidewall-angle, and thickness of the patterned samples quickly and non-destructively. The present work describes the application of Mueller matrix spectroscopic ellipsometry (MMSE) based scatterometry to optically characterize DSA patterned line- space grating and contact hole structures fabricated with phase-separated polystyrene-b-polymethylmethacrylate (PS-b-PMMA) at various integration steps of BCP DSA based patterning process. This work focuses on understanding the efficacy of MMSE base scatterometry for characterizing complex DSA structures. For example, the use of symmetry-antisymmetry properties associated with Mueller matrix (MM) elements to understand the topography of the periodic nanostructures and measure defectivity. Simulations (the forward problem approach of scatterometry) are used to investigate MM elements' sensitivity to changes in DSA structure such as one vs. two contact hole patterns and predict sensitivity to dimensional changes. A regression-based approach is used to extract feature shape parameters of the DSA structures by fitting simulated optical spectra to experimental optical spectra. Detection of the DSA defects is a key to reducing defect density for eventual manufacturability and production use of DSA process. Simulations of optical models of structures containing defects are used to evaluate the sensitivity of MM elements to DSA defects. This study describes the application of MMSE to determine the DSA pattern defectivity via spectral comparisons based on optical anisotropy and depolarization. The use of depolarization and optical anisotropy for characterization of experimental MMSE data is a very recent development in scatterometry. In addition, reconstructed scatterometry models are used to calculate line edge roughness in 28 nm pitch Si fins fabricated using DSA patterning process.

Point defects in Cd(Zn)Te and TlBr: Theory

NASA Astrophysics Data System (ADS)

Lordi, Vincenzo

2013-09-01

The effects of various crystal defects on the performances of CdTe, CdZnxTe (CZT), and TlBr for room-temperature high-energy radiation detection are examined using first-principles theoretical methods. The predictive, parameter-free, atomistic approaches used provide fundamental understanding of defect properties that are difficult to measure and also allow rapid screening of possibilities for material engineering, such as optimal doping and annealing conditions. Several recent examples from the author's work are reviewed, including: (i) accurate calculations of the thermodynamic and electronic properties of native point defects and point defect complexes in CdTe and CZT; (ii) the effects of Zn alloying on the native point defect properties in CZT; (iii) point defect diffusion and binding leading to Te clustering in Cd(Zn)Te; (iv) the profound effect of native point defects—principally vacancies—on the intrinsic material properties of TlBr, particularly its electronic and ionic conductivity; and (v) a study on doping TlBr to independently control the electronic and ionic conductivity.

Defects in doped LaGaO3 anionic conductors: linking NMR spectral features, local environments, and defect thermodynamics.

PubMed

Blanc, Frédéric; Middlemiss, Derek S; Gan, Zhehong; Grey, Clare P

2011-11-09

Doped lanthanum gallate perovskites (LaGaO(3)) constitute some of the most promising electrolyte materials for solid oxide fuel cells operating in the intermediate temperature regime. Here, an approach combining experimental multinuclear NMR spectroscopy with density functional theory total energy and GIPAW NMR calculations yields a comprehensive understanding of the structural and defect chemistries of Sr- and Mg-doped LaGaO(3) anionic conductors. The DFT energetics demonstrate that Ga-V(O)-Ga (V(O) = oxygen vacancy) environments are favored (vs Ga-V(O)-Mg, Mg-V(O)-Mg and Mg-O-Mg-V(O)-Ga) across a range y = 0.0625, 0.125, and 0.25 of fractional Mg contents in LaGa(1-y)Mg(y)O(3-y/2). The results are interpreted in terms of doping and mean phase formation energies (relative to binary oxides) and are compared with previous calculations and experimental calorimetry data. Experimental multinuclear NMR data reveal that while Mg sites remain six-fold coordinated across the range of phase stoichiometries, albeit with significant structural disorder, a stoichiometry-dependent minority of the Ga sites resonate at a shift consistent with Ga(V) coordination, demonstrating that O vacancies preferentially locate in the first anion coordination shell of Ga. The strong Mg-V(O) binding inferred by previous studies is not observed here. The (17)O NMR spectra reveal distinct resonances that can be assigned by using the GIPAW NMR calculations to anions occupying equatorial and axial positions with respect to the Ga(V)-V(O) axis. The disparate shifts displayed by these sites are due to the nature and extent of the structural distortions caused by the O vacancies.

Field-enhanced route to generating anti-Frenkel pairs in HfO2

NASA Astrophysics Data System (ADS)

Schie, Marcel; Menzel, Stephan; Robertson, John; Waser, Rainer; De Souza, Roger A.

2018-03-01

The generation of anti-Frenkel pairs (oxygen vacancies and oxygen interstitials) in monoclinic and cubic HfO2 under an applied electric field is examined. A thermodynamic model is used to derive an expression for the critical field strength required to generate an anti-Frenkel pair. The critical field strength of EaFcr˜101GVm-1 obtained for HfO2 exceeds substantially the field strengths routinely employed in the forming and switching operations of resistive switching HfO2 devices, suggesting that field-enhanced defect generation is negligible. Atomistic simulations with molecular static (MS) and molecular dynamic (MD) approaches support this finding. The MS calculations indicated a high formation energy of Δ EaF≈8 eV for the infinitely separated anti-Frenkel pair, and only a decrease to Δ EaF≈6 eV for the adjacent anti-Frenkel pair. The MD simulations showed no defect generation in either phase for E <3 GVm-1 , and only sporadic defect generation in the monoclinic phase (at E =3 GVm-1 ) with fast (trec<4 ps ) recombination. At even higher E but below EaFcr both monoclinic and cubic structures became unstable as a result of field-induced deformation of the ionic potential wells. Further MD investigations starting with preexisting anti-Frenkel pairs revealed recombination of all pairs within trec<1 ps , even for the case of neutral vacancies and charged interstitials, for which formally there is no electrostatic attraction between the defects. In conclusion, we find no physically reasonable route to generating point-defects in HfO2 by an applied field.

Interlayer Communication in Aurivillius Vanadate to Enable Defect Structures and Charge Ordering.

PubMed

Zhang, Yaoqing; Yamamoto, Takafumi; Green, Mark A; Kageyama, Hiroshi; Ueda, Yutaka

2015-11-16

The fluorite-like [Bi2O2](2+) layer is a fundamental building unit in a great variety of layered compounds. Here in this contribution, we presented a comprehensive study on an unusual Aurivillius phase Bi3.6V2O10 with respect to its defect chemistry and polymorphism control as well as implications for fast oxide ion transport at lower temperatures. The bismuth oxide layer in Bi4V2O11 is found to tolerate a large number of Bi vacancies without breaking the high temperature prototype I4/mmm structure (γ-phase). On cooling, an orthorhombic distortion occurs to the γ-phase, giving rise to a different type of phase (B-phase) in the intermediate temperature region. Cooling to room temperature causes a further transition to an oxygen-vacancy ordered A-phase, which is accompanied by the charge ordering of V(4+) and V(5+) cations, providing magnetic (d(1)) and nonmagnetic (d(0)) chains along the a axis. This is a novel charge ordering transition in terms of the concomitant change of oxygen coordination. Interestingly, upon quenching, both the γ- and B-phase can be kinetically trapped, enabling the structural probing of the two phases at ambient temperature. Driven by the thermodynamic forces, the oxide anion in the γ-phase undergoes an interlayer diffusion process to reshuffle the compositions of both Bi-O and V-O layers.

Effect of composition and strain on the electrical properties of LaNiO3 thin films

NASA Astrophysics Data System (ADS)

Zhu, Mingwei; Komissinskiy, Philipp; Radetinac, Aldin; Vafaee, Mehran; Wang, Zhanjie; Alff, Lambert

2013-09-01

The Ni content of LaNi1-xO3 epitaxial thin films grown by pulsed laser deposition has been varied by ablation from targets with different composition. While tensile strain and Ni substoichiometry reduce the conductivity, nearly stoichiometric and unstrained films show reproducibly resistivities below 100 μΩ × cm. Since the thermodynamic instability of the Ni3+ state drives defect formation, Ni defect engineering is the key to obtain highly conducting LaNiO3 thin films.

Space charge induced surface stresses: implications in ceria and other ionic solids.

PubMed

Sheldon, Brian W; Shenoy, Vivek B

2011-05-27

Volume changes associated with point defects in space charge layers can produce strains that substantially alter thermodynamic equilibrium near surfaces in ionic solids. For example, near-surface compressive stresses exceeding -10 GPa are predicted for ceria. The magnitude of this effect is consistent with anomalous lattice parameter increases that occur in ceria nanoparticles. These stresses should significantly alter defect concentrations and key transport properties in a wide range of materials (e.g., ceria electrolytes in fuel cells). © 2011 American Physical Society

A new parameter-free soft-core potential for silica and its application to simulation of silica anomalies

DOE Office of Scientific and Technical Information (OSTI.GOV)

Izvekov, Sergei, E-mail: sergiy.izvyekov.civ@mail.mil; Rice, Betsy M.

2015-12-28

A core-softening of the effective interaction between oxygen atoms in water and silica systems and its role in developing anomalous thermodynamic, transport, and structural properties have been extensively debated. For silica, the progress with addressing these issues has been hampered by a lack of effective interaction models with explicit core-softening. In this work, we present an extension of a two-body soft-core interatomic force field for silica recently reported by us [S. Izvekov and B. M. Rice, J. Chem. Phys. 136(13), 134508 (2012)] to include three-body forces. Similar to two-body interaction terms, the three-body terms are derived using parameter-free force-matching ofmore » the interactions from ab initio MD simulations of liquid silica. The derived shape of the O–Si–O three-body potential term affirms the existence of repulsion softening between oxygen atoms at short separations. The new model shows a good performance in simulating liquid, amorphous, and crystalline silica. By comparing the soft-core model and a similar model with the soft-core suppressed, we demonstrate that the topology reorganization within the local tetrahedral network and the O–O core-softening are two competitive mechanisms responsible for anomalous thermodynamic and kinetic behaviors observed in liquid and amorphous silica. The studied anomalies include the temperature of density maximum locus and anomalous diffusivity in liquid silica, and irreversible densification of amorphous silica. We show that the O–O core-softened interaction enhances the observed anomalies primarily through two mechanisms: facilitating the defect driven structural rearrangements of the silica tetrahedral network and modifying the tetrahedral ordering induced interactions toward multiple characteristic scales, the feature which underlies the thermodynamic anomalies.« less

On the interplay of point defects and Cd in non-polar ZnCdO films

NASA Astrophysics Data System (ADS)

Zubiaga, A.; Reurings, F.; Tuomisto, F.; Plazaola, F.; García, J. A.; Kuznetsov, A. Yu.; Egger, W.; Zúñiga-Pérez, J.; Muñoz-Sanjosé, V.

2013-01-01

Non-polar ZnCdO films, grown over m- and r-sapphire with a Cd concentration ranging between 0.8% and 5%, have been studied by means of slow positron annihilation spectroscopy (PAS) combined with chemical depth profiling by secondary ion mass spectroscopy and Rutherford back-scattering. Vacancy clusters and Zn vacancies with concentrations up to 1017 cm-3 and 1018 cm-3, respectively, have been measured inside the films. Secondary ion mass spectroscopy results show that most Cd stays inside the ZnCdO film but the diffused atoms can penetrate up to 1.3 μm inside the ZnO buffer. PAS results give an insight to the structure of the meta-stable ZnCdO above the thermodynamical solubility limit of 2%. A correlation between the concentration of vacancy clusters and Cd has been measured. The concentration of Zn vacancies is one order of magnitude larger than in as-grown non-polar ZnO films and the vacancy cluster are, at least partly, created by the aggregation of smaller Zn vacancy related defects. The Zn vacancy related defects and the vacancy clusters accumulate around the Cd atoms as a way to release the strain induced by the substitutional CdZn in the ZnO crystal.

FIRST-PRINCIPLES CALCULATIONS OF INTRINSIC DEFECTS AND Mg TRANSMUTANTS IN 3C-SiC

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hu, Shenyang Y.; Setyawan, Wahyu; Van Ginhoven, Renee M.

2013-09-25

Silicon carbide (SiC) possesses many desirable attributes for applications in high-temperature and neutron radiation environments. These attributes include excellent dimensional and thermodynamic stability, low activation, high strength, and high thermal conductivity. Therefore, SiC based materials draw broad attention as structural materials for the first wall (FW) and blanket in fusion power plants. Under the severe high-energy neutron environment of D-T fusion systems, SiC suffers significant transmutation resulting in both gaseous and metallic transmutants. Recent calculations by Sawan, et al. [2] predict that at a fast neutron dose of ~100 dpa, there will be about 0.5 at% Mg generated in SiCmore » through nuclear transmutation. Other transmutation products, including 0.15 at% Al, 0.2 at% Be and 2.2 at% He, also emerge. Formation and migration energies of point defects in 3C-SiC have been widely investigated using density functional theory (DFT). However, the properties of defects associated with transmutants are currently not well understood. Fundamental understanding of where the transmutation products go and how they affect microstructure evolution of SiC composites will help to predict property evolution and performance of SiC-based materials in fusion reactors.« less

Near Surface Stoichiometry in UO 2 : A Density Functional Theory Study

DOE Office of Scientific and Technical Information (OSTI.GOV)

Yu, Jianguo; Valderrama, Billy; Henderson, Hunter B.

2015-01-01

The mechanisms of oxygen stoichiometry variation in UO 2at different temperature and oxygen partial pressure are important for understanding the dynamics of microstructure in these crystals. However, very limited experimental studies have been performed to understand the atomic structure of UO 2near surface and defect effects of near surface on stoichiometry in which the system can exchange atoms with the external reservoir. In this study, the near (110) surface relaxation and stoichiometry in UO 2have been studied with density functional theory (DFT) calculations. On the basis of the point-defect model (PDM), a general expression for the near surface stoichiometric variationmore » is derived by using DFT total-energy calculations and atomistic thermodynamics, in an attempt to pin down the mechanisms of oxygen exchange between the gas environment and defected UO 2. By using the derived expression, it is observed that, under poor oxygen conditions, the stoichiometry of near surface is switched from hyperstoichiometric at 300 K with a depth around 3 nm to near-stoichiometric at 1000 K and hypostoichiometric at 2000 K. Furthermore, at very poor oxygen concentrations and high temperatures, our results also suggest that the bulk of the UO 2prefers to be hypostoichiometric, although the surface is near-stoichiometric.« less

Near surface stoichiometry in UO 2: A density functional theory study

DOE Office of Scientific and Technical Information (OSTI.GOV)

Yu, Jianguo; Valderrama, Billy; Henderson, Hunter B.

2015-08-01

The mechanisms of oxygen stoichiometry variation in UO 2 at different temperature and oxygen partial pressure are important for understanding the dynamics of microstructure in these crystals. However, very limited experimental studies have been performed to understand the atomic structure of UO 2 near surface and defect effects of near surface on stoichiometry in which the system can exchange atoms with the external reservoir. In this study, the near (110) surface relaxation and stoichiometry in UO 2 have been studied with density functional theory (DFT) calculations. On the basis of the point-defect model (PDM), a general expression for the nearmore » surface stoichiometric variation is derived by using DFT total-energy calculations and atomistic thermodynamics, in an attempt to pin down the mechanisms of oxygen exchange between the gas environment and defected UO 2. By using the derived expression, it is observed that, under poor oxygen conditions, the stoichiometry of near surface is switched from hyperstoichiometric at 300 K with a depth around 3 nm to near-stoichiometric at 1000 K and hypostoichiometric at 2000 K. Furthermore, at very poor oxygen concentrations and high temperatures, our results also suggest that the bulk of the UO 2 prefers to be hypostoichiometric, although the surface is near-stoichiometric.« less

Designing Radiation Resistance in Materials for Fusion Energy

NASA Astrophysics Data System (ADS)

Zinkle, S. J.; Snead, L. L.

2014-07-01

Proposed fusion and advanced (Generation IV) fission energy systems require high-performance materials capable of satisfactory operation up to neutron damage levels approaching 200 atomic displacements per atom with large amounts of transmutant hydrogen and helium isotopes. After a brief overview of fusion reactor concepts and radiation effects phenomena in structural and functional (nonstructural) materials, three fundamental options for designing radiation resistance are outlined: Utilize matrix phases with inherent radiation tolerance, select materials in which vacancies are immobile at the design operating temperatures, or engineer materials with high sink densities for point defect recombination. Environmental and safety considerations impose several additional restrictions on potential materials systems, but reduced-activation ferritic/martensitic steels (including thermomechanically treated and oxide dispersion-strengthened options) and silicon carbide ceramic composites emerge as robust structural materials options. Materials modeling (including computational thermodynamics) and advanced manufacturing methods are poised to exert a major impact in the next ten years.

Defect topologies in chiral liquid crystals confined to mesoscopic channels

DOE Office of Scientific and Technical Information (OSTI.GOV)

Schlotthauer, Sergej, E-mail: s.schlotthauer@mailbox.tu-berlin.de; Skutnik, Robert A.; Stieger, Tillmann

2015-05-21

We present Monte Carlo simulations in the grand canonical and canonical ensembles of a chiral liquid crystal confined to mesochannels of variable sizes and geometries. The mesochannels are taken to be quasi-infinite in one dimension but finite in the two other directions. Under thermodynamic conditions chosen and for a selected value of the chirality coupling constant, the bulk liquid crystal exhibits structural characteristics of a blue phase II. This is established through the tetrahedral symmetry of disclination lines and the characteristic simple-cubic arrangement of double-twist helices formed by the liquid-crystal molecules along all three axes of a Cartesian coordinate system.more » If the blue phase II is then exposed to confinement, the interplay between its helical structure, various anchoring conditions at the walls of the mesochannels, and the shape of the mesochannels gives rise to a broad variety of novel, qualitative disclination-line structures that are reported here for the first time.« less

Long-term stable water vapor permeation barrier properties of SiN/SiCN/SiN nanolaminated multilayers grown by plasma-enhanced chemical vapor deposition at extremely low pressures

DOE Office of Scientific and Technical Information (OSTI.GOV)

Choi, Bum Ho, E-mail: bhchoi@kitech.re.kr; Lee, Jong Ho

2014-08-04

We investigated the water vapor permeation barrier properties of 30-nm-thick SiN/SiCN/SiN nanolaminated multilayer structures grown by plasma enhanced chemical vapor deposition at 7 mTorr. The derived water vapor transmission rate was 1.12 × 10{sup −6} g/(m{sup 2} day) at 85 °C and 85% relative humidity, and this value was maintained up to 15 000 h of aging time. The X-ray diffraction patterns revealed that the nanolaminated film was composed of an amorphous phase. A mixed phase was observed upon performing high resolution transmission electron microscope analysis, which indicated that a thermodynamically stable structure was formed. It was revealed amorphous SiN/SiCN/SiN multilayer structures that are freemore » from intermixed interface defects effectively block water vapor permeation into active layer.« less

Theoretical Investigations into Defected Graphene for Electrochemical Reduction of CO 2

DOE PAGES

Siahrostami, Samira; Jiang, Kun; Karamad, Mohammadreza; ...

2017-10-10

Here, despite numerous experimental efforts that have been dedicated to studying carbon-based materials for electrochemical reduction of CO 2, a rationalization of the associated trends in the intrinsic activity of different active motifs has so far been elusive. In the present work, we employ density functional theory calculations to examine a variety of different active sites in N-doped graphene to give a comprehensive outline of the trends in activity. We find that adsorption energies of COOH* and CO* do not follow the linear scaling relationships observed for the pure transition metals, and this unique scaling is rationalized through differences inmore » electronic structure between transition metals and defected graphene. This finding rationalizes most of the experimental observations on the carbon-based materials which present promising catalysts for the two-electron reduction of CO 2 to CO. With this simple thermodynamic analysis, we identify several active sites that are expected to exhibit a comparable or even better activity to the state-of-the-art gold catalyst, and several configurations are suggested to be selective for CO 2RR over HER.« less

Revealing Charge Transport Mechanisms in Li 2 S 2 for Li–Sulfur Batteries

DOE Office of Scientific and Technical Information (OSTI.GOV)

Liu, Zhixiao; Balbuena, Perla B.; Mukherjee, Partha P.

Besides lithium sulfide (Li 2S), lithium persulfide (Li 2S 2) is another solid discharge product in lithium-sulfur (Li-S) batteries. Revealing the charge transport mechanism in the discharge products is important for developing an effective strategy to improve the performance of Li-S batteries. Li 2S 2 cannot transport free electrons due to its wide bandgap between the valence band maximum (VBM) and conduction band minimum (VBM). However, electron polarons (p -) and hole polarons (p +) can appear in solid Li 2S 2 due to the unique molecular orbital structure of the S 2 2- anion. The thermodynamic and kinetic propertiesmore » of native defects are investigated. It is found that negatively charged Li vacancies (V Li-) and p + are the main native defects with a low formation energy of 0.77 eV. The predominant charge carrier is p + because p + has a high mobility. Thus, the electronic conductivity related to p + diffusion is dependent on temperature, and high temperatures are preferred to increase the conductivity.« less

Revealing Charge Transport Mechanisms in Li 2 S 2 for Li–Sulfur Batteries

DOE PAGES

Liu, Zhixiao; Balbuena, Perla B.; Mukherjee, Partha P.

2017-03-06

Besides lithium sulfide (Li 2S), lithium persulfide (Li 2S 2) is another solid discharge product in lithium-sulfur (Li-S) batteries. Revealing the charge transport mechanism in the discharge products is important for developing an effective strategy to improve the performance of Li-S batteries. Li 2S 2 cannot transport free electrons due to its wide bandgap between the valence band maximum (VBM) and conduction band minimum (VBM). However, electron polarons (p -) and hole polarons (p +) can appear in solid Li 2S 2 due to the unique molecular orbital structure of the S 2 2- anion. The thermodynamic and kinetic propertiesmore » of native defects are investigated. It is found that negatively charged Li vacancies (V Li-) and p + are the main native defects with a low formation energy of 0.77 eV. The predominant charge carrier is p + because p + has a high mobility. Thus, the electronic conductivity related to p + diffusion is dependent on temperature, and high temperatures are preferred to increase the conductivity.« less

Degree of polymerization of glucan chains shapes the structure fluctuations and melting thermodynamics of a cellulose microfibril.

PubMed

Chang, Rakwoo; Gross, Adam S; Chu, Jhih-Wei

2012-07-19

A Staggered LATtice (SLAT) model is developed for modeling cellulose microfibrils. The simple representation of molecular packing and interactions employed in SLAT allows simulations of structure fluctuations and phase transition of cellulose microfibrils at sufficiently long and large scales for comparison with experiments. Glucan chains in the microfibril are modeled as connected monomers, each corresponding to a cellobiose subunit, and the surrounding space around the cellulose is composed of solvent cells. Interaction parameters of monomer-monomer interactions were parametrized based on the results of atomistic molecular dynamics simulations. The monomer-solvent interaction was optimized to give a melting temperature of ∼695 K for the 36-glucan chain model cellulose microfibril, which is consistent with the estimation based on experimental data. Monte Carlo simulations of the SLAT model also capture experimentally measured X-ray diffraction patterns of cellulose as a function of temperature, including the region of melting transition, as well as predict the highly flexible regions in the microfibril. Beyond the diameter of ∼3 nm, we found that melting temperature of the cellulose microfibril is not significantly shifted by changing the thickness. On the other hand, a slight decrease in the degree of polymerization of glucan chains is shown to enhance structure fluctuations through the ends of glucan chains, i.e., the defect sites, and thereby significantly reduce the melting temperature. Analysis of the sizes, densities, and lifetimes of defect structures in the microfibril indicates a significant extent of fluctuations on the surfaces even at room temperature and that defect statistics are strong but distinct functions of temperature and solvent quality. The SLAT model is the first of its kind for simulating cellulosic materials, and this work shows that it can be used to incorporate information obtained from atomistic simulations and experimental data to enable the aforementioned findings through computation.

Carbon substitution for oxygen in silicates in planetary interiors

PubMed Central

Sen, Sabyasachi; Widgeon, Scarlett J.; Navrotsky, Alexandra; Mera, Gabriela; Tavakoli, Amir; Ionescu, Emanuel; Riedel, Ralf

2013-01-01

Amorphous silicon oxycarbide polymer-derived ceramics (PDCs), synthesized from organometallic precursors, contain carbon- and silica-rich nanodomains, the latter with extensive substitution of carbon for oxygen, linking Si-centered SiOxC4-x tetrahedra. Calorimetric studies demonstrated these PDCs to be thermodynamically more stable than a mixture of SiO2, C, and silicon carbide. Here, we show by multinuclear NMR spectroscopy that substitution of C for O is also attained in PDCs with depolymerized silica-rich domains containing lithium, associated with SiOxC4-x tetrahedra with nonbridging oxygen. We suggest that significant (several percent) substitution of C for O could occur in more complex geological silicate melts/glasses in contact with graphite at moderate pressure and high temperature and may be thermodynamically far more accessible than C for Si substitution. Carbon incorporation will change the local structure and may affect physical properties, such as viscosity. Analogous carbon substitution at grain boundaries, at defect sites, or as equilibrium states in nominally acarbonaceous crystalline silicates, even if present at levels at 10–100 ppm, might form an extensive and hitherto hidden reservoir of carbon in the lower crust and mantle. PMID:24043830

Carbon substitution for oxygen in silicates in planetary interiors.

PubMed

Sen, Sabyasachi; Widgeon, Scarlett J; Navrotsky, Alexandra; Mera, Gabriela; Tavakoli, Amir; Ionescu, Emanuel; Riedel, Ralf

2013-10-01

Amorphous silicon oxycarbide polymer-derived ceramics (PDCs), synthesized from organometallic precursors, contain carbon- and silica-rich nanodomains, the latter with extensive substitution of carbon for oxygen, linking Si-centered SiO(x)C(4-x) tetrahedra. Calorimetric studies demonstrated these PDCs to be thermodynamically more stable than a mixture of SiO2, C, and silicon carbide. Here, we show by multinuclear NMR spectroscopy that substitution of C for O is also attained in PDCs with depolymerized silica-rich domains containing lithium, associated with SiO(x)C(4-x) tetrahedra with nonbridging oxygen. We suggest that significant (several percent) substitution of C for O could occur in more complex geological silicate melts/glasses in contact with graphite at moderate pressure and high temperature and may be thermodynamically far more accessible than C for Si substitution. Carbon incorporation will change the local structure and may affect physical properties, such as viscosity. Analogous carbon substitution at grain boundaries, at defect sites, or as equilibrium states in nominally acarbonaceous crystalline silicates, even if present at levels at 10-100 ppm, might form an extensive and hitherto hidden reservoir of carbon in the lower crust and mantle.

Mesoscale simulation of the formation and dynamics of lipid-structured poly(ethylene oxide)-block-poly(methyl methacrylate) diblock copolymers.

PubMed

Mu, Dan; Li, Jian-Quan; Feng, Sheng-Yu

2015-05-21

Twelve poly(ethylene oxide)-block-poly(methyl methacrylate) (PEO-b-PMMA) copolymers with lipid-like structures were designed and investigated by MesoDyn simulation. Spherical and worm-like micelles as well as bicontinuous, lamellar and defected lamellar phases were obtained. A special structure, designated B2412, with two lipid structures connected by their heads, was found to undergo four stages prior to forming a spherical micelle phase. Two possible assembly mechanisms were found via thermodynamic and dynamic process analyses; namely, the fusion and fission of micelles in dynamic equilibrium during the adjustment stage. Water can be encapsulated into these micelles, which can affect their size, particularly in low concentration aqueous solutions. The assignment of weak negative charges to the hydrophilic EO blocks resulted in a clear effect on micelle size. Surprisingly, the largest effect was observed with EO blocks with -0.5 e, wherein an ordered perfect hexagonal phase was formed. The obtained results can be applied in numerous fields of study, including adsorption, catalysis, controlled release and drug delivery.

Optimization of self-interstitial clusters in 3C-SiC with genetic algorithm

NASA Astrophysics Data System (ADS)

Ko, Hyunseok; Kaczmarowski, Amy; Szlufarska, Izabela; Morgan, Dane

2017-08-01

Under irradiation, SiC develops damage commonly referred to as black spot defects, which are speculated to be self-interstitial atom clusters. To understand the evolution of these defect clusters and their impacts (e.g., through radiation induced swelling) on the performance of SiC in nuclear applications, it is important to identify the cluster composition, structure, and shape. In this work the genetic algorithm code StructOpt was utilized to identify groundstate cluster structures in 3C-SiC. The genetic algorithm was used to explore clusters of up to ∼30 interstitials of C-only, Si-only, and Si-C mixtures embedded in the SiC lattice. We performed the structure search using Hamiltonians from both density functional theory and empirical potentials. The thermodynamic stability of clusters was investigated in terms of their composition (with a focus on Si-only, C-only, and stoichiometric) and shape (spherical vs. planar), as a function of the cluster size (n). Our results suggest that large Si-only clusters are likely unstable, and clusters are predominantly C-only for n ≤ 10 and stoichiometric for n > 10. The results imply that there is an evolution of the shape of the most stable clusters, where small clusters are stable in more spherical geometries while larger clusters are stable in more planar configurations. We also provide an estimated energy vs. size relationship, E(n), for use in future analysis.

Thermodynamic inspection of concrete using a controlled heat source

NASA Astrophysics Data System (ADS)

Milne, James M.

1990-10-01

Concrete is not quite such a non-destructable material as many are led to believe. It can deteriorate with time due to changes in the chemistry, the effect of moisture penetration and the corrosion of reinforcing steel bars. Much of this damage occurs relatively close to the surface, sometimes revealed by discolourations or the presence of cracks and sometimes as spallation when the corrosion products of steel cause delamination of the near surface concrete. These effects may occur in good quality concrete but their severity and rapidity of onset may be enhanced by fabrication defects when aggregates may not be to specification or the packing conditions cause porosity. It may thus be months or even years afterwards that these defects come to light. As a consequence a new industry has been formed to inspect concrete structures which may include X-ray equipment, linac accelerators, gamma isotope sources, ultrasonics, radar and of course thermography. Each of these nethods will have their own particular attractive features and merits. But most of these activities tend to be used more as a "fire fighting" service than as one ensuring regular maintenance of critical structures or even as quality control of structures during building. Quite often it seems that Non-destructive Testing is turned into a litigation service for dissatisfied customers and thermography is no stranger to this topic. It is heartening to see that the ASTM organisation in the USA and British Standards are encouraging and developing suitable standards for the inspection of concrete by thermographic techniques.

Locality of the Thomas-Fermi-von Weizsäcker Equations

NASA Astrophysics Data System (ADS)

Nazar, F. Q.; Ortner, C.

2017-06-01

We establish a pointwise stability estimate for the Thomas-Fermi-von Weiz-säcker (TFW) model, which demonstrates that a local perturbation of a nuclear arrangement results also in a local response in the electron density and electrostatic potential. The proof adapts the arguments for existence and uniqueness of solutions to the TFW equations in the thermodynamic limit by Catto et al. (The mathematical theory of thermodynamic limits: Thomas-Fermi type models. Oxford mathematical monographs. The Clarendon Press, Oxford University Press, New York, 1998). To demonstrate the utility of this combined locality and stability result we derive several consequences, including an exponential convergence rate for the thermodynamic limit, partition of total energy into exponentially localised site energies (and consequently, exponential locality of forces), and generalised and strengthened results on the charge neutrality of local defects.

Colloidal membranes: The rich confluence of geometry and liquid crystals

NASA Astrophysics Data System (ADS)

Kaplan, Cihan Nadir

A simple and experimentally realizable model system of chiral symmetry breaking is liquid-crystalline monolayers of aligned, identical hard rods. In these materials, tuning the chirality at the molecular level affects the geometry at systems level, thereby inducing a myriad of morphological transitions. This thesis presents theoretical studies motivated by the rich phenomenology of these colloidal monolayers. High molecular chirality leads to assemblages of rods exhibiting macroscopic handedness. In the first part we consider one such geometry, twisted ribbons, which are minimal surfaces to a double helix. By employing a theoretical approach that combines liquid-crystalline order with the preferred shape, we focus on the phase transition from simple flat monolayers to these twisted structures. In these monolayers, regions of broken chiral symmetry nucleate at the interfaces, as in a chiral smectic A sample. The second part particularly focuses on the detailed structure and thermodynamic stability of two types of observed interfaces, the monolayer edge and domain walls in simple flat monolayers. Both the edge and "twist-walls" are quasi-one-dimensional bands of molecular twist deformations dictated by local chiral interactions and surface energy considerations. We develop a unified theory of these interfaces by utilizing the de Gennes framework accompanied by appropriate surface energy terms. The last part turns to colloidal "cookies", which form in mixtures of rods with opposite handedness. These elegant structures are essentially flat monolayers surrounded by an array of local, three dimensional cusp defects. We reveal the thermodynamic and structural characteristics of cookies. Furthermore, cookies provide us with a simple relation to determine the intrinsic curvature modulus of our model system, an important constant associated with topological properties of membranes. Our results may have impacts on a broader class of soft thin films.

Theoretical Studies of Nonuniform Orientational Order in Liquid Crystals and Active Particles

NASA Astrophysics Data System (ADS)

Duzgun, Ayhan

I investigate three systems that exhibit complex patterns in orientational order, which are controlled by geometry interacting with the dynamics of phase transitions, metastability, and activity. 1. Liquid Crystal Elastomers: Liquid-crystal elastomers are remarkable materials that combine the elastic properties of cross-linked polymer networks with the anisotropy of liquid crystals. Any distortion of the polymer network affects the nematic order of the liquid crystal, and, likewise, any change in the magnitude or direction of the nematic order influences the shape of the elastomer. When elastomers are prepared without any alignment, they develop disordered polydomain structures as they are cooled into the nematic phase. To model these polydomain structures, I develop a dynamic theory for the isotropic-nematic transition in elastomers. 2. Active Brownian Particles: Unlike equilibrium systems, active matter is not governed by the conventional laws of thermodynamics. I perform Langevin dynamics simulations and analytic calculations to explore how systems cross over from equilibrium to active behavior as the activity is increased. Based on these results, I calculate how the pressure depends on wall curvature, and hence make analytic predictions for the motion of curved tracers and other effects of confinement in active matter systems. 3. Skyrmions in Liquid Crystals: Skyrmions are localized topological defects in the orientation of an order parameter field, without a singularity in the magnitude of the field. For many years, such defects have been studied in the context of chiral liquid crystals--for example, as bubbles in a confined cholesteric phase or as double-twist tubes in a blue phase. More recently, skyrmions have been investigated extensively in the context of chiral magnets. In this project, I compare skyrmions in chiral liquid crystals with the analogous magnetic defects. Through simulations based on the nematic order tensor, I model both isolated skyrmions and periodic defect lattices.

Structure of the thermodynamic arrow of time in classical and quantum theories

NASA Astrophysics Data System (ADS)

Korzekwa, Kamil

2017-05-01

In this work we analyze the structure of the thermodynamic arrow of time, defined by transformations that leave the thermal equilibrium state unchanged, in classical (incoherent) and quantum (coherent) regimes. We note that in the infinite-temperature limit, the thermodynamic ordering of states in both regimes exhibits a lattice structure. This means that when energy does not matter and the only thermodynamic resource is given by information, the thermodynamic arrow of time has a very specific structure. Namely, for any two states at present there exists a unique state in the past consistent with them and with all possible joint pasts. Similarly, there also exists a unique state in the future consistent with those states and with all possible joint futures. We also show that the lattice structure in the classical regime is broken at finite temperatures, i.e., when energy is a relevant thermodynamic resource. Surprisingly, however, we prove that in the simplest quantum scenario of a two-dimensional system, this structure is preserved at finite temperatures. We provide the physical interpretation of these results by introducing and analyzing the history erasure process, and point out that quantum coherence may be a necessary resource for the existence of an optimal erasure process.

An open canvas--2D materials with defects, disorder, and functionality.

PubMed

Zou, Xiaolong; Yakobson, Boris I

2015-01-20

CONSPECTUS: While some exceptional properties are unique to graphene only (its signature Dirac-cone gapless dispersion, carrier mobility, record strength), other features are common to other two-dimensional materials. The broader family "beyond graphene" offers greater choices to be explored and tailored for various applications. Transition metal dichalcogenides (TMDCs), hexagonal boron nitride (h-BN), and 2D layers of pure elements, like phosphorus or boron, can complement or even surpass graphene in many ways and uses, ranging from electronics and optoelectronics to catalysis and energy storage. Their availability greatly relies on chemical vapor deposition growth of large samples, which are highly polycrystalline and include interfaces such as edges, heterostructures, and grain boundaries, as well as dislocations and point defects. These imperfections do not always degrade the material properties, but they often bring new physics and even useful functionality. It turns particularly interesting in combination with the sheer openness of all 2D sheets, fully exposed to the environment, which, as we show herein, can change and tune the defect structures and consequently all their qualities, from electronic levels, conductivity, magnetism, and optics to structural mobility of dislocations and catalytic activities. In this Account, we review our progress in understanding of various defects. We begin by expressing the energy of an arbitrary graphene edge analytically, so that the environment is regarded by "chemical phase shift". This has profound implications for graphene and carbon nanotube growth. Generalization of this equation to heteroelemental BN gives a method to determine the energy for arbitrary edges of BN, depending on the partial chemical potentials. This facilitates the tuning of the morphology and electronic and magnetic properties of pure BN or hybrid BN|C systems. Applying a similar method to three-atomic-layer TMDCs reveals more diverse edge structures for thermodynamically stable flakes. Moreover, CVD samples show new types of edge reconstruction, providing insight into the nonequilibrium growth process. Combining dislocation theory with first-principles computations, we could predict the dislocation cores for BN and TMDC and reveal their variable chemical makeup. This lays the foundation for the unique sensitivity to ambient conditions. For example, partial occupation of the defect states for dislocations in TMDCs renders them intrinsically magnetic. The exchange coupling between electrons from neighboring dislocations in grain boundaries further makes them half-metallic, which may find its applications in spintronics. Finally, brief discussion of monoelemental 2D-layer phosphorus and especially the structures and growth routes of 2D boron shows how theoretical assessment can help the quest for new synthetic routes.

Solid State Ionics: from Michael Faraday to green energy-the European dimension.

PubMed

Funke, Klaus

2013-08-01

Solid State Ionics has its roots essentially in Europe. First foundations were laid by Michael Faraday who discovered the solid electrolytes Ag 2 S and PbF 2 and coined terms such as cation and anion , electrode and electrolyte . In the 19th and early 20th centuries, the main lines of development toward Solid State Ionics, pursued in Europe, concerned the linear laws of transport, structural analysis, disorder and entropy and the electrochemical storage and conversion of energy. Fundamental contributions were then made by Walther Nernst, who derived the Nernst equation and detected ionic conduction in heterovalently doped zirconia, which he utilized in his Nernst lamp. Another big step forward was the discovery of the extraordinary properties of alpha silver iodide in 1914. In the late 1920s and early 1930s, the concept of point defects was established by Yakov Il'ich Frenkel, Walter Schottky and Carl Wagner, including the development of point-defect thermodynamics by Schottky and Wagner. In terms of point defects, ionic (and electronic) transport in ionic crystals became easy to visualize. In an 'evolving scheme of materials science', point disorder precedes structural disorder, as displayed by the AgI-type solid electrolytes (and other ionic crystals), by ion-conducting glasses, polymer electrolytes and nano-composites. During the last few decades, much progress has been made in finding and investigating novel solid electrolytes and in using them for the preservation of our environment, in particular in advanced solid state battery systems, fuel cells and sensors. Since 1972, international conferences have been held in the field of Solid State Ionics, and the International Society for Solid State Ionics was founded at one of them, held at Garmisch-Partenkirchen, Germany, in 1987.

Solid State Ionics: from Michael Faraday to green energy—the European dimension

PubMed Central

Funke, Klaus

2013-01-01

Solid State Ionics has its roots essentially in Europe. First foundations were laid by Michael Faraday who discovered the solid electrolytes Ag2S and PbF2 and coined terms such as cation and anion, electrode and electrolyte. In the 19th and early 20th centuries, the main lines of development toward Solid State Ionics, pursued in Europe, concerned the linear laws of transport, structural analysis, disorder and entropy and the electrochemical storage and conversion of energy. Fundamental contributions were then made by Walther Nernst, who derived the Nernst equation and detected ionic conduction in heterovalently doped zirconia, which he utilized in his Nernst lamp. Another big step forward was the discovery of the extraordinary properties of alpha silver iodide in 1914. In the late 1920s and early 1930s, the concept of point defects was established by Yakov Il'ich Frenkel, Walter Schottky and Carl Wagner, including the development of point-defect thermodynamics by Schottky and Wagner. In terms of point defects, ionic (and electronic) transport in ionic crystals became easy to visualize. In an ‘evolving scheme of materials science’, point disorder precedes structural disorder, as displayed by the AgI-type solid electrolytes (and other ionic crystals), by ion-conducting glasses, polymer electrolytes and nano-composites. During the last few decades, much progress has been made in finding and investigating novel solid electrolytes and in using them for the preservation of our environment, in particular in advanced solid state battery systems, fuel cells and sensors. Since 1972, international conferences have been held in the field of Solid State Ionics, and the International Society for Solid State Ionics was founded at one of them, held at Garmisch-Partenkirchen, Germany, in 1987. PMID:27877585

Dirac structures in nonequilibrium thermodynamics

NASA Astrophysics Data System (ADS)

Gay-Balmaz, François; Yoshimura, Hiroaki

2018-01-01

Dirac structures are geometric objects that generalize both Poisson structures and presymplectic structures on manifolds. They naturally appear in the formulation of constrained mechanical systems. In this paper, we show that the evolution equations for nonequilibrium thermodynamics admit an intrinsic formulation in terms of Dirac structures, both on the Lagrangian and the Hamiltonian settings. In the absence of irreversible processes, these Dirac structures reduce to canonical Dirac structures associated with canonical symplectic forms on phase spaces. Our geometric formulation of nonequilibrium thermodynamic thus consistently extends the geometric formulation of mechanics, to which it reduces in the absence of irreversible processes. The Dirac structures are associated with the variational formulation of nonequilibrium thermodynamics developed in the work of Gay-Balmaz and Yoshimura, J. Geom. Phys. 111, 169-193 (2017a) and are induced from a nonlinear nonholonomic constraint given by the expression of the entropy production of the system.

Defect phase diagram for doping of Ga2O3

NASA Astrophysics Data System (ADS)

Lany, Stephan

2018-04-01

For the case of n-type doping of β-Ga2O3 by group 14 dopants (C, Si, Ge, Sn), a defect phase diagram is constructed from defect equilibria calculated over a range of temperatures (T), O partial pressures (pO2), and dopant concentrations. The underlying defect levels and formation energies are determined from first-principles supercell calculations with GW bandgap corrections. Only Si is found to be a truly shallow donor, C is a deep DX-like (lattice relaxed donor) center, and Ge and Sn have defect levels close to the conduction band minimum. The thermodynamic modeling includes the effect of association of dopant-defect pairs and complexes, which causes the net doping to decline when exceeding a certain optimal dopant concentration. The optimal doping levels are surprisingly low, between about 0.01% and 1% of cation substitution, depending on the (T, pO2) conditions. Considering further the stability constraints due to sublimation of molecular Ga2O, specific predictions of optimized pO2 and Si dopant concentrations are given. The incomplete passivation of dopant-defect complexes in β-Ga2O3 suggests a design rule for metastable doping above the solubility limit.

Icosahedral stereographic projections in three dimensions for use in dark field TEM.

PubMed

Bourdillon, Antony J

2013-08-01

Thermodynamics require that rapidly cooled crystals and quasicrystals are relatively defective. Yet, without convenient 3-dimensional indexation both at crystal poles and in diffraction planes, or Kikuchi maps, it is difficult to identify the defects by dark field transmission electron microscopy. For two phase Al6Mn, these maps are derived. They relate i-Al6Mn to the standard face centered cubic, matrix crystals. An example of their usefulness in determining interfacial characteristics is described. Indices are integral powers on an irrational number. Copyright © 2013 Elsevier Ltd. All rights reserved.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Castro, Ricardo

The report describes in details the achievements of the project addressing the performance of nanomaterials in radioactive environments. The project addresses the fundamentals of the role of interface features on the defect dynamics during irradiation and present models to predict behavior based on thermodynamic properties. Papers and products, including formation of students in this strategic area, are presented in details as well.

Computational design of surfaces, nanostructures and optoelectronic materials

NASA Astrophysics Data System (ADS)

Choudhary, Kamal

Properties of engineering materials are generally influenced by defects such as point defects (vacancies, interstitials, substitutional defects), line defects (dislocations), planar defects (grain boundaries, free surfaces/nanostructures, interfaces, stacking faults) and volume defects (voids). Classical physics based molecular dynamics and quantum physics based density functional theory can be useful in designing materials with controlled defect properties. In this thesis, empirical potential based molecular dynamics was used to study the surface modification of polymers due to energetic polyatomic ion, thermodynamics and mechanics of metal-ceramic interfaces and nanostructures, while density functional theory was used to screen substituents in optoelectronic materials. Firstly, polyatomic ion-beams were deposited on polymer surfaces and the resulting chemical modifications of the surface were examined. In particular, S, SC and SH were deposited on amorphous polystyrene (PS), and C2H, CH3, and C3H5 were deposited on amorphous poly (methyl methacrylate) (PMMA) using molecular dynamics simulations with classical reactive empirical many-body (REBO) potentials. The objective of this work was to elucidate the mechanisms by which the polymer surface modification took place. The results of the work could be used in tailoring the incident energy and/or constituents of ion beam for obtaining a particular chemistry inside the polymer surface. Secondly, a new Al-O-N empirical potential was developed within the charge optimized many body (COMB) formalism. This potential was then used to examine the thermodynamic stability of interfaces and mechanical properties of nanostructures composed of aluminum, its oxide and its nitride. The potentials were tested for these materials based on surface energies, defect energies, bulk phase stability, the mechanical properties of the most stable bulk phase, its phonon properties as well as with a genetic algorithm based evolution theory of the materials to ensure that no spurious phases had a lower cohesive energy. Thirdly, lanthanide doped and co-doped Y3Al5O 12 were examined using density functional theory (DFT) with semi-local and local functional. Theoretical results were compared and validated with experimental data and new co-doped materials with high efficiency were predicted. Finally, Transition element doped CH3NH3PbI3 were studied with DFT for validation of the model with experimental data and replacement materials for toxic Pb were predicted.

Density functional theory in the solid state

PubMed Central

Hasnip, Philip J.; Refson, Keith; Probert, Matt I. J.; Yates, Jonathan R.; Clark, Stewart J.; Pickard, Chris J.

2014-01-01

Density functional theory (DFT) has been used in many fields of the physical sciences, but none so successfully as in the solid state. From its origins in condensed matter physics, it has expanded into materials science, high-pressure physics and mineralogy, solid-state chemistry and more, powering entire computational subdisciplines. Modern DFT simulation codes can calculate a vast range of structural, chemical, optical, spectroscopic, elastic, vibrational and thermodynamic phenomena. The ability to predict structure–property relationships has revolutionized experimental fields, such as vibrational and solid-state NMR spectroscopy, where it is the primary method to analyse and interpret experimental spectra. In semiconductor physics, great progress has been made in the electronic structure of bulk and defect states despite the severe challenges presented by the description of excited states. Studies are no longer restricted to known crystallographic structures. DFT is increasingly used as an exploratory tool for materials discovery and computational experiments, culminating in ex nihilo crystal structure prediction, which addresses the long-standing difficult problem of how to predict crystal structure polymorphs from nothing but a specified chemical composition. We present an overview of the capabilities of solid-state DFT simulations in all of these topics, illustrated with recent examples using the CASTEP computer program. PMID:24516184

Size-dependent pressure-induced amorphization: a thermodynamic panorama.

PubMed

Machon, Denis; Mélinon, Patrice

2015-01-14

Below a critical particle size, some pressurized compounds (e.g. TiO2, Y2O3, PbTe) undergo a crystal-to-amorphous transformation instead of a polymorphic transition. This effect reflects the greater propensity of nanomaterials for amorphization. In this work, a panorama of thermodynamic interpretations is given: first, a descriptive analysis based on the energy landscape concept gives a general comprehension of the balance between thermodynamics and kinetics to obtain an amorphous state. Then, a formal approach based on Gibbs energy to describe the thermodynamics and phase transitions in nanoparticles gives a basic explanation of size-dependent pressure-induced amorphization. The features of this transformation (amorphization occurs at pressures lower than the polymorphic transition pressure!) and the nanostructuration can be explained in an elaborated model based on the Ginzburg-Landau theory of phase transition and on percolation theory. It is shown that the crossover between polymorphic transition and amorphization is highly dependent on the defect density and interfacial energy, i.e., on the synthesis process. Their behavior at high pressure is a quality control test for the nanoparticles.

Modeling of the interfacial separation work in relation to impurity concentration in adjoining materials

NASA Astrophysics Data System (ADS)

Alekseev, Ilia M.; Makhviladze, Tariel M.; Minushev, Airat Kh.; Sarychev, Mikhail E.

2009-10-01

On the basis of the general thermodynamic approach developed in a model describing the influence of point defects on the separation work at an interface of solid materials is developed. The kinetic equations describing the defect exchange between the interface and the material bulks are formulated. The model have been applied to the case when joined materials contain such point defects as impurity atoms (interstitial and substitutional), concretized the main characteristic parameters required for a numerical modeling as well as clarified their domains of variability. The results of the numerical modeling concerning the dependences on impurity concentrations and the temperature dependences are obtained and analyzed. Particularly, the effects of interfacial strengthening and adhesion incompatibility predicted analytically for the case of impurity atoms are verified and analyzed.

Modeling of the interfacial separation work in relation to impurity concentration in adjoining materials

NASA Astrophysics Data System (ADS)

Alekseev, Ilia M.; Makhviladze, Tariel M.; Minushev, Airat Kh.; Sarychev, Mikhail E.

2010-02-01

On the basis of the general thermodynamic approach developed in a model describing the influence of point defects on the separation work at an interface of solid materials is developed. The kinetic equations describing the defect exchange between the interface and the material bulks are formulated. The model have been applied to the case when joined materials contain such point defects as impurity atoms (interstitial and substitutional), concretized the main characteristic parameters required for a numerical modeling as well as clarified their domains of variability. The results of the numerical modeling concerning the dependences on impurity concentrations and the temperature dependences are obtained and analyzed. Particularly, the effects of interfacial strengthening and adhesion incompatibility predicted analytically for the case of impurity atoms are verified and analyzed.

Carbon as a source for yellow luminescence in GaN: Isolated C{sub N} defect or its complexes

DOE Office of Scientific and Technical Information (OSTI.GOV)

Christenson, Sayre G.; Xie, Weiyu; Sun, Y. Y., E-mail: suny4@rpi.edu

2015-10-07

We study three carbon defects in GaN, isolated C{sub N} and its two complexes with donors C{sub N}–O{sub N}, and C{sub N}–Si{sub Ga}, as a cause of the yellow luminescence using accurate hybrid density functional calculation, which includes the semi-core Ga 3d electrons as valence electrons and uses a larger 300-atom supercell. We show that the isolated C{sub N} defect yields good agreement with experiment on the photoluminescence (PL) peak position, zero-phonon line, and thermodynamic defect transition level. We find that the defect state of the complexes that is involved in the PL process is the same as that ofmore » the C{sub N} defect. The role of the positively charged donors (O{sub N} or Si{sub Ga}) next to C{sub N} is to blue-shift the PL peak. Therefore, the complexes cannot be responsible for the same PL peak as isolated C{sub N}. Our detailed balance analysis further suggests that under thermal equilibrium at typical growth temperature, the concentration of isolated C{sub N} defect is orders of magnitude higher than the defect complexes, which is a result of the small binding energy in these complexes.« less

Point Defect Properties of Cd(Zn)Te and TlBr for Room-Temperature Gamma Radiation Detectors

NASA Astrophysics Data System (ADS)

Lordi, Vincenzo

2013-03-01

The effects of various crystal defects in CdTe, Cd1-xZnxTe (CZT), and TlBr are critical for their performance as room-temperature gamma radiation detectors. We use predictive first principles theoretical methods to provide fundamental, atomic scale understanding of the defect properties of these materials to enable design of optimal growth and processing conditions, such as doping, annealing, and stoichiometry. Several recent cases will be reviewed, including (i) accurate calculations of the thermodynamic and electronic properties of native point defects and point defect complexes in CdTe and CZT; (ii) the effects of Zn alloying on the native point defect properties of CZT; (iii) point defect diffusion and binding related to Te clustering in Cd(Zn)Te; (iv) the profound effect of native point defects--principally vacancies--on the intrinsic material properties of TlBr, particularly electronic and ionic conductivity; (v) tailored doping of TlBr to independently control the electronic and ionic conductivity; and (vi) the effects of metal impurities on the electronic properties and device performance of TlBr detectors. Prepared by LLNL under Contract DE-AC52-07NA27344 with support from the National Nuclear Security Administration Office of Nonproliferation and Verification Research and Development NA-22.

Thermodynamic stability of RNA structures formed by CNG trinucleotide repeats. Implication for prediction of RNA structure.

PubMed

Broda, Magdalena; Kierzek, Elzbieta; Gdaniec, Zofia; Kulinski, Tadeusz; Kierzek, Ryszard

2005-08-16

Trinucleotide repeat expansion diseases (TREDs) are correlated with elongation of CNG DNA and RNA repeats to pathological level. This paper shows, for the first time, complete data concerning thermodynamic stabilities of RNA with CNG trinucleotide repeats. Our studies include the stability of oligoribonucleotides composed of two to seven of CAG, CCG, CGG, and CUG repeats. The thermodynamic parameters of helix propagation correlated with the presence of multiple N-N mismatches within CNG RNA duplexes were also determined. Moreover, the total stability of CNG RNA hairpins, as well as the contribution of trinucleotide repeats placed only in the stem or loop regions, was evaluated. The improved thermodynamic parameters allow to predict much more accurately the thermodynamic stabilities and structures of CNG RNAs.

Tip-induced domain structures and polarization switching in ferroelectric amino acid glycine

DOE Office of Scientific and Technical Information (OSTI.GOV)

Seyedhosseini, E., E-mail: Seyedhosseini@ua.pt; Ivanov, M.; Bdikin, I.

2015-08-21

Bioorganic ferroelectrics and piezoelectrics are becoming increasingly important in view of their intrinsic compatibility with biological environment and biofunctionality combined with strong piezoelectric effect and a switchable polarization at room temperature. Here, we study tip-induced domain structures and polarization switching in the smallest amino acid β-glycine, representing a broad class of non-centrosymmetric amino acids. We show that β-glycine is indeed a room-temperature ferroelectric and polarization can be switched by applying a bias to non-polar cuts via a conducting tip of atomic force microscope (AFM). Dynamics of these in-plane domains is studied as a function of an applied voltage and pulsemore » duration. The domain shape is dictated by polarization screening at the domain boundaries and mediated by growth defects. Thermodynamic theory is applied to explain the domain propagation induced by the AFM tip. Our findings suggest that the properties of β-glycine are controlled by the charged domain walls which in turn can be manipulated by an external bias.« less

Path-integral simulation of solids.

PubMed

Herrero, C P; Ramírez, R

2014-06-11

The path-integral formulation of the statistical mechanics of quantum many-body systems is described, with the purpose of introducing practical techniques for the simulation of solids. Monte Carlo and molecular dynamics methods for distinguishable quantum particles are presented, with particular attention to the isothermal-isobaric ensemble. Applications of these computational techniques to different types of solids are reviewed, including noble-gas solids (helium and heavier elements), group-IV materials (diamond and elemental semiconductors), and molecular solids (with emphasis on hydrogen and ice). Structural, vibrational, and thermodynamic properties of these materials are discussed. Applications also include point defects in solids (structure and diffusion), as well as nuclear quantum effects in solid surfaces and adsorbates. Different phenomena are discussed, as solid-to-solid and orientational phase transitions, rates of quantum processes, classical-to-quantum crossover, and various finite-temperature anharmonic effects (thermal expansion, isotopic effects, electron-phonon interactions). Nuclear quantum effects are most remarkable in the presence of light atoms, so that especial emphasis is laid on solids containing hydrogen as a constituent element or as an impurity.

The thermodynamic properties of pyrrhotite and pyrite: A re-evaluation

NASA Astrophysics Data System (ADS)

Barker, W. W.; Parks, T. C.

1986-10-01

On a plot of log sulfur activity versus inverse absolute temperature, the variation in published pyrite/pyrrhotite curves below 500°C is larger than expected from the precision of the measurements. The precise data by RAU (1976) fall between interpretations by SCOTT and BARNES (1971) and by TOULMIN and BARTON (1964) and are recommended. Scott and Barnes calibrated sulfur fugacities in the system Fe-Zn-S, against the data of Toulmin and Barton, but this involved a double extrapolation of empirical relationships, to and from a region where fugacities in pyrrhotite are unmeasured. Regular-solution models offer no improvement. An apparent interruption in the properties of the high-temperature pyrrhotite solid solution, at the composition Fe 7S 8 ( POWELL, 1983) is probably due to the inclusion of metastable microdomains of monoclinic pyrrhotite in some of Rau's experimental runs, rather than to an equilibrium change of structure. Hence, the uncertainties of extrapolation are unlikely to account for the displacement of the pyrite/pyrrhotite curve of Scott and Barnes. There may be a systematic error in the composition of pyrrhotite inferred by Scott and Barnes from X-ray lattice spacings, due to the effects of preparation-dependent ordering. Other influences on pyrrhotite thermodynamics are discussed. There is a maximum in the pyrrhotite fundamental unit-cell parameter, "a," as composition is changed. This maximum shifts towards the Fe-rich boundary of pyrrhotite as temperature is increased, so it suggests a contribution from intrinsic defects, even at low temperatures. The thermodynamic effects of pressure need recalculating to suit these unit-cell data.

Structure, processing, and properties of potatoes

NASA Astrophysics Data System (ADS)

Lloyd, Isabel K.; Kolos, Kimberly R.; Menegaux, Edmond C.; Luo, Huy; McCuen, Richard H.; Regan, Thomas M.

1992-06-01

The objective of this experiment and lesson intended for high school students in an engineering or materials science course or college freshmen is to demonstrate the relation between processing, structure, and thermodynamic and physical properties. The specific objectives are to show the effect of structure and structural changes on thermodynamic properties (specific heat) and physical properties (compressive strength); to illustrate the first law of thermodynamics; to compare boiling a potato in water with cooking it in a microwave in terms of the rate of structural change and the energy consumed to 'process' the potato; and to demonstrate compression testing.

Structure, processing, and properties of potatoes

NASA Technical Reports Server (NTRS)

Lloyd, Isabel K.; Kolos, Kimberly R.; Menegaux, Edmond C.; Luo, Huy; Mccuen, Richard H.; Regan, Thomas M.

1992-01-01

The objective of this experiment and lesson intended for high school students in an engineering or materials science course or college freshmen is to demonstrate the relation between processing, structure, and thermodynamic and physical properties. The specific objectives are to show the effect of structure and structural changes on thermodynamic properties (specific heat) and physical properties (compressive strength); to illustrate the first law of thermodynamics; to compare boiling a potato in water with cooking it in a microwave in terms of the rate of structural change and the energy consumed to 'process' the potato; and to demonstrate compression testing.

Fluctuation relation based continuum model for thermoviscoplasticity in metals

NASA Astrophysics Data System (ADS)

Roy Chowdhury, Shubhankar; Roy, Debasish; Reddy, J. N.; Srinivasa, Arun

2016-11-01

A continuum plasticity model for metals is presented from considerations of non-equilibrium thermodynamics. Of specific interest is the application of a fluctuation relation that subsumes the second law of thermodynamics en route to deriving the evolution equations for the internal state variables. The modelling itself is accomplished in a two-temperature framework that appears naturally by considering the thermodynamic system to be composed of two weakly interacting subsystems, viz. a kinetic vibrational subsystem corresponding to the atomic lattice vibrations and a configurational subsystem of the slower degrees of freedom describing the motion of defects in a plastically deforming metal. An apparently physical nature of the present model derives upon considering the dislocation density, which characterizes the configurational subsystem, as a state variable. Unlike the usual constitutive modelling aided by the second law of thermodynamics that merely provides a guideline to select the admissible (though possibly non-unique) processes, the present formalism strictly determines the process or the evolution equations for the thermodynamic states while including the effect of fluctuations. The continuum model accommodates finite deformation and describes plastic deformation in a yield-free setup. The theory here is essentially limited to face-centered cubic metals modelled with a single dislocation density as the internal variable. Limited numerical simulations are presented with validation against relevant experimental data.

Thermodynamic behavior of glassy state of structurally related compounds.

PubMed

Kaushal, Aditya Mohan; Bansal, Arvind Kumar

2008-08-01

Thermodynamic properties of amorphous pharmaceutical forms are responsible for enhanced solubility as well as poor physical stability. The present study was designed to investigate the differences in thermodynamic parameters arising out of disparate molecular structures and associations for four structurally related pharmaceutical compounds--celecoxib, valdecoxib, rofecoxib, and etoricoxib. Conventional and modulated temperature differential scanning calorimetry were employed to study glass forming ability and thermodynamic behavior of the glassy state of model compounds. Glass transition temperature of four glassy compounds was in a close range of 327.6-331.8 K, however, other thermodynamic parameters varied considerably. Kauzmann temperature, strength parameter and fragility parameter showed rofecoxib glass to be most fragile of the four compounds. Glass forming ability of the compounds fared similar in the critical cooling rate experiments, suggesting that different factors were determining the glass forming ability and subsequent behavior of the compounds in glassy state. A comprehensive understanding of such thermodynamic facets of amorphous form would help in rationalizing the approaches towards development of stable glassy pharmaceuticals.

The stability of a crystal with diamond structure for patchy particles with tetrahedral symmetry.

PubMed

Noya, Eva G; Vega, Carlos; Doye, Jonathan P K; Louis, Ard A

2010-06-21

The phase diagram of model anisotropic particles with four attractive patches in a tetrahedral arrangement has been computed at two different values of the range of the potential, with the aim of investigating the conditions under which a diamond crystal can be formed. We find that the diamond phase is never stable for our longer-ranged potential. At low temperatures and pressures, the fluid freezes into a body-centered-cubic solid that can be viewed as two interpenetrating diamond lattices with a weak interaction between the two sublattices. Upon compression, an orientationally ordered face-centered-cubic crystal becomes more stable than the body-centered-cubic crystal, and at higher temperatures, a plastic face-centered-cubic phase is stabilized by the increased entropy due to orientational disorder. A similar phase diagram is found for the shorter-ranged potential, but at low temperatures and pressures, we also find a region over which the diamond phase is thermodynamically favored over the body-centered-cubic phase. The higher vibrational entropy of the diamond structure with respect to the body-centered-cubic solid explains why it is stable even though the enthalpy of the latter phase is lower. Some preliminary studies on the growth of the diamond structure starting from a crystal seed were performed. Even though the diamond phase is never thermodynamically stable for the longer-ranged model, direct coexistence simulations of the interface between the fluid and the body-centered-cubic crystal and between the fluid and the diamond crystal show that at sufficiently low pressures, it is quite probable that in both cases the solid grows into a diamond crystal, albeit involving some defects. These results highlight the importance of kinetic effects in the formation of diamond crystals in systems of patchy particles.

GENERIC Integrators: Structure Preserving Time Integration for Thermodynamic Systems

NASA Astrophysics Data System (ADS)

Öttinger, Hans Christian

2018-04-01

Thermodynamically admissible evolution equations for non-equilibrium systems are known to possess a distinct mathematical structure. Within the GENERIC (general equation for the non-equilibrium reversible-irreversible coupling) framework of non-equilibrium thermodynamics, which is based on continuous time evolution, we investigate the possibility of preserving all the structural elements in time-discretized equations. Our approach, which follows Moser's [1] construction of symplectic integrators for Hamiltonian systems, is illustrated for the damped harmonic oscillator. Alternative approaches are sketched.

Conditioning and Robustness of RNA Boltzmann Sampling under Thermodynamic Parameter Perturbations.

PubMed

Rogers, Emily; Murrugarra, David; Heitsch, Christine

2017-07-25

Understanding how RNA secondary structure prediction methods depend on the underlying nearest-neighbor thermodynamic model remains a fundamental challenge in the field. Minimum free energy (MFE) predictions are known to be "ill conditioned" in that small changes to the thermodynamic model can result in significantly different optimal structures. Hence, the best practice is now to sample from the Boltzmann distribution, which generates a set of suboptimal structures. Although the structural signal of this Boltzmann sample is known to be robust to stochastic noise, the conditioning and robustness under thermodynamic perturbations have yet to be addressed. We present here a mathematically rigorous model for conditioning inspired by numerical analysis, and also a biologically inspired definition for robustness under thermodynamic perturbation. We demonstrate the strong correlation between conditioning and robustness and use its tight relationship to define quantitative thresholds for well versus ill conditioning. These resulting thresholds demonstrate that the majority of the sequences are at least sample robust, which verifies the assumption of sampling's improved conditioning over the MFE prediction. Furthermore, because we find no correlation between conditioning and MFE accuracy, the presence of both well- and ill-conditioned sequences indicates the continued need for both thermodynamic model refinements and alternate RNA structure prediction methods beyond the physics-based ones. Copyright © 2017. Published by Elsevier Inc.

Thermodynamics of strain-induced crystallization of random copolymers.

PubMed

Nie, Yijing; Gao, Huanhuan; Wu, Yixian; Hu, Wenbing

2014-01-14

Industrial semi-crystalline polymers contain various kinds of sequence defects, which behave like non-crystallizable comonomer units on random copolymers. We performed dynamic Monte Carlo simulations of strain-induced crystallization of random copolymers with various contents of comonomers at high temperatures. We observed that the onset strains of crystallization shift up with the increase of comonomer contents and temperatures. The behaviors can be predicted well by a combination of Flory's theories on the melting-point shifting-down of random copolymers and on the melting-point shifting-up of strain-induced crystallization. Our thermodynamic results are fundamentally important for us to understand the rubber strain-hardening, the plastic molding, the film stretching as well as the fiber spinning.

Crack initiation and potential hot-spot formation around a cylindrical defect under dynamic compression

NASA Astrophysics Data System (ADS)

Ma, Xiao; Li, Xinguo; Zheng, Xianxu; Li, Kewu; Hu, Qiushi; Li, Jianling

2017-11-01

In recent decades, the hot-spot theory of condensed-phase explosives has been a compelling focus of scientific investigation attracting many researchers. The defect in the polymeric binder of the polymer-bonded explosive is called the intergranular defect. In this study, the real polymeric binder was substituted by poly(methyl methacrylate) (PMMA) as it is transparent and has similar thermodynamic properties to some binders. A set of modified split Hopkinson pressure bars equipped with a time-resolved shadowgraph was used to study the process of crack initiation and potential hot-spot formation around a cylindrical defect in PMMA. The new and significant phenomenon that the opening-mode crack emerged earlier than the shearing-mode crack from the cylindrical defect has been published for the first time in this paper. Furthermore, a two-dimensional numerical simulation was performed to show the evolution of both the stress field and the temperature field. The simulation results were in good agreement with the experiment. Finally, the law of potential hot-spot formation is discussed in detail.

Defect chemistry and characterization of Hg(1-x)Cd(x)Te

NASA Technical Reports Server (NTRS)

Vydyanath, H. R.

1981-01-01

Undoped mercury cadmium telluride crystals were subjected to high temperature equilibration at temperatures ranging from 400 C to 655 C in various Hg atmospheres. Hall effect and mobility measurements were carried out on the crystals quenched to room temperature subsequent to the high temperature equilibration. The variation of the hole concentration in the cooled crystals at 77 K as a function of the partial pressure of Hg at the equlibration temperatures, together with a comparison of the hole mobility in the undoped samples with that in the copper and phosphorous doped samples yielded a defect model for the undoped crystals, according to which, the undoped crystals are essentially intrinsic at the equilibration temperatures and the native acceptor defects are doubly ionized. Native donor defects appear to be negligible in concentration, implying that the p to n conversion in these alloys is mainly due to residual foreign donor impurities. The thermodynamic constants for the intrinsic excitation process as well as for the incorporation of the doubly ionized native acceptor defects in the undoped crystals were obtained.

Origin of n-type conductivity in two-dimensional InSe: In atoms from surface adsorption and van der Waals gap

NASA Astrophysics Data System (ADS)

Wang, Hui; Shi, Jun-jie; Huang, Pu; Ding, Yi-min; Wu, Meng; Cen, Yu-lang; Yu, Tongjun

2018-04-01

Recently, two-dimensional (2D) InSe nanosheet becomes a promising material for electronic and optoelectronic nano-devices due to its excellent electron transport, wide bandgap tunability and good metal contact. The inevitable native point defects are essential in determining its characteristics and device performance. Here we investigate the defect formation energy and thermodynamic transition levels for the most important native defects and clarify the physical origin of n-type conductivity in unintentionally doped 2D InSe by using the powerful first-principles calculations. We find that both surface In adatom and Se vacancy are the key defects, and the In adatom, donated 0.65 electrons to the host, causes the n-type conductivity in monolayer InSe under In-rich conditions. For bilayer or few-layer InSe, the In interstitial within the van der Waals gap, transferred 0.68 electrons to InSe, is found to be the most stable donor defect, which dominates the n-type character. Our results are significant for understanding the defect nature of 2D InSe and improving the related nano-device performance.

Structural stability and energetics of grain boundary triple junctions in face centered cubic materials

NASA Astrophysics Data System (ADS)

Adlakha, I.; Solanki, K. N.

2015-03-01

We present a systematic study to elucidate the role of triple junctions (TJs) and their constituent grain boundaries on the structural stability of nanocrystalline materials. Using atomistic simulations along with the nudge elastic band calculations, we explored the atomic structural and thermodynamic properties of TJs in three different fcc materials. We found that the magnitude of excess energy at a TJ was directly related to the atomic density of the metal. Further, the vacancy binding and migration energetics in the vicinity of the TJ were examined as they play a crucial role in the structural stability of NC materials. The resolved line tension which takes into account the stress buildup at the TJ was found to be a good measure in predicting the vacancy binding tendency near the TJ. The activation energy for vacancy migration along the TJ was directly correlated with the measured excess energy. Finally, we show that the resistance for vacancy diffusion increased for TJs with larger excess stored energy and the defect mobility at some TJs is slower than their constituent GBs. Hence, our results have general implications on the diffusional process in NC materials and provide new insight into stabilizing NC materials with tailored TJs.

Structural Stability and Defect Energetics of ZnO from Diffusion Quantum Monte Carlo

DOE PAGES

Santana Palacio, Juan A.; Krogel, Jaron T.; Kim, Jeongnim; ...

2015-04-28

We have applied the many-body ab-initio diffusion quantum Monte Carlo (DMC) method to study Zn and ZnO crystals under pressure, and the energetics of the oxygen vacancy, zinc interstitial and hydrogen impurities in ZnO. We show that DMC is an accurate and practical method that can be used to characterize multiple properties of materials that are challenging for density functional theory approximations. DMC agrees with experimental measurements to within 0.3 eV, including the band-gap of ZnO, the ionization potential of O and Zn, and the atomization energy of O2, ZnO dimer, and wurtzite ZnO. DMC predicts the oxygen vacancy asmore » a deep donor with a formation energy of 5.0(2) eV under O-rich conditions and thermodynamic transition levels located between 1.8 and 2.5 eV from the valence band maximum. Our DMC results indicate that the concentration of zinc interstitial and hydrogen impurities in ZnO should be low under n-type, and Zn- and H-rich conditions because these defects have formation energies above 1.4 eV under these conditions. Comparison of DMC and hybrid functionals shows that these DFT approximations can be parameterized to yield a general correct qualitative description of ZnO. However, the formation energy of defects in ZnO evaluated with DMC and hybrid functionals can differ by more than 0.5 eV.« less

Stability of vacancy-type defect clusters in Ni based on first-principles and molecular dynamics simulations

DOE PAGES

Zhao, Shijun; Zhang, Yanwen; Weber, William J.

2017-10-17

Using first-principles calculations based on density-functional theory, the energetics of different vacancy-type defects, including voids, stacking fault tetrahedra (SFT) and vacancy loops, in Ni are investigated. It is found that voids are more stable than SFT at 0 K, which is also the case after taking into account the volumetric strains. By carrying out ab initio molecular dynamics simulations at temperatures up to 1000 K, direct transformations from vacancy loops and voids into SFT are observed. Our results suggest the importance of temperature effects in determining thermodynamic stability of vacancy clusters in face-centered cubic metals.

Defect phase diagram for doping of Ga 2O 3

DOE PAGES

Lany, Stephan

2018-04-01

For the case of n-type doping of β-Ga 2O 3 by group 14 dopants (C, Si, Ge, Sn), a defect phase diagram is constructed from defect equilibria calculated over a range of temperatures (T), O partial pressures (pO 2), and dopant concentrations. The underlying defect levels and formation energies are determined from first-principles supercell calculations with GW bandgap corrections. Only Si is found to be a truly shallow donor, C is a deep DX-like (lattice relaxed donor) center, and Ge and Sn have defect levels close to the conduction band minimum. The thermodynamic modeling includes the effect of association ofmore » dopant-defect pairs and complexes, which causes the net doping to decline when exceeding a certain optimal dopant concentration. The optimal doping levels are surprisingly low, between about 0.01% and 1% of cation substitution, depending on the (T, pO 2) conditions. Considering further the stability constraints due to sublimation of molecular Ga 2O, specific predictions of optimized pO 2 and Si dopant concentrations are given. To conclude, the incomplete passivation of dopant-defect complexes in β-Ga 2O 3 suggests a design rule for metastable doping above the solubility limit.« less

Defect phase diagram for doping of Ga 2O 3

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lany, Stephan

For the case of n-type doping of β-Ga 2O 3 by group 14 dopants (C, Si, Ge, Sn), a defect phase diagram is constructed from defect equilibria calculated over a range of temperatures (T), O partial pressures (pO 2), and dopant concentrations. The underlying defect levels and formation energies are determined from first-principles supercell calculations with GW bandgap corrections. Only Si is found to be a truly shallow donor, C is a deep DX-like (lattice relaxed donor) center, and Ge and Sn have defect levels close to the conduction band minimum. The thermodynamic modeling includes the effect of association ofmore » dopant-defect pairs and complexes, which causes the net doping to decline when exceeding a certain optimal dopant concentration. The optimal doping levels are surprisingly low, between about 0.01% and 1% of cation substitution, depending on the (T, pO 2) conditions. Considering further the stability constraints due to sublimation of molecular Ga 2O, specific predictions of optimized pO 2 and Si dopant concentrations are given. To conclude, the incomplete passivation of dopant-defect complexes in β-Ga 2O 3 suggests a design rule for metastable doping above the solubility limit.« less

Effects of fO2, fH2O and aoxide on formation and density of extended planar defects in olivine

NASA Astrophysics Data System (ADS)

Burgess, K.; Cooper, R. F.

2011-12-01

Melt inclusions are used in geochemistry to inform our understanding of many physiochemical processes taking place in the mantle, such as melting, melt-rock interactions and magma mixing. Fundamental to this interpretation of melt inclusions is the assumption that they act as closed systems, i.e., they are chemically isolated after trapping and preserve primitive magma compositions. However, recent work indicates that volatiles (e.g., H and F) can be rapidly reset [Portnyagin et al., 2008], and the diffusion mechanisms and rates in tracer diffusion experiments, specifically of REEs, are a matter of some debate [Spandler and O'Neill, 2010; Cherniak, 2010]. The compendium of observations and experiments suggests a role of planar extended defects in effecting and affecting diffusion kinetics in olivine. Planar extended defects are the exothermic condensation of charged point defects into two-dimensional structures, their third dimension insufficient (i.e., sub-unit cell) to describe them as a unique phase. These planar defects, in a manner similar to mechanisms of "pipe" diffusion along dislocations and of grain boundary diffusion, can lead to measured diffusivities far greater than the lattice diffusivity, and their overall effect on flux is proportional to their spatial density [cf. Hart, 1957]. High-resolution TEM and AEM investigation of experimental olivine-basalt samples show the presence of planar defects near the olivine-melt interface, with the area fraction of the high-contrast defects in the images being greatest at high fO2 and/or fH2O while temperature has an effect on the defect dimensions but not total areal density. EDS analysis of the interface regions indicate high Ti/Ca and Ti/Al ratios compared to the glass; the stability of intercalated humite-type defects in olivine, a planar defect type found in some natural olivines [e.g., Risold et al., 2001; Hermann et al., 2007], is increased to higher temperature by the incorporation of Ti. Activities of oxides clearly affect the presence and density of the defects. Olivine-ilmenite experiments were also carried out in varying fO2 and fH2O conditions. Thermodynamic calculations for concentrations of point defects, defect association(s) and defect condensation in olivine can relate experimental data for measured diffusivities to discerning natural conditions where condensed-defect, fast-path diffusion in olivine could be significant. Planar extended defects can potentially play a role in the kinetics of deformation of olivine in the mantle, particularly as the condensation reaction lowers the activity of mobile point defects. Cherniak, Am. Mineral. 95 (2010) 362-368. Hart, Acta Met. 5 (1957) 597. Hermann et al., Contrib. Mineral. Petrol. 153 (2007) 417-428. Portnyagin et al., Earth Planet. Sci.Lett. 272 (2008) 541-552. Risold et al., Contrib. Mineral. Petrol. 142 (2001) 619-628. Spandler and O'Neill, Contrib. Mineral. Petrol. 159 (2010) 791-818.

Correlation between defect transition levels and thermoelectric operational temperature of doped CrSi2

NASA Astrophysics Data System (ADS)

Singh, Abhishek; Pandey, Tribhuwan

2014-03-01

The performance of a thermoelectric material is quantified by figure of merit ZT. The challenge in achieving high ZT value requires simultaneously high thermopower, high electrical conductivity and low thermal conductivity at optimal carrier concentration. So far doping is the most versatile approach used for modifying thermoelectric properties. Previous studies have shown that doping can significantly improve the thermoelectric performance, however the tuning the operating temperature of a thermoelectric device is a main issue. Using first principles density functional theory, we report for CrSi2, a linear relationship between thermodynamic charge state transition levels of defects and temperature at which thermopower peaks. We show for doped CrSi2 that the peak of thermopower occurs at the temperature Tm, which corresponds to the position of defect transition level. Therefore, by modifying the defect transition level, a thermoelectric material with a given operational temperature can be designed. The authors thankfully acknowledge support from ADA under NpMASS.

Non-random walk diffusion enhances the sink strength of semicoherent interfaces

DOE PAGES

Vattré, A.; Jourdan, T.; Ding, H.; ...

2016-01-29

Clean, safe and economical nuclear energy requires new materials capable of withstanding severe radiation damage. One strategy of imparting radiation resistance to solids is to incorporate into them a high density of solid-phase interfaces capable of absorbing and annihilating radiation-induced defects. Here we show that elastic interactions between point defects and semicoherent interfaces lead to a marked enhancement in interface sink strength. Our conclusions stem from simulations that integrate first principles, object kinetic Monte Carlo and anisotropic elasticity calculations. Surprisingly, the enhancement in sink strength is not due primarily to increased thermodynamic driving forces, but rather to reduced defect migrationmore » barriers, which induce a preferential drift of defects towards interfaces. The sink strength enhancement is highly sensitive to the detailed character of interfacial stresses, suggesting that ‘super-sink’ interfaces may be designed by optimizing interface stress fields. Lastly, such interfaces may be used to create materials with unprecedented resistance to radiation-induced damage.« less

Discerning Thermodynamic Basis of Self-Organization in Critical Zone Structure and Function

NASA Astrophysics Data System (ADS)

Richardson, M.; Kumar, P.

2017-12-01

Self-organization characterizes the spontaneous emergence of order. Self-organization in the Critical Zone, the region of Earth's skin from below the groundwater table to the top of the vegetation canopy, involves the interaction of biotic and abiotic processes occurring through a hierarchy of temporal and spatial scales. The self-organization is sustained through input of energy and material in an open system framework, and the resulting formations are called dissipative structures. Why do these local states of organization form and how are they thermodynamically favorable? We hypothesize that structure formation is linked to energy conversion and matter throughput rates across driving gradients. Furthermore, we predict that structures in the Critical Zone evolve based on local availability of nutrients, water, and energy. By considering ecosystems as open thermodynamic systems, we model and study the throughput signatures on short times scales to determine origins and characteristics of ecosystem structure. This diagnostic approach allows us to use fluxes of matter and energy to understand the thermodynamic drivers of the system. By classifying the fluxes and dynamics in a system, we can identify patterns to determine the thermodynamic drivers for organized states. Additionally, studying the partitioning of nutrients, water, and energy throughout ecosystems through dissipative structures will help identify reasons for structure shapes and how these shapes impact major Critical Zone functions.

Investigating homology between proteins using energetic profiles.

PubMed

Wrabl, James O; Hilser, Vincent J

2010-03-26

Accumulated experimental observations demonstrate that protein stability is often preserved upon conservative point mutation. In contrast, less is known about the effects of large sequence or structure changes on the stability of a particular fold. Almost completely unknown is the degree to which stability of different regions of a protein is generally preserved throughout evolution. In this work, these questions are addressed through thermodynamic analysis of a large representative sample of protein fold space based on remote, yet accepted, homology. More than 3,000 proteins were computationally analyzed using the structural-thermodynamic algorithm COREX/BEST. Estimated position-specific stability (i.e., local Gibbs free energy of folding) and its component enthalpy and entropy were quantitatively compared between all proteins in the sample according to all-vs.-all pairwise structural alignment. It was discovered that the local stabilities of homologous pairs were significantly more correlated than those of non-homologous pairs, indicating that local stability was indeed generally conserved throughout evolution. However, the position-specific enthalpy and entropy underlying stability were less correlated, suggesting that the overall regional stability of a protein was more important than the thermodynamic mechanism utilized to achieve that stability. Finally, two different types of statistically exceptional evolutionary structure-thermodynamic relationships were noted. First, many homologous proteins contained regions of similar thermodynamics despite localized structure change, suggesting a thermodynamic mechanism enabling evolutionary fold change. Second, some homologous proteins with extremely similar structures nonetheless exhibited different local stabilities, a phenomenon previously observed experimentally in this laboratory. These two observations, in conjunction with the principal conclusion that homologous proteins generally conserved local stability, may provide guidance for a future thermodynamically informed classification of protein homology.

Wetting and Dewetting Transitions on Submerged Superhydrophobic Surfaces with Hierarchical Structures.

PubMed

Wu, Huaping; Yang, Zhe; Cao, Binbin; Zhang, Zheng; Zhu, Kai; Wu, Bingbing; Jiang, Shaofei; Chai, Guozhong

2017-01-10

The wetting transition on submersed superhydrophobic surfaces with hierarchical structures and the influence of trapped air on superhydrophobic stability are predicted based on the thermodynamics and mechanical analyses. The dewetting transition on the hierarchically structured surfaces is investigated, and two necessary thermodynamic conditions and a mechanical balance condition for dewetting transition are proposed. The corresponding thermodynamic phase diagram of reversible transition and the critical reversed pressure well explain the experimental results reported previously. Our theory provides a useful guideline for precise controlling of breaking down and recovering of superhydrophobicity by designing superhydrophobic surfaces with hierarchical structures under water.

Modeling Fission Product Sorption in Graphite Structures

DOE Office of Scientific and Technical Information (OSTI.GOV)

Szlufarska, Izabela; Morgan, Dane; Allen, Todd

2013-04-08

The goal of this project is to determine changes in adsorption and desorption of fission products to/from nuclear-grade graphite in response to a changing chemical environment. First, the project team will employ principle calculations and thermodynamic analysis to predict stability of fission products on graphite in the presence of structural defects commonly observed in very high- temperature reactor (VHTR) graphites. Desorption rates will be determined as a function of partial pressure of oxygen and iodine, relative humidity, and temperature. They will then carry out experimental characterization to determine the statistical distribution of structural features. This structural information will yield distributionsmore » of binding sites to be used as an input for a sorption model. Sorption isotherms calculated under this project will contribute to understanding of the physical bases of the source terms that are used in higher-level codes that model fission product transport and retention in graphite. The project will include the following tasks: Perform structural characterization of the VHTR graphite to determine crystallographic phases, defect structures and their distribution, volume fraction of coke, and amount of sp2 versus sp3 bonding. This information will be used as guidance for ab initio modeling and as input for sorptivity models; Perform ab initio calculations of binding energies to determine stability of fission products on the different sorption sites present in nuclear graphite microstructures. The project will use density functional theory (DFT) methods to calculate binding energies in vacuum and in oxidizing environments. The team will also calculate stability of iodine complexes with fission products on graphite sorption sites; Model graphite sorption isotherms to quantify concentration of fission products in graphite. The binding energies will be combined with a Langmuir isotherm statistical model to predict the sorbed concentration of fission products on each type of graphite site. The model will include multiple simultaneous adsorbing species, which will allow for competitive adsorption effects between different fission product species and O and OH (for modeling accident conditions).« less

Thermodynamic and Kinematic Flow Characteristics of Some Developing and Non-Developing Disturbances in Predict

DTIC Science & Technology

2014-12-01

normal ( 1S ) and parallel ( 2S ) strain rates squared. U and V are the zonal and meridional velocities and the x and y subscripts indicate partial...between developing and non-developing tropical disturbances appears to lie with the kinematic flow boundary structure and thermodynamic properties ...tropical disturbances appears to lie with the kinematic flow boundary structure and thermodynamic properties hypothesized in the marsupial paradigm

Consistency of the structure of Legendre transform in thermodynamics with the Kolmogorov-Nagumo average

NASA Astrophysics Data System (ADS)

Scarfone, A. M.; Matsuzoe, H.; Wada, T.

2016-09-01

We show the robustness of the structure of Legendre transform in thermodynamics against the replacement of the standard linear average with the Kolmogorov-Nagumo nonlinear average to evaluate the expectation values of the macroscopic physical observables. The consequence of this statement is twofold: 1) the relationships between the expectation values and the corresponding Lagrange multipliers still hold in the present formalism; 2) the universality of the Gibbs equation as well as other thermodynamic relations are unaffected by the structure of the average used in the theory.

Damage Tolerance of Large Shell Structures

NASA Technical Reports Server (NTRS)

Minnetyan, L.; Chamis, C. C.

1999-01-01

Progressive damage and fracture of large shell structures is investigated. A computer model is used for the assessment of structural response, progressive fracture resistance, and defect/damage tolerance characteristics. Critical locations of a stiffened conical shell segment are identified. Defective and defect-free computer models are simulated to evaluate structural damage/defect tolerance. Safe pressurization levels are assessed for the retention of structural integrity at the presence of damage/ defects. Damage initiation, growth, accumulation, and propagation to fracture are included in the simulations. Damage propagation and burst pressures for defective and defect-free shells are compared to evaluate damage tolerance. Design implications with regard to defect and damage tolerance of a large steel pressure vessel are examined.

Critical Role of Water and Oxygen Defects in C-O Scission during CO2 Reduction on Zn2GeO4(010).

PubMed

Yang, Jing; Li, Yanlu; Zhao, Xian; Fan, Weiliu

2018-03-27

Exploration of catalyst structure and environmental sensitivity for C-O bond scission is essential for improving the conversion efficiency because of the inertness of CO 2 . We performed density functional theory calculations to understand the influence of the properties of adsorbed water and the reciprocal action with oxygen vacancy on the CO 2 dissociation mechanism on Zn 2 GeO 4 (010). When a perfect surface was hydrated, the introduction of H 2 O was predicted to promote the scission step by two modes based on its appearance, with the greatest enhancement from dissociative adsorbed H 2 O. The dissociative H 2 O lowers the barrier and reaction energy of CO 2 dissociation through hydrogen bonding to preactivate the C-O bond and assisted scission via a COOH intermediate. The perfect surface with bidentate-binding H 2 O was energetically more favorable for CO 2 dissociation than the surface with monodentate-binding H 2 O. Direct dissociation was energetically favored by the former, whereas monodentate H 2 O facilitated the H-assisted pathway. The defective surface exhibited a higher reactivity for CO 2 decomposition than the perfect surface because the generation of oxygen vacancies could disperse the product location. When the defective surface was hydrated, the reciprocal action for vacancy and surface H 2 O on CO 2 dissociation was related to the vacancy type. The presence of H 2 O substantially decreased the reaction energy for the direct dissociation of CO 2 on O 2c1 - and O 3c2 -defect surfaces, which converts the endoergic reaction to an exoergic reaction. However, the increased decomposition barrier made the step kinetically unfavorable and reduced the reaction rate. When H 2 O was present on the O 2c2 -defect surface, both the barrier and reaction energy for direct dissociation were invariable. This result indicated that the introduction of H 2 O had little effect on the kinetics and thermodynamics. Moreover, the H-assisted pathway was suppressed on all hydrated defect surfaces. These results provide a theoretical perspective for the design of highly efficient catalysts.

Using Structured Examples and Prompting Reflective Questions to Correct Misconceptions about Thermodynamic Concepts

ERIC Educational Resources Information Center

Olakanmi, E. O.; Doyoyo, M.

2014-01-01

This paper explores the effectiveness of using "structured examples in concert with prompting reflective questions" to address misconceptions held by mechanical engineering students about thermodynamic principles by employing pre-test and post-test design, a structured questionnaire, lecture room observation, and participants'…

Theoretical limits on the stability of single-phase kesterite-Cu{sub 2}ZnSnS{sub 4}

DOE Office of Scientific and Technical Information (OSTI.GOV)

Sarker, Pranab; Huda, Muhammad N., E-mail: huda@uta.edu; Al-Jassim, Mowafak M.

2015-01-21

The single-phase stability of Cu{sub 2}ZnSnS{sub 4} (CZTS), after an intrinsic defect was incorporated in it, has been examined here for the first time based on ab initio calculations. The stability analysis of such a non-stoichiometric-defect incorporated CZTS shows that the single-phase formation is unlikely at thermodynamic equilibrium conditions. In addition, the effective growth condition of CZTS is determined and quantified for all the elements (Cu-poor, Zn-rich, Sn-poor, and S-rich) to extract maximum photovoltaic efficiency from CZTS. These conditions promote (i) spontaneous formation of Cu vacancy (V{sub Cu}), which might benefit p-type conduction, and (ii) the co-existence of ZnS whilemore » suppressing other harmful defects and secondary phases. Further, the results presented here explain the unavailability of single-phase CZTS to date.« less

Nature of electron trap states under inversion at In0.53Ga0.47As/Al2O3 interfaces

NASA Astrophysics Data System (ADS)

Colleoni, Davide; Pourtois, Geoffrey; Pasquarello, Alfredo

2017-03-01

In and Ga impurities substitutional to Al in the oxide layer resulting from diffusion out of the substrate are identified as candidates for electron traps under inversion at In0.53Ga0.47As/Al2O3 interfaces. Through density-functional calculations, these defects are found to be thermodynamically stable in amorphous Al2O3 and to be able to capture two electrons in a dangling bond upon breaking bonds with neighboring O atoms. Through a band alignment based on hybrid functional calculations, it is inferred that the corresponding defect levels lie at ˜1 eV above the conduction band minimum of In0.53Ga0.47As, in agreement with measured defect densities. These results support the technological importance of avoiding cation diffusion into the oxide layer.

Dynamics of vacancies in two-dimensional Lennard-Jones crystals

NASA Astrophysics Data System (ADS)

Yao, Zhenwei; Olvera de La Cruz, Monica

2015-03-01

Vacancies represent an important class of crystallographic defects, and their behaviors can be strongly coupled with relevant material properties. We report the rich dynamics of vacancies in two-dimensional Lennard-Jones crystals in several thermodynamic states. Specifically, we numerically observe significantly faster diffusion of the 2-point vacancy with two missing particles in comparison with other types of vacancies; it opens the possibility of doping 2-point vacancies into atomic materials to enhance atomic migration. In addition, the resulting dislocations in the healing of a long vacancy suggest the intimate connection between vacancies and topological defects that may provide an extra dimension in the engineering of defects in extensive crystalline materials for desired properties. We thank the financial support from the U.S. Department of Commerce, National Institute of Standards and Technology, the Office of the Director of Defense Research and Engineering (DDR&E) and the Air Force Office of Scientific Research.

Large effect of columnar defects on the thermodynamic properties of Bi2Sr2CaCu2O8 single crystals

NASA Astrophysics Data System (ADS)

van der Beek, C. J.; Konczykowski, M.; Li, T. W.; Kes, P. H.; Benoit, W.

1996-07-01

The introduction of columnar defects by irradiation with 5.8-GeV Pb ions is shown to affect significantly the reversible magnetic properties of Bi2Sr2CaCu2O8+δ single crystals. Notably, the suppression of superconducting fluctuations on length scales greater than the separation between columns leads to the disappearance of the ``crossing point'' in the critical fluctuation regime. At lower temperatures, the strong modification of the vortex energy due to pinning leads to an important change of the reversible magnetization. The analysis of the latter permits the direct determination of the pinning energy.

Dependence of Morphology of SiOx Nanowires on the Supersaturation of Au-Si Alloy Liquid Droplets Formed on the Au-Coated Si Substrate

NASA Astrophysics Data System (ADS)

Zhang, Han; Li, Ji-Xue; Jin, Ai-Zi; Zhang, Ze

2001-11-01

A thermodynamic theory about the dependence of morphology of SiOx nanowires on the super-saturation of alloy liquid droplets has been proposed on the basis of the vapour-liquid-solid growth mechanism and has been supported experimentally. By changing the Si concentration in the Au-Si liquid droplets formed on the Au-coated Si substrate, firework-, tulip- and bud-shaped SiOx nanowires were synthesized by a thermal evaporation method and distributed concentrically around some void defects in the Si substrate. Voids were formed underneath the surface of the Si substrate during the thermal evaporation at 850°C and resulted in the Si-concentration deficient thus different saturation of Au-Si droplets. Electron microscopy analysis showed that the nanowires had an amorphous structure and were terminated by Au-Si particles.

Dilatonic BTZ black holes with power-law field

NASA Astrophysics Data System (ADS)

Hendi, S. H.; Eslam Panah, B.; Panahiyan, S.; Sheykhi, A.

2017-04-01

Motivated by low energy effective action of string theory and numerous applications of BTZ black holes, we will consider minimal coupling between dilaton and nonlinear electromagnetic fields in three dimensions. The main goal is studying thermodynamical structure of black holes in this set up. Temperature and heat capacity of these black holes are investigated and a picture regarding their phase transitions is given. In addition, the role and importance of studying the mass of black holes is highlighted. We will see how different parameters modify thermodynamical quantities, hence thermodynamical structure of these black holes. In addition, geometrical thermodynamics is used to investigate thermodynamical properties of these black holes. In this regard, the successful method is presented and the nature of interaction around bound and phase transition points is studied.

Structure and stability of CaH 2 surfaces: on the possibility of electron-rich surfaces in metal hydrides for catalysis

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ong, Phuong-Vu; Johnson, Lewis E.; Hosono, Hideo

Structure, thermodynamic stability, and electronic properties of CaH 2 surfaces in (001),(110), and (111) crystallographic orientations are investigated using ab initio modeling. We show that stoichiometric surfaces terminated with a hydrogen atomic plane are the most energetically favorable and discuss properties of hydrogen vacancies (VH) at these surfaces. The average calculated work function of the most stable pristine surfaces (~5.2 eV) is in agree-ment with experimental data for powder samples. Neutral hydrogen vacancies host localized electrons and induce defect states in the band gap, thereby shifting the effective work function to much lower values of ~2.7 eV. Surface VH aremore » predicted to aggregate into dimers and form electron-rich centers (e -)Ca 2+(e -) stable to over 800 K. These results suggest that hydrogen-deficient surfaces of CaH 2 can host a large concentration of localized electrons and, thus, give rise to new catalytic functionalities involving electron transfer between the surface, catalysts supported on it, and reacting species.« less

Synthesis of ALD zinc oxide and thin film materials optimization for UV photodetector applications

NASA Astrophysics Data System (ADS)

Tapily, Kandabara Nouhoum

Zinc oxide (ZnO) is a direct, wide bandgap semiconductor material. It is thermodynamically stable in the wurtzite structure at ambient temperature conditions. ZnO has very interesting optical and electrical properties and is a suitable candidate for numerous optoelectronic applications such as solar cells, LEDs and UV-photodetectors. ZnO is a naturally n-type semiconductor. Due to the lack of reproducible p-type ZnO, achieving good homojunction ZnO-based photodiodes such as UV-photodetectors remains a challenge. Meanwhile, heterojunction structures of ZnO with p-type substrates such as SiC, GaN, NiO, AlGaN, Si etc. are used; however, those heterojunction diodes suffer from low efficiencies. ZnO is an n-type material with numerous intrinsic defect levels responsible for the electrical and optical behaviors. Presently, there is no clear consensus about the origin of those defects. In this work, ZnO was synthesized by atomic layer deposition (ALD). ALD is a novel deposition technique suitable for nanotechnology engineering that provides unique features such as precise control of ZnO thin film with atomic resolution, high uniformity, good conformity and high aspect ratio. Using this novel deposition technique, the ALD ZnO deposition process was developed and optimized using diethyl zinc as the precursor for zinc and water vapor as the oxygen source. In order to optimize the film quality for use in electronic applications, the physical, mechanical and electrical properties were investigated. The structural and mechanical properties of the ALD ZnO thin films were investigated by X-ray diffraction (XRD), transmission electron microscopy (TEM), atomic force microscopy (AFM), scanning electron microscopy (SEM), spectroscopic Ellipsometry, X-ray photoelectron spectroscopy (XPS), Raman spectroscopy, UV-VIS absorption and nanoindentation. The electrical characterizations were performed using C-V, I-V, DLTS, Hall Effect, and four-point probe. The intrinsic defects responsible for the electrical and optical properties of the ALD ZnO films were analyzed and identified. ALD ZnO based electronic devices were fabricated, optimized and their electrical characteristics measured. The photocurrent characteristics of ALD ZnO were also optimized, and high efficiency UV-photodetectors were achieved.

Variable-amplitude oscillatory shear response of amorphous materials.

PubMed

Perchikov, Nathan; Bouchbinder, Eran

2014-06-01

Variable-amplitude oscillatory shear tests are emerging as powerful tools to investigate and quantify the nonlinear rheology of amorphous solids, complex fluids, and biological materials. Quite a few recent experimental and atomistic simulation studies demonstrated that at low shear amplitudes, an amorphous solid settles into an amplitude- and initial-conditions-dependent dissipative limit cycle, in which back-and-forth localized particle rearrangements periodically bring the system to the same state. At sufficiently large shear amplitudes, the amorphous system loses memory of the initial conditions, exhibits chaotic particle motions accompanied by diffusive behavior, and settles into a stochastic steady state. The two regimes are separated by a transition amplitude, possibly characterized by some critical-like features. Here we argue that these observations support some of the physical assumptions embodied in the nonequilibrium thermodynamic, internal-variables based, shear-transformation-zone model of amorphous viscoplasticity; most notably that "flow defects" in amorphous solids are characterized by internal states between which they can make transitions, and that structural evolution is driven by dissipation associated with plastic deformation. We present a rather extensive theoretical analysis of the thermodynamic shear-transformation-zone model for a variable-amplitude oscillatory shear protocol, highlighting its success in accounting for various experimental and simulational observations, as well as its limitations. Our results offer a continuum-level theoretical framework for interpreting the variable-amplitude oscillatory shear response of amorphous solids and may promote additional developments.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wiedemeier, Heribert, E-mail: wiedeh@rpi.edu

The observed linear (Na-, K-halides) and near-linear (Mg-, Sr-, Zn-, Cd-, and Hg-chalcogenides) dependences of Schottky constants on reciprocal interatomic distances yield the relation logK{sub S}=((s{sub s}1/T)+i{sub s})1/d{sub (A−B)}+(s{sub i}1/T)+i{sub i}, where K{sub S} is the product of metal and non-metal thermal equilibrium vacancy concentrations, and s{sub s}, i{sub s}, s{sub i} and i{sub i} are the group specific slope and intercept values obtained from an extended analysis of the above log K{sub S} versus 1/d{sub (A−B)} data. The previously reported linear dependences of log K{sub S} on the Born–Haber lattice energies [1] are the basis for combining the earliermore » results [1] with the Born–Mayer lattice energy equation to yield a new thermodynamic relationship, namely logK{sub S}=−(2.303nRT){sup −1}(c{sub (B−M)}/d{sub (A−B)}−I{sub e}), where c{sub (B−M)} is the product of the constants of the Born–Mayer equation and I{sub e} is the metal ionization energy of the above compounds. These results establish a correlation between point defect concentrations and basic thermodynamic, coulombic, and structural solid state properties for selected I–VII and II–VI semiconductor materials. - Graphical abstract: Display Omitted.« less

Advancing viral RNA structure prediction: measuring the thermodynamics of pyrimidine-rich internal loops

PubMed Central

Phan, Andy; Mailey, Katherine; Saeki, Jessica; Gu, Xiaobo

2017-01-01

Accurate thermodynamic parameters improve RNA structure predictions and thus accelerate understanding of RNA function and the identification of RNA drug binding sites. Many viral RNA structures, such as internal ribosome entry sites, have internal loops and bulges that are potential drug target sites. Current models used to predict internal loops are biased toward small, symmetric purine loops, and thus poorly predict asymmetric, pyrimidine-rich loops with >6 nucleotides (nt) that occur frequently in viral RNA. This article presents new thermodynamic data for 40 pyrimidine loops, many of which can form UU or protonated CC base pairs. Uracil and protonated cytosine base pairs stabilize asymmetric internal loops. Accurate prediction rules are presented that account for all thermodynamic measurements of RNA asymmetric internal loops. New loop initiation terms for loops with >6 nt are presented that do not follow previous assumptions that increasing asymmetry destabilizes loops. Since the last 2004 update, 126 new loops with asymmetry or sizes greater than 2 × 2 have been measured. These new measurements significantly deepen and diversify the thermodynamic database for RNA. These results will help better predict internal loops that are larger, pyrimidine-rich, and occur within viral structures such as internal ribosome entry sites. PMID:28213527

Deconstructing thermodynamic parameters of a coupled system from site-specific observables.

PubMed

Chowdhury, Sandipan; Chanda, Baron

2010-11-02

Cooperative interactions mediate information transfer between structural domains of a protein molecule and are major determinants of protein function and modulation. The prevalent theories to understand the thermodynamic origins of cooperativity have been developed to reproduce the complex behavior of a global thermodynamic observable such as ligand binding or enzyme activity. However, in most cases the measurement of a single global observable cannot uniquely define all the terms that fully describe the energetics of the system. Here we establish a theoretical groundwork for analyzing protein thermodynamics using site-specific information. Our treatment involves extracting a site-specific parameter (defined as χ value) associated with a structural unit. We demonstrate that, under limiting conditions, the χ value is related to the direct interaction terms associated with the structural unit under observation and its intrinsic activation energy. We also introduce a site-specific interaction energy term (χ(diff)) that is a function of the direct interaction energy of that site with every other site in the system. When combined with site-directed mutagenesis and other molecular level perturbations, analyses of χ values of site-specific observables may provide valuable insights into protein thermodynamics and structure.

Examining the Chemical and Structural Properties that Influence the Sensitivity of Energetic Nitrate Esters

DOE PAGES

Manner, Virginia W.; Cawkwell, Marc; Kober, Edward M.; ...

2018-03-09

The sensitivity of explosives is controlled by factors that span from intrinsic chemical reactivity and chemical intramolecular effects to mesoscale structure and defects, and has been a topic of extensive study for over 50 years. Due to these complex competing chemical and physical elements, a unifying relationship between molecular framework, crystal structure, and sensitivity has yet to be developed. In order to move towards this goal, ideally experimental studies should be performed on systems with small, systematic structural modifications, with modeling utilized to interpret experimental results. Pentaerythritol tetranitrate (PETN) is a common nitrate ester explosive that has been widely studiedmore » due to its use in military and commercial explosives. We have synthesized PETN derivatives with modified sensitivity characteristics by substituting the CCH 2ONO 2 moiety with other substituents, including CH, CNH 2, CNH3X, CCH 3, and PO. We relate the handling sensitivity properties of each PETN derivative to its structural properties, and discuss the potential roles of thermodynamic properties such as heat capacity and heat of formation, thermal stability, crystal structure, compressibility, and inter- and intramolecular hydrogen bonding on impact sensitivity. Reactive molecular dynamics (MD) simulations of the C/H/N/O-based PETN-derivatives have been performed under cook-off conditions that mimic those accessed in impact tests. These simulations infer how changes in chemistry affect the subsequent decomposition pathways.« less

Examining the Chemical and Structural Properties that Influence the Sensitivity of Energetic Nitrate Esters

DOE Office of Scientific and Technical Information (OSTI.GOV)

Manner, Virginia W.; Cawkwell, Marc; Kober, Edward M.

The sensitivity of explosives is controlled by factors that span from intrinsic chemical reactivity and chemical intramolecular effects to mesoscale structure and defects, and has been a topic of extensive study for over 50 years. Due to these complex competing chemical and physical elements, a unifying relationship between molecular framework, crystal structure, and sensitivity has yet to be developed. In order to move towards this goal, ideally experimental studies should be performed on systems with small, systematic structural modifications, with modeling utilized to interpret experimental results. Pentaerythritol tetranitrate (PETN) is a common nitrate ester explosive that has been widely studiedmore » due to its use in military and commercial explosives. We have synthesized PETN derivatives with modified sensitivity characteristics by substituting the CCH 2ONO 2 moiety with other substituents, including CH, CNH 2, CNH3X, CCH 3, and PO. We relate the handling sensitivity properties of each PETN derivative to its structural properties, and discuss the potential roles of thermodynamic properties such as heat capacity and heat of formation, thermal stability, crystal structure, compressibility, and inter- and intramolecular hydrogen bonding on impact sensitivity. Reactive molecular dynamics (MD) simulations of the C/H/N/O-based PETN-derivatives have been performed under cook-off conditions that mimic those accessed in impact tests. These simulations infer how changes in chemistry affect the subsequent decomposition pathways.« less

Atomic-scale properties of Ni-based FCC ternary, and quaternary alloys

DOE Office of Scientific and Technical Information (OSTI.GOV)

Tamm, Artur; Aabloo, Alvo; Klintenberg, Mattias

2015-08-26

The aim of our study is to characterize some atomic-scale properties of Ni-based FCC multicomponent alloys. For this purpose, we use Monte Carlo method combined with density functional theory calculations to study short-range order (SRO), atomic displacements, electronic density of states, and magnetic moments in equimolar ternary NiCrCo, and quaternary NiCrCoFe alloys. The salient features for the ternary alloy are a negative SRO parameter between Ni Cr and a positive between Cr Cr pairs as well as a weakly magnetic state. For the quaternary alloy we predict negative SRO parameter for Ni Cr and Ni Fe pairs and positive formore » Cr Cr and Fe Fe pairs. Atomic displacements for both ternary and quaternary alloys are negligible. In contrast to the ternary, the quaternary alloy shows a complex magnetic structure. The electronic structure of the ternary and quaternary alloys shows differences near the Fermi energy between a random solid solution and the predicted structure with SRO. Despite that, the calculated EXAFS spectra does not show enough contrast to discriminate between random and ordered structures. Finally, the predicted SRO has an impact on point-defect energetics, electron phonon coupling and thermodynamic functions and thus, SRO should not be neglected when studying properties of these two alloys.« less

A thermodynamic review of cryogenic refrigeration cycles for liquefaction of natural gas

NASA Astrophysics Data System (ADS)

Chang, Ho-Myung

2015-12-01

A thermodynamic review is presented on cryogenic refrigeration cycles for the liquefaction process of natural gas. The main purpose of this review is to examine the thermodynamic structure of various cycles and provide a theoretical basis for selecting a cycle in accordance with different needs and design criteria. Based on existing or proposed liquefaction processes, sixteen ideal cycles are selected and the optimal conditions to achieve their best thermodynamic performance are investigated. The selected cycles include standard and modified versions of Joule-Thomson (JT) cycle, Brayton cycle, and their combined cycle with pure refrigerants (PR) or mixed refrigerants (MR). Full details of the cycles are presented and discussed in terms of FOM (figure of merit) and thermodynamic irreversibility. In addition, a new method of nomenclature is proposed to clearly identify the structure of cycles by abbreviation.

Fisher Information, Entropy, and the Second and Third Laws of Thermodynamics

EPA Science Inventory

We propose Fisher Information as a new calculable thermodynamic property that can be shown to follow the Second and the Third Laws of Thermodynamics. Fisher Information is, however, qualitatively different from entropy and potentially possessing a great deal more structure. Hence...

Structural, electronic, elastic, and thermodynamic properties of CaSi, Ca2Si, and CaSi2 phases from first-principles calculations

NASA Astrophysics Data System (ADS)

Li, X. D.; Li, K.; Wei, C. H.; Han, W. D.; Zhou, N. G.

2018-06-01

The structural, electronic, elastic, and thermodynamic properties of CaSi, Ca2Si, and CaSi2 are systematically investigated by using first-principles calculations method based on density functional theory (DFT). The calculated formation enthalpies and cohesive energies show that CaSi2 possesses the greatest structural stability and CaSi has the strongest alloying ability. The structural stability of the three phases is compared according to electronic structures. Further analysis on electronic structures indicates that the bonding of these phases exhibits the combinations of metallic, covalent, and ionic bonds. The elastic constants are calculated, and the bulk modulus, shear modulus, Young's modulus, Poisson's ratio, and anisotropy factor of polycrystalline materials are deduced. Additionally, the thermodynamic properties were theoretically predicted and discussed.

Electronic structure, thermodynamic properties and hydrogenation of LaPtIn and CePtIn compounds by ab-initio methods

DOE Office of Scientific and Technical Information (OSTI.GOV)

Jezierski, Andrzej, E-mail: andrzej.jezierski@ifmpan.poznan.pl; Szytuła, Andrzej

2016-02-15

The electronic structures and thermodynamic properties of LaPtIn and CePtIn are studied by means of ab-initio full-relativistic full-potential local orbital basis (FPLO) method within densities functional (DFT) methodologies. We have also examined the influence of hydrogen on the electronic structure and stability of CePtInH and LaPtInH systems. The positions of the hydrogen atoms have been found from the minimum of the total energy. Our calculations have shown that band structure and topology of the Fermi surfaces changed significantly during the hydrogenation. The thermodynamic properties (bulk modulus, Debye temperatures, constant pressure heat capacity) calculated in quasi-harmonic Debye-Grüneisen model are in amore » good agreement with the experimental data. We have applied different methods of the calculation of the equation of states (EOS) (Murnaghan, Birch-Murnaghan, Poirier–Tarantola, Vinet). The thermodynamic properties are presented for the pressure 0« less

Noncanonical structures and their thermodynamics of DNA and RNA under molecular crowding: beyond the Watson-Crick double helix.

PubMed

Sugimoto, Naoki

2014-01-01

How does molecular crowding affect the stability of nucleic acid structures inside cells? Water is the major solvent component in living cells, and the properties of water in the highly crowded media inside cells differ from that in buffered solution. As it is difficult to measure the thermodynamic behavior of nucleic acids in cells directly and quantitatively, we recently developed a cell-mimicking system using cosolutes as crowding reagents. The influences of molecular crowding on the structures and thermodynamics of various nucleic acid sequences have been reported. In this chapter, we discuss how the structures and thermodynamic properties of nucleic acids differ under various conditions such as highly crowded environments, compartment environments, and in the presence of ionic liquids, and the major determinants of the crowding effects on nucleic acids are discussed. The effects of molecular crowding on the activities of ribozymes and riboswitches on noncanonical structures of DNA- and RNA-like quadruplexes that play important roles in transcription and translation are also described. © 2014 Elsevier Inc. All rights reserved.

TiO2--a prototypical memristive material.

PubMed

Szot, K; Rogala, M; Speier, W; Klusek, Z; Besmehn, A; Waser, R

2011-06-24

Redox-based memristive switching has been observed in many binary transition metal oxides and related compounds. Since, on the one hand, many recent reports utilize TiO(2) for their studies of the memristive phenomenon and, on the other hand, there is a long history of the electronic structure and the crystallographic structure of TiO(2) under the impact of reduction and oxidation processes, we selected this material as a prototypical material to provide deeper insight into the mechanisms behind memristive switching. In part I, we briefly outline the results of the historical and recent studies of electroforming and resistive switching of TiO(2)-based cells. We describe the (tiny) stoichiometrical range for TiO(2 - x) as a homogeneous compound, the aggregation of point defects (oxygen vacancies) into extended defects, and the formation of the various Magnéli phases. Furthermore, we discuss the driving forces for these solid-state reactions from the thermodynamical point of view. In part II, we provide new experimental details about the hierarchical transformation of TiO(2) single crystals into Magnéli phases, and vice versa, under the influence of chemical, electrical and thermal gradients, on the basis of the macroscopic and nanoscopic measurements. Those include thermogravimetry, high-temperature x-ray diffraction (XRD), high-temperature conductivity measurements, as well as low-energy electron diffraction (LEED), x-ray photoelectron spectroscopy (XPS), and LC-AFM (atomic force microscope equipped with a conducting tip) studies. Conclusions are drawn concerning the relevant parameters that need to be controlled in order to tailor the memristive properties.

Ionics of nanoheterogeneous materials

NASA Astrophysics Data System (ADS)

Uvarov, Nikolay F.

2007-05-01

The results of studies of composite ionic conductors are considered. The relationship between their properties and the ionic salt disordering and the interfacial interaction between the components of the material is analysed. Special attention is paid to models that describe the surface disordering and the mechanism of defect formation. The methods of calculation of physicochemical characteristics of composites, the thermodynamic stability and peculiarities of the genesis of the nanocomposite morphology are discussed.

Defects Associated with Soldification of Melt Processed Superalloys for the Aerospace Industry

DTIC Science & Technology

2008-07-23

resulting computational model will be in a form that is usable in their efforts to design new alloys and processing routes. Given the broad research...thermodynamics modeling by Asta and Woodward. The permeability of dendritic arrays in superalloys has been determined using three-dimensional reconstructions of...the solid-liquid mush and finite-element fluid simulations by Pollock and Spowart. Close interaction with industry ensured that computational

Study on the intrinsic defects in ZnO by combing first-principle and thermodynamic calculations

NASA Astrophysics Data System (ADS)

Ma, Changmin; Liu, Tingyu; Chang, Qiuxiang

2015-11-01

In this paper, the intrinsic point defects in ZnO crystal have been studied by the approach that integrates first-principles, thermodynamic calculations and the contributions of vibrational entropy. With temperature increasing and oxygen partial pressure decreasing, the formation energies of oxygen vacancy (VO), zinc interstitial (Zni) and zinc anti-site (ZnO) are decreasing, while it increases for zinc vacancy (VZn), oxygen interstitial (Oi) and oxygen anti-site (OZn). They are more sensitive to temperature than oxygen partial pressure. There are two interesting phenomena. First, VO or VZn have the lowest formation energies for whole Fermi level at special environment condition (such as at T = 300K, about PO2 = 10-10atm or T = 1500K, about PO2 = 104atm) and intrinsic p-type doping of ZnO is possible by VZn at these special conditions. Second, VO as donors have lowest formation energy for all Fermi level at high temperature and low oxygen partial pressure (T = 1500K, PO2 = 10-10atm). According to our analysis, the VO could produce n-type doping in ZnO at these special conditions and change p-type ZnO to n-type ZnO at condition from low temperature and high oxygen partial pressure to high temperature and low oxygen partial pressure.

Anomalous contact angle hysteresis of a captive bubble: advancing contact line pinning.

PubMed

Hong, Siang-Jie; Chang, Feng-Ming; Chou, Tung-He; Chan, Seong Heng; Sheng, Yu-Jane; Tsao, Heng-Kwong

2011-06-07

Contact angle hysteresis of a sessile drop on a substrate consists of continuous invasion of liquid phase with the advancing angle (θ(a)) and contact line pinning of liquid phase retreat until the receding angle (θ(r)) is reached. Receding pinning is generally attributed to localized defects that are more wettable than the rest of the surface. However, the defect model cannot explain advancing pinning of liquid phase invasion driven by a deflating bubble and continuous retreat of liquid phase driven by the inflating bubble. A simple thermodynamic model based on adhesion hysteresis is proposed to explain anomalous contact angle hysteresis of a captive bubble quantitatively. The adhesion model involves two solid–liquid interfacial tensions (γ(sl) > γ(sl)′). Young’s equation with γ(sl) gives the advancing angle θ(a) while that with γ(sl)′ due to surface rearrangement yields the receding angle θ(r). Our analytical analysis indicates that contact line pinning represents frustration in surface free energy, and the equilibrium shape corresponds to a nondifferential minimum instead of a local minimum. On the basis of our thermodynamic model, Surface Evolver simulations are performed to reproduce both advancing and receding behavior associated with a captive bubble on the acrylic glass.

[Thermodynamics of the origin of life, evolution and aging].

PubMed

Gladyshev, G P

2014-01-01

Briefly discusses the history of the search of thermodynamic approach to explain the origin of life, evolution and aging of living beings. The origin of life is the result of requirement by the quasi-equilibrium hierarchical thermodynamics, in particular, the supramolecular thermodynamics. The evolution and aging of living beings is accompanied with changes of chemical and supramolecular compositions of living bodies, as well as with changes in the composition and structure of all hierarchies of the living world. The thermodynamic principle of substance stability predicts the existence of a single genetic code in our universe. The thermodynamic theory optimizes physiology and medicine and recommends antiaging diets and medicines. Hierarchical thermodynamics forms the design diversity of culture and art. The thermodynamic theory of origin of life, evolution and aging is the development of Clausius-Gibbs thermodynamics. Hierarchical thermodynamics is the mirror of Darwin-Wallace's-theory.

Molecular simulation of the thermodynamic, structural, and vapor-liquid equilibrium properties of neon

NASA Astrophysics Data System (ADS)

Vlasiuk, Maryna; Frascoli, Federico; Sadus, Richard J.

2016-09-01

The thermodynamic, structural, and vapor-liquid equilibrium properties of neon are comprehensively studied using ab initio, empirical, and semi-classical intermolecular potentials and classical Monte Carlo simulations. Path integral Monte Carlo simulations for isochoric heat capacity and structural properties are also reported for two empirical potentials and one ab initio potential. The isobaric and isochoric heat capacities, thermal expansion coefficient, thermal pressure coefficient, isothermal and adiabatic compressibilities, Joule-Thomson coefficient, and the speed of sound are reported and compared with experimental data for the entire range of liquid densities from the triple point to the critical point. Lustig's thermodynamic approach is formally extended for temperature-dependent intermolecular potentials. Quantum effects are incorporated using the Feynman-Hibbs quantum correction, which results in significant improvement in the accuracy of predicted thermodynamic properties. The new Feynman-Hibbs version of the Hellmann-Bich-Vogel potential predicts the isochoric heat capacity to an accuracy of 1.4% over the entire range of liquid densities. It also predicts other thermodynamic properties more accurately than alternative intermolecular potentials.

Damage of composite structures: Detection technique, dynamic response and residual strength

NASA Astrophysics Data System (ADS)

Lestari, Wahyu

2001-10-01

Reliable and accurate health monitoring techniques can prevent catastrophic failures of structures. Conventional damage detection methods are based on visual or localized experimental methods and very often require prior information concerning the vicinity of the damage or defect. The structure must also be readily accessible for inspections. The techniques are also labor intensive. In comparison to these methods, health-monitoring techniques that are based on the structural dynamic response offers unique information on failure of structures. However, systematic relations between the experimental data and the defect are not available and frequently, the number of vibration modes needed for an accurate identification of defects is much higher than the number of modes that can be readily identified in the experiment. These motivated us to develop an experimental data based detection method with systematic relationships between the experimentally identified information and the analytical or mathematical model representing the defective structures. The developed technique use changes in vibrational curvature modes and natural frequencies. To avoid misinterpretation of the identified information, we also need to understand the effects of defects on the structural dynamic response prior to developing health-monitoring techniques. In this thesis work we focus on two type of defects in composite structures, namely delamination and edge notch like defect. Effects of nonlinearity due to the presence of defect and due to the axial stretching are studied for beams with delamination. Once defects are detected in a structure, next concern is determining the effects of the defects on the strength of the structure and its residual stiffness under dynamic loading. In this thesis, energy release rate due to dynamic loading in a delaminated structure is studied, which will be a foundation toward determining the residual strength of the structure.

A miniaturized technique for assessing protein thermodynamics and function using fast determination of quantitative cysteine reactivity.

PubMed

Isom, Daniel G; Marguet, Philippe R; Oas, Terrence G; Hellinga, Homme W

2011-04-01

Protein thermodynamic stability is a fundamental physical characteristic that determines biological function. Furthermore, alteration of thermodynamic stability by macromolecular interactions or biochemical modifications is a powerful tool for assessing the relationship between protein structure, stability, and biological function. High-throughput approaches for quantifying protein stability are beginning to emerge that enable thermodynamic measurements on small amounts of material, in short periods of time, and using readily accessible instrumentation. Here we present such a method, fast quantitative cysteine reactivity, which exploits the linkage between protein stability, sidechain protection by protein structure, and structural dynamics to characterize the thermodynamic and kinetic properties of proteins. In this approach, the reaction of a protected cysteine and thiol-reactive fluorogenic indicator is monitored over a gradient of temperatures after a short incubation time. These labeling data can be used to determine the midpoint of thermal unfolding, measure the temperature dependence of protein stability, quantify ligand-binding affinity, and, under certain conditions, estimate folding rate constants. Here, we demonstrate the fQCR method by characterizing these thermodynamic and kinetic properties for variants of Staphylococcal nuclease and E. coli ribose-binding protein engineered to contain single, protected cysteines. These straightforward, information-rich experiments are likely to find applications in protein engineering and functional genomics. Copyright © 2010 Wiley-Liss, Inc.

Insight into the microscopic structure of an AdS black hole from a thermodynamical phase transition.

PubMed

Wei, Shao-Wen; Liu, Yu-Xiao

2015-09-11

Comparing with an ordinary thermodynamic system, we investigate the possible microscopic structure of a charged anti-de Sitter black hole completely from the thermodynamic viewpoint. The number density of the black hole molecules is introduced to measure the microscopic degrees of freedom of the black hole. We found that the number density suffers a sudden change accompanied by a latent heat when the black hole system crosses the small-large black hole coexistence curve, while when the system passes the critical point, it encounters a second-order phase transition with a vanishing latent heat due to the continuous change of the number density. Moreover, the thermodynamic scalar curvature suggests that there is a weak attractive interaction between two black hole molecules. These phenomena might cast new insight into the underlying microscopic structure of a charged anti-de Sitter black hole.

Stochastic thermodynamics across scales: Emergent inter-attractoral discrete Markov jump process and its underlying continuous diffusion

NASA Astrophysics Data System (ADS)

Santillán, Moisés; Qian, Hong

2013-01-01

We investigate the internal consistency of a recently developed mathematical thermodynamic structure across scales, between a continuous stochastic nonlinear dynamical system, i.e., a diffusion process with Langevin and Fokker-Planck equations, and its emergent discrete, inter-attractoral Markov jump process. We analyze how the system’s thermodynamic state functions, e.g. free energy F, entropy S, entropy production ep, free energy dissipation Ḟ, etc., are related when the continuous system is described with coarse-grained discrete variables. It is shown that the thermodynamics derived from the underlying, detailed continuous dynamics gives rise to exactly the free-energy representation of Gibbs and Helmholtz. That is, the system’s thermodynamic structure is the same as if one only takes a middle road and starts with the natural discrete description, with the corresponding transition rates empirically determined. By natural we mean in the thermodynamic limit of a large system, with an inherent separation of time scales between inter- and intra-attractoral dynamics. This result generalizes a fundamental idea from chemistry, and the theory of Kramers, by incorporating thermodynamics: while a mechanical description of a molecule is in terms of continuous bond lengths and angles, chemical reactions are phenomenologically described by a discrete representation, in terms of exponential rate laws and a stochastic thermodynamics.

An Integrated Approach to Thermodynamics in the Introductory Physics Course.

ERIC Educational Resources Information Center

Alonso, Marcelo; Finn, Edward J.

1995-01-01

Presents an approach to combine the empirical approach of classical thermodynamics with the structural approach of statistical mechanics. Topics covered include dynamical foundation of the first law; mechanical work, heat, radiation, and the first law; thermal equilibrium; thermal processes; thermodynamic probability; entropy; the second law;…

Ideal gas thermodynamic properties for the phenyl, phenoxy, and o-biphenyl radicals

NASA Technical Reports Server (NTRS)

Burcat, A.; Zeleznik, F. J.; Mcbride, B. J.

1985-01-01

Ideal gas thermodynamic properties of the phenyl and o-biphenyl radicals, their deuterated analogs and the phenoxy radical were calculated to 5000 K using estimated vibrational frequencies and structures. The ideal gas thermodynamic properties of benzene, biphenyl, their deuterated analogs and phenyl were also calculated.

Thermodynamic characterization of networks using graph polynomials

NASA Astrophysics Data System (ADS)

Ye, Cheng; Comin, César H.; Peron, Thomas K. DM.; Silva, Filipi N.; Rodrigues, Francisco A.; Costa, Luciano da F.; Torsello, Andrea; Hancock, Edwin R.

2015-09-01

In this paper, we present a method for characterizing the evolution of time-varying complex networks by adopting a thermodynamic representation of network structure computed from a polynomial (or algebraic) characterization of graph structure. Commencing from a representation of graph structure based on a characteristic polynomial computed from the normalized Laplacian matrix, we show how the polynomial is linked to the Boltzmann partition function of a network. This allows us to compute a number of thermodynamic quantities for the network, including the average energy and entropy. Assuming that the system does not change volume, we can also compute the temperature, defined as the rate of change of entropy with energy. All three thermodynamic variables can be approximated using low-order Taylor series that can be computed using the traces of powers of the Laplacian matrix, avoiding explicit computation of the normalized Laplacian spectrum. These polynomial approximations allow a smoothed representation of the evolution of networks to be constructed in the thermodynamic space spanned by entropy, energy, and temperature. We show how these thermodynamic variables can be computed in terms of simple network characteristics, e.g., the total number of nodes and node degree statistics for nodes connected by edges. We apply the resulting thermodynamic characterization to real-world time-varying networks representing complex systems in the financial and biological domains. The study demonstrates that the method provides an efficient tool for detecting abrupt changes and characterizing different stages in network evolution.

Thermodynamics of manganese oxides: Sodium, potassium, and calcium birnessite and cryptomelane

PubMed Central

Birkner, Nancy; Navrotsky, Alexandra

2017-01-01

Manganese oxides with layer and tunnel structures occur widely in nature and inspire technological applications. Having variable compositions, these structures often are found as small particles (nanophases). This study explores, using experimental thermochemistry, the role of composition, oxidation state, structure, and surface energy in the their thermodynamic stability. The measured surface energies of cryptomelane, sodium birnessite, potassium birnessite and calcium birnessite are all significantly lower than those of binary manganese oxides (Mn3O4, Mn2O3, and MnO2), consistent with added stabilization of the layer and tunnel structures at the nanoscale. Surface energies generally decrease with decreasing average manganese oxidation state. A stabilizing enthalpy contribution arises from increasing counter-cation content. The formation of cryptomelane from birnessite in contact with aqueous solution is favored by the removal of ions from the layered phase. At large surface area, surface-energy differences make cryptomelane formation thermodynamically less favorable than birnessite formation. In contrast, at small to moderate surface areas, bulk thermodynamics and the energetics of the aqueous phase drive cryptomelane formation from birnessite, perhaps aided by oxidation-state differences. Transformation among birnessite phases of increasing surface area favors compositions with lower surface energy. These quantitative thermodynamic findings explain and support qualitative observations of phase-transformation patterns gathered from natural and synthetic manganese oxides. PMID:28130549

Advancing viral RNA structure prediction: measuring the thermodynamics of pyrimidine-rich internal loops.

PubMed

Phan, Andy; Mailey, Katherine; Saeki, Jessica; Gu, Xiaobo; Schroeder, Susan J

2017-05-01

Accurate thermodynamic parameters improve RNA structure predictions and thus accelerate understanding of RNA function and the identification of RNA drug binding sites. Many viral RNA structures, such as internal ribosome entry sites, have internal loops and bulges that are potential drug target sites. Current models used to predict internal loops are biased toward small, symmetric purine loops, and thus poorly predict asymmetric, pyrimidine-rich loops with >6 nucleotides (nt) that occur frequently in viral RNA. This article presents new thermodynamic data for 40 pyrimidine loops, many of which can form UU or protonated CC base pairs. Uracil and protonated cytosine base pairs stabilize asymmetric internal loops. Accurate prediction rules are presented that account for all thermodynamic measurements of RNA asymmetric internal loops. New loop initiation terms for loops with >6 nt are presented that do not follow previous assumptions that increasing asymmetry destabilizes loops. Since the last 2004 update, 126 new loops with asymmetry or sizes greater than 2 × 2 have been measured. These new measurements significantly deepen and diversify the thermodynamic database for RNA. These results will help better predict internal loops that are larger, pyrimidine-rich, and occur within viral structures such as internal ribosome entry sites. © 2017 Phan et al.; Published by Cold Spring Harbor Laboratory Press for the RNA Society.

Effects of defects in composite structures

NASA Technical Reports Server (NTRS)

Sendeckyj, G. P.

1983-01-01

The effect of defects in composite structures is addressed. Defects in laminates such as wrinkles, foreign particles, scratches and breaks are discussed. Effects of plygap plywaviness and machining defects are also studied.

Signal Transduction in Histidine Kinases: Insights from New Structures

PubMed Central

Bhate, Manasi P.; Molnar, Kathleen S.; Goulian, Mark; DeGrado, William F.

2015-01-01

Histidine kinases (HKs) are major players in bacterial signaling. There has been an explosion of new HK crystal structures in the last five years. We globally analyze the structures of HKs to yield insights into the mechanisms by which signals are transmitted to and across protein structures in this family. We interpret known enzymological data in the context of new structural data to show how asymmetry across the dimer interface is a key feature of signal transduction in HKs, and discuss how different HK domains undergo asymmetric-to-symmetric transitions during signal transduction and catalysis. A thermodynamic framework for signaling that encompasses these various properties is presented and the consequences of weak thermodynamic coupling are discussed. The synthesis of observations from enzymology, structural biology, protein engineering and thermodynamics paves the way for a deeper molecular understanding of histidine kinase signal transduction. PMID:25982528

Structural evolution dynamics in fusion of sumanenes and corannulenes: defects formation and self-healing mechanism

NASA Astrophysics Data System (ADS)

Sorkin, Anastassia; Su, Haibin

2018-06-01

The fusion processes of structures consisting of various combinations between sumanene and corannulene, leading to the formation of graphene nanoribbons (GNRs) under heating are simulated by density-functional-based tight-binding molecular dynamics. Distinct stages are unraveled in the course of GNR formation. Firstly, the carbon fragments coalescence into highly strained framework. Secondly, structural reconstruction invokes breaking most strained bonds to form a GNR structure containing numerous defects. Lastly, defects are remedied by the delicate ‘edge-facilitated self-healing’ process through two synergized edge-related effects: elevated mobility of defects and promoted structure reconstructions owing to the remarkable dynamics associated with edges. Importantly, detailed dynamics in the course of forming GNRs with defects and grain boundaries simulated in this work is valuable to provide better understanding at the atomistic scale of defect formation as well as self-healing in the context of the sp2 carbon network. In particular, edges play important roles in not only generating Stone–Wales (SW), 5-8-5 types of defects, 8-5-5-8 and pentagon–heptagon grain boundaries. In addition, our simulations predict the existence of one novel defect, coined as the Inverse SW defect, which is to be confirmed in future experimental studies. This study of dynamic structural evolution reveals that edges are prone to intrinsic and extrinsic modifications such as atomic-scale defects, structural distortions and inhomogeneity.

Effect of Urea on the Thermodynamics of Hexadecyltrimethylammonium Bromide Micelle Formation in Aqueous Solutions

NASA Astrophysics Data System (ADS)

Velikov, A. A.

2018-02-01

The effect of urea on the thermodynamics of hexadecyltrimethylammonium bromide (CTAB) micelle formation in aqueous urea solutions was studied by isothermal titration microcalorimetry. The thermodynamic functions of Δ H, Δ G, and Δ S of CTAB micelle formation were calculated. The critical micelle concentrations (CMC) were determined. The addition of urea to the solution decreased the micelle formation entropy. This was attributed to the "lowering" of the structural temperature of the solution, which led to an increased number of hydrogen bonds and structure formation of water.

Application of Ultrasonic Phased Array Technology to the Detection of Defect in Composite Stiffened-structures

NASA Astrophysics Data System (ADS)

Zhou, Yuan-Qi; Zhan, Li-Hua

2016-05-01

Composite stiffened-structure consists of the skin and stringer has been widely used in aircraft fuselage and wings. The main purpose of the article is to detect the composite material reinforced structure accurately and explore the relationship between defect formation and structural elements or curing process. Based on ultrasonic phased array inspection technology, the regularity of defects in the manufacture of composite materials are obtained, the correlation model between actual defects and nondestructive testing are established. The article find that the forming quality of deltoid area in T-stiffened structure is obviously improved by pre-curing, the defects of hat-stiffened structure are affected by the mandrel. The results show that the ultrasonic phased array inspection technology can be an effectively way for the detection of composite stiffened-structures, which become an important means to control the defects of composite and improve the quality of the product.

Contact symmetries and Hamiltonian thermodynamics

DOE Office of Scientific and Technical Information (OSTI.GOV)

Bravetti, A., E-mail: bravetti@correo.nucleares.unam.mx; Lopez-Monsalvo, C.S., E-mail: cesar.slm@correo.nucleares.unam.mx; Nettel, F., E-mail: Francisco.Nettel@roma1.infn.it

It has been shown that contact geometry is the proper framework underlying classical thermodynamics and that thermodynamic fluctuations are captured by an additional metric structure related to Fisher’s Information Matrix. In this work we analyse several unaddressed aspects about the application of contact and metric geometry to thermodynamics. We consider here the Thermodynamic Phase Space and start by investigating the role of gauge transformations and Legendre symmetries for metric contact manifolds and their significance in thermodynamics. Then we present a novel mathematical characterization of first order phase transitions as equilibrium processes on the Thermodynamic Phase Space for which the Legendremore » symmetry is broken. Moreover, we use contact Hamiltonian dynamics to represent thermodynamic processes in a way that resembles the classical Hamiltonian formulation of conservative mechanics and we show that the relevant Hamiltonian coincides with the irreversible entropy production along thermodynamic processes. Therefore, we use such property to give a geometric definition of thermodynamically admissible fluctuations according to the Second Law of thermodynamics. Finally, we show that the length of a curve describing a thermodynamic process measures its entropy production.« less

Design principles for radiation-resistant solid solutions

NASA Astrophysics Data System (ADS)

Schuler, Thomas; Trinkle, Dallas R.; Bellon, Pascal; Averback, Robert

2017-05-01

We develop a multiscale approach to quantify the increase in the recombined fraction of point defects under irradiation resulting from dilute solute additions to a solid solution. This methodology provides design principles for radiation-resistant materials. Using an existing database of solute diffusivities, we identify Sb as one of the most efficient solutes for this purpose in a Cu matrix. We perform density-functional-theory calculations to obtain binding and migration energies of Sb atoms, vacancies, and self-interstitial atoms in various configurations. The computed data informs the self-consistent mean-field formalism to calculate transport coefficients, allowing us to make quantitative predictions of the recombined fraction of point defects as a function of temperature and irradiation rate using homogeneous rate equations. We identify two different mechanisms according to which solutes lead to an increase in the recombined fraction of point defects; at low temperature, solutes slow down vacancies (kinetic effect), while at high temperature, solutes stabilize vacancies in the solid solution (thermodynamic effect). Extension to other metallic matrices and solutes are discussed.

Huge critical current density and tailored superconducting anisotropy in SmFeAsO₀.₈F₀.₁₅ by low-density columnar-defect incorporation.

PubMed

Fang, L; Jia, Y; Mishra, V; Chaparro, C; Vlasko-Vlasov, V K; Koshelev, A E; Welp, U; Crabtree, G W; Zhu, S; Zhigadlo, N D; Katrych, S; Karpinski, J; Kwok, W K

2013-01-01

Iron-based superconductors could be useful for electricity distribution and superconducting magnet applications because of their relatively high critical current densities and upper critical fields. SmFeAsO₀.₈F₀.₁₅ is of particular interest as it has the highest transition temperature among these materials. Here we show that by introducing a low density of correlated nano-scale defects into this material by heavy-ion irradiation, we can increase its critical current density to up to 2 × 10⁷ A cm⁻² at 5 K--the highest ever reported for an iron-based superconductor--without reducing its critical temperature of 50 K. We also observe a notable reduction in the thermodynamic superconducting anisotropy, from 8 to 4 upon irradiation. We develop a model based on anisotropic electron scattering that predicts that the superconducting anisotropy can be tailored via correlated defects in semimetallic, fully gapped type II superconductors.

Anisotropic D3-D5 black holes with unquenched flavors

NASA Astrophysics Data System (ADS)

Penín, José Manuel; Ramallo, Alfonso V.; Zoakos, Dimitrios

2018-02-01

We construct a black hole geometry generated by the intersection of N c color D3- branes and N f flavor D5-branes along a 2+1 dimensional subspace. Working in the Veneziano limit in which N f is large and distributing homogeneously the D5-branes in the internal space, we calculate the solution of the equations of motion of supergravity plus sources which includes the backreaction of the flavor branes. The solution is analytic and dual to a 2+1 dimensional defect in a 3+1 dimensional gauge theory, with N f massless hypermultiplets living in the defect. The smeared background we obtain can be regarded as the holographic realization of a multilayered system. We study the thermodynamics of the resulting spatially anisotropic geometry and compute the first and second order transport coefficients for perturbations propagating along the defect. We find that, in our system, the dynamics of excitations within a layer can be described by a stack of effective D2-branes.

First-principles investigation on the composition of Ni-Si precipitates formed in irradiated stainless steels

NASA Astrophysics Data System (ADS)

Chen, Dongyue; Murakami, Kenta; Dohi, Kenji; Nishida, Kenji; Ohnuma, Toshiharu; Soneda, Naoki; Li, Zhengcao; Liu, Li; Sekimura, Naoto

2017-10-01

Recent atom probe tomography (APT) study has revealed the complicated nature of Ni-Si precipitates in irradiated stainless steels. Although Ni3Si γ‧ phase has been confirmed under transmission electron microscopy (TEM), the Ni/Si ratio of the precipitates detected by APT is smaller than its theoretical value 3. An interpretation of the APT results is provided in this work by considering the lattice defects in the Ni3Si γ‧ phase. Using first principles calculations, Si substitutions on Ni sites were found to be the most thermodynamically stable among all the single defects considered here. Although two such substitutional defects are repulsive to each other, the repulsion decreases quickly as their separation distance grows. By keeping a large enough distance between each other, multiple Si substitutions can appear at high densities in the γ‧ phase, which can be one important contributor to the small Ni/Si atom ratio in Ni-Si precipitates observed by APT.

Thermodynamics of protein folding using a modified Wako-Saitô-Muñoz-Eaton model.

PubMed

Tsai, Min-Yeh; Yuan, Jian-Min; Teranishi, Yoshiaki; Lin, Sheng Hsien

2012-09-01

Herein, we propose a modified version of the Wako-Saitô-Muñoz-Eaton (WSME) model. The proposed model introduces an empirical temperature parameter for the hypothetical structural units (i.e., foldons) in proteins to include site-dependent thermodynamic behavior. The thermodynamics for both our proposed model and the original WSME model were investigated. For a system with beta-hairpin topology, a mathematical treatment (contact-pair treatment) to facilitate the calculation of its partition function was developed. The results show that the proposed model provides better insight into the site-dependent thermodynamic behavior of the system, compared with the original WSME model. From this site-dependent point of view, the relationship between probe-dependent experimental results and model's thermodynamic predictions can be explained. The model allows for suggesting a general principle to identify foldon behavior. We also find that the backbone hydrogen bonds may play a role of structural constraints in modulating the cooperative system. Thus, our study may contribute to the understanding of the fundamental principles for the thermodynamics of protein folding.

Physical and mechanical metallurgy of zirconium alloys for nuclear applications: a multi-scale computational study

DOE Office of Scientific and Technical Information (OSTI.GOV)

Glazoff, Michael Vasily

2014-10-01

In the post-Fukushima world, the stability of materials under extreme conditions is an important issue for the safety of nuclear reactors. Because the nuclear industry is going to continue using advanced zirconium cladding materials in the foreseeable future, it become critical to gain fundamental understanding of the several interconnected problems. First, what are the thermodynamic and kinetic factors affecting the oxidation and hydrogen pick-up by these materials at normal, off-normal conditions, and in long-term storage? Secondly, what protective coatings (if any) could be used in order to gain extremely valuable time at off-normal conditions, e.g., when temperature exceeds the criticalmore » value of 2200°F? Thirdly, the kinetics of oxidation of such protective coating or braiding needs to be quantified. Lastly, even if some degree of success is achieved along this path, it is absolutely critical to have automated inspection algorithms allowing identifying defects of cladding as soon as possible. This work strives to explore these interconnected factors from the most advanced computational perspective, utilizing such modern techniques as first-principles atomistic simulations, computational thermodynamics of materials, diffusion modeling, and the morphological algorithms of image processing for defect identification. Consequently, it consists of the four parts dealing with these four problem areas preceded by the introduction and formulation of the studied problems. In the 1st part an effort was made to employ computational thermodynamics and ab initio calculations to shed light upon the different stages of oxidation of ziraloys (2 and 4), the role of microstructure optimization in increasing their thermal stability, and the process of hydrogen pick-up, both in normal working conditions and in long-term storage. The 2nd part deals with the need to understand the influence and respective roles of the two different plasticity mechanisms in Zr nuclear alloys: twinning (at low T) and crystallographic slip (higher T’s). For that goal, a description of the advanced plasticity model is outlined featuring the non-associated flow rule in hcp materials including Zr. The 3rd part describes the kinetic theory of oxidation of the several materials considered to be perspective coating materials for Zr alloys: SiC and ZrSiO 4. In the 4th part novel and advanced projectional algorithms for defect identification in zircaloy coatings are described. In so doing, the author capitalized on some 12 years of his applied industrial research in this area. Our conclusions and recommendations are presented in the 5th part of this work, along with the list of used literature and the scripts for atomistic, thermodynamic, kinetic, and morphological computations.« less

Anisotropy and temperature dependence of structural, thermodynamic, and elastic properties of crystalline cellulose Iβ: a first-principles investigation

Treesearch

ShunLi Shang; Louis G. Hector Jr.; Paul Saxe; Zi-Kui Liu; Robert J. Moon; Pablo D. Zavattieri

2014-01-01

Anisotropy and temperature dependence of structural, thermodynamic and elastic properties of crystalline cellulose Iβ were computed with first-principles density functional theory (DFT) and a semi-empirical correction for van der Waals interactions. Specifically, we report the computed temperature variation (up to 500...

Visualization and automatic detection of defect distribution in GaN atomic structure from sampling Moiré phase.

PubMed

Wang, Qinghua; Ri, Shien; Tsuda, Hiroshi; Kodera, Masako; Suguro, Kyoichi; Miyashita, Naoto

2017-09-19

Quantitative detection of defects in atomic structures is of great significance to evaluating product quality and exploring quality improvement process. In this study, a Fourier transform filtered sampling Moire technique was proposed to visualize and detect defects in atomic arrays in a large field of view. Defect distributions, defect numbers and defect densities could be visually and quantitatively determined from a single atomic structure image at low cost. The effectiveness of the proposed technique was verified from numerical simulations. As an application, the dislocation distributions in a GaN/AlGaN atomic structure in two directions were magnified and displayed in Moire phase maps, and defect locations and densities were detected automatically. The proposed technique is able to provide valuable references to material scientists and engineers by checking the effect of various treatments for defect reduction. © 2017 IOP Publishing Ltd.

Photoelectrochemical Properties and Behavior of α-SnWO4 Photoanodes Synthesized by Hydrothermal Conversion of WO3 Films.

PubMed

Zhu, Zhehao; Sarker, Pranab; Zhao, Chenqi; Zhou, Lite; Grimm, Ronald L; Huda, Muhammad N; Rao, Pratap M

2017-01-18

Metal oxides with moderate band gaps are desired for efficient production of hydrogen from sunlight and water via photoelectrochemical (PEC) water splitting. Here, we report an α-SnWO 4 photoanode synthesized by hydrothermal conversion of WO 3 films that achieves photon to current conversion at wavelengths up to 700 nm (1.78 eV). This photoanode is promising for overall PEC water-splitting because the flat-band potential and voltage of photocurrent onset are more negative than the potential of hydrogen evolution. Furthermore, the photoanode utilizes a large portion of the solar spectrum. However, the photocurrent density reaches only a small fraction of that which is theoretically possible. Density functional theory based thermodynamic and electronic structure calculations were performed to elucidate the nature and impact of defects in α-SnWO 4 prepared by this synthetic route, from which hole localization at Sn-at-W antisite defects was determined to be a likely cause for the poor photocurrent. Measurements further showed that the photocurrent decreases over time due to surface oxidation, which was suppressed by improving the kinetics of hole transfer at the semiconductor/electrolyte interface. Alternative synthetic methods and the addition of protective coatings and/or oxygen evolution catalysts are suggested to improve the PEC performance and stability of this promising α-SnWO 4 material.

Computer Simulations of Intrinsically Disordered Proteins

NASA Astrophysics Data System (ADS)

Chong, Song-Ho; Chatterjee, Prathit; Ham, Sihyun

2017-05-01

The investigation of intrinsically disordered proteins (IDPs) is a new frontier in structural and molecular biology that requires a new paradigm to connect structural disorder to function. Molecular dynamics simulations and statistical thermodynamics potentially offer ideal tools for atomic-level characterizations and thermodynamic descriptions of this fascinating class of proteins that will complement experimental studies. However, IDPs display sensitivity to inaccuracies in the underlying molecular mechanics force fields. Thus, achieving an accurate structural characterization of IDPs via simulations is a challenge. It is also daunting to perform a configuration-space integration over heterogeneous structural ensembles sampled by IDPs to extract, in particular, protein configurational entropy. In this review, we summarize recent efforts devoted to the development of force fields and the critical evaluations of their performance when applied to IDPs. We also survey recent advances in computational methods for protein configurational entropy that aim to provide a thermodynamic link between structural disorder and protein activity.

Perspective: Structural fluctuation of protein and Anfinsen's thermodynamic hypothesis

NASA Astrophysics Data System (ADS)

Hirata, Fumio; Sugita, Masatake; Yoshida, Masasuke; Akasaka, Kazuyuki

2018-01-01

The thermodynamics hypothesis, casually referred to as "Anfinsen's dogma," is described theoretically in terms of a concept of the structural fluctuation of protein or the first moment (average structure) and the second moment (variance and covariance) of the structural distribution. The new theoretical concept views the unfolding and refolding processes of protein as a shift of the structural distribution induced by a thermodynamic perturbation, with the variance-covariance matrix varying. Based on the theoretical concept, a method to characterize the mechanism of folding (or unfolding) is proposed. The transition state, if any, between two stable states is interpreted as a gap in the distribution, which is created due to an extensive reorganization of hydrogen bonds among back-bone atoms of protein and with water molecules in the course of conformational change. Further perspective to applying the theory to the computer-aided drug design, and to the material science, is briefly discussed.

Thermodynamics of Accelerating Black Holes.

PubMed

Appels, Michael; Gregory, Ruth; Kubizňák, David

2016-09-23

We address a long-standing problem of describing the thermodynamics of an accelerating black hole. We derive a standard first law of black hole thermodynamics, with the usual identification of entropy proportional to the area of the event horizon-even though the event horizon contains a conical singularity. This result not only extends the applicability of black hole thermodynamics to realms previously not anticipated, it also opens a possibility for studying novel properties of an important class of exact radiative solutions of Einstein equations describing accelerated objects. We discuss the thermodynamic volume, stability, and phase structure of these black holes.

Thermodynamics of third-order Lovelock-AdS black holes in the presence of Born-Infeld type nonlinear electrodynamics

NASA Astrophysics Data System (ADS)

Hendi, S. H.; Dehghani, A.

2015-03-01

In this paper, we obtain topological black hole solutions of third-order Lovelock gravity coupled with two classes of Born-Infeld-type nonlinear electrodynamics with anti-de Sitter asymptotic structure. We investigate geometric and thermodynamics properties of the solutions and obtain conserved quantities of the black holes. We examine the first law of thermodynamics and find that the conserved and thermodynamic quantities of the black hole solutions satisfy the first law of thermodynamics. Finally, we calculate the heat capacity and determinant of the Hessian matrix to evaluate thermal stability in both canonical and grand canonical ensembles. Moreover, we consider the extended phase space thermodynamics to obtain a generalized first law of thermodynamics as well as the extended Smarr formula.

Dynamical stability of plutonium alloys

NASA Astrophysics Data System (ADS)

Torrent, Marc; Dorado, Boris; Bieder, Jordan

Plutonium sits at the center of the actinide series and marks the transition between localization and delocalization of the 5 f electrons. From a metallurgical standpoint, the monoclinic α phase (stable at low T) is brittle, not suitable for engineering applications, as opposed to the ductile fcc δ phase (stable at 580K). The δ - α transition can be avoided by alloying δ-Pu with ''deltagen'' elements. There is a wide unexplored area for Pu when it comes to lattice dynamics. Due to the changes in the composition, the dynamical stability of is constantly challenged. Displ. cascades are created in the material, which in turn produce numerous of point defects. Therefore, the accumulation of defects preclude a thermodynamic equilibrium. Given the importance for engineering applications, it is crucial that we understand the mechanisms that lead to stabilization with respect to the alloy composition. We use first-principles calculations to provide evidence of the effect of defects/impurities (C, O, Al, Fe, Ni, Ga, Ce, U, Am) on the dynamical stability of δ-Pu. We show that this phase is dynamically unstable at low T and that it depends on the 5 f orbital occupancies. We investigate how defects affect the stability by comparing the phonon DoS.

Thermodynamics of Alloys: Studies of Nickel-Gallium, Nickel-Germanium and Nickel-Rhodium Alloys.

DTIC Science & Technology

NICKEL ALLOYS, *GALLIUM ALLOYS, *GERMANIUM ALLOYS, * RHODIUM ALLOYS, *PHASE STUDIES, THERMODYNAMICS, INTERMETALLIC COMPOUNDS, FREE ENERGY, ENTROPY, HEAT OF FORMATION, CRYSTAL STRUCTURE, UNITED KINGDOM.

Solid-solution thermodynamics in Al-Li alloys

NASA Astrophysics Data System (ADS)

Alekseev, A. A.; Lukina, E. A.

2016-05-01

The relative equilibrium concentrations of lithium atoms distributed over different electron-structural states has been estimated. The possibility of the existence of various nonequilibrium electron-structural states of Li atoms in the solid solution in Al has been substantiated thermodynamically. Upon the decomposition of the supersaturated solid solution, the supersaturation on three electron-structural states of Li atoms that arises upon the quenching of the alloy can lead to the formation of lithium-containing phases in which the lithium atoms enter in one electron-structural state.

Effects of physical properties on thermo-fluids cavitating flows

NASA Astrophysics Data System (ADS)

Chen, T. R.; Wang, G. Y.; Huang, B.; Li, D. Q.; Ma, X. J.; Li, X. L.

2015-12-01

The aims of this paper are to study the thermo-fluid cavitating flows and to evaluate the effects of physical properties on cavitation behaviours. The Favre-averaged Navier-Stokes equations with the energy equation are applied to numerically investigate the liquid nitrogen cavitating flows around a NASA hydrofoil. Meanwhile, the thermodynamic parameter Σ is used to assess the thermodynamic effects on cavitating flows. The results indicate that the thermodynamic effects on the thermo-fluid cavitating flows significantly affect the cavitation behaviours, including pressure and temperature distribution, the variation of physical properties, and cavity structures. The thermodynamic effects can be evaluated by physical properties under the same free-stream conditions. The global sensitivity analysis of liquid nitrogen suggests that ρv, Cl and L significantly influence temperature drop and cavity structure in the existing numerical framework, while pv plays the dominant role when these properties vary with temperature. The liquid viscosity μl slightly affects the flow structure via changing the Reynolds number Re equivalently, however, it hardly affects the temperature distribution.

Heat of supersaturation-limited amyloid burst directly monitored by isothermal titration calorimetry.

PubMed

Ikenoue, Tatsuya; Lee, Young-Ho; Kardos, József; Yagi, Hisashi; Ikegami, Takahisa; Naiki, Hironobu; Goto, Yuji

2014-05-06

Amyloid fibrils form in supersaturated solutions via a nucleation and growth mechanism. Although the structural features of amyloid fibrils have become increasingly clearer, knowledge on the thermodynamics of fibrillation is limited. Furthermore, protein aggregation is not a target of calorimetry, one of the most powerful approaches used to study proteins. Here, with β2-microglobulin, a protein responsible for dialysis-related amyloidosis, we show direct heat measurements of the formation of amyloid fibrils using isothermal titration calorimetry (ITC). The spontaneous fibrillation after a lag phase was accompanied by exothermic heat. The thermodynamic parameters of fibrillation obtained under various protein concentrations and temperatures were consistent with the main-chain dominated structural model of fibrils, in which overall packing was less than that of the native structures. We also characterized the thermodynamics of amorphous aggregation, enabling the comparison of protein folding, amyloid fibrillation, and amorphous aggregation. These results indicate that ITC will become a promising approach for clarifying comprehensively the thermodynamics of protein folding and misfolding.

Polarization Coupling in Ferroelectric Multilayers as a Function of Interface Charge Concentration

NASA Astrophysics Data System (ADS)

Okatan, Mahmut; Mantese, Joseph; Alpay, Pamir

2009-03-01

Intriguing properties of multilayered and graded ferroelectrics follow from the electrostatic and electromechanical interactions. The strength of the interlayer coupling depends on the concentration of interfacial defects with short-range local electrostatic fields. Defects may locally relax polarization differences and thus reduce the commensurate bound charge concentration at the interlayer interfaces. In this talk, we develop a theoretical analysis based on non-linear thermodynamics coupled with basic electrostatic relations to understand the role of charge compensation at the interlayer interfaces. The results show multilayered ferroelectrics with systematic variations in the composition may display a colossal dielectric response depending upon the interlayer electrostatic interactions. It is expected that other properties such as the pyroelectric and piezoelectric response will yield concomitant increases through the dielectric permittivity.

A Delicate Interplay of Structure, Dynamics, and Thermodynamics for Function: A High Pressure NMR Study of Outer Surface Protein A

PubMed Central

Kitahara, Ryo; Simorellis, Alana K.; Hata, Kazumi; Maeno, Akihiro; Yokoyama, Shigeyuki; Koide, Shohei; Akasaka, Kazuyuki

2012-01-01

Outer surface protein A (OspA) is a crucial protein in the infection of Borrelia burgdorferi causing Lyme disease. We studied conformational fluctuations of OspA with high-pressure 15N/1H two-dimensional NMR along with high-pressure fluorescence spectroscopy. We found evidence within folded, native OspA for rapid local fluctuations of the polypeptide backbone in the nonglobular single layer β-sheet connecting the N- and C-terminal domains with τ << ms, which may give the two domains certain independence in mobility and thermodynamic stability. Furthermore, we found that folded, native OspA is in equilibrium (τ >> ms) with a minor conformer I, which is almost fully disordered and hydrated for the entire C-terminal part of the polypeptide chain from β8 to the C-terminus. Conformer I is characterized with ΔG0 = 32 ± 9 kJ/mol and ΔV0 = −140 ± 40 mL/mol, populating only ∼0.001% at 40°C at 0.1 MPa, pH 5.9. Because in the folded conformer the receptor binding epitope of OspA is buried in the C-terminal domain, its transition into conformer I under in vivo conditions may be critical for the infection of B. burgdorferi. The formation and stability of the peculiar conformer I are apparently supported by a large packing defect or cavity located in the C-terminal domain. PMID:22385863

Allosteric modulation balances thermodynamic stability and restores function of ΔF508 CFTR

PubMed Central

Aleksandrov, Andrei A.; Kota, Pradeep; Cui, Liying; Jensen, Tim; Alekseev, Alexey E.; Reyes, Santiago; He, Lihua; Gentzsch, Martina; Aleksandrov, Luba A.; Dokholyan, Nikolay V.; Riordan, John R.

2013-01-01

Most cystic fibrosis is caused by a deletion of a single residue (F508) in CFTR that disrupts the folding and biosynthetic maturation of the ion channel protein. Progress towards understanding the underlying mechanisms and overcoming the defect remain incomplete. Here we show that the thermal instability of human ΔF508 CFTR channel activity evident in both cell-attached membrane patches and planar phospholipid bilayers is not observed in corresponding mutant CFTRs of several non-mammalian species. These more stable orthologs are distinguished from their mammalian counterparts by the substitution of proline residues at several key dynamic locations in the first nucleotide domain (NBD1), including the structurally diverse region (SDR), the gamma phosphate switch loop and the Regulatory Insertion (RI). Molecular Dynamic analyses revealed that addition of the prolines could reduce flexibility at these locations and increase the temperatures of unfolding transitions of ΔF508 NBD1 to that of the wild-type. Introduction of these prolines experimentally into full-length human ΔF508 CFTR together with the already recognized I539T suppressor mutation, also in the SDR, restored channel function and thermodynamic stability as well as its trafficking to and lifetime at the cell surface. Thus, while cellular manipulations that circumvent its culling by quality control systems leave ΔF508 CFTR dysfunctional at physiological temperature, restoration of the delicate balance between the dynamic protein’s inherent stability and channel activity returns a near-normal state. PMID:22406676

First principles calculation of material properties of group IV elements and III-V compounds

NASA Astrophysics Data System (ADS)

Malone, Brad Dean

This thesis presents first principles calculations on the properties of group IV elements and group III-V compounds. It includes investigations into what structure a material is likely to form in, and given that structure, what are its electronic, optical, and lattice dynamical properties as well as what are the properties of defects that might be introduced into the sample. The thesis is divided as follows: • Chapter 1 contains some of the conceptual foundations used in the present work. These involve the major approximations which allow us to approach the problem of systems with huge numbers of interacting electrons and atomic cores. • Then, in Chapter 2, we discuss one of the major limitations to the DFT formalism introduced in Chapter 1, namely its inability to predict the quasiparticle spectra of materials and in particular the band gap of a semiconductor. We introduce a Green's function approach to the electron self-energy Sigma known as the GW approximation and use it to compute the quasiparticle band structures of a number of group IV and III-V semiconductors. • In Chapter 3 we present a first-principles study of a number of high-pressure metastable phases of Si with tetrahedral bonding. The phases studied include all experimentally determined phases that result from decompression from the metallic beta-Sn phase, specifically the BC8 (Si-III), hexagonal diamond (Si-IV), and R8 (Si-XII). In addition to these, we also study the hypothetical ST12 structure found upon decompression from beta-Sn in germanium. • Our attention is then turned to the first principles calculations of optical properties in Chapter 4. The Bethe-Salpeter equation is then solved to obtain the optical spectrum of this material including electron-hole interactions. The calculated optical spectrum is compared with experimental data for other forms of silicon commonly used in photovoltaic devices, namely the cubic, polycrystalline, and amorphous forms. • In Chapter 5 we present first principles calculations of the quasiparticle and optical excitation spectra of recently predicted silicon and germanium polytypes in the body-centered-tetragonal (bct) structure. The quasiparticle spectra calculated within the GW approximation predict that both silicon and germanium in the bct structure are small band gap materials. The optical spectra are then evaluated by solving the Bethe-Salpeter equation taking into account. • We examine the low-pressure phases of Ge in Chapter 6 by performing first principles calculations of the electronic structure and lattice dynamics of the R8, BC8, ST12, and hexagonal diamond structures of Ge. To aid future experimental investigation, we include predictions of the Raman-active frequencies of these phases as well as present the full phonon dispersion throughout the zone. • In Chapter 7 we demonstrate how first principles calculations can be used to predict new structures. In a study aimed at finding new useful forms of silicon, we use an ab initio random structure searching (AIRSS) method to identify a new phase of silicon in the Ibamstructure. The Ibam phase is found to be semimetallic within density functional theory with a small band overlap, and it is expected that quasiparticle corrections using the GW approximation would yield a semiconducting state with a small band gap. • We present a first-principles study of boron and phosphorus substitutional defects in Si-XII in Chapter 8. Recent result from nanoindentation experiments reveal that the Si-XII phase is semiconducting and has the interesting property that it can be doped n- and p-type at room temperature without an annealing step. Using the hybrid functional of Heyd, Scuseria, and Ernzerhof (HSE), we examine the formation energies of the B and P defects at the two distinct atomic sites in Si-XII to find on which site the substitutional defects are more easily accommodated. We also estimate the thermodynamic transition levels of each defect in its relevant charge states. (Abstract shortened by UMI.).

First-principles study on the phase transitions, crystal stabilities and thermodynamic properties of TiN under high pressure

NASA Astrophysics Data System (ADS)

Sun, Xinjun; Liu, Changdong; Guo, Yongliang; Sun, Deyan; Ke, Xuezhi

2018-03-01

The structural and thermodynamic properties of titanium nitride (TiN) have been investigated by merging first-principles calculations and particle-swarm algorithm. The three phases are identified for TiN, including the B1, the P63 / mmc, and the B2 phases. A new phase of anti-TiP structure with the space group P63 / mmc has been predicted. The calculated phase transition from the B1 to the P63 / mmc occurs at 270 GPa. The vibrational, elastic, and thermodynamic properties for the three phases have been calculated and discussed.

Solitons in Crystalline Processes; Statistical thermodynamics of structural phase transitions and mesoscopic disorder

NASA Astrophysics Data System (ADS)

Fujimoto, Minoru

2017-11-01

Solitons in Crystalline Processes is an introduction to the statistical thermodynamics of phase transitions in crystallized solids. This book is written as an introductory treatise with respect to the soliton concept, from structural transitions where the crystal symmetry changes, to magnets and superconductors, describing the role of nonlinear excitations in detail.

Theoretical study of isostructural compounds MTe2 (M = Ni, Pd and Pt) on structure and thermodynamic properties under high pressures

NASA Astrophysics Data System (ADS)

Lei, Jin-Qiao; Liu, Ke; Huang, Sha; Mao, Xiao-Chun; Hou, Bao-Sen; Tan, Jiao; Zhou, Xiao-Lin

2017-11-01

The mechanical, electronic and thermodynamic properties of MTe2 (M = Ni, Pd and Pt) under high pressure were investigated via the first-principles calculations. According to our calculations of these trigonal crystals (space group of P3M1, No: 164), we found that all of them are fulfilled by the mechanical stability criteria under 31 GPa (for NiTe2), 37 GPa (for PdTe2) and 73 GPa (for PtTe2). The study on their structures revealed the elastic anisotropy of these isostructural compounds. Electronic structure calculations show that MTe2 are semi-metal. On the basis of the quasi-harmonic Debye model, we also researches their thermodynamic properties.

Xenon Defects in Uranium Dioxide From First Principles and Interatomic Potentials

NASA Astrophysics Data System (ADS)

Thompson, Alexander

In this thesis, we examine the defect energetics and migration energies of xenon atoms in uranium dioxide (UO2) from first principles and interatomic potentials. We also parameterize new, accurate interatomic potentials for xenon and uranium dioxide. To achieve accurate energetics and provide a foundation for subsequent calculations, we address difficulties in finding consistent energetics within Hubbard U corrected density functional theory (DFT+U). We propose a method of slowly ramping the U parameter in order to guide the calculation into low energy orbital occupations. We find that this method is successful for a variety of materials. We then examine the defect energetics of several noble gas atoms in UO2 for several different defect sites. We show that the energy to incorporate large noble gas atoms into interstitial sites is so large that it is energetically favorable for a Schottky defect cluster to be created to relieve the strain. We find that, thermodynamically, xenon will rarely ever be in the interstitial site of UO2. To study larger defects associated with the migration of xenon in UO 2, we turn to interatomic potentials. We benchmark several previously published potentials against DFT+U defect energetics and migration barriers. Using a combination of molecular dynamics and nudged elastic band calculations, we find a new, low energy migration pathway for xenon in UO2. We create a new potential for xenon that yields accurate defect energetics. We fit this new potential with a method we call Iterative Potential Refinement that parameterizes potentials to first principles data via a genetic algorithm. The potential finds accurate energetics for defects with relatively low amounts of strain (xenon in defect clusters). It is important to find accurate energetics for these sorts of low-strain defects because they essentially represent small xenon bubbles. Finally, we parameterize a new UO2 potential that simultaneously yields accurate vibrational properties and defect energetics, important properties for UO2 because of the high temperature and defective reactor environment.. Previously published potentials could only yield accurate defect energetics or accurate phonons, but never both.

The thermodynamic scale of inorganic crystalline metastability

PubMed Central

Sun, Wenhao; Dacek, Stephen T.; Ong, Shyue Ping; Hautier, Geoffroy; Jain, Anubhav; Richards, William D.; Gamst, Anthony C.; Persson, Kristin A.; Ceder, Gerbrand

2016-01-01

The space of metastable materials offers promising new design opportunities for next-generation technological materials, such as complex oxides, semiconductors, pharmaceuticals, steels, and beyond. Although metastable phases are ubiquitous in both nature and technology, only a heuristic understanding of their underlying thermodynamics exists. We report a large-scale data-mining study of the Materials Project, a high-throughput database of density functional theory–calculated energetics of Inorganic Crystal Structure Database structures, to explicitly quantify the thermodynamic scale of metastability for 29,902 observed inorganic crystalline phases. We reveal the influence of chemistry and composition on the accessible thermodynamic range of crystalline metastability for polymorphic and phase-separating compounds, yielding new physical insights that can guide the design of novel metastable materials. We further assert that not all low-energy metastable compounds can necessarily be synthesized, and propose a principle of ‘remnant metastability’—that observable metastable crystalline phases are generally remnants of thermodynamic conditions where they were once the lowest free-energy phase. PMID:28138514

Tight-binding calculation studies of vacancy and adatom defects in graphene

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zhang, Wei; Lu, Wen-Cai; Zhang, Hong-Xing

2016-02-19

Computational studies of complex defects in graphene usually need to deal with a larger number of atoms than the current first-principles methods can handle. We show a recently developed three-center tight-binding potential for carbon is very efficient for large scale atomistic simulations and can accurately describe the structures and energies of various defects in graphene. Using the three-center tight-binding potential, we have systematically studied the stable structures and formation energies of vacancy and embedded-atom defects of various sizes up to 4 vacancies and 4 embedded atoms in graphene. In conclusion, our calculations reveal low-energy defect structures and provide a moremore » comprehensive understanding of the structures and stability of defects in graphene.« less

Box 6: Nanoscale Defects

NASA Astrophysics Data System (ADS)

Alves, Eduardo; Breese, Mark

Defects affect virtually all properties of crystalline materials, and their role is magnified in nanoscale structures. In this box we describe the different type of defects with particular emphasis on point and linear defects. Above zero Kelvin all real materials have a defect population within their structure, which affects either their crystalline, electronic or optical properties. It is common to attribute a negative connotation to the presence of defects. However, a perfect silicon crystal or any other defect-free semiconductor would have a limited functionality and might even be useless.

Thermodynamic stability of boron: the role of defects and zero point motion.

PubMed

van Setten, Michiel J; Uijttewaal, Matthé A; de Wijs, Gilles A; de Groot, Robert A

2007-03-07

Its low weight, high melting point, and large degree of hardness make elemental boron a technologically interesting material. The large number of allotropes, mostly containing over a hundred atoms in the unit cell, and their difficult characterization challenge both experimentalists and theoreticians. Even the ground state of this element is still under discussion. For over 30 years, scientists have attempted to determine the relative stability of alpha- and beta-rhombohedral boron. We use density functional calculations in the generalized gradient approximation to study a broad range of possible beta-rhombohedral structures containing interstitial atoms and partially occupied sites within a 105 atoms framework. The two most stable structures are practically degenerate in energy and semiconducting. One contains the experimental 320 atoms in the hexagonal unit cell, and the other contains 106 atoms in the triclinic unit cell. When populated with the experimental 320 electrons, the 106 atom structure exhibits a band gap of 1.4 eV and an in-gap hole trap at 0.35 eV above the valence band, consistent with known experiments. The total energy of these two structures is 23 meV/B lower than the original 105 atom framework, but it is still 1 meV/B above the alpha phase. Adding zero point energies finally makes the beta phase the ground state of elemental boron by 3 meV/B. At finite temperatures, the difference becomes even larger.

Thermodynamics and kinetics of RNA tertiary structure formation in the junctionless hairpin ribozyme.

PubMed

White, Neil A; Hoogstraten, Charles G

2017-09-01

The hairpin ribozyme consists of two RNA internal loops that interact to form the catalytically active structure. This docking transition is a rare example of intermolecular formation of RNA tertiary structure without coupling to helix annealing. We have used temperature-dependent surface plasmon resonance (SPR) to characterize the thermodynamics and kinetics of RNA tertiary structure formation for the junctionless form of the ribozyme, in which loops A and B reside on separate molecules. We find docking to be strongly enthalpy-driven and to be accompanied by substantial activation barriers for association and dissociation, consistent with the structural reorganization of both internal loops upon complex formation. Comparisons with the parallel analysis of a ribozyme variant carrying a 2'-O-methyl modification at the self-cleavage site and with published data in other systems reveal a surprising diversity of thermodynamic signatures, emphasizing the delicate balance of contributions to the free energy of formation of RNA tertiary structure. Copyright © 2017 Elsevier B.V. All rights reserved.

Effect of point defects on the electronic density states of SnC nanosheets: First-principles calculations

NASA Astrophysics Data System (ADS)

Majidi, Soleyman; Achour, Amine; Rai, D. P.; Nayebi, Payman; Solaymani, Shahram; Beryani Nezafat, Negin; Elahi, Seyed Mohammad

In this work, we investigated the electronic and structural properties of various defects including single Sn and C vacancies, double vacancy of the Sn and C atoms, anti-sites, position exchange and the Stone-Wales (SW) defects in SnC nanosheets by using density-functional theory (DFT). We found that various vacancy defects in the SnC monolayer can change the electronic and structural properties. Our results show that the SnC is an indirect band gap compound, with the band gap of 2.10 eV. The system turns into metal for both structure of the single Sn and C vacancies. However, for the double vacancy contained Sn and C atoms, the structure remains semiconductor with the direct band gap of 0.37 eV at the G point. We also found that for anti-site defects, the structure remains semiconductor and for the exchange defect, the structure becomes indirect semiconductor with the K-G point and the band gap of 0.74 eV. Finally, the structure of SW defect remains semiconductor with the direct band gap at K point with band gap of 0.54 eV.

Analysis of Helium Segregation on Surfaces of Plasma-Exposed Tungsten

NASA Astrophysics Data System (ADS)

Maroudas, Dimitrios; Hu, Lin; Hammond, Karl; Wirth, Brian

2015-11-01

We report a systematic theoretical and atomic-scale computational study of implanted helium segregation on surfaces of tungsten, which is considered as a plasma facing component in nuclear fusion reactors. We employ a hierarchy of atomic-scale simulations, including molecular statics to understand the origin of helium surface segregation, targeted molecular-dynamics (MD) simulations of near-surface cluster reactions, and large-scale MD simulations of implanted helium evolution in plasma-exposed tungsten. We find that small, mobile helium clusters (of 1-7 He atoms) in the near-surface region are attracted to the surface due to an elastic interaction force. This thermodynamic driving force induces drift fluxes of these mobile clusters toward the surface, facilitating helium segregation. Moreover, the clusters' drift toward the surface enables cluster reactions, most importantly trap mutation, at rates much higher than in the bulk material. This cluster dynamics has significant effects on the surface morphology, near-surface defect structures, and the amount of helium retained in the material upon plasma exposure.

Unravelling the origin of the giant Zn deficiency in wurtzite type ZnO nanoparticles

PubMed Central

Renaud, Adèle; Cario, Laurent; Rocquelfelte, Xavier; Deniard, Philippe; Gautron, Eric; Faulques, Eric; Das, Tilak; Cheviré, François; Tessier, Franck; Jobic, Stéphane

2015-01-01

Owing to its high technological importance for optoelectronics, zinc oxide received much attention. In particular, the role of defects on its physical properties has been extensively studied as well as their thermodynamical stability. In particular, a large concentration of Zn vacancies in ZnO bulk materials is so far considered highly unstable. Here we report that the thermal decomposition of zinc peroxide produces wurtzite-type ZnO nanoparticles with an extraordinary large amount of zinc vacancies (>15%). These Zn vacancies segregate at the surface of the nanoparticles, as confirmed by ab initio calculations, to form a pseudo core-shell structure made of a dense ZnO sphere coated by a Zn free oxo-hydroxide mono layer. In others terms, oxygen terminated surfaces are privileged over zinc-terminated surfaces for passivation reasons what accounts for the Zn off-stoichiometry observed in ultra-fine powdered samples. Such Zn-deficient Zn1-xO nanoparticles exhibit an unprecedented photoluminescence signature suggesting that the core-shell-like edifice drastically influences the electronic structure of ZnO. This nanostructuration could be at the origin of the recent stabilisation of p-type charge carriers in nitrogen-doped ZnO nanoparticles. PMID:26333510

Effects of sudden density changes in disordered superconductors and semiconductors

NASA Astrophysics Data System (ADS)

Assi, Hiba; Chaturvedi, Harshwardhan; Pleimling, Michel; Täuber, Uwe

Vortices in type-II superconductors in the presence of extended, linear defects display the strongly pinned Bose glass phase at low temperatures. This disorder-dominated thermodynamic state is characterized by suppressed lateral flux line fluctuations and very slow structural relaxation kinetics: The vortices migrate between different columnar pinning centers to minimize the mutual repulsive interactions and eventually optimize the system's pinning configuration. To monitor the flux lines' late-time structural relaxations, we employ a mapping between an effectively two-dimensional Bose glass system and a modified Coulomb glass model, originally developed to describe disordered semiconductors at low temperatures. By means of Monte Carlo simulations, we investigate the effects of the introduction of random bare site energies and sudden changes in the vortex or charge carrier density on the soft Coulomb gap that appears in the density of states due to the emerging spatial anticorrelations. The non-equilibrium relaxation properties of the Bose and Coulomb glass states and the ensuing aging kinetics are studied through the two-time density autocorrelation function and its various scaling forms. Research supported by the U.S. Department of Energy, Office of Basic Energy Sciences, Division of Materials Sciences and Engineering under Award DE-FG02-09ER46613.

The role of titanium nitride supports for single-atom platinum-based catalysts in fuel cell technology.

PubMed

Zhang, Ren-Qin; Lee, Tae-Hun; Yu, Byung-Deok; Stampfl, Catherine; Soon, Aloysius

2012-12-28

As a first step towards a microscopic understanding of single-Pt atom-dispersed catalysts on non-conventional TiN supports, we present density-functional theory (DFT) calculations to investigate the adsorption properties of Pt atoms on the pristine TiN(100) surface, as well as the dominant influence of surface defects on the thermodynamic stability of platinized TiN. Optimized atomic geometries, energetics, and analysis of the electronic structure of the Pt/TiN system are reported for various surface coverages of Pt. We find that atomic Pt does not bind preferably to the clean TiN surface, but under typical PEM fuel cell operating conditions, i.e. strongly oxidizing conditions, TiN surface vacancies play a crucial role in anchoring the Pt atom for its catalytic function. Whilst considering the energetic stability of the Pt/TiN structures under varying N conditions, embedding Pt at the surface N-vacancy site is found to be the most favorable under N-lean conditions. Thus, the system of embedding Pt at the surface N-vacancy sites on TiN(100) surfaces could be promising catalysts for PEM fuel cells.

Description of quantum coherence in thermodynamic processes requires constraints beyond free energy.

PubMed

Lostaglio, Matteo; Jennings, David; Rudolph, Terry

2015-03-10

Recent studies have developed fundamental limitations on nanoscale thermodynamics, in terms of a set of independent free energy relations. Here we show that free energy relations cannot properly describe quantum coherence in thermodynamic processes. By casting time-asymmetry as a quantifiable, fundamental resource of a quantum state, we arrive at an additional, independent set of thermodynamic constraints that naturally extend the existing ones. These asymmetry relations reveal that the traditional Szilárd engine argument does not extend automatically to quantum coherences, but instead only relational coherences in a multipartite scenario can contribute to thermodynamic work. We find that coherence transformations are always irreversible. Our results also reveal additional structural parallels between thermodynamics and the theory of entanglement.

Description of quantum coherence in thermodynamic processes requires constraints beyond free energy

NASA Astrophysics Data System (ADS)

Lostaglio, Matteo; Jennings, David; Rudolph, Terry

2015-03-01

Recent studies have developed fundamental limitations on nanoscale thermodynamics, in terms of a set of independent free energy relations. Here we show that free energy relations cannot properly describe quantum coherence in thermodynamic processes. By casting time-asymmetry as a quantifiable, fundamental resource of a quantum state, we arrive at an additional, independent set of thermodynamic constraints that naturally extend the existing ones. These asymmetry relations reveal that the traditional Szilárd engine argument does not extend automatically to quantum coherences, but instead only relational coherences in a multipartite scenario can contribute to thermodynamic work. We find that coherence transformations are always irreversible. Our results also reveal additional structural parallels between thermodynamics and the theory of entanglement.

Description of quantum coherence in thermodynamic processes requires constraints beyond free energy

PubMed Central

Lostaglio, Matteo; Jennings, David; Rudolph, Terry

2015-01-01

Recent studies have developed fundamental limitations on nanoscale thermodynamics, in terms of a set of independent free energy relations. Here we show that free energy relations cannot properly describe quantum coherence in thermodynamic processes. By casting time-asymmetry as a quantifiable, fundamental resource of a quantum state, we arrive at an additional, independent set of thermodynamic constraints that naturally extend the existing ones. These asymmetry relations reveal that the traditional Szilárd engine argument does not extend automatically to quantum coherences, but instead only relational coherences in a multipartite scenario can contribute to thermodynamic work. We find that coherence transformations are always irreversible. Our results also reveal additional structural parallels between thermodynamics and the theory of entanglement. PMID:25754774

Imaging the atomic structure and local chemistry of platelets in natural type Ia diamond

NASA Astrophysics Data System (ADS)

Olivier, E. J.; Neethling, J. H.; Kroon, R. E.; Naidoo, S. R.; Allen, C. S.; Sawada, H.; van Aken, P. A.; Kirkland, A. I.

2018-03-01

In the past decades, many efforts have been devoted to characterizing {001} platelet defects in type Ia diamond. It is known that N is concentrated at the defect core. However, an accurate description of the atomic structure of the defect and the role that N plays in it is still unknown. Here, by using aberration-corrected transmission electron microscopy and electron energy-loss spectroscopy we have determined the atomic arrangement within platelet defects in a natural type Ia diamond and matched it to a prevalent theoretical model. The platelet has an anisotropic atomic structure with a zigzag ordering of defect pairs along the defect line. The electron energy-loss near-edge fine structure of both carbon K- and nitrogen K-edges obtained from the platelet core is consistent with a trigonal bonding arrangement at interstitial sites. The experimental observations support an interstitial aggregate mode of formation for platelet defects in natural diamond.

Imaging the atomic structure and local chemistry of platelets in natural type Ia diamond.

PubMed

Olivier, E J; Neethling, J H; Kroon, R E; Naidoo, S R; Allen, C S; Sawada, H; van Aken, P A; Kirkland, A I

2018-03-01

In the past decades, many efforts have been devoted to characterizing {001} platelet defects in type Ia diamond. It is known that N is concentrated at the defect core. However, an accurate description of the atomic structure of the defect and the role that N plays in it is still unknown. Here, by using aberration-corrected transmission electron microscopy and electron energy-loss spectroscopy we have determined the atomic arrangement within platelet defects in a natural type Ia diamond and matched it to a prevalent theoretical model. The platelet has an anisotropic atomic structure with a zigzag ordering of defect pairs along the defect line. The electron energy-loss near-edge fine structure of both carbon K- and nitrogen K-edges obtained from the platelet core is consistent with a trigonal bonding arrangement at interstitial sites. The experimental observations support an interstitial aggregate mode of formation for platelet defects in natural diamond.

Thermodynamics-hydration relationships within loops that affect G-quadruplexes under molecular crowding conditions.

PubMed

Fujimoto, Takeshi; Nakano, Shu-ichi; Sugimoto, Naoki; Miyoshi, Daisuke

2013-01-31

We systematically investigated the effects of loop length on the conformation, thermodynamic stability, and hydration of DNA G-quadruplexes under dilute and molecular crowding conditions in the presence of Na(+). Structural analysis showed that molecular crowding induced conformational switches of oligonucleotides with the longer guanine stretch and the shorter thymine loop. Thermodynamic parameters further demonstrated that the thermodynamic stability of G-quadruplexes increased by increasing the loop length from two to four, whereas it decreased by increasing the loop length from four to six. Interestingly, we found by osmotic pressure analysis that the number of water molecules released from the G-quadruplex decreased with increasing thermodynamic stability. We assumed that base-stacking interactions within the loops not only stabilized the whole G-quadruplex structure but also created hydration sites by accumulating nucleotide functional groups. The molecular crowding effects on the stability of G-quadruplexes composed of abasic sites, which reduce the stacking interactions at the loops, further demonstrated that G-quadruplexes with fewer stacking interactions within the loops released a larger number of water molecules upon folding. These results showed that the stacking interactions within the loops determined the thermodynamic stability and hydration of the whole G-quadruplex.

Thermodynamics of RNA duplexes modified with unlocked nucleic acid nucleotides

PubMed Central

Pasternak, Anna; Wengel, Jesper

2010-01-01

Thermodynamics provides insights into the influence of modified nucleotide residues on stability of nucleic acids and is crucial for designing duplexes with given properties. In this article, we introduce detailed thermodynamic analysis of RNA duplexes modified with unlocked nucleic acid (UNA) nucleotide residues. We investigate UNA single substitutions as well as model mismatch and dangling end effects. UNA residues placed in a central position makes RNA duplex structure less favourable by 4.0–6.6 kcal/mol. Slight destabilization, by ∼0.5–1.5 kcal/mol, is observed for 5′- or 3′-terminal UNA residues. Furthermore, thermodynamic effects caused by UNA residues are extremely additive with ΔG°37 conformity up to 98%. Direct mismatches involving UNA residues decrease the thermodynamic stability less than unmodified mismatches in RNA duplexes. Additionally, the presence of UNA residues adjacent to unpaired RNA residues reduces mismatch discrimination. Thermodynamic analysis of UNA 5′- and 3′-dangling ends revealed that stacking interactions of UNA residues are always less favourable than that of RNA residues. Finally, circular dichroism spectra imply no changes in overall A-form structure of UNA–RNA/RNA duplexes relative to the unmodified RNA duplexes. PMID:20562222

What is life? Bio-physical perspectives.

PubMed

Gladyshev, G P

2009-01-01

Life arises and develops in gravitationally bound atomic systems, under certain conditions, in the presence of the inflow of energy. A condition of structural dynamic reactivity to the energy inflow qualifies what are anthropomorphically considered as "alive objects". Alive objects, in this perspective, include such rudimentary animate atomic structures as the retinal molecule C20H28o to the herpes simplex virus C102H152N26o29 to the human being, a twenty-six element atomic structure, which can be quantified further as thermodynamic quasi-closed supramolecular systems, which are part of natural open systems. These systems appear and evolve in periodic conditions near to internal equilibrium. This systems attribute of dynamic life can be understood further by the determination and use of mathematical "state functions", which are functions that quantify the state of a system defined by the ensemble of physical quantities: temperature, pressure, composition, etc., which characterize the system, but neither by its surroundings nor by its history. In this view, the phenomenon of a life is easily understood as a general consequence of the laws of the universe, in particular, the laws of thermodynamics, which in the geocentric perspective translate to a formulation of "hierarchical thermodynamics" and a "principle of substance stability". The formation of living thermodynamic structures, in short, arises on the nanolevel by a constantly varying environment that causes variety of living forms. The definition of a life as the bio-chemical-physical phenomenon can thus be given on the basis of the exact sciences, i. e. chemistry, physics, and thermodynamics, without mention of numerous private attributes of a living substance and without physically baseless models of mathematical modeling, such as Prigoginean thermodynamics.

Screening Libraries of Semifluorinated Arylene Bisimides to Discover and Predict Thermodynamically Controlled Helical Crystallization.

PubMed

Ho, Ming-Shou; Partridge, Benjamin E; Sun, Hao-Jan; Sahoo, Dipankar; Leowanawat, Pawaret; Peterca, Mihai; Graf, Robert; Spiess, Hans W; Zeng, Xiangbing; Ungar, Goran; Heiney, Paul A; Hsu, Chain-Shu; Percec, Virgil

2016-12-12

Synthesis, structural, and retrostructural analysis of a library containing 16 self-assembling perylene (PBI), 1,6,7,12-tetrachloroperylene (Cl 4 PBI), naphthalene (NBI), and pyromellitic (PMBI) bisimides functionalized with environmentally friendly AB 3 chiral racemic semifluorinated minidendrons at their imide groups via m = 0, 1, 2, and 3 methylene units is reported. These semifluorinated compounds melt at lower temperatures than homologous hydrogenated compounds, permitting screening of all their thermotropic phases via structural analysis to discover thermodynamically controlled helical crystallization from propeller-like, cogwheel, and tilted molecules as well as lamellar-like structures. Thermodynamically controlled helical crystallization was discovered for propeller-like PBI, Cl 4 PBI and NBI with m = 0. Unexpectedly, assemblies of twisted Cl 4 PBIs exhibit higher order than those of planar PBIs. PBI with m = 1, 2, and 3 form a thermodynamically controlled columnar hexagonal 2D lattice of tilted helical columns with intracolumnar order. PBI and Cl 4 PBI with m = 1 crystallize via a recently discovered helical cogwheel mechanism, while NBI and PMBI with m = 1 form tilted helical columns. PBI, NBI and PMBI with m = 2 generate lamellar-like structures. 3D and 2D assemblies of PBI with m = 1, 2, and 3, NBI with m = 1 and PMBI with m = 2 exhibit 3.4 Å π-π stacking. The library approach applied here and in previous work enabled the discovery of six assemblies which self-organize via thermodynamic control into 3D and 2D periodic arrays, and provides molecular principles to predict the supramolecular structure of electronically active components.

The Personal Computer in Mechanical Engineering Thermodynamics Courses.

ERIC Educational Resources Information Center

Romer, I. C., Jr.; Balmer, R. T.

1986-01-01

Describes experiences over several semesters with microcomputers in a mechanical engineering applied thermodynamics course. Includes course objectives, computer assignment structure, typical assignments, prewritten versus student-written software, and other topic areas. (JN)

Thermodynamic model of natural, medieval and nuclear waste glass durability

DOE Office of Scientific and Technical Information (OSTI.GOV)

Jantzen, C.M.; Plodinec, M.J.

1983-01-01

A thermodynamic model of glass durability based on hydration of structural units has been applied to natural glass, medieval window glasses, and glasses containing nuclear waste. The relative durability predicted from the calculated thermodynamics correlates directly with the experimentally observed release of structural silicon in the leaching solution in short-term laboratory tests. By choosing natural glasses and ancient glasses whose long-term performance is known, and which bracket the durability of waste glasses, the long-term stability of nuclear waste glasses can be interpolated among these materials. The current Savannah River defense waste glass formulation is as durable as natural basalt frommore » the Hanford Reservation (10/sup 6/ years old). The thermodynamic hydration energy is shown to be related to the bond energetics of the glass. 69 references, 2 figures, 1 table.« less

Student Oriented Approaches in the Teaching of Thermodynamics at Universities--Developing an Effective Course Structure

ERIC Educational Resources Information Center

Partanen, Lauri

2016-01-01

The aim of this study was to apply current pedagogical research in order to develop an effective course and exercise structure for a physical chemistry thermodynamics course intended for second or third year university students of chemistry. A mixed-method approach was used to measure the impact the changes had on student learning. In its final…

Theory and computer simulation of hard-core Yukawa mixtures: thermodynamical, structural and phase coexistence properties.

PubMed

Mkanya, Anele; Pellicane, Giuseppe; Pini, Davide; Caccamo, Carlo

2017-09-13

We report extensive calculations, based on the modified hypernetted chain (MHNC) theory, on the hierarchical reference theory (HRT), and on Monte Carlo simulations, of thermodynamical, structural and phase coexistence properties of symmetric binary hard-core Yukawa mixtures (HCYM) with attractive interactions at equal species concentration. The obtained results are throughout compared with those available in the literature for the same systems. It turns out that the MHNC predictions for thermodynamic and structural quantities are quite accurate in comparison with the MC data. The HRT is equally accurate for thermodynamics, and slightly less accurate for structure. Liquid-vapor (LV) and liquid-liquid (LL) consolute coexistence conditions as emerging from simulations, are also highly satisfactorily reproduced by both the MHNC and HRT for relatively long ranged potentials. When the potential range reduces, the MHNC faces problems in determining the LV binodal line; however, the LL consolute line and the critical end point (CEP) temperature and density turn out to be still satisfactorily predicted within this theory. The HRT also predicts with good accuracy the CEP position. The possibility of employing liquid state theories HCYM for the purpose of reliably determining phase equilibria in multicomponent colloidal fluids of current technological interest, is discussed.

Theory and computer simulation of hard-core Yukawa mixtures: thermodynamical, structural and phase coexistence properties

NASA Astrophysics Data System (ADS)

Mkanya, Anele; Pellicane, Giuseppe; Pini, Davide; Caccamo, Carlo

2017-09-01

We report extensive calculations, based on the modified hypernetted chain (MHNC) theory, on the hierarchical reference theory (HRT), and on Monte Carlo simulations, of thermodynamical, structural and phase coexistence properties of symmetric binary hard-core Yukawa mixtures (HCYM) with attractive interactions at equal species concentration. The obtained results are throughout compared with those available in the literature for the same systems. It turns out that the MHNC predictions for thermodynamic and structural quantities are quite accurate in comparison with the MC data. The HRT is equally accurate for thermodynamics, and slightly less accurate for structure. Liquid-vapor (LV) and liquid-liquid (LL) consolute coexistence conditions as emerging from simulations, are also highly satisfactorily reproduced by both the MHNC and HRT for relatively long ranged potentials. When the potential range reduces, the MHNC faces problems in determining the LV binodal line; however, the LL consolute line and the critical end point (CEP) temperature and density turn out to be still satisfactorily predicted within this theory. The HRT also predicts with good accuracy the CEP position. The possibility of employing liquid state theories HCYM for the purpose of reliably determining phase equilibria in multicomponent colloidal fluids of current technological interest, is discussed.

Metal viscoplasticity with two-temperature thermodynamics and two dislocation densities

NASA Astrophysics Data System (ADS)

Roy Chowdhury, Shubhankar; Kar, Gurudas; Roy, Debasish; Reddy, J. N.

2018-03-01

Posed within the two-temperature theory of non-equilibrium thermodynamics, we propose a model for thermoviscoplastic deformation in metals. We incorporate the dynamics of dislocation densities-mobile and forest—that play the role of internal state variables in the formulation. The description based on two temperatures appears naturally when one recognizes that the thermodynamic system undergoing viscoplastic deformation is composed of two weakly interacting subsystems, viz. a kinetic-vibrational subsystem of the vibrating atomic lattices and a configurational subsystem of the slower degrees of freedom relating to defect motion, each with its own temperature. Starting with a basic model that involves only homogeneous deformation, a three-dimensional model for inhomogeneous viscoplasticity applicable to finite deformation is charted out in an overstress driven viscoplastic deformation framework. The model shows how the coupled evolutions of mobile and forest dislocation densities, which are critically influenced by the dynamics of configurational temperature, govern the strength and ductility of the metal. Unlike most contemporary models, the current proposal also affords a prediction of certain finer details as observed in the experimental data on stress-strain behaviour of metals and this in turn enhances the understanding of the evolving and interacting dislocation densities.

A phase field model for segregation and precipitation induced by irradiation in alloys

NASA Astrophysics Data System (ADS)

Badillo, A.; Bellon, P.; Averback, R. S.

2015-04-01

A phase field model is introduced to model the evolution of multicomponent alloys under irradiation, including radiation-induced segregation and precipitation. The thermodynamic and kinetic components of this model are derived using a mean-field model. The mobility coefficient and the contribution of chemical heterogeneity to free energy are rescaled by the cell size used in the phase field model, yielding microstructural evolutions that are independent of the cell size. A new treatment is proposed for point defect clusters, using a mixed discrete-continuous approach to capture the stochastic character of defect cluster production in displacement cascades, while retaining the efficient modeling of the fate of these clusters using diffusion equations. The model is tested on unary and binary alloy systems using two-dimensional simulations. In a unary system, the evolution of point defects under irradiation is studied in the presence of defect clusters, either pre-existing ones or those created by irradiation, and compared with rate theory calculations. Binary alloys with zero and positive heats of mixing are then studied to investigate the effect of point defect clustering on radiation-induced segregation and precipitation in undersaturated solid solutions. Lastly, irradiation conditions and alloy parameters leading to irradiation-induced homogeneous precipitation are investigated. The results are discussed in the context of experimental results reported for Ni-Si and Al-Zn undersaturated solid solutions subjected to irradiation.

Structural and thermodynamic analysis of modified nucleosides in self-assembled DNA cross-tiles.

PubMed

Hakker, Lauren; Marchi, Alexandria N; Harris, Kimberly A; LaBean, Thomas H; Agris, Paul F

2014-01-01

DNA Holliday junctions are important natural strand-exchange structures that form during homologous recombination. Immobile four-arm junctions, analogs to Holliday junctions, have been designed to self-assemble into cross-tile structures by maximizing Watson-Crick base pairing and fixed crossover points. The cross-tiles, self-assembled from base pair recognition between designed single-stranded DNAs, form higher order lattice structures through cohesion of self-associating sticky ends. These cross-tiles have 16 unpaired nucleosides in the central loop at the junction of the four duplex stems. The importance of the centralized unpaired nucleosides to the structure's thermodynamic stability and self-assembly is unknown. Cross-tile DNA nanostructures were designed and constructed from nine single-stranded DNAs with four shell strands, four arms, and a central loop containing 16 unpaired bases. The 16 unpaired bases were either 2'-deoxyribothymidines, 2'-O-methylribouridines, or abasic 1',2'-dideoxyribonucleosides. Thermodynamic profiles and structural base-stacking contributions were assessed using UV absorption spectroscopy during thermal denaturation and circular dichroism spectroscopy, respectively, and the resulting structures were observed by atomic force microscopy. There were surprisingly significant changes in the thermodynamic and structural properties of lattice formation as a result of altering only the 16 unpaired, centralized nucleosides. The 16 unpaired 2'-O-methyluridines were stabilizing and produced uniform tubular structures. In contrast, the abasic nucleosides were destabilizing producing a mixture of structures. These results strongly indicate the importance of a small number of centrally located unpaired nucleosides within the structures. Since minor modifications lead to palpable changes in lattice formation, DNA cross-tiles present an easily manipulated structure convenient for applications in biomedical and biosensing devices.

Substituent effect on the thermodynamic solubility of structural analogs: relative contribution of crystal packing and hydration.

PubMed

Ozaki, Shunsuke; Nakagawa, Yoshiaki; Shirai, Osamu; Kano, Kenji

2014-11-01

Thermodynamic analysis of the solubility of benzoylphenylurea (BPU) derivatives was conducted to investigate the relative importance of crystal packing and hydration for improving solubility with minor structural modification. The contribution of crystal packing to solubility was evaluated from the change in Gibbs energy on the transition from the crystalline to liquid state. Hydration Gibbs energy was estimated using a linear free-energy relationship between octanol-water partition coefficients and gas-water partition coefficients. The established solubility model satisfactorily explained the relative thermodynamic solubility of the model compounds and revealed that crystal packing and hydration equally controlled solubility of the structural analogs. All hydrophobic substituents were undesirable for solubility in terms of hydration, as expected. On the other hand, some of these hydrophobic substituents destabilized crystal packing and improved the solubility of the BPU derivatives when their impact on crystal packing exceeded their negative influence on hydration. The replacement of a single substituent could cause more than a 10-fold enhancement in thermodynamic solubility; this degree of improvement was comparable to that generally achieved by amorphous formulations. Detailed analysis of thermodynamic solubility will allow us to better understand the true substituent effect and design drug-like candidates efficiently. © 2014 Wiley Periodicals, Inc. and the American Pharmacists Association.

First-principles study of transition-metal nitrides as diffusion barriers against Al

DOE Office of Scientific and Technical Information (OSTI.GOV)

Mei, Zhi-Gang; Yacout, Abdellatif M.; Kim, Yeon Soo

2016-04-01

Using density-functional theory based first-principles calculations we provided a comparative study of the diffusion barrier properties of TiN, ZrN, and HfN against Al for U-Mo dispersion fuel applications. We firstly examined the thermodynamic stability of these transition-metal nitrides with Al. The calculated heats of reaction show that both TiN and ZrN are thermodynamically unstable diffusion barrier materials, which might be decomposed by Al at relatively high temperatures. As a comparison, HfN is a stable diffusion barrier material for Al. To evaluate the kinetic stability of these nitride systems against Al diffusion, we investigated the diffusion mechanisms of Al in TiN,more » ZrN and HfN using atomic scale simulations. The effect of non-stoichiometry on the defect formation and Al migration was systematically studied. (C) 2015 ELSEVIER B.V. All rights reserved« less

Calculation of open and closed system elastic coefficients for multicomponent solids

NASA Astrophysics Data System (ADS)

Mishin, Y.

2015-06-01

Thermodynamic equilibrium in multicomponent solids subject to mechanical stresses is a complex nonlinear problem whose exact solution requires extensive computations. A few decades ago, Larché and Cahn proposed a linearized solution of the mechanochemical equilibrium problem by introducing the concept of open system elastic coefficients [Acta Metall. 21, 1051 (1973), 10.1016/0001-6160(73)90021-7]. Using the Ni-Al solid solution as a model system, we demonstrate that open system elastic coefficients can be readily computed by semigrand canonical Monte Carlo simulations in conjunction with the shape fluctuation approach. Such coefficients can be derived from a single simulation run, together with other thermodynamic properties needed for prediction of compositional fields in solid solutions containing defects. The proposed calculation approach enables streamlined solutions of mechanochemical equilibrium problems in complex alloys. Second order corrections to the linear theory are extended to multicomponent systems.

Energy Transformations of Soil Organic Matter in a Changing World

NASA Astrophysics Data System (ADS)

Herrmann, A. M.; Coucheney, E.; Grice, S. M.; Ritz, K.; Harris, J.

2011-12-01

The role of soils in governing the terrestrial carbon balance is acknowledged as being important but remains poorly understood within the context of climate change. Soils exchange energy with their surroundings and are therefore open systems thermodynamically, but little is known how energy transformations of decomposition processes are affected by temperature. Soil organic matter and the soil biomass can be conceptualised as analogous to the 'fuel' and 'biological engine' of the earth, respectively, and are pivotal in driving the belowground carbon cycle. Thermodynamic principles of soil organic matter decomposition were evaluated by means of isothermal microcalorimetry (TAM Air, TA Instruments, Sollentuna Sweden: (i) Mineral forest soils from the Flakaliden long-term nitrogen fertilisation experiment (Sweden) were amended with a range of different substrates representing structurally simple to complex, ecologically pertinent organic matter and heat signatures were determined at temperatures between 5 and 25°C. (ii) Thermodynamic and resource-use efficiencies of the biomass were determined in arable soils which received contrasting long-term management regimes with respect to organic matter and nitrogen since 1956. The work showed that (i) structurally labile components have higher activation energy and temperature dependence than structurally more complex organic components. This is, however, in contrast to the thermodynamic argument which suggests the opposite that reactions metabolising structurally complex, aromatic components have higher temperature dependence than reactions metabolising structurally more labile components. (ii) Microbial communities exposed to long-term stress by heavy metal and low pH were less thermodynamic efficient and showed a decrease in resource-use efficiency in comparison with conventional input regimes. Differences in efficiencies were mirrored in both the phenotypic and functional profiles of the communities. We will present our findings illustrating the capacity of isothermal microcalorimetry to evaluate temperature dependencies of soil organic matter decomposition, associated energy transformations and thermodynamic principles in soil ecosystems.

Defect classification in sparsity-based structural health monitoring

NASA Astrophysics Data System (ADS)

Golato, Andrew; Ahmad, Fauzia; Santhanam, Sridhar; Amin, Moeness G.

2017-05-01

Guided waves have gained popularity in structural health monitoring (SHM) due to their ability to inspect large areas with little attenuation, while providing rich interactions with defects. For thin-walled structures, the propagating waves are Lamb waves, which are a complex but well understood type of guided waves. Recent works have cast the defect localization problem of Lamb wave based SHM within the sparse reconstruction framework. These methods make use of a linear model relating the measurements with the scene reflectivity under the assumption of point-like defects. However, most structural defects are not perfect points but tend to assume specific forms, such as surface cracks or internal cracks. Knowledge of the "type" of defects is useful in the assessment phase of SHM. In this paper, we present a dual purpose sparsity-based imaging scheme which, in addition to accurately localizing defects, properly classifies the defects present simultaneously. The proposed approach takes advantage of the bias exhibited by certain types of defects toward a specific Lamb wave mode. For example, some defects strongly interact with the anti-symmetric modes, while others strongly interact with the symmetric modes. We build model based dictionaries for the fundamental symmetric and anti-symmetric wave modes, which are then utilized in unison to properly localize and classify the defects present. Simulated data of surface and internal defects in a thin Aluminum plate are used to validate the proposed scheme.

Investigating the Defect Structures in Transparent Conducting Oxides Using X-ray and Neutron Scattering Techniques

PubMed Central

González, Gabriela B.

2012-01-01

Transparent conducting oxide (TCO) materials are implemented into a wide variety of commercial devices because they possess a unique combination of high optical transparency and high electrical conductivity. Created during the processing of the TCOs, defects within the atomic-scale structure are responsible for their desirable optical and electrical properties. Therefore, studying the defect structure is essential to a better understanding of the behavior of transparent conductors. X-ray and neutron scattering techniques are powerful tools to investigate the atomic lattice structural defects in these materials. This review paper presents some of the current developments in the study of structural defects in n-type TCOs using x-ray diffraction (XRD), neutron diffraction, extended x-ray absorption fine structure (EXAFS), pair distribution functions (PDFs), and x-ray fluorescence (XRF). PMID:28817010

Redox levels in aqueous solution: Effect of van der Waals interactions and hybrid functionals.

PubMed

Ambrosio, Francesco; Miceli, Giacomo; Pasquarello, Alfredo

2015-12-28

We investigate redox levels in aqueous solution using a combination of ab initio molecular dynamics (MD) simulations and thermodynamic integration methods. The molecular dynamics are performed with both the semilocal Perdew-Burke-Ernzerhof functional and a nonlocal functional (rVV10) accounting for van der Waals (vdW) interactions. The band edges are determined through three different schemes, namely, from the energy of the highest occupied and of the lowest unoccupied Kohn-Sham states, from total-energy differences, and from a linear extrapolation of the density of states. It is shown that the latter does not depend on the system size while the former two are subject to significant finite-size effects. For the redox levels, we provide a formulation in analogy to the definition of charge transition levels for defects in crystalline materials. We consider the H(+)/H2 level defining the standard hydrogen electrode, the OH(-)/OH(∗) level corresponding to the oxidation of the hydroxyl ion, and the H2O/OH(∗) level for the dehydrogenation of water. In spite of the large structural modifications induced in liquid water, vdW interactions do not lead to any significant structural effect on the calculated band gap and band edges. The effect on the redox levels is also small since the solvation properties of ionic species are little affected by vdW interactions. Since the electronic properties are not significantly affected by the underlying structural properties, it is justified to perform hybrid functional calculations on the configurations of our MD simulations. The redox levels calculated as a function of the fraction α of Fock exchange are found to remain constant, reproducing a general behavior previously observed for charge transition levels of defects. Comparison with experimental values shows very good agreement. At variance, the band edges and the band gap evolve linearly with α. For α ≃ 0.40, we achieve a band gap, band-edge positions, and redox levels in overall good agreement with experiment.

Depth-Profiling Electronic and Structural Properties of Cu(In,Ga)(S,Se)2 Thin-Film Solar Cell.

PubMed

Chiang, Ching-Yu; Hsiao, Sheng-Wei; Wu, Pin-Jiun; Yang, Chu-Shou; Chen, Chia-Hao; Chou, Wu-Ching

2016-09-14

Utilizing a scanning photoelectron microscope (SPEM) and grazing-incidence X-ray powder diffraction (GIXRD), we studied the electronic band structure and the crystalline properties of the pentanary Cu(In,Ga)(S,Se)2 (CIGSSe) thin-film solar cell as a function of sample depth on measuring the thickness-gradient sample. A novel approach is proposed for studying the depth-dependent information on thin films, which can provide a gradient thickness and a wide cross-section of the sample by polishing process. The results exhibit that the CIGSSe absorber layer possesses four distinct stoichiometries. The growth mechanism of this distinctive compositional distribution formed by a two-stage process is described according to the thermodynamic reaction and the manufacturing process. On the basis of the depth-profiling results, the gradient profiles of the conduction and valence bands were constructed to elucidate the performance of the electrical properties (in this case, Voc = 620 mV, Jsc = 34.6 mA/cm(2), and η = 14.04%); the valence-band maxima (VBM) measured with a SPEM in the spectroscopic mode coincide with this band-structure model, except for a lowering of the VBM observed in the surface region of the absorber layer due to the ordered defect compound (ODC). In addition, the depth-dependent texturing X-ray diffraction pattern presents the crystalline quality and the residual stress for each depth of a thin-film device. We find that the randomly oriented grains in the bottom region of the absorber layer and the different residual stress between the underlying Mo and the absorber interface, which can deteriorate the electrical performance due to peeling-off effect. An anion interstitial defect can be observed on comparing the anion concentration of the elemental distribution with crystalline composition; a few excess sulfur atoms insert in interstitial sites at the front side of the absorber layer, whereas the interstitial selenium atoms insert at the back side.

Redox levels in aqueous solution: Effect of van der Waals interactions and hybrid functionals

NASA Astrophysics Data System (ADS)

Ambrosio, Francesco; Miceli, Giacomo; Pasquarello, Alfredo

2015-12-01

We investigate redox levels in aqueous solution using a combination of ab initio molecular dynamics (MD) simulations and thermodynamic integration methods. The molecular dynamics are performed with both the semilocal Perdew-Burke-Ernzerhof functional and a nonlocal functional (rVV10) accounting for van der Waals (vdW) interactions. The band edges are determined through three different schemes, namely, from the energy of the highest occupied and of the lowest unoccupied Kohn-Sham states, from total-energy differences, and from a linear extrapolation of the density of states. It is shown that the latter does not depend on the system size while the former two are subject to significant finite-size effects. For the redox levels, we provide a formulation in analogy to the definition of charge transition levels for defects in crystalline materials. We consider the H+/H2 level defining the standard hydrogen electrode, the OH-/OH∗ level corresponding to the oxidation of the hydroxyl ion, and the H2O/OH∗ level for the dehydrogenation of water. In spite of the large structural modifications induced in liquid water, vdW interactions do not lead to any significant structural effect on the calculated band gap and band edges. The effect on the redox levels is also small since the solvation properties of ionic species are little affected by vdW interactions. Since the electronic properties are not significantly affected by the underlying structural properties, it is justified to perform hybrid functional calculations on the configurations of our MD simulations. The redox levels calculated as a function of the fraction α of Fock exchange are found to remain constant, reproducing a general behavior previously observed for charge transition levels of defects. Comparison with experimental values shows very good agreement. At variance, the band edges and the band gap evolve linearly with α. For α ≃ 0.40, we achieve a band gap, band-edge positions, and redox levels in overall good agreement with experiment.

Structural, electronic, magnetic and thermodynamic properties of Ni1-xTixO alloys an ab initio calculation and Monte Carlo study

NASA Astrophysics Data System (ADS)

Klaa, K.; Labidi, S.; Masrour, R.; Jabar, A.; Labidi, M.; Amara, A.; Drici, A.; Hlil, E. K.; Ellouze, M.

2018-06-01

Structural, electronic, magnetic and thermodynamic main features for Ni1-xTixO ternary alloys in rock-salt structure with Ti content in the range ? were studied using the full potential Linearized augmented plane wave (FP-LAPW) method within density functional theory. The exchange-correlation potential was calculated by the generalized gradient approximation. The analysis of the electronic density of states curves allowed the computation of the magnetic moments which are considered to lie along (010) axes. The thermodynamic stability of this alloy was investigated by calculating the excess enthalpy of mixing ? as well as the phase diagram. In addition, the Monte Carlo simulations have been exploited to calculate the transition temperature and magnetic coercive field in the alloy.

Thermodynamic heuristics with case-based reasoning: combined insights for RNA pseudoknot secondary structure.

PubMed

Al-Khatib, Ra'ed M; Rashid, Nur'Aini Abdul; Abdullah, Rosni

2011-08-01

The secondary structure of RNA pseudoknots has been extensively inferred and scrutinized by computational approaches. Experimental methods for determining RNA structure are time consuming and tedious; therefore, predictive computational approaches are required. Predicting the most accurate and energy-stable pseudoknot RNA secondary structure has been proven to be an NP-hard problem. In this paper, a new RNA folding approach, termed MSeeker, is presented; it includes KnotSeeker (a heuristic method) and Mfold (a thermodynamic algorithm). The global optimization of this thermodynamic heuristic approach was further enhanced by using a case-based reasoning technique as a local optimization method. MSeeker is a proposed algorithm for predicting RNA pseudoknot structure from individual sequences, especially long ones. This research demonstrates that MSeeker improves the sensitivity and specificity of existing RNA pseudoknot structure predictions. The performance and structural results from this proposed method were evaluated against seven other state-of-the-art pseudoknot prediction methods. The MSeeker method had better sensitivity than the DotKnot, FlexStem, HotKnots, pknotsRG, ILM, NUPACK and pknotsRE methods, with 79% of the predicted pseudoknot base-pairs being correct.

Extreme Entropy-Enthalpy Compensation in a Drug Resistant Variant of HIV-1 Protease

PubMed Central

King, Nancy M.; Prabu-Jeyabalan, Moses; Bandaranayake, Rajintha M.; Nalam, Madhavi N. L.; Nalivaika, Ellen A.; Özen, Ayşegül; Haliloglu, Türkan; Yılmaz, Neşe Kurt; Schiffer, Celia A.

2012-01-01

The development of HIV-1 protease inhibitors has been the historic paradigm of rational structure-based drug design, where structural and thermodynamic analyses have assisted in the discovery of novel inhibitors. While the total enthalpy and entropy change upon binding determine the affinity, often the thermodynamics are considered in terms of inhibitor properties only. In the current study, profound changes are observed in the binding thermodynamics of a drug resistant variant compared to wild-type HIV-1 protease, irrespective of the inhibitor bound. This variant (Flap+) has a combination of flap and active site mutations and exhibits extremely large entropy-enthalpy compensation compared to wild-type protease, 5–15 kcal/mol, while losing only 1–3 kcal/mol in total binding free energy for any of six FDA approved inhibitors. Although entropy-enthalpy compensation has been previously observed for a variety of systems, never have changes of this magnitude been reported. The co-crystal structures of Flap+ protease with four of the inhibitors were determined and compared with complexes of both the wildtype protease and another drug resistant variant that does not exhibit this energetic compensation. Structural changes conserved across the Flap+ complexes, which are more pronounced for the flaps covering the active site, likely contribute to the thermodynamic compensation. The finding that drug resistant mutations can profoundly modulate the relative thermodynamic properties of a therapeutic target independent of the inhibitor presents a new challenge for rational drug design. PMID:22712830

Thermodynamics and Cation Diffusion in the Oxygen Ion Conductor Lsgm

NASA Astrophysics Data System (ADS)

Martin, M.; Schulz, O.

Perovskite type oxides based on LaGaO3 are of large technical interest because of their high oxygen-ion conductivity. Lanthanum gallate doped with Sr on A- and Mg on B-sites, La1-xSrxGa1-yMgyO3-(x+y)/2 (LSGM), reaches higher oxygen-ion conductivities than yttria-doped zirconia (YSZ). Thus LSGM represents a promising alternative for YSZ as electrolyte in solid oxide fuel cells (SOFC). Cells using thin LSGM-layers as electrolyte are expected to operate at intermediate temperatures around 700°C for more than 30000 hours without severe degradation. A potential long term degradation effect of LSGM is kinetic demixing of the electrolyte, caused by different cation diffusion coefficients. In this paper we report on experimental studies concerning the phase diagram of LSGM and the diffusion of cations. Cation self-diffusion of 139La, 84Sr and 25Mg and cation impurity diffusion of 144Nd, 89Y and 56Fe in polycrystalline LSGM samples was investigated by secondary ion mass spectrometry (SIMS) for temperatures between 900°C and 1400°C. It was found that diffusion occurs by means of bulk and grain boundaries. The bulk diffusion coefficients are similar for all cations with activation energies which are strongly dependent on temperature. At high temperatures, the activation energies are about 5 eV, while at low temperatures values of about 2 eV are found. These results are explained by a frozen in defect structure at low temperatures. This means that the observed activation energy at low temperatures represents only the migration energy of the different cations while the observed activation energy at high temperatures is the sum of the defect formation energy and the migration energy. The migration energies for all cations are nearly identical, although 139La, 84Sr and 144Nd are occupying A-sites while 25Mg and 56Fe are occupying B-sites in the perovskite-structure. To explain these experimental findings we propose a defect cluster containing cation vacancies in both the A- and the B-sublattice and anion vacancies as well.

Misoriented grain boundaries vicinal to the (1 1 1) <1 1¯0> twin in nickel Part I: Thermodynamics & temperature-dependent structure

DOE PAGES

O’Brien, Christopher J.; Medlin, Douglas L.; Foiles, Stephen M.

2016-03-30

Here, grain boundary-engineered materials are of immense interest for their corrosion resistance, fracture resistance and microstructural stability. This work contributes to a larger goal of understanding both the structure and thermodynamic properties of grain boundaries vicinal (within ±30°) to the Σ3(1 1 1) <1 1¯0> (coherent twin) boundary which is found in grain boundary-engineered materials. The misoriented boundaries vicinal to the twin show structural changes at elevated temperatures. In the case of nickel, this transition temperature is substantially below the melting point and at temperatures commonly reached during processing, making the existence of such boundaries very likely in applications. Thus,more » the thermodynamic stability of such features is thoroughly investigated in order to predict and fully understand the structure of boundaries vicinal to twins. Low misorientation angle grain boundaries (|θ| ≲ 16°) show distinct ±1/3(1 1 1) disconnections which accommodate misorientation in opposite senses. The two types of disconnection have differing low-temperature structures which show different temperature-dependent behaviours with one type undergoing a structural transition at approximately 600 K. At misorientation angles greater than approximately ±16°, the discrete disconnection nature is lost as the disconnections merge into one another. Free energy calculations demonstrate that these high-angle boundaries, which exhibit a transition from a planar to a faceted structure, are thermodynamically more stable in the faceted configuration.« less

The Thermodynamic Properties of Cubanite

NASA Technical Reports Server (NTRS)

Berger, E. L.; Lauretta, D. S.; Keller, L. P.

2012-01-01

CuFe2S3 exists in two polymorphs, a low-temperature orthorhombic form (cubanite) and a high-temperature cubic form (isocubanite). Cubanite has been identified in the CI-chondrite and Stardust collections. However, the thermodynamic properties of cubanite have neither been measured nor estimated. Our derivation of a thermodynamic model for cubanite allows constraints to be placed on the formation conditions. This data, along with the temperature constraint afforded by the crystal structure, can be used to assess the environments in which cubanite formation is (or is not) thermodynamically favored.

Thermodynamic metrics and optimal paths.

PubMed

Sivak, David A; Crooks, Gavin E

2012-05-11

A fundamental problem in modern thermodynamics is how a molecular-scale machine performs useful work, while operating away from thermal equilibrium without excessive dissipation. To this end, we derive a friction tensor that induces a Riemannian manifold on the space of thermodynamic states. Within the linear-response regime, this metric structure controls the dissipation of finite-time transformations, and bestows optimal protocols with many useful properties. We discuss the connection to the existing thermodynamic length formalism, and demonstrate the utility of this metric by solving for optimal control parameter protocols in a simple nonequilibrium model.

Theoretical exploration of various lithium peroxide crystal structures in a Li-air battery

DOE PAGES

Lau, Kah; Qiu, Dantong; Luo, Xiangyi; ...

2015-01-14

We describe a series of metastable Li₂O₂ crystal structures involving different orientations and displacements of the O₂²⁻ peroxy ions based on the known Li₂O₂ crystal structure. Within the vicinity of the chemical potential ΔG ~ 0.20 eV/Li from the thermodynamic ground state of the Li₂O₂ crystal structure (i.e., Föppl structure), all of these newly found metastable Li₂O₂ crystal structures are found to be insulating and high-k materials, and they have a common unique signature of an O₂²⁻ O-O vibration mode (ω ~ 799–865 cm⁻¹), which is in the range of that commonly observed in Li-air battery experiments, regardless of themore » random O₂²⁻ orientations and the symmetry in the crystal lattice. From XRD patterns analysis, the commercially available Li₂O₂ powder is confirmed to be the thermodynamic ground state Föppl-like structure. However, for Li₂O₂ compounds that are grown electrochemically under the environment of Li-O₂ cells, we found that the XRD patterns alone are not sufficient for structural identification of these metastable Li₂O₂ crystalline phases due to the poor crystallinity of the sample. In addition, the commonly known Raman signal of O₂²⁻ vibration mode is also found to be insufficient to validate the possible existence of these newly predicted Li₂O₂ crystal structures, as all of them similarly share the similar O₂²⁻ vibration mode. However considering that the discharge voltage in most Li-O₂ cells are typically several tenths of an eV below the thermodynamic equilibrium for the formation of ground state Föppl structure, the formation of these metastable Li₂O₂ crystal structures appears to be thermodynamically feasible.« less

Synthesis and characterization of novel electronic materials with volatile species

NASA Astrophysics Data System (ADS)

Zhizhong, Tang

In this thesis, two novel electronic materials, including semiconductor ZnGeAs2 and dielectric Ba(Zn1/3Ta 2/3)O3 were studied. The growth, characterization and application of ZnGeAs2 in photovoltaics were explored. The structure, optic and electric properties of expitaxial Ba(Zn1/3Ta2/3)O 3 films were also reported. ZnGeAs2 films were grown by pulsed laser deposition from the home-made target. The composition study showed that the Ge element incorporation rate remained constant, while the Zn and As incorporation rates decrease monotonically at elevated growth temperatures. Prototype of photovoltaic cell made with heterojunction p-ZnGeAs2/n-CdS/n+-SnO2 diode showed 0.14 Volt open circuit voltage under ˜100 mW/cm2 lab lamp illumination (1 sun) and 0.45 Volt Voc under 100 mW/cm 2 green LED illumination. Thermal decomposition studied of bulk ZnGeAs2 showed that the Zn and As dissociation rate from ZnGeAs2 approaches one monolayer per second at around 425 °C with activation energy of 1.08 eV. Thermodynamic and kinetic analysis showed that synthesis of ZnGeAs2 thin film is a metastable process involving a competition between the forward reaction which depends on the arrival of reactants at the growth surface, and the reverse kinetically-limited decomposition reaction. Ba(Zn1/3Ta2/3)O3 (100) dielectric thin films grown on MgO (100) substrates by pulsed laser deposition. The thin film structure, optic and electric properties were systematically characterized. Advanced electronic structure calculations were used to guide the interpretation of the experimental data. The Ba(Zn1/3Ta2/3)O3 films have an indirect optical band gap of ˜3.0 eV and a refractive index of 1.91 in the visible spectral range, with dielectric constant of 25 and dissipation factor of 0.0025 at 100 kHz. The Ba(Zn1/3Ta 2/3)O3 films exhibit a small thermally-activated Ohmic leakage current at high fields (<250 KV/cm) and high temperatures (<200 °C) with an activation energy of 0.85 eV. Ba(Zn1/3Ta2/3)O3 dielectric ceramics powder was used to synthesize Metallo-Dielectric Electromagnetic Band Gap structures by ceramic injection molding. Capacitive series and shunt defects were introduced in Metallo-Dielectric Electromagnetic Band Gap structures to generate sub-wavelength resonances. The frequency responses of both defect-free and defect-laden EBG structures were characterized at microwave frequencies and were found to agree with the results of electromagnetic simulations using the commercial HFSS modeling package.

Thermodynamics of organisms in the context of dynamic energy budget theory.

PubMed

Sousa, Tânia; Mota, Rui; Domingos, Tiago; Kooijman, S A L M

2006-11-01

We carry out a thermodynamic analysis to an organism. It is applicable to any type of organism because (1) it is based on a thermodynamic formalism applicable to all open thermodynamic systems and (2) uses a general model to describe the internal structure of the organism--the dynamic energy budget (DEB) model. Our results on the thermodynamics of DEB organisms are the following. (1) Thermodynamic constraints for the following types of organisms: (a) aerobic and exothermic, (b) anaerobic and exothermic, and (c) anaerobic and endothermic; showing that anaerobic organisms have a higher thermodynamic flexibility. (2) A way to compute the changes in the enthalpy and in the entropy of living biomass that accompany changes in growth rate solving the problem of evaluating the thermodynamic properties of biomass as a function of the amount of reserves. (3) Two expressions for Thornton's coefficient that explain its experimental variability and theoretically underpin its use in metabolic studies. (4) A mechanism that organisms in non-steady-state use to rid themselves of internal entropy production: "dilution of entropy production by growth." To demonstrate the practical applicability of DEB theory to quantify thermodynamic changes in organisms we use published data on Klebsiella aerogenes growing aerobically in a continuous culture. We obtain different values for molar entropies of the reserve and the structure of Klebsiella aerogenes proving that the reserve density concept of DEB theory is essential in discussions concerning (a) the relationship between organization and entropy and (b) the mechanism of storing entropy in new biomass. Additionally, our results suggest that the entropy of dead biomass is significantly different from the entropy of living biomass.

Solubility of oxygen in CdS single crystals and their physicochemical properties

DOE Office of Scientific and Technical Information (OSTI.GOV)

Morozova, N. K., E-mail: MorozovaNK@mail.ru; Kanakhin, A. A.; Shnitnikov, A. S.

2016-07-15

The specific features of oxygen dissolution in CdS using the example of single crystals grown by the gas-transport method with deviations from stoichiometry at 1100°C are considered. The effect of various types of intrinsic point defects in crystals of different composition on the form in the presence of oxygen is analyzed. It is shown that the most stable composition thermodynamically is that corresponding to nonstoichiometric “self-activated cadmium sulphide” stabilized with oxygen.

Transient Dissipation and Structural Costs of Physical Information Transduction

NASA Astrophysics Data System (ADS)

Boyd, Alexander B.; Mandal, Dibyendu; Riechers, Paul M.; Crutchfield, James P.

2017-06-01

A central result that arose in applying information theory to the stochastic thermodynamics of nonlinear dynamical systems is the information-processing second law (IPSL): the physical entropy of the Universe can decrease if compensated by the Shannon-Kolmogorov-Sinai entropy change of appropriate information-carrying degrees of freedom. In particular, the asymptotic-rate IPSL precisely delineates the thermodynamic functioning of autonomous Maxwellian demons and information engines. How do these systems begin to function as engines, Landauer erasers, and error correctors? We identify a minimal, and thus inescapable, transient dissipation of physical information processing, which is not captured by asymptotic rates, but is critical to adaptive thermodynamic processes such as those found in biological systems. A component of transient dissipation, we also identify an implementation-dependent cost that varies from one physical substrate to another for the same information processing task. Applying these results to producing structured patterns from a structureless information reservoir, we show that "retrodictive" generators achieve the minimal costs. The results establish the thermodynamic toll imposed by a physical system's structure as it comes to optimally transduce information.

Vibration of carbon nanotubes with defects: order reduction methods

NASA Astrophysics Data System (ADS)

Hudson, Robert B.; Sinha, Alok

2018-03-01

Order reduction methods are widely used to reduce computational effort when calculating the impact of defects on the vibrational properties of nearly periodic structures in engineering applications, such as a gas-turbine bladed disc. However, despite obvious similarities these techniques have not yet been adapted for use in analysing atomic structures with inevitable defects. Two order reduction techniques, modal domain analysis and modified modal domain analysis, are successfully used in this paper to examine the changes in vibrational frequencies, mode shapes and mode localization caused by defects in carbon nanotubes. The defects considered are isotope defects and Stone-Wales defects, though the methods described can be extended to other defects.

Structural, electronic and photocatalytic properties of atomic defective BiI3 monolayers

NASA Astrophysics Data System (ADS)

Yan, Huang; Ziyu, Hu; Xu, Gong; Xiaohong, Shao

2018-01-01

The structural, electronic and photocatalytic properties of five vacancy-containing 2D BiI3 monolayers are investigated by the first-principle calculations. The electronic structures show that the five structures are stable and have comparable binding energies to that of the pristine BiI3 monolayer, and the defects can tune the band gaps. Optical spectra indicate that the five structures retain high absorption capacity for visible light. The spin-orbit coupling (SOC) effect is found to play an important role in the band edge of defective structures, and the VBi and VBi-I3 defective BiI3 monolayers can make absolute band edges straddle water redox potentials more easily.

Predicting RNA pseudoknot folding thermodynamics

PubMed Central

Cao, Song; Chen, Shi-Jie

2006-01-01

Based on the experimentally determined atomic coordinates for RNA helices and the self-avoiding walks of the P (phosphate) and C4 (carbon) atoms in the diamond lattice for the polynucleotide loop conformations, we derive a set of conformational entropy parameters for RNA pseudoknots. Based on the entropy parameters, we develop a folding thermodynamics model that enables us to compute the sequence-specific RNA pseudoknot folding free energy landscape and thermodynamics. The model is validated through extensive experimental tests both for the native structures and for the folding thermodynamics. The model predicts strong sequence-dependent helix-loop competitions in the pseudoknot stability and the resultant conformational switches between different hairpin and pseudoknot structures. For instance, for the pseudoknot domain of human telomerase RNA, a native-like and a misfolded hairpin intermediates are found to coexist on the (equilibrium) folding pathways, and the interplay between the stabilities of these intermediates causes the conformational switch that may underlie a human telomerase disease. PMID:16709732

First-principles calculations of the thermodynamic properties of transuranium elements in a molten salt medium

NASA Astrophysics Data System (ADS)

Noh, Seunghyo; Kwak, Dohyun; Lee, Juseung; Kang, Joonhee; Han, Byungchan

2014-03-01

We utilized first-principles density-functional-theory (DFT) calculations to evaluate the thermodynamic feasibility of a pyroprocessing methodology for reducing the volume of high-level radioactive materials and recycling spent nuclear fuels. The thermodynamic properties of transuranium elements (Pu, Np and Cm) were obtained in electrochemical equilibrium with a LiCl-KCl molten salt as ionic phases and as adsorbates on a W(110) surface. To accomplish the goal, we rigorously calculated the double layer interface structures on an atomic resolution, on the thermodynamically most stable configurations on W(110) surfaces and the chemical activities of the transuranium elements for various coverages of those elements. Our results indicated that the electrodeposition process was very sensitive to the atomic level structures of Cl ions at the double-layer interface. Our studies are easily expandable to general electrochemical applications involving strong redox reactions of transition metals in non-aqueous solutions.

BDA: A novel method for identifying defects in body-centered cubic crystals.

PubMed

Möller, Johannes J; Bitzek, Erik

2016-01-01

The accurate and fast identification of crystallographic defects plays a key role for the analysis of atomistic simulation output data. For face-centered cubic (fcc) metals, most existing structure analysis tools allow for the direct distinction of common defects, such as stacking faults or certain low-index surfaces. For body-centered cubic (bcc) metals, on the other hand, a robust way to identify such defects is currently not easily available. We therefore introduce a new method for analyzing atomistic configurations of bcc metals, the BCC Defect Analysis (BDA). It uses existing structure analysis algorithms and combines their results to uniquely distinguish between typical defects in bcc metals. In essence, the BDA method offers the following features:•Identification of typical defect structures in bcc metals.•Reduction of erroneously identified defects by iterative comparison to the defects in the atom's neighborhood.•Availability as ready-to-use Python script for the widespread visualization tool OVITO [http://ovito.org].

The relationship between grain boundary structure, defect mobility, and grain boundary sink efficiency

PubMed Central

Uberuaga, Blas Pedro; Vernon, Louis J.; Martinez, Enrique; Voter, Arthur F.

2015-01-01

Nanocrystalline materials have received great attention due to their potential for improved functionality and have been proposed for extreme environments where the interfaces are expected to promote radiation tolerance. However, the precise role of the interfaces in modifying defect behavior is unclear. Using long-time simulations methods, we determine the mobility of defects and defect clusters at grain boundaries in Cu. We find that mobilities vary significantly with boundary structure and cluster size, with larger clusters exhibiting reduced mobility, and that interface sink efficiency depends on the kinetics of defects within the interface via the in-boundary annihilation rate of defects. Thus, sink efficiency is a strong function of defect mobility, which depends on boundary structure, a property that evolves with time. Further, defect mobility at boundaries can be slower than in the bulk, which has general implications for the properties of polycrystalline materials. Finally, we correlate defect energetics with the volumes of atomic sites at the boundary. PMID:25766999

The relationship between grain boundary structure, defect mobility, and grain boundary sink efficiency

DOE PAGES

Uberuaga, Blas Pedro; Vernon, Louis J.; Martinez, Enrique; ...

2015-03-13

Nanocrystalline materials have received great attention due to their potential for improved functionality and have been proposed for extreme environments where the interfaces are expected to promote radiation tolerance. However, the precise role of the interfaces in modifying defect behavior is unclear. Using long-time simulations methods, we determine the mobility of defects and defect clusters at grain boundaries in Cu. We find that mobilities vary significantly with boundary structure and cluster size, with larger clusters exhibiting reduced mobility, and that interface sink efficiency depends on the kinetics of defects within the interface via the in-boundary annihilation rate of defects. Thus,more » sink efficiency is a strong function of defect mobility, which depends on boundary structure, a property that evolves with time. Further, defect mobility at boundaries can be slower than in the bulk, which has general implications for the properties of polycrystalline materials. Finally, we correlate defect energetics with the volumes of atomic sites at the boundary.« less

Simulation of Rutherford backscattering spectrometry from arbitrary atom structures.

PubMed

Zhang, S; Nordlund, K; Djurabekova, F; Zhang, Y; Velisa, G; Wang, T S

2016-10-01

Rutherford backscattering spectrometry in a channeling direction (RBS/C) is a powerful tool for analysis of the fraction of atoms displaced from their lattice positions. However, it is in many cases not straightforward to analyze what is the actual defect structure underlying the RBS/C signal. To reveal insights of RBS/C signals from arbitrarily complex defective atomic structures, we develop here a method for simulating the RBS/C spectrum from a set of arbitrary read-in atom coordinates (obtained, e.g., from molecular dynamics simulations). We apply the developed method to simulate the RBS/C signals from Ni crystal structures containing randomly displaced atoms, Frenkel point defects, and extended defects, respectively. The RBS/C simulations show that, even for the same number of atoms in defects, the RBS/C signal is much stronger for the extended defects. Comparison with experimental results shows that the disorder profile obtained from RBS/C signals in ion-irradiated Ni is due to a small fraction of extended defects rather than a large number of individual random atoms.

Simulation of Rutherford backscattering spectrometry from arbitrary atom structures

NASA Astrophysics Data System (ADS)

Zhang, S.; Nordlund, K.; Djurabekova, F.; Zhang, Y.; Velisa, G.; Wang, T. S.

2016-10-01

Rutherford backscattering spectrometry in a channeling direction (RBS/C) is a powerful tool for analysis of the fraction of atoms displaced from their lattice positions. However, it is in many cases not straightforward to analyze what is the actual defect structure underlying the RBS/C signal. To reveal insights of RBS/C signals from arbitrarily complex defective atomic structures, we develop here a method for simulating the RBS/C spectrum from a set of arbitrary read-in atom coordinates (obtained, e.g., from molecular dynamics simulations). We apply the developed method to simulate the RBS/C signals from Ni crystal structures containing randomly displaced atoms, Frenkel point defects, and extended defects, respectively. The RBS/C simulations show that, even for the same number of atoms in defects, the RBS/C signal is much stronger for the extended defects. Comparison with experimental results shows that the disorder profile obtained from RBS/C signals in ion-irradiated Ni is due to a small fraction of extended defects rather than a large number of individual random atoms.

Active nematic emulsions

PubMed Central

Hardoüin, Jérôme; Sagués, Francesc

2018-01-01

The formation of emulsions from multiple immiscible fluids is governed by classical concepts such as surface tension, differential chemical affinity and viscosity, and the action of surface-active agents. Much less is known about emulsification when one of the components is active and thus inherently not constrained by the laws of thermodynamic equilibrium. We demonstrate one such realization consisting in the encapsulation of an active liquid crystal (LC)–like gel, based on microtubules and kinesin molecular motors, into a thermotropic LC. These active nematic emulsions exhibit a variety of dynamic behaviors that arise from the cross-talk between topological defects separately residing in the active and passive components. Using numerical simulations, we show a feedback mechanism by which active flows continuously drive the passive defects that, in response, resolve the otherwise degenerated trajectories of the active defects. Our experiments show that the choice of surfactant, which stabilizes the active/passive interface, allows tuning the regularity of the self-sustained dynamic events. The hybrid active-passive system demonstrated here provides new perspectives for dynamic self-assembly driven by an active material but regulated by the equilibrium properties of the passive component. PMID:29740605

Active nematic emulsions.

PubMed

Guillamat, Pau; Kos, Žiga; Hardoüin, Jérôme; Ignés-Mullol, Jordi; Ravnik, Miha; Sagués, Francesc

2018-04-01

The formation of emulsions from multiple immiscible fluids is governed by classical concepts such as surface tension, differential chemical affinity and viscosity, and the action of surface-active agents. Much less is known about emulsification when one of the components is active and thus inherently not constrained by the laws of thermodynamic equilibrium. We demonstrate one such realization consisting in the encapsulation of an active liquid crystal (LC)-like gel, based on microtubules and kinesin molecular motors, into a thermotropic LC. These active nematic emulsions exhibit a variety of dynamic behaviors that arise from the cross-talk between topological defects separately residing in the active and passive components. Using numerical simulations, we show a feedback mechanism by which active flows continuously drive the passive defects that, in response, resolve the otherwise degenerated trajectories of the active defects. Our experiments show that the choice of surfactant, which stabilizes the active/passive interface, allows tuning the regularity of the self-sustained dynamic events. The hybrid active-passive system demonstrated here provides new perspectives for dynamic self-assembly driven by an active material but regulated by the equilibrium properties of the passive component.

Finite-volume spectra of the Lee-Yang model

NASA Astrophysics Data System (ADS)

Bajnok, Zoltan; el Deeb, Omar; Pearce, Paul A.

2015-04-01

We consider the non-unitary Lee-Yang minimal model in three different finite geometries: (i) on the interval with integrable boundary conditions labelled by the Kac labels ( r, s) = (1 , 1) , (1 , 2), (ii) on the circle with periodic boundary conditions and (iii) on the periodic circle including an integrable purely transmitting defect. We apply φ 1,3 integrable perturbations on the boundary and on the defect and describe the flow of the spectrum. Adding a Φ1,3 integrable perturbation to move off-criticality in the bulk, we determine the finite size spectrum of the massive scattering theory in the three geometries via Thermodynamic Bethe Ansatz (TBA) equations. We derive these integral equations for all excitations by solving, in the continuum scaling limit, the TBA functional equations satisfied by the transfer matrices of the associated A 4 RSOS lattice model of Forrester and Baxter in Regime III. The excitations are classified in terms of ( m, n) systems. The excited state TBA equations agree with the previously conjectured equations in the boundary and periodic cases. In the defect case, new TBA equations confirm previously conjectured transmission factors.

Towards direct synthesis of alane: A predicted defect-mediated pathway confirmed experimentally

DOE PAGES

Wang, Lin -Lin; Herwadkar, Aditi; Reich, Jason M.; ...

2016-08-18

Here, alane (AlH 3) is a unique energetic material that has not found a broad practical use for over 70 years because it is difficult to synthesize directly from its elements. Using density functional theory, we examine the defect-mediated formation of alane monomers on Al(111) in a two-step process: (1) dissociative adsorption of H 2 and (2) alane formation, which are both endothermic on a clean surface. Only with Ti dopant to facilitate H 2 dissociation and vacancies to provide Al adatoms, both processes become exothermic. In agreement, in situ scanning tunneling microscopy showed that during H 2 exposure, alanemore » monomers and clusters form primarily in the vicinity of Al vacancies and Ti atoms. Moreover, ball milling of the Al samples with Ti (providing necessary defects) showed a 10 % conversion of Al into AlH 3 or closely related species at 344 bar H 2, indicating that the predicted pathway may lead to the direct synthesis of alane from elements at pressures much lower than the 104 bar expected from bulk thermodynamics.« less

Thermodynamics and Kinetics of Three Mg-H-VN Complexes in Mg:GaN from Combined First-Principles Calculation and Experiment

NASA Astrophysics Data System (ADS)

Lee, Donghwa; Mitchell, Brandon; Fujiwara, Y.; Dierolf, V.

2014-05-01

An understanding of the formation and dissociation process of Mg-H defects in GaN is of paramount importance for high efficient GaN-based solid-state lighting. Through a combination of first-principle calculations and experimental observations, we find the existence of three types of Mg related centers forming different Mg-H-VN complexes in Mg:GaN. Our study shows that the three different arrangements, which differ by the relative position of the H, determine the degree of acceptor passivation by changing their charge state from +3 to +1. The energetic study demonstrates that the relative stability of the defect complexes can vary with the location of the Fermi level, as well as thermal annealing and electron beam irradiation. The inclusion of a VN is shown to produce an additional variance in optical spectra associated with Mg acceptor activation, resulting from changes in the defect configurations and charge states. Our study shows that these three Mg-H-VN complexes are key components for understanding the Mg acceptor activation and passivation processes.

On the mechanical stability of the body-centered cubic phase and the emergence of a metastable cI16 phase in classical hard sphere solids

NASA Astrophysics Data System (ADS)

Warshavsky, Vadim B.; Ford, David M.; Monson, Peter A.

2018-01-01

The stability of the body-centered cubic (bcc) solid phase of classical hard spheres is of intrinsic interest and is also relevant to the development of perturbation theories for bcc solids of other model systems. Using canonical ensemble Monte Carlo, we simulated systems initialized in a perfect bcc lattice at various densities in the solid region. We observed that the systems rapidly evolved into one of four structures that then persisted for the duration of the simulation. Remarkably, one of these structures was identified as cI16, a cubic crystalline structure with 16 particles in the unit cell, which has recently been observed experimentally in lithium and sodium solids at high pressures. The other three structures do not exhibit crystalline order but are characterized by common patterns in the radial distribution function and bond-orientational order parameter distribution; we refer to them as bcc-di, with i ranging from 1 to 3. We found similar outcomes when employing any of the three single occupancy cell (SOC) restrictions commonly used in the literature. We also ran long constant-pressure simulations with box shape fluctuations initiated from bcc and cI16 initial configurations. At lower pressures, all the systems evolved to defective face-centered cubic (fcc) or hexagonal close-packed (hcp) structures. At higher pressures, most of the systems initiated as bcc evolved to cI16 with some evolving to defective fcc/hcp. High pressure systems initiated from cI16 remained in that structure. We computed the chemical potential of cI16 using the Einstein crystal reference method and found that it is higher than that of fcc by ˜0.5kT-2.5kT over the pressure range studied, with the difference increasing with pressure. We find that the undistorted bcc solid, even with constant-volume and SOC restrictions applied, is so mechanically unstable that it is unsuitable for consideration as a metastable phase or as a reference system for studying bcc phases of other systems. On the other hand, cI16 is a mechanically stable structure that can spontaneously emerge from a bcc starting point but it is thermodynamically metastable relative to fcc or hcp.

Tunable thermodynamic activity of LaxSr1–xMnyAl1–yO3–δ (0 ≤ x ≤ 1, 0 ≤ y ≤ 1) perovskites for solar thermochemical fuel synthesis† †Electronic supplementary information (ESI) available: Computational details, comprehensive XRD analyses, oxygen nonstoichiometry measurements and thermodynamic characterization of the perovskites. See DOI: 10.1039/c6ta06644e Click here for additional data file.

PubMed Central

Ezbiri, M.; Takacs, M.; Theiler, D.; Steinfeld, A.

2017-01-01

Nonstoichiometric metal oxides with variable valence are attractive redox materials for thermochemical and electrochemical fuel processing. To guide the design of advanced redox materials for solar-driven splitting of CO2 and/or H2O to produce CO and/or H2 (syngas), we investigate the equilibrium thermodynamics of the LaxSr1–xMnyAl1–yO3–δ perovskite family (0 ≤ x ≤ 1, 0 ≤ y ≤ 1) and La0.6Ca0.4Mn0.8Al0.2O3–δ, and compare them to those of CeO2 as the baseline. Oxygen nonstoichiometry measurements from 1573 to 1773 K and from 0.206 to 180 mbar O2 show a tunable reduction extent, increasing with increasing Sr content. Maximal nonstoichiometry of 0.32 is established with La0.2Sr0.8Mn0.8Al0.2O3–δ at 1773 K and 2.37 mbar O2. As a trend, we find that oxygen capacities are most sensitive to the A-cation composition. Partial molar enthalpy, entropy and Gibbs free energy changes for oxide reduction are extracted from the experimental data using defect models for Mn4+/Mn3+ and Mn3+/Mn2+ redox couples. We find that perovskites exhibit typically decreasing enthalpy changes with increasing nonstoichiometries. This desirable characteristic is most pronounced by La0.6Sr0.4Mn0.4Al0.6O3–δ, rendering it attractive for CO2 and H2O splitting. Generally, perovskites show lower enthalpy and entropy changes than ceria, resulting in more favorable reduction but less favorable oxidation equilibria. The energy penalties due to larger temperature swings and excess oxidants are discussed in particular. Using electronic structure theory, we conclude with a practical methodology estimating thermodynamic activity to rationally design perovskites with variable stoichiometry and valence. PMID:28580143

Birth Defects

MedlinePlus

... both. Some birth defects like cleft lip or neural tube defects are structural problems that can be ... during pregnancy is a key factor in causing neural tube defects. For most birth defects, the cause ...

Actinic imaging and evaluation of phase structures on EUV lithography masks

DOE Office of Scientific and Technical Information (OSTI.GOV)

Mochi, Iacopo; Goldberg, Kenneth; Huh, Sungmin

2010-09-28

The authors describe the implementation of a phase-retrieval algorithm to reconstruct phase and complex amplitude of structures on EUV lithography masks. Many native defects commonly found on EUV reticles are difficult to detect and review accurately because they have a strong phase component. Understanding the complex amplitude of mask features is essential for predictive modeling of defect printability and defect repair. Besides printing in a stepper, the most accurate way to characterize such defects is with actinic inspection, performed at the design, EUV wavelength. Phase defect and phase structures show a distinct through-focus behavior that enables qualitative evaluation of themore » object phase from two or more high-resolution intensity measurements. For the first time, phase of structures and defects on EUV masks were quantitatively reconstructed based on aerial image measurements, using a modified version of a phase-retrieval algorithm developed to test optical phase shifting reticles.« less

Mechanical and thermodynamic properties of AlX (X = N, P, As) compounds

NASA Astrophysics Data System (ADS)

Xu, Lifang; Bu, Wei

2017-09-01

The Vickers hardness of various AlX (X = N, P, As) compound polymorphs were calculated with the bond resistance model. Thermodynamic properties, such as vibrational entropy, constant volume specific heat and Debye temperatures, were calculated using phonon dispersion relations and phonon density of states (DOS). The calculated values are in good agreement with the previous experimental and theoretical data. For the same structure of AlX (X = N, P, As) compounds, their hardness and Debye temperatures both decrease with the X atomic number. The wurtzite (wz) and zincblende (zb) structures of the same compounds AlX share an almost identical hardness, but have different Debye temperatures. The difference between wz and zb structures increases as the atomic number of X increases. The thermodynamic properties reveal that the constant volume specific heat approaches the Dulong-Petit rule at high temperatures.

Structure-Thermodynamics-Antioxidant Activity Relationships of Selected Natural Phenolic Acids and Derivatives: An Experimental and Theoretical Evaluation

PubMed Central

Zheng, Jie; Liang, Guizhao

2015-01-01

Phenolic acids and derivatives have potential biological functions, however, little is known about the structure-activity relationships and the underlying action mechanisms of these phenolic acids to date. Herein we investigate the structure-thermodynamics-antioxidant relationships of 20 natural phenolic acids and derivatives using DPPH• scavenging assay, density functional theory calculations at the B3LYP/6-311++G(d,p) levels of theory, and quantitative structure-activity relationship (QSAR) modeling. Three main working mechanisms (HAT, SETPT and SPLET) are explored in four micro-environments (gas-phase, benzene, water and ethanol). Computed thermodynamics parameters (BDE, IP, PDE, PA and ETE) are compared with the experimental radical scavenging activities against DPPH•. Available theoretical and experimental investigations have demonstrated that the extended delocalization and intra-molecular hydrogen bonds are the two main contributions to the stability of the radicals. The C = O or C = C in COOH, COOR, C = CCOOH and C = CCOOR groups, and orthodiphenolic functionalities are shown to favorably stabilize the specific radical species to enhance the radical scavenging activities, while the presence of the single OH in the ortho position of the COOH group disfavors the activities. HAT is the thermodynamically preferred mechanism in the gas phase and benzene, whereas SPLET in water and ethanol. Furthermore, our QSAR models robustly represent the structure-activity relationships of these explored compounds in polar media. PMID:25803685

Structure-thermodynamics-antioxidant activity relationships of selected natural phenolic acids and derivatives: an experimental and theoretical evaluation.

PubMed

Chen, Yuzhen; Xiao, Huizhi; Zheng, Jie; Liang, Guizhao

2015-01-01

Phenolic acids and derivatives have potential biological functions, however, little is known about the structure-activity relationships and the underlying action mechanisms of these phenolic acids to date. Herein we investigate the structure-thermodynamics-antioxidant relationships of 20 natural phenolic acids and derivatives using DPPH• scavenging assay, density functional theory calculations at the B3LYP/6-311++G(d,p) levels of theory, and quantitative structure-activity relationship (QSAR) modeling. Three main working mechanisms (HAT, SETPT and SPLET) are explored in four micro-environments (gas-phase, benzene, water and ethanol). Computed thermodynamics parameters (BDE, IP, PDE, PA and ETE) are compared with the experimental radical scavenging activities against DPPH•. Available theoretical and experimental investigations have demonstrated that the extended delocalization and intra-molecular hydrogen bonds are the two main contributions to the stability of the radicals. The C = O or C = C in COOH, COOR, C = CCOOH and C = CCOOR groups, and orthodiphenolic functionalities are shown to favorably stabilize the specific radical species to enhance the radical scavenging activities, while the presence of the single OH in the ortho position of the COOH group disfavors the activities. HAT is the thermodynamically preferred mechanism in the gas phase and benzene, whereas SPLET in water and ethanol. Furthermore, our QSAR models robustly represent the structure-activity relationships of these explored compounds in polar media.

A thermodynamic definition of protein domains.

PubMed

Porter, Lauren L; Rose, George D

2012-06-12

Protein domains are conspicuous structural units in globular proteins, and their identification has been a topic of intense biochemical interest dating back to the earliest crystal structures. Numerous disparate domain identification algorithms have been proposed, all involving some combination of visual intuition and/or structure-based decomposition. Instead, we present a rigorous, thermodynamically-based approach that redefines domains as cooperative chain segments. In greater detail, most small proteins fold with high cooperativity, meaning that the equilibrium population is dominated by completely folded and completely unfolded molecules, with a negligible subpopulation of partially folded intermediates. Here, we redefine structural domains in thermodynamic terms as cooperative folding units, based on m-values, which measure the cooperativity of a protein or its substructures. In our analysis, a domain is equated to a contiguous segment of the folded protein whose m-value is largely unaffected when that segment is excised from its parent structure. Defined in this way, a domain is a self-contained cooperative unit; i.e., its cooperativity depends primarily upon intrasegment interactions, not intersegment interactions. Implementing this concept computationally, the domains in a large representative set of proteins were identified; all exhibit consistency with experimental findings. Specifically, our domain divisions correspond to the experimentally determined equilibrium folding intermediates in a set of nine proteins. The approach was also proofed against a representative set of 71 additional proteins, again with confirmatory results. Our reframed interpretation of a protein domain transforms an indeterminate structural phenomenon into a quantifiable molecular property grounded in solution thermodynamics.

Characterization and manipulation of individual defects in insulating hexagonal boron nitride using scanning tunnelling microscopy.

PubMed

Wong, Dillon; Velasco, Jairo; Ju, Long; Lee, Juwon; Kahn, Salman; Tsai, Hsin-Zon; Germany, Chad; Taniguchi, Takashi; Watanabe, Kenji; Zettl, Alex; Wang, Feng; Crommie, Michael F

2015-11-01

Defects play a key role in determining the properties and technological applications of nanoscale materials and, because they tend to be highly localized, characterizing them at the single-defect level is of particular importance. Scanning tunnelling microscopy has long been used to image the electronic structure of individual point defects in conductors, semiconductors and ultrathin films, but such single-defect electronic characterization remains an elusive goal for intrinsic bulk insulators. Here, we show that individual native defects in an intrinsic bulk hexagonal boron nitride insulator can be characterized and manipulated using a scanning tunnelling microscope. This would typically be impossible due to the lack of a conducting drain path for electrical current. We overcome this problem by using a graphene/boron nitride heterostructure, which exploits the atomically thin nature of graphene to allow the visualization of defect phenomena in the underlying bulk boron nitride. We observe three different defect structures that we attribute to defects within the bulk insulating boron nitride. Using scanning tunnelling spectroscopy we obtain charge and energy-level information for these boron nitride defect structures. We also show that it is possible to manipulate the defects through voltage pulses applied to the scanning tunnelling microscope tip.

Nanoscale interfacial defect shedding in a growing nematic droplet.

PubMed

Gurevich, Sebastian; Provatas, Nikolas; Rey, Alejandro

2017-08-01

Interfacial defect shedding is the most recent known mechanism for defect formation in a thermally driven isotropic-to-nematic phase transition. It manifests in nematic-isotropic interfaces going through an anchoring switch. Numerical computations in planar geometry established that a growing nematic droplet can undergo interfacial defect shedding, nucleating interfacial defect structures that shed into the bulk as +1/2 point defects. By extending the study of interfacial defect shedding in a growing nematic droplet to larger length and time scales, and to three dimensions, we unveil an oscillatory growth mode involving shape and anchoring transitions that results in a controllable regular distributions of point defects in planar geometry, and complex structures of disclination lines in three dimensions.

First principles investigation of structural, mechanical, dynamical and thermodynamic properties of AgMg under pressure

NASA Astrophysics Data System (ADS)

Cui, Rong Hua; Chao Dong, Zheng; Gui Zhong, Chong

2017-12-01

The effects of pressure on the structural, mechanical, dynamical and thermodynamic properties of AgMg have been investigated using first principles based on density functional theory. The optimized lattice constants agree well with previous experimental and theoretical results. The bulk modulus, shear modulus, Young’s modulus, Poisson’s ratio and Debye temperature under pressures were calculated. The calculated results of Cauchy pressure and B/G ratio indicate that AgMg shows ductile nature. Phonon dispersion curves suggest the dynamical stability of AgMg. The pressure dependent behavior of thermodynamic properties are calculated, the Helmholtz free energy and internal energy increase with increase of pressure, while entropy and heat capacity decrease.

Integrative energy-systems design: System structure from thermodynamic optimization

NASA Astrophysics Data System (ADS)

Ordonez, Juan Carlos

This thesis deals with the application of thermodynamic optimization to find optimal structure and operation conditions of energy systems. Chapter 1 outlines the thermodynamic optimization of a combined power and refrigeration system subject to constraints. It is shown that the thermodynamic optimum is reached by distributing optimally the heat exchanger inventory. Chapter 2 considers the maximization of power extraction from a hot stream in the presence of phase change. It shows that when the receiving (cold) stream boils in a counterflow heat exchanger, the thermodynamic optimization consists of locating the optimal capacity rate of the cold stream. Chapter 3 shows that the main architectural features of a counterflow heat exchanger can be determined based on thermodynamic optimization subject to volume constraint. Chapter 4 addresses two basic issues in the thermodynamic optimization of environmental control systems (ECS) for aircraft: realistic limits for the minimal power requirement, and design features that facilitate operation at minimal power consumption. Several models of the ECS-Cabin interaction are considered and it is shown that in all the models the temperature of the air stream that the ECS delivers to the cabin can be optimized for operation at minimal power. In chapter 5 it is shown that the sizes (weights) of heat and fluid flow systems that function on board vehicles such as aircraft can be derived from the maximization of overall (system level) performance. Chapter 6 develops analytically the optimal sizes (hydraulic diameters) of parallel channels that penetrate and cool a volume with uniformly distributed internal heat generation and Chapter 7 shows analytically and numerically how an originally uniform flow structure transforms itself into a nonuniform one when the objective is to minimize global flow losses. It is shown that flow maldistribution and the abandonment of symmetry are necessary for the development of flow structures with minimal resistance. In the second part of the chapter, the flow medium is continuous and permeated by Darcy flow. As flow systems become smaller and more compact, the flow systems themselves become "designed porous media".

Analyzing the defect structure of CuO-doped PZT and KNN piezoelectrics from electron paramagnetic resonance.

PubMed

Jakes, Peter; Kungl, Hans; Schierholz, Roland; Eichel, Rüdiger-A

2014-09-01

The defect structure for copper-doped sodium potassium niobate (KNN) ferroelectrics has been analyzed with respect to its defect structure. In particular, the interplay between the mutually compensating dimeric (Cu(Nb)'''-V(O)··) and trimeric (V(O)··-Cu(Nb)'''-V(O)··)· defect complexes with 180° and non-180° domain walls has been analyzed and compared to the effects from (Cu'' - V(O)··)(x)× dipoles in CuO-doped lead zirconate titanate (PZT). Attempts are made to relate the rearrangement of defect complexes to macroscopic electromechanical properties.

Nonlinear Impedance Analysis of La 0.4Sr 0.6Co 0.2Fe 0.8O 3-δ Thin Film Oxygen Electrodes

DOE PAGES

Geary, Tim C.; Lee, Dongkyu; Shao-Horn, Yang; ...

2016-07-23

Here, linear and nonlinear electrochemical impedance spectroscopy (EIS, NLEIS) were used to study 20 nm thin film La 0.6Sr 0.4Co 0.2Fe 0.8O 3-δ (LSCF-6428) electrodes at 600°C in oxygen environments. LSCF films were epitaxially deposited on single crystal yttria-stabilized zirconia (YSZ) with a 5 nm gadolinium-doped ceria (GDC) protective interlayer. Impedance measurements reveal an oxygen storage capacity similar to independent thermogravimetry measurements on semi-porous pellets. However, the impedance data fail to obey a homogeneous semiconductor point-defect model. Two consistent scenarios were considered: a homogeneous film with non-ideal thermodynamics (constrained by thermogravimetry measurements), or an inhomogeneous film (constrained by a semiconductormore » point-defect model with a Sr maldistribution). The latter interpretation suggests that gradients in Sr composition would have to extend beyond the space-charge region of the gas-electrode interface. While there is growing evidence supporting an equilibrium Sr segregation at the LSCF surface monolayer, a long-range, non-equilibrium Sr stratification caused by electrode processing conditions offers a possible explanation for the large volume of highly reducible LSCF. Additionally, all thin films exhibited fluctuations in both linear and nonlinear impedance over the hundred-hour measurement period. This behavior is inconsistent with changes solely in the surface rate coefficient and possibly caused by variations in the surface thermodynamics over exposure time.« less

Defect modes in a stacked structure of chiral photonic crystals.

PubMed

Chen, Jiun-Yeu; Chen, Lien-Wen

2005-06-01

An optical propagation simulation is carried out for the study of photonic defect modes in a stacked structure of cholesteric liquid crystal films with spatially varying pitch. The defects are introduced by a pitch jump and a phase jump in the cholesteric helix. The effect of a finite sample thickness on transmission of the defect mode and on the required polarization of incident light to create the defect mode is discussed. For normal and near-normal incidence of circularly polarized light with the same handedness as structure, the defect caused by a pitch jump results in discrete peaks within a forbidden band in the transmission. The particular spectrum is similar to the feature of a Fabry-Pérot interferometer. By introducing an additional phase jump, linear blueshifts of the defect modes in transmission spectra are correlated with an increase in the twist angle.

Real time studies of Elastic Moduli Pu Aging using Resonant Ultrasound Spectroscopy

NASA Astrophysics Data System (ADS)

Maiorov, Boris

Elastic moduli are fundamental thermodynamic susceptibilities that connect directly to thermodynamics, electronic structure and give important information about mechanical properties. To determine the time evolution of the elastic properties in 239Pu and it Ga alloys, is imperative to study its phase stability and self-irradiation damage process. The most-likely sources of these changes include a) ingrowth of radioactive decay products like He and U, b) the introduction of radiation damage, c) δ-phase instabilities towards α-Pu or to Pu3Ga. The measurement of mechanical resonance frequencies can be made with extreme precision and used to compute the elastic moduli without corrections giving important insight in this problem. Using Resonant Ultrasound Spectroscopy, we measured the time dependence of the mechanical resonance frequencies of fine-grained polycrystalline δ-phase 239Pu, from 300K up to 480K. At room temperature, the shear modulus shows an increase in time (stiffening), but the bulk modulus decreases (softening). These are the first real-time measurements of room temperature aging of the elastic moduli, and the changes are consistent with elastic moduli measurements performed on 44 year old δ-Pu. As the temperature is increased, the rate of change increases exponentially, with both moduli becoming stiffer with time. For T>420K an abrupt change in the time dependence is observed indicating that the bulk and shear moduli have opposite rates of change. Our measurements provide a basis for ruling out the decomposition of δ-Pu towards α-Pu or Pu3Ga, and indicate a complex defect-related scenario from which we are gathering important clues.

Band Structure Characteristics of Nacreous Composite Materials with Various Defects

NASA Astrophysics Data System (ADS)

Yin, J.; Zhang, S.; Zhang, H. W.; Chen, B. S.

2016-06-01

Nacreous composite materials have excellent mechanical properties, such as high strength, high toughness, and wide phononic band gap. In order to research band structure characteristics of nacreous composite materials with various defects, supercell models with the Brick-and-Mortar microstructure are considered. An efficient multi-level substructure algorithm is employed to discuss the band structure. Furthermore, two common systems with point and line defects and varied material parameters are discussed. In addition, band structures concerning straight and deflected crack defects are calculated by changing the shear modulus of the mortar. Finally, the sensitivity of band structures to the random material distribution is presented by considering different volume ratios of the brick. The results reveal that the first band gap of a nacreous composite material is insensitive to defects under certain conditions. It will be of great value to the design and synthesis of new nacreous composite materials for better dynamic properties.

Elastic dependence of defect modes in one-dimensional photonic crystals with a cholesteric elastomer slab

NASA Astrophysics Data System (ADS)

Avendanño, Carlos G.; Martínez, Daniel

2018-07-01

We studied the transmission spectra in a one-dimensional dielectric multilayer photonic structure containing a cholesteric liquid crystal elastomer layer as a defect. For circularly polarized incident electromagnetic waves, we analyzed the optical defect modes induced in the band gap spectrum as a function of the incident angle and the axial strain applied along the same axis as the periodic medium. The physical parameters of the structure were chosen in such a way the photonic band gap of the cholesteric elastomer lies inside that of the multilayer. We found that, in addition to the defect modes associated with the thickness of the defect layer and the anisotropy of the elastic polymer, two new defect modes appear at both band edges of the cholesteric structure, whose amplitudes and spectral positions can be elastically tuned. Particularly, we showed that, at normal incidence, the defect modes shift toward the long-wavelength region with the strain; whereas, for constant elongation, such defects move toward larger frequencies with the incidence angle.

Free Energy Defect Model for the Cu-In-Ga-Se Tetrahedral Lattice

NASA Astrophysics Data System (ADS)

Stanbery, B. J.

2003-03-01

The most efficient thin-film photovoltaic converters of solar insolation to electrical power have recently achieved conversion efficiencies exceeding 19%, and are based on light absorbing layers containing the binary alloy (CuInSe_2)_1-X(CuGaSe_2)X of the α phases of these ternary chalcopyrite compounds. A statistical quantum mechanical model of the thermodynamic equilibrium defect structure of the tetrahedral lattice of copper, indium, and selenium with composition in the domain between that of the stoichiometric CuIn_1-XGa_XSe2 alloy and the β phase Cu(In_1-XGa_X)_3Se5 composition is presented. Compositions more copper-deficient than the latter have been reported experimentally to result in a breakdown of the tetrahedral coordination characteristic of the chalcopyrite lattice. These computations are based on a cluster expansion algorithm that minimizes the total free energy of the system using the Gibbs-Duhem equation to compute quasichemical reaction equilibria between the neutral clusters, and explicitly incorporates Fermi-Dirac statistics to determine their ionization equilibria and consequent carrier concentrations in the conduction and valence bands. The results are consistent with recent experimental evidence that the stoichiometric CuIn_1-XGa_XSe2 composition segregates in equilibrium into a two-phase mixture of a copper-deficient quaternary Cu_1-γIn_1-XGa_XSe2 composition and the binary Cu_2-δSe compound. The model predicts that the hole majority carrier (p-type) can only be achieved in the equilibrium single-phase chalcopyrite lattice with compositions that correspond to Cu_1-γIn_1-XGa_XSe_2+ɛ with γ and ɛ >0. This predicted requirement for selenium enrichment compared to the stoichiometric CuIn_1-XGa_XSe2 alloy composition for the dominance of holes over electrons as the majority carrier type is consistent with experimental evidence, and is explained in terms of a transition of the dominant lattice defect from the selenium vacancy in the stoichiometric case to the copper vacancy defect in the selenium-enriched lattice. This result is of particular importance since all CuIn_1-XGa_XSe2 thin-film solar cells utilize p-type absorber films.

Thermodynamics and Structural Evolution during a Reversible Vesicle-Micelle Transition of a Vitamin-Derived Bolaamphiphile Induced by Sodium Cholate.

PubMed

Tian, Jun-Nan; Ge, Bing-Qiang; Shen, Yun-Feng; He, Yu-Xuan; Chen, Zhong-Xiu

2016-03-09

Interaction of endogenous sodium cholate (SC) with dietary amphiphiles would induce structural evolution of the self-assembled aggregates, which inevitably affects the hydrolysis of fat in the gut. Current work mainly focused on the interaction of bile salts with classical double-layered phospholipid vesicles. In this paper, the thermodynamics and structural evolution during the interaction of SC with novel unilamellar vesicles formed from vitamin-derived zwitterionic bolaamphiphile (DDO) were characterized. It was revealed that an increased temperature and the presence of NaCl resulted in narrowed micelle-vesicle coexistence and enlarged the vesicle region. The coexistence of micelles and vesicles mainly came from the interaction of monomeric SC with DDO vesicles, whereas micellar SC contributed to the total solubilization of DDO vesicles. This research may enrich the thermodynamic mechanism behind the structure transition of the microaggregates formed by amphiphiles in the gut. It will also contribute to the design of food formulation and drug delivery system.

Two-state thermodynamics and the possibility of a liquid-liquid phase transition in supercooled TIP4P/2005 water

DOE Office of Scientific and Technical Information (OSTI.GOV)

Singh, Rakesh S.; Debenedetti, Pablo G.; Biddle, John W.

Water shows intriguing thermodynamic and dynamic anomalies in the supercooled liquid state. One possible explanation of the origin of these anomalies lies in the existence of a metastable liquid-liquid phase transition (LLPT) between two (high and low density) forms of water. While the anomalies are observed in experiments on bulk and confined water and by computer simulation studies of different water-like models, the existence of a LLPT in water is still debated. Unambiguous experimental proof of the existence of a LLPT in bulk supercooled water is hampered by fast ice nucleation which is a precursor of the hypothesized LLPT. Moreover,more » the hypothesized LLPT, being metastable, in principle cannot exist in the thermodynamic limit (infinite size, infinite time). Therefore, computer simulations of water models are crucial for exploring the possibility of the metastable LLPT and the nature of the anomalies. In this work, we present new simulation results in the NVT ensemble for one of the most accurate classical molecular models of water, TIP4P/2005. To describe the computed properties and explore the possibility of a LLPT, we have applied two-structure thermodynamics, viewing water as a non-ideal mixture of two interconvertible local structures (“states”). The results suggest the presence of a liquid-liquid critical point and are consistent with the existence of a LLPT in this model for the simulated length and time scales. We have compared the behavior of TIP4P/2005 with other popular water-like models, namely, mW and ST2, and with real water, all of which are well described by two-state thermodynamics. In view of the current debate involving different studies of TIP4P/2005, we discuss consequences of metastability and finite size in observing the liquid-liquid separation. We also address the relationship between the phenomenological order parameter of two-structure thermodynamics and the microscopic nature of the low-density structure.« less

Simulation of Rutherford backscattering spectrometry from arbitrary atom structures

DOE PAGES

Zhang, S.; Univ. of Helsinki; Nordlund, Kai; ...

2016-10-25

Rutherford backscattering spectrometry in a channeling direction (RBS/C) is a powerful tool for analysis of the fraction of atoms displaced from their lattice positions. However, it is in many cases not straightforward to analyze what is the actual defect structure underlying the RBS/C signal. To reveal insights of RBS/C signals from arbitrarily complex defective atomic structures, we develop in this paper a method for simulating the RBS/C spectrum from a set of arbitrary read-in atom coordinates (obtained, e.g., from molecular dynamics simulations). We apply the developed method to simulate the RBS/C signals from Ni crystal structures containing randomly displaced atoms,more » Frenkel point defects, and extended defects, respectively. The RBS/C simulations show that, even for the same number of atoms in defects, the RBS/C signal is much stronger for the extended defects. Finally, comparison with experimental results shows that the disorder profile obtained from RBS/C signals in ion-irradiated Ni is due to a small fraction of extended defects rather than a large number of individual random atoms.« less

Atomistic simulation of defect formation and structure transitions in U-Mo alloys in swift heavy ion irradiation

NASA Astrophysics Data System (ADS)

Kolotova, L. N.; Starikov, S. V.

2017-11-01

In irradiation of swift heavy ions, the defects formation frequently takes place in crystals. High energy transfer into the electronic subsystem and relaxations processes lead to the formation of structural defects and cause specific effects, such as the track formation. There is a large interest to understanding of the mechanisms of defects/tracks formation due to the heating of the electron subsystem. In this work, the atomistic simulation of defects formation and structure transitions in U-Mo alloys in irradiation of swift heavy ions has been carried out. We use the two-temperature atomistic model with explicit account of electron pressure and electron thermal conductivity. This two-temperature model describes ionic subsystem by means of molecular dynamics while the electron subsystem is considered in the continuum approach. The various mechanisms of structure changes in irradiation are examined. In particular, the simulation results indicate that the defects formation may be produced without melting and subsequent crystallization. Threshold stopping power of swift ions for the defects formation in irradiation in the various conditions are calculated.

Average structure and local configuration of excess oxygen in UO(2+x).

PubMed

Wang, Jianwei; Ewing, Rodney C; Becker, Udo

2014-03-19

Determination of the local configuration of interacting defects in a crystalline, periodic solid is problematic because defects typically do not have a long-range periodicity. Uranium dioxide, the primary fuel for fission reactors, exists in hyperstoichiometric form, UO(2+x). Those excess oxygen atoms occur as interstitial defects, and these defects are not random but rather partially ordered. The widely-accepted model to date, the Willis cluster based on neutron diffraction, cannot be reconciled with the first-principles molecular dynamics simulations present here. We demonstrate that the Willis cluster is a fair representation of the numerical ratio of different interstitial O atoms; however, the model does not represent the actual local configuration. The simulations show that the average structure of UO(2+x) involves a combination of defect structures including split di-interstitial, di-interstitial, mono-interstitial, and the Willis cluster, and the latter is a transition state that provides for the fast diffusion of the defect cluster. The results provide new insights in differentiating the average structure from the local configuration of defects in a solid and the transport properties of UO(2+x).

RNA Thermodynamic Structural Entropy

PubMed Central

Garcia-Martin, Juan Antonio; Clote, Peter

2015-01-01

Conformational entropy for atomic-level, three dimensional biomolecules is known experimentally to play an important role in protein-ligand discrimination, yet reliable computation of entropy remains a difficult problem. Here we describe the first two accurate and efficient algorithms to compute the conformational entropy for RNA secondary structures, with respect to the Turner energy model, where free energy parameters are determined from UV absorption experiments. An algorithm to compute the derivational entropy for RNA secondary structures had previously been introduced, using stochastic context free grammars (SCFGs). However, the numerical value of derivational entropy depends heavily on the chosen context free grammar and on the training set used to estimate rule probabilities. Using data from the Rfam database, we determine that both of our thermodynamic methods, which agree in numerical value, are substantially faster than the SCFG method. Thermodynamic structural entropy is much smaller than derivational entropy, and the correlation between length-normalized thermodynamic entropy and derivational entropy is moderately weak to poor. In applications, we plot the structural entropy as a function of temperature for known thermoswitches, such as the repression of heat shock gene expression (ROSE) element, we determine that the correlation between hammerhead ribozyme cleavage activity and total free energy is improved by including an additional free energy term arising from conformational entropy, and we plot the structural entropy of windows of the HIV-1 genome. Our software RNAentropy can compute structural entropy for any user-specified temperature, and supports both the Turner’99 and Turner’04 energy parameters. It follows that RNAentropy is state-of-the-art software to compute RNA secondary structure conformational entropy. Source code is available at https://github.com/clotelab/RNAentropy/; a full web server is available at http://bioinformatics.bc.edu/clotelab/RNAentropy, including source code and ancillary programs. PMID:26555444

RNA Thermodynamic Structural Entropy.

PubMed

Garcia-Martin, Juan Antonio; Clote, Peter

2015-01-01

Conformational entropy for atomic-level, three dimensional biomolecules is known experimentally to play an important role in protein-ligand discrimination, yet reliable computation of entropy remains a difficult problem. Here we describe the first two accurate and efficient algorithms to compute the conformational entropy for RNA secondary structures, with respect to the Turner energy model, where free energy parameters are determined from UV absorption experiments. An algorithm to compute the derivational entropy for RNA secondary structures had previously been introduced, using stochastic context free grammars (SCFGs). However, the numerical value of derivational entropy depends heavily on the chosen context free grammar and on the training set used to estimate rule probabilities. Using data from the Rfam database, we determine that both of our thermodynamic methods, which agree in numerical value, are substantially faster than the SCFG method. Thermodynamic structural entropy is much smaller than derivational entropy, and the correlation between length-normalized thermodynamic entropy and derivational entropy is moderately weak to poor. In applications, we plot the structural entropy as a function of temperature for known thermoswitches, such as the repression of heat shock gene expression (ROSE) element, we determine that the correlation between hammerhead ribozyme cleavage activity and total free energy is improved by including an additional free energy term arising from conformational entropy, and we plot the structural entropy of windows of the HIV-1 genome. Our software RNAentropy can compute structural entropy for any user-specified temperature, and supports both the Turner'99 and Turner'04 energy parameters. It follows that RNAentropy is state-of-the-art software to compute RNA secondary structure conformational entropy. Source code is available at https://github.com/clotelab/RNAentropy/; a full web server is available at http://bioinformatics.bc.edu/clotelab/RNAentropy, including source code and ancillary programs.

A new idea for broad band reflector and tunable multichannel filter of one dimensional symmetric photonic crystal with magnetized cold plasma defects

NASA Astrophysics Data System (ADS)

Kumar, Asish; Singh, Prabal P.; Thapa, Khem B.

2018-05-01

The optical properties of one-dimensional periodic structure composed by SiO2 and dielectric (air) layers with asymmetric and symmetric forms studied. The transmittance for symmetric periodic defective structure analyzed by introducing one, two, three layers of magnetized cold plasma (MCP) in one-dimensional periodic structure. We found better result for symmetric defect of three layer of the MCP compare to the other defective structures. On the basis of our calculated results, we proposed a new idea for broadband reflector at lower frequency range as well as the multichannel filter at higher frequency range.

Study of defects and vacancies in structural properties of Mn, co-doped oxides: ZnO

NASA Astrophysics Data System (ADS)

Kumar, Harish; Kaushik, A.; Alvi, P. A.; Dalela, B.; Dalela, S.

2018-05-01

The paper deals with the Structural properties on Mn, Co doped oxides ZnO samples using XRD, Positron Annihilation Lifetime (PAL) Spectra and Raman Spectra. The Mn, Co doped ZnO samples crystallize in a wurtzite structure without any impurity phases in XRD Spectra. The defect state of these samples has been investigated by using positron annihilation lifetime (PAL) spectroscopy technique in which all the relevant lifetime parameters are measured for all the spectra. The results are explained in the direction of doping concentration in these samples in terms of defects structure on Zn lattice site VZn and oxygen defects Vo.

Synthesis and study of electrolytic materials with a high-energy defect structure and a developed surface

NASA Astrophysics Data System (ADS)

Gryzunova, N. N.; Vikarchuk, A. A.; Tyur'kov, M. N.

2016-10-01

The defect structure of the electrolytic copper coatings formed upon mechanical activation of a cathode is described. These coatings are shown to have a fragmented structure containing disclination-type defects, namely, terminating dislocation, disclination and twin boundaries; partial disclinations, misorientation bands; and twin layers. They have both growth and deformation origins. The mechanisms of formation of the structural defects are discussed. It is experimentally proved that part of the elastic energy stored in the crystal volume during electrocrystallization can be converted into surface energy. As a result, catalytically active materials with a large developed surface can be synthesized.

First-principles study of structural, electronic, and optical properties of surface defects in GaAs(001) - β2(2x4)

NASA Astrophysics Data System (ADS)

Bacuyag, Dhonny; Escaño, Mary Clare Sison; David, Melanie; Tani, Masahiko

2018-06-01

We performed first-principles calculations based on density functional theory (DFT) to investigate the role of point defects in the structural, electronic, and optical properties of the GaAs(001)- β2(2x4). In terms of structural properties, AsGa is the most stable defect structure, consistent with experiments. With respect to the electronic structure, band structures revealed the existence of sub-band and midgap states for all defects. The induced sub-bands and midgap states originated from the redistributions of charges towards these defects and neighboring atoms. The presence of these point defects introduced deep energy levels characteristic of EB3 (0.97 eV), EL4 (0.52 eV), and EL2 (0.82 eV) for AsGa, GaAs, GaV, respectively. The optical properties are found to be strongly related to these induced gap states. The calculated onset values in the absorption spectra, corresponding to the energy gaps, confirmed the absorption below the known bulk band gap of 1.43 eV. These support the possible two-step photoabsorption mediated by midgap states as observed in experiments.

U(v) in metal uranates: A combined experimental and theoretical study of MgUO 4, CrUO 4, and FeUO 4

DOE PAGES

Guo, Xiaofeng; Tiferet, Eitan; Qi, Liang; ...

2016-01-01

Although pentavalent uranium can exist in aqueous solution, its presence in the solid state is uncommon. Metal monouranates, MgUO 4, CrUO 4 and FeUO 4 were synthesized for detailed structural and energetic investigations. Structural characteristics of these uranates used powder X-ray diffraction, synchrotron X-ray absorption spectroscopy, X-ray photoelectron spectroscopy, and 57Fe-Mossbauer spectroscopy. Enthalpies of formation were measured by high temperature oxide melt solution calorimetry. Density functional theory (DFT) calculations provided both structural and energetic information. The measured structural and thermodynamic properties show good consistency with those predicted from DFT. The presence of U 5+ has been solidly confirmed in CrUOmore » 4 and FeUO 4, which are thermodynamically stable compounds, and the origin and stability of U 5+ in the system was elaborated by DFT. Lastly, the structural and thermodynamic behaviour of U 5+ elucidated in this work is relevant to fundamental actinide redox chemistry and to applications in the nuclear industry and radioactive waste disposal.« less

A computational investigation of the thermodynamics and structure in colloid and polymer mixtures

NASA Astrophysics Data System (ADS)

Mahynski, Nathan Alexander

In this dissertation I use computational tools to study the structure and thermodynamics of colloid-polymer mixtures. I show that fluid-fluid phase separation in mixtures of colloids and linear polymers cannot be universally reduced using polymer-based scaling principles since these assume the binodals exist in a single scaling regime, whereas accurate simulations clearly demonstrate otherwise. I show that rethinking these solutions in terms of multiple length scales is necessary to properly explain the thermodynamic stability and structure of these fluid phases, and produce phase diagrams in nearly quantitative agreement with experimental results. I then extend this work to encompass more geometrically complex "star" polymers revealing how the phase behavior for many of these binary mixtures may be mapped onto that of mixtures containing only linear polymers. I further consider the depletion-driven crystallization of athermal colloidal hard spheres induced by polymers. I demonstrate how the partitioning of a finite amount of polymer into the colloidal crystal phase implies that the polymer's architecture can be tailored to interact with the internal void structure of different crystal polymorphs uniquely, thus providing a direct route to thermodynamically stabilizing one arbitrarily chosen structure over another, e.g., the hexagonal close-packed crystal over the face-centered cubic. I then begin to generalize this result by considering the consequences of thermal interactions and complex polymer architectures. These principles lay the groundwork for intelligently engineering co-solute additives in crystallizing colloidal suspensions that can be used to thermodynamically isolate single crystal morphologies. Finally, I examine the competition between self-assembly and phase separation in polymer-grafted nanoparticle systems by comparing and contrasting the validity of two different models for grafted nanoparticles: "nanoparticle amphiphiles" versus "patchy particles." The latter suggests these systems have some utility in forming novel "equilibrium gel" phases, however, I find that considering grafted nanoparticles as amphiphiles provides a qualitatively accurate description of their thermodynamics revealing either first-order phase separation into two isotropic phases or continuous self-assembly. I find no signs of empty liquid formation, suggesting that these nanoparticles do not provide a route to such phases.

Magnesium Nanoparticles for Hydrogen Storage: Structure, Kinetics and Thermodynamics

NASA Astrophysics Data System (ADS)

Pasquini, L.; Brighi, M.; Montone, A.; Vittori Antisari, M.; Dam, B.; Palmisano, V.; Bonetti, E.

2012-08-01

Magnesium nanoparticles coated by a native oxide shell and decorated by palladium clusters were synthesized by the inert gas condensation technique. The kinetics and thermodynamics of hydrogen sorption were investigated by Sieverts measurements at high temperature and by optical hydrogenography close to ambient temperature. The structure and morphology of the nanoparticles were studied by electron microscopy and X-ray diffraction both in the as-prepared state and after hydrogen sorption cycles.

Insight into the Li2CO3-K2CO3 eutectic mixture from classical molecular dynamics: Thermodynamics, structure, and dynamics

NASA Astrophysics Data System (ADS)

Corradini, Dario; Coudert, François-Xavier; Vuilleumier, Rodolphe

2016-03-01

We use molecular dynamics simulations to study the thermodynamics, structure, and dynamics of the Li2CO3-K2CO3 (62:38 mol. %) eutectic mixture. We present a new classical non-polarizable force field for this molten salt mixture, optimized using experimental and first principles molecular dynamics simulations data as reference. This simple force field allows efficient molecular simulations of phenomena at long time scales. We use this optimized force field to describe the behavior of the eutectic mixture in the 900-1100 K temperature range, at pressures between 0 and 5 GPa. After studying the equation of state in these thermodynamic conditions, we present molecular insight into the structure and dynamics of the melt. In particular, we present an analysis of the temperature and pressure dependence of the eutectic mixture's self-diffusion coefficients, viscosity, and ionic conductivity.

Insight into the Li2CO3-K2CO3 eutectic mixture from classical molecular dynamics: Thermodynamics, structure, and dynamics.

PubMed

Corradini, Dario; Coudert, François-Xavier; Vuilleumier, Rodolphe

2016-03-14

We use molecular dynamics simulations to study the thermodynamics, structure, and dynamics of the Li2CO3-K2CO3 (62:38 mol. %) eutectic mixture. We present a new classical non-polarizable force field for this molten salt mixture, optimized using experimental and first principles molecular dynamics simulations data as reference. This simple force field allows efficient molecular simulations of phenomena at long time scales. We use this optimized force field to describe the behavior of the eutectic mixture in the 900-1100 K temperature range, at pressures between 0 and 5 GPa. After studying the equation of state in these thermodynamic conditions, we present molecular insight into the structure and dynamics of the melt. In particular, we present an analysis of the temperature and pressure dependence of the eutectic mixture's self-diffusion coefficients, viscosity, and ionic conductivity.

Thermodynamic prediction of protein neutrality.

PubMed

Bloom, Jesse D; Silberg, Jonathan J; Wilke, Claus O; Drummond, D Allan; Adami, Christoph; Arnold, Frances H

2005-01-18

We present a simple theory that uses thermodynamic parameters to predict the probability that a protein retains the wild-type structure after one or more random amino acid substitutions. Our theory predicts that for large numbers of substitutions the probability that a protein retains its structure will decline exponentially with the number of substitutions, with the severity of this decline determined by properties of the structure. Our theory also predicts that a protein can gain extra robustness to the first few substitutions by increasing its thermodynamic stability. We validate our theory with simulations on lattice protein models and by showing that it quantitatively predicts previously published experimental measurements on subtilisin and our own measurements on variants of TEM1 beta-lactamase. Our work unifies observations about the clustering of functional proteins in sequence space, and provides a basis for interpreting the response of proteins to substitutions in protein engineering applications.

Thermodynamic prediction of protein neutrality

PubMed Central

Bloom, Jesse D.; Silberg, Jonathan J.; Wilke, Claus O.; Drummond, D. Allan; Adami, Christoph; Arnold, Frances H.

2005-01-01

We present a simple theory that uses thermodynamic parameters to predict the probability that a protein retains the wild-type structure after one or more random amino acid substitutions. Our theory predicts that for large numbers of substitutions the probability that a protein retains its structure will decline exponentially with the number of substitutions, with the severity of this decline determined by properties of the structure. Our theory also predicts that a protein can gain extra robustness to the first few substitutions by increasing its thermodynamic stability. We validate our theory with simulations on lattice protein models and by showing that it quantitatively predicts previously published experimental measurements on subtilisin and our own measurements on variants of TEM1 β-lactamase. Our work unifies observations about the clustering of functional proteins in sequence space, and provides a basis for interpreting the response of proteins to substitutions in protein engineering applications. PMID:15644440

Structural, vibrational and thermodynamic properties of Mg2 FeH6 complex hydride

NASA Astrophysics Data System (ADS)

Zhou, H. L.; Yu, Y.; Zhang, H. F.; Gao, T.

2011-02-01

Mg2FeH6, which has one of the highest hydrogen storage capacities among Mg based 3d-transitional metal hydrides, is considered as an attractive material for hydrogen storage. Within density-functional perturbation theory (DFPT), we have investigated the structural, vibrational and thermodynamic properties of Mg2FeH6. The band structure calculation shows that this compound is a semiconductor with a direct X-X energy gap of 1.96 eV. The calculated phonon frequencies for the Raman-active and the infrared-active modes are assigned. The phonon dispersion curves together with the corresponding phonon density of states and longitudinal-transverse optical (LO-TO) splitting are also calculated. Findings are also presented for the temperature-dependent behaviors of some thermodynamic properties such as free energy, internal energy, entropy and heat capacity within the quasi-harmonic approximation based on the calculated phonon density of states.

Thermodynamic properties and static structure factor for a Yukawa fluid in the mean spherical approximation.

PubMed

Montes-Perez, J; Cruz-Vera, A; Herrera, J N

2011-12-01

This work presents the full analytic expressions for the thermodynamic properties and the static structure factor for a hard sphere plus 1-Yukawa fluid within the mean spherical approximation. To obtain these properties of the fluid type Yukawa analytically it was necessary to solve an equation of fourth order for the scaling parameter on a large scale. The physical root of this equation was determined by imposing physical conditions. The results of this work are obtained from seminal papers of Blum and Høye. We show that is not necessary the use the series expansion to solve the equation for the scaling parameter. We applied our theoretical result to find the thermodynamic and the static structure factor for krypton. Our results are in good agreement with those obtained in an experimental form or by simulation using the Monte Carlo method.

Structural defects in GaN revealed by Transmission Electron Microscopy

DOE Office of Scientific and Technical Information (OSTI.GOV)

Liliental-Weber, Zuzanna

This paper reviews the various types of structural defects observed by Transmission Electron Microscopy in GaN heteroepitaxial layers grown on foreign substrates and homoepitaxial layers grown on bulk GaN substrates. The structural perfection of these layers is compared to the platelet self-standing crystals grown by High Nitrogen Pressure Solution. Defects in undoped and Mg doped GaN are discussed. Lastly, some models explaining the formation of inversion domains in heavily Mg doped layers that are possible defects responsible for the difficulties of p-doping in GaN are also reviewed.

Structural defects in GaN revealed by Transmission Electron Microscopy

DOE PAGES

Liliental-Weber, Zuzanna

2014-09-08

This paper reviews the various types of structural defects observed by Transmission Electron Microscopy in GaN heteroepitaxial layers grown on foreign substrates and homoepitaxial layers grown on bulk GaN substrates. The structural perfection of these layers is compared to the platelet self-standing crystals grown by High Nitrogen Pressure Solution. Defects in undoped and Mg doped GaN are discussed. Lastly, some models explaining the formation of inversion domains in heavily Mg doped layers that are possible defects responsible for the difficulties of p-doping in GaN are also reviewed.

Biophysical Analysis of Apolipoprotein E3 Variants Linked with Development of Type III Hyperlipoproteinemia

PubMed Central

Georgiadou, Dimitra; Chroni, Angeliki; Vezeridis, Alexander; Zannis, Vassilis I.; Stratikos, Efstratios

2011-01-01

Background Apolipoprotein E (apoE) is a major protein of the lipoprotein transport system that plays important roles in lipid homeostasis and protection from atherosclerosis. ApoE is characterized by structural plasticity and thermodynamic instability and can undergo significant structural rearrangements as part of its biological function. Mutations in the 136–150 region of the N-terminal domain of apoE, reduce its low density lipoprotein (LDL) receptor binding capacity and have been linked with lipoprotein disorders, such as type III hyperlipoproteinemia (HLP) in humans. However, the LDL-receptor binding defects for these apoE variants do not correlate well with the severity of dyslipidemia, indicating that these variants may carry additional properties that contribute to their pathogenic potential. Methodology/Principal Findings In this study we examined whether three type III HLP predisposing apoE3 variants, namely R136S, R145C and K146E affect the biophysical properties of the protein. Circular dichroism (CD) spectroscopy revealed that these mutations do not significantly alter the secondary structure of the protein. Thermal and chemical unfolding analysis revealed small thermodynamic alterations in each variant compared to wild-type apoE3, as well as effects in the reversibility of the unfolding transition. All variants were able to remodel multillamelar 1,2-Dimyristoyl-sn-glycero-3-phosphocholine (DMPC) vesicles, but R136S and R145C had reduced kinetics. Dynamic light scattering analysis indicated that the variant R136S exists in a higher-order oligomerization state in solution. Finally, 1-anilinonaphthalene-8-sulfonic acid (ANS) binding suggested that the variant R145C exposes a larger amount of hydrophobic surface to the solvent. Conclusions/Significance Overall, our findings suggest that single amino acid changes in the functionally important region 136–150 of apoE3 can affect the molecule's stability and conformation in solution and may underlie functional consequences. However, the magnitude and the non-concerted nature of these changes, make it unlikely that they constitute a distinct unifying mechanism leading to type III HLP pathogenesis. PMID:22069485

Topological defects in electric double layers of ionic liquids at carbon interfaces

DOE PAGES

Black, Jennifer M.; Okatan, Mahmut Baris; Feng, Guang; ...

2015-06-07

The structure and properties of the electrical double layer in ionic liquids is of interest in a wide range of areas including energy storage, catalysis, lubrication, and many more. Theories describing the electrical double layer for ionic liquids have been proposed, however a full molecular level description of the double layer is lacking. To date, studies have been predominantly focused on ion distributions normal to the surface, however the 3D nature of the electrical double layer in ionic liquids requires a full picture of the double layer structure not only normal to the surface, but also in plane. Here wemore » utilize 3D force mapping to probe the in plane structure of an ionic liquid at a graphite interface and report the direct observation of the structure and properties of topological defects. The observation of ion layering at structural defects such as step-edges, reinforced by molecular dynamics simulations, defines the spatial resolution of the method. Observation of defects allows for the establishment of the universality of ionic liquid behavior vs. separation from the carbon surface and to map internal defect structure. In conclusion, these studies offer a universal pathway for probing the internal structure of topological defects in soft condensed matter on the nanometer level in three dimensions.« less

First-principles calculations of the structural, elastic and thermodynamic properties of mackinawite (FeS) and pyrite (FeS2)

NASA Astrophysics Data System (ADS)

Wen, Xiangli; Liang, Yuxuan; Bai, Pengpeng; Luo, Bingwei; Fang, Teng; Yue, Luo; An, Teng; Song, Weiyu; Zheng, Shuqi

2017-11-01

The thermodynamic properties of Fe-S compounds with different crystal structure are very different. In this study, the structural, elastic and thermodynamic properties of mackinawite (FeS) and pyrite (FeS2) were investigated by first-principles calculations. Examination of the electronic density of states shows that mackinawite (FeS) is metallic and that pyrite (FeS2) is a semiconductor with a band gap of Eg = 1.02 eV. Using the stress-strain method, the elastic properties including the bulk modulus and shear modulus were derived from the elastic Cij data. Density functional perturbation theory (DFPT) calculations within the quasi-harmonic approximation (QHA) were used to calculate the thermodynamic properties, and the two Fe-S compounds are found to be dynamically stable. The isothermal bulk modulus, thermal expansion coefficient, heat capacities, Gibbs free energy and entropy of the Fe-S compounds are obtained by first-principles phonon calculations. Furthermore, the temperature of the mackinawite (FeS) ⟶ pyrite (FeS2) phase transition at 0 GPa was predicted. Based on the calculation results, the model for prediction of Fe-S compounds in the Fe-H2S-H2O system was improved.

Rectangular microstrip antenna with corrugation like defects at radiating edge: A new approach to reduce cross polarization radiation

NASA Astrophysics Data System (ADS)

Pawar, U. A.; Mondal, D.; Nagaraju, A.; Chakraborty, S.; Singh, L. L. K.; Chattopadhyay, S.

2018-03-01

In this paper, single layer, simple and compact RMA, with corrugation like defects at the radiating edge, is studied thoroughly to reduce XP radiation from the patch. Unlike the earlier works reported on defected ground structure integrated patches and defect patch structures, in this work, corrugation like linear defects have been placed at the radiating edges of the patch to reduce cross polarisation radiation. Around 30-40 dB of CP-XP isolation is observed in H-plane with 7% impedance bandwidth and in E-plane also, more than 55 dB CP-XP isolation is found. The proposed structure is very simple to design and easy to fabricate.

Thermodynamics of fission products in UO(2 ± x).

PubMed

Nerikar, P V; Liu, X-Y; Uberuaga, B P; Stanek, C R; Phillpot, S R; Sinnott, S B

2009-10-28

The stabilities of selected fission products-Xe, Cs, and Sr-are investigated as a function of non-stoichiometry x in UO(2 ± x). In particular, density functional theory (DFT) is used to calculate the incorporation and solution energies of these fission products at the anion and cation vacancy sites, at the divacancy, and at the bound Schottky defect. In order to reproduce the correct insulating state of UO(2), the DFT calculations are performed using spin polarization and with the Hubbard U term. In general, higher charge defects are more soluble in the fuel matrix and the solubility of fission products increases as the hyperstoichiometry increases. The solubility of fission product oxides is also explored. Cs(2)O is observed as a second stable phase and SrO is found to be soluble in the UO(2) matrix for all stoichiometries. These observations mirror experimentally observed phenomena.

Developpement de techniques numeriques pour l'estimation, la modelisation et la prediction de proprietes thermodynamiques et structurales de systems metalliques a fort ordonnancement chimique

NASA Astrophysics Data System (ADS)

Harvey, Jean-Philippe

In this work, the possibility to calculate and evaluate with a high degree of precision the Gibbs energy of complex multiphase equilibria for which chemical ordering is explicitly and simultaneously considered in the thermodynamic description of solid (short range order and long range order) and liquid (short range order) metallic phases is studied. The cluster site approximation (CSA) and the cluster variation method (CVM) are implemented in a new minimization technique of the Gibbs energy of multicomponent and multiphase systems to describe the thermodynamic behaviour of metallic solid solutions showing strong chemical ordering. The modified quasichemical model in the pair approximation (MQMPA) is also implemented in the new minimization algorithm presented in this work to describe the thermodynamic behaviour of metallic liquid solutions. The constrained minimization technique implemented in this work consists of a sequential quadratic programming technique based on an exact Newton’s method (i.e. the use of exact second derivatives in the determination of the Hessian of the objective function) combined to a line search method to identify a direction of sufficient decrease of the merit function. The implementation of a new algorithm to perform the constrained minimization of the Gibbs energy is justified by the difficulty to identify, in specific cases, the correct multiphase assemblage of a system where the thermodynamic behaviour of the equilibrium phases is described by one of the previously quoted models using the FactSage software (ex.: solid_CSA+liquid_MQMPA; solid1_CSA+solid2_CSA). After a rigorous validation of the constrained Gibbs energy minimization algorithm using several assessed binary and ternary systems found in the literature, the CVM and the CSA models used to describe the energetic behaviour of metallic solid solutions present in systems with key industrial applications such as the Cu-Zr and the Al-Zr systems are parameterized using fully consistent thermodynamic an structural data generated from a Monte Carlo (MC) simulator also implemented in the framework of this project. In this MC simulator, the modified embedded atom model in the second nearest neighbour formalism (MEAM-2NN) is used to describe the cohesive energy of each studied structure. A new Al-Zr MEAM-2NN interatomic potential needed to evaluate the cohesive energy of the condensed phases of this system is presented in this work. The thermodynamic integration (TI) method implemented in the MC simulator allows the evaluation of the absolute Gibbs energy of the considered solid or liquid structures. The original implementation of the TI method allowed us to evaluate theoretically for the first time all the thermodynamic mixing contributions (i.e., mixing enthalpy and mixing entropy contributions) of a metallic liquid (Cu-Zr and Al-Zr) and of a solid solution (face-centered cubic (FCC) Al-Zr solid solution) described by the MEAM-2NN. Thermodynamic and structural data obtained from MC and molecular dynamic simulations are then used to parameterize the CVM for the Al-Zr FCC solid solution and the MQMPA for the Al-Zr and the Cu-Zr liquid phase respectively. The extended thermodynamic study of these systems allow the introduction of a new type of configuration-dependent excess parameters in the definition of the thermodynamic function of solid solutions described by the CVM or the CSA. These parameters greatly improve the precision of these thermodynamic models based on experimental evidences found in the literature. A new parameterization approach of the MQMPA model of metallic liquid solutions is presented throughout this work. In this new approach, calculated pair fractions obtained from MC/MD simulations are taken into account as well as configuration-independent volumetric relaxation effects (regular like excess parameters) in order to parameterize precisely the Gibbs energy function of metallic melts. The generation of a complete set of fully consistent thermodynamic, physical and structural data for solid, liquid, and stoichiometric compounds and the subsequent parameterization of their respective thermodynamic model lead to the first description of the complete Al-Zr phase diagram in the range of composition [0 ≤ XZr ≤ 5 / 9] based on theoretical and fully consistent thermodynamic properties. MC and MD simulations are performed for the Al-Zr system to define for the first time the precise thermodynamic behaviour of the amorphous phase for its entire range of composition. Finally, all the thermodynamic models for the liquid phase, the FCC solid solution and the amorphous phase are used to define conditions based on thermodynamic and volumetric considerations that favor the amorphization of Al-Zr alloys.

An EQT-based cDFT approach for thermodynamic properties of confined fluid mixtures

NASA Astrophysics Data System (ADS)

Motevaselian, M. H.; Aluru, N. R.

2017-04-01

We present an empirical potential-based quasi-continuum theory (EQT) to predict the structure and thermodynamic properties of confined fluid mixtures. The central idea in the EQT is to construct potential energies that integrate important atomistic details into a continuum-based model such as the Nernst-Planck equation. The EQT potentials can be also used to construct the excess free energy functional, which is required for the grand potential in the classical density functional theory (cDFT). In this work, we use the EQT-based grand potential to predict various thermodynamic properties of a confined binary mixture of hydrogen and methane molecules inside graphene slit channels of different widths. We show that the EQT-cDFT predictions for the structure, surface tension, solvation force, and local pressure tensor profiles are in good agreement with the molecular dynamics simulations. Moreover, we study the effect of different bulk compositions and channel widths on the thermodynamic properties. Our results reveal that the composition of methane in the mixture can significantly affect the ordering of molecules and thermodynamic properties under confinement. In addition, we find that graphene is selective to methane molecules.

Thermodynamic forces in coarse-grained simulations

NASA Astrophysics Data System (ADS)

Noid, William

Atomically detailed molecular dynamics simulations have profoundly advanced our understanding of the structure and interactions in soft condensed phases. Nevertheless, despite dramatic advances in the methodology and resources for simulating atomically detailed models, low-resolution coarse-grained (CG) models play a central and rapidly growing role in science. CG models not only empower researchers to investigate phenomena beyond the scope of atomically detailed simulations, but also to precisely tailor models for specific phenomena. However, in contrast to atomically detailed simulations, which evolve on a potential energy surface, CG simulations should evolve on a free energy surface. Therefore, the forces in CG models should reflect the thermodynamic information that has been eliminated from the CG configuration space. As a consequence of these thermodynamic forces, CG models often demonstrate limited transferability and, moreover, rarely provide an accurate description of both structural and thermodynamic properties. In this talk, I will present a framework that clarifies the origin and impact of these thermodynamic forces. Additionally, I will present computational methods for quantifying these forces and incorporating their effects into CG MD simulations. As time allows, I will demonstrate applications of this framework for liquids, polymers, and interfaces. We gratefully acknowledge the support of the National Science Foundation via CHE 1565631.

Nondestructive optical testing of the materials surface structure based on liquid crystals

NASA Astrophysics Data System (ADS)

Tomilin, M. G.; Stafeev, S. K.

2011-08-01

Thin layers of nematic liquid crystals (NLCs) may be used as recording media for visualizing structural and microrelief defects, distribution of low power physical fields and modifications of the surface. NLCs are more sensitive in comparison with cholesteric and smectic LCs having super molecular structures. The detecting properties of NLCs are based on local layers deformation, induced by surface fields and observed in polarizing microscope. The structural surface defects or physical field's distribution are dramatically change the distribution of surface tension. Surface defects recording becomes possible if NLC deformed structure is illuminated in transparent or reflective modes and observed in optical polarizing microscope and appearing image is compared with background structure. In this case one observes not the real defect but the local deformation in NLCs. The theory was developed to find out the real size of defects. The resolution of NLC layer is more than 2000 lines/mm. The fields of NLC application are solid crystals symmetry, minerals, metals, semiconductors, polymers and glasses structure inhomogeneities and optical coatings defects detecting. The efficiency of NLC method in biophotonics is illustrated by objective detecting cancer tissues character and visualizing the interaction traces of grippe viruses with antibodies. NLCs may detect solvent components structure in tea, wine and perfume giving unique information of their structure. It presents diagnostic information alternative to dyes and fluorescence methods. For the first time the structures of some juices and beverages are visualized to illustrate the unique possibilities of NLCs.

Progressive Fracture of Fiber Composite Thin Shell Structures Under Internal Pressure and Axial Loads

NASA Technical Reports Server (NTRS)

Gotsis, Pascal K.; Chamis, Christos C.; Minnetyan, Levon

1996-01-01

Graphite/epoxy composite thin shell structures were simulated to investigate damage and fracture progression due to internal pressure and axial loading. Defective and defect-free structures (thin cylinders) were examined. The three different laminates examined had fiber orientations of (90/0/+/-0)(sub s), where 0 is 45, 60, and 75 deg. CODSTRAN, an integrated computer code that scales up constituent level properties to the structural level and accounts for all possible failure modes, was used to simulate composite degradation under loading. Damage initiation, growth, accumulation, and propagation to fracture were included in the simulation. Burst pressures for defective and defect-free shells were compared to evaluate damage tolerance. The results showed that damage initiation began with matrix failure whereas damage and/or fracture progression occurred as a result of additional matrix failure and fiber fracture. In both thin cylinder cases examined (defective and defect-free), the optimum layup configuration was (90/0/+/-60)(sub s) because it had the best damage tolerance with respect to the burst pressure.

Structural hierarchies define toughness and defect-tolerance despite simple and mechanically inferior brittle building blocks

NASA Astrophysics Data System (ADS)

Sen, Dipanjan; Buehler, Markus J.

2011-07-01

Mineralized biological materials such as bone, sea sponges or diatoms provide load-bearing and armor functions and universally feature structural hierarchies from nano to macro. Here we report a systematic investigation of the effect of hierarchical structures on toughness and defect-tolerance based on a single and mechanically inferior brittle base material, silica, using a bottom-up approach rooted in atomistic modeling. Our analysis reveals drastic changes in the material crack-propagation resistance (R-curve) solely due to the introduction of hierarchical structures that also result in a vastly increased toughness and defect-tolerance, enabling stable crack propagation over an extensive range of crack sizes. Over a range of up to four hierarchy levels, we find an exponential increase in the defect-tolerance approaching hundred micrometers without introducing additional mechanisms or materials. This presents a significant departure from the defect-tolerance of the base material, silica, which is brittle and highly sensitive even to extremely small nanometer-scale defects.

Decoupling the Effects of Mass Density and Hydrogen-, Oxygen-, and Aluminum-Based Defects on Optoelectronic Properties of Realistic Amorphous Alumina.

PubMed

Riffet, Vanessa; Vidal, Julien

2017-06-01

The search for functional materials is currently hindered by the difficulty to find significant correlation between constitutive properties of a material and its functional properties. In the case of amorphous materials, the diversity of local structures, chemical composition, impurities and mass densities makes such a connection difficult to be addressed. In this Letter, the relation between refractive index and composition has been investigated for amorphous AlO x materials, including nonstoichiometric AlO x , emphasizing the role of structural defects and the absence of effect of the band gap variation. It is found that the Newton-Drude (ND) relation predicts the refractive index from mass density with a rather high level of precision apart from some structures displaying structural defects. Our results show especially that O- and Al-based defects act as additive local disturbance in the vicinity of band gap, allowing us to decouple the mass density effects from defect effects (n = n[ND] + Δn defect ).

Waltzing route toward double-helix formation in cholesteric shells

NASA Astrophysics Data System (ADS)

Darmon, Alexandre; Benzaquen, Michael; Seč, David; Čopar, Simon; Dauchot, Olivier; Lopez-Leon, Teresa

2016-08-01

Liquid crystals, when confined to a spherical shell, offer fascinating possibilities for producing artificial mesoscopic atoms, which could then self-assemble into materials structured at a nanoscale, such as photonic crystals or metamaterials. The spherical curvature of the shell imposes topological constraints in the molecular ordering of the liquid crystal, resulting in the formation of defects. Controlling the number of defects, that is, the shell valency, and their positions, is a key success factor for the realization of those materials. Liquid crystals with helical cholesteric order offer a promising, yet unexplored way of controlling the shell defect configuration. In this paper, we study cholesteric shells with monovalent and bivalent defect configurations. By bringing together experiments and numerical simulations, we show that the defects appearing in these two configurations have a complex inner structure, as recently reported for simulated droplets. Bivalent shells possess two highly structured defects, which are composed of a number of smaller defect rings that pile up through the shell. Monovalent shells have a single radial defect, which is composed of two nonsingular defect lines that wind around each other in a double-helix structure. The stability of the bivalent configuration against the monovalent one is controlled by c = h/p, where h is the shell thickness and p the cholesteric helical pitch. By playing with the shell geometry, we can trigger the transition between the two configurations. This transition involves a fascinating waltz dynamics, where the two defects come closer while turning around each other.

A review of defects and disorder in multinary tetrahedrally bonded semiconductors [Defects and disorder in multinary tetrahedrally bonded semiconductors studied by experiment and theory

DOE PAGES

Baranowski, Lauryn L.; Zawadzki, Pawel; Lany, Stephan; ...

2016-11-10

Defects are critical to understanding the electronic properties of semiconducting compounds, for applications such as light-emitting diodes, transistors, photovoltaics, and thermoelectrics. In this review, we describe our work investigating defects in tetrahedrally bonded, multinary semiconductors, and discuss the place of our research within the context of publications by other groups. We applied experimental and theory techniques to understand point defects, structural disorder, and extended antisite defects in one semiconductor of interest for photovoltaic applications, Cu 2SnS 3. We contrast our findings on Cu 2SnS 3 with other chemically related Cu-Sn-S compounds, as well as structurally related compounds such as Cumore » 2ZnSnS 4 and Cu(In,Ga)Se 2. We find that evaluation of point defects alone is not sufficient to understand defect behavior in multinary tetrahedrally bonded semiconductors. In the case of Cu 2SnS 3 and Cu 2ZnSnS 4, structural disorder and entropy-driven cation clustering can result in nanoscale compositional inhomogeneities which detrimentally impact the electronic transport. Therefore, it is not sufficient to assess only the point defect behavior of new multinary tetrahedrally bonded compounds; effects such as structural disorder and extended antisite defects must also be considered. Altogether, this review provides a framework for evaluating tetrahedrally bonded semiconducting compounds with respect to their defect behavior for photovoltaic and other applications, and suggests new materials that may not be as prone to such imperfections.« less

A review of defects and disorder in multinary tetrahedrally bonded semiconductors [Defects and disorder in multinary tetrahedrally bonded semiconductors studied by experiment and theory

DOE Office of Scientific and Technical Information (OSTI.GOV)

Baranowski, Lauryn L.; Zawadzki, Pawel; Lany, Stephan

Defects are critical to understanding the electronic properties of semiconducting compounds, for applications such as light-emitting diodes, transistors, photovoltaics, and thermoelectrics. In this review, we describe our work investigating defects in tetrahedrally bonded, multinary semiconductors, and discuss the place of our research within the context of publications by other groups. We applied experimental and theory techniques to understand point defects, structural disorder, and extended antisite defects in one semiconductor of interest for photovoltaic applications, Cu 2SnS 3. We contrast our findings on Cu 2SnS 3 with other chemically related Cu-Sn-S compounds, as well as structurally related compounds such as Cumore » 2ZnSnS 4 and Cu(In,Ga)Se 2. We find that evaluation of point defects alone is not sufficient to understand defect behavior in multinary tetrahedrally bonded semiconductors. In the case of Cu 2SnS 3 and Cu 2ZnSnS 4, structural disorder and entropy-driven cation clustering can result in nanoscale compositional inhomogeneities which detrimentally impact the electronic transport. Therefore, it is not sufficient to assess only the point defect behavior of new multinary tetrahedrally bonded compounds; effects such as structural disorder and extended antisite defects must also be considered. Altogether, this review provides a framework for evaluating tetrahedrally bonded semiconducting compounds with respect to their defect behavior for photovoltaic and other applications, and suggests new materials that may not be as prone to such imperfections.« less

On Teaching Thermodynamics

ERIC Educational Resources Information Center

Debbasch, F.

2011-01-01

The logical structure of classical thermodynamics is presented in a modern, geometrical manner. The first and second law receive clear, operatively oriented statements and the Gibbs free energy extremum principle is fully discussed. Applications relevant to chemistry, such as phase transitions, dilute solutions theory and, in particular, the law…

Entropy in self-similar shock profiles

DOE Office of Scientific and Technical Information (OSTI.GOV)

Margolin, Len G.; Reisner, Jon Michael; Jordan, Pedro M.

In this paper, we study the structure of a gaseous shock, and in particular the distribution of entropy within, in both a thermodynamics and a statistical mechanics context. The problem of shock structure has a long and distinguished history that we review. We employ the Navier–Stokes equations to construct a self–similar version of Becker’s solution for a shock assuming a particular (physically plausible) Prandtl number; that solution reproduces the well–known result of Morduchow & Libby that features a maximum of the equilibrium entropy inside the shock profile. We then construct an entropy profile, based on gas kinetic theory, that ismore » smooth and monotonically increasing. The extension of equilibrium thermodynamics to irreversible processes is based in part on the assumption of local thermodynamic equilibrium. We show that this assumption is not valid except for the weakest shocks. Finally, we conclude by hypothesizing a thermodynamic nonequilibrium entropy and demonstrating that it closely estimates the gas kinetic nonequilibrium entropy within a shock.« less

Entropy in self-similar shock profiles

DOE PAGES

Margolin, Len G.; Reisner, Jon Michael; Jordan, Pedro M.

2017-07-16

In this paper, we study the structure of a gaseous shock, and in particular the distribution of entropy within, in both a thermodynamics and a statistical mechanics context. The problem of shock structure has a long and distinguished history that we review. We employ the Navier–Stokes equations to construct a self–similar version of Becker’s solution for a shock assuming a particular (physically plausible) Prandtl number; that solution reproduces the well–known result of Morduchow & Libby that features a maximum of the equilibrium entropy inside the shock profile. We then construct an entropy profile, based on gas kinetic theory, that ismore » smooth and monotonically increasing. The extension of equilibrium thermodynamics to irreversible processes is based in part on the assumption of local thermodynamic equilibrium. We show that this assumption is not valid except for the weakest shocks. Finally, we conclude by hypothesizing a thermodynamic nonequilibrium entropy and demonstrating that it closely estimates the gas kinetic nonequilibrium entropy within a shock.« less

Hamiltonian and Thermodynamic Modeling of Quantum Turbulence

NASA Astrophysics Data System (ADS)

Grmela, Miroslav

2010-10-01

The state variables in the novel model introduced in this paper are the fields playing this role in the classical Landau-Tisza model and additional fields of mass, entropy (or temperature), superfluid velocity, and gradient of the superfluid velocity, all depending on the position vector and another tree dimensional vector labeling the scale, describing the small-scale structure developed in 4He superfluid experiencing turbulent motion. The fluxes of mass, momentum, energy, and entropy in the position space as well as the fluxes of energy and entropy in scales, appear in the time evolution equations as explicit functions of the state variables and of their conjugates. The fundamental thermodynamic relation relating the fields to their conjugates is left in this paper undetermined. The GENERIC structure of the equations serves two purposes: (i) it guarantees that solutions to the governing equations, independently of the choice of the fundamental thermodynamic relation, agree with the observed compatibility with thermodynamics, and (ii) it is used as a guide in the construction of the novel model.

An EQT-cDFT approach to determine thermodynamic properties of confined fluids.

PubMed

Mashayak, S Y; Motevaselian, M H; Aluru, N R

2015-06-28

We present a continuum-based approach to predict the structure and thermodynamic properties of confined fluids at multiple length-scales, ranging from a few angstroms to macro-meters. The continuum approach is based on the empirical potential-based quasi-continuum theory (EQT) and classical density functional theory (cDFT). EQT is a simple and fast approach to predict inhomogeneous density and potential profiles of confined fluids. We use EQT potentials to construct a grand potential functional for cDFT. The EQT-cDFT-based grand potential can be used to predict various thermodynamic properties of confined fluids. In this work, we demonstrate the EQT-cDFT approach by simulating Lennard-Jones fluids, namely, methane and argon, confined inside slit-like channels of graphene. We show that the EQT-cDFT can accurately predict the structure and thermodynamic properties, such as density profiles, adsorption, local pressure tensor, surface tension, and solvation force, of confined fluids as compared to the molecular dynamics simulation results.

Thermodynamic database for proteins: features and applications.

PubMed

Gromiha, M Michael; Sarai, Akinori

2010-01-01

We have developed a thermodynamic database for proteins and mutants, ProTherm, which is a collection of a large number of thermodynamic data on protein stability along with the sequence and structure information, experimental methods and conditions, and literature information. This is a valuable resource for understanding/predicting the stability of proteins, and it can be accessible at http://www.gibk26.bse.kyutech.ac.jp/jouhou/Protherm/protherm.html . ProTherm has several features including various search, display, and sorting options and visualization tools. We have analyzed the data in ProTherm to examine the relationship among thermodynamics, structure, and function of proteins. We describe the progress on the development of methods for understanding/predicting protein stability, such as (i) relationship between the stability of protein mutants and amino acid properties, (ii) average assignment method, (iii) empirical energy functions, (iv) torsion, distance, and contact potentials, and (v) machine learning techniques. The list of online resources for predicting protein stability has also been provided.

Thermodynamic model of a solid with RKKY interaction and magnetoelastic coupling

NASA Astrophysics Data System (ADS)

Balcerzak, T.; Szałowski, K.; Jaščur, M.

2018-04-01

Thermodynamic description of a model system with magnetoelastic coupling is presented. The elastic, vibrational, electronic and magnetic energy contributions are taken into account. The long-range RKKY interaction is considered together with the nearest-neighbour direct exchange. The generalized Gibbs potential and the set of equations of state are derived, from which all thermodynamic functions are self-consistently obtained. Thermodynamic properties are calculated numerically for FCC structure for arbitrary external pressure, magnetic field and temperature, and widely discussed. In particular, for some parameters of interaction potential and electron concentration corresponding to antiferromagnetic phase, the existence of negative thermal expansion coefficient is predicted.

Torsional anharmonicity in the conformational thermodynamics of flexible molecules

NASA Astrophysics Data System (ADS)

Miller, Thomas F., III; Clary, David C.

We present an algorithm for calculating the conformational thermodynamics of large, flexible molecules that combines ab initio electronic structure theory calculations with a torsional path integral Monte Carlo (TPIMC) simulation. The new algorithm overcomes the previous limitations of the TPIMC method by including the thermodynamic contributions of non-torsional vibrational modes and by affordably incorporating the ab initio calculation of conformer electronic energies, and it improves the conventional ab initio treatment of conformational thermodynamics by accounting for the anharmonicity of the torsional modes. Using previously published ab initio results and new TPIMC calculations, we apply the algorithm to the conformers of the adrenaline molecule.

Graphene materials having randomly distributed two-dimensional structural defects

DOEpatents

Kung, Harold H; Zhao, Xin; Hayner, Cary M; Kung, Mayfair C

2013-10-08

Graphene-based storage materials for high-power battery applications are provided. The storage materials are composed of vertical stacks of graphene sheets and have reduced resistance for Li ion transport. This reduced resistance is achieved by incorporating a random distribution of structural defects into the stacked graphene sheets, whereby the structural defects facilitate the diffusion of Li ions into the interior of the storage materials.

Graphene materials having randomly distributed two-dimensional structural defects

DOEpatents

Kung, Harold H.; Zhao, Xin; Hayner, Cary M.; Kung, Mayfair C.

2016-05-31

Graphene-based storage materials for high-power battery applications are provided. The storage materials are composed of vertical stacks of graphene sheets and have reduced resistance for Li ion transport. This reduced resistance is achieved by incorporating a random distribution of structural defects into the stacked graphene sheets, whereby the structural defects facilitate the diffusion of Li ions into the interior of the storage materials.

Binding thermodynamics discriminates fragments from druglike compounds: a thermodynamic description of fragment-based drug discovery.

PubMed

Williams, Glyn; Ferenczy, György G; Ulander, Johan; Keserű, György M

2017-04-01

Small is beautiful - reducing the size and complexity of chemical starting points for drug design allows better sampling of chemical space, reveals the most energetically important interactions within protein-binding sites and can lead to improvements in the physicochemical properties of the final drug. The impact of fragment-based drug discovery (FBDD) on recent drug discovery projects and our improved knowledge of the structural and thermodynamic details of ligand binding has prompted us to explore the relationships between ligand-binding thermodynamics and FBDD. Information on binding thermodynamics can give insights into the contributions to protein-ligand interactions and could therefore be used to prioritise compounds with a high degree of specificity in forming key interactions. Copyright © 2016 Elsevier Ltd. All rights reserved.

Thermodynamics of organic compounds

NASA Astrophysics Data System (ADS)

Gammon, B. E.; Smith, N. K.

1982-11-01

This research program consisted of an integrated and interrelated effort of basic and applied research in chemical thermodynamics and thermochemistry. Knowledge of variation of physical and thermodynamic properties with molecular structure was used to select compounds for study that because of high ring strain or unusual steric effects may have good energy characteristics per unit volume or per unit mass and thus be useful in the synthesis of high energy fuels. These materials were synthesized, and their thermodynamic properties were evaluated. In cooperation with researcher at Wright-Patterson Air Force Base, ramjet fuels currently in use were subjected to careful thermodynamic evaluation by measurements of heat capacity, enthalpy of combustion and vapor pressure. During the last year of this effort, seven kerosene-type fuels produced by British Petroleum and seven jet fuels produced from shale oil were studied.

Advancing density functional theory to finite temperatures: methods and applications in steel design

NASA Astrophysics Data System (ADS)

Hickel, T.; Grabowski, B.; Körmann, F.; Neugebauer, J.

2012-02-01

The performance of materials such as steels, their high strength and formability, is based on an impressive variety of competing mechanisms on the microscopic/atomic scale (e.g. dislocation gliding, solid solution hardening, mechanical twinning or structural phase transformations). Whereas many of the currently available concepts to describe these mechanisms are based on empirical and experimental data, it becomes more and more apparent that further improvement of materials needs to be based on a more fundamental level. Recent progress for methods based on density functional theory (DFT) now makes the exploration of chemical trends, the determination of parameters for phenomenological models and the identification of new routes for the optimization of steel properties feasible. A major challenge in applying these methods to a true materials design is, however, the inclusion of temperature-driven effects on the desired properties. Therefore, a large range of computational tools has been developed in order to improve the capability and accuracy of first-principles methods in determining free energies. These combine electronic, vibrational and magnetic effects as well as structural defects in an integrated approach. Based on these simulation tools, one is now able to successfully predict mechanical and thermodynamic properties of metals with a hitherto not achievable accuracy.

Modeling of Interface and Internal Disorder Applied to XRD Analysis of Ag-Based Nano-Multilayers.

PubMed

Ariosa, Daniel; Cancellieri, Claudia; Araullo-Peters, Vicente; Chiodi, Mirco; Klyatskina, Elizaveta; Janczak-Rusch, Jolanta; Jeurgens, Lars P H

2018-06-20

Multilayered structures are a promising route to tailor electronic, magnetic, optical, and/or mechanical properties and durability of functional materials. Sputter deposition at room temperature, being an out-of-equilibrium process, introduces structural defects and confers to these nanosystems an intrinsic thermodynamical instability. As-deposited materials exhibit a large amount of internal atomic displacements within each constituent block as well as severe interface roughness between different layers. To access and characterize the internal multilayer disorder and its thermal evolution, X-ray diffraction investigation and analysis are performed systematically at differently grown Ag-Ge/aluminum nitride (AlN) multilayers (co-deposited, sequentially deposited with and without radio frequency (RF) bias) samples and after high-temperature annealing treatment. We report here on model calculations based on a kinematic formalism describing the displacement disorder both within the multilayer blocks and at the interfaces to reproduce the experimental X-ray diffraction intensities. Mixing and displacements at the interface are found to be considerably reduced after thermal treatment for co- and sequentially deposited Ag-Ge/AlN samples. The application of a RF bias during the deposition causes the highest interface mixing and introduces random intercalates in the AlN layers. X-ray analysis is contrasted to transmission electron microscopy pictures to validate the approach.

Strontium-free rare earth perovskite ferrites with fast oxygen exchange kinetics: Experiment and theory

NASA Astrophysics Data System (ADS)

Berger, Christian; Bucher, Edith; Windischbacher, Andreas; Boese, A. Daniel; Sitte, Werner

2018-03-01

The Sr-free mixed ionic electronic conducting perovskites La0.8Ca0.2FeO3-δ (LCF82) and Pr0.8Ca0.2FeO3-δ (PCF82) were synthesized via a glycine-nitrate process. Crystal structure, phase purity, and lattice constants were determined by XRD and Rietveld analysis. The oxygen exchange kinetics and the electronic conductivity were obtained from in-situ dc-conductivity relaxation experiments at 600-800 °C and 1×10-3≤pO2/bar≤0.1. Both LCF82 and PCF82 show exceptionally fast chemical surface exchange coefficients and chemical diffusion coefficients of oxygen. The oxygen nonstochiometry of LCF82 and PCF82 was determined by precision thermogravimetry. A point defect model was used to calculate the thermodynamic factors of oxygen and to estimate self-diffusion coefficients and ionic conductivities. Density Functional Theory (DFT) calculations on the crystal structure, oxygen vacancy formation as well as oxygen migration energies are in excellent agreement with the experimental values. Due to their favourable properties both LCF82 and PCF82 are of interest for applications in solid oxide fuel cell cathodes, solid oxide electrolyser cell anodes, oxygen separation membranes, catalysts, or electrochemical sensors.

Advancing density functional theory to finite temperatures: methods and applications in steel design.

PubMed

Hickel, T; Grabowski, B; Körmann, F; Neugebauer, J

2012-02-08

The performance of materials such as steels, their high strength and formability, is based on an impressive variety of competing mechanisms on the microscopic/atomic scale (e.g. dislocation gliding, solid solution hardening, mechanical twinning or structural phase transformations). Whereas many of the currently available concepts to describe these mechanisms are based on empirical and experimental data, it becomes more and more apparent that further improvement of materials needs to be based on a more fundamental level. Recent progress for methods based on density functional theory (DFT) now makes the exploration of chemical trends, the determination of parameters for phenomenological models and the identification of new routes for the optimization of steel properties feasible. A major challenge in applying these methods to a true materials design is, however, the inclusion of temperature-driven effects on the desired properties. Therefore, a large range of computational tools has been developed in order to improve the capability and accuracy of first-principles methods in determining free energies. These combine electronic, vibrational and magnetic effects as well as structural defects in an integrated approach. Based on these simulation tools, one is now able to successfully predict mechanical and thermodynamic properties of metals with a hitherto not achievable accuracy.

Defect formation energy in pyrochlore: the effect of crystal size

NASA Astrophysics Data System (ADS)

Wang, Jianwei; Ewing, Rodney C.; Becker, Udo

2014-09-01

Defect formation energies of point defects of two pyrochlores Gd2Ti2O7 and Gd2Zr2O7 as a function of crystal size were calculated. Density functional theory with plane-wave basis sets and the projector-augmented wave method were used in the calculations. The results show that the defect formation energies of the two pyrochlores diverge as the size decreases to the nanometer range. For Gd2Ti2O7 pyrochlore, the defect formation energy is higher at nanometers with respect to that of the bulk, while it is lower for Gd2Zr2O7. The lowest defect formation energy for Gd2Zr2O7 is found at 15-20 Å. The different behaviors of the defect formation energies as a function of crystal size are caused by different structural adjustments around the defects as the size decreases. For both pyrochlore compositions at large sizes, the defect structures are similar to those of the bulk. As the size decreases, for Gd2Ti2O7, additional structure distortions appear at the surfaces, which cause the defect formation energy to increase. For Gd2Zr2O7, additional oxygen Frenkel pair defects are introduced, which reduce the defect formation energy. As the size further decreases, increased structure distortions occur at the surfaces, which cause the defect formation energy to increase. Based on a hypothesis that correlates the energetics of defect formation and radiation response for complex oxides, the calculated results suggest that at nanometer range Gd2Ti2O7 pyrochlore is expected to have a lower radiation tolerance, and those of Gd2Zr2O7 pyrochlore to have a higher radiation tolerance. The highest radiation tolerance for Gd2Zr2O7 pyrochlore is expected to be found at ˜2 nanometers.

Thermodynamic Presynthetic Considerations for Ring-Opening Polymerization

PubMed Central

2016-01-01

The need for polymers for high-end applications, coupled with the desire to mimic nature’s macromolecular machinery fuels the development of innovative synthetic strategies every year. The recently acquired macromolecular-synthetic tools increase the precision and enable the synthesis of polymers with high control and low dispersity. However, regardless of the specificity, the polymerization behavior is highly dependent on the monomeric structure. This is particularly true for the ring-opening polymerization of lactones, in which the ring size and degree of substitution highly influence the polymer formation properties. In other words, there are two important factors to contemplate when considering the particular polymerization behavior of a specific monomer: catalytic specificity and thermodynamic equilibrium behavior. This perspective focuses on the latter and undertakes a holistic approach among the different lactones with regard to the equilibrium thermodynamic polymerization behavior and its relation to polymer synthesis. This is summarized in a monomeric overview diagram that acts as a presynthetic directional cursor for synthesizing highly specific macromolecules; the means by which monomer equilibrium conversion relates to starting temperature, concentration, ring size, degree of substitution, and its implications for polymerization behavior are discussed. These discussions emphasize the importance of considering not only the catalytic system but also the monomer size and structure relations to thermodynamic equilibrium behavior. The thermodynamic equilibrium behavior relation with a monomer structure offers an additional layer of complexity to our molecular toolbox and, if it is harnessed accordingly, enables a powerful route to both monomer formation and intentional macromolecular design. PMID:26795940

Thermodynamic Presynthetic Considerations for Ring-Opening Polymerization.

PubMed

Olsén, Peter; Odelius, Karin; Albertsson, Ann-Christine

2016-03-14

The need for polymers for high-end applications, coupled with the desire to mimic nature's macromolecular machinery fuels the development of innovative synthetic strategies every year. The recently acquired macromolecular-synthetic tools increase the precision and enable the synthesis of polymers with high control and low dispersity. However, regardless of the specificity, the polymerization behavior is highly dependent on the monomeric structure. This is particularly true for the ring-opening polymerization of lactones, in which the ring size and degree of substitution highly influence the polymer formation properties. In other words, there are two important factors to contemplate when considering the particular polymerization behavior of a specific monomer: catalytic specificity and thermodynamic equilibrium behavior. This perspective focuses on the latter and undertakes a holistic approach among the different lactones with regard to the equilibrium thermodynamic polymerization behavior and its relation to polymer synthesis. This is summarized in a monomeric overview diagram that acts as a presynthetic directional cursor for synthesizing highly specific macromolecules; the means by which monomer equilibrium conversion relates to starting temperature, concentration, ring size, degree of substitution, and its implications for polymerization behavior are discussed. These discussions emphasize the importance of considering not only the catalytic system but also the monomer size and structure relations to thermodynamic equilibrium behavior. The thermodynamic equilibrium behavior relation with a monomer structure offers an additional layer of complexity to our molecular toolbox and, if it is harnessed accordingly, enables a powerful route to both monomer formation and intentional macromolecular design.

A Unified Theory of Non-Ideal Gas Lattice Boltzmann Models

NASA Technical Reports Server (NTRS)

Luo, Li-Shi

1998-01-01

A non-ideal gas lattice Boltzmann model is directly derived, in an a priori fashion, from the Enskog equation for dense gases. The model is rigorously obtained by a systematic procedure to discretize the Enskog equation (in the presence of an external force) in both phase space and time. The lattice Boltzmann model derived here is thermodynamically consistent and is free of the defects which exist in previous lattice Boltzmann models for non-ideal gases. The existing lattice Boltzmann models for non-ideal gases are analyzed and compared with the model derived here.

Energetics of drug-DNA interactions.

PubMed

Chaires, J B

1997-01-01

Understanding the thermodynamics of drug binding to DNA is of both practical and fundamental interest. The practical interest lies in the contribution that thermodynamics can make to the rational design process for the development of new DNA targeted drugs. Thermodynamics offer key insights into the molecular forces that drive complex formation that cannot be obtained by structural or computational studies alone. The fundamental interest in these interactions lies in what they can reveal about the general problems of parsing and predicting ligand binding free energies. For these problems, drug-DNA interactions offer several distinct advantages, among them being that the structures of many drug-DNA complexes are known at high resolution and that such structures reveal that in many cases the drug acts as a rigid body, with little conformational change upon binding. Complete thermodynamic profiles (delta G, delta H, delta S, delta Cp) for numerous drug-DNA interactions have been obtained, with the help of high-sensitivity microcalorimetry. The purpose of this article is to offer a perspective on the interpretation of these thermodynamics parameters, and in particular how they might be correlated with known structural features. Obligatory conformational changes in the DNA to accommodate intercalators and the loss of translational and rotational freedom upon complex formation both present unfavorable free energy barriers for binding. Such barriers must be overcome by favorable free energy contributions from the hydrophobic transfer of ligand from solution into the binding site, polyelectrolyte contributions from coupled ion release, and molecular interactions (hydrogen and ionic bonds, van der Waals interactions) that form within the binding site. Theoretical and semiempirical tools that allow estimates of these contributions to be made will be discussed, and their use in dissecting experimental data illustrated. This process, even at the current level of approximation, can shed considerable light on the drug-DNA binding process.

An analytical coarse-graining method which preserves the free energy, structural correlations, and thermodynamic state of polymer melts from the atomistic to the mesoscale.

PubMed

McCarty, J; Clark, A J; Copperman, J; Guenza, M G

2014-05-28

Structural and thermodynamic consistency of coarse-graining models across multiple length scales is essential for the predictive role of multi-scale modeling and molecular dynamic simulations that use mesoscale descriptions. Our approach is a coarse-grained model based on integral equation theory, which can represent polymer chains at variable levels of chemical details. The model is analytical and depends on molecular and thermodynamic parameters of the system under study, as well as on the direct correlation function in the k → 0 limit, c0. A numerical solution to the PRISM integral equations is used to determine c0, by adjusting the value of the effective hard sphere diameter, dHS, to agree with the predicted equation of state. This single quantity parameterizes the coarse-grained potential, which is used to perform mesoscale simulations that are directly compared with atomistic-level simulations of the same system. We test our coarse-graining formalism by comparing structural correlations, isothermal compressibility, equation of state, Helmholtz and Gibbs free energies, and potential energy and entropy using both united atom and coarse-grained descriptions. We find quantitative agreement between the analytical formalism for the thermodynamic properties, and the results of Molecular Dynamics simulations, independent of the chosen level of representation. In the mesoscale description, the potential energy of the soft-particle interaction becomes a free energy in the coarse-grained coordinates which preserves the excess free energy from an ideal gas across all levels of description. The structural consistency between the united-atom and mesoscale descriptions means the relative entropy between descriptions has been minimized without any variational optimization parameters. The approach is general and applicable to any polymeric system in different thermodynamic conditions.

The importance of mRNA structure in determining the pathogenicity of synonymous and non-synonymous mutations in haemophilia

PubMed Central

Hamasaki-Katagiri, Nobuko; Lin, Brian C.; Simon, Jonathan; Hunt, Ryan C.; Schiller, Tal; Russek-Cohen, Estelle; Komar, Anton A.; Bar, Haim; Kimchi-Sarfaty, Chava

2016-01-01

Introduction Mutational analysis is commonly used to support the diagnosis and management of haemophilia. This has allowed for the generation of large mutation databases which provide unparalleled insight into genotype-phenotype relationships. Haemophilia is associated with inversions, deletions, insertions, nonsense and missense mutations. Both synonymous and non-synonymous mutations influence the base pairing of messenger RNA (mRNA), which can alter mRNA structure, cellular half-life and ribosome processivity/elongation. However, the role of mRNA structure in determining the pathogenicity of point mutations in haemophilia has not been evaluated. Aim To evaluate mRNA thermodynamic stability and associated RNA prediction software as a means to distinguish between neutral and disease-associated mutations in haemophilia. Methods Five mRNA structure prediction software programs were used to assess the thermodynamic stability of mRNA fragments carrying neutral vs. disease-associated and synonymous vs. non-synonymous point mutations in F8, F9 and a third X-linked gene, DMD (dystrophin). Results In F8 and DMD, disease-associated mutations tend to occur in more structurally stable mRNA regions, represented by lower MFE (minimum free energy) levels. In comparing multiple software packages for mRNA structure prediction, a 101–151 nucleotide fragment length appears to be a feasible range for structuring future studies. Conclusion mRNA thermodynamic stability is one predictive characteristic, which when combined with other RNA and protein features, may offer significant insight when screening sequencing data for novel disease-associated mutations. Our results also suggest potential utility in evaluating the mRNA thermodynamic stability profile of a gene when determining the viability of interchanging codons for biological and therapeutic applications. PMID:27933712

Modification of electronic structure, magnetic structure, and topological phase of bismuthene by point defects

NASA Astrophysics Data System (ADS)

Kadioglu, Yelda; Kilic, Sevket Berkay; Demirci, Salih; Aktürk, O. Üzengi; Aktürk, Ethem; Ciraci, Salim

2017-12-01

This paper reveals how the electronic structure, magnetic structure, and topological phase of two-dimensional (2D), single-layer structures of bismuth are modified by point defects. We first showed that a free-standing, single-layer, hexagonal structure of bismuth, named h-bismuthene, exhibits nontrivial band topology. We then investigated interactions between single foreign adatoms and bismuthene structures, which comprise stability, bonding, electronic structure, and magnetic structures. Localized states in diverse locations of the band gap and resonant states in band continua of bismuthene are induced upon the adsorption of different adatoms, which modify electronic and magnetic properties. Specific adatoms result in reconstruction around the adsorption site. Single vacancies and divacancies can form readily in bismuthene structures and remain stable at high temperatures. Through rebondings, Stone-Whales-type defects are constructed by divacancies, which transform into a large hole at high temperature. Like adsorbed adatoms, vacancies induce also localized gap states, which can be eliminated through rebondings in divacancies. We also showed that not only the optical and magnetic properties, but also the topological features of pristine h-bismuthene can be modified by point defects. The modification of the topological features depends on the energies of localized states and also on the strength of coupling between point defects.

Thermodynamic insights into 2-thiouridine-enhanced RNA hybridization

PubMed Central

Larsen, Aaron T.; Fahrenbach, Albert C.; Sheng, Jia; Pian, Julia; Szostak, Jack W.

2015-01-01

Nucleobase modifications dramatically alter nucleic acid structure and thermodynamics. 2-thiouridine (s2U) is a modified nucleobase found in tRNAs and known to stabilize U:A base pairs and destabilize U:G wobble pairs. The recently reported crystal structures of s2U-containing RNA duplexes do not entirely explain the mechanisms responsible for the stabilizing effect of s2U or whether this effect is entropic or enthalpic in origin. We present here thermodynamic evaluations of duplex formation using ITC and UV thermal denaturation with RNA duplexes containing internal s2U:A and s2U:U pairs and their native counterparts. These results indicate that s2U stabilizes both duplexes. The stabilizing effect is entropic in origin and likely results from the s2U-induced preorganization of the single-stranded RNA prior to hybridization. The same preorganizing effect is likely responsible for structurally resolving the s2U:U pair-containing duplex into a single conformation with a well-defined H-bond geometry. We also evaluate the effect of s2U on single strand conformation using UV- and CD-monitored thermal denaturation and on nucleoside conformation using 1H NMR spectroscopy, MD and umbrella sampling. These results provide insights into the effects that nucleobase modification has on RNA structure and thermodynamics and inform efforts toward improving both ribozyme-catalyzed and nonenzymatic RNA copying. PMID:26240387

Massive Interfacial Reconstruction at Misfit Dislocations in Metal/Oxide Interfaces

DOE Office of Scientific and Technical Information (OSTI.GOV)

Choudhury, Samrat; Morgan, Dane; Uberuaga, Blas P.

Electronic structure calculations were performed to study the role of misfit dislocations on the structure and chemistry of a metal/oxide interface. We found that a chemical imbalance exists at the misfit dislocation which leads to dramatic changes in the point defect content at the interface – stabilizing the structure requires removing as much as 50% of the metal atoms and insertion of a large number of oxygen interstitials. The exact defect composition that stabilizes the interface is sensitive to the external oxygen partial pressure. We relate the preferred defect structure at the interface to a competition between chemical and strainmore » energies as defects are introduced.« less

Massive Interfacial Reconstruction at Misfit Dislocations in Metal/Oxide Interfaces

DOE PAGES

Choudhury, Samrat; Morgan, Dane; Uberuaga, Blas P.

2014-10-17

Electronic structure calculations were performed to study the role of misfit dislocations on the structure and chemistry of a metal/oxide interface. We found that a chemical imbalance exists at the misfit dislocation which leads to dramatic changes in the point defect content at the interface – stabilizing the structure requires removing as much as 50% of the metal atoms and insertion of a large number of oxygen interstitials. The exact defect composition that stabilizes the interface is sensitive to the external oxygen partial pressure. We relate the preferred defect structure at the interface to a competition between chemical and strainmore » energies as defects are introduced.« less

Insights into the Molecular Mechanisms of Alzheimer's and Parkinson's Diseases with Molecular Simulations: Understanding the Roles of Artificial and Pathological Missense Mutations in Intrinsically Disordered Proteins Related to Pathology.

PubMed

Coskuner-Weber, Orkid; Uversky, Vladimir N

2018-01-24

Amyloid-β and α-synuclein are intrinsically disordered proteins (IDPs), which are at the center of Alzheimer's and Parkinson's disease pathologies, respectively. These IDPs are extremely flexible and do not adopt stable structures. Furthermore, both amyloid-β and α-synuclein can form toxic oligomers, amyloid fibrils and other type of aggregates in Alzheimer's and Parkinson's diseases. Experimentalists face challenges in investigating the structures and thermodynamic properties of these IDPs in their monomeric and oligomeric forms due to the rapid conformational changes, fast aggregation processes and strong solvent effects. Classical molecular dynamics simulations complement experiments and provide structural information at the atomic level with dynamics without facing the same experimental limitations. Artificial missense mutations are employed experimentally and computationally for providing insights into the structure-function relationships of amyloid-β and α-synuclein in relation to the pathologies of Alzheimer's and Parkinson's diseases. Furthermore, there are several natural genetic variations that play a role in the pathogenesis of familial cases of Alzheimer's and Parkinson's diseases, which are related to specific genetic defects inherited in dominant or recessive patterns. The present review summarizes the current understanding of monomeric and oligomeric forms of amyloid-β and α-synuclein, as well as the impacts of artificial and pathological missense mutations on the structural ensembles of these IDPs using molecular dynamics simulations. We also emphasize the recent investigations on residual secondary structure formation in dynamic conformational ensembles of amyloid-β and α-synuclein, such as β-structure linked to the oligomerization and fibrillation mechanisms related to the pathologies of Alzheimer's and Parkinson's diseases. This information represents an important foundation for the successful and efficient drug design studies.

Role of Defects on Regioselectivity of Nano Pristine Graphene.

PubMed

Kudur Jayaprakash, Gururaj; Casillas, Norberto; Astudillo-Sánchez, Pablo D; Flores-Moreno, Roberto

2016-11-17

Here analytical Fukui functions based on density functional theory are applied to investigate the redox reactivity of pristine and defected graphene lattices. A carbon H-terminated graphene structure (with 96 carbon atoms) and a graphene defected surface with Stone-Wales rearrangement and double vacancy defects are used as models. Pristine sp 2 -hybridized, hexagonal arranged carbon atoms exhibit a symmetric reactivity. In contrast, common carbon atoms at reconstructed polygons in Stone-Wales and double vacancy graphene display large reactivity variations. The improved reactivity and the regioselectivity at defected graphene is correlated to structural changes that caused carbon-carbon bond length variations at defected zones.

Shape-Controlled Synthesis of Colloidal Metal Nanocrystals: Thermodynamic versus Kinetic Products.

PubMed

Xia, Younan; Xia, Xiaohu; Peng, Hsin-Chieh

2015-07-01

This Perspective provides a contemporary understanding of the shape evolution of colloidal metal nanocrystals under thermodynamically and kinetically controlled conditions. It has been extremely challenging to investigate this subject in the setting of one-pot synthesis because both the type and number of seeds involved would be changed whenever the experimental conditions are altered, making it essentially impossible to draw conclusions when comparing the outcomes of two syntheses conducted under different conditions. Because of the uncertainty about seeds, most of the mechanistic insights reported in literature for one-pot syntheses of metal nanocrystals with different shapes are either incomplete or ambiguous, and some of them might be misleading or even wrong. Recently, with the use of well-defined seeds for such syntheses, it became possible to separate growth from nucleation and therefore investigate the explicit role(s) played by a specific thermodynamic or kinetic parameter in directing the evolution of colloidal metal nanocrystals into a specific shape. Starting from single-crystal seeds enclosed by a mix of {100}, {111}, and {110} facets, for example, one can obtain colloidal nanocrystals with diversified shapes by adjusting various thermodynamic or kinetic parameters. The mechanistic insights learnt from these studies can also be extended to account for the products of conventional one-pot syntheses that involve self-nucleation only. The knowledge can be further applied to many other types of seeds with twin defects or stacking faults, making it an exciting time to design and synthesize colloidal metal nanocrystals with the shapes sought for a variety of fundamental studies and technologically important applications.

7 CFR 1924.253 - Definitions.

Code of Federal Regulations, 2010 CFR

2010-01-01

... structural defect. (d) Structural defect. A defect in the dwelling or unit, installation or set-up of a unit... of the dwelling or unit or site such as faulty wiring, or failure of sewage disposal or water supply systems located on the property securing the loan caused by faulty materials or improper installation. (3...

Electronic and structural properties of vacancies and hydrogen adsorbates on trilayer graphene

NASA Astrophysics Data System (ADS)

Menezes, Marcos G.; Capaz, Rodrigo B.

2015-08-01

Using ab initio calculations, we study the electronic and structural properties of vacancies and hydrogen adsorbates on trilayer graphene. Those defects are found to share similar low-energy electronic features, since they both remove a pz electron from the honeycomb lattice and induce a defect level near the Fermi energy. However, a vacancy also leaves unpaired σ electrons on the lattice, which lead to important structural differences and also contribute to magnetism. We explore both ABA and ABC stackings and compare properties such as formation energies, magnetic moments, spin density and the local density of states (LDOS) of the defect levels. These properties show a strong sensitivity to the layer in which the defect is placed and smaller sensitivities to sublattice placing and stacking type. Finally, for the ABC trilayer, we also study how these states behave in the presence of an external field, which opens a tunable gap in the band structure of the non-defective system. The pz defect states show a strong hybridization with band states as the field increases, with reduction and eventually loss of magnetization, and a non-magnetic, midgap-like state is found when the defect is at the middle layer.

Electronic and Structural Properties of Vacancies and Hydrogen Adsorbates on Trilayer Graphene

NASA Astrophysics Data System (ADS)

Menezes, Marcos; Capaz, Rodrigo

2015-03-01

Using ab initio calculations, we study the electronic and structural properties of vacancies and hydrogen adsorbates on trilayer graphene. Those defects are found to share similar low-energy electronic features, since they both remove a pz electron from the honeycomb lattice and induce a defect level near the Fermi energy. However, a vacancy also leaves unpaired σ electrons on the lattice, which lead to important structural differences and also contribute to magnetism. We explore both ABA and ABC stackings and compare properties such as formation energies, magnetic moments, spin density and the local density of states (LDOS) of the defect levels. These properties show a strong sensitivity to the layer in which the defect is placed and smaller sensitivities to sublattice placing and stacking type. Finally, for the ABC trilayer, we also study how these states behave in the presence of an external electrical field, which opens a tunable gap in the band structure of the non-defective system. The pz defect states show a strong hybridization with band states as the field increases, with reduction and eventually loss of magnetization, and a non-magnetic, midgap-like state is found when the defect is at the middle layer.

Defects in Arsenic Implanted p + -n- and n + -p- Structures Based on MBE Grown CdHgTe Films

NASA Astrophysics Data System (ADS)

Izhnin, I. I.; Fitsych, E. I.; Voitsekhovskii, A. V.; Korotaev, A. G.; Mynbaev, K. D.; Varavin, V. S.; Dvoretsky, S. A.; Mikhailov, N. N.; Yakushev, M. V.; Bonchyk, A. Yu.; Savytskyy, H. V.; Świątek, Z.

2018-02-01

Complex studies of the defect structure of arsenic-implanted (with the energy of 190 keV) Cd x Hg 1-x Te ( x = 0.22) films grown by molecular-beam epitaxy are carried out. The investigations were performed using secondary-ion mass spectroscopy, transmission electron microscopy, optical reflection in the visible region of the spectrum, and electrical measurements. Radiation donor defects were studied in n +- p- and n +- n-structures obtained by implantation and formed on the basis of p-type and n-type materials, respectively, without activation annealing. It is shown that in the layer of the distribution of implanted ions, a layer of large extended defects with low density is formed in the near-surface region followed by a layer of smaller extended defects with larger density. A different character of accumulation of electrically active donor defects in the films with and without a protective graded-gap surface layer has been revealed. It is demonstrated that p +- n- structures are formed on the basis of n-type material upon activation of arsenic in the process of postimplantation thermal annealing with 100% activation of impurity and complete annihilation of radiation donor defects.

Wafer-scale Thermodynamically Stable GaN Nanorods via Two-Step Self-Limiting Epitaxy for Optoelectronic Applications

NASA Astrophysics Data System (ADS)

Kum, Hyun; Seong, Han-Kyu; Lim, Wantae; Chun, Daemyung; Kim, Young-Il; Park, Youngsoo; Yoo, Geonwook

2017-01-01

We present a method of epitaxially growing thermodynamically stable gallium nitride (GaN) nanorods via metal-organic chemical vapor deposition (MOCVD) by invoking a two-step self-limited growth (TSSLG) mechanism. This allows for growth of nanorods with excellent geometrical uniformity with no visible extended defects over a 100 mm sapphire (Al2O3) wafer. An ex-situ study of the growth morphology as a function of growth time for the two self-limiting steps elucidate the growth dynamics, which show that formation of an Ehrlich-Schwoebel barrier and preferential growth in the c-plane direction governs the growth process. This process allows monolithic formation of dimensionally uniform nanowires on templates with varying filling matrix patterns for a variety of novel electronic and optoelectronic applications. A color tunable phosphor-free white light LED with a coaxial architecture is fabricated as a demonstration of the applicability of these nanorods grown by TSSLG.

Active Oxygen Vacancy Site for Methanol Synthesis from CO2 Hydrogenation on In2O3(110): A DFT Study

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ye, Jingyun; Liu, Changjun; Mei, Donghai

2013-06-03

Methanol synthesis from CO2 hydrogenation on the defective In2O3(110) surface with surface oxygen vacancies has been investigated using periodic density functional theory calculations. The relative stabilities of six possible surface oxygen vacancies numbered from Ov1 to Ov6 on the perfect In2O3(110) surface were examined. The calculated oxygen vacancy formation energies show that the D1 surface with the Ov1 defective site is the most thermodynamically favorable while the D4 surface with the Ov4 defective site is the least stable. Two different methanol synthesis routes from CO2 hydrogenation over both D1 and D4 surfaces were studied and the D4 surface was foundmore » to be more favorable for CO2 activation and hydrogenation. On the D4 surface, one of the O atoms of the CO2 molecule fills in the Ov4 site upon adsorption. Hydrogenation of CO2 to HCOO on the D4 surface is both thermodynamically and kinetically favorable. Further hydrogenation of HCOO involves both forming the C-H bond and breaking the C-O bond, resulting in H2CO and hydroxyl. The HCOO hydrogenation is slightly endothermic with an activation barrier of 0.57 eV. A high barrier of 1.14 eV for the hydrogenation of H2CO to H3CO indicates that this step is the rate-limiting step in the methanol synthesis on the defective In2O3(110) surface. We gratefully acknowledge the supports from the National Natural Science Foundation of China (#20990223) and from US Department of Energy, Basic Energy Science program (DE-FG02-05ER46231). D. Mei was supported by the US Department of Energy, Office of Basic Energy Sciences, Division of Chemical Sciences, Geosciences & Biosciences. The computations were performed in part using the Molecular Science Computing Facility in the William R. Wiley Environmental Molecular Sciences Laboratory (EMSL), which is a U.S. Department of Energy national scientific user facility located at Pacific Northwest National Laboratory in Richland, Washington. PNNL is a multiprogram national laboratory operated for DOE by Battelle.« less

Amplified emission and modified spectral features in an opal hetero-structure mediated by passive defect mode localization

NASA Astrophysics Data System (ADS)

Rout, Dipak; Kumar, Govind; Vijaya, R.

2018-01-01

A photonic crystal hetero-structure consisting of a passive planar defect of SiO2 thin film sandwiched between two identical opals grown by inward growing self-assembly method using Rhodamine-B dye-doped polystyrene microspheres is studied for the characteristics of dye emission. The optical properties and the defect mode characteristics of the hetero-structure are studied from the reflection and transmission measurements. Laser-induced fluorescence from the hetero-structure showed amplified and spectrally narrowed emission compared to the photonic crystal emphasizing the role of the defect mode and distributed feedback. The enhanced emission is also complemented by the reduction in fluorescence decay time in the case of the hetero-structure in comparison to the 3D photonic crystals.

Delamination Defect Detection Using Ultrasonic Guided Waves in Advanced Hybrid Structural Elements

NASA Astrophysics Data System (ADS)

Yan, Fei; Qi, Kevin ``Xue''; Rose, Joseph L.; Weiland, Hasso

2010-02-01

Nondestructive testing for multilayered structures is challenging because of increased numbers of layers and plate thicknesses. In this paper, ultrasonic guided waves are applied to detect delamination defects inside a 23-layer Alcoa Advanced Hybrid Structural plate. A semi-analytical finite element (SAFE) method generates dispersion curves and wave structures in order to select appropriate wave structures to detect certain defects. One guided wave mode and frequency is chosen to achieve large in-plane displacements at regions of interest. The interactions of the selected mode with defects are simulated using finite element models. Experiments are conducted and compared with bulk wave measurements. It is shown that guided waves can detect deeply embedded damages inside thick multilayer fiber-metal laminates with suitable mode and frequency selection.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Sivak, David; Crooks, Gavin

A fundamental problem in modern thermodynamics is how a molecular-scale machine performs useful work, while operating away from thermal equilibrium without excessive dissipation. To this end, we derive a friction tensor that induces a Riemannian manifold on the space of thermodynamic states. Within the linear-response regime, this metric structure controls the dissipation of finite-time transformations, and bestows optimal protocols with many useful properties. We discuss the connection to the existing thermodynamic length formalism, and demonstrate the utility of this metric by solving for optimal control parameter protocols in a simple nonequilibrium model.

Radioactivity and Environmental Security in the Oceans: New Research and Policy Priorities in the Arctic and North Atlantic

DTIC Science & Technology

1993-06-09

within the framework of an update for the computer database "DiaNIK" which has been developed at the Vernadsky Institute of Geochemistry and Analytical...chemical thermodynamic data for minerals and mineral-forming substances. The structure of thermodynamic database "DiaNIK" is based on the principles...in the database . A substantial portion of the thermodynamic values recommended by "DiaNIK" experts for the substances in User Version 3.1 resulted from

Investigation of surface potentials in reduced graphene oxide flake by Kelvin probe force microscopy

NASA Astrophysics Data System (ADS)

Negishi, Ryota; Takashima, Kai; Kobayashi, Yoshihiro

2018-06-01

The surface potential (SP) of reduced graphene oxide (rGO) flakes prepared by thermal treatments of GO under several conditions was analyzed by Kelvin probe force microscopy. The low-crystalline rGO flakes in which a significant amount of oxygen functional groups and structural defects remain have a much lower SP than mechanically exfoliated graphene free from oxygen and defects. On the other hand, the highly crystalline rGO flake after a thermal treatment for the efficient removal of oxygen functional groups and healing of structural defects except for domain boundary shows SP equivalent to that of the mechanically exfoliated graphene. These results indicate that the work function of rGO is sensitively modulated by oxygen functional groups and structural defects remaining after the thermal reduction process, but is not affected significantly by the domain boundary remaining after the healing of structural defects through the thermal treatment at high temperature.

Invited review liquid crystal models of biological materials and silk spinning.

PubMed

Rey, Alejandro D; Herrera-Valencia, Edtson E

2012-06-01

A review of thermodynamic, materials science, and rheological liquid crystal models is presented and applied to a wide range of biological liquid crystals, including helicoidal plywoods, biopolymer solutions, and in vivo liquid crystals. The distinguishing characteristics of liquid crystals (self-assembly, packing, defects, functionalities, processability) are discussed in relation to biological materials and the strong correspondence between different synthetic and biological materials is established. Biological polymer processing based on liquid crystalline precursors includes viscoelastic flow to form and shape fibers. Viscoelastic models for nematic and chiral nematics are reviewed and discussed in terms of key parameters that facilitate understanding and quantitative information from optical textures and rheometers. It is shown that viscoelastic modeling the silk spinning process using liquid crystal theories sheds light on textural transitions in the duct of spiders and silk worms as well as on tactoidal drops and interfacial structures. The range and consistency of the predictions demonstrates that the use of mesoscopic liquid crystal models is another tool to develop the science and biomimetic applications of mesogenic biological soft matter. Copyright © 2011 Wiley Periodicals, Inc.

Ab Initio Simulations of Temperature Dependent Phase Stability and Martensitic Transitions in NiTi

NASA Technical Reports Server (NTRS)

Haskins, Justin B.; Thompson, Alexander E.; Lawson, John W.

2016-01-01

For NiTi based alloys, the shape memory effect is governed by a transition from a low-temperature martensite phase to a high-temperature austenite phase. Despite considerable experimental and computational work, basic questions regarding the stability of the phases and the martensitic phase transition remain unclear even for the simple case of binary, equiatomic NiTi. We perform ab initio molecular dynamics simulations to describe the temperature-dependent behavior of NiTi and resolve several of these outstanding issues. Structural correlation functions and finite temperature phonon spectra are evaluated to determine phase stability. In particular, we show that finite temperature, entropic effects stabilize the experimentally observed martensite (B19') and austenite (B2) phases while destabilizing the theoretically predicted (B33) phase. Free energy computations based on ab initio thermodynamic integration confirm these results and permit estimates of the transition temperature between the phases. In addition to the martensitic phase transition, we predict a new transition between the B33 and B19' phases. The role of defects in suppressing these phase transformations is discussed.

Electronic and thermodynamic properties of layered Hf2Sfrom first-principles calculations

NASA Astrophysics Data System (ADS)

Nandadasa, Chandani; Yoon, Mina; Kim, Seong-Gon; Erwin, Steve; Kim, Sungho; Kim, Sung Wng; Lee, Kimoon

Theoretically we explored two stable phases of inorganic fullerene-like structure of the layered dihafnium sulfide (Hf2 S) . We investigated structural and electronic properties of the two phases of Hf2 S by using first-principles calculations. Our calculation identifies experimentally observed anti-NbS2 structure of Hf2 S . Our electronic calculation results indicate that the density of states of anti- NbS2 structure of Hf2 S at fermi level is less than that of the other phase of Hf2 S . To study the relative stability of different phases at finite temperature Helmholtz free energies of two phases are obtained using density functional theory and density functional perturbation theory. The free energy of the anti-NbS2 structure of Hf2 S always lies below the free energy of the other phase by confirming the most stable structure of Hf2 S . The phonon dispersion, phonon density of states including partial density of states and total density of states are obtained within density functional perturbation theory. Our calculated zero-pressure phonon dispersion curves confirm that the thermodynamic stability of Hf2 S structures. For further investigation of thermodynamic properties, the temperature dependency of thermal expansion, heat capacities at constant pressure and volume are evaluated within the quasiharmonic approximations (QHA).

Thermodynamic Studies for Drug Design and Screening

PubMed Central

Garbett, Nichola C.; Chaires, Jonathan B.

2012-01-01

Introduction A key part of drug design and development is the optimization of molecular interactions between an engineered drug candidate and its binding target. Thermodynamic characterization provides information about the balance of energetic forces driving binding interactions and is essential for understanding and optimizing molecular interactions. Areas covered This review discusses the information that can be obtained from thermodynamic measurements and how this can be applied to the drug development process. Current approaches for the measurement and optimization of thermodynamic parameters are presented, specifically higher throughput and calorimetric methods. Relevant literature for this review was identified in part by bibliographic searches for the period 2004 – 2011 using the Science Citation Index and PUBMED and the keywords listed below. Expert opinion The most effective drug design and development platform comes from an integrated process utilizing all available information from structural, thermodynamic and biological studies. Continuing evolution in our understanding of the energetic basis of molecular interactions and advances in thermodynamic methods for widespread application are essential to realize the goal of thermodynamically-driven drug design. Comprehensive thermodynamic evaluation is vital early in the drug development process to speed drug development towards an optimal energetic interaction profile while retaining good pharmacological properties. Practical thermodynamic approaches, such as enthalpic optimization, thermodynamic optimization plots and the enthalpic efficiency index, have now matured to provide proven utility in design process. Improved throughput in calorimetric methods remains essential for even greater integration of thermodynamics into drug design. PMID:22458502

Analysis of oxygen potential of (U 0.7Pu 0.3)O 2±x and (U 0.8Pu 0.2)O 2±x based on point defect chemistry

NASA Astrophysics Data System (ADS)

Kato, Masato; Konashi, Kenji; Nakae, Nobuo

2009-06-01

Stoichiometries in (U 0.7Pu 0.3)O 2±x and (U 0.8Pu 0.2)O 2±x were analyzed with the experimental data of oxygen potential based on point defect chemistry. The relationship between the deviation x of stoichiometric composition and the oxygen partial pressure P was evaluated using a Kröger-Vink diagram. The concentrations of the point defects in uranium and plutonium mixed oxide (MOX) were estimated from the measurement data of oxygen potentials as functions of temperature and P. The analysis results showed that x was proportional to PO2±1/2 near the stoichiometric region of both (U 0.7Pu 0.3)O 2±x and (U 0.8Pu 0.2)O 2±x, which suggested that intrinsic ionization was the dominant defect. A model to calculate oxygen potential was derived and it represented the experimental data accurately. Further, the model estimated the thermodynamic data, ΔH and ΔS, of stoichiometric (U 0.7Pu 0.3)O 2.00 and (U 0.8Pu 0.2)O 2.00 as -552.5 kJ·mol -1 and -149.7 J·mol -1, and -674.0 kJ · mol -1 and -219.4 J · mol -1, respectively.

Deformation in amorphous–crystalline nanolaminates—an effective-temperature theory and interaction between defects

DOE PAGES

Lieou, Charles K. C.; Mayeur, Jason R.; Beyerlein, Irene J.

2017-02-24

Experiments and atomic-scale simulations suggest that the transmission of plasticity carriers in deforming amorphous–crystalline nanolaminates is mediated by the biphase interface between the amorphous and crystalline layers. In this study, we present a micromechanics model for these biphase nanolaminates that describes defect interactions through the amorphous–crystalline interface (ACI). The model is based on an effective-temperature framework to achieve a unified description of the slow, configurational atomic rearrangements in both phases when driven out of equilibrium. We show how the second law of thermodynamics constrains the density of defects and the rate of configurational rearrangements, and apply this framework to dislocationsmore » in crystalline solids and shear transformation zones (STZs) in amorphous materials. The effective-temperature formulation enables us to interpret the observed movement of dislocations to the ACI and the production of STZs at the interface as a 'diffusion' of configurational disorder across the material. Finally, we demonstrate favorable agreement with experimental findings reported in (Kim et al 2011 Adv. Funct. Mater. 21 4550–4), and demonstrate how the ACI acts as a sink of dislocations and a source of STZs.« less

Thermodynamics of Polaronic States in Artificial Spin Ice

NASA Astrophysics Data System (ADS)

Farhan, Alan

Artificial spin ices represent a class of systems consisting of lithographically patterned nanomagnets arranged in two-dimensional geometries. They were initially introduced as a two-dimensional analogue to geometrically frustrated pyrochlore spin ice, and the most recent introduction of artificial spin ice systems with thermally activated moment fluctuations not only delivered the possibility to directly investigate geometrical frustration and emergent phenomena with real space imaging, but also paved the way to design and investigate new two-dimensional magnetic metamaterials, where material properties can be directly manipulated giving rise to properties that do not exist in nature. Here, taking advantage of cryogenic photoemission electron microscopy, and using the concept of emergent magnetic charges, we are able to directly visualize the creation and annihilation of screened emergent magnetic monopole defects in artificial spin ice. We observe that these polaronic states arise as intermediate states, separating an energetically excited out-of-equilibrium state and low-energy equilibrium configurations. They appear as a result of a local screening effect between emergent magnetic charge defects and their neighboring magnetic charges, thus forming a transient minimum, before the system approaches a global minimum with the least amount of emergent magnetic charge defects. This project is funded by the Swiss National Science Foundation.

Fast ion conductivity in strained defect-fluorite structure created by ion tracks in Gd 2Ti 2O 7

DOE PAGES

Aidhy, Dilpuneet S.; Sachan, Ritesh; Zarkadoula, Eva; ...

2015-11-10

In this research, the structure and ion-conducting properties of the defect-fluorite ring structure formed around amorphous ion-tracks by swift heavy ion irradiation of Gd 2Ti 2O 7 pyrochlore are investigated. High angle annular dark field imaging complemented with ion-track molecular dynamics simulations show that the atoms in the ring structure are disordered, and have relatively larger cation-cation interspacing than in the bulk pyrochlore, illustrating the presence of tensile strain in the ring region. Density functional theory calculations show that the non-equilibrium defect-fluorite structure can be stabilized by tensile strain. The pyrochlore to defect-fluorite structure transformation in the ring region ismore » predicted to be induced by recrystallization during a melt-quench process and stabilized by tensile strain. Static pair-potential calculations show that planar tensile strain lowers oxygen vacancy migration barriers in pyrochlores, in agreement with recent studies on fluorite and perovskite materials. From these results, it is suggested that strain engineering could be simultaneously used to stabilize the defect-fluorite structure and gain control over its high ion-conducting properties.« less

Strain-induced structural defects and their effects on the electrochemical performances of silicon core/germanium shell nanowire heterostructures

DOE PAGES

Lin, Yung-Chen; Kim, Dongheun; Li, Zhen; ...

2016-12-14

Here we report on strain-induced structural defect formation in core Si nanowire of Si/Ge core/shell nanowire heterostructure and influences of the structural defects on the electrochemical performances in lithium-ion battery anodes based on Si/Ge core/shell nanowire heterostructures. The induced structural defects consisting of stacking faults and dislocations in the core Si nanowire were observed for the first time. The generation of stacking faults in Si/Ge core/shell nanowire heterostructure is observed to prefer settling in either only Ge shell region or in both Ge shell and Si core regions and is associated with the increase of the shell volume fraction. Themore » relax of misfit strain in [112] oriented core/shell nanowire heterostructure leads to subsequent gliding of Shockley partial dislocations, preferentially forming the twins. The observation of cross-over defect formation is of great importance for the understanding of heteroepitaxy in radial heterostructures at nanoscale and building the three dimensional heterostructures for the various applications. In addition, the effect of the defect formation on nanomaterial’s functionality is investigated by electrochemical performance test. The Si/Ge core/shell nanowire heterostructures enhance the gravimetric capacity of lithium ion battery anodes under fast charging/discharging rates compared to Si nanowires. However, the induced structural defects hamper lithiation of the Si/Ge core/shell nanowire heterostructure.« less

Strain-induced structural defects and their effects on the electrochemical performances of silicon core/germanium shell nanowire heterostructures

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lin, Yung-Chen; Kim, Dongheun; Li, Zhen

Here we report on strain-induced structural defect formation in core Si nanowire of Si/Ge core/shell nanowire heterostructure and influences of the structural defects on the electrochemical performances in lithium-ion battery anodes based on Si/Ge core/shell nanowire heterostructures. The induced structural defects consisting of stacking faults and dislocations in the core Si nanowire were observed for the first time. The generation of stacking faults in Si/Ge core/shell nanowire heterostructure is observed to prefer settling in either only Ge shell region or in both Ge shell and Si core regions and is associated with the increase of the shell volume fraction. Themore » relax of misfit strain in [112] oriented core/shell nanowire heterostructure leads to subsequent gliding of Shockley partial dislocations, preferentially forming the twins. The observation of cross-over defect formation is of great importance for the understanding of heteroepitaxy in radial heterostructures at nanoscale and building the three dimensional heterostructures for the various applications. In addition, the effect of the defect formation on nanomaterial’s functionality is investigated by electrochemical performance test. The Si/Ge core/shell nanowire heterostructures enhance the gravimetric capacity of lithium ion battery anodes under fast charging/discharging rates compared to Si nanowires. However, the induced structural defects hamper lithiation of the Si/Ge core/shell nanowire heterostructure.« less

Thermodynamics, kinetics, and catalytic effect of dehydrogenation from MgH2 stepped surfaces and nanocluster: a DFT study

NASA Astrophysics Data System (ADS)

Reich, Jason; Wang, Linlin; Johnson, Duane

2013-03-01

We detail the results of a Density Functional Theory (DFT) based study of hydrogen desorption, including thermodynamics and kinetics with(out) catalytic dopants, on stepped (110) rutile and nanocluster MgH2. We investigate competing configurations (optimal surface and nanoparticle configurations) using simulated annealing with additional converged results at 0 K, necessary for finding the low-energy, doped MgH2 nanostructures. Thermodynamics of hydrogen desorption from unique dopant sites will be shown, as well as activation energies using the Nudged Elastic Band algorithm. To compare to experiment, both stepped structures and nanoclusters are required to understanding and predict the effects of ball milling. We demonstrate how these model systems relate to the intermediary sized structures typically seen in ball milling experiments.

Structural stability, elastic and thermodynamic properties of Au-Cu alloys from first-principles calculations

NASA Astrophysics Data System (ADS)

Kong, Ge-Xing; Ma, Xiao-Juan; Liu, Qi-Jun; Li, Yong; Liu, Zheng-Tang

2018-03-01

Using first-principles calculations method based on density functional theory (DFT) with the Perdew-Burke-Ernzerhof (PBE) implementation of the generalized gradient approximation (GGA), we investigate the structural, elastic and thermodynamic properties of gold-copper intermetallic compounds (Au-Cu ICs). The calculated lattice parameters are in excellent agreement with experimental data. The elastic constants show that all the investigated Au-Cu alloys are mechanically stable. Elastic properties, including the shear modulus, Young's modulus, Poisson's ratio and Pugh's indicator, of the intermetallic compounds are evaluated and discussed, with special attention to the remarkable anisotropy displayed by Au-Cu ICs. Thermodynamic and transport properties including the Debye temperature, thermal conductivity and melting point are predicted from the averaged sound velocity and elastic moduli, using semi-empirical formulas.

MOLECULAR THEORY OF HYDROPHOBIC EFFECTS: "She is too mean to have her name repeated."*

NASA Astrophysics Data System (ADS)

Pratt, Lawrence R.

2002-10-01

This paper reviews the molecular theory of hydrophobic effects relevant to biomolecular structure and assembly in aqueous solution. Recent progress has resulted in simple, validated molecular statistical thermodynamic theories and clarification of confusing theories of decades ago. Current work is resolving effects of wider variations of thermodynamic state, e.g., pressure denaturation of soluble proteins, and more exotic questions such as effects of surface chemistry in treating stability of macromolecular structures in aqueous solution.

Raman spectroscopic studies of defect structures and phase transition in hyper-stoichiometric UO(2+x).

PubMed

He, Heming; Shoesmith, David

2010-07-28

A method to determine the defect structures in hyper-stoichiometric UO(2+x) using a combination of XRD and Raman spectroscopy has been developed. A sequence of phase transitions, from cubic to tetragonal symmetry, occurs with increasing degree of non-stoichiometry. This sequence proceeds from a cubic phase through an intermediate t''-type tetragonal (axial ratio c/a = 1) phase to a final t-type tetragonal (c/a not = 1) phase. Four distinct structural defect regions can be identified in the stoichiometry range, UO(2) to U(3)O(7): (i) a random point defect structure (x (in UO(2+x)) < or = 0.05); (ii) a non-stoichiometry region (0.05 < or = x < or = 0.15) over which point defects are gradually eliminated and replaced by the Willis 2:2:2 cluster; (iii) a mixture of Willis and cuboctahedral clusters (0.15 < or = x < or = 0.23); (iv) the cuboctahedral cluster (x > or = 0.23). The geometry and steric arrangement of these defects is primarily determined by the concentration of the excess-oxygen interstitials.

Drastic stabilization of parallel DNA hybridizations by a polylysine comb-type copolymer with hydrophilic graft chain.

PubMed

Miyoshi, Daisuke; Ueda, Yu-Mi; Shimada, Naohiko; Nakano, Shu-Ichi; Sugimoto, Naoki; Maruyama, Atsushi

2014-09-01

Electrostatic interactions play a major role in protein-DNA interactions. As a model system of a cationic protein, herein we focused on a comb-type copolymer of a polycation backbone and dextran side chains, poly(L-lysine)-graft-dextran (PLL-g-Dex), which has been reported to form soluble interpolyelectrolyte complexes with DNA strands. We investigated the effects of PLL-g-Dex on the conformation and thermodynamics of DNA oligonucleotides forming various secondary structures. Thermodynamic analysis of the DNA structures showed that the parallel conformations involved in both DNA duplexes and triplexes were significantly and specifically stabilized by PLL-g-Dex. On the basis of thermodynamic parameters, it was further possible to design DNA switches that undergo structural transition responding to PLL-g-Dex from an antiparallel duplex to a parallel triplex even with mismatches in the third strand hybridization. These results suggest that polycationic molecules are able to induce structural polymorphism of DNA oligonucleotides, because of the conformation-selective stabilization effects. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

On correction of model of stabilization of distribution of concentration of radiation defects in a multilayer structure with account experiment data

NASA Astrophysics Data System (ADS)

Pankratov, E. L.

2018-05-01

We introduce a model of redistribution of point radiation defects, their interaction between themselves and redistribution of their simplest complexes (divacancies and diinterstitials) in a multilayer structure. The model gives a possibility to describe qualitatively nonmonotonicity of distributions of concentrations of radiation defects on interfaces between layers of the multilayer structure. The nonmonotonicity was recently found experimentally. To take into account the nonmonotonicity we modify recently used in literature model for analysis of distribution of concentration of radiation defects. To analyze the model we used an approach of solution of boundary problems, which could be used without crosslinking of solutions on interfaces between layers of the considered multilayer structures.

Tunable thermodynamic activity of La x Sr1-x Mn y Al1-y O3-δ (0 ≤ x ≤ 1, 0 ≤ y ≤ 1) perovskites for solar thermochemical fuel synthesis.

PubMed

Ezbiri, M; Takacs, M; Theiler, D; Michalsky, R; Steinfeld, A

2017-02-28

Nonstoichiometric metal oxides with variable valence are attractive redox materials for thermochemical and electrochemical fuel processing. To guide the design of advanced redox materials for solar-driven splitting of CO 2 and/or H 2 O to produce CO and/or H 2 (syngas), we investigate the equilibrium thermodynamics of the La x Sr 1- x Mn y Al 1- y O 3- δ perovskite family (0 ≤ x ≤ 1, 0 ≤ y ≤ 1) and La 0.6 Ca 0.4 Mn 0.8 Al 0.2 O 3- δ , and compare them to those of CeO 2 as the baseline. Oxygen nonstoichiometry measurements from 1573 to 1773 K and from 0.206 to 180 mbar O 2 show a tunable reduction extent, increasing with increasing Sr content. Maximal nonstoichiometry of 0.32 is established with La 0.2 Sr 0.8 Mn 0.8 Al 0.2 O 3- δ at 1773 K and 2.37 mbar O 2 . As a trend, we find that oxygen capacities are most sensitive to the A-cation composition. Partial molar enthalpy, entropy and Gibbs free energy changes for oxide reduction are extracted from the experimental data using defect models for Mn 4+ /Mn 3+ and Mn 3+ /Mn 2+ redox couples. We find that perovskites exhibit typically decreasing enthalpy changes with increasing nonstoichiometries. This desirable characteristic is most pronounced by La 0.6 Sr 0.4 Mn 0.4 Al 0.6 O 3- δ , rendering it attractive for CO 2 and H 2 O splitting. Generally, perovskites show lower enthalpy and entropy changes than ceria, resulting in more favorable reduction but less favorable oxidation equilibria. The energy penalties due to larger temperature swings and excess oxidants are discussed in particular. Using electronic structure theory, we conclude with a practical methodology estimating thermodynamic activity to rationally design perovskites with variable stoichiometry and valence.

Predicting structural properties of fluids by thermodynamic extrapolation

NASA Astrophysics Data System (ADS)

Mahynski, Nathan A.; Jiao, Sally; Hatch, Harold W.; Blanco, Marco A.; Shen, Vincent K.

2018-05-01

We describe a methodology for extrapolating the structural properties of multicomponent fluids from one thermodynamic state to another. These properties generally include features of a system that may be computed from an individual configuration such as radial distribution functions, cluster size distributions, or a polymer's radius of gyration. This approach is based on the principle of using fluctuations in a system's extensive thermodynamic variables, such as energy, to construct an appropriate Taylor series expansion for these structural properties in terms of intensive conjugate variables, such as temperature. Thus, one may extrapolate these properties from one state to another when the series is truncated to some finite order. We demonstrate this extrapolation for simple and coarse-grained fluids in both the canonical and grand canonical ensembles, in terms of both temperatures and the chemical potentials of different components. The results show that this method is able to reasonably approximate structural properties of such fluids over a broad range of conditions. Consequently, this methodology may be employed to increase the computational efficiency of molecular simulations used to measure the structural properties of certain fluid systems, especially those used in high-throughput or data-driven investigations.

Cubic and orthorhombic structures of aluminum hydride Al H3 predicted by a first-principles study

NASA Astrophysics Data System (ADS)

Ke, Xuezhi; Kuwabara, Akihide; Tanaka, Isao

2005-05-01

The most stable structure of aluminum hydride AlH3 is believed to be a hexagonal symmetry. However, using the density functional theory, we have identified two more stable structures for the AlH3 with the cubic and orthorhombic symmetries. Based on the quasiharmonic approximation, the cubic and orthorhombic AlH3 are almost degenerate when the zero-point energies are included. The geometric and electronic structures, the phonon, and the thermodynamic properties for the hexagonal, cubic, and orthorhombic AlH3 have been studied by means of density functional theory and direct ab initio force constant approach. The calculated electronic structures, phonon density of states, and thermodynamic functions [including S(T) and H(T)-H(0) ] for the three hydrides are similar. The results show that these three hydrides have negative enthalpies of formation, but positive free energies of formation. This conclusion is the same as that made by Wolverton for the hexagonal AlH3 [Phys. Rev. B 69, 144109 (2004)]. The thermodynamic properties indicate that the orthorhombic and cubic AlH3 should be more difficult to dissociate than the hexagonal AlH3 .

Thermodynamics of micellization from heat-capacity measurements.

PubMed

Šarac, Bojan; Bešter-Rogač, Marija; Lah, Jurij

2014-06-23

Differential scanning calorimetry (DSC), the most important technique for studying the thermodynamics of structural transitions of biological macromolecules, is seldom used in quantitative thermodynamic studies of surfactant micellization/demicellization. The reason for this could be ascribed to an insufficient understanding of the temperature dependence of the heat capacity of surfactant solutions (DSC data) in terms of thermodynamics, which leads to problems with the design of experiments and interpretation of the output signals. We address these issues by careful design of DSC experiments performed with solutions of ionic and nonionic surfactants at various surfactant concentrations, and individual and global mass-action model analysis of the obtained DSC data. Our approach leads to reliable thermodynamic parameters of micellization for all types of surfactants, comparable with those obtained by using isothermal titration calorimetry (ITC). In summary, we demonstrate that DSC can be successfully used as an independent method to obtain temperature-dependent thermodynamic parameters for micellization. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Course 12: Proteins: Structural, Thermodynamic and Kinetic Aspects

NASA Astrophysics Data System (ADS)

Finkelstein, A. V.

1 Introduction 2 Overview of protein architectures and discussion of physical background of their natural selection 2.1 Protein structures 2.2 Physical selection of protein structures 3 Thermodynamic aspects of protein folding 3.1 Reversible denaturation of protein structures 3.2 What do denatured proteins look like? 3.3 Why denaturation of a globular protein is the first-order phase transition 3.4 "Gap" in energy spectrum: The main characteristic that distinguishes protein chains from random polymers 4 Kinetic aspects of protein folding 4.1 Protein folding in vivo 4.2 Protein folding in vitro (in the test-tube) 4.3 Theory of protein folding rates and solution of the Levinthal paradox

Intrinsic thermodynamics of inhibitor binding to human carbonic anhydrase IX.

PubMed

Linkuvienė, Vaida; Matulienė, Jurgita; Juozapaitienė, Vaida; Michailovienė, Vilma; Jachno, Jelena; Matulis, Daumantas

2016-04-01

Human carbonic anhydrase 9th isoform (CA IX) is an important marker of numerous cancers and is increasingly interesting as a potential anticancer drug target. Various synthetic aromatic sulfonamide-bearing compounds are being designed as potent inhibitors of CA IX. However, sulfonamide compound binding to CA IX is linked to several reactions, the deprotonation of the sulfonamide amino group and the protonation of the CA active site Zn(II)-bound hydroxide. These linked reactions significantly affect the affinities and other thermodynamic parameters such as enthalpies and entropies of binding. The observed and intrinsic affinities of compound binding to CA IX were determined by the fluorescent thermal shift assay. The enthalpies and entropies of binding were determined by the isothermal titration calorimetry. The pKa of CA IX was determined to be 6.8 and the enthalpy of CA IX-Zn(II)-bound hydroxide protonation was -24 kJ/mol. These values enabled the analysis of intrinsic thermodynamics of a library of compounds binding to CA IX. The most strongly binding compounds exhibited the intrinsic affinity of 0.01 nM and the observed affinity of 2 nM. The intrinsic thermodynamic parameters of compound binding to CA IX helped to draw the compound structure to thermodynamics relationship. It is important to distinguish the intrinsic from observed parameters of any disease target protein interaction with its inhibitors as drug candidates when drawing detailed compound structure to thermodynamics correlations. Copyright © 2016 Elsevier B.V. All rights reserved.

Transforming graphene nanoribbons into nanotubes by use of point defects.

PubMed

Sgouros, A; Sigalas, M M; Papagelis, K; Kalosakas, G

2014-03-26

Using molecular dynamics simulations with semi-empirical potentials, we demonstrate a method to fabricate carbon nanotubes (CNTs) from graphene nanoribbons (GNRs), by periodically inserting appropriate structural defects into the GNR crystal structure. We have found that various defect types initiate the bending of GNRs and eventually lead to the formation of CNTs. All kinds of carbon nanotubes (armchair, zigzag, chiral) can be produced with this method. The structural characteristics of the resulting CNTs, and the dependence on the different type and distribution of the defects, were examined. The smallest (largest) CNT obtained had a diameter of ∼ 5 Å (∼ 39 Å). Proper manipulation of ribbon edges controls the chirality of the CNTs formed. Finally, the effect of randomly distributed defects on the ability of GNRs to transform into CNTs is considered.

Toward superconducting critical current by design

DOE PAGES

Sadovskyy, Ivan A.; Jia, Ying; Leroux, Maxime; ...

2016-03-31

The interaction of vortex matter with defects in applied superconductors directly determines their current carrying capacity. Defects range from chemically grown nanostructures and crystalline imperfections to the layered structure of the material itself. The vortex-defect interactions are non-additive in general, leading to complex dynamic behavior that has proven difficult to capture in analytical models. With recent rapid progress in computational powers, a new paradigm has emerged that aims at simulation assisted design of defect structures with predictable ‘critical-current-by-design’: analogous to the materials genome concept of predicting stable materials structures of interest. We demonstrate the feasibility of this paradigm by combiningmore » large-scale time-dependent Ginzburg-Landau numerical simulations with experiments on commercial high temperature superconductor (HTS) containing well-controlled correlated defects.« less

Unified framework to evaluate panmixia and migration direction among multiple sampling locations.

PubMed

Beerli, Peter; Palczewski, Michal

2010-05-01

For many biological investigations, groups of individuals are genetically sampled from several geographic locations. These sampling locations often do not reflect the genetic population structure. We describe a framework using marginal likelihoods to compare and order structured population models, such as testing whether the sampling locations belong to the same randomly mating population or comparing unidirectional and multidirectional gene flow models. In the context of inferences employing Markov chain Monte Carlo methods, the accuracy of the marginal likelihoods depends heavily on the approximation method used to calculate the marginal likelihood. Two methods, modified thermodynamic integration and a stabilized harmonic mean estimator, are compared. With finite Markov chain Monte Carlo run lengths, the harmonic mean estimator may not be consistent. Thermodynamic integration, in contrast, delivers considerably better estimates of the marginal likelihood. The choice of prior distributions does not influence the order and choice of the better models when the marginal likelihood is estimated using thermodynamic integration, whereas with the harmonic mean estimator the influence of the prior is pronounced and the order of the models changes. The approximation of marginal likelihood using thermodynamic integration in MIGRATE allows the evaluation of complex population genetic models, not only of whether sampling locations belong to a single panmictic population, but also of competing complex structured population models.

Effect of precursor solutions stirring on deep level defects concentration and spatial distribution in low temperature aqueous chemical synthesis of zinc oxide nanorods

DOE Office of Scientific and Technical Information (OSTI.GOV)

Alnoor, Hatim, E-mail: hatim.alnoor@liu.se; Chey, Chan Oeurn; Pozina, Galia

Hexagonal c-axis oriented zinc oxide (ZnO) nanorods (NRs) with 120-300 nm diameters are synthesized via the low temperature aqueous chemical route at 80 °C on silver-coated glass substrates. The influence of varying the precursor solutions stirring durations on the concentration and spatial distributions of deep level defects in ZnO NRs is investigated. Room temperature micro-photoluminesnce (μ-PL) spectra were collected for all samples. Cathodoluminescence (CL) spectra of the as-synthesized NRs reveal a significant change in the intensity ratio of the near band edge emission (NBE) to the deep-level emission (DLE) peaks with increasing stirring durations. This is attributed to the variation inmore » the concentration of the oxygen-deficiency with increasing stirring durations as suggested from the X-ray photoelectron spectroscopy analysis. Spatially resolved CL spectra taken along individual NRs revealed that stirring the precursor solutions for relatively short duration (1-3 h), which likely induced high super saturation under thermodynamic equilibrium during the synthesis process, is observed to favor the formation of point defects moving towards the tip of the NRs. In contrary, stirring for longer duration (5-15 h) will induce low super saturation favoring the formation of point defects located at the bottom of the NRs. These findings demonstrate that it is possible to control the concentration and spatial distribution of deep level defects in ZnO NRs by varying the stirring durations of the precursor solutions.« less

Co-operative intra-protein structural response due to protein-protein complexation revealed through thermodynamic quantification: study of MDM2-p53 binding

NASA Astrophysics Data System (ADS)

Samanta, Sudipta; Mukherjee, Sanchita

2017-10-01

The p53 protein activation protects the organism from propagation of cells with damaged DNA having oncogenic mutations. In normal cells, activity of p53 is controlled by interaction with MDM2. The well understood p53-MDM2 interaction facilitates design of ligands that could potentially disrupt or prevent the complexation owing to its emergence as an important objective for cancer therapy. However, thermodynamic quantification of the p53-peptide induced structural changes of the MDM2-protein remains an area to be explored. This study attempts to understand the conformational free energy and entropy costs due to this complex formation from the histograms of dihedral angles generated from molecular dynamics simulations. Residue-specific quantification illustrates that, hydrophobic residues of the protein contribute maximum to the conformational thermodynamic changes. Thermodynamic quantification of structural changes of the protein unfold the fact that, p53 binding provides a source of inter-element cooperativity among the protein secondary structural elements, where the highest affected structural elements (α2 and α4) found at the binding site of the protein affects faraway structural elements (β1 and Loop1) of the protein. The communication perhaps involves water mediated hydrogen bonded network formation. Further, we infer that in inhibitory F19A mutation of P53, though Phe19 is important in the recognition process, it has less prominent contribution in the stability of the complex. Collectively, this study provides vivid microscopic understanding of the interaction within the protein complex along with exploring mutation sites, which will contribute further to engineer the protein function and binding affinity.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Putilov, L.P., E-mail: lev.putilov@gmail.com; Tsidilkovski, V.I.

The impact of deep acceptor centers on defect thermodynamics and oxidation of wide-band-gap acceptor-doped perovskites without mixed-valence cations is studied. These deep centers are formed by the acceptor-bound small hole polarons whose stabilization energy can be high enough (significantly higher than the hole-acceptor Coulomb interaction energy). It is shown that the oxidation enthalpy ΔH{sub ox} of oxide is determined by the energy ε{sub A} of acceptor-bound states along with the formation energy E{sub V} of oxygen vacancies. The oxidation reaction is demonstrated to be either endothermic or exothermic, and the regions of ε{sub A} and E{sub V} values corresponding tomore » the positive or negative ΔH{sub ox} are determined. The contribution of acceptor-bound holes to the defect thermodynamics strongly depends on the acceptor states depth ε{sub A}: it becomes negligible at ε{sub A} less than a certain value (at which the acceptor levels are still deep). With increasing ε{sub A}, the concentration of acceptor-bound small hole polarons can reach the values comparable to the dopant content. The results are illustrated with the acceptor-doped BaZrO{sub 3} as an example. It is shown that the experimental data on the bulk hole conductivity of barium zirconate can be described both in the band transport model and in the model of hopping small polarons localized on oxygen ions away from the acceptor centers. Depending on the ε{sub A} magnitude, the oxidation reaction can be either endothermic or exothermic for both mobility mechanisms.« less

Study on control of defect mode in hybrid mirror chirped porous silicon photonic crystal

NASA Astrophysics Data System (ADS)

Chen, Ying; Luo, Pei; Han, Yangyang; Cui, Xingning; He, Lei

2018-03-01

Based on the optical resonance principle and the tight-binding theory, a hybrid mirror chirped porous silicon photonic crystal is proposed. The control of the defect mode in hybrid mirror chirped porous silicon photonic crystal is studied. Through the numerical simulation, the control regulations of the defect modes resulted by the number of the periodical layers for the fundamental unit and the cascading number of the chirped structures are analyzed, and the split and the degeneration of the defect modes resulted by the change of the relative location between the mirror structures and the quasi-mirror structures are discussed. The simulation results show that the band gap would be broadened with the increase of the chirp quantity and the layer number of unilateral chirp. Adjusting the structural parameters of the hybrid mirror structure, the multimode characteristics will occur in the band gap. The more the cascading number of the chirped units, the more the number of the filtering channels will be. In addition, with the increase of the relative location between the mirror structures and the quasi-mirror structures, the degeneration of the defect modes will occur and can obtain high Q value. The structure can provide effective theoretical references for the design the multi-channel filters and high Q value sensors.

Thermodynamic Model Formulations for Inhomogeneous Solids with Application to Non-isothermal Phase Field Modelling

NASA Astrophysics Data System (ADS)

Gladkov, Svyatoslav; Kochmann, Julian; Reese, Stefanie; Hütter, Markus; Svendsen, Bob

2016-04-01

The purpose of the current work is the comparison of thermodynamic model formulations for chemically and structurally inhomogeneous solids at finite deformation based on "standard" non-equilibrium thermodynamics [SNET: e. g. S. de Groot and P. Mazur, Non-equilibrium Thermodynamics, North Holland, 1962] and the general equation for non-equilibrium reversible-irreversible coupling (GENERIC) [H. C. Öttinger, Beyond Equilibrium Thermodynamics, Wiley Interscience, 2005]. In the process, non-isothermal generalizations of standard isothermal conservative [e. g. J. W. Cahn and J. E. Hilliard, Free energy of a non-uniform system. I. Interfacial energy. J. Chem. Phys. 28 (1958), 258-267] and non-conservative [e. g. S. M. Allen and J. W. Cahn, A macroscopic theory for antiphase boundary motion and its application to antiphase domain coarsening. Acta Metall. 27 (1979), 1085-1095; A. G. Khachaturyan, Theory of Structural Transformations in Solids, Wiley, New York, 1983] diffuse interface or "phase-field" models [e. g. P. C. Hohenberg and B. I. Halperin, Theory of dynamic critical phenomena, Rev. Modern Phys. 49 (1977), 435-479; N. Provatas and K. Elder, Phase Field Methods in Material Science and Engineering, Wiley-VCH, 2010.] for solids are obtained. The current treatment is consistent with, and includes, previous works [e. g. O. Penrose and P. C. Fife, Thermodynamically consistent models of phase-field type for the kinetics of phase transitions, Phys. D 43 (1990), 44-62; O. Penrose and P. C. Fife, On the relation between the standard phase-field model and a "thermodynamically consistent" phase-field model. Phys. D 69 (1993), 107-113] on non-isothermal systems as a special case. In the context of no-flux boundary conditions, the SNET- and GENERIC-based approaches are shown to be completely consistent with each other and result in equivalent temperature evolution relations.

Quantitative Analysis of Defects in Silicon. [to predict energy conversion efficiency of silicon samples for solar cells

NASA Technical Reports Server (NTRS)

Natesh, R.; Smith, J. M.; Qidwai, H. A.; Bruce, T.

1979-01-01

The evaluation and prediction of the conversion efficiency for a variety of silicon samples with differences in structural defects, such as grain boundaries, twin boundaries, precipitate particles, dislocations, etc. are discussed. Quantitative characterization of these structural defects, which were revealed by etching the surface of silicon samples, is performed by using an image analyzer. Due to different crystal growth and fabrication techniques the various types of silicon contain a variety of trace impurity elements and structural defects. The two most important criteria in evaluating the various silicon types for solar cell applications are cost and conversion efficiency.

Structural characterization of terrestrial microbial Mn oxides from Pinal Creek, AZ

USGS Publications Warehouse

Bargar, J.R.; Fuller, C.C.; Marcus, M.A.; Brearley, A.J.; Perez De la Rosa, M.; Webb, S.M.; Caldwell, W.A.

2009-01-01

The microbial catalysis of Mn(II) oxidation is believed to be a dominant source of abundant sorption- and redox-active Mn oxides in marine, freshwater, and subsurface aquatic environments. In spite of their importance, environmental oxides of known biogenic origin have generally not been characterized in detail from a structural perspective. Hyporheic zone Mn oxide grain coatings at Pinal Creek, Arizona, a metals-contaminated stream, have been identified as being dominantly microbial in origin and are well studied from bulk chemistry and contaminant hydrology perspectives. This site thus presents an excellent opportunity to study the structures of terrestrial microbial Mn oxides in detail. XRD and EXAFS measurements performed in this study indicate that the hydrated Pinal Creek Mn oxide grain coatings are layer-type Mn oxides with dominantly hexagonal or pseudo-hexagonal layer symmetry. XRD and TEM measurements suggest the oxides to be nanoparticulate plates with average dimensions on the order of 11 nm thick ?? 35 nm diameter, but with individual particles exhibiting thickness as small as a single layer and sheets as wide as 500 nm. The hydrated oxides exhibit a 10-?? basal-plane spacing and turbostratic disorder. EXAFS analyses suggest the oxides contain layer Mn(IV) site vacancy defects, and layer Mn(III) is inferred to be present, as deduced from Jahn-Teller distortion of the local structure. The physical geometry and structural details of the coatings suggest formation within microbial biofilms. The biogenic Mn oxides are stable with respect to transformation into thermodynamically more stable phases over a time scale of at least 5 months. The nanoparticulate layered structural motif, also observed in pure culture laboratory studies, appears to be characteristic of biogenic Mn oxides and may explain the common occurrence of this mineral habit in soils and sediments. ?? 2008 Elsevier Ltd.

Crystal structure correlations with the intrinsic thermodynamics of human carbonic anhydrase inhibitor binding

PubMed Central

Smirnov, Alexey; Zubrienė, Asta; Manakova, Elena; Gražulis, Saulius

2018-01-01

The structure-thermodynamics correlation analysis was performed for a series of fluorine- and chlorine-substituted benzenesulfonamide inhibitors binding to several human carbonic anhydrase (CA) isoforms. The total of 24 crystal structures of 16 inhibitors bound to isoforms CA I, CA II, CA XII, and CA XIII provided the structural information of selective recognition between a compound and CA isoform. The binding thermodynamics of all structures was determined by the analysis of binding-linked protonation events, yielding the intrinsic parameters, i.e., the enthalpy, entropy, and Gibbs energy of binding. Inhibitor binding was compared within structurally similar pairs that differ by para- or meta-substituents enabling to obtain the contributing energies of ligand fragments. The pairs were divided into two groups. First, similar binders—the pairs that keep the same orientation of the benzene ring exhibited classical hydrophobic effect, a less exothermic enthalpy and a more favorable entropy upon addition of the hydrophobic fragments. Second, dissimilar binders—the pairs of binders that demonstrated altered positions of the benzene rings exhibited the non-classical hydrophobic effect, a more favorable enthalpy and variable entropy contribution. A deeper understanding of the energies contributing to the protein-ligand recognition should lead toward the eventual goal of rational drug design where chemical structures of ligands could be designed based on the target protein structure. PMID:29503769

Structural and Thermodynamic Properties of Amyloid-β Peptides: Impact of Fragment Size

NASA Astrophysics Data System (ADS)

Kitahara, T.; Wise-Scira, O.; Coskuner, O.

2010-10-01

Alzheimer's disease is a progressive neurodegenerative disease whose physiological characteristics include the accumulation of amyloid-containing deposits in the brain and consequent synapse and neuron loss. Unfortunately, most widely used drugs for the treatment can palliate the outer symptoms but cannot cure the disease itself. Hence, developing a new drug that can cure it. Most recently, the ``early aggregation and monomer'' hypothesis has become popular and a few drugs have been developed based on this hypothesis. Detailed understanding of the amyloid-β peptide structure can better help us to determine more effective treatment strategies; indeed, the structure of Amyloid has been studied extensively employing experimental and theoretical tools. Nevertheless, those studies have employed different fragment sizes of Amyloid and characterized its conformational nature in different media. Thus, the structural properties might be different from each other and provide a reason for the existing debates in the literature. Here, we performed all-atom MD simulations and present the structural and thermodynamic properties of Aβ1-16, Aβ1-28, and Aβ1-42 in the gas phase and in aqueous solution. Our studies show that the overall structures, secondary structures, and the calculated thermodynamic properties change with increasing peptide size. In addition, we find that the structural properties of those peptides are different from each other in the gas phase and in aqueous solution.

Solvation Structure and Thermodynamic Mapping (SSTMap): An Open-Source, Flexible Package for the Analysis of Water in Molecular Dynamics Trajectories.

PubMed

Haider, Kamran; Cruz, Anthony; Ramsey, Steven; Gilson, Michael K; Kurtzman, Tom

2018-01-09

We have developed SSTMap, a software package for mapping structural and thermodynamic water properties in molecular dynamics trajectories. The package introduces automated analysis and mapping of local measures of frustration and enhancement of water structure. The thermodynamic calculations are based on Inhomogeneous Fluid Solvation Theory (IST), which is implemented using both site-based and grid-based approaches. The package also extends the applicability of solvation analysis calculations to multiple molecular dynamics (MD) simulation programs by using existing cross-platform tools for parsing MD parameter and trajectory files. SSTMap is implemented in Python and contains both command-line tools and a Python module to facilitate flexibility in setting up calculations and for automated generation of large data sets involving analysis of multiple solutes. Output is generated in formats compatible with popular Python data science packages. This tool will be used by the molecular modeling community for computational analysis of water in problems of biophysical interest such as ligand binding and protein function.

Thermodynamics. [algebraic structure

NASA Technical Reports Server (NTRS)

Zeleznik, F. J.

1976-01-01

The fundamental structure of thermodynamics is purely algebraic, in the sense of atopological, and it is also independent of partitions, composite systems, the zeroth law, and entropy. The algebraic structure requires the notion of heat, but not the first law. It contains a precise definition of entropy and identifies it as a purely mathematical concept. It also permits the construction of an entropy function from heat measurements alone when appropriate conditions are satisfied. Topology is required only for a discussion of the continuity of thermodynamic properties, and then the weak topology is the relevant topology. The integrability of the differential form of the first law can be examined independently of Caratheodory's theorem and his inaccessibility axiom. Criteria are established by which one can determine when an integrating factor can be made intensive and the pseudopotential extensive and also an entropy. Finally, a realization of the first law is constructed which is suitable for all systems whether they are solids or fluids, whether they do or do not exhibit chemical reactions, and whether electromagnetic fields are or are not present.

Structural and Thermodynamic Factors of Suppressed Interdiffusion Kinetics in Multi-component High-entropy Materials

PubMed Central

Chang, Shou-Yi; Li, Chen-En; Huang, Yi-Chung; Hsu, Hsun-Feng; Yeh, Jien-Wei; Lin, Su-Jien

2014-01-01

We report multi-component high-entropy materials as extraordinarily robust diffusion barriers and clarify the highly suppressed interdiffusion kinetics in the multi-component materials from structural and thermodynamic perspectives. The failures of six alloy barriers with different numbers of elements, from unitary Ti to senary TiTaCrZrAlRu, against the interdiffusion of Cu and Si were characterized, and experimental results indicated that, with more elements incorporated, the failure temperature of the barriers increased from 550 to 900°C. The activation energy of Cu diffusion through the alloy barriers was determined to increase from 110 to 163 kJ/mole. Mechanistic analyses suggest that, structurally, severe lattice distortion strains and a high packing density caused by different atom sizes, and, thermodynamically, a strengthened cohesion provide a total increase of 55 kJ/mole in the activation energy of substitutional Cu diffusion, and are believed to be the dominant factors of suppressed interdiffusion kinetics through the multi-component barrier materials. PMID:24561911

Insight into the Li{sub 2}CO{sub 3}–K{sub 2}CO{sub 3} eutectic mixture from classical molecular dynamics: Thermodynamics, structure, and dynamics

DOE Office of Scientific and Technical Information (OSTI.GOV)

Corradini, Dario; Vuilleumier, Rodolphe, E-mail: rodolphe.vuilleumier@ens.fr; Sorbonne Universités, UPMC Univ. Paris 06, PASTEUR, 75005 Paris

We use molecular dynamics simulations to study the thermodynamics, structure, and dynamics of the Li{sub 2}CO{sub 3}–K{sub 2}CO{sub 3} (62:38 mol. %) eutectic mixture. We present a new classical non-polarizable force field for this molten salt mixture, optimized using experimental and first principles molecular dynamics simulations data as reference. This simple force field allows efficient molecular simulations of phenomena at long time scales. We use this optimized force field to describe the behavior of the eutectic mixture in the 900–1100 K temperature range, at pressures between 0 and 5 GPa. After studying the equation of state in these thermodynamic conditions, wemore » present molecular insight into the structure and dynamics of the melt. In particular, we present an analysis of the temperature and pressure dependence of the eutectic mixture’s self-diffusion coefficients, viscosity, and ionic conductivity.« less

Reovirus FAST Proteins Drive Pore Formation and Syncytiogenesis Using a Novel Helix-Loop-Helix Fusion-Inducing Lipid Packing Sensor

PubMed Central

Sarker, Muzaddid; de Antueno, Roberto; Langelaan, David N.; Parmar, Hiren B.; Shin, Kyungsoo; Rainey, Jan K.; Duncan, Roy

2015-01-01

Pore formation is the most energy-demanding step during virus-induced membrane fusion, where high curvature of the fusion pore rim increases the spacing between lipid headgroups, exposing the hydrophobic interior of the membrane to water. How protein fusogens breach this thermodynamic barrier to pore formation is unclear. We identified a novel fusion-inducing lipid packing sensor (FLiPS) in the cytosolic endodomain of the baboon reovirus p15 fusion-associated small transmembrane (FAST) protein that is essential for pore formation during cell-cell fusion and syncytiogenesis. NMR spectroscopy and mutational studies indicate the dependence of this FLiPS on a hydrophobic helix-loop-helix structure. Biochemical and biophysical assays reveal the p15 FLiPS preferentially partitions into membranes with high positive curvature, and this partitioning is impeded by bis-ANS, a small molecule that inserts into hydrophobic defects in membranes. Most notably, the p15 FLiPS can be functionally replaced by heterologous amphipathic lipid packing sensors (ALPS) but not by other membrane-interactive amphipathic helices. Furthermore, a previously unrecognized amphipathic helix in the cytosolic domain of the reptilian reovirus p14 FAST protein can functionally replace the p15 FLiPS, and is itself replaceable by a heterologous ALPS motif. Anchored near the cytoplasmic leaflet by the FAST protein transmembrane domain, the FLiPS is perfectly positioned to insert into hydrophobic defects that begin to appear in the highly curved rim of nascent fusion pores, thereby lowering the energy barrier to stable pore formation. PMID:26061049

Leveraging Environmental Correlations: The Thermodynamics of Requisite Variety

NASA Astrophysics Data System (ADS)

Boyd, Alexander B.; Mandal, Dibyendu; Crutchfield, James P.

2017-06-01

Key to biological success, the requisite variety that confronts an adaptive organism is the set of detectable, accessible, and controllable states in its environment. We analyze its role in the thermodynamic functioning of information ratchets—a form of autonomous Maxwellian Demon capable of exploiting fluctuations in an external information reservoir to harvest useful work from a thermal bath. This establishes a quantitative paradigm for understanding how adaptive agents leverage structured thermal environments for their own thermodynamic benefit. General ratchets behave as memoryful communication channels, interacting with their environment sequentially and storing results to an output. The bulk of thermal ratchets analyzed to date, however, assume memoryless environments that generate input signals without temporal correlations. Employing computational mechanics and a new information-processing Second Law of Thermodynamics (IPSL) we remove these restrictions, analyzing general finite-state ratchets interacting with structured environments that generate correlated input signals. On the one hand, we demonstrate that a ratchet need not have memory to exploit an uncorrelated environment. On the other, and more appropriate to biological adaptation, we show that a ratchet must have memory to most effectively leverage structure and correlation in its environment. The lesson is that to optimally harvest work a ratchet's memory must reflect the input generator's memory. Finally, we investigate achieving the IPSL bounds on the amount of work a ratchet can extract from its environment, discovering that finite-state, optimal ratchets are unable to reach these bounds. In contrast, we show that infinite-state ratchets can go well beyond these bounds by utilizing their own infinite "negentropy". We conclude with an outline of the collective thermodynamics of information-ratchet swarms.

The thermodynamics of bipolarity: a bifurcation model of bipolar illness and bipolar character and its psychotherapeutic applications.

PubMed

Sabelli, H C; Carlson-Sabelli, L; Javaid, J I

1990-11-01

Two models dominate current formulations of bipolar illness: the homeostatic model implicit in Freud's psychodynamics and most neuroamine deficit/excess theories; and the oscillatory model of exaggerated biological rhythms. The homeostatic model is based on the closed systems approach of classic thermodynamics, while the oscillatory model requires the open systems approach of modern thermodynamics. Here we present a thermodynamic model of bipolarity that includes both homeostatic and oscillatory features and adds the most important feature of open systems thermodynamics: the creation of novel structures in bifurcation processes. According to the proposed model, bipolarity is the result of exaggerated biological energy that augments homeostatic, oscillatory and creative psychological processes. Only low-energy closed systems tend to rest ("point attractor") and entropic disorder. Open processes containing and exchanging energy fluctuate between opposite states ("periodic attractors"); they are characteristic of most physiological rhythms and are exaggerated in bipolar subjects. At higher energies, their strong fluctuations destroy pre-existing patterns and structures, produce turbulence ("chaotic attractors"), which sudden switches between opposite states, and create new and more complex structures. Likewise, high-energy bipolars develop high spontaneity, great fluctuations between opposite moods, internal and interpersonal chaos, and enhanced creativity (personal, artistic, professional) as well as psychopathology (personality deviations, psychotic delusions). Offered here is a theoretical explanation of the dual--creative and destructive--nature of bipolarity in terms of the new enantiodromic concept of entropy generalized by process theory. Clinically, this article offers an integrative model of bipolarity that accounts for many clinical features and contributes to a definition of the bipolar personality.

Theoretical investigation of the structural stabilities, optoelectronic properties and thermodynamic characteristics of GaPxSb1-x ternary alloys

NASA Astrophysics Data System (ADS)

Oumelaz, F.; Nemiri, O.; Boumaza, A.; Ghemid, S.; Meradji, H.; Bin Omran, S.; El Haj Hassan, F.; Rai, D. P.; Khenata, R.

2018-06-01

In this theoretical study, we have investigated the structural, phase transition, electronic, thermodynamic and optical properties of GaPxSb1-x ternary alloys. Our calculations are performed with the WIEN2k code based on density functional theory using the full-potential linearized augmented plane wave method. For the electron exchange-correlation potential, a generalized gradient approximation within Wu-Cohen scheme is considered. The recently developed Tran-Blaha modified Becke-Johnson potential has also been used to improve the underestimated band gap. The structural properties, including the lattice constants, the bulk moduli and their pressure derivatives are in very good agreement with the available experimental data and theoretical results. Several structural phase transitions were studied here to establish the stable structure and to predict the phase transition under hydrostatic pressure. The computed transition pressure (Pt) of the material of our interest from the zinc blende (B3) to the rock salt (B1) phase has been determined and found to agree well with the experimental and theoretical data. The calculated band structure shows that GaSb binary compound and the ternary alloys are direct band gap semiconductors. Optical parameters such as the dielectric constants and the refractive indices are calculated and analyzed. The thermodynamic results are also interpreted and analyzed.

Quantitative determination of anti-structured defects applied to alloys of a wide chemical range

NASA Astrophysics Data System (ADS)

Zhang, Jing; Chen, Zheng; Wang, Yongxin; Lu, Yanli

2016-11-01

Anti-structured defects bridge atom migration among heterogeneous sublattices facilitating diffusion but could also result in the collapse of ordered structure. Component distribution Ni75Al x V25-x alloys are investigated using a microscopic phase field model to illuminate relations between anti-structured defects and composition, precipitate order, precipitate type, and phase stability. The Ni75Al x V25-x alloys undergo single Ni3V (stage I), dual Ni3Al and Ni3V (stage II with Ni3V prior; and stage III with Ni3Al prior), and single Ni3Al (stage IV) with enhanced aluminum level. For Ni3V phase, anti-structured defects (VNi1, NiV, except VNi2) and substitution defects (AlNi1, AlNi2, AlV) exhibit a positive correlation to aluminum in stage I, the positive trend becomes to negative correlation or smooth during stage II. For Ni3Al phase, anti-structured defects (AlNi, NiAl) and substitution defects (VNi, VAl) have a positive correlation to aluminum in stage II, but NiAl goes down since stage III and lasts to stage IV. VNi and VAl fluctuate when Ni3Al precipitates prior, but go down drastically in stage IV. Precipitate type conversion of single Ni3V/dual (Ni3V+Ni3Al) affects Ni3V defects, while dual (Ni3V+Ni3Al)/single Ni3Al has little effect on Ni3Al defects. Precipitate order swap occurred in the dual phase region affects on Ni3Al defects but not on Ni3V. Project supported by the Natural Science Basic Research Plan in Shaanxi Province of China (Grant No. 2016JQ5014), the Fundamental Research Funds for the Central Universities, China (Grant No. 3102014JCQ01024), the Research Fund of the State Key Laboratory of Solidification Processing (NWPU), China (Grant No. 114-QP-2014), the Specialized Research Fund for the Doctoral Program of Higher Education of China (Grant No. 20136102120021), and the National Natural Science Foundation of China (Grant Nos. 51474716 and 51475378).

Subminiature eddy current transducers for studying metal- dielectric junctions

NASA Astrophysics Data System (ADS)

Dmitriev, S.; Katasonov, A.; Malikov, V.; Sagalakov, A.; Davydchenko, M.; Shevtsova, L.; Ishkov, A.

2016-11-01

Based on an eddy current transducer (ECT), a probe has been designed to research metal-dielectric structures. The measurement procedure allowing one to detect defects in laminate composites with a high accuracy is described. The transducer was tested on the layered structure consisting of paper and aluminum layers with a thickness of 100 μm each in which the model defect was placed. The dependences of the ECT signal on the defect in this structure are given.

Characterization of Local Carrier Dynamics in AlN and AlGaN Films using High Spatial- and Time-resolution Cathodoluminescence Spectroscopy

DTIC Science & Technology

2012-10-12

21/2012 Abstract: In order to assess the impacts of structural and point defects on the local carrier (exciton) recombination dynamics in...quantitatively understood as functions of structural / point defect and impurity concentrations (crystal imperfections). However, only few papers [5...NOTES 14. ABSTRACT In order to assess the impacts of structural and point defects on the local carrier (exciton) recombination dynamics in wide bandgap

Electronic structure properties of deep defects in hBN

NASA Astrophysics Data System (ADS)

Dev, Pratibha; Prdm Collaboration

In recent years, the search for room-temperature solid-state qubit (quantum bit) candidates has revived interest in the study of deep-defect centers in semiconductors. The charged NV-center in diamond is the best known amongst these defects. However, as a host material, diamond poses several challenges and so, increasingly, there is an interest in exploring deep defects in alternative semiconductors such as hBN. The layered structure of hBN makes it a scalable platform for quantum applications, as there is a greater potential for controlling the location of the deep defect in the 2D-matrix through careful experiments. Using density functional theory-based methods, we have studied the electronic and structural properties of several deep defects in hBN. Native defects within hBN layers are shown to have high spin ground states that should survive even at room temperature, making them interesting solid-state qubit candidates in a 2D matrix. Partnership for Reduced Dimensional Material (PRDM) is part of the NSF sponsored Partnerships for Research and Education in Materials (PREM).

Photoluminescence of Molecular Beam Epitaxy-Grown Mercury Cadmium Telluride: Comparison of HgCdTe/GaAs and HgCdTe/Si Technologies

NASA Astrophysics Data System (ADS)

Mynbaev, K. D.; Bazhenov, N. L.; Dvoretsky, S. A.; Mikhailov, N. N.; Varavin, V. S.; Marin, D. V.; Yakushev, M. V.

2018-05-01

Properties of HgCdTe films grown by molecular beam epitaxy on GaAs and Si substrates have been studied by performing variable-temperature photoluminescence (PL) measurements. A substantial difference in defect structure between films grown on GaAs (013) and Si (013) substrates was revealed. HgCdTe/GaAs films were mostly free of defect-related energy levels within the bandgap, which was confirmed by PL and carrier lifetime measurements. By contrast, the properties of HgCdTe/Si films are affected by uncontrolled point defects. These could not be always associated with typical "intrinsic" HgCdTe defects, such as mercury vacancies, so consideration of other defects, possibly inherent in HgCdTe/Si structures, was required. The post-growth annealing was found to have a positive effect on the defect structure by reducing the full-widths at half-maximum of excitonic PL lines for both types of films and lowering the concentration of defects specific to HgCdTe/Si.

Electronic structure and STM images simulation of defects on hBN/ black-phosphorene heterostructures: A theoretical study

NASA Astrophysics Data System (ADS)

Ospina, D. A.; Cisternas, E.; Duque, C. A.; Correa, J. D.

2018-03-01

By first principles calculations which include van der Waals interactions, we studied the electronic structure of hexagonal boron-nitride/black-phosphorene heterostructures (hBN/BP). In particular the role of several kind of defects on the electronic properties of black-phosphorene monolayer and hBN/BP heterostructure was analyzed. The defects under consideration were single and double vacancies, as well Stone-Wale type defects, all of them present in the phosphorene layer. In this way, we found that the electronic structure of the hBN/BP is modified according the type of defect that is introduced. As a remarkable feature, our results show occupied states at the Fermi Level introduced by a single vacancy in the energy gap of the hBN/BP heterostructure. Additionally, we performed simulations of scanning tunneling microscopy images. These simulations show that is possible to discriminate the kind of defect even when the black-phosphorene monolayer is part of the heterostructure hBN/BP. Our results may help to discriminate among several kind of defects during experimental characterization of these novel materials.

Analysis of Radiation Effects in Silicon using Kinetic Monte Carlo Methods

DOE PAGES

Hehr, Brian Douglas

2014-11-25

The transient degradation of semiconductor device performance under irradiation has long been an issue of concern. Neutron irradiation can instigate the formation of quasi-stable defect structures, thereby introducing new energy levels into the bandgap that alter carrier lifetimes and give rise to such phenomena as gain degradation in bipolar junction transistors. Normally, the initial defect formation phase is followed by a recovery phase in which defect-defect or defect-dopant interactions modify the characteristics of the damaged structure. A kinetic Monte Carlo (KMC) code has been developed to model both thermal and carrier injection annealing of initial defect structures in semiconductor materials.more » The code is employed to investigate annealing in electron-irradiated, p-type silicon as well as the recovery of base current in silicon transistors bombarded with neutrons at the Los Alamos Neutron Science Center (LANSCE) “Blue Room” facility. Our results reveal that KMC calculations agree well with these experiments once adjustments are made, within the appropriate uncertainty bounds, to some of the sensitive defect parameters.« less

Extracting and identifying concrete structural defects in GPR images

NASA Astrophysics Data System (ADS)

Ye, Qiling; Jiao, Liangbao; Liu, Chuanxin; Cao, Xuehong; Huston, Dryver; Xia, Tian

2018-03-01

Traditionally most GPR data interpretations are performed manually. With the advancement of computing technologies, how to automate GPR data interpretation to achieve high efficiency and accuracy has become an active research subject. In this paper, analytical characterizations of major defects in concrete structures, including delamination, air void and moisture in GPR images, are performed. In the study, the image features of different defects are compared. Algorithms are developed for defect feature extraction and identification. For validations, both simulation results and field test data are utilized.

Observation of 'hidden' planar defects in boron carbide nanowires and identification of their orientations.

PubMed

Guan, Zhe; Cao, Baobao; Yang, Yang; Jiang, Youfei; Li, Deyu; Xu, Terry T

2014-01-15

The physical properties of nanostructures strongly depend on their structures, and planar defects in particular could significantly affect the behavior of the nanowires. In this work, planar defects (twins or stacking faults) in boron carbide nanowires are extensively studied by transmission electron microscopy (TEM). Results show that these defects can easily be invisible, i.e., no presence of characteristic defect features like modulated contrast in high-resolution TEM images and streaks in diffraction patterns. The simplified reason of this invisibility is that the viewing direction during TEM examination is not parallel to the (001)-type planar defects. Due to the unique rhombohedral structure of boron carbide, planar defects are only distinctive when the viewing direction is along the axial or short diagonal directions ([100], [010], or 1¯10) within the (001) plane (in-zone condition). However, in most cases, these three characteristic directions are not parallel to the viewing direction when boron carbide nanowires are randomly dispersed on TEM grids. To identify fault orientations (transverse faults or axial faults) of those nanowires whose planar defects are not revealed by TEM, a new approach is developed based on the geometrical analysis between the projected preferred growth direction of a nanowire and specific diffraction spots from diffraction patterns recorded along the axial or short diagonal directions out of the (001) plane (off-zone condition). The approach greatly alleviates tedious TEM examination of the nanowire and helps to establish the reliable structure-property relations. Our study calls attention to researchers to be extremely careful when studying nanowires with potential planar defects by TEM. Understanding the true nature of planar defects is essential in tuning the properties of these nanostructures through manipulating their structures.

Entropy-Driven Folding of an RNA Helical Junction: An Isothermal Titration Calorimetric Analysis of the Hammerhead Ribozyme†

PubMed Central

Mikulecky, Peter J.; Takach, Jennifer C.; Feig, Andrew L.

2008-01-01

Helical junctions are extremely common motifs in naturally occurring RNAs, but little is known about the thermodynamics that drive their folding. Studies of junction folding face several challenges: non-two-state folding behavior, superposition of secondary and tertiary structural energetics, and drastically opposing enthalpic and entropic contributions to folding. Here we describe a thermodynamic dissection of the folding of the hammerhead ribozyme, a three-way RNA helical junction, by using isothermal titration calorimetry of bimolecular RNA constructs. By using this method, we show that tertiary folding of the hammerhead core occurs with a highly unfavorable enthalpy change, and is therefore entropically driven. Furthermore, the enthalpies and heat capacities of core folding are the same whether supported by monovalent or divalent ions. These properties appear to be general to the core sequence of bimolecular hammerhead constructs. We present a model for the ion-induced folding of the hammerhead core that is similar to those advanced for the folding of much larger RNAs, involving ion-induced collapse to a structured, non-native state accompanied by rearrangement of core residues to produce the native fold. In agreement with previous enzymological and structural studies, our thermodynamic data suggest that the hammerhead structure is stabilized in vitro predominantly by diffusely bound ions. Our approach addresses several significant challenges that accompany the study of junction folding, and should prove useful in defining the thermodynamic determinants of stability in these important RNA motifs. PMID:15134461

A computational microscopy study of nanostructural evolution in irradiated pressure vessel steels

NASA Astrophysics Data System (ADS)

Odette, G. R.; Wirth, B. D.

1997-11-01

Nanostructural features that form in reactor pressure vessel steels under neutron irradiation at around 300°C lead to significant hardening and embrittlement. Continuum thermodynamic-kinetic based rate theories have been very successful in modeling the general characteristics of the copper and manganese nickel rich precipitate evolution, often the dominant source of embrittlement. However, a more detailed atomic scale understanding of these features is needed to interpret experimental measurements and better underpin predictive embrittlement models. Further, other embrittling features, believed to be subnanometer defect (vacancy)-solute complexes and small regions of modest enrichment of solutes are not well understood. A general approach to modeling embrittlement nanostructures, based on the concept of a computational microscope, is described. The objective of the computational microscope is to self-consistently integrate atomic scale simulations with other sources of information, including a wide range of experiments. In this work, lattice Monte Carlo (LMC) simulations are used to resolve the chemically and structurally complex nature of CuMnNiSi precipitates. The LMC simulations unify various nanoscale analytical characterization methods and basic thermodynamics. The LMC simulations also reveal that significant coupled vacancy and solute clustering takes place during cascade aging. The cascade clustering produces the metastable vacancy-cluster solute complexes that mediate flux effects. Cascade solute clustering may also play a role in the formation of dilute atmospheres of solute enrichment and enhance the nucleation of manganese-nickel rich precipitates at low Cu levels. Further, the simulations suggest that complex, highly correlated processes (e.g. cluster diffusion, formation of favored vacancy diffusion paths and solute scavenging vacancy cluster complexes) may lead to anomalous fast thermal aging kinetics at temperatures below about 450°C. The potential technical significance of these phenomena is described.

Thermodynamic and Kinetic Properties of Metal Hydrides from First-Principles Calculations

NASA Astrophysics Data System (ADS)

Michel, Kyle Jay

In an effort to minimize the worldwide dependence on fossil fuels, much research has focused on the development of hydrogen fuel cell vehicles. Among the many challenges currently facing the transition to such an alternative energy economy is the storage of hydrogen in an economical and practical way. One class of materials that has presented itself as a possible candidate is solid metal hydrides. These materials chemically bind hydrogen and on heating, release the gas which can then be used to generate power as needed for the vehicle. In order to meet guidelines that have been set for such a storage system, hydrogen must be released rapidly in a narrow temperature range of -40 to 80°C with all reactions being reversible. This sets both thermodynamic and kinetic requirements for the design of candidate metal hydrides. First-principles calculations are well-suited for the task of exploring reactions involving metal hydrides. Here, density-functional theory is used to calculate properties of these materials at the quantum mechanical level of accuracy. In particular, three systems have been investigated: 1. Li-Mg-N-H. Reactions between all known compounds in this system are systematically investigated in order to predict thermodynamically allowed reactions that release hydrogen. The properties of these reactions are compared to the requirements set for hydrogen storage systems. Additionally, ground-state structures are predicted for Li2Mg(NH)2 and Li 4Mg(NH)3. 2. Na-Al-H. The kinetics of mass transport during the (de)hydrogenation of the well-known metal hydride NaAlH4 are investigated. A model is developed to study the flux of native defects through phases involved in these reactions. Since it is also known that titanium is an effective catalyst for both dehydrogenation and rehydrogenation, the effect of Ti substitution in bulk lattices on the kinetics of mass transport is investigated. Results are compared to experiments in order to determine if mass transport represents the rate-limiting process during de- or rehydrogenation and what the effect of Ti may be. 3. Si-H. Properties of the recently synthesized compound SiH4(H 2)2 are investigated. Under high pressures, hydrogen binding to SiH4 exhibits characteristics of both physical and chemical bonds. A ground-state structure is predicted for this phase and the vibrational and bonding properties are investigated in order to determine the origin of the unusual binding between H2 and SiH4.

Pressure-induced structural modifications of rare-earth hafnate pyrochlore

NASA Astrophysics Data System (ADS)

Turner, Katlyn M.; Rittman, Dylan R.; Heymach, Rachel A.; Tracy, Cameron L.; Turner, Madison L.; Fuentes, Antonio F.; Mao, Wendy L.; Ewing, Rodney C.

2017-06-01

Complex oxides with the pyrochlore (A2B2O7) and defect-fluorite ((A,B)4O7) structure-types undergo structural transformations under high-pressure. Rare-earth hafnates (A2Hf2O7) form the pyrochlore structure for A  =  La-Tb and the defect-fluorite structure for A  =  Dy-Lu. High-pressure transformations in A2Hf2O7 pyrochlore (A  =  Sm, Eu, Gd) and defect-fluorite (A  =  Dy, Y, Yb) were investigated up to ~50 GPa and characterized by in situ Raman spectroscopy and synchrotron x-ray diffraction (XRD). Raman spectra at ambient pressure revealed that all compositions, including the defect-fluorites, have some pyrochlore-type short-range order. In situ high-pressure synchrotron XRD showed that all of the rare earth hafnates investigated undergo a pressure-induced phase transition to a cotunnite-like (orthorhombic) structure that begins between 18 and 25 GPa. The phase transition to the cotunnite-like structure is not complete at 50 GPa, and upon release of pressure, the hafnates transform to defect-fluorite with an amorphous component. For all compositions, in situ Raman spectroscopy showed that disordering occurs gradually with increasing pressure. Pyrochlore-structured hafnates retain their short-range order to a higher pressure (30 GPa vs.  <10 GPa) than defect-fluorite-structured hafnates. Rare earth hafnates quenched from 50 GPa show Raman spectra consistent with weberite-type structures, as also reported for irradiated rare-earth stannates. The second-order Birch-Murnaghan equation of state fit gives a bulk modulus of ~250 GPa for hafnates with the pyrochlore structure, and ~400 GPa for hafnates with the defect-fluorite structure. Dy2Hf2O7 is intermediate in its response, with some pyrochlore-type ordering, based on Raman spectroscopy and the equation of state, with a bulk modulus of ~300 GPa. As predicted based on the similar ionic radius of Zr4+ and Hf4+, rare-earth hafnates show similar behavior to that reported for rare earth zirconates at high pressure.

Pressure-induced structural modifications of rare-earth hafnate pyrochlore.

PubMed

Turner, Katlyn M; Rittman, Dylan R; Heymach, Rachel A; Tracy, Cameron L; Turner, Madison L; Fuentes, Antonio F; Mao, Wendy L; Ewing, Rodney C

2017-06-28

Complex oxides with the pyrochlore (A 2 B 2 O 7 ) and defect-fluorite ((A,B) 4 O 7 ) structure-types undergo structural transformations under high-pressure. Rare-earth hafnates (A 2 Hf 2 O 7 ) form the pyrochlore structure for A  =  La-Tb and the defect-fluorite structure for A  =  Dy-Lu. High-pressure transformations in A 2 Hf 2 O 7 pyrochlore (A  =  Sm, Eu, Gd) and defect-fluorite (A  =  Dy, Y, Yb) were investigated up to ~50 GPa and characterized by in situ Raman spectroscopy and synchrotron x-ray diffraction (XRD). Raman spectra at ambient pressure revealed that all compositions, including the defect-fluorites, have some pyrochlore-type short-range order. In situ high-pressure synchrotron XRD showed that all of the rare earth hafnates investigated undergo a pressure-induced phase transition to a cotunnite-like (orthorhombic) structure that begins between 18 and 25 GPa. The phase transition to the cotunnite-like structure is not complete at 50 GPa, and upon release of pressure, the hafnates transform to defect-fluorite with an amorphous component. For all compositions, in situ Raman spectroscopy showed that disordering occurs gradually with increasing pressure. Pyrochlore-structured hafnates retain their short-range order to a higher pressure (30 GPa vs.  <10 GPa) than defect-fluorite-structured hafnates. Rare earth hafnates quenched from 50 GPa show Raman spectra consistent with weberite-type structures, as also reported for irradiated rare-earth stannates. The second-order Birch-Murnaghan equation of state fit gives a bulk modulus of ~250 GPa for hafnates with the pyrochlore structure, and ~400 GPa for hafnates with the defect-fluorite structure. Dy 2 Hf 2 O 7 is intermediate in its response, with some pyrochlore-type ordering, based on Raman spectroscopy and the equation of state, with a bulk modulus of ~300 GPa. As predicted based on the similar ionic radius of Zr 4+ and Hf 4+ , rare-earth hafnates show similar behavior to that reported for rare earth zirconates at high pressure.

Infinitesimal Legendre symmetry in the Geometrothermodynamics programme

DOE Office of Scientific and Technical Information (OSTI.GOV)

García-Peláez, D., E-mail: dgarciap@up.edu.mx; Universidad Panamericana, Tecoyotitla 366. Col. Ex Hacienda Guadalupe Chimalistac, 01050 México D.F., México; López-Monsalvo, C. S., E-mail: cesar.slm@correo.nucleares.unam.mx

2014-08-15

The work within the Geometrothermodynamics programme rests upon the metric structure for the thermodynamic phase-space. Such structure exhibits discrete Legendre symmetry. In this work, we study the class of metrics which are invariant along the infinitesimal generators of Legendre transformations. We solve the Legendre-Killing equation for a K-contact general metric. We consider the case with two thermodynamic degrees of freedom, i.e., when the dimension of the thermodynamic phase-space is five. For the generic form of contact metrics, the solution of the Legendre-Killing system is unique, with the sole restriction that the only independent metric function – Ω – should bemore » dragged along the orbits of the Legendre generator. We revisit the ideal gas in the light of this class of metrics. Imposing the vanishing of the scalar curvature for this system results in a further differential equation for the metric function Ω which is not compatible with the Legendre invariance constraint. This result does not allow us to use Quevedo's interpretation of the curvature scalar as a measure of thermodynamic interaction for this particular class.« less

Equilibrium econophysics: A unified formalism for neoclassical economics and equilibrium thermodynamics

NASA Astrophysics Data System (ADS)

Sousa, Tânia; Domingos, Tiago

2006-11-01

We develop a unified conceptual and mathematical structure for equilibrium econophysics, i.e., the use of concepts and tools of equilibrium thermodynamics in neoclassical microeconomics and vice versa. Within this conceptual structure the results obtained in microeconomic theory are: (1) the definition of irreversibility in economic behavior; (2) the clarification that the Engel curve and the offer curve are not descriptions of real processes dictated by the maximization of utility at constant endowment; (3) the derivation of a relation between elasticities proving that economic elasticities are not all independent; (4) the proof that Giffen goods do not exist in a stable equilibrium; (5) the derivation that ‘economic integrability’ is equivalent to the generalized Le Chatelier principle and (6) the definition of a first order phase transition, i.e., a transition between separate points in the utility function. In thermodynamics the results obtained are: (1) a relation between the non-dimensional isothermal and adiabatic compressibilities and the increase or decrease in the thermodynamic potentials; (2) the distinction between mathematical integrability and optimization behavior and (3) the generalization of the Clapeyron equation.