transition state structures: Topics by Science.gov

Sample records for transition state structures

Enzymatic Transition States, Transition-State Analogs, Dynamics, Thermodynamics, and Lifetimes

PubMed Central

Schramm, Vern L.

2017-01-01

Experimental analysis of enzymatic transition-state structures uses kinetic isotope effects (KIEs) to report on bonding and geometry differences between reactants and the transition state. Computational correlation of experimental values with chemical models permits three-dimensional geometric and electrostatic assignment of transition states formed at enzymatic catalytic sites. The combination of experimental and computational access to transition-state information permits (a) the design of transition-state analogs as powerful enzymatic inhibitors, (b) exploration of protein features linked to transition-state structure, (c) analysis of ensemble atomic motions involved in achieving the transition state, (d) transition-state lifetimes, and (e) separation of ground-state (Michaelis complexes) from transition-state effects. Transition-state analogs with picomolar dissociation constants have been achieved for several enzymatic targets. Transition states of closely related isozymes indicate that the protein’s dynamic architecture is linked to transition-state structure. Fast dynamic motions in catalytic sites are linked to transition-state generation. Enzymatic transition states have lifetimes of femtoseconds, the lifetime of bond vibrations. Binding isotope effects (BIEs) reveal relative reactant and transition-state analog binding distortion for comparison with actual transition states. PMID:21675920
Parameter optimization on the convergence surface of path simulations

NASA Astrophysics Data System (ADS)

Chandrasekaran, Srinivas Niranj

Computational treatments of protein conformational changes tend to focus on the trajectories themselves, despite the fact that it is the transition state structures that contain information about the barriers that impose multi-state behavior. PATH is an algorithm that computes a transition pathway between two protein crystal structures, along with the transition state structure, by minimizing the Onsager-Machlup action functional. It is rapid but depends on several unknown input parameters whose range of different values can potentially generate different transition-state structures. Transition-state structures arising from different input parameters cannot be uniquely compared with those generated by other methods. I outline modifications that I have made to the PATH algorithm that estimates these input parameters in a manner that circumvents these difficulties, and describe two complementary tests that validate the transition-state structures found by the PATH algorithm. First, I show that although the PATH algorithm and two other approaches to computing transition pathways produce different low-energy structures connecting the initial and final ground-states with the transition state, all three methods agree closely on the configurations of their transition states. Second, I show that the PATH transition states are close to the saddle points of free-energy surfaces connecting initial and final states generated by replica-exchange Discrete Molecular Dynamics simulations. I show that aromatic side-chain rearrangements create similar potential energy barriers in the transition-state structures identified by PATH for a signaling protein, a contractile protein, and an enzyme. Finally, I observed, but cannot account for, the fact that trajectories obtained for all-atom and Calpha-only simulations identify transition state structures in which the Calpha atoms are in essentially the same positions. The consistency between transition-state structures derived by different algorithms for unrelated protein systems argues that although functionally important protein conformational change trajectories are to a degree stochastic, they nonetheless pass through a well-defined transition state whose detailed structural properties can rapidly be identified using PATH. In the end, I outline the strategies that could enhance the efficiency and applicability of PATH.
Three key residues form a critical contact network in a protein folding transition state

NASA Astrophysics Data System (ADS)

Vendruscolo, Michele; Paci, Emanuele; Dobson, Christopher M.; Karplus, Martin

2001-02-01

Determining how a protein folds is a central problem in structural biology. The rate of folding of many proteins is determined by the transition state, so that a knowledge of its structure is essential for understanding the protein folding reaction. Here we use mutation measurements-which determine the role of individual residues in stabilizing the transition state-as restraints in a Monte Carlo sampling procedure to determine the ensemble of structures that make up the transition state. We apply this approach to the experimental data for the 98-residue protein acylphosphatase, and obtain a transition-state ensemble with the native-state topology and an average root-mean-square deviation of 6Å from the native structure. Although about 20 residues with small positional fluctuations form the structural core of this transition state, the native-like contact network of only three of these residues is sufficient to determine the overall fold of the protein. This result reveals how a nucleation mechanism involving a small number of key residues can lead to folding of a polypeptide chain to its unique native-state structure.
A modified PATH algorithm rapidly generates transition states comparable to those found by other well established algorithms

PubMed Central

Chandrasekaran, Srinivas Niranj; Das, Jhuma; Dokholyan, Nikolay V.; Carter, Charles W.

2016-01-01

PATH rapidly computes a path and a transition state between crystal structures by minimizing the Onsager-Machlup action. It requires input parameters whose range of values can generate different transition-state structures that cannot be uniquely compared with those generated by other methods. We outline modifications to estimate these input parameters to circumvent these difficulties and validate the PATH transition states by showing consistency between transition-states derived by different algorithms for unrelated protein systems. Although functional protein conformational change trajectories are to a degree stochastic, they nonetheless pass through a well-defined transition state whose detailed structural properties can rapidly be identified using PATH. PMID:26958584
Engineered Bi-Histidine Metal Chelation Sites Map the Structure of the Mechanical Unfolding Transition State of an Elastomeric Protein Domain GB1

PubMed Central

Shen, Tao; Cao, Yi; Zhuang, Shulin; Li, Hongbin

2012-01-01

Determining the structure of the transition state is critical for elucidating the mechanism behind how proteins fold and unfold. Due to its high free energy, however, the transition state generally cannot be trapped and studied directly using traditional structural biology methods. Thus, characterizing the structure of the transition state that occurs as proteins fold and unfold remains a major challenge. Here, we report a novel (to our knowledge) method that uses engineered bi-histidine (bi-His) metal-binding sites to directly map the structure of the mechanical unfolding transition state of proteins. This method is adapted from the traditional ψ-value analysis, which uses engineered bi-His metal chelation sites to probe chemical (un)folding transition-state structure. The ϕM2+U-value is defined as ΔΔG‡-N/ΔΔGU-N, which is the energetic effects of metal chelation by the bi-His site on the unfolding energy barrier (ΔG‡-N) relative to its thermodynamic stability (ΔGU-N) and can be used to obtain information about the transition state in the mutational site. As a proof of principle, we used the small protein GB1 as a model system and set out to map its mechanical unfolding transition-state structure. Using single-molecule atomic force microscopy and spectrofluorimetry, we directly quantified the effect of divalent metal ion binding on the mechanical unfolding free energy and thermodynamic stability of GB1, which allowed us to quantify ϕM2+U-values for different sites in GB1. Our results enabled us to map the structure of the mechanical unfolding transition state of GB1. Within GB1’s mechanical unfolding transition state, the interface between force-bearing β-strands 1 and 4 is largely disrupted, and the first β-hairpin is partially disordered while the second β-hairpin and the α-helix remain structured. Our results demonstrate the unique application of ψ-value analysis in elucidating the structure of the transition state that occurs during the mechanical unfolding process, offering a potentially powerful new method for investigating the design of novel elastomeric proteins. PMID:22947942
Engineered bi-histidine metal chelation sites map the structure of the mechanical unfolding transition state of an elastomeric protein domain GB1.

PubMed

Shen, Tao; Cao, Yi; Zhuang, Shulin; Li, Hongbin

2012-08-22

Determining the structure of the transition state is critical for elucidating the mechanism behind how proteins fold and unfold. Due to its high free energy, however, the transition state generally cannot be trapped and studied directly using traditional structural biology methods. Thus, characterizing the structure of the transition state that occurs as proteins fold and unfold remains a major challenge. Here, we report a novel (to our knowledge) method that uses engineered bi-histidine (bi-His) metal-binding sites to directly map the structure of the mechanical unfolding transition state of proteins. This method is adapted from the traditional ψ-value analysis, which uses engineered bi-His metal chelation sites to probe chemical (un)folding transition-state structure. The φ(M2+)(U)-value is defined as ΔΔG(‡-N)/ΔΔG(U-N), which is the energetic effects of metal chelation by the bi-His site on the unfolding energy barrier (ΔG(‡-N)) relative to its thermodynamic stability (ΔG(U-N)) and can be used to obtain information about the transition state in the mutational site. As a proof of principle, we used the small protein GB1 as a model system and set out to map its mechanical unfolding transition-state structure. Using single-molecule atomic force microscopy and spectrofluorimetry, we directly quantified the effect of divalent metal ion binding on the mechanical unfolding free energy and thermodynamic stability of GB1, which allowed us to quantify φ(M2+)(U)-values for different sites in GB1. Our results enabled us to map the structure of the mechanical unfolding transition state of GB1. Within GB1's mechanical unfolding transition state, the interface between force-bearing β-strands 1 and 4 is largely disrupted, and the first β-hairpin is partially disordered while the second β-hairpin and the α-helix remain structured. Our results demonstrate the unique application of ψ-value analysis in elucidating the structure of the transition state that occurs during the mechanical unfolding process, offering a potentially powerful new method for investigating the design of novel elastomeric proteins. Copyright © 2012 Biophysical Society. Published by Elsevier Inc. All rights reserved.
Multi-path variational transition state theory for chemical reaction rates of complex polyatomic species: ethanol + OH reactions.

PubMed

Zheng, Jingjing; Truhlar, Donald G

2012-01-01

Complex molecules often have many structures (conformations) of the reactants and the transition states, and these structures may be connected by coupled-mode torsions and pseudorotations; some but not all structures may have hydrogen bonds in the transition state or reagents. A quantitative theory of the reaction rates of complex molecules must take account of these structures, their coupled-mode nature, their qualitatively different character, and the possibility of merging reaction paths at high temperature. We have recently developed a coupled-mode theory called multi-structural variational transition state theory (MS-VTST) and an extension, called multi-path variational transition state theory (MP-VTST), that includes a treatment of the differences in the multi-dimensional tunneling paths and their contributions to the reaction rate. The MP-VTST method was presented for unimolecular reactions in the original paper and has now been extended to bimolecular reactions. The MS-VTST and MP-VTST formulations of variational transition state theory include multi-faceted configuration-space dividing surfaces to define the variational transition state. They occupy an intermediate position between single-conformation variational transition state theory (VTST), which has been used successfully for small molecules, and ensemble-averaged variational transition state theory (EA-VTST), which has been used successfully for enzyme kinetics. The theories are illustrated and compared here by application to three thermal rate constants for reactions of ethanol with hydroxyl radical--reactions with 4, 6, and 14 saddle points.
Probing the transition state for nucleic acid hybridization using phi-value analysis.

PubMed

Kim, Jandi; Shin, Jong-Shik

2010-04-27

Genetic regulation by noncoding RNA elements such as microRNA and small interfering RNA (siRNA) involves hybridization of a short single-stranded RNA with a complementary segment in a target mRNA. The physical basis of the hybridization process between the structured nucleic acids is not well understood primarily because of the lack of information about the transition-state structure. Here we use transition-state theory, inspired by phi-value analysis in protein folding studies, to provide quantitative analysis of the relationship between changes in the secondary structure stability and the activation free energy. Time course monitoring of the hybridization reaction was performed under pseudo-steady-state conditions using a single fluorophore. The phi-value analysis indicates that the native secondary structure remains intact in the transition state. The nativelike transition state was confirmed via examination of the salt dependence of the hybridization kinetics, indicating that the number of sodium ions associated with the transition state was not substantially affected by changes in the native secondary structure. These results propose that hybridization between structured nucleic acids undergoes a transition state leading to formation of a nucleation complex and then is followed by sequential displacement of preexisting base pairings involving successive small energy barriers. The proposed mechanism might provide new insight into physical processes during small RNA-mediated gene silencing, which is essential to selection of a target mRNA segment for siRNA design.
Theoretical studies of the transition state structures and free energy barriers for base-catalyzed hydrolysis of amides

PubMed Central

Xiong, Ying; Zhan, Chang-Guo

2010-01-01

The transition state structures and free energy barriers for the rate-determining step (i.e. the formation of a tetrahedral intermediate) of base-catalyzed hydrolysis of a series of amides in aqueous solution have been studied by performing first-principle electronic structure calculations using a hybrid supermolecule-polarizable continuum approach. The calculated results and a revisit of recently reported experimental proton inventory data reveal that the favorable transition state structure optimized for the tetrahedral intermediate formation of hydroxide ion-catalyzed hydrolysis of formamide may have three solvating water molecules remaining on the attacking hydroxide oxygen and two additional water molecules attached to the carbonyl oxygen of formamide. The calculated results have also demonstrated interesting substituent effects on the optimized transition state geometries, on the transition-state stabilization, and on the calculated free energy barriers for the base-catalyzed hydrolysis of amides. When some or all of the hydrogen atoms of formamide are replaced by methyl groups, the total number of water molecules hydrogen-bonding with the attacking hydroxide in the transition state decreases from three for formamide to two for N-methylacetamide, N,N-dimethylformamide (DMF), and N,N-dimethylacetamide (DMA). The larger substituents of the amide hinder the solvent water molecules approaching the attacking hydroxide oxygen in the transition state and, therefore, destabilize the transition state structure and increase the free energy barrier. By using the optimized most favorable transition state structures, the calculated free energy barriers, i.e. 21.6 (or 21.7), 22.7, 23.1, and 26.0 kcal/mol for formamide, N-methylacetamide, DMF, and DMA, respectively, are in good agreement with the available experimental free energy barriers, i.e. 21.2, 21.5, 22.6, and 24.1 kcal/mol for formamide, N-methylacetamide, DMF, and DMA, respectively. PMID:17107116
Transition State Geometry Measurements from 13C Isotope Effects. The Experimental Transition State for the Epoxidation of Alkenes with Oxaziridines

PubMed Central

Hirschi, Jennifer S.; Takeya, Tetsuya; Hang, Chao; Singleton, Daniel A.

2009-01-01

We suggest here and evaluate a methodology for the measurement of specific interatomic distances from a combination of theoretical calculations and experimentally measured 13C kinetic isotope effects. This process takes advantage of a broad diversity of transition structures available for the epoxidation of 2-methyl-2-butene with oxaziridines. From the isotope effects calculated for these transition structures, a theory-independent relationship between the C-O bond distances of the newly forming bonds and the isotope effects is established. Within the precision of the measurement, this relationship in combination with the experimental isotope effects provides a highly accurate picture of the C-O bonds forming at the transition state. The diversity of transition structures also allows an evaluation of the Schramm process for defining transition state geometries based on calculations at non-stationary points, and the methodology is found to be reasonably accurate. PMID:19146405
Stabilization of different types of transition states in a single enzyme active site: QM/MM analysis of enzymes in the alkaline phosphatase superfamily.

PubMed

Hou, Guanhua; Cui, Qiang

2013-07-17

The first step for the hydrolysis of a phosphate monoester (pNPP(2-)) in enzymes of the alkaline phosphatase (AP) superfamily, R166S AP and wild-type NPP, is studied using QM/MM simulations based on an approximate density functional theory (SCC-DFTBPR) and a recently introduced QM/MM interaction Hamiltonian. The calculations suggest that similar loose transition states are involved in both enzymes, despite the fact that phosphate monoesters are the cognate substrates for AP but promiscuous substrates for NPP. The computed loose transition states are clearly different from the more synchronous ones previously calculated for diester reactions in the same AP enzymes. Therefore, our results explicitly support the proposal that AP enzymes are able to recognize and stabilize different types of transition states in a single active site. Analysis of the structural features of computed transition states indicates that the plastic nature of the bimetallic site plays a minor role in accommodating multiple types of transition states and that the high degree of solvent accessibility of the AP active site also contributes to its ability to stabilize diverse transition-state structures without the need of causing large structural distortions of the bimetallic motif. The binding mode of the leaving group in the transition state highlights that vanadate may not always be an ideal transition state analog for loose phosphoryl transfer transition states.
Non-Congruence of Thermally Induced Structural and Electronic Transitions in VO2

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

Nag, Joyeeta; HaglundJr., Richard F; Payzant, E Andrew

2012-01-01

The multifunctional properties of vanadium dioxide (VO2) arise from coupled first-order phase transitions: an insulator-to-metal transition (IMT) and a structural phase transition (SPT) from monoclinic to tetragonal. The characteristic signatures of the IMT and SPT are the hysteresis loops that track the phase transition from nucleation to stabilization of a new phase and back. A long-standing question about the mechanism of the VO2 phase transition is whether and how the almost-simultaneous electronic and structural transitions are related. Here we report independent measurements of the IMT and SPT hystereses in epitaxial VO2 films with differing morphologies. We show that, in bothmore » cases, the hystereses are not congruent, that the structural change requires more energy to reach completion. This result is independent of nanoscale morphology, so that the non- congruence is an intrinsic property of the VO2 phase transition. Our conclusion is supported by effective-medium calculations of the dielectric function incorporating the measured volume fractions of the monoclinic and tetragonal states. The results are consistent with the existence of an monoclinic correlated metallic state in which the electron- electron correlations characteristic of the monoclinic state begin to disappear before the transition to the tetragonal structural state.« less
A residue in helical conformation in the native state adopts a β-strand conformation in the folding transition state despite its high and canonical Φ-value.

PubMed

Zarrine-Afsar, Arash; Dahesh, Samira; Davidson, Alan R

2012-05-01

Delineating structures of the transition states in protein folding reactions has provided great insight into the mechanisms by which proteins fold. The most common method for obtaining this information is Φ-value analysis, which is carried out by measuring the changes in the folding and unfolding rates caused by single amino acid substitutions at various positions within a given protein. Canonical Φ-values range between 0 and 1, and residues displaying high values within this range are interpreted to be important in stabilizing the transition state structure, and to elicit this stabilization through native-like interactions. Although very successful in defining the general features of transition state structures, Φ-value analysis can be confounded when non-native interactions stabilize this state. In addition, direct information on backbone conformation within the transition state is not provided. In the work described here, we have investigated structure formation at a conserved β-bulge (with helical conformation) in the Fyn SH3 domain by characterizing the effects of substituting all natural amino acids at one position within this structural motif. By comparing the effects on folding rates of these substitutions with database-derived local structure propensity values, we have determined that this position adopts a non-native backbone conformation in the folding transition state. This result is surprising because this position displays a high and canonical Φ-value of 0.7. This work emphasizes the potential role of non-native conformations in folding pathways and demonstrates that even positions displaying high and canonical Φ-values may, nevertheless, adopt a non-native conformation in the transition state. Copyright © 2012 Wiley Periodicals, Inc.
Folding of a LysM Domain: Entropy-Enthalpy Compensation in the Transition State of an Ideal Two-state Folder

PubMed Central

Nickson, Adrian A.; Stoll, Kate E.; Clarke, Jane

2008-01-01

Protein-engineering methods (Φ-values) were used to investigate the folding transition state of a lysin motif (LysM) domain from Escherichia coli membrane-bound lytic murein transglycosylase D. This domain consists of just 48 structured residues in a symmetrical βααβ arrangement and is the smallest αβ protein yet investigated using these methods. An extensive mutational analysis revealed a highly robust folding pathway with no detectable transition state plasticity, indicating that LysM is an example of an ideal two-state folder. The pattern of Φ-values denotes a highly polarised transition state, with significant formation of the helices but no structure within the β-sheet. Remarkably, this transition state remains polarised after circularisation of the domain, and exhibits an identical Φ-value pattern; however, the interactions within the transition state are uniformly weaker in the circular variant. This observation is supported by results from an Eyring analysis of the folding rates of the two proteins. We propose that the folding pathway of LysM is dominated by enthalpic rather than entropic considerations, and suggest that the lower entropy cost of formation of the circular transition state is balanced, to some extent, by the lower enthalpy of contacts within this structure. PMID:18538343
Effect of Zn2+ binding and enzyme active site on the transition state for RNA 2'-O-transphosphorylation interpreted through kinetic isotope effects.

PubMed

Chen, Haoyuan; Piccirilli, Joseph A; Harris, Michael E; York, Darrin M

2015-11-01

Divalent metal ions, due to their ability to stabilize high concentrations of negative charge, are important for RNA folding and catalysis. Detailed models derived from the structures and kinetics of enzymes and from computational simulations have been developed. However, in most cases the specific catalytic modes involving metal ions and their mechanistic roles and effects on transition state structures remain controversial. Valuable information about the nature of the transition state is provided by measurement of kinetic isotope effects (KIEs). However, KIEs reflect changes in all bond vibrational modes that differ between the ground state and transition state. QM calculations are therefore essential for developing structural models of the transition state and evaluating mechanistic alternatives. Herein, we present computational models for Zn2+ binding to RNA 2'O-transphosphorylation reaction models that aid in the interpretation of KIE experiments. Different Zn2+ binding modes produce distinct KIE signatures, and one binding mode involving two zinc ions is in close agreement with KIEs measured for non-enzymatic catalysis by Zn2+ aquo ions alone. Interestingly, the KIE signatures in this specific model are also very close to those in RNase A catalysis. These results allow a quantitative connection to be made between experimental KIE measurements and transition state structure and bonding, and provide insight into RNA 2'O-ransphosphorylation reactions catalyzed by metal ions and enzymes. This article is part of a Special Issue entitled: Enzyme Transition States from Theory and Experiment. Copyright © 2015. Published by Elsevier B.V.
Pressure-Induced Structural Phase Transition in CeNi: X-ray and Neutron Scattering Studies and First-Principles Calculations

DOE PAGES

Mirmelstein, A.; Podlesnyak, Andrey A.; dos Santos, Antonio M.; ...

2015-08-03

The pressure-induced structural phase transition in the intermediate-valence compound CeNi has been investigated by x-ray and neutron powder diffraction techniques. It is shown that the structure of the pressure-induced CeNi phase (phases) can be described in terms of the Pnma space group. Equations of state for CeNi on both sides of the phase transition are derived and an approximate P-T phase diagram is suggested for P<8 GPa and T<300 K. The observed Cmcm→Pnma structural transition is then analyzed using density functional theory calculations, which successfully reproduce the ground state volume, the phase transition pressure, and the volume collapse associated withmore » the phase transition.« less
Rationalizing the role of structural motif and underlying electronic structure in the finite temperature behavior of atomic clusters

NASA Astrophysics Data System (ADS)

Susan, Anju; Joshi, Kavita

2014-04-01

Melting in finite size systems is an interesting but complex phenomenon. Many factors affect melting and owing to their interdependencies it is a challenging task to rationalize their roles in the phase transition. In this work, we demonstrate how structural motif of the ground state influences melting transition in small clusters. Here, we report a case with clusters of aluminum and gallium having same number of atoms, valence electrons, and similar structural motif of the ground state but drastically different melting temperatures. We have employed Born-Oppenheimer molecular dynamics to simulate the solid-like to liquid-like transition in these clusters. Our simulations have reproduced the experimental trends fairly well. Further, the detailed analysis of isomers has brought out the role of the ground state structure and underlying electronic structure in the finite temperature behavior of these clusters. For both clusters, isomers accessible before cluster melts have striking similarities and does have strong influence of the structural motif of the ground state. Further, the shape of the heat capacity curve is similar in both the cases but the transition is more spread over for Al36 which is consistent with the observed isomerization pattern. Our simulations also suggest a way to characterize transition region on the basis of accessibility of the ground state at a specific temperature.
Efficient Transition State Optimization of Periodic Structures through Automated Relaxed Potential Energy Surface Scans.

PubMed

Plessow, Philipp N

2018-02-13

This work explores how constrained linear combinations of bond lengths can be used to optimize transition states in periodic structures. Scanning of constrained coordinates is a standard approach for molecular codes with localized basis functions, where a full set of internal coordinates is used for optimization. Common plane wave-codes for periodic boundary conditions almost exlusively rely on Cartesian coordinates. An implementation of constrained linear combinations of bond lengths with Cartesian coordinates is described. Along with an optimization of the value of the constrained coordinate toward the transition states, this allows transition optimization within a single calculation. The approach is suitable for transition states that can be well described in terms of broken and formed bonds. In particular, the implementation is shown to be effective and efficient in the optimization of transition states in zeolite-catalyzed reactions, which have high relevance in industrial processes.
A liquid-liquid transition in supercooled aqueous solution related to the HDA-LDA transition

NASA Astrophysics Data System (ADS)

Woutersen, Sander; Ensing, Bernd; Hilbers, Michiel; Zhao, Zuofeng; Angell, C. Austen

2018-03-01

Simulations and theory suggest that the thermodynamic anomalies of water may be related to a phase transition between two supercooled liquid states, but so far this phase transition has not been observed experimentally because of preemptive ice crystallization. We used calorimetry, infrared spectroscopy, and molecular dynamics simulations to investigate a water-rich hydrazinium trifluoroacetate solution in which the local hydrogen bond structure surrounding a water molecule resembles that in neat water at elevated pressure, but which does not crystallize upon cooling. Instead, this solution underwent a sharp, reversible phase transition between two homogeneous liquid states. The hydrogen-bond structures of these two states are similar to those established for high- and low-density amorphous (HDA and LDA) water. Such structural similarity supports theories that predict a similar sharp transition in pure water under pressure if ice crystallization could be suppressed.
M1 transitions between low-lying states in the sdg-IBM-2

NASA Astrophysics Data System (ADS)

Casperson, Robert; Werner, Volker

2006-10-01

The interplay between collective and single-particle degrees of freedom for nuclei in the A=90 region have recently been under investigation. In Molybdenum and Ruthenium nuclei, collective symmetric and mixed-symmetric structures have been identified, while in Zirconium, underlying shell-structure plays an enhanced role. Collective symmetric structures appear when protons and neutrons are in phase, whereas mixed-symmetric structures occur when they are not. The one-phonon 2^+ mixed-symmetric state was identified from strong M1 transitions to the 2^+1 state. Similar transitions were observed between higher-spin states, and are predicted by the shell model. These phenomena will be investigated within the sdg Interacting Boson Model 2 in order to obtain a better understanding about the structure of the states involved, and results from first model calculations will be presented. Work supported by US DOE under grant number DE-FG02-91ER-40609.

Direct measurement of the low temperature spin state transitions in La1-xSrxCoO3 (0.05 < x < 0.3)

NASA Astrophysics Data System (ADS)

Gulec, A.; Klie, R. F.

2014-12-01

Sr-doped LaCoO3 has a complex magnetic phase diagram, which is believed to be directly correlated to changes in the crystal structure and ordering of the Co3+ spin states. In this work, we study the low temperature Co3+-ion spin state transitions in Sr-doped LaCoO3 around the critical doping concentration where a metal to insulator transition has been observed using electron energy-loss spectroscopy of the O K-edge combined with the Co L-edge fine structure. We measure the local spin state of the Co3+-ions and we demonstrate that the Co3+ spin-state transition only occurs in La0.95Sr0.05CoO3 single-crystal materials in the temperature range accessible by LN2 in-situ cooling, while no structural symmetry change is observed. The presence of this low-temperature spin-state transition in La1-xSrxCoO3 (x < 0.17) has been proposed as the origin of the percolative magnetic ordering in doped LaCoO3.
Exploring proton transfer in 1,2,3-triazole-triazolium dimer with ab initio method

NASA Astrophysics Data System (ADS)

Li, Ailin; Yan, Tianying; Shen, Panwen

Ab initio calculations are utilized to search for transition state structures for proton transfer in the 1,2,3-triazole-triazolium complexes on the basis of optimized dimers. The result suggests six transition state structures for single proton transfer in the complexes, most of which are coplanar. The energy barriers, between different stable and transition states structures with zero point energy (ZPE) corrections, show that proton transfer occurs at room temperature with coplanar configuration that has the lowest energy. The results clearly support that reorientation gives triazole flexibility for proton transfer.
Effect of Zn2+ binding and enzyme active site on the transition state for RNA 2′-O-transphosphorylation interpreted through kinetic isotope effects

PubMed Central

Chen, Haoyuan; Piccirilli, Joseph A.; Harris, Michael E.; York, Darrin M.

2016-01-01

Divalent metal ions, due to their ability to stabilize high concentrations of negative charge, are important for RNA folding and catalysis. Detailed models derived from the structures and kinetics of enzymes and from computational simulations have been developed. However, in most cases the specific catalytic modes involving metal ions and their mechanistic roles and effects on transition state structures remains controversial. Valuable information about the nature of the transition state is provided by measurement of kinetic isotope effects (KIEs). However, KIEs reflect changes in all bond vibrational modes that differ between the ground state and transition state. QM calculations are therefore essential for developing structural models of the transition state and evaluating mechanistic alternatives. Herein, we present computational models for Zn2+ binding to RNA 2′O-transphosphorylation reaction models that aid in the interpretation of KIE experiments. Different Zn2+ binding modes produce distinct KIE signatures, and one binding mode involving two zinc ions is in close agreement with KIEs measured for non-enzymatic catalysis by Zn2+ aquo ions alone. Interestingly, the KIE signatures in this specific model are also very close to those in RNase A catalysis. These results allow a quantitative connection to be made between experimental KIE measurements and transition state structure and bonding, and provide insight into RNA 2′O-transphosphorylation reactions catalyzed by metal ions and enzymes. PMID:25812974
Structural, vibrational, and electronic topological transitions of Bi1.5Sb0.5Te1.8Se1.2 under pressure

NASA Astrophysics Data System (ADS)

Kim, Joon-Seok; Juneja, Rinkle; Salke, Nilesh P.; Palosz, Witold; Swaminathan, Venkataraman; Trivedi, Sudhir; Singh, Abhishek K.; Akinwande, Deji; Lin, Jung-Fu

2018-03-01

Topological insulators have been the subject of intense research interest due to their unique surface states that are topologically protected against scattering or defects. However, the relationship between the crystal structure and topological insulator state remains to be clarified. Here, we show the effects of hydrostatic pressure on the structural, vibrational, and topological properties of the topological insulator Bi1.5Sb0.5Te1.8Se1.2 up to 45 GPa using X-ray diffraction and Raman spectroscopy in a diamond anvil cell, together with first-principles theoretical calculations. Two pressure-induced structural phase transitions were observed: from ambient rhombohedral R 3 ¯ m phase to a monoclinic C2/m phase at ˜13 GPa, and to a disordered I4/mmm phase at ˜22 GPa. In addition, the alloy undergoes several electronic transitions within the R 3 ¯ m phase: indirect to direct bulk band gap transition at ˜5.8 GPa, bulk gap closing with an appearance of Dirac semimetal (DSM) state at ˜8.2 GPa, and to a trivial semimetal state at ˜12.1 GPa. Anomalies in c/a ratio and Raman full width at half maximum that coincide with the DSM phase suggest the contribution of electron-phonon coupling to the transition. Compared to binary end members Bi2Te3, Bi2Se3, and Sb2Te3, the structural phase transition and anomaly were observed at higher pressures in Bi1.5Sb0.5Te1.8Se1.2. These results suggest that the topological transitions are precursors to the structural phase transitions.
Experimental and computational analysis of the transition state for ribonuclease A-catalyzed RNA 2′-O-transphosphorylation

PubMed Central

Gu, Hong; Zhang, Shuming; Wong, Kin-Yiu; Radak, Brian K.; Dissanayake, Thakshila; Kellerman, Daniel L.; Dai, Qing; Miyagi, Masaru; Anderson, Vernon E.; York, Darrin M.; Piccirilli, Joseph A.; Harris, Michael E.

2013-01-01

Enzymes function by stabilizing reaction transition states; therefore, comparison of the transition states of enzymatic and nonenzymatic model reactions can provide insight into biological catalysis. Catalysis of RNA 2′-O-transphosphorylation by ribonuclease A is proposed to involve electrostatic stabilization and acid/base catalysis, although the structure of the rate-limiting transition state is uncertain. Here, we describe coordinated kinetic isotope effect (KIE) analyses, molecular dynamics simulations, and quantum mechanical calculations to model the transition state and mechanism of RNase A. Comparison of the 18O KIEs on the 2′O nucleophile, 5′O leaving group, and nonbridging phosphoryl oxygens for RNase A to values observed for hydronium- or hydroxide-catalyzed reactions indicate a late anionic transition state. Molecular dynamics simulations using an anionic phosphorane transition state mimic suggest that H-bonding by protonated His12 and Lys41 stabilizes the transition state by neutralizing the negative charge on the nonbridging phosphoryl oxygens. Quantum mechanical calculations consistent with the experimental KIEs indicate that expulsion of the 5′O remains an integral feature of the rate-limiting step both on and off the enzyme. Electrostatic interactions with positively charged amino acid site chains (His12/Lys41), together with proton transfer from His119, render departure of the 5′O less advanced compared with the solution reaction and stabilize charge buildup in the transition state. The ability to obtain a chemically detailed description of 2′-O-transphosphorylation transition states provides an opportunity to advance our understanding of biological catalysis significantly by determining how the catalytic modes and active site environments of phosphoryl transferases influence transition state structure. PMID:23878223
A liquid-liquid transition in supercooled aqueous solution related to the HDA-LDA transition.

PubMed

Woutersen, Sander; Ensing, Bernd; Hilbers, Michiel; Zhao, Zuofeng; Angell, C Austen

2018-03-09

Simulations and theory suggest that the thermodynamic anomalies of water may be related to a phase transition between two supercooled liquid states, but so far this phase transition has not been observed experimentally because of preemptive ice crystallization. We used calorimetry, infrared spectroscopy, and molecular dynamics simulations to investigate a water-rich hydrazinium trifluoroacetate solution in which the local hydrogen bond structure surrounding a water molecule resembles that in neat water at elevated pressure, but which does not crystallize upon cooling. Instead, this solution underwent a sharp, reversible phase transition between two homogeneous liquid states. The hydrogen-bond structures of these two states are similar to those established for high- and low-density amorphous (HDA and LDA) water. Such structural similarity supports theories that predict a similar sharp transition in pure water under pressure if ice crystallization could be suppressed. Copyright © 2018 The Authors, some rights reserved; exclusive licensee American Association for the Advancement of Science. No claim to original U.S. Government Works.
Structural changes and fluctuations of proteins. I. A statistical thermodynamic model.

PubMed

Ikegami, A

1977-01-01

A general theory of the structural changes and fluctuations of proteins has been proposed based on statistical thermodynamic considerations at the chain level. The "structure" of protein was assumed to be characterized by the state of secondary bonds between unique pairs of specific sites on peptide chains. Every secondary bond changes between the bonded and unbonded states by thermal agitation and the "structure" is continuously fluctuating. The free energy of the "structural state" that is defined by the fraction of secondary bonds in the bonded state has been expressed by the bond energy, the cooperative interaction between bonds, the mixing entropy of bonds, and the entropy of polypeptide chains. The most probable "structural state" can be simply determined by graphical analysis and the effect of temperature or solvent composition on it is discussed. The temperature dependence of the free energy, the probability distribution of structural states and the specific heat have been calculted for two examples of structural change. The theory predicts two different types of structural changes from the ordered to disorderd state, a "structured transition" and a "gradual structural change" with rising temperature. In the "structural transition", the probability distribution has two maxima in the temperature range of transition. In the "gradual structural change", the probabilty distribution has only one maximum during the change. A considerable fraction of secondary bonds is in the unbounded state and is always fluctuating even in the ordered state at room temperature. Such structural flucutations in a single protein molecule have been discussed quantitatively. The theory is extended to include small molecules which bind to the protein molecule and affect the structural state. The changes of structural state caused by specific and non-specific binding and allosteric effects are explained in a unified manner.
A Possible Operational Motivation for the Orthocomplementation in Quantum Structures

NASA Astrophysics Data System (ADS)

D'Hooghe, Bart

2010-11-01

In the foundations of quantum mechanics Gleason’s theorem dictates the uniqueness of the state transition probability via the inner product of the corresponding state vectors in Hilbert space, independent of which measurement context induces this transition. We argue that the state transition probability should not be regarded as a secondary concept which can be derived from the structure on the set of states and properties, but instead should be regarded as a primitive concept for which measurement context is crucial. Accordingly, we adopt an operational approach to quantum mechanics in which a physical entity is defined by the structure of its set of states, set of properties and the possible (measurement) contexts which can be applied to this entity. We put forward some elementary definitions to derive an operational theory from this State-COntext-Property (SCOP) formalism. We show that if the SCOP satisfies a Gleason-like condition, namely that the state transition probability is independent of which measurement context induces the change of state, then the lattice of properties is orthocomplemented, which is one of the ‘quantum axioms’ used in the Piron-Solèr representation theorem for quantum systems. In this sense we obtain a possible physical meaning for the orthocomplementation widely used in quantum structures.
Free energy landscape of activation in a signaling protein at atomic resolution

PubMed Central

Pontiggia, F.; Pachov, D.V.; Clarkson, M.W.; Villali, J.; Hagan, M.F.; Pande, V.S.; Kern, D.

2015-01-01

The interconversion between inactive and active protein states, traditionally described by two static structures, is at the heart of signaling. However, how folded states interconvert is largely unknown due to the inability to experimentally observe transition pathways. Here we explore the free energy landscape of the bacterial response regulator NtrC by combining computation and NMR, and discover unexpected features underlying efficient signaling. We find that functional states are defined purely in kinetic and not structural terms. The need of a well-defined conformer, crucial to the active state, is absent in the inactive state, which comprises a heterogeneous collection of conformers. The transition between active and inactive states occurs through multiple pathways, facilitated by a number of nonnative transient hydrogen bonds, thus lowering the transition barrier through both entropic and enthalpic contributions. These findings may represent general features for functional conformational transitions within the folded state. PMID:26073309
Navigating ligand protein binding free energy landscapes: universality and diversity of protein folding and molecular recognition mechanisms

NASA Astrophysics Data System (ADS)

Verkhivker, Gennady M.; Rejto, Paul A.; Bouzida, Djamal; Arthurs, Sandra; Colson, Anthony B.; Freer, Stephan T.; Gehlhaar, Daniel K.; Larson, Veda; Luty, Brock A.; Marrone, Tami; Rose, Peter W.

2001-03-01

Thermodynamic and kinetic aspects of ligand-protein binding are studied for the methotrexate-dihydrofolate reductase system from the binding free energy profile constructed as a function of the order parameter. Thermodynamic stability of the native complex and a cooperative transition to the unique native structure suggest the nucleation kinetic mechanism at the equilibrium transition temperature. Structural properties of the transition state ensemble and the ensemble of nucleation conformations are determined by kinetic simulations of the transmission coefficient and ligand-protein association pathways. Structural analysis of the transition states and the nucleation conformations reconciles different views on the nucleation mechanism in protein folding.
Potential energy surface of cyclooctatetraene

NASA Astrophysics Data System (ADS)

Andrés, José L.; Castaño, Obis; Morreale, Antonio; Palmeiro, Raul; Gomperts, Roberto

1998-01-01

We present a theoretical study of the cyclooctatetraene (COT) molecule. Seven COT structures are located on the singlet ground state potential energy surface. Four of them, which present D2d (tub), Cs (bicyclo[4.2.0]octa-2,4,7-triene or BOT), C2h (chair) and D4 (crown) symmetries are stable species, and the other three are transition state structures showing Cs, D4h, and D8h symmetry. We discuss the symmetry of wave functions for these stationary points. Geometries, energies, and harmonic vibrational frequencies of these structures, and energy gaps between singlet-triplet states and low-lying singlets are presented. For the planar D4h and D8h structures, Jahn-Teller and tunneling effects have also been discussed. Ring inversion, bond shifting and valence isomerization reactive channels from the tub COT conformer are discussed from the point of view of the corresponding transition state structures. Where possible, in order to lend support to this theoretical information comparisons with recent transition state spectroscopy data are made.
Nonequilibrium phase transition in a self-activated biological network.

PubMed

Berry, Hugues

2003-03-01

We present a lattice model for a two-dimensional network of self-activated biological structures with a diffusive activating agent. The model retains basic and simple properties shared by biological systems at various observation scales, so that the structures can consist of individuals, tissues, cells, or enzymes. Upon activation, a structure emits a new mobile activator and remains in a transient refractory state before it can be activated again. Varying the activation probability, the system undergoes a nonequilibrium second-order phase transition from an active state, where activators are present, to an absorbing, activator-free state, where each structure remains in the deactivated state. We study the phase transition using Monte Carlo simulations and evaluate the critical exponents. As they do not seem to correspond to known values, the results suggest the possibility of a separate universality class.
Status of Credentialing Structures Related to Secondary Transition: A State-Level Policy Analysis

ERIC Educational Resources Information Center

Simonsen, Monica L.; Novak, Jeanne A.; Mazzotti, Valerie L.

2018-01-01

To understand the current status of transition-related credentialing systems in driving personnel preparation, it is necessary to identify which state education and rehabilitation services agencies are currently providing certification and licensure in the area of secondary transition. The purpose of this study was to examine the current state of…
Revealing the hidden structural phases of FeRh

NASA Astrophysics Data System (ADS)

Kim, Jinwoong; Ramesh, R.; Kioussis, Nicholas

2016-11-01

Ab initio electronic structure calculations reveal that tetragonal distortion has a dramatic effect on the relative stability of the various magnetic structures (C-, A-, G-, A'-AFM, and FM) of FeRh giving rise to a wide range of novel stable/metastable structures and magnetic phase transitions between these states. We predict that the cubic G-AFM structure, which was believed thus far to be the ground state, is metastable and that the tetragonally expanded G-AFM is the stable structure. The low energy barrier separating these states suggests phase coexistence at room temperature. We propose an A'-AFM phase to be the global ground state among all magnetic phases which arises from the strain-induced tuning of the exchange interactions. The results elucidate the underlying mechanism for the recent experimental findings of electric-field control of magnetic phase transition driven via tetragonal strain. The magnetic phase transitions open interesting prospects for exploiting strain engineering for the next-generation memory devices.
Pionic transitions from X(3872) to {chi}{sub cJ}

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

Dubynskiy, S.; Voloshin, M.B.; William, I.

2008-01-01

We consider transitions from the resonance X(3872) to the {chi}{sub cJ} states of charmonium with emission of one or two pions as a means of studying the structure of the X resonance. We find that the relative rates for these transitions to the final states with different J significantly depend on whether the initial state is a pure charmonium state or a four-quark/molecular state.
Family Structure States and Transitions: Associations with Children's Well-Being during Middle Childhood

ERIC Educational Resources Information Center

Magnuson, Katherine; Berger, Lawrence M.

2009-01-01

Using longitudinal data from the Maternal and Child Supplement of the National Longitudinal Survey of Youth (N = 3,862) and Hierarchical Linear Models, we estimated associations of family structure states and transitions with children's achievement and behavior trajectories during middle childhood. Results suggest that residing in a single-mother…
Influences of P doping on magnetic phase transition and structure in MnCoSi ribbon

NASA Astrophysics Data System (ADS)

Du, Qian-Heng; Chen, Guo-Fu; Yang, Wen-Yun; Hua, Mu-Xin; Du, Hong-Lin; Wang, Chang-Sheng; Liu, Shun-Quan; Hang, Jing-Zhi; Zhou, Dong; Zhang, Yan; Yan, Jin-Bo

2015-06-01

The structure and magnetic properties of MnCoSi1- x Px (x = 0.05-0.50) are systematically investigated. With P content increasing, the lattice parameter a increases monotonically while both b and c decrease. At the same time, the temperature of metamagnetic transition from a low-temperature non-collinear ferromagnetic state to a high-temperature ferromagnetic state decreases and a new magnetic transition from a higher-magnetization ferromagnetic state to a lower-magnetization ferromagnetic state is observed in each of these compounds for the first time. This is explained by the changes of crystal structure and distance between Mn and Si atoms with the increase of temperature according to the high-temperature XRD result. The metamagnetic transition is found to be a second-order magnetic transition accompanied by a low inversed magnetocaloric effect (1.0 J·kg-1·K-1 at 5 T) with a large temperature span (190 K at 5 T) compared with the scenario of MnCoSi. The changes in the order of metamagnetic transition and structure make P-doped MoCoSi compounds good candidates for the study of magnetoelastic coupling and the modulation of magnetic phase transition. Project supported by the National Natural Science Foundation of China (Grant No. 11275013), the Fund from the National Physics Laboratory, China Academy of Engineering Physics (Grant No. 2013DB01), and the National Key Basic Research Program of China (Grant No. 2010CB833104).
Origins of the structural phase transitions in MoTe2 and WTe2

NASA Astrophysics Data System (ADS)

Kim, Hyun-Jung; Kang, Seoung-Hun; Hamada, Ikutaro; Son, Young-Woo

2017-05-01

Layered transition metal dichalcogenides MoTe2 and WTe2 share almost similar lattice constants as well as topological electronic properties except their structural phase transitions. While the former shows a first-order phase transition between monoclinic and orthorhombic structures, the latter does not. Using a recently proposed van der Waals density functional method, we investigate structural stability of the two materials and uncover that the disparate phase transitions originate from delicate differences between their interlayer bonding states near the Fermi energy. By exploiting the relation between the structural phase transitions and the low energy electronic properties, we show that a charge doping can control the transition substantially, thereby suggesting a way to stabilize or to eliminate their topological electronic energy bands.
Tension-dependent structural deformation alters single-molecule transition kinetics.

PubMed

Sudhanshu, B; Mihardja, S; Koslover, E F; Mehraeen, S; Bustamante, C; Spakowitz, A J

2011-02-01

We analyze the response of a single nucleosome to tension, which serves as a prototypical biophysical measurement where tension-dependent deformation alters transition kinetics. We develop a statistical-mechanics model of a nucleosome as a wormlike chain bound to a spool, incorporating fluctuations in the number of bases bound, the spool orientation, and the conformations of the unbound polymer segments. With the resulting free-energy surface, we perform dynamic simulations that permit a direct comparison with experiments. This simple approach demonstrates that the experimentally observed structural states at nonzero tension are a consequence of the tension and that these tension-induced states cease to exist at zero tension. The transitions between states exhibit substantial deformation of the unbound polymer segments. The associated deformation energy increases with tension; thus, the application of tension alters the kinetics due to tension-induced deformation of the transition states. This mechanism would arise in any system where the tether molecule is deformed in the transition state under the influence of tension.
Tension-dependent structural deformation alters single-molecule transition kinetics

PubMed Central

Sudhanshu, B.; Mihardja, S.; Koslover, E. F.; Mehraeen, S.; Bustamante, C.; Spakowitz, A. J.

2011-01-01

We analyze the response of a single nucleosome to tension, which serves as a prototypical biophysical measurement where tension-dependent deformation alters transition kinetics. We develop a statistical-mechanics model of a nucleosome as a wormlike chain bound to a spool, incorporating fluctuations in the number of bases bound, the spool orientation, and the conformations of the unbound polymer segments. With the resulting free-energy surface, we perform dynamic simulations that permit a direct comparison with experiments. This simple approach demonstrates that the experimentally observed structural states at nonzero tension are a consequence of the tension and that these tension-induced states cease to exist at zero tension. The transitions between states exhibit substantial deformation of the unbound polymer segments. The associated deformation energy increases with tension; thus, the application of tension alters the kinetics due to tension-induced deformation of the transition states. This mechanism would arise in any system where the tether molecule is deformed in the transition state under the influence of tension. PMID:21245354

Description of strong M1 transitions between 4^+ states at N=52 within the sdg-IBM-2

NASA Astrophysics Data System (ADS)

Casperson, R. J.; Werner, V.; Heinze, S.

2009-10-01

The interplay between collective and single-particle degrees of freedom for nuclei near the N=50 shell closure have recently been under investigation. In Molybdenum and Ruthenium nuclei, collective symmetric and mixed-symmetric structures have been identified, while in Zirconium, underlying shell-structure plays an enhanced role. The one-phonon 2^+ mixed-symmetry state was identified from its strong M1 transition to the 2^+1 state. Similar transitions were observed between 4^+ states in ^94Mo and ^92Zr, and shell model calculations indicate that hexadecapole excitations play a role. These phenomena will be investigated within the sdg-Interacting Boson Model-2 in order to gain a better understanding about the structure of the states involved, and to which extent the hexadecapole degree of freedom is important at relatively low energies. First calculations within this model, using an F-spin conserving Hamiltonian to disentangle symmetric and mixed- symmetric structures, will be presented and compared to data.
Structural phases arising from reconstructive and isostructural transitions in high-melting-point oxides under hydrostatic pressure: A first-principles study

NASA Astrophysics Data System (ADS)

Tian, Hao; Kuang, Xiao-Yu; Mao, Ai-Jie; Yang, Yurong; Xu, Changsong; Sayedaghaee, S. Omid; Bellaiche, L.

2018-01-01

High-melting-point oxides of chemical formula A B O3 with A =Ca , Sr, Ba and B =Zr , Hf are investigated as a function of hydrostatic pressure up to 200 GPa by combining first-principles calculations with a particle swarm optimization method. Ca- and Sr-based systems: (1) first undergo a reconstructive phase transition from a perovskite state to a novel structure that belongs to the post-post-perovskite family and (2) then experience an isostructural transition to a second, also new post-post-perovskite state at higher pressures, via the sudden formation of a specific out-of-plane B -O bond. In contrast, the studied Ba compounds evolve from a perovskite phase to a third novel post-post-perovskite structure via another reconstructive phase transition. The original characteristics of these three different post-post-perovskite states are emphasized. Unusual electronic properties, including significant piezochromic effects and an insulator-metal transition, are also reported and explained.
Kinetic mechanism for reversible structural transition in MoTe2 induced by excess charge carriers

NASA Astrophysics Data System (ADS)

Rubel, O.

2018-06-01

Kinetic of a reversible structural transition between insulating (2H) and metallic (1T ') phases in a monolayer MoTe2 due to an electrostatic doping is studied using first-principle calculations. The driving force for the structural transition is the energy gained by transferring excess electrons from the bottom of the conduction band to lower energy gapless states in the metallic phase as have been noticed in earlier studies. The corresponding structural transformation involves dissociation of Mo-Te bonds (one per formula unit), which results in a kinetic energy barrier of 0.83 eV. The transformation involves a consecutive movement of atoms similar to a domain wall motion. The presence of excess charge carriers modifies not only the total energy of the initial and final states, but also lowers an energy of the transition state. An experimentally observed hysteresis in the switching process can be attributed to changes in the kinetic energy barrier due to its dependence on the excess carrier density.
Titanium α-ω phase transformation pathway and a predicted metastable structure

DOE PAGES

Zarkevich, Nickolai A.; Johnson, Duane D.

2016-01-15

A titanium is a highly utilized metal for structural lightweighting and its phases, transformation pathways (transition states), and structures have scientific and industrial importance. Using a proper solid-state nudged elastic band method employing two climbing images combined with density functional theory DFT + U methods for accurate energetics, we detail the pressure-induced α (ductile) to ω (brittle) transformation at the coexistence pressure. We also find two transition states along the minimal-enthalpy path and discover a metastable body-centered orthorhombic structure, with stable phonons, a lower density than the end-point phases, and decreasing stability with increasing pressure.
Band structure dynamics in indium wires

NASA Astrophysics Data System (ADS)

Chávez-Cervantes, M.; Krause, R.; Aeschlimann, S.; Gierz, I.

2018-05-01

One-dimensional indium wires grown on Si(111) substrates, which are metallic at high temperatures, become insulating below ˜100 K due to the formation of a charge density wave (CDW). The physics of this transition is not conventional and involves a multiband Peierls instability with strong interband coupling. This CDW ground state is readily destroyed with femtosecond laser pulses resulting in a light-induced insulator-to-metal phase transition. The current understanding of this transition remains incomplete, requiring measurements of the transient electronic structure to complement previous investigations of the lattice dynamics. Time- and angle-resolved photoemission spectroscopy with extreme ultraviolet radiation is applied to this end. We find that the transition from the insulating to the metallic band structure occurs within ˜660 fs, which is a fraction of the amplitude mode period. The long lifetime of the transient state (>100 ps) is attributed to trapping in a metastable state in accordance with previous work.
Negative thermal expansion near two structural quantum phase transitions

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

Occhialini, Connor A.; Handunkanda, Sahan U.; Said, Ayman

Recent experimental work has revealed that the unusually strong, isotropic structural negative thermal expansion in cubic perovskite ionic insulator ScF3 occurs in excited states above a ground state tuned very near a structural quantum phase transition, posing a question of fundamental interest as to whether this special circumstance is related to the anomalous behavior. To test this hypothesis, we report an elastic and inelastic x-ray scattering study of a second system Hg2I2 also tuned near a structural quantum phase transition while retaining stoichiometric composition and high crystallinity. We find similar behavior and significant negative thermal expansion below 100 K formore » dimensions along the body-centered-tetragonal c axis, bolstering the connection between negative thermal expansion and zero-temperature structural transitions.We identify the common traits between these systems and propose a set of materials design principles that can guide discovery of newmaterials exhibiting negative thermal expansion« less
Negative thermal expansion near two structural quantum phase transitions

NASA Astrophysics Data System (ADS)

Occhialini, Connor A.; Handunkanda, Sahan U.; Said, Ayman; Trivedi, Sudhir; Guzmán-Verri, G. G.; Hancock, Jason N.

2017-12-01

Recent experimental work has revealed that the unusually strong, isotropic structural negative thermal expansion in cubic perovskite ionic insulator ScF3 occurs in excited states above a ground state tuned very near a structural quantum phase transition, posing a question of fundamental interest as to whether this special circumstance is related to the anomalous behavior. To test this hypothesis, we report an elastic and inelastic x-ray scattering study of a second system Hg2I2 also tuned near a structural quantum phase transition while retaining stoichiometric composition and high crystallinity. We find similar behavior and significant negative thermal expansion below 100 K for dimensions along the body-centered-tetragonal c axis, bolstering the connection between negative thermal expansion and zero-temperature structural transitions. We identify the common traits between these systems and propose a set of materials design principles that can guide discovery of new materials exhibiting negative thermal expansion.
Communication: Electronic flux induced by crossing the transition state

NASA Astrophysics Data System (ADS)

Jia, Dongming; Manz, Jörn; Yang, Yonggang

2018-01-01

We present a new effect of chemical reactions, e.g., isomerizations, that occurs when the reactants pass along the transition state, on the way to products. It is based on the well-known fact that at the transition state, the electronic structure of one isomer changes to the other. We discover that this switch of electronic structure causes a strong electronic flux that is well distinguishable from the usual flux of electrons that travel with the nuclei. As a simple but clear example, the effect is demonstrated here for bond length isomerization of Na2 (21Σu+), with adiabatic crossing the barrier between the inner and outer wells of the double minimum potential that support different "Rydberg" and "ionic" type electronic structures, respectively.
Pressure-decoupled magnetic and structural transitions of the parent compound of iron-based 122 superconductors BaFe2As2

PubMed Central

Wu, J. J.; Lin, Jung-Fu; Wang, X. C.; Liu, Q. Q.; Zhu, J. L.; Xiao, Y. M.; Chow, P.; Jin, Changqing

2013-01-01

The recent discovery of iron ferropnictide superconductors has received intensive concern in connection with magnetically involved superconductors. Prominent features of ferropnictide superconductors are becoming apparent: the parent compounds exhibit an antiferromagnetic ordered spin density wave (SDW) state, the magnetic-phase transition is always accompanied by a crystal structural transition, and superconductivity can be induced by suppressing the SDW phase via either chemical doping or applied external pressure to the parent state. These features generated considerable interest in the interplay between magnetism and structure in chemically doped samples, showing crystal structure transitions always precede or coincide with magnetic transition. Pressure-tuned transition, on the other hand, would be more straightforward to superconducting mechanism studies because there are no disorder effects caused by chemical doping; however, remarkably little is known about the interplay in the parent compounds under controlled pressure due to the experimental challenge of in situ measuring both of magnetic and crystal structure evolution at high pressure and low temperatures. Here we show from combined synchrotron Mössbauer and X-ray diffraction at high pressures that the magnetic ordering surprisingly precedes the structural transition at high pressures in the parent compound BaFe2As2, in sharp contrast to the chemical-doping case. The results can be well understood in terms of the spin fluctuations in the emerging nematic phase before the long-range magnetic order that sheds light on understanding how the parent compound evolves from a SDW state to a superconducting phase, a key scientific inquiry of iron-based superconductors. PMID:24101468
Role of the Disulfide Bond in Prion Protein Amyloid Formation: A Thermodynamic and Kinetic Analysis.

PubMed

Honda, Ryo

2018-02-27

Prion diseases are associated with the structural conversion of prion protein (PrP) to a β-sheet-rich aggregate, PrP Sc . Previous studies have indicated that a reduction of the disulfide bond linking C179 and C214 of PrP yields an amyloidlike β-rich aggregate in vitro. To gain mechanistic insights into the reduction-induced aggregation, here I characterized how disulfide bond reduction modulates the protein folding/misfolding landscape of PrP, by examining 1) the equilibrium stabilities of the native (N) and aggregated states relative to the unfolded (U) state, 2) the transition barrier separating the U and aggregated states, and 3) the final structure of amyloidlike misfolded aggregates. Kinetic and thermodynamic experiments revealed that disulfide bond reduction decreases the equilibrium stabilities of both the N and aggregated states by ∼3 kcal/mol, without changing either the amyloidlike aggregate structure, at least at the secondary structural level, or the transition barrier of aggregation. Therefore, disulfide bond reduction modulates the protein folding/misfolding landscape by entropically stabilizing disordered states, including the U and transition state of aggregation. This also indicates that the equilibrium stability of the N state, but not the transition barrier of aggregation, is the dominant factor determining the reduction-induced aggregation of PrP. Copyright © 2017 Biophysical Society. Published by Elsevier Inc. All rights reserved.
Disorder-Induced Topological State Transition in Photonic Metamaterials

NASA Astrophysics Data System (ADS)

Liu, Changxu; Gao, Wenlong; Yang, Biao; Zhang, Shuang

2017-11-01

The topological state transition has been widely studied based on the quantized topological band invariant such as the Chern number for the system without intense randomness that may break the band structures. We numerically demonstrate the disorder-induced state transition in the photonic topological systems for the first time. Instead of applying the ill-defined topological band invariant in a disordered system, we utilize an empirical parameter to unambiguously illustrate the state transition of the topological metamaterials. Before the state transition, we observe a robust surface state with well-confined electromagnetic waves propagating unidirectionally, immune to the disorder from permittivity fluctuation up to 60% of the original value. During the transition, a hybrid state composed of a quasiunidirectional surface mode and intensively localized hot spots is established, a result of the competition between the topological protection and Anderson localization.
Electronic structure of negative charge transfer CaFeO3 across the metal-insulator transition

NASA Astrophysics Data System (ADS)

Rogge, Paul C.; Chandrasena, Ravini U.; Cammarata, Antonio; Green, Robert J.; Shafer, Padraic; Lefler, Benjamin M.; Huon, Amanda; Arab, Arian; Arenholz, Elke; Lee, Ho Nyung; Lee, Tien-Lin; Nemšák, Slavomír; Rondinelli, James M.; Gray, Alexander X.; May, Steven J.

2018-01-01

We investigated the metal-insulator transition for epitaxial thin films of the perovskite CaFeO3, a material with a significant oxygen ligand hole contribution to its electronic structure. We find that biaxial tensile and compressive strain suppress the metal-insulator transition temperature. By combining hard x-ray photoelectron spectroscopy, soft x-ray absorption spectroscopy, and density functional calculations, we resolve the element-specific changes to the electronic structure across the metal-insulator transition. We demonstrate that the Fe sites undergo no observable spectroscopic change between the metallic and insulating states, whereas the O electronic configuration undergoes significant changes. This strongly supports the bond-disproportionation model of the metal-insulator transition for CaFeO3 and highlights the importance of ligand holes in its electronic structure. By sensitively measuring the ligand hole density, however, we find that it increases by ˜5 -10 % in the insulating state, which we ascribe to a further localization of electron charge on the Fe sites. These results provide detailed insight into the metal-insulator transition of negative charge transfer compounds and should prove instructive for understanding metal-insulator transitions in other late transition metal compounds such as the nickelates.
Exploring Molecular Speciation and Crystallization Mechanism of Amorphous 2-Phenylamino Nicotinic Acid.

PubMed

Kalra, Arjun; Lubach, Joseph W; Munson, Eric J; Li, Tonglei

2018-02-07

Molecular understanding of phase stability and transition of the amorphous state helps in formulation and manufacturing of poorly-soluble drugs. Crystallization of a model compound, 2-phenylamino nicotinic acid (2PNA), from the amorphous state was studied using solid-state analytical methods. Our previous report suggests that 2PNA molecules mainly develop intermolecular -COOH∙∙∙pyridine N (acid-pyridine) interactions in the amorphous state. In the current study, the molecular speciation is explored with regard to the phase transition from the amorphous to the crystalline state. Using spectroscopic techniques, the molecular interactions and structural evolvement during the recrystallization from the glassy state were investigated. The results unveiled that the structurally heterogeneous amorphous state contains acid-pyridine aggregates - either as hydrogen-bonded neutral molecules or as zwitterions - as well as a population of carboxylic acid dimers. Phase transition from the amorphous state results in crystal structures composed of carboxylic acid dimer (acid-acid) synthon or acid-pyridine chains depending on the crystallization conditions employed. The study underlines the structural evolvement, as well as its impact on the metastability, of amorphous samples from local, supramolecular assemblies to long-range intermolecular ordering through crystallization.
Dynamics Sampling in Transition Pathway Space.

PubMed

Zhou, Hongyu; Tao, Peng

2018-01-09

The minimum energy pathway contains important information describing the transition between two states on a potential energy surface (PES). Chain-of-states methods were developed to efficiently calculate minimum energy pathways connecting two stable states. In the chain-of-states framework, a series of structures are generated and optimized to represent the minimum energy pathway connecting two states. However, multiple pathways may exist connecting two existing states and should be identified to obtain a full view of the transitions. Therefore, we developed an enhanced sampling method, named as the direct pathway dynamics sampling (DPDS) method, to facilitate exploration of a PES for multiple pathways connecting two stable states as well as addition minima and their associated transition pathways. In the DPDS method, molecular dynamics simulations are carried out on the targeting PES within a chain-of-states framework to directly sample the transition pathway space. The simulations of DPDS could be regulated by two parameters controlling distance among states along the pathway and smoothness of the pathway. One advantage of the chain-of-states framework is that no specific reaction coordinates are necessary to generate the reaction pathway, because such information is implicitly represented by the structures along the pathway. The chain-of-states setup in a DPDS method greatly enhances the sufficient sampling in high-energy space between two end states, such as transition states. By removing the constraint on the end states of the pathway, DPDS will also sample pathways connecting minima on a PES in addition to the end points of the starting pathway. This feature makes DPDS an ideal method to directly explore transition pathway space. Three examples demonstrate the efficiency of DPDS methods in sampling the high-energy area important for reactions on the PES.
Dynamically Switching the Polarization State of Light Based on the Phase Transition of Vanadium Dioxide

NASA Astrophysics Data System (ADS)

Jia, Zhi-Yong; Shu, Fang-Zhou; Gao, Ya-Jun; Cheng, Feng; Peng, Ru-Wen; Fan, Ren-Hao; Liu, Yongmin; Wang, Mu

2018-03-01

There have been great endeavors devoted to manipulating the polarization state of light by plasmonic nanostructures in recent decades. However, the topic of active polarizers has attracted much less attention. We present a composite plasmonic nanostructure consisting of vanadium dioxide that can dynamically modulate the polarization state of the reflected light through a thermally induced phase transition of vanadium dioxide. We design a system consisting of anisotropic plasmonic nanostructures with vanadium dioxide that exhibits distinct reflections subjected to different linearly polarized incidence at room temperature and in the heated state. Under a particular linearly polarized incidence, the polarization state of the reflected light changes at room temperature, and reverts to its original polarization state above the phase-transition temperature. The composite structure can also be used to realize a dynamically switchable infrared image, wherein a pattern can be visualized at room temperature while it disappears above the phase-transition temperature. The composite structure could be potentially used for versatile optical modulators, molecular detection, and polarimetric imaging.
High-temperature high-pressure properties of silica from Quantum Monte Carlo and Density Functional Perturbation Theory

NASA Astrophysics Data System (ADS)

Cohen, R. E.; Driver, K.; Wu, Z.; Militzer, B.; Rios, P. L.; Towler, M.; Needs, R.

2009-03-01

We have used diffusion quantum Monte Carlo (DMC) with the CASINO code with thermal free energies from phonons computed using density functional perturbation theory (DFPT) with the ABINIT code to obtain phase transition curves and thermal equations of state of silica phases under pressure. We obtain excellent agreement with experiments for the metastable phase transition from quartz to stishovite. The local density approximation (LDA) incorrectly gives stishovite as the ground state. The generalized gradient approximation (GGA) correctly gives quartz as the ground state, but does worse than LDA for the equations of state. DMC, variational quantum Monte Carlo (VMC), and DFT all give good results for the ferroelastic transition of stishovite to the CaCl2 structure, and LDA or the WC exchange correlation potentials give good results within a given silica phase. The δV and δH from the CaCl2 structure to α-PbO2 is small, giving uncertainly in the theoretical transition pressure. It is interesting that DFT has trouble with silica transitions, although the electronic structures of silica are insulating, simple closed-shell with ionic/covalent bonding. It seems like the errors in DFT are from not precisely giving the ion sizes.
Exploring the Conformational Transitions of Biomolecular Systems Using a Simple Two-State Anisotropic Network Model

PubMed Central

Jo, Sunhwan; Bahar, Ivet; Roux, Benoît

2014-01-01

Biomolecular conformational transitions are essential to biological functions. Most experimental methods report on the long-lived functional states of biomolecules, but information about the transition pathways between these stable states is generally scarce. Such transitions involve short-lived conformational states that are difficult to detect experimentally. For this reason, computational methods are needed to produce plausible hypothetical transition pathways that can then be probed experimentally. Here we propose a simple and computationally efficient method, called ANMPathway, for constructing a physically reasonable pathway between two endpoints of a conformational transition. We adopt a coarse-grained representation of the protein and construct a two-state potential by combining two elastic network models (ENMs) representative of the experimental structures resolved for the endpoints. The two-state potential has a cusp hypersurface in the configuration space where the energies from both the ENMs are equal. We first search for the minimum energy structure on the cusp hypersurface and then treat it as the transition state. The continuous pathway is subsequently constructed by following the steepest descent energy minimization trajectories starting from the transition state on each side of the cusp hypersurface. Application to several systems of broad biological interest such as adenylate kinase, ATP-driven calcium pump SERCA, leucine transporter and glutamate transporter shows that ANMPathway yields results in good agreement with those from other similar methods and with data obtained from all-atom molecular dynamics simulations, in support of the utility of this simple and efficient approach. Notably the method provides experimentally testable predictions, including the formation of non-native contacts during the transition which we were able to detect in two of the systems we studied. An open-access web server has been created to deliver ANMPathway results. PMID:24699246
Molecular dynamics simulation of bovine pancreatic ribonuclease A-CpA and transition state-like complexes.

PubMed

Formoso, Elena; Matxain, Jon M; Lopez, Xabier; York, Darrin M

2010-06-03

The mechanisms of enzymes are intimately connected with their overall structure and dynamics in solution. Experimentally, it is considerably challenging to provide detailed atomic level information about the conformational events that occur at different stages along the chemical reaction path. Here, theoretical tools may offer new potential insights that complement those obtained from experiments that may not yield an unambiguous mechanistic interpretation. In this study, we apply molecular dynamics simulations of bovine pancreatic ribonuclease A, an archetype ribonuclease, to study the conformational dynamics, structural relaxation, and differential solvation that occur at discrete stages of the transesterification and cleavage reaction. Simulations were performed with explicit solvation with rigorous electrostatics and utilize recently developed molecular mechanical force field parameters for transphosphorylation and hydrolysis transition state analogues. Herein, we present results for the enzyme complexed with the dinucleotide substrate cytidilyl-3',5'-adenosine (CpA) in the reactant, and transphosphorylation and hydrolysis transition states. A detailed analysis of active site structures and hydrogen-bond patterns is presented and compared. The integrity of the overall backbone structure is preserved in the simulations and supports a mechanism whereby His12 stabilizes accumulating negative charge at the transition states through hydrogen-bond donation to the nonbridge oxygens. Lys41 is shown to be highly versatile along the reaction coordinate and can aid in the stabilization of the dianionic transition state, while being poised to act as a general acid catalyst in the hydrolysis step.
Molecular Dynamics Simulation of Bovine Pancreatic Ribonuclease A - CpA and Transition State-like Complexes

PubMed Central

Formoso, Elena; Matxain, Jon M.; Lopez, Xabier; York, Darrin M.

2010-01-01

The mechanisms of enzymes are intimately connected with their overall structure and dynamics in solution. Experimentally it is considerably challenging to provide detailed atomic level information about the conformational events that occur at different stages along the chemical reaction path. Here, theoretical tools may offer new potential insights that complement those obtained from experiments that may not yield an unambiguous mechanistic interpretation. In this study we apply molecular dynamics simulations of bovine pancreatic ribonuclease A, an archetype ribonuclease, in order to study the conformational dynamics, structural relaxation, and differential solvation that occurs at discreet stages of the transesterification and cleavage reaction. Simulations were performed with explicit solvation with rigorous electrostatics, and utilize recently developed molecular mechanical force field parameters for transphosphorylation and hydrolysis transition state analogs. Herein, we present results for the enzyme complexed with the dinucleotide substrate cytidilyl-3′,5′-adenosine (CpA) in the reactant, and transphosphorylation and hydrolysis transition states. A detailed analysis of active site structures and hydrogen bond patterns are presented and compared. The integrity of the overall backbone structure is preserved in the simulations, and support a mechanism whereby His12 stabilizes accumulating negative charge at the transition states through hydrogen bond donation to the non-bridge oxygens. Lys41 is shown to be highly versatile along the reaction coordinate, and can aid in the stabilization of the dianionic transition state, while being poised to act as a general acid catalyst in the hydrolysis step. PMID:20455590
Structural-Phase Transformations of CuZn Alloy Under Thermal-Impact Cycling

NASA Astrophysics Data System (ADS)

Potekaev, A. I.; Chaplygina, A. A.; Kulagina, V. V.; Chaplygin, P. A.; Starostenkov, M. D.; Grinkevich, L. S.

2017-02-01

Using the Monte Carlo method, special features of structural - phase transformations in β-brass are investigated during thermal impact using thermal cycling as an example (a number of successive order - disorder and disorder - order phase transitions in the course of several heating - cooling cycles). It is shown that a unique hysteresis is observed after every heating and cooling cycle, whose presence indicates irreversibility of the processes, which suggests a difference in the structural - phase states both in the heating and cooling stages. A conclusion is drawn that the structural - phase transformations in the heating and cooling stages occur within different temperature intervals, where the thermodynamic stimuli of one or the other structural - phase state are low. This is also demonstrated both in the plots of configurational energy, long- and short-range order parameter, atomic structure variations, and structural - phase state distributions. Simultaneously, there coexist ordered and disordered phases and a certain collection of superstructure domains. This implies the presence of low - stability states in the vicinity of the order - disorder phase transition. The results of investigations demonstrate that the structural - phase transitions within two successive heating and cooling cycles at the same temperature are different in both stages. These changes, though not revolutionary, occur in every cycle and decrease with the increasing cycle number. In fact, the system undergoes training with a tendency towards a certain sequence of structural - phase states.

Crystal structure of the unactivated ribulose 1,5-bisphosphate carboxylase/oxygenase complexed with a transition state analog, 2-carboxy-D-arabinitol 1,5-bisphosphate.

PubMed Central

Zhang, K. Y.; Cascio, D.; Eisenberg, D.

1994-01-01

The crystal structure of unactivated ribulose 1,5-bisphosphate carboxylase/oxygenase from Nicotiana tabacum complexed with a transition state analog, 2-carboxy-D-arabinitol 1,5-bisphosphate, was determined to 2.7 A resolution by X-ray crystallography. The transition state analog binds at the active site in an extended conformation. As compared to the binding of the same analog in the activated enzyme, the analog binds in a reverse orientation. The active site Lys 201 is within hydrogen bonding distance of the carboxyl oxygen of the analog. Loop 6 (residues 330-339) remains open and flexible upon binding of the analog in the unactivated enzyme, in contrast to the closed and ordered loop 6 in the activated enzyme complex. The transition state analog is exposed to solvent due to the open conformation of loop 6. PMID:8142899
Magnetic structure of NiS2 -xSex

NASA Astrophysics Data System (ADS)

Yano, S.; Louca, Despina; Yang, J.; Chatterjee, U.; Bugaris, D. E.; Chung, D. Y.; Peng, L.; Grayson, M.; Kanatzidis, Mercouri G.

2016-01-01

NiS2 -2 xSex is revisited to determine the magnetic structure using neutron diffraction and magnetic representational analysis. Upon cooling, the insulating parent compound, NiS2, becomes antiferromagnetic with two successive magnetic transitions. The first transition (M 1 ) occurs at TN˜39 K with Γ1ψ1 symmetry and a magnetic propagation vector of k =(000 ) . The second transition (M 2 ) occurs at TN˜30 K with k =(0.5 ,0.5 ,0.5 ) and a Γ1ψ2 symmetry with face-centered translations, giving rise to four possible magnetic domains. With doping, the system becomes metallic. The transition to the M 2 state is suppressed prior to x =0.4 while the M 1 state persists. The M 1 magnetic structure gradually vanishes by x ˜0.8 at a lower concentration than previously reported. The details of the magnetic structures are provided.
Catalytic transitions in the human MDR1 P-glycoprotein drug binding sites.

PubMed

Wise, John G

2012-06-26

Multidrug resistance proteins that belong to the ATP-binding cassette family like the human P-glycoprotein (ABCB1 or Pgp) are responsible for many failed cancer and antiviral chemotherapies because these membrane transporters remove the chemotherapeutics from the targeted cells. Understanding the details of the catalytic mechanism of Pgp is therefore critical to the development of inhibitors that might overcome these resistances. In this work, targeted molecular dynamics techniques were used to elucidate catalytically relevant structures of Pgp. Crystal structures of homologues in four different conformations were used as intermediate targets in the dynamics simulations. Transitions from conformations that were wide open to the cytoplasm to transition state conformations that were wide open to the extracellular space were studied. Twenty-six nonredundant transitional protein structures were identified from these targeted molecular dynamics simulations using evolutionary structure analyses. Coupled movement of nucleotide binding domains (NBDs) and transmembrane domains (TMDs) that form the drug binding cavities were observed. Pronounced twisting of the NBDs as they approached each other as well as the quantification of a dramatic opening of the TMDs to the extracellular space as the ATP hydrolysis transition state was reached were observed. Docking interactions of 21 known transport ligands or inhibitors were analyzed with each of the 26 transitional structures. Many of the docking results obtained here were validated by previously published biochemical determinations. As the ATP hydrolysis transition state was approached, drug docking in the extracellular half of the transmembrane domains seemed to be destabilized as transport ligand exit gates opened to the extracellular space.
Pressure-induced magneto-structural transition in iron via a modified solid-state nudged elastic band method

NASA Astrophysics Data System (ADS)

Zarkevich, Nikolai A.; Johnson, Duane D.

2015-03-01

Materials under pressure may exhibit critical electronic and structural transitions that affect equation of states, as known for superconductors and the magneto-structural transformations of iron with both geophysical and planetary implications. While experiments often use constant-pressure (diamond-anvil cell, DAC) measurements, many theoretical results address a constant-volume transitions, which avoid issues with magnetic collapse but cannot be directly compared to experiment. We establish a modified solid-state nudge elastic band (MSS-NEB) method to handle magnetic systems that may exhibit moment (and volume) collapse during transformation. We apply it to the pressure-induced transformation in iron between the low-pressure body-centered cubic (bcc) and the high-pressure hexagonal close-packed (hcp) phases, find the bcc-hcp equilibrium coexistence pressure and a transitional pathway, and compare to shock and DAC experiments. We use methods developed with support by the U.S. Department of Energy (DE-FG02-03ER46026 and DE-AC02-07CH11358). Ames Laboratory is operated for the DOE by Iowa State University under contract DE-AC02-07CH11358.
Temperature-driven topological transition in 1T'-MoTe2

NASA Astrophysics Data System (ADS)

Berger, Ayelet Notis; Andrade, Erick; Kerelsky, Alexander; Edelberg, Drew; Li, Jian; Wang, Zhijun; Zhang, Lunyong; Kim, Jaewook; Zaki, Nader; Avila, Jose; Chen, Chaoyu; Asensio, Maria C.; Cheong, Sang-Wook; Bernevig, Bogdan A.; Pasupathy, Abhay N.

2018-01-01

The topology of Weyl semimetals requires the existence of unique surface states. Surface states have been visualized in spectroscopy measurements, but their connection to the topological character of the material remains largely unexplored. 1T'-MoTe2, presents a unique opportunity to study this connection. This material undergoes a phase transition at 240 K that changes the structure from orthorhombic (putative Weyl semimetal) to monoclinic (trivial metal), while largely maintaining its bulk electronic structure. Here, we show from temperature-dependent quasiparticle interference measurements that this structural transition also acts as a topological switch for surface states in 1T'-MoTe2. At low temperature, we observe strong quasiparticle scattering, consistent with theoretical predictions and photoemission measurements for the surface states in this material. In contrast, measurements performed at room temperature show the complete absence of the scattering wavevectors associated with the trivial surface states. These distinct quasiparticle scattering behaviors show that 1T'-MoTe2 is ideal for separating topological and trivial electronic phenomena via temperature-dependent measurements.
Disappearance of dielectric anomaly in spite of presence of structural phase transition in reduced BaTiO3: Effect of defect states within the bandgap

NASA Astrophysics Data System (ADS)

Sagdeo, Archna; Nagwanshi, Anjali; Pokhriyal, Preeti; Sinha, A. K.; Rajput, Parasmani; Mishra, Vikash; Sagdeo, P. R.

2018-04-01

We report the structural, optical, ferroelectric, and dielectric properties of reduced BaTiO3 samples. For this purpose, oxygen vacancies in BaTiO3 are created by heating these samples with a Ti metal in a vacuum environment at different temperatures. It is observed that with an increase in oxygen deficiencies, the c/a ratio decreases as compared to that of the oxygen treated sample. The ferroelectric properties of the oxygen deficient samples are visibly different as compared to those of the oxygen treated sample. The disappearance of the P-E loop and the anomaly in the temperature variation of the dielectric constant have been observed; however, the structural phase transition corresponding to ferroelectric phase transitions still persists. Thus, it appears that the anomaly in dielectric data and the presence of the P-E loop are getting masked possibly by the Maxwell-Wagner effect. The presence of Ti+3 states in the prepared samples has been confirmed by X-ray absorption near edge structure measurements. The Kubelka-Munk optical absorption shows the presence of extra states below fundamental transition, indicating the emergence of new electronic states within the bandgap, which might be due to Ti+3 states. These new states appear at different energy positions, and with different intensities for different samples, which are reduced in the presence of Ti. These new states within the bandgap appear to modify the electronic structure, thereby reducing the overall bandgap, and hence, they seem to modify the ferroelectric and dielectric properties of the samples. Our results may be treated as experimental evidence for theoretically proposed defect states in oxygen deficient or reduced BaTiO3.
Different secondary structure elements as scaffolds for protein folding transition states of two homologous four-helix bundles.

PubMed

Teilum, Kaare; Thormann, Thorsten; Caterer, Nigel R; Poulsen, Heidi I; Jensen, Peter H; Knudsen, Jens; Kragelund, Birthe B; Poulsen, Flemming M

2005-04-01

Comparison of the folding processes for homologue proteins can provide valuable information about details in the interactions leading to the formation of the folding transition state. Here the folding kinetics of 18 variants of yACBP and 3 variants of bACBP have been studied by Phi-value analysis. In combination with Phi-values from previous work, detailed insight into the transition states for folding of both yACBP and bACBP has been obtained. Of the 16 sequence positions that have been studied in both yACBP and bACBP, 5 (V12, I/L27, Y73, V77, and L80) have high Phi-values and appear to be important for the transition state formation in both homologues. Y31, A34, and A69 have high Phi-values only in yACBP, while F5, A9, and I74 have high Phi-values only in bACBP. Thus, additional interactions between helices A2 and A4 appear to be important for the transition state of yACBP, whereas additional interactions between helices A1 and A4 appear to be important for the transition state of bACBP. To examine whether these differences could be assigned to different packing of the residues in the native state, a solution structure of yACBP was determined by NMR. Small changes in the packing of the hydrophobic side-chains, which strengthen the interactions between helices A2 and A4, are observed in yACBP relative to bACBP. It is suggested that different structure elements serve as scaffolds for the folding of the 2 ACBP homologues. (c) 2005 Wiley-Liss, Inc.
Effects of ITS on transit system cost structures

DOT National Transportation Integrated Search

2002-10-01

The operation of public transit system has undergone significant changes over the past five decades. In the 1960s, most U.S. transit systems were privately owned and received little federal assistance. Most transit systems in the United States are cu...
Quantum Theory of Hyperfine Structure Transitions in Diatomic Molecules.

ERIC Educational Resources Information Center

Klempt, E.; And Others

1979-01-01

Described is an advanced undergraduate laboratory experiment in which radio-frequency transitions between molecular hyperfine structure states may be observed. Aspects of the quantum theory applied to the analysis of this physical system, are discussed. (Authors/BT)
Catch and Release: Orbital Symmetry Guided Reaction Dynamics from a Freed “Tension Trapped Transition State”

DOE PAGES

Wang, Junpeng; Ong, Mitchell T.; Kouznetsova, Tatiana B.; ...

2015-08-31

The dynamics of reactions at or in the immediate vicinity of transition states are critical to reaction rates and product distributions, but direct experimental probes of those dynamics are rare. In this paper, s-trans, s-trans 1,3-diradicaloid transition states are trapped by tension along the backbone of purely cis-substituted gem-difluorocyclopropanated polybutadiene using the extensional forces generated by pulsed sonication of dilute polymer solutions. Once released, the branching ratio between symmetry-allowed disrotatory ring closing (of which the trapped diradicaloid structure is the transition state) and symmetry-forbidden conrotatory ring closing (whose transition state is nearby) can be inferred. Finally, net conrotatory ring closingmore » occurred in 5.0 ± 0.5% of the released transition states, in excellent agreement with ab initio molecular dynamics simulations.« less
Comparison of successive transition states for folding reveals alternative early folding pathways of two homologous proteins

PubMed Central

Calosci, Nicoletta; Chi, Celestine N.; Richter, Barbara; Camilloni, Carlo; Engström, Åke; Eklund, Lars; Travaglini-Allocatelli, Carlo; Gianni, Stefano; Vendruscolo, Michele; Jemth, Per

2008-01-01

The energy landscape theory provides a general framework for describing protein folding reactions. Because a large number of studies, however, have focused on two-state proteins with single well-defined folding pathways and without detectable intermediates, the extent to which free energy landscapes are shaped up by the native topology at the early stages of the folding process has not been fully characterized experimentally. To this end, we have investigated the folding mechanisms of two homologous three-state proteins, PTP-BL PDZ2 and PSD-95 PDZ3, and compared the early and late transition states on their folding pathways. Through a combination of Φ value analysis and molecular dynamics simulations we obtained atomic-level structures of the transition states of these homologous three-state proteins and found that the late transition states are much more structurally similar than the early ones. Our findings thus reveal that, while the native state topology defines essentially in a unique way the late stages of folding, it leaves significant freedom to the early events, a result that reflects the funneling of the free energy landscape toward the native state. PMID:19033470
Flow Topology Transition via Global Bifurcation in Thermally Driven Turbulence

NASA Astrophysics Data System (ADS)

Xie, Yi-Chao; Ding, Guang-Yu; Xia, Ke-Qing

2018-05-01

We report an experimental observation of a flow topology transition via global bifurcation in a turbulent Rayleigh-Bénard convection. This transition corresponds to a spontaneous symmetry breaking with the flow becomes more turbulent. Simultaneous measurements of the large-scale flow (LSF) structure and the heat transport show that the LSF bifurcates from a high heat transport efficiency quadrupole state to a less symmetric dipole state with a lower heat transport efficiency. In the transition zone, the system switches spontaneously and stochastically between the two long-lived metastable states.
Pressure-Induced Structural Transition and Enhancement of Energy Gap of CuAlO2

NASA Astrophysics Data System (ADS)

Nakanishi, Akitaka

2011-02-01

By using first-principles calculations, we studied the stable crystal structures and energy gaps of CuAlO2 under high pressure. Our simulation shows that CuAlO2 transforms from a delafossite structure to a leaning delafossite structure. The critical pressure of the transition was determined to be 60 GPa. The energy gap of CuAlO2 increases through the structural transition due to the enhanced covalency of Cu 3d and O 2p states. We found that a chalcopyrite structure does not appear as a stable structure under high pressure.
First-principles study of high-pressure structural phase transitions of magnesium

NASA Astrophysics Data System (ADS)

Liu, Qiuxiang; Fan, Changzeng; Zhang, Ruijun

2009-06-01

The structural phase transitions for the hcp, bcc, dhcp, and fcc of magnesium at hydrostatic pressures larger than about 200 GPa at zero temperature are studied by first-principles total energy calculations. The plane-wave basis pseudopotential method has been adopted, in which the generalized gradient approximation implanted in the CASTEP code is employed. By comparing the enthalpy differences of the hcp structure with other three structures under different pressures, it can be seen that when the pressure becomes higher than about 65, 130, and 190 GPa, the bcc, dhcp, and fcc structures become more stable relative to the hcp structure, respectively. Due to the lowest enthalpy value of the bcc structure above 65 GPa, it can be deduced that magnesium may transform to the bcc structure from the ground state hcp structure around 65 GPa, but no further phase transitions occur without additionally applying high temperature. In addition, the equation of state of magnesium is calculated, indicating that bcc structure is the softest phase.
Collective dynamics in heterogeneous networks of neuronal cellular automata

NASA Astrophysics Data System (ADS)

Manchanda, Kaustubh; Bose, Amitabha; Ramaswamy, Ramakrishna

2017-12-01

We examine the collective dynamics of heterogeneous random networks of model neuronal cellular automata. Each automaton has b active states, a single silent state and r - b - 1 refractory states, and can show 'spiking' or 'bursting' behavior, depending on the values of b. We show that phase transitions that occur in the dynamical activity can be related to phase transitions in the structure of Erdõs-Rényi graphs as a function of edge probability. Different forms of heterogeneity allow distinct structural phase transitions to become relevant. We also show that the dynamics on the network can be described by a semi-annealed process and, as a result, can be related to the Boolean Lyapunov exponent.
Structural Insights into the Calcium-Mediated Allosteric Transition in the C-Terminal Domain of Calmodulin from Nuclear Magnetic Resonance Measurements.

PubMed

Kukic, Predrag; Lundström, Patrik; Camilloni, Carlo; Evenäs, Johan; Akke, Mikael; Vendruscolo, Michele

2016-01-12

Calmodulin is a two-domain signaling protein that becomes activated upon binding cooperatively two pairs of calcium ions, leading to large-scale conformational changes that expose its binding site. Despite significant advances in understanding the structural biology of calmodulin functions, the mechanistic details of the conformational transition between closed and open states have remained unclear. To investigate this transition, we used a combination of molecular dynamics simulations and nuclear magnetic resonance (NMR) experiments on the Ca(2+)-saturated E140Q C-terminal domain variant. Using chemical shift restraints in replica-averaged metadynamics simulations, we obtained a high-resolution structural ensemble consisting of two conformational states and validated such an ensemble against three independent experimental data sets, namely, interproton nuclear Overhauser enhancements, (15)N order parameters, and chemical shift differences between the exchanging states. Through a detailed analysis of this structural ensemble and of the corresponding statistical weights, we characterized a calcium-mediated conformational transition whereby the coordination of Ca(2+) by just one oxygen of the bidentate ligand E140 triggers a concerted movement of the two EF-hands that exposes the target binding site. This analysis provides atomistic insights into a possible Ca(2+)-mediated activation mechanism of calmodulin that cannot be achieved from static structures alone or from ensemble NMR measurements of the transition between conformations.
The Profession of Transition Specialization: In Search of an Identity

ERIC Educational Resources Information Center

Breault, Dawn E.

2016-01-01

This qualitative phenomenological dissertation examined the overall profession of transition specialization; in particular the perceptions of transition specialists regarding the sufficiency of their professional preparation and development. Fifteen transition specialists from the six states participated via semi-structured interviews. Major…
Transition States and transition state analogue interactions with enzymes.

PubMed

Schramm, Vern L

2015-04-21

Enzymatic transition states have lifetimes of a few femtoseconds (fs). Computational analysis of enzyme motions leading to transition state formation suggests that local catalytic site motions on the fs time scale provide the mechanism to locate transition states. An experimental test of protein fs motion and its relation to transition state formation can be provided by isotopically heavy proteins. Heavy enzymes have predictable mass-altered bond vibration states without altered electrostatic properties, according to the Born-Oppenheimer approximation. On-enzyme chemistry is slowed in most heavy proteins, consistent with altered protein bond frequencies slowing the search for the transition state. In other heavy enzymes, structural changes involved in reactant binding and release are also influenced. Slow protein motions associated with substrate binding and catalytic site preorganization are essential to allow the subsequent fs motions to locate the transition state and to facilitate the efficient release of products. In the catalytically competent geometry, local groups move in stochastic atomic motion on the fs time scale, within transition state-accessible conformations created by slower protein motions. The fs time scale for the transition state motions does not permit thermodynamic equilibrium between the transition state and stable enzyme states. Isotopically heavy enzymes provide a diagnostic tool for fast coupled protein motions to transition state formation and mass-dependent conformational changes. The binding of transition state analogue inhibitors is the opposite in catalytic time scale to formation of the transition state but is related by similar geometries of the enzyme-transition state and enzyme-inhibitor interactions. While enzymatic transition states have lifetimes as short as 10(-15) s, transition state analogues can bind tightly to enzymes with release rates greater than 10(3) s. Tight-binding transition state analogues stabilize the rare but evolved enzymatic geometry to form the transition state. Evolution to efficient catalysis optimized this geometry and its stabilization by a transition state mimic results in tight binding. Release rates of transition state analogues are orders of magnitude slower than product release in normal catalytic function. During catalysis, product release is facilitated by altered chemistry. Compared to the weak associations found in Michaelis complexes, transition state analogues involve strong interactions related to those in the transition state. Optimum binding of transition state analogues occurs when the complex retains the system motions intrinsic to transition state formation. Conserved dynamic motion retains the entropic components of inhibitor complexes, improving the thermodynamics of analogue binding.
Energy, fine structure, hyperfine structure, and radiative transition rates of the high-lying multi-excited states for B-like neon

NASA Astrophysics Data System (ADS)

Zhang, Chun Mei; Chen, Chao; Sun, Yan; Gou, Bing Cong; Shao, Bin

2015-04-01

The Rayleigh-Ritz variational method with multiconfiguration interaction wave functions is used to obtain the energies of high-lying multi-excited quartet states 1 s 22 s2 pnl and 1 s 22 p 2 nl 4Pe,o ( n ≥ 2) in B-like neon, including the mass polarization and relativistic corrections. The fine structure and hyperfine structure of the excited quartet states for this system are investigated. Configuration structures of the high-lying multi-excited series are further identified by relativistic corrections and fine structure splittings. The transition rates and wavelengths are also calculated. Calculated wavelengths include the quantum electrodynamic effects. The results are compared with other theoretical and experimental data in the literature.
Coupled channels description of the α-decay fine structure

NASA Astrophysics Data System (ADS)

Delion, D. S.; Ren, Zhongzhou; Dumitrescu, A.; Ni, Dongdong

2018-05-01

We review the coupled channels approach of α transitions to excited states. The α-decaying states are identified as narrow outgoing Gamow resonances in an α-daughter potential. The real part of the eigenvalue corresponds to the Q-value, while the imaginary part determines the half of the total α-decay width. We first review the calculations describing transitions to rotational states treated by the rigid rotator model, in even–even, odd-mass and odd–odd nuclei. It is found that the semiclassical method overestimates the branching ratios to excited 4+ for some even–even α-emitters and fails in explaining the unexpected inversion of branching ratios of some odd-mass nuclei, while the coupled-channels results show good agreement with the experimental data. Then, we review the coupled channels method for α-transitions to 2+ vibrational and transitional states. We present the results of the Coherent State Model that describes in a unified way the spectra of vibrational, transitional and rotational nuclei. We evidence general features of the α-decay fine structure, namely the linear dependence between α-intensities and excitation energy, the linear correlation between the strength of the α-core interaction and spectroscopic factor, and the inverse correlation between the nuclear collectivity, given by electromagnetic transitions, and α-clustering.

Theoretical Study of Energy Levels and Transition Probabilities of Boron Atom

NASA Astrophysics Data System (ADS)

Tian Yi, Zhang; Neng Wu, Zheng

2009-08-01

Full Text PDF Though the electrons configuration for boron atom is simple and boron atom has long been of interest for many researchers, the theoretical studies for properties of BI are not systematic, there are only few results reported on energy levels of high excited states of boron, and transition measurements are generally restricted to transitions involving ground states and low excited states without considering fine structure effects, provided only multiplet results, values for transitions between high excited states are seldom performed. In this article, by using the scheme of the weakest bound electron potential model theory calculations for energy levels of five series are performed and with the same method we give the transition probabilities between excited states with considering fine structure effects. The comprehensive set of calculations attempted in this paper could be of some value to workers in the field because of the lack of published calculations for the BI systems. The perturbations coming from foreign perturbers are taken into account in studying the energy levels. Good agreement between our results and the accepted values taken from NIST has been obtained. We also reported some values of energy levels and transition probabilities not existing on the NIST data bases.
THE ROLE OF METASTABLE STATES IN POLYMER PHASE TRANSITIONS: Concepts, Principles, and Experimental Observations

NASA Astrophysics Data System (ADS)

Cheng, Stephen Z. D.; Keller, Andrew

1998-08-01

Polymer phases can be described in the same way as phases in other condensed matter using a number density operator and its correlation functions. This description requires the understanding of symmetry operations and order at different atomic and molecular levels. Statistical mechanics provides a link between the microscopic description of the structure and motion and the macroscopic thermodynamic properties. Within the limits of the laws of thermodynamics, polymers exhibit a rich variety of phase transition behaviors. By definition, a first-order phase transition describes a transformation that involves a sudden change of thermodynamic properties at its transition temperature, whereas higher-order phase transitions are classified as critical phenomena. Of special interest is the role of metastability in phase and phase transition behaviors. Although a metastable state possesses a local free energy minimum, it is not at the global equilibrium. Furthermore, metastable states can also be associated with phase sizes. Metastable behavior is also observed in phase transformations that are impeded by kinetic limitations along the pathway to thermodynamic equilibrium. This is illustrated in structural and morphological investigations of crystallization and mesophase transitions, liquid-liquid phase separation, vitrification, and gel formation, as well as combinations of transformation processes. In these cases, the metastable state often becomes the dominant state for the entire system and is observed over a range of time and size scales. This review describes the general principles of metastability in polymer phases and phase transitions and provides illustrations from current experimental works in selected areas.
Laser Induced Optical Pumping Measurements of Cross Sections for Fine and Hyperfine Structure Transitions in Sodium Induced by Collisions with Helium Argon Atoms

NASA Technical Reports Server (NTRS)

Dobson, Chris C.; Sung, C. C.

1998-01-01

Optical pumping of the ground states of sodium can radically alter the shape of the laser induced fluorescence excitation spectrum, complicating measurements of temperature, pressure, etc., which are based on these spectra. Modeling of the fluorescence using rate equations for the eight hyperfine states of the sodium D manifolds can be used to quantify the contribution to the ground state pumping of transitions among the hyperfine excited states induced by collisions with buffer gas atoms. This model is used here to determine, from the shape of experimental spectra, cross sections for (Delta)F transitions of the P(sub 3/2) state induced by collisions with helium and argon atoms, for a range of values assumed for the P(sub 1/2), (Delta)F cross sections. The hyperfine cross sections measured using this method, which is thought to be novel, are compared with cross sections for transitions involving polarized magnetic substates, m(sub F), measured previously using polarization sensitive absorption. Also, fine structure transition ((Delta)J) cross sections were measured in the pumped vapor, giving agreement with previous measurements made in the absence of pumping.
Laser-Induced Optical Pumping Measurements of Cross Section for Fine- and Hyperfine-Structure Transitions in Sodium Induced by Collisions with Helium and Argon Atoms

NASA Technical Reports Server (NTRS)

Dobson, Chris C.; Sung, C. C.

1999-01-01

Optical pumping of the ground states of sodium can radically alter the shape of the laser-induced fluorescence excitation spectrum, complicating measurements of temperature, pressure, etc., which are based on these spectra. Modeling of the fluorescence using rate equations for the eight hyperfine states of the sodium D manifolds can be used to quantify the contribution to the ground state pumping of transitions among the hyperfine excited states induced by collisions with buffer gas atoms. This model is used here to determine, from the shape of experimental spectra, cross sections lor DELTA.F transitions of the P(sub 3/2) state induced by collisions with helium and argon atoms, for a range of values assumed for the P(sub 1/2), DELTA.F cross sections. The hyperfine cross sections measured using this method, which to our knowledge is novel, are compared with cross sections for transitions involving polarized magnetic substates m(sub F) measured previously using polarization sensitive absorption. Also, fine-structure transition cross sections were measured in the pumped vapor, giving agreement with previous measurements made in the absence of pumping.
Importance of electronegativity differences and surface structure in molecular dissociation reactions at transition metal surfaces.

PubMed

Crawford, Paul; Hu, P

2006-12-14

The dissociative adsorption of N2 has been studied at both monatomic steps and flat regions on the surfaces of the 4d transition metals from Zr to Pd. Using density functional theory (DFT) calculations, we have determined and analyzed the trends in both straight reactivity and structure sensitivity across the periodic table. With regards to reactivity, we find that the trend in activation energy (Ea) is determined mainly by a charge transfer from the surface metal atoms to the N atoms during transition state formation, namely, the degree of ionicity of the N-surface bond at the transition state. Indeed, we find that the strength of the metal-N bond at the transition state (and therefore the trend in Ea) can be predicted by the difference in Mulliken electronegativity between the metal and N. Structure sensitivity is analyzed in terms of geometric and electronic effects. We find that the lowering of Ea due to steps is more pronounced on the right-hand side of the periodic table. It is found that for the early transition metals the geometric and electronic effects work in opposition when going from terrace to step active site. In the case of the late 4d metals, however, these effects work in combination, producing a more marked reduction in Ea.
Vibrational spectroscopic study on polymorphism of erucic acid and palmitoleic acid: γ1→α1 and γ→α reversible solid state phase transitions

NASA Astrophysics Data System (ADS)

Kaneko, Fumitoshi; Yamazaki, Kazuhiro; Kobayashi, Masamichi; Sato, Kiyotaka; Suzuki, Masao

1994-08-01

The infrared and Raman spectra of four polymorphic phases (α, α1, γ and γ1) of erucic acid ( cis-13-docosenoic acid) and those of two polymorphic phases (α and γ) of palmitoleic acid ( cis-9-hexadecenoic acid) were investigated. The γ and γ1 phases of erucic acid were analyzed on the basis of crystal structures determined by us. There were large spectral differences between γ and γ1 phases, which could be ascribed to the differences in the conformation of cis-olefin groups and the subcell structure. Two types of reversible solid state phase transitions (γ→α and γ1→α1 transitions) were followed by the infrared and Raman spectra. It was concluded that the mechanism of the γ→α phase transition of erucic and palmitoleic acids is essentially the same as that of oleic acid previously reported by us [ J. Phys. Chem.90, 6371 (1986)], i.e. this phase transition is of order-disorder type accompanied by a conformational disordering at the methyl-terminal chain. Spectral changes on the γ1→α1 transition suggested that a similar structural change took place during this transition but there were large structural differences between α and α1.
Structure of siderite FeCO[subscript 3] to 56 GPa and hysteresis of its spin-pairing transition

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

Lavina, Barbara; Dera, Przemyslaw; Downs, Robert T.

2010-09-17

The structure of siderite, FeCO{sub 3}, was determined to 56 GPa, beyond the spin-pairing transition of its iron d electrons. Fe{sup 2+} in the siderite structure is in the high-spin state at low pressures and transforms to the low-spin (LS) state over a narrow pressure range, 44 to 45 GPa, that is concomitant with a shrinkage of the octahedral bond distance by 4%, and a volume collapse of 10%. The structural rearrangements associated with the electronic transition are nearly isotropic in contrast with other properties of siderite, which mostly are highly anisotropic. Robust refinements of the crystal structure from single-crystalmore » x-ray diffraction data were performed at small pressure intervals in order to accurately evaluate the variation in the interatomic distances and to define the geometry of the carbonate hosting LS-Fe{sup 2+}. Thermal vibrations are remarkably lowered in the LS-Sd as shown by atomic displacement parameters. The formation of like-spin domains at the transition shows a hysteresis of more than 3 GPa, compatible with a strong cooperative contribution of neighboring clusters to the transition.« less
Design of biomimetic catalysts by molecular imprinting in synthetic polymers: the role of transition state stabilization.

PubMed

Wulff, Günter; Liu, Junqiu

2012-02-21

The impressive efficiency and selectivity of biological catalysts has engendered a long-standing effort to understand the details of enzyme action. It is widely accepted that enzymes accelerate reactions through their steric and electronic complementarity to the reactants in the rate-determining transition states. Thus, tight binding to the transition state of a reactant (rather than to the corresponding substrate) lowers the activation energy of the reaction, providing strong catalytic activity. Debates concerning the fundamentals of enzyme catalysis continue, however, and non-natural enzyme mimics offer important additional insight in this area. Molecular structures that mimic enzymes through the design of a predetermined binding site that stabilizes the transition state of a desired reaction are invaluable in this regard. Catalytic antibodies, which can be quite active when raised against stable transition state analogues of the corresponding reaction, represent particularly successful examples. Recently, synthetic chemistry has begun to match nature's ability to produce antibody-like binding sites with high affinities for the transition state. Thus, synthetic, molecularly imprinted polymers have been engineered to provide enzyme-like specificity and activity, and they now represent a powerful tool for creating highly efficient catalysts. In this Account, we review recent efforts to develop enzyme models through the concept of transition state stabilization. In particular, models for carboxypeptidase A were prepared through the molecular imprinting of synthetic polymers. On the basis of successful experiments with phosphonic esters as templates to arrange amidinium groups in the active site, the method was further improved by combining the concept of transition state stabilization with the introduction of special catalytic moieties, such as metal ions in a defined orientation in the active site. In this way, the imprinted polymers were able to provide both an electrostatic stabilization for the transition state through the amidinium group as well as a synergism of transition state recognition and metal ion catalysis. The result was an excellent catalyst for carbonate hydrolysis. These enzyme mimics represent the most active catalysts ever prepared through the molecular imprinting strategy. Their catalytic activity, catalytic efficiency, and catalytic proficiency clearly surpass those of the corresponding catalytic antibodies. The active structures in natural enzymes evolve within soluble proteins, typically by the refining of the folding of one polypeptide chain. To incorporate these characteristics into synthetic polymers, we used the concept of transition state stabilization to develop soluble, nanosized carboxypeptidase A models using a new polymerization method we term the "post-dilution polymerization method". With this methodology, we were able to prepare soluble, highly cross-linked, single-molecule nanoparticles. These particles have controlled molecular weights (39 kDa, for example) and, on average, one catalytically active site per particle. Our strategies have made it possible to obtain efficient new enzyme models and further advance the structural and functional analogy with natural enzymes. Moreover, this bioinspired design based on molecular imprinting in synthetic polymers offers further support for the concept of transition state stabilization in catalysis.
The folding transition state of Protein L is extensive with non-native interactions (and not small and polarized)

PubMed Central

Yoo, Tae Yeon; Adhikari, Aashish; Xia, Zhen; Huynh, Tien; Freed, Karl F.; Zhou, Ruhong; Sosnick, Tobin R.

2012-01-01

Progress in understanding protein folding relies heavily upon an interplay between experiment and theory. In particular, readily interpretable experimental data are required that can be meaningfully compared to simulations. According to standard mutational φ analysis, the transition state for Protein L contains only a single hairpin. However, we demonstrate here using ψ analysis with engineered metal ion binding sites that the transition state is extensive, containing the entire four-stranded β sheet. Underreporting of the structural content of the transition state by φ analysis also occurs for acyl phosphatase1, ubiquitin2 and BdpA3. The carboxy terminal hairpin in the transition state of Protein L is found to be non-native, a significant result that agrees with our PDB-based backbone sampling and all-atom simulations. The non-native character partially explains the failure of accepted experimental and native-centric computational approaches to adequately describe the transition state. Hence, caution is required even when an apparent agreement exists between experiment and theory, thus highlighting the importance of having alternative methods for characterizing transition states. PMID:22522126
Pressure-induced electronic topological transitions in the charge-density-wave material In 4 Se 3

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

Zhang, Yuhang; Song, Liyan; Shao, Xuecheng

2017-08-01

High-pressure in situ angle dispersive X-ray diffraction (ADXRD) measurements were performed on the charge-density-wave (CDW) material In4Se3 up to 48.8 GPa. Pressure-induced structural changes were observed at 7.0 and 34.2 GPa, respectively. Using the CALYPSO methodology, the first high-pressure phase was solved as an exotic Pca21 structure. The compressional behaviors of the initial Pnnm and the Pca21 phases were all determined. Combined with first-principle calculations, we find that, unexpectedly, the Pnnm phase probably experiences twice electronic topological transitions (ETTs), from the initial possible CDW state to a semimetallic state at about 2.3 GPa and then back to a possible CDWmore » state at around 3.5 GPa, which was uncovered for the first time in CDW systems. In the both possible CDW states, pressure provokes a decrease of band-gap. The observation of a bulk metallic state was ascribed to structural transition to the Pca21 phase. Besides, based on electronic band structure calculations, the thermoelectric property of the Pnnm phase under compression was discussed. Our results show that pressure play a dramatic role in tuning In4Se3's structure and transport properties.« less
Two-Dimensional Wetting Transition Modeling with the Potts Model

NASA Astrophysics Data System (ADS)

Lopes, Daisiane M.; Mombach, José C. M.

2017-12-01

A droplet of a liquid deposited on a surface structured in pillars may have two states of wetting: (1) Cassie-Baxter (CB), the liquid remains on top of the pillars, also known as heterogeneous wetting, or (2) Wenzel, the liquid fills completely the cavities of the surface, also known as homogeneous wetting. Studies show that between these two states, there is an energy barrier that, when overcome, results in the transition of states. The transition can be achieved by changes in geometry parameters of the surface, by vibrations of the surface or by evaporation of the liquid. In this paper, we present a comparison of two-dimensional simulations of the Cassie-Wenzel transition on pillar-structured surfaces using the cellular Potts model (CPM) with studies performed by Shahraz et al. In our work, we determine a transition diagram by varying the surface parameters such as the interpillar distance ( G) and the pillar height ( H). Our results were compared to those obtained by Shahraz et al. obtaining good agreement.
Typology of State Types: Persistence and Transition

DTIC Science & Technology

2015-04-28

is the lack of positive transition among the weakest states. Our findings are derived from a minimalist construct of a refined time series dataset...states based on a „ minimalist ‟ construct of the Country Indicators for Foreign Policy (CIFP) fragile states project and its core structural...begin with the rationale for developing a minimalist construct of a state typology model (STM), similar to the approach taken by Gravingholt, Ziaja
Nuclear structure properties of the double-charge-exchange transition amplitudes

NASA Astrophysics Data System (ADS)

Auerbach, N.; Zheng, D. C.

1992-03-01

Nuclear structure aspects of the double-charge-exchange (DCX) reaction on nuclei are studied. Using a variety of DCX-type two-body transition operators, we explore the influence of two-body correlations among valence nucleons on the DCX transition amplitudes to the isobaric analog state and to other nonanalog J π=0+ states. In particular, the question of the spin dependence and of the range of the DCX transition operators is explored and the behavior of the transition amplitudes as a function of the valence nucleon number is studied. It is shown that the two-amplitude DCX formula derived by Auerbach, Gibbs, and Piasetzky for a single j n configuration holds also in some cases when configuration mixing is strong. DCX-type transitions from the Ca and Ni isotopes to the Ti and Zn isotopes and from 56Fe to 56Ni are the subject of this study.
Excited state conformational dynamics in carotenoids: dark intermediates and excitation energy transfer.

PubMed

Beck, Warren F; Bishop, Michael M; Roscioli, Jerome D; Ghosh, Soumen; Frank, Harry A

2015-04-15

A consideration of the excited state potential energy surfaces of carotenoids develops a new hypothesis for the nature of the conformational motions that follow optical preparation of the S2 (1(1)Bu(+)) state. After an initial displacement from the Franck-Condon geometry along bond length alternation coordinates, it is suggested that carotenoids pass over a transition-state barrier leading to twisted conformations. This hypothesis leads to assignments for several dark intermediate states encountered in femtosecond spectroscopic studies. The Sx state is assigned to the structure reached upon the onset of torsional motions near the transition state barrier that divides planar and twisted structures on the S2 state potential energy surface. The X state, detected recently in two-dimensional electronic spectra, corresponds to a twisted structure well past the barrier and approaching the S2 state torsional minimum. Lastly, the S(∗) state is assigned to a low lying S1 state structure with intramolecular charge transfer character (ICT) and a pyramidal conformation. It follows that the bent and twisted structures of carotenoids that are found in photosynthetic light-harvesting proteins yield excited-state structures that favor the development of an ICT character and optimized energy transfer yields to (bacterio)chlorophyll acceptors. Copyright © 2015 Elsevier Inc. All rights reserved.
Epitaxial strain-mediated spin-state transitions: can we switch off magnetism?

NASA Astrophysics Data System (ADS)

Rondinelli, James; Spaldin, Nicola

2008-03-01

We use first-principles density functional theory calculations to explore spin-state transitions in epitaxially strained LaCoO3. While high-spin to low-spin state transitions in minerals are common in geophysics, where pressures can reach over 200 GPa, we explore whether heteroepitaxial strain can achieve similar transitions with moderate strain in thin films. LaCoO3 is known to undergo a low-spin (S=0, t2g^6eg^0) to intermediate-spin (S=1, t2g^5eg^1) or high-spin (S=2, t2g^4eg^2) state transition with increasing temperature, and thus makes it a promising candidate material for strain-mediated spin transitions. Here we discuss the physics of the low-spin transition and changes in the electronic structure of LaCoO3, most notably, the metal-insulator transition that accompanies the spin-state transitions with epitaxial strain. As thin film growth techniques continue to reach atomic-level precision, we suggest this is another approach for controlling magnetism in complex oxide heterostructures.
[Artificial Cysteine Bridges on the Surface of Green Fluorescent Protein Affect Hydration of Its Transition and Intermediate States].

PubMed

Melnik, T N; Nagibina, G S; Surin, A K; Glukhova, K A; Melnik, B S

2018-01-01

Studying the effect of cysteine bridges on different energy levels of multistage folding proteins will enable a better understanding of the process of folding and functioning of globular proteins. In particular, it will create prospects for directed change in the stability and rate of protein folding. In this work, using the method of differential scanning microcalorimetry, we have studied the effect of three cysteine bridges introduced in different structural elements of the green fluorescent protein on the denaturation enthalpies, activation energies, and heat-capacity increments when this protein passes from native to intermediate and transition states. The studies have allowed us to confirm that, with this protein denaturation, the process hardly damages the structure initially, but then changes occur in the protein structure in the region of 4-6 beta sheets. The cysteine bridge introduced in this region decreases the hydration of the second transition state and increases the hydration of the second intermediate state during the thermal denaturation of the green fluorescent protein.
Tendency to occupy a statistically dominant spatial state of the flow as a driving force for turbulent transition.

PubMed

Chekmarev, Sergei F

2013-03-01

The transition from laminar to turbulent fluid motion occurring at large Reynolds numbers is generally associated with the instability of the laminar flow. On the other hand, since the turbulent flow characteristically appears in the form of spatially localized structures (e.g., eddies) filling the flow field, a tendency to occupy such a structured state of the flow cannot be ruled out as a driving force for turbulent transition. To examine this possibility, we propose a simple analytical model that treats the flow as a collection of localized spatial structures, each of which consists of elementary cells in which the behavior of the particles (atoms or molecules) is uncorrelated. This allows us to introduce the Reynolds number, associating it with the ratio between the total phase volume for the system and that for the elementary cell. Using the principle of maximum entropy to calculate the most probable size distribution of the localized structures, we show that as the Reynolds number increases, the elementary cells group into the localized structures, which successfully explains turbulent transition and some other general properties of turbulent flows. An important feature of the present model is that a bridge between the spatial-statistical description of the flow and hydrodynamic equations is established. We show that the basic assumptions underlying the model, i.e., that the particles are indistinguishable and elementary volumes of phase space exist in which the state of the particles is uncertain, are involved in the derivation of the Navier-Stokes equation. Taking into account that the model captures essential features of turbulent flows, this suggests that the driving force for the turbulent transition is basically the same as in the present model, i.e., the tendency of the system to occupy a statistically dominant state plays a key role. The instability of the flow at high Reynolds numbers can then be a mechanism to initiate structural rearrangement of the flow to find this state.
The structure and energetics of the HCN → HNC transition state

NASA Astrophysics Data System (ADS)

Lee, Timothy J.; Rendell, Alistair P.

1991-03-01

The optimum geometries and quadratic force constants of HCN, HNC and the transition state connecting them have been determined at the single and double excitation coupled-cluster (CCSD) and CCSD(T) levels of theory. Energy differences were evaluated using the CCSD and CCSD(T) methods in conjunction with large atomic natural orbital basis sets containing g-type basis functions on the heavy atoms and f-type functions on hydrogen. The most reliable structure obtained for the transition state has bond distances of 1.194, 1.188 and 1.389 Å for rCN, rCH and rNH, respectively. Including a correction for zero-point vibrational energies, the transition state is predicted to be 44.6 ± 1.0 kcal/mol above the HCN isomer, while HNC is predicted to be 14.4 ± 1.0 kcal/mol above HCN. The latter value is in excellent agreement with the most recent experimental determination (14.8 ± 2.0 kcal/mol).
Transition state analogues in structures of ricin and saporin ribosome-inactivating proteins

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

Ho, Meng-Chiao; Sturm, Matthew B.; Almo, Steven C.

2010-01-12

Ricin A-chain (RTA) and saporin-L1 (SAP) catalyze adenosine depurination of 28S rRNA to inhibit protein synthesis and cause cell death. We present the crystal structures of RTA and SAP in complex with transition state analogue inhibitors. These tight-binding inhibitors mimic the sarcin-ricin recognition loop of 28S rRNA and the dissociative ribocation transition state established for RTA catalysis. RTA and SAP share unique purine-binding geometry with quadruple {pi}-stacking interactions between adjacent adenine and guanine bases and 2 conserved tyrosines. An arginine at one end of the {pi}-stack provides cationic polarization and enhanced leaving group ability to the susceptible adenine. Common featuresmore » of these ribosome-inactivating proteins include adenine leaving group activation, a remarkable lack of ribocation stabilization, and conserved glutamates as general bases for activation of the H{sub 2}O nucleophile. Catalytic forces originate primarily from leaving group activation evident in both RTA and SAP in complex with transition state analogues.« less
δ-Deuterium Isotope Effects as Probes for Transition-State Structures of Isoprenoid Substrates

PubMed Central

2015-01-01

The biosynthetic pathways to isoprenoid compounds involve transfer of the prenyl moiety in allylic diphosphates to electron-rich (nucleophilic) acceptors. The acceptors can be many types of nucleophiles, while the allylic diphosphates only differ in the number of isoprene units and stereochemistry of the double bonds in the hydrocarbon moieties. Because of the wide range of nucleophilicities of naturally occurring acceptors, the mechanism for prenyltransfer reactions may be dissociative or associative with early to late transition states. We have measured δ-secondary kinetic isotope effects operating through four bonds for substitution reactions with dimethylallyl derivatives bearing deuterated methyl groups at the distal (C3) carbon atom in the double bond under dissociative and associative conditions. Computational studies with density functional theory indicate that the magnitudes of the isotope effects correlate with the extent of bond formation between the allylic moiety and the electron-rich acceptor in the transition state for alkylation and provide insights into the structures of the transition states for associative and dissociative alkylation reactions. PMID:24665882

Christopher Chang | NREL

Science.gov Websites

transition metal systems, macromolecular dynamics, comparative chemical bonding analysis, electron transfer . Research Interests Dynamics and control on discrete structures, including excited-state transition metal
The mechanism of the converter domain rotation in the recovery stroke of myosin motor protein

PubMed Central

Baumketner, Andrij

2012-01-01

Upon ATP binding, myosin motor protein is found in two alternative conformations, pre-recovery state M* and post-recovery state M**. The transition from one state to the other, known as the recovery stroke, plays a key role in the myosin functional cycle. Despite much recent research, the microscopic details of this transition remain elusive. A critical step in the recovery stroke is the rotation of the converter domain from “up” position in pre-recovery state to “down” position in post-recovery state that leads to the swing of the lever arm attached to it. In this work, we demonstrate that the two rotational states of the converter domain are determined by the interactions within a small structural motif in the force-generating region of the protein that can be accurately modeled on computers using atomic representation and explicit solvent. Our simulations show that the transition between the two states is controlled by a small helix (SH1) located next to the relay helix and relay loop. A small translation in the position of SH1 away from the relay helix is seen to trigger the transition from “up” state to “down” state. The transition is driven by a cluster of hydrophobic residues I687, F487 and F506 that make significant contributions to the stability of both states. The proposed mechanism agrees well with the available structural and mutational studies. PMID:22855405
Anomalous structural transition of confined hard squares.

PubMed

Gurin, Péter; Varga, Szabolcs; Odriozola, Gerardo

2016-11-01

Structural transitions are examined in quasi-one-dimensional systems of freely rotating hard squares, which are confined between two parallel walls. We find two competing phases: one is a fluid where the squares have two sides parallel to the walls, while the second one is a solidlike structure with a zigzag arrangement of the squares. Using transfer matrix method we show that the configuration space consists of subspaces of fluidlike and solidlike phases, which are connected with low probability microstates of mixed structures. The existence of these connecting states makes the thermodynamic quantities continuous and precludes the possibility of a true phase transition. However, thermodynamic functions indicate strong tendency for the phase transition and our replica exchange Monte Carlo simulation study detects several important markers of the first order phase transition. The distinction of a phase transition from a structural change is practically impossible with simulations and experiments in such systems like the confined hard squares.
Effective collision strengths for the electron impact excitation of Mg

NASA Astrophysics Data System (ADS)

Hudson, C. E.; Ramsbottom, C. A.; Norrington, P. H.; Scott, M. P.

2008-05-01

Electron impact excitation collision strengths for fine structure transitions of Mg,have been determined by a Breit-Pauli R-matrix calculation. The target states are represented by configuration interaction wavefunctions and consist of the 19 lowest LS states, having configurations 2s^22p^4, 2s2p^5, 2p^6, 2s^22p^33s and 2s^22p^33p. These target states give rise to 37 fine structure levels and 666 possible transitions. The effective collision strengths are calculated by averaging the electron collision strengths over a Maxwellian distribution of electron velocities. Effective collision strengths for transitions between the fine structure levels are given for electron temperatures in the range 10Te(K) = 3.0 - 7.0. Results are compared with the previous R-matrix calculation of Butler & Zeippen (AASS, 1994) and the recent Distorted Wave evaluations of Bhatia, Landi & Eissner (ADNDT, 2006).
Binding energy of donor impurity states and optical absorption in the Tietz-Hua quantum well under an applied electric field

NASA Astrophysics Data System (ADS)

Al, E. B.; Kasapoglu, E.; Sakiroglu, S.; Duque, C. A.; Sökmen, I.

2018-04-01

For a quantum well which has the Tietz-Hua potential, the ground and some excited donor impurity binding energies and the total absorption coefficients, including linear and third order nonlinear terms for the transitions between the related impurity states with respect to the structure parameters and the impurity position as well as the electric field strength are investigated. The binding energies were obtained using the effective-mass approximation within a variational scheme and the optical transitions between any two impurity states were calculated by using the density matrix formalism and the perturbation expansion method. Our results show that the effects of the electric field and the structure parameters on the optical transitions are more pronounced. So we can adjust the red or blue shift in the peak position of the absorption coefficient by changing the strength of the electric field as well as the structure parameters.
Interplay of Cu and oxygen vacancy in optical transitions and screening of excitons in ZnO:Cu films

NASA Astrophysics Data System (ADS)

Darma, Yudi; Seng Herng, Tun; Marlina, Resti; Fauziah, Resti; Ding, Jun; Rusydi, Andrivo

2014-02-01

We study room temperature optics and electronic structures of ZnO:Cu films as a function of Cu concentration using a combination of spectroscopic ellipsometry, photoluminescence, and ultraviolet-visible absorption spectroscopy. Mid-gap optical states, interband transitions, and excitons are observed and distinguishable. We argue that the mid-gap states are originated from interactions of Cu and oxygen vacancy (Vo). They are located below conduction band (Zn4s) and above valence band (O2p) promoting strong green emission and narrowing optical band gap. Excitonic states are screened and its intensities decrease upon Cu doping. Our results show the importance of Cu and Vo driving the electronic structures and optical transitions in ZnO:Cu films.
OsB 2 and RuB 2, ultra-incompressible, hard materials: First-principles electronic structure calculations

NASA Astrophysics Data System (ADS)

Chiodo, S.; Gotsis, H. J.; Russo, N.; Sicilia, E.

2006-07-01

Recently it has been reported that osmium diboride has an unusually large bulk modulus combined with high hardness, and consequently is a most interesting candidate as an ultra-incompressible and hard material. The electronic and structural properties of the transition metal diborides OsB 2 and RuB 2 have been calculated within the local density approximation (LDA). It is shown that the high hardness is the result of covalent bonding between transition metal d states and boron p states in the orthorhombic structure.
Role of entropy and structural parameters in the spin-state transition of LaCoO3

NASA Astrophysics Data System (ADS)

Chakrabarti, Bismayan; Birol, Turan; Haule, Kristjan

2017-11-01

The spin-state transition in LaCoO3 has eluded description for decades despite concerted theoretical and experimental effort. In this study, we approach this problem using fully charge self-consistent density functional theory + embedded dynamical mean field theory (DFT+DMFT). We show from first principles that LaCoO3 cannot be described by a single, pure spin state at any temperature. Instead, we observe a gradual change in the population of higher-spin multiplets with increasing temperature, with the high-spin multiplets being excited at the onset of the spin-state transition followed by the intermediate-spin multiplets being excited at the metal-insulator-transition temperature. We explicitly elucidate the critical role of lattice expansion and oxygen octahedral rotations in the spin-state transition. We also reproduce, from first principles, that the spin-state transition and the metal-insulator transition in LaCoO3 occur at different temperature scales. In addition, our results shed light on the importance of electronic entropy in driving the spin-state transition, which has so far been ignored in all first-principles studies of this material.
Structure-guided Protein Transition Modeling with a Probabilistic Roadmap Algorithm.

PubMed

Maximova, Tatiana; Plaku, Erion; Shehu, Amarda

2016-07-07

Proteins are macromolecules in perpetual motion, switching between structural states to modulate their function. A detailed characterization of the precise yet complex relationship between protein structure, dynamics, and function requires elucidating transitions between functionally-relevant states. Doing so challenges both wet and dry laboratories, as protein dynamics involves disparate temporal scales. In this paper we present a novel, sampling-based algorithm to compute transition paths. The algorithm exploits two main ideas. First, it leverages known structures to initialize its search and define a reduced conformation space for rapid sampling. This is key to address the insufficient sampling issue suffered by sampling-based algorithms. Second, the algorithm embeds samples in a nearest-neighbor graph where transition paths can be efficiently computed via queries. The algorithm adapts the probabilistic roadmap framework that is popular in robot motion planning. In addition to efficiently computing lowest-cost paths between any given structures, the algorithm allows investigating hypotheses regarding the order of experimentally-known structures in a transition event. This novel contribution is likely to open up new venues of research. Detailed analysis is presented on multiple-basin proteins of relevance to human disease. Multiscaling and the AMBER ff14SB force field are used to obtain energetically-credible paths at atomistic detail.
Structure of Mandelate Racemase with Bound Intermediate Analogues Benzohydroxamate and Cupferron†

PubMed Central

Lietzan, Adam D.; Nagar, Mitesh; Pellmann, Elise A.; Bourque, Jennifer R.; Bearne, Stephen L.; St Maurice, Martin

2012-01-01

Mandelate racemase (MR, EC 5.1.2.2) from Pseudomonas putida catalyzes the Mg2+-dependent interconversion of the enantiomers of mandelate, stabilizing the altered substrate in the transition state by 26 kcal/mol relative to the substrate in the ground state. To understand the origins of this binding discrimination, we solved the X-ray crystal structures of wild-type MR complexed with two analogues of the putative aci-carboxylate intermediate, benzohydroxamate and cupferron, to 2.2-Å resolution. Benzohydroxamate is shown to be a reasonable mimic of the transition state/intermediate since its binding affinity to 21 MR variants correlates well with changes in the free energy of transition state stabilization afforded by these variants. Both benzohydroxamate and cupferron chelate the active site divalent metal ion and are bound in a conformation with the phenyl ring coplanar with the hydroxamate and diazeniumdiolate moieties, respectively. Structural overlays of MR complexed with benzohydroxamate, cupferron, and the ground state analogue (S)-atrolacatate reveal that the para-carbon of the substrate phenyl ring moves by 0.8–1.2 Å between the ground state and intermediate state, consistent with the proposal that the phenyl ring moves during MR catalysis while the polar groups remain relatively fixed. Although the overall protein structure of MR with bound intermediate analogues is very similar to MR with bound (S)-atrolactate, the intermediate-Mg2+ distance shortens, suggesting a tighter complex with the catalytic Mg2+. In addition, Tyr 54 moves nearer to the phenyl ring of the bound intermediate analogues, contributing to an overall constriction of the active site cavity. However, site-directed mutagenesis experiments revealed that the role of Tyr 54 in MR catalysis is relatively minor, suggesting that alterations in enzyme structure that contribute to discrimination between the altered substrate in the transition state and the ground state by this proficient enzyme are extremely subtle. PMID:22264153
Analysis of the E2 transitions for /sup 3/H-/alpha/ cluster states of /sup 7/Li by the resonating group method

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

Xu Pu; Zhao Xuan; Zeng Fanan

1989-07-01

It is suggested that the ground state and the 1st, 2nd, and 3rd excited states of /sup 7/Li are /sup 3/H-/alpha/ cluster-structure states. Using the resonating group method (RGM), the eigenvalues and eigenfunctions of these states as well as the reduced E2 transition probabilities between these states are calculated and are consistent with the experimental values. The results show that the RGM is much better than the harmonic oscillator model used by Bernheim /ital et/ /ital al/. in predicting the E2 transition rates.
Feshbach resonances in the exit channel of the F + CH3OH → HF + CH3O reaction observed using transition-state spectroscopy

NASA Astrophysics Data System (ADS)

Weichman, Marissa L.; Devine, Jessalyn A.; Babin, Mark C.; Li, Jun; Guo, Lifen; Ma, Jianyi; Guo, Hua; Neumark, Daniel M.

2017-10-01

The transition state governs how chemical bonds form and cleave during a chemical reaction and its direct characterization is a long-standing challenge in physical chemistry. Transition state spectroscopy experiments based on negative-ion photodetachment provide a direct probe of the vibrational structure and metastable resonances that are characteristic of the reactive surface. Dynamical resonances are extremely sensitive to the topography of the reactive surface and provide an exceptional point of comparison with theory. Here we study the seven-atom F + CH3OH → HF + CH3O reaction using slow photoelectron velocity-map imaging spectroscopy of cryocooled CH3OHF- anions. These measurements reveal spectral features associated with a manifold of vibrational Feshbach resonances and bound states supported by the post-transition state potential well. Quantum dynamical calculations yield excellent agreement with the experimental results, allow the assignment of spectral structure and demonstrate that the key dynamics of complex bimolecular reactions can be captured with a relatively simple theoretical framework.
Feshbach resonances in the exit channel of the F + CH3OH → HF + CH3O reaction observed using transition-state spectroscopy.

PubMed

Weichman, Marissa L; DeVine, Jessalyn A; Babin, Mark C; Li, Jun; Guo, Lifen; Ma, Jianyi; Guo, Hua; Neumark, Daniel M

2017-10-01

The transition state governs how chemical bonds form and cleave during a chemical reaction and its direct characterization is a long-standing challenge in physical chemistry. Transition state spectroscopy experiments based on negative-ion photodetachment provide a direct probe of the vibrational structure and metastable resonances that are characteristic of the reactive surface. Dynamical resonances are extremely sensitive to the topography of the reactive surface and provide an exceptional point of comparison with theory. Here we study the seven-atom F + CH 3 OH → HF + CH 3 O reaction using slow photoelectron velocity-map imaging spectroscopy of cryocooled CH 3 OHF - anions. These measurements reveal spectral features associated with a manifold of vibrational Feshbach resonances and bound states supported by the post-transition state potential well. Quantum dynamical calculations yield excellent agreement with the experimental results, allow the assignment of spectral structure and demonstrate that the key dynamics of complex bimolecular reactions can be captured with a relatively simple theoretical framework.
Electronic correlation in magnetic contributions to structural energies

NASA Astrophysics Data System (ADS)

Haydock, Roger

For interacting electrons the density of transitions [see http://arxiv.org/abs/1405.2288] replaces the density of states in calculations of structural energies. Extending previous work on paramagnetic metals, this approach is applied to correlation effects on the structural stability of magnetic transition metals. Supported by the H. V. Snyder Gift to the University of Oregon.
Nanodisperse transition metal electrodes (NTME) for electrochemical cells

DOEpatents

Striebel, Kathryn A.; Wen, Shi-Jie

2000-01-01

Disclosed are transition metal electrodes for electrochemical cells using gel-state and solid-state polymers. The electrodes are suitable for use in primary and secondary cells. The electrodes (either negative electrode or positive electrode) are characterized by uniform dispersion of the transition metal at the nanoscale in the polymer. The transition metal moiety is structurally amorphous, so no capacity fade should occur due to lattice expansion/contraction mechanisms. The small grain size, amorphous structure and homogeneous distribution provide improved charge/discharge cycling performance, and a higher initial discharge rate capability. The cells can be cycled at high current densities, limited only by the electrolyte conductivity. A method of making the electrodes (positive and negative), and their usage in electrochemical cells are disclosed.
Structural transition in lanthanum gallate and transformation of the fine structure of the EPR spectrum of a Gd3+ impurity center

NASA Astrophysics Data System (ADS)

Vazhenin, V. A.; Guseva, V. B.; Fokin, A. V.; Potapov, A. P.; Artyomov, M. Yu.

2011-04-01

Abrupt changes in resonance positions, hysteretic temperature behavior, and coexistence of phases, which indicate a first-order phase transition, have been revealed from measurements of temperature dependences of the EPR spectra of Gd3+ and Mn4+ centers in the vicinity of the structural transition of lanthanum gallate. The transformation of monoclinic Gd3+ centers into trigonal Gd3+ centers upon the phase transition has been used to estimate the adequacy of two approximations of the superposition model for parameters of the zero-field splitting of the ground state.
Ultrafast X-Ray Diffraction Studies of the Phase Transitions and Equation of State of Scandium Shock Compressed to 82 GPa

DOE PAGES

Briggs, R.; Gorman, M. G.; Coleman, A. L.; ...

2017-01-09

Using x-ray diffraction at the Linac Coherent Light Source x-ray free-electron laser, we have determined simultaneously and self-consistently the phase transitions and equation of state (EOS) of the lightest transition metal, scandium, under shock compression. On compression scandium undergoes a structural phase transition between 32 and 35 GPa to the same bcc structure seen at high temperatures at ambient pressures, and then a further transition at 46 GPa to the incommensurate host-guest polymorph found above 21 GPa in static compression at room temperature. Furthermore, shock melting of the host-guest phase is observed between 53 and 72 GPa with the disappearancemore » of Bragg scattering and the growth of a broad asymmetric diffraction peak from the high-density liquid.« less
Ultrafast X-Ray Diffraction Studies of the Phase Transitions and Equation of State of Scandium Shock Compressed to 82 GPa.

PubMed

Briggs, R; Gorman, M G; Coleman, A L; McWilliams, R S; McBride, E E; McGonegle, D; Wark, J S; Peacock, L; Rothman, S; Macleod, S G; Bolme, C A; Gleason, A E; Collins, G W; Eggert, J H; Fratanduono, D E; Smith, R F; Galtier, E; Granados, E; Lee, H J; Nagler, B; Nam, I; Xing, Z; McMahon, M I

2017-01-13

Using x-ray diffraction at the Linac Coherent Light Source x-ray free-electron laser, we have determined simultaneously and self-consistently the phase transitions and equation of state (EOS) of the lightest transition metal, scandium, under shock compression. On compression scandium undergoes a structural phase transition between 32 and 35 GPa to the same bcc structure seen at high temperatures at ambient pressures, and then a further transition at 46 GPa to the incommensurate host-guest polymorph found above 21 GPa in static compression at room temperature. Shock melting of the host-guest phase is observed between 53 and 72 GPa with the disappearance of Bragg scattering and the growth of a broad asymmetric diffraction peak from the high-density liquid.
Imaging ultrafast excited state pathways in transition metal complexes by X-ray transient absorption and scattering using X-ray free electron laser source

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

Chen, Lin X.; Shelby, Megan L.; Lestrange, Patrick J.

2016-01-01

This report will describe our recent studies of transition metal complex structural dynamics on the fs and ps time scales using an X-ray free electron laser source, Linac Coherent Light Source (LCLS). Ultrafast XANES spectra at the Ni K-edge of nickel(II) tetramesitylporphyrin (NiTMP) were successfully measured for optically excited state at a timescale from 100 fs to 50 ps, providing insight into its sub-ps electronic and structural relaxation processes. Importantly, a transient reduced state Ni(I) (π, 3dx2-y2) electronic state is captured through the interpretation of a short-lived excited state absorption on the low-energy shoulder of the edge, which is aidedmore » by the computation of X-ray transitions for postulated excited electronic states. The observed and computed inner shell to valence orbital transition energies demonstrate and quantify the influence of electronic configuration on specific metal orbital energies. A strong influence of the valence orbital occupation on the inner shell orbital energies indicates that one should not use the transition energy from 1s to other orbitals to draw conclusions about the d-orbital energies. For photocatalysis, a transient electronic configuration could influence d-orbital energies up to a few eV and any attempt to steer the reaction pathway should account for this to ensure that external energies can be used optimally in driving desirable processes. NiTMP structural evolution and the influence of the porphyrin macrocycle conformation on relaxation kinetics can be likewise inferred from this study.« less
From the granular Leidenfrost state to buoyancy-driven convection.

PubMed

Rivas, Nicolas; Thornton, Anthony R; Luding, Stefan; van der Meer, Devaraj

2015-04-01

Grains inside a vertically vibrated box undergo a transition from a density-inverted and horizontally homogeneous state, referred to as the granular Leidenfrost state, to a buoyancy-driven convective state. We perform a simulational study of the precursors of such a transition and quantify their dynamics as the bed of grains is progressively fluidized. The transition is preceded by transient convective states, which increase their correlation time as the transition point is approached. Increasingly correlated convective flows lead to density fluctuations, as quantified by the structure factor, that also shows critical behavior near the transition point. The amplitude of the modulations in the vertical velocity field are seen to be best described by a quintic supercritical amplitude equation with an additive noise term. The validity of such an amplitude equation, and previously observed collective semiperiodic oscillations of the bed of grains, suggests a new interpretation of the transition analogous to a coupled chain of vertically vibrated damped oscillators. Increasing the size of the container shows metastability of convective states, as well as an overall invariant critical behavior close to the transition.

Interfacial states and far-from-equilibrium transitions in the epitaxial growth and erosion on (110) crystal surfaces

NASA Astrophysics Data System (ADS)

Levandovsky, Artem; Golubović, Leonardo; Moldovan, Dorel

2006-12-01

We discuss the far-from-equilibrium interfacial phenomena occurring in the multilayer homoepitaxial growth and erosion on (110) crystal surfaces. Experimentally, these rectangular symmetry surfaces exhibit a multitude of interesting nonequilibrium interfacial structures, such as the rippled one-dimensional periodic states that are not present in the homoepitaxial growth and erosion on the high symmetry (100) and (111) crystal surfaces. Within a unified phenomenological model, we reveal and elucidate this multitude of states on (110) surfaces as well as the transitions between them. By analytic arguments and numerical simulations, we address experimentally observed transitions between two types of rippled states on (110) surfaces. We discuss several intermediary interface states intervening, via consecutive transitions, between the two rippled states. One of them is the rhomboidal pyramid state, theoretically predicted by Golubovic [Phys. Rev. Lett. 89, 266104 (2002)] and subsequently seen, by de Mongeot and co-workers, in the epitaxial erosion of Cu(110) and Rh(110) surfaces [A. Molle , Phys. Rev. Lett. 93, 256103 (2004), and A. Molle , Phys. Rev. B 73, 155418 (2006)]. In addition, we find a number of interesting intermediary states having structural properties somewhere between those of rippled and pyramidal states. Prominent among them are the rectangular rippled states of long rooflike objects (huts) recently seen on Ag(110) surface. We also predict the existence of a striking interfacial structure that carries nonzero, persistent surface currents. Periodic surface currents vortex lattice formed in this so-called buckled rippled interface state is a far-from-equilibrium relative of the self-organized convective flow patterns in hydrodynamic systems. We discuss the coarsening growth of the multitude of the interfacial states on (110) crystal surfaces.
Jet-cooled laser-induced fluorescence spectroscopy of cyclohexoxy: rotational and fine structure of molecules in nearly degenerate electronic States.

PubMed

Liu, Jinjun; Miller, Terry A

2014-12-26

The rotational structure of the previously observed B̃(2)A' ← X̃(2)A″ and B̃(2)A' ← Ã(2)A' laser-induced fluorescence spectra of jet-cooled cyclohexoxy radical (c-C6H11O) [ Zu, L.; Liu, J.; Tarczay, G.; Dupré, P; Miller, T. A. Jet-cooled laser spectroscopy of the cyclohexoxy radical. J. Chem. Phys. 2004 , 120 , 10579 ] has been analyzed and simulated using a spectroscopic model that includes the coupling between the nearly degenerate X̃ and Ã states separated by ΔE. The rotational and fine structure of these two states is reproduced by a 2-fold model using one set of molecular constants including rotational constants, spin-rotation constants (ε's), the Coriolis constant (Aζt), the quenched spin-orbit constant (aζed), and the vibronic energy separation between the two states (ΔE0). The energy level structure of both states can also be reproduced using an isolated-state asymmetric top model with rotational constants and effective spin-rotation constants (ε's) and without involving Coriolis and spin-orbit constants. However, the spin-orbit interaction introduces transitions that have no intensity using the isolated-state model but appear in the observed spectra. The line intensities are well simulated using the 2-fold model with an out-of-plane (b-) transition dipole moment for the B̃ ← X̃ transitions and in-plane (a and c) transition dipole moment for the B̃ ← Ã transitions, requiring the symmetry for the X̃ (Ã) state to be A″ (A'), which is consistent with a previous determination and opposite to that of isopropoxy, the smallest secondary alkoxy radical. The experimentally determined Ã-X̃ separation and the energy level ordering of these two states with different (A' and A″) symmetries are consistent with quantum chemical calculations. The 2-fold model also enables the independent determination of the two contributions to the Ã-X̃ separation: the relativistic spin-orbit interaction (magnetic effect) and the nonrelativistic vibronic separation between the lowest vibrational energy levels of these two states due to both electrostatic interaction (Coulombic effect) and difference in zero-point energies (kinetic effect).
MHD Simulation for Investigating the Dynamic State Transition Responsible for a Solar Eruption in Active Region 12158

NASA Astrophysics Data System (ADS)

Lee, Hwanhee; Magara, Tetsuya

2018-06-01

We present a magnetohydrodynamic model of solar eruption based on the dynamic state transition from the quasi-static state to the eruptive state of an active region (AR) magnetic field. For the quasi-static state before an eruption, we consider the existence of a slow solar wind originating from an AR, which may continuously make the AR magnetic field deviate from mechanical equilibrium. In this model, we perform a three-dimensional magnetohydrodynamic simulation of AR 12158 producing a coronal mass ejection, where the initial magnetic structure of the simulation is given by a nonlinear force-free field derived from an observed photospheric vector magnetic field. We then apply a pressure-driven outflow to the upper part of the magnetic structure to achieve a quasi-static pre-eruptive state. The simulation shows that the eruptive process observed in this AR may be caused by the dynamic state transition of an AR magnetic field, which is essentially different from the destabilization of a static magnetic field. The dynamic state transition is determined from the shape evolution of the magnetic field line according to the κH-mechanism. This work demonstrates how the mechanism works to produce a solar eruption in the dynamic solar corona governed by the gravitational field and the continuous outflows of solar wind.
27Al-NMR studies of the structural phase transition in LaPd2Al2

NASA Astrophysics Data System (ADS)

Aoyama, Taisuke; Kobayashi, Fumiaki; Kotegawa, Hisashi; Tou, Hideki; Doležal, Petr; Kriegner, Dominik; Javorský, Pavel; Uhlířová, Klára

2018-05-01

We performed 27Al-NMR measurements for the CaBe2Ge2 type single crystalline LaPd2Al2 in the temperature range from 100 K to 5 K to investigate the origin of the structural phase transition. We found that the line profile of the 27Al-NMR spectrum does not change entirely on passing through the structural phase transition at Tst. Meanwhile, the peak position of the central line slightly change (≈ 30 ppm) below 70 K, suggesting the orbital shift changes below Tst. The present 27Al-NMR studies evidence that the local electronic state at Al site is hardly affected by the structural phase transition.
Toward a social justice theory of demographic transition: lessons from India's Kerala State.

PubMed

Ratcliffe, J W

1983-06-01

Recent research evidence, which suggests that observed demographic trends and patterns are largely consequences of broad structural changes in society, has raised serious doubts about the validity of traditional demographic theory and the framework for action it has generated. This theoretical essay 1st recasts classical demographic transition theory in general systems terms in order to make it consistent with the evidence and to place the processes of fertility and mortality in a larger social context. The demographic transition experience of Kerala State, India is then recounted to provide a concrete example of the demographic response in society to structural reforms based primarily on equity considerations.
Structural and electronic properties of the transition layer at the SiO{sub 2}/4H-SiC interface

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

Li, Wenbo; Wang, Dejun, E-mail: dwang121@dlut.edu.cn; Zhao, Jijun

Using first-principles methods, we generate an amorphous SiO{sub 2}/4H-SiC interface with a transition layer. Based this interface model, we investigate the structural and electronic properties of the interfacial transition layer. The calculated Si 2p core-level shifts for this interface are comparable to the experimental data, indicating that various SiC{sub x}O{sub y} species should be present in this interface transition layer. The analysis of the electronic structures reveals that the tetrahedral SiC{sub x}O{sub y} structures cannot introduce any of the defect states at the interface. Interestingly, our transition layer also includes a C-C=C trimer and SiO{sub 5} configurations, which lead tomore » the generation of interface states. The accurate positions of Kohn-Sham energy levels associated with these defects are further calculated within the hybrid functional scheme. The Kohn-Sham energy levels of the carbon trimer and SiO{sub 5} configurations are located near the conduction and valence band of bulk 4H-SiC, respectively. The result indicates that the carbon trimer occurred in the transition layer may be a possible origin of near interface traps. These findings provide novel insight into the structural and electronic properties of the realistic SiO{sub 2}/SiC interface.« less
Speeding Up Sigmatropic Shifts-To Halve or to Hold.

PubMed

Tantillo, Dean J

2016-04-19

Catalysis is common. Rational catalyst design, however, is at the frontier of chemical science. Although the histories of physical organic and synthetic organic chemistry boast key chapters involving [3s,3s] sigmatropic shifts, catalysis of these reactions is much less common than catalysis of ostensibly more complex processes. The comparative dearth of catalysts for sigmatropic shifts is perhaps a result of the perception that transition state structures for these reactions, like their reactants, are nonpolar and therefore not amenable to selective stabilization and its associated barrier lowering. However, as demonstrated in this Account, transition state structures for [3s,3s] sigmatropic shifts can in fact have charge distributions that differ significantly from those of reactants, even for hydrocarbon substrates, allowing for barriers to be decreased and rates increased. In some cases, differences in charge distribution result from the inclusion of heteroatoms at specific positions in reactants, but in other cases differences are actually induced by catalysts. Perhaps surprisingly, strategies for complexation of transition state structures that remain nonpolar are also possible. In general, the strategies for catalysis employed can be characterized as involving either mechanistic intervention, where a catalyst induces a change from the concerted mechanism expected for a [3s,3s] sigmatropic shift to a multistep process (cutting the transformation into halves or smaller pieces) whose overall barrier is decreased relative to the concerted process, or transition state complexation, where a catalyst simply binds (holds) more tightly to the transition state structure for a [3s,3s] sigmatropic shift than to the reactant, leading to a lower barrier in the presence of the catalyst. Both of these strategies can be considered to be biomimetic in that enzymes frequently induce multistep processes and utilize selective transition state stabilization for the steps involved. In addition, transition state complexation was the principle around which catalytic antibodies were originally designed. The field of catalysis of sigmatropic shifts is now ready for rational design. The studies described here all provide evidence for the origins of rate acceleration, derived in large part from the results of quantum chemical calculations, that can now be applied to the design of new catalysts for [3s,3s] and other sigmatropic shifts.
Gated access to the pore of a P2X receptor: structural implications for closed-open transitions.

PubMed

Kracun, Sebastian; Chaptal, Vincent; Abramson, Jeff; Khakh, Baljit S

2010-03-26

P2X receptors are ligand-gated cation channels that transition from closed to open states upon binding ATP. The crystal structure of the closed zebrafish P2X4.1 receptor directly reveals that the ion-conducting pathway is formed by three transmembrane domain 2 (TM2) alpha-helices, each being provided by the three subunits of the trimer. However, the transitions in TM2 that accompany channel opening are incompletely understood and remain unresolved. In this study, we quantified gated access to Cd(2+) at substituted cysteines in TM2 of P2X2 receptors in the open and closed states. Our data for the closed state are consistent with the zebrafish P2X4.1 structure, with isoleucines and threonines (Ile-332 and Thr-336) positioned one helical turn apart lining the channel wall on approach to the gate. Our data for the open state reveal gated access to deeper parts of the pore (Thr-339, Val-343, Asp-349, and Leu-353), suggesting the closed channel gate is between Thr-336 and Thr-339. We also found unexpected interactions between native Cys-348 and D349C that result in tight Cd(2+) binding deep within the intracellular vestibule in the open state. Interpreted with a P2X2 receptor structural model of the closed state, our data suggest that the channel gate opens near Thr-336/Thr-339 and is accompanied by movement of the pore-lining regions, which narrow toward the cytosolic end of TM2 in the open state. Such transitions would relieve the barrier to ion flow and render the intracellular vestibule less splayed during channel opening in the presence of ATP.
Study of transitional doubly-odd /sup 186/Ir and /sup 184/Ir

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

Ben Braham, A.; Bourgeois, C.; Kilcher, P.

1987-12-10

The transitional doubly-odd iridium nuclei with A = 184 and 186 have been studied from the ..beta../sup +//EC decay of the corresponding platinum isotopes using the on-line mass separator ISOCELE. Configurations can be reasonably Attributed to the low-lying states of /sup 184/Ir in agreement with results already known. On the other hand an E3 transition observed in /sup 186/Ir suggests that the known long-lived 1.7h 2/sup -/ state is located at 137.5 keV above the 16h 5/sup +/ state, raising questions about structure of this latter state.
Spectroscopic Studies on Unfolding Processes of Apo-Neuroglobin Induced by Guanidine Hydrochloride and Urea

PubMed Central

Zhang, Cui; Gao, Chaohui; Qiu, Zhanglei

2013-01-01

Neuroglobin (Ngb), a recently discovered globin, is predominantly expressed in the brain, retina, and other nerve tissues of vertebrates. The unfolding processes of apo-neuroglobin (apoNgb) induced by guanidine hydrochloride (GdnHCl) and urea were investigated by spectroscopic methods. In the unfolding processes, apoNgb's tertiary structural transition was monitored by the changes of intrinsic fluorescence emission spectra, and its secondary structural transition was measured by the changes of far-ultraviolet circular dichroism (CD) spectra. In addition, 8-anilino-1-naphthalenesulfonic acid (ANS), a hydrophobic cluster binding dye, was also used to monitor the unfolding process of apoNgb and to explore its intermediates. Results showed that GdnHCl-induced unfolding of apoNgb was via a three-state pathway, that is, Native state (N) → Intermediate state (I) → Unfolded state (U), during which the intermediate was inferred by an increase in fluorescence intensity and the change of CD value. Gibbs free energy changes are 10.2 kJ·mol−1 for the first unfolding transition and 14.0 kJ·mol−1 for the second transition. However, urea-induced unfolding of apoNgb only underwent a two-state transition: Native state (N) → Partially unfolded state (P). The result showed that GdnHCl can efficiently affect the conformational states of apoNgb compared with those of urea. The work will benefit to have an understanding of the unfolding mechanism of apoNgb induced by GdnHCl and urea. PMID:23984347
Role of Entropy and Structural Parameters in the Spin State Transition of LaCoO3

NASA Astrophysics Data System (ADS)

Chakrabarti, Bismayan; Birol, Turan; Haule, Kristjan

The spin state transition in LaCoO3 has eluded description for decades despite concerted theoretical and experimental effort. In this study, we approach this problem using fully charge consistent Density Functional Theory + Dynamical Mean Field Theory (DFT+DMFT). We show, from first principles, that LaCoO3 cannot be described by a single, pure spin state at any temperature, but instead shows a gradual change in the population of higher spin multiples as temperature is increased. We explicitly elucidate the critical role of the lattice expansion and oxygen octahedral rotations in the spin state transition. We also show that the spin state transition and the metal-insulator transition in the compound occur at different temperatures. In addition, our results shed light on the importance of electronic entropy, which has so far been ignored in all first principles studies of this material.
Optimal trajectories of brain state transitions

PubMed Central

Gu, Shi; Betzel, Richard F.; Mattar, Marcelo G.; Cieslak, Matthew; Delio, Philip R.; Grafton, Scott T.; Pasqualetti, Fabio; Bassett, Danielle S.

2017-01-01

The complexity of neural dynamics stems in part from the complexity of the underlying anatomy. Yet how white matter structure constrains how the brain transitions from one cognitive state to another remains unknown. Here we address this question by drawing on recent advances in network control theory to model the underlying mechanisms of brain state transitions as elicited by the collective control of region sets. We find that previously identified attention and executive control systems are poised to affect a broad array of state transitions that cannot easily be classified by traditional engineering-based notions of control. This theoretical versatility comes with a vulnerability to injury. In patients with mild traumatic brain injury, we observe a loss of specificity in putative control processes, suggesting greater susceptibility to neurophysiological noise. These results offer fundamental insights into the mechanisms driving brain state transitions in healthy cognition and their alteration following injury. PMID:28088484
Investigation of a Structural Phase Transition and Magnetic Structure of Na 2BaFe(VO 4) 2: A Triangular Magnetic Lattice with a Ferromagnetic Ground State

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

Sanjeewa, Liurukara D.; Garlea, Vasile O.; McGuire, Michael A.

The structural and magnetic properties of a glaserite-type Na 2BaFe(VO 4) 2 compound, featuring a triangular magnetic lattice of Fe 2+ (S = 2), are reported. Temperature dependent X-ray single crystal studies indicate that at room temperature the system adopts a trigonal Pmore » $$\\bar{3}$$ m1 structure and undergoes a structural phase transition to a C2/c monoclinic phase slightly below room temperature (T s = 288 K). This structural transition involves a tilting of Fe–O–V bond angles and strongly influences the magnetic correlation within the Fe triangular lattice. The magnetic susceptibility measurements reveal a ferromagnetic transition near 7 K. Single crystal neutron diffraction confirms the structural distortion and the ferromagnetic spin ordering in Na 2BaFe(VO 4) 2. The magnetic structure of the ordered state is modeled in the magnetic space group C2'/c' that implies a ferromagnetic order of the a and c moment components and antiferromagnetic arrangement for the b components. Altogether, the Fe magnetic moments form ferromagnetic layers that are stacked along the c-axis, where the spins point along one of the (111) facets of the FeO 6 octahedron.« less
Investigation of a Structural Phase Transition and Magnetic Structure of Na 2BaFe(VO 4) 2: A Triangular Magnetic Lattice with a Ferromagnetic Ground State

DOE PAGES

Sanjeewa, Liurukara D.; Garlea, Vasile O.; McGuire, Michael A.; ...

2017-12-07

The structural and magnetic properties of a glaserite-type Na 2BaFe(VO 4) 2 compound, featuring a triangular magnetic lattice of Fe 2+ (S = 2), are reported. Temperature dependent X-ray single crystal studies indicate that at room temperature the system adopts a trigonal Pmore » $$\\bar{3}$$ m1 structure and undergoes a structural phase transition to a C2/c monoclinic phase slightly below room temperature (T s = 288 K). This structural transition involves a tilting of Fe–O–V bond angles and strongly influences the magnetic correlation within the Fe triangular lattice. The magnetic susceptibility measurements reveal a ferromagnetic transition near 7 K. Single crystal neutron diffraction confirms the structural distortion and the ferromagnetic spin ordering in Na 2BaFe(VO 4) 2. The magnetic structure of the ordered state is modeled in the magnetic space group C2'/c' that implies a ferromagnetic order of the a and c moment components and antiferromagnetic arrangement for the b components. Altogether, the Fe magnetic moments form ferromagnetic layers that are stacked along the c-axis, where the spins point along one of the (111) facets of the FeO 6 octahedron.« less
Nonequilibrium transitions in complex networks: A model of social interaction

NASA Astrophysics Data System (ADS)

Klemm, Konstantin; Eguíluz, Víctor M.; Toral, Raúl; San Miguel, Maxi

2003-02-01

We analyze the nonequilibrium order-disorder transition of Axelrod’s model of social interaction in several complex networks. In a small-world network, we find a transition between an ordered homogeneous state and a disordered state. The transition point is shifted by the degree of spatial disorder of the underlying network, the network disorder favoring ordered configurations. In random scale-free networks the transition is only observed for finite size systems, showing system size scaling, while in the thermodynamic limit only ordered configurations are always obtained. Thus, in the thermodynamic limit the transition disappears. However, in structured scale-free networks, the phase transition between an ordered and a disordered phase is restored.
Effects of Catalytic Action and Ligand Binding on Conformational Ensembles of Adenylate Kinase.

PubMed

Onuk, Emre; Badger, John; Wang, Yu Jing; Bardhan, Jaydeep; Chishti, Yasmin; Akcakaya, Murat; Brooks, Dana H; Erdogmus, Deniz; Minh, David D L; Makowski, Lee

2017-08-29

Crystal structures of adenylate kinase (AdK) from Escherichia coli capture two states: an "open" conformation (apo) obtained in the absence of ligands and a "closed" conformation in which ligands are bound. Other AdK crystal structures suggest intermediate conformations that may lie on the transition pathway between these two states. To characterize the transition from open to closed states in solution, X-ray solution scattering data were collected from AdK in the apo form and with progressively increasing concentrations of five different ligands. Scattering data from apo AdK are consistent with scattering predicted from the crystal structure of AdK in the open conformation. In contrast, data from AdK samples saturated with Ap5A do not agree with that calculated from AdK in the closed conformation. Using cluster analysis of available structures, we selected representative structures in five conformational states: open, partially open, intermediate, partially closed, and closed. We used these structures to estimate the relative abundances of these states for each experimental condition. X-ray solution scattering data obtained from AdK with AMP are dominated by scattering from AdK in the open conformation. For AdK in the presence of high concentrations of ATP and ADP, the conformational ensemble shifts to a mixture of partially open and closed states. Even when AdK is saturated with Ap5A, a significant proportion of AdK remains in a partially open conformation. These results are consistent with an induced-fit model in which the transition of AdK from an open state to a closed state is initiated by ATP binding.
Transition state analysis of Trypanosoma cruzi uridine phosphorylase-catalyzed arsenolysis of uridine

PubMed Central

Silva, Rafael G.; Vetticatt, Mathew J.; Merino, Emilio F.; Cassera, Maria B.; Schramm, Vern L.

2011-01-01

Uridine phosphorylase catalyzes the reversible phosphorolysis of uridine and 2′-deoxyuridine to generate uracil and (2-deoxy)ribose 1-phosphate, an important step in the pyrimidine salvage pathway. The coding sequence annotated as a putative nucleoside phosphorylase in the Trypanosoma cruzi genome was overexpressed in Escherichia coli, purified to homogeneity, and shown to be a homodimeric uridine phosphorylase, with similar specificity for uridine and 2′-deoxyuridine, and undetectable activity towards thymidine and purine nucleosides. Competitive kinetic isotope effects (KIEs) were measured and corrected for a forward commitment factor using arsenate as the nucleophile. The intrinsic KIEs are: 1′-14C = 1.103, 1,3-15N2 = 1.034, 3-15N = 1.004, 1-15N = 1.030, 1′-3H = 1.132, 2′-2H = 1.086 and 5′-3H2 = 1.041 for this reaction. Density functional theory was employed to quantitatively interpret the KIEs in terms of transition state structure and geometry. Matching of experimental KIEs to proposed transition state structures suggests an almost synchronous, SN2-like transition state model, in which the ribosyl moiety possesses significant bond order to both nucleophile and leaving group. Natural bond orbital analysis allowed a comparison of the charge distribution pattern between the ground state and the transition state model. PMID:21599004
Optical study of phase transitions in single-crystalline RuP

NASA Astrophysics Data System (ADS)

Chen, R. Y.; Shi, Y. G.; Zheng, P.; Wang, L.; Dong, T.; Wang, N. L.

2015-03-01

RuP single crystals of MnP-type orthorhombic structure were synthesized by the Sn flux method. Temperature-dependent x-ray diffraction measurements reveal that the compound experiences two structural phase transitions, which are further confirmed by enormous anomalies shown in temperature-dependent resistivity and magnetic susceptibility. Particularly, the resistivity drops monotonically upon temperature cooling below the second transition, indicating that the material shows metallic behavior, in sharp contrast with the insulating ground state of polycrystalline samples. Optical conductivity measurements were also performed in order to unravel the mechanism of these two transitions. The measurement revealed a sudden reconstruction of band structure over a broad energy scale and a significant removal of conducting carriers below the first phase transition, while a charge-density-wave-like energy gap opens below the second phase transition.
Pressure Induced Liquid-to-Liquid Transition in Zr-based Supercooled Melts and Pressure Quenched Glasses.

PubMed

Dmowski, W; Gierlotka, S; Wang, Z; Yokoyama, Y; Palosz, B; Egami, T

2017-07-26

Through high-energy x-ray diffraction and atomic pair density function analysis we find that Zr-based metallic alloy, heated to the supercooled liquid state under hydrostatic pressure and then quenched to room temperature, exhibits a distinct glassy structure. The PDF indicates that the Zr-Zr distances in this glass are significantly reduced compared to those quenched without pressure. Annealing at the glass transition temperature at ambient pressure reverses structural changes and the initial glassy state is recovered. This result suggests that pressure causes a liquid-to-liquid phase transition in this metallic alloy supercooled melt. Such a pressure induced transition is known for covalent liquids, but has not been observed for metallic liquids. The High Pressure Quenched glasses are stable in ambient conditions after decompression.
Direct Simulation and Theoretical Study of Sub- and Supersonic Wakes

NASA Astrophysics Data System (ADS)

Hickey, Jean-Pierre

Wakes are constitutive components of engineering, aeronautical and geophysical flows. Despite their canonical nature, many fundamental questions surrounding wakes remain unanswered. The present work studies the nature of archetypal planar splitter-plate wakes in the sub- and supersonic regimes from a theoretical as well as a numerical perspective. A highly-parallelizable computational fluid dynamic solver was developed, from scratch, for the very-large scale direct numerical simulations of high-speed free shear flows. Wakes maintain a near indelible memory of their origins; thus, changes to the state of the flow on the generating body lead to multiple self-similar states in the far wake. To understand the source of the lack of universality, three distinct wake evolution scenarios are investigated in the incompressible limit: the Kelvin-Helmholtz transition, the bypass transition in an asymmetric wake and the initially turbulent wake. The multiplicity of self-similar states is the result of a plurality of far wake structural organizations, which maintains the memory of the flow. The structural organization is predicated on the presence or absence of near wake anti-symmetric perturbations (as a result of shedding, instability modes and/or trailing edge receptivity). The plurality of large-scale structural organization contrasts with the commonality observed in the mid-sized structures, which are dominated by inclined vortical rods, and not, as previously assumed, by horseshoe structures. The compressibility effects are a direct function of the maximal velocity defect in the wake and are therefore only important in the transitional region - the far wake having an essentially incompressible character. The compressibility simultaneously modifies the growth rate and wavelength of the primary instability mode with a concomitant effect on the emerging transitional structures. As a direct result, the spanwise rollers have an increasing ellipticity and cross-wake domain of influence with the increasing Mach number of the wake. Consequently, structural pairing - a key feature of wake transition - is inhibited at a critical Mach number, which greatly modifies the transitional dynamics. In idealized wakes, the increased stability caused by the compressibility effects leads to a vortex breakdown of secondary structures prior to the full transition of the principal mode. These findings open the door to novel mixing enhancement and flow control possibilities in the high-speed wake transition. Keywords: FLUID DYNAMICS, DIRECT NUMERICAL SIMULATIONS, FREE SHEAR FLOWS, TURBULENCE, NUMERICAL METHODS

The ground state of the Frenkel-Kontorova model

NASA Astrophysics Data System (ADS)

Babushkin, A. Yu.; Abkaryan, A. K.; Dobronets, B. S.; Krasikov, V. S.; Filonov, A. N.

2016-09-01

The continual approximation of the ground state of the discrete Frenkel-Kontorova model is tested using a symmetric algorithm of numerical simulation. A "kaleidoscope effect" is found, which means that the curves representing the dependences of the relative extension of an N-atom chain vary periodically with increasing N. Stairs of structural transitions for N ≫ 1 are analyzed by the channel selection method with the approximation N = ∞. Images of commensurable and incommensurable structures are constructed. The commensurable-incommensurable phase transitions are stepwise.
Half-Metallic Ferromagnetism and Stability of Transition Metal Pnictides and Chalcogenides

NASA Astrophysics Data System (ADS)

Liu, Bang-Gui

It is highly desirable to explore robust half-metallic ferromagnetic materials compatible with important semiconductors for spintronic applications. A state-of-the-art full potential augmented plane wave method within the densityfunctional theory is reliable enough for this purpose. In this chapter we review theoretical research on half-metallic ferromagnetism and structural stability of transition metal pnictides and chalcogenides. We show that some zincblende transition metal pnictides are half-metallic and the half-metallic gap can be fairly wide, which is consistent with experiment. Systematic calculations reveal that zincblende phases of CrTe, CrSe, and VTe are excellent half-metallic ferromagnets. These three materials have wide half-metallic gaps, are low in total energy with respect to the corresponding ground-state phases, and, importantly, are structurally stable. Halfmetallic ferromagnetism is also found in wurtzite transition metal pnictides and chalcogenides and in transition-metal doped semiconductors as well as deformed structures. Some of these half-metallic materials could be grown epitaxially in the form of ultrathin .lms or layers suitable for real spintronic applications.
LaCu6-xAgx : A promising host of an elastic quantum critical point

NASA Astrophysics Data System (ADS)

Poudel, L.; Cruz, C. de la; Koehler, M. R.; McGuire, M. A.; Keppens, V.; Mandrus, D.; Christianson, A. D.

2018-05-01

Structural properties of LaCu6-xAgx have been investigated using neutron and x-ray diffraction, and resonant ultrasound spectroscopy (RUS) measurements. Diffraction measurements indicate a continuous structural transition from orthorhombic (Pnma) to monoclinic (P21 / c) structure. RUS measurements show softening of natural frequencies at the structural transition, consistent with the elastic nature of the structural ground state. The structural transition temperatures in LaCu6-xAgx decrease with Ag composition until the monoclinic phase is completely suppressed at xc = 0.225 . All of the evidence is consistent with the presence of an elastic quantum critical point in LaCu6-xAgx .
LaCu 6-xAg x: A promising host of an elastic quantum critical point

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

Poudel, Lekh; Dela Cruz, Clarina R.; Koehler, Michael R.

Structural properties of LaCu 6-xAg x have been investigated using neutron and x-ray diffraction, and resonant ultrasound spectroscopy (RUS) measurements. Diffraction measurements indicate a continuous structural transition from orthorhombic (Pnma) to monoclinic (P2₁/C) structure. RUS measurements show softening of natural frequencies at the structural transition, consistent with the elastic nature of the structural ground state. The structural transition temperatures in LaCu 6-xAg x decrease with Ag composition until the monoclinic phase is completely suppressed at x c=0.225. All of the evidence is consistent with the presence of an elastic quantum critical point in LaCu 6-xAg x.
The American Experience in the Transition from Vocational Schools to Work: A Report to the United Nations Education, Scientific, and Cultural Organization. International Symposium on Problems of Transition from Technical and Vocational Schools to Work (Berlin, German Democratic Republic, 14-18 April, 1980).

ERIC Educational Resources Information Center

Dunham, Daniel B.

This paper discusses the central problems and issues of the transition from school to worklife in the United States. Developed from a framework which outlines the structure of the education system and the place of vocational-technical education within it, the paper addresses measures the United States has taken to facilitate the transition from…
Strain tuning of electronic structure in Bi 4Ti 3O 12-LaCoO 3 epitaxial thin films

DOE PAGES

Choi, Woo Seok; Lee, Ho Nyung

2015-05-08

In this study, we investigated the crystal and electronic structures of ferroelectric Bi 4Ti 3O 12 single-crystalline thin films site-specifically substituted with LaCoO 3 (LCO). The epitaxial films were grown by pulsed laser epitaxy on NdGaO 3 and SrTiO 3 substrates to vary the degree of strain. With increasing the LCO substitution, we observed a systematic increase in the c-axis lattice constant of the Aurivillius phase related with the modification of pseudo-orthorhombic unit cells. These compositional and structural changes resulted in a systematic decrease in the band gap, i.e., the optical transition energy between the oxygen 2p and transition-metal 3dmore » states, based on a spectroscopic ellipsometry study. In particular, the Co 3d state seems to largely overlap with the Ti t 2g state, decreasing the band gap. Interestingly, the applied tensile strain facilitates the band-gap narrowing, demonstrating that epitaxial strain is a useful tool to tune the electronic structure of ferroelectric transition-metal oxides.« less
Automated Transition State Search and Its Application to Diverse Types of Organic Reactions.

PubMed

Jacobson, Leif D; Bochevarov, Art D; Watson, Mark A; Hughes, Thomas F; Rinaldo, David; Ehrlich, Stephan; Steinbrecher, Thomas B; Vaitheeswaran, S; Philipp, Dean M; Halls, Mathew D; Friesner, Richard A

2017-11-14

Transition state search is at the center of multiple types of computational chemical predictions related to mechanistic investigations, reactivity and regioselectivity predictions, and catalyst design. The process of finding transition states in practice is, however, a laborious multistep operation that requires significant user involvement. Here, we report a highly automated workflow designed to locate transition states for a given elementary reaction with minimal setup overhead. The only essential inputs required from the user are the structures of the separated reactants and products. The seamless workflow combining computational technologies from the fields of cheminformatics, molecular mechanics, and quantum chemistry automatically finds the most probable correspondence between the atoms in the reactants and the products, generates a transition state guess, launches a transition state search through a combined approach involving the relaxing string method and the quadratic synchronous transit, and finally validates the transition state via the analysis of the reactive chemical bonds and imaginary vibrational frequencies as well as by the intrinsic reaction coordinate method. Our approach does not target any specific reaction type, nor does it depend on training data; instead, it is meant to be of general applicability for a wide variety of reaction types. The workflow is highly flexible, permitting modifications such as a choice of accuracy, level of theory, basis set, or solvation treatment. Successfully located transition states can be used for setting up transition state guesses in related reactions, saving computational time and increasing the probability of success. The utility and performance of the method are demonstrated in applications to transition state searches in reactions typical for organic chemistry, medicinal chemistry, and homogeneous catalysis research. In particular, applications of our code to Michael additions, hydrogen abstractions, Diels-Alder cycloadditions, carbene insertions, and an enzyme reaction model involving a molybdenum complex are shown and discussed.
Electronic transitions of tantalum monofluoride

NASA Astrophysics Data System (ADS)

Ng, K. F.; Zou, Wenli; Liu, Wenjian; Cheung, A. S.-C.

2017-03-01

The electronic transition spectrum of the tantalum monofluoride (TaF) molecule in the spectral region between 448 and 560 nm has been studied using the technique of laser-ablation/reaction free jet expansion and laser induced fluorescence spectroscopy. The TaF molecule was produced by reacting laser-ablated tantalum atoms with sulfur hexafluoride gas seeded in argon. Twenty-two vibrational bands with resolved rotational structure have been recorded and analyzed, which were organized into seven electronic transitions. The X3Σ-(0+) state has been identified to be the ground state and the determined equilibrium bond length, re, and vibrational frequency, ωe, are 1.8184 Å and 700.1 cm-1, respectively. The low-lying Λ-S states and Ω sub-states of TaF were also theoretically studied at the MRCISD+Q level of theory with spin-orbit coupling. The Ω = 0+ and 2 sub-states from the -3Σ and 3Φ state have been found to be the ground and the first excited states, respectively, which agrees well with our experimental determinations. This work represents the first experimental investigation of the molecular structure of the TaF molecule.
Transition probability spaces in loop quantum gravity

NASA Astrophysics Data System (ADS)

Guo, Xiao-Kan

2018-03-01

We study the (generalized) transition probability spaces, in the sense of Mielnik and Cantoni, for spacetime quantum states in loop quantum gravity. First, we show that loop quantum gravity admits the structures of transition probability spaces. This is exemplified by first checking such structures in covariant quantum mechanics and then identifying the transition probability spaces in spin foam models via a simplified version of general boundary formulation. The transition probability space thus defined gives a simple way to reconstruct the discrete analog of the Hilbert space of the canonical theory and the relevant quantum logical structures. Second, we show that the transition probability space and in particular the spin foam model are 2-categories. Then we discuss how to realize in spin foam models two proposals by Crane about the mathematical structures of quantum gravity, namely, the quantum topos and causal sites. We conclude that transition probability spaces provide us with an alternative framework to understand various foundational questions of loop quantum gravity.
Structural and topological phase transitions on the German Stock Exchange

NASA Astrophysics Data System (ADS)

Wiliński, M.; Sienkiewicz, A.; Gubiec, T.; Kutner, R.; Struzik, Z. R.

2013-12-01

We find numerical and empirical evidence for dynamical, structural and topological phase transitions on the (German) Frankfurt Stock Exchange (FSE) in the temporal vicinity of the worldwide financial crash. Using the Minimal Spanning Tree (MST) technique, a particularly useful canonical tool of the graph theory, two transitions of the topology of a complex network representing the FSE were found. The first transition is from a hierarchical scale-free MST representing the stock market before the recent worldwide financial crash, to a superstar-like MST decorated by a scale-free hierarchy of trees representing the market’s state for the period containing the crash. Subsequently, a transition is observed from this transient, (meta)stable state of the crash to a hierarchical scale-free MST decorated by several star-like trees after the worldwide financial crash. The phase transitions observed are analogous to the ones we obtained earlier for the Warsaw Stock Exchange and more pronounced than those found by Onnela-Chakraborti-Kaski-Kertész for the S&P 500 index in the vicinity of Black Monday (October 19, 1987) and also in the vicinity of January 1, 1998. Our results provide an empirical foundation for the future theory of dynamical, structural and topological phase transitions on financial markets.
Indicators of ecosystem function identify alternate states in the sagebrush steppe.

PubMed

Kachergis, Emily; Rocca, Monique E; Fernandez-Gimenez, Maria E

2011-10-01

Models of ecosystem change that incorporate nonlinear dynamics and thresholds, such as state-and-transition models (STMs), are increasingly popular tools for land management decision-making. However, few models are based on systematic collection and documentation of ecological data, and of these, most rely solely on structural indicators (species composition) to identify states and transitions. As STMs are adopted as an assessment framework throughout the United States, finding effective and efficient ways to create data-driven models that integrate ecosystem function and structure is vital. This study aims to (1) evaluate the utility of functional indicators (indicators of rangeland health, IRH) as proxies for more difficult ecosystem function measurements and (2) create a data-driven STM for the sagebrush steppe of Colorado, USA, that incorporates both ecosystem structure and function. We sampled soils, plant communities, and IRH at 41 plots with similar clayey soils but different site histories to identify potential states and infer the effects of management practices and disturbances on transitions. We found that many IRH were correlated with quantitative measures of functional indicators, suggesting that the IRH can be used to approximate ecosystem function. In addition to a reference state that functions as expected for this soil type, we identified four biotically and functionally distinct potential states, consistent with the theoretical concept of alternate states. Three potential states were related to management practices (chemical and mechanical shrub treatments and seeding history) while one was related only to ecosystem processes (erosion). IRH and potential states were also related to environmental variation (slope, soil texture), suggesting that there are environmental factors within areas with similar soils that affect ecosystem dynamics and should be noted within STMs. Our approach generated an objective, data-driven model of ecosystem dynamics for rangeland management. Our findings suggest that the IRH approximate ecosystem processes and can distinguish between alternate states and communities and identify transitions when building data-driven STMs. Functional indicators are a simple, efficient way to create data-driven models that are consistent with alternate state theory. Managers can use them to improve current model-building methods and thus apply state-and-transition models more broadly for land management decision-making.
Millimeter-Wave Spectroscopy, X-ray Crystal Structure, and Quantum Chemical Studies of Diketene: Resolving Ambiguities Concerning the Structure of the Ketene Dimer.

PubMed

Orr, Vanessa L; Esselman, Brian J; Dorman, P Matisha; Amberger, Brent K; Guzei, Ilia A; Woods, R Claude; McMahon, Robert J

2016-10-06

The pure rotational spectrum of diketene has been studied in the millimeter-wave region from ∼240 to 360 GHz. For the ground vibrational state and five vibrationally excited satellites (ν 24 , 2ν 24 , 3ν 24 , 4ν 24 , and ν 16 ), the observed spectrum allowed for the measurement, assignment, and least-squares fitting a total of more than 10 000 distinct rotational transitions. In each case, the transitions were fit to single-state, complete or near-complete sextic centrifugally distorted rotor models to near experimental error limits using Kisiel's ASFIT. Additionally, we obtained less satisfactory least-squares fits to single-state centrifugally distorted rotor models for three additional vibrational states: ν 24 + ν 16 , ν 23 , and 5ν 24 . The structure of diketene was optimized at the CCSD(T)/ANO1 level, and the vibration-rotation interaction (α i ) values for each normal mode were determined with a CCSD(T)/ANO1 VPT2 anharmonic frequency calculation. These α i values were helpful in identifying the previously unreported ν 16 and ν 23 fundamental states. We obtained a single-crystal X-ray structure of diketene at -173 °C. The bond distances are increased in precision by more than an order of magnitude compared to those in the 1958 X-ray crystal structure. The improved accuracy of the crystal structure geometry resolves the discrepancy between previous computational and experimental structures. The rotational transition frequencies provided herein should be useful for a millimeter-wave or terahertz search for diketene in the interstellar medium.
Current instability and burnout of HEMT structures

NASA Astrophysics Data System (ADS)

Vashchenko, V. A.; Sinkevitch, V. F.

1996-06-01

The burnout mechanism and region of high conductivity formation under breakdown of pseudomorphic GalnAs/GaAlAs and GaAs/GaAlAs HEMT structures have been studied in a pulsed and direct current (d.c.) regime. Peculiarities of the HEMT breakdown have been compared with a GaAs MESFET structure of the same topology. It appears that in all types of investigated structures the drain voltage increase is limited by the transition into a high conductivity state as a result of "parasitic" avalanche-injection conductivity modulation of the undoped GaAs or i-GaAs layer. It has been established that the transition into a high conductivity state is caused by holes from the drain avalanche region in the channel and is the result of a mutual intensification of the avalanche generation rate near the drain and the injection level from the source contact. It turns out that under a typical gate bias operation the transition in the high conductivity state is accompanied by a negative differential conductivity (NDC) and results in the formation of high current density filaments. The resulting high local overheating in the filament region is the cause of local melting and burnout of the HEMT structures.
Structural model of the open–closed–inactivated cycle of prokaryotic voltage-gated sodium channels

PubMed Central

Bagnéris, Claire; Naylor, Claire E.; McCusker, Emily C.

2015-01-01

In excitable cells, the initiation of the action potential results from the opening of voltage-gated sodium channels. These channels undergo a series of conformational changes between open, closed, and inactivated states. Many models have been proposed for the structural transitions that result in these different functional states. Here, we compare the crystal structures of prokaryotic sodium channels captured in the different conformational forms and use them as the basis for examining molecular models for the activation, slow inactivation, and recovery processes. We compare structural similarities and differences in the pore domains, specifically in the transmembrane helices, the constrictions within the pore cavity, the activation gate at the cytoplasmic end of the last transmembrane helix, the C-terminal domain, and the selectivity filter. We discuss the observed differences in the context of previous models for opening, closing, and inactivation, and present a new structure-based model for the functional transitions. Our proposed prokaryotic channel activation mechanism is then compared with the activation transition in eukaryotic sodium channels. PMID:25512599
Urea-temperature phase diagrams capture the thermodynamics of denatured state expansion that accompany protein unfolding

PubMed Central

Tischer, Alexander; Auton, Matthew

2013-01-01

We have analyzed the thermodynamic properties of the von Willebrand factor (VWF) A3 domain using urea-induced unfolding at variable temperature and thermal unfolding at variable urea concentrations to generate a phase diagram that quantitatively describes the equilibrium between native and denatured states. From this analysis, we were able to determine consistent thermodynamic parameters with various spectroscopic and calorimetric methods that define the urea–temperature parameter plane from cold denaturation to heat denaturation. Urea and thermal denaturation are experimentally reversible and independent of the thermal scan rate indicating that all transitions are at equilibrium and the van't Hoff and calorimetric enthalpies obtained from analysis of individual thermal transitions are equivalent demonstrating two-state character. Global analysis of the urea–temperature phase diagram results in a significantly higher enthalpy of unfolding than obtained from analysis of individual thermal transitions and significant cross correlations describing the urea dependence of and that define a complex temperature dependence of the m-value. Circular dichroism (CD) spectroscopy illustrates a large increase in secondary structure content of the urea-denatured state as temperature increases and a loss of secondary structure in the thermally denatured state upon addition of urea. These structural changes in the denatured ensemble make up ∼40% of the total ellipticity change indicating a highly compact thermally denatured state. The difference between the thermodynamic parameters obtained from phase diagram analysis and those obtained from analysis of individual thermal transitions illustrates that phase diagrams capture both contributions to unfolding and denatured state expansion and by comparison are able to decipher these contributions. PMID:23813497
Equation of State of Structured Matter at Finite Temperature

NASA Astrophysics Data System (ADS)

Maruyama, T.; Yasutake, N.; Tatsumi, T.

We investigate the properties of nuclear matter at the first-order phase transitions such as liquid-gas phase transition and hadron-quark phase transition. As a general feature of the first-order phase transitions of matter consisting of many species of charged particles, there appears a mixed phases with geometrical structures called ``pasta'' due to the balance of the Coulomb repulsion and the surface tension between two phases [G.~D.~Ravenhall, C.~J.~Pethick and J.~R.~Wilson, Phys. Rev. Lett. 50 (1983), 2066. M.~Hashimoto, H.~Seki and M.~Yamada, Prog. Theor. Phys. 71 (1984), 320.] The equation of state (EOS) of mixed phase is different from the one obtained by a bulk application of the Gibbs conditions or by the Maxwell construction due to the effects of the non-uniform structure. We show that the charge screening and strong surface tension make the EOS close to that of the Maxwell construction. The thermal effects are elucidated as well as the above finite-size effects.
Characterization of pH-sensitive molecular switches that trigger the structural transition of vesicular stomatitis virus glycoprotein from the postfusion state toward the prefusion state.

PubMed

Ferlin, Anna; Raux, Hélène; Baquero, Eduard; Lepault, Jean; Gaudin, Yves

2014-11-01

Vesicular stomatitis virus (VSV; the prototype rhabdovirus) fusion is triggered at low pH and mediated by glycoprotein G, which undergoes a low-pH-induced structural transition. A unique feature of rhabdovirus G is that its conformational change is reversible. This allows G to recover its native prefusion state at the viral surface after its transport through the acidic Golgi compartments. The crystal structures of G pre- and postfusion states have been elucidated, leading to the identification of several acidic amino acid residues, clustered in the postfusion trimer, as potential pH-sensitive switches controlling the transition back toward the prefusion state. We mutated these residues and produced a panel of single and double mutants whose fusion properties, conformational change characteristics, and ability to pseudotype a virus lacking the glycoprotein gene were assayed. Some of these mutations were also introduced in the genome of recombinant viruses which were further characterized. We show that D268, located in the segment consisting of residues 264 to 273, which refolds into postfusion helix F during G structural transition, is the major pH sensor while D274, D395, and D393 have additional contributions. Furthermore, a single passage of recombinant virus bearing the mutation D268L (which was demonstrated to stabilize the G postfusion state) resulted in a pseudorevertant with a compensatory second mutation, L271P. This revealed that the propensity of the segment of residues 264 to 273 to refold into helix F has to be finely tuned since either an increase (mutation D268L alone) or a decrease (mutation L271P alone) of this propensity is detrimental to the virus. Vesicular stomatitis virus enters cells via endocytosis. Endosome acidification induces a structural transition of its unique glycoprotein (G), which mediates fusion between viral and endosomal membranes. G conformational change is reversible upon increases in pH. This allows G to recover its native prefusion state at the viral surface after its transport through the acidic Golgi compartments. We mutated five acidic residues, proposed to be pH-sensitive switches controlling the structural transition back toward the prefusion state. Our results indicate that residue D268 is the major pH sensor, while other acidic residues have additional contributions, and reveal that the propensity of the segment consisting of residues 264 to 273 to adopt a helical conformation is finely regulated. This segment might be a good target for antiviral compounds. Copyright © 2014, American Society for Microbiology. All Rights Reserved.
Existence problem of proton semi-bubble structure in the 21 + state of 34Si

NASA Astrophysics Data System (ADS)

Wu, Feng; Bai, C. L.; Yao, J. M.; Zhang, H. Q.; Zhang, X. Z.

2017-09-01

The fully self-consistent Hartree-Fock (HF) plus random phase approximation (RPA) based on Skyrme-type interaction is used to study the existence problem of proton semi-bubble structure in the 21+ state of 34Si. The experimental excitation energy and the transition strength of the 21+ state in 34Si can be reproduced quite well. The tensor effect is also studied. It is shown that the tensor interaction has a notable impact on the excitation energy of the 21+ state and a small effect on the B( E2) value. Besides, its effect on the density distributions in the ground and 21+ state of 34Si is negligible. Our present results with T36 and T44 show that the 21+ state of 34Si is mainly caused by proton transition from π 1d_{5/2} orbit to π 2s_{1/2} orbit, and the existence of a proton semi-bubble structure in this state is very unlikely.
OPTICAL ABSORPTION SPECTRUM OF ANTIFERROMAGNETIC MNF2.

DTIC Science & Technology

separated in energy and easily identifiable, (3) has a very simple ground state, and (4) has a well studied magnon structure, an investigation was...undertaken of the excited states in the hope of observing other magnetic dipole transitions and their accompanying magnon sidebands. This study was...similarities between the magnon sidebands in several excited states of the Mn(+2) ion, and to determine the importance of spin assisted transitions in
Experimental Evidence for a Structural-Dynamical Transition in Trajectory Space.

PubMed

Pinchaipat, Rattachai; Campo, Matteo; Turci, Francesco; Hallett, James E; Speck, Thomas; Royall, C Patrick

2017-07-14

Among the key insights into the glass transition has been the identification of a nonequilibrium phase transition in trajectory space which reveals phase coexistence between the normal supercooled liquid (active phase) and a glassy state (inactive phase). Here, we present evidence that such a transition occurs in experiments. In colloidal hard spheres, we find a non-Gaussian distribution of trajectories leaning towards those rich in locally favored structures (LFSs), associated with the emergence of slow dynamics. This we interpret as evidence for a nonequilibrium transition to an inactive LFS-rich phase. Reweighting trajectories reveals a first-order phase transition in trajectory space between a normal liquid and a LFS-rich phase. We also find evidence for a purely dynamical transition in trajectory space.

Pressure Induced Liquid-to-Liquid Transition in Zr-based Supercooled Melts and Pressure Quenched Glasses

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

Dmowski, W.; Gierlotka, S.; Wang, Z.

Through high-energy x-ray diffraction and atomic pair density function analysis we find that Zr-based metallic alloy, heated to the supercooled liquid state under hydrostatic pressure and then quenched to room temperature, exhibits a distinct glassy structure. The PDF indicates that the Zr-Zr distances in this glass are significantly reduced compared to those quenched without pressure. Annealing at the glass transition temperature at ambient pressure reverses structural changes and the initial glassy state is recovered. This result suggests that pressure causes a liquid-to-liquid phase transition in this metallic alloy supercooled melt. Such a pressure induced transition is known for covalent liquids,more » but has not been observed for metallic liquids. The High Pressure Quenched glasses are stable in ambient conditions after decompression.« less
Relaxation mode analysis and Markov state relaxation mode analysis for chignolin in aqueous solution near a transition temperature

NASA Astrophysics Data System (ADS)

Mitsutake, Ayori; Takano, Hiroshi

2015-09-01

It is important to extract reaction coordinates or order parameters from protein simulations in order to investigate the local minimum-energy states and the transitions between them. The most popular method to obtain such data is principal component analysis, which extracts modes of large conformational fluctuations around an average structure. We recently applied relaxation mode analysis for protein systems, which approximately estimates the slow relaxation modes and times from a simulation and enables investigations of the dynamic properties underlying the structural fluctuations of proteins. In this study, we apply this relaxation mode analysis to extract reaction coordinates for a system in which there are large conformational changes such as those commonly observed in protein folding/unfolding. We performed a 750-ns simulation of chignolin protein near its folding transition temperature and observed many transitions between the most stable, misfolded, intermediate, and unfolded states. We then applied principal component analysis and relaxation mode analysis to the system. In the relaxation mode analysis, we could automatically extract good reaction coordinates. The free-energy surfaces provide a clearer understanding of the transitions not only between local minimum-energy states but also between the folded and unfolded states, even though the simulation involved large conformational changes. Moreover, we propose a new analysis method called Markov state relaxation mode analysis. We applied the new method to states with slow relaxation, which are defined by the free-energy surface obtained in the relaxation mode analysis. Finally, the relaxation times of the states obtained with a simple Markov state model and the proposed Markov state relaxation mode analysis are compared and discussed.
Deacylation transition states of a bacterial DD-peptidase.

PubMed

Adediran, S A; Kumar, I; Pratt, R F

2006-10-31

Beta-lactam antibiotics restrict bacterial growth by inhibiting DD-peptidases. These enzymes catalyze the final transpeptidation step in bacterial cell wall biosynthesis. Although much structural information is now available for these enzymes, the mechanism of the actual transpeptidation reaction has not been studied in detail. The reaction is known to involve a double-displacement mechanism with an acyl-enzyme intermediate, which can be attacked by water, specific amino acids, peptides, and other acyl acceptors. We describe in this paper an investigation of acyl acceptor specificity and assess the need for general base catalysis in the deacylation transition state of the Streptomyces R61 DD-peptidase. We show, by the criterion of solvent deuterium kinetic isotope effect measurements and proton inventories, that the transition states of specific and nonspecific substrates are very similar, at least with respect to proton motion. The transition states for attack (tetrahedral intermediate formation) by d-amino acids and Gly-l-Xaa dipeptides do not include a general base catalyst, while such catalysis is essential for reaction with water and d-alpha-hydroxy acids. D-Alpha-hydroxy acids act as acyl acceptors for glycyl substrates but not for more specific d-alanyl substrates; hydroxy acids actually behave, more generally, as mixed inhibitors of the DD-peptidase. The structural and mechanistic bases of these observations are discussed; they should inform transition state analogue design.
Enhanced conformational sampling technique provides an energy landscape view of large-scale protein conformational transitions.

PubMed

Shao, Qiang

2016-10-26

Large-scale conformational changes in proteins are important for their functions. Tracking the conformational change in real time at the level of a single protein molecule, however, remains a great challenge. In this article, we present a novel in silico approach with the combination of normal mode analysis and integrated-tempering-sampling molecular simulation (NMA-ITS) to give quantitative data for exploring the conformational transition pathway in multi-dimensional energy landscapes starting only from the knowledge of the two endpoint structures of the protein. The open-to-closed transitions of three proteins, including nCaM, AdK, and HIV-1 PR, were investigated using NMA-ITS simulations. The three proteins have varied structural flexibilities and domain communications in their respective conformational changes. The transition state structure in the conformational change of nCaM and the associated free-energy barrier are in agreement with those measured in a standard explicit-solvent REMD simulation. The experimentally measured transition intermediate structures of the intrinsically flexible AdK are captured by the conformational transition pathway measured here. The dominant transition pathways between the closed and fully open states of HIV-1 PR are very similar to those observed in recent REMD simulations. Finally, the evaluated relaxation times of the conformational transitions of three proteins are roughly at the same level as reported experimental data. Therefore, the NMA-ITS method is applicable for a variety of cases, providing both qualitative and quantitative insights into the conformational changes associated with the real functions of proteins.
Structure of vortices in superfluid 3He A-like phase in uniaxially stretched aerogel

NASA Astrophysics Data System (ADS)

Aoyama, Kazushi; Ikeda, Ryusuke

2009-02-01

Possible vortex-core transitions in A-like phase of superfluid 3He in uniaxially stretched aerogel are investigated. Since the global anisotropy in this system induces the polar pairing state in a narrow range close to the superfluid transition in addition to the A-like and B-like phases, the polar state may occur in the core of a vortex in the A-like phase identified with the ABM pairing state, like in the case of the bulk B phase where a core including the ABM state is realized at higher pressures. We examine the core structure of a single vortex under the boundary condition compatible with the Mermin-Ho vortex in the presence of the dipole interaction. Following Salomaa and Volovik's approach, we numerically solve the Ginzburg-Landau equation for an axially symmetric vortex and, by examining its stability against nonaxisymmetric perturbations, discuss possible vortex core states. It is found that a first order transition on core states may occur on warming from an axisymmetric vortex with a nonunitary core to a singular vortex with the polar core.
Localization-delocalization transition of electrons at the percolation threshold of semiconductor GaAs1-xNx alloys: The appearance of a mobility edge

NASA Astrophysics Data System (ADS)

Alberi, K.; Fluegel, B.; Beaton, D. A.; Ptak, A. J.; Mascarenhas, A.

2012-07-01

Electrons in semiconductor alloys have generally been described in terms of Bloch states that evolve from constructive interference of electron waves scattering from perfectly periodic potentials, despite the loss of structural periodicity that occurs on alloying. Using the semiconductor alloy GaAs1-xNx as a prototype, we demonstrate a localized to delocalized transition of the electronic states at a percolation threshold, the emergence of a mobility edge, and the onset of an abrupt perturbation to the host GaAs electronic structure, shedding light on the evolution of electronic structure in these abnormal alloys.
Intrinsic exciton-state mixing and nonlinear optical properties in transition metal dichalcogenide monolayers

NASA Astrophysics Data System (ADS)

Glazov, M. M.; Golub, L. E.; Wang, G.; Marie, X.; Amand, T.; Urbaszek, B.

2017-01-01

Optical properties of transition metal dichalcogenides monolayers are controlled by Wannier-Mott excitons forming a series of 1 s ,2 s ,2 p ,... hydrogen-like states. We develop the theory of the excited excitonic states energy spectrum fine structure. We predict that p - and s -shell excitons are mixed due to the specific D3 h point symmetry of the transition metal dichalcogenide monolayers. Hence, both s - and p -shell excitons are active in both single- and two-photon processes, providing an efficient mechanism of second harmonic generation. The corresponding contribution to the nonlinear susceptibility is calculated.
Structure and Inhibition of Quorum Sensing Target from Streptococcus pneumoniae

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

Singh,V.; Shi, W.; Almo, S.

2006-01-01

Streptococcus pneumoniae 5'-methylthioadenosine/S-adenosylhomocysteine hydrolase (MTAN) catalyzes the hydrolytic deadenylation of its substrates to form adenine and 5-methylthioribose or S-ribosylhomocysteine (SRH). MTAN is not found in mammals but is involved in bacterial quorum sensing. MTAN gene disruption affects the growth and pathogenicity of bacteria, making it a target for antibiotic design. Kinetic isotope effects and computational studies have established a dissociative S{sub N}1 transition state for Escherichia coli MTAN, and transition state analogues resembling the transition state are powerful inhibitors of the enzyme [Singh, V., Lee, J. L., Nunez, S., Howell, P. L., and Schramm, V. L. (2005) Biochemistry 44, 11647-11659].more » The sequence of MTAN from S. pneumoniae is 40% identical to that of E. coli MTAN, but S. pneumoniae MTAN exhibits remarkably distinct kinetic and inhibitory properties. 5'-Methylthio-Immucillin-A (MT-ImmA) is a transition state analogue resembling an early S{sub N}1 transition state. It is a weak inhibitor of S. pneumoniae MTAN with a K{sub i} of 1.0 {mu}M. The X-ray structure of S. pneumoniae MTAN with MT-ImmA indicates a dimer with the methylthio group in a flexible hydrophobic pocket. Replacing the methyl group with phenyl (PhT-ImmA), tolyl (p-TolT-ImmA), or ethyl (EtT-ImmA) groups increases the affinity to give K{sub i} values of 335, 60, and 40 nM, respectively. DADMe-Immucillins are geometric and electrostatic mimics of a fully dissociated transition state and bind more tightly than Immucillins. MT-DADMe-Immucillin-A inhibits with a K{sub i} value of 24 nM, and replacing the 5'-methyl group with p-Cl-phenyl (p-Cl-PhT-DADMe-ImmA) gave a K{sub i}* value of 0.36 nM. The inhibitory potential of DADMe-Immucillins relative to the Immucillins supports a fully dissociated transition state structure for S. pneumoniae MTAN. Comparison of active site contacts in the X-ray crystal structures of E. coli and S. pneumoniae MTAN with MT-ImmA would predict equal binding, yet most analogues bind 10{sup 3}-10{sup 4}-fold more tightly to the E. coli enzyme. Catalytic site efficiency is primarily responsible for this difference since k{sub cat}/K{sub m} for S. pneumoniae MTAN is decreased 845-fold relative to that of E. coli MTAN.« less
Band structure of the quasi two-dimensional purple molybdenum bronze

NASA Astrophysics Data System (ADS)

Guyot, H.; Balaska, H.; Perrier, P.; Marcus, J.

2006-09-01

The molybdenum purple bronze KMo 6O 17 is quasi two-dimensional (2D) metallic oxide that shows a Peierls transition towards a metallic charge density wave state. Since this specific transition is directly related to the electron properties of the normal state, we have investigated the electronic structure of this bronze at room temperature. The shape of the Mo K1s absorption edge reveals the presence of distorted MoO 6 octahedra in the crystallographic structure. Photoemission experiments evidence a large conduction band, with a bandwidth of 800 meV and confirm the metallic character of this bronze. A wide depleted zone separates the conduction band from the valence band that exhibits a fourfold structure, directly connected to the octahedral symmetry of the Mo sites. The band structure is determined by ARUPS in two main directions of the (0 0 1) Brillouin zone. It exhibits some unpredicted features but corroborates the earlier theoretical band structure and Fermi surface. It confirms the hidden one-dimensionality of KMo 6O 17 that has been proposed to explain the origin of the Peierls transition in this 2D compound.
Λ-enhanced grey molasses on the D2 transition of Rubidium-87 atoms.

PubMed

Rosi, Sara; Burchianti, Alessia; Conclave, Stefano; Naik, Devang S; Roati, Giacomo; Fort, Chiara; Minardi, Francesco

2018-01-22

Laser cooling based on dark states, i.e. states decoupled from light, has proven to be effective to increase the phase-space density of cold trapped atoms. Dark-states cooling requires open atomic transitions, in contrast to the ordinary laser cooling used for example in magneto-optical traps (MOTs), which operate on closed atomic transitions. For alkali atoms, dark-states cooling is therefore commonly operated on the D 1 transition nS 1/2 → nP 1/2 . We show that, for 87 Rb, thanks to the large hyperfine structure separations the use of this transition is not strictly necessary and that "quasi-dark state" cooling is efficient also on the D 2 line, 5S 1/2 → 5P 3/2 . We report temperatures as low as (4.0 ± 0.3) μK and an increase of almost an order of magnitude in the phase space density with respect to ordinary laser sub-Doppler cooling.
Pressure-induced quantum phase transition in the quantum antiferromagnet CsFeCl3

NASA Astrophysics Data System (ADS)

Hayashida, Shohei; Zaharko, Oksana; Kurita, Nobuyuki; Tanaka, Hidekazu; Hagihala, Masato; Soda, Minoru; Itoh, Shinichi; Uwatoko, Yoshiya; Masuda, Takatsugu

2018-04-01

We have studied the pressure-induced quantum phase transition in the singlet-ground-state antiferromagnet CsFeCl3. Neutron diffraction experiments under pressure evidence the magnetic long-range order at low temperatures. Magnetic structure analysis reveals a 120∘ structure with a propagation vector of kmag=(1 /3 ,1 /3 ,0 ) . The estimated critical exponent of the order parameter suggests that CsFeCl3 belongs to the universality class of U (1 ) ×Z2 symmetry which is expected to realize the chiral liquid state.
Separated oscillatory field microwave measurement of the n=2 3P1 to n=2 3P2 fine-structure interval of helium

NASA Astrophysics Data System (ADS)

Borbely, Joseph S.

2009-11-01

The fine-structure constant is a fundamental constant of nature that represents the strength of the coupling interaction between charged particles. Comparison of high-precision theory and high-precision experiment of the n=2 3PJ fine-structure intervals of helium will allow for a determination of the fine-structure constant. The 23P1(mJ=0)-to-23P 2(mJ=0) magnetic-dipole transition in helium is measured to be 2 291 177.53(35) kHz using Ramsey separated oscillatory fields. A thermal beam of 23S1 metastable helium atoms is produced in a DC discharge source and enters a chamber where a vertical DC magnetic field lifts the degeneracy of the mJ states. Initially, the 2 3S1(mJ=-1, 0, 1) states are equally populated. A linearly polarized 1083-nm diode laser drives the 23S 1(mJ=0) atoms up to the 23P0(m J=0) state, emptying the 23S1(mJ=0) state. A 15-ns laser pulse drives the 23S1(m J=+1)-to-23P1(mJ=0) transitions and this laser pulse is followed by two microwave pulses that drive the 2.29-GHz 23P1(mJ=0)-to-23P 2(mJ=0) transition. The atoms which undergo this microwave transition can spontaneously decay to the previously-emptied 23S 1(mJ=0) state. The 23P1(m J=0) state is forbidden to decay to the 23S1(m J=0) state since the transition has a zero electric-dipole matrix element. Therefore, any re-population of the 23S1(m J=0) state is a direct indication that the 2.29-GHz microwave transition has been driven. A linearly polarized 1083-nm diode laser detects the 2 3S1(mJ=0) atoms by exciting them up to the 2 3P0(mJ=0) state and the radiation from the resulting spontaneous decay is observed by focusing it onto a liquid-nitrogen-cooled InGaAs photodiode. The two microwave pulses are alternatively in phase or 180°out of phase and the difference of these signals versus microwave frequency leads to a Ramsey separated oscillatory field interference pattern.
The electronic structures of AlN and InN wurtzite nanowires

NASA Astrophysics Data System (ADS)

Xiong, Wen; Li, Dong-Xiao

2017-07-01

We derive the relations between the analogous seven Luttinger-Kohn parameters and six Rashba-Sheka-Pikus parameters for wurtzite semiconductors, which can be used to investigate the electronic structures of some wurtzite semiconductors such as AlN and InN materials, including their low-dimensional structures. As an example, the electronic structures of AlN and InN nanowires are calculated by using the derived relations and six-band effective-mass k · p theory. Interestingly, it is found that the ground hole state of AlN nanowires is always a pure S state whether the radius R is small (1 nm) or large (6 nm), and the ground hole state only contains | Z 〉 Bloch orbital component. Therefore, AlN nanowires is the ideal low-dimensional material for the production of purely linearly polarized π light, unlike ZnO nanowires, which emits plane-polarized σ light. However, the ground hole state of InN nanowires can be tuned from a pure S state to a mixed P state when the radius R is larger than 2.6 nm, which will make the polarized properties of the lowest optical transition changes from linearly polarized π light to plane-polarized σ light. Meanwhile, the valence band structures of InN nanowires will present strong band-crossings when the radius R increases to 6 nm, and through the detail analysis of possible transitions of InN nanowires at the Γ point, we find some of the neighbor optical transitions are almost degenerate, because the spin-orbit splitting energy of InN material is only 0.001 eV. Therefore, it is concluded that the electronic structures and optical properties of InN nanowires present great differences with that of AlN nanowires.
Radiationless Transitions and Excited-State Absorption in Tunable Laser Materials

DTIC Science & Technology

1992-09-01

chromium - doped halide elpasolites K2 NaGaF 6 , K2 NaScF6 and Cs2NaYCl 6 , and on the laser-active TI0 (l) color center in KCI. Luminescence lifetime...Non-radiative transitions, transition metals, chromium , ¶SLWmER o E tunable lasers, high pressure, luminescence, color centers ൙. SECURITY O...quenching and excited-state absorption are major loss mechanisms. Low-crystal-field chromium complexes in ordered perovskites of cubic elpasolite structure
Complex band structures of transition metal dichalcogenide monolayers with spin-orbit coupling effects

NASA Astrophysics Data System (ADS)

Szczęśniak, Dominik; Ennaoui, Ahmed; Ahzi, Saïd

2016-09-01

Recently, the transition metal dichalcogenides have attracted renewed attention due to the potential use of their low-dimensional forms in both nano- and opto-electronics. In such applications, the electronic and transport properties of monolayer transition metal dichalcogenides play a pivotal role. The present paper provides a new insight into these essential properties by studying the complex band structures of popular transition metal dichalcogenide monolayers (MX 2, where M = Mo, W; X = S, Se, Te) while including spin-orbit coupling effects. The conducted symmetry-based tight-binding calculations show that the analytical continuation from the real band structures to the complex momentum space leads to nonlinear generalized eigenvalue problems. Herein an efficient method for solving such a class of nonlinear problems is presented and yields a complete set of physically relevant eigenvalues. Solutions obtained by this method are characterized and classified into propagating and evanescent states, where the latter states manifest not only monotonic but also oscillatory decay character. It is observed that some of the oscillatory evanescent states create characteristic complex loops at the direct band gap of MX 2 monolayers, where electrons can directly tunnel between the band gap edges. To describe these tunneling currents, decay behavior of electronic states in the forbidden energy region is elucidated and their importance within the ballistic transport regime is briefly discussed.
Phase diagram of the ultrafast photoinduced insulator-metal transition in vanadium dioxide

NASA Astrophysics Data System (ADS)

Cocker, T. L.; Titova, L. V.; Fourmaux, S.; Holloway, G.; Bandulet, H.-C.; Brassard, D.; Kieffer, J.-C.; El Khakani, M. A.; Hegmann, F. A.

2012-04-01

We use time-resolved terahertz spectroscopy to probe the ultrafast dynamics of the insulator-metal phase transition induced by femtosecond laser pulses in a nanogranular vanadium dioxide (VO2) film. Based on the observed thresholds for characteristic transient terahertz dynamics, a phase diagram of critical pump fluence versus temperature for the insulator-metal phase transition in VO2 is established for the first time over a broad range of temperatures down to 17 K. We find that both Mott and Peierls mechanisms are present in the insulating state and that the photoinduced transition is nonthermal. We propose a critical-threshold model for the ultrafast photoinduced transition based on a critical density of electrons and a critical density of coherently excited phonons necessary for the structural transition to the metallic state. As a result, evidence is found at low temperatures for an intermediate metallic state wherein the Mott state is melted but the Peierls distortion remains intact, consistent with recent theoretical predictions. Finally, the observed terahertz conductivity dynamics above the photoinduced transition threshold reveal nucleation and growth of metallic nanodomains over picosecond time scales.
Tautomerization, molecular structure, transition state structure, and vibrational spectra of 2-aminopyridines: a combined computational and experimental study.

PubMed

Al-Otaibi, Jamelah S

2015-01-01

2-amino pyridine derivatives have attracted considerable interest because they are useful precursors for the synthesis of a variety of heterocyclic compounds possessing a medicinal value. In this work we aim to study both structural and electronic as well as high quality vibrational spectra for 2-amino-3-methylpyridine (2A3MP) and 2-amino-4-methylpyridine (2A4MP). Møller-Plesset perturbation theory (MP2/6-31G(d) and MP2/6-31++G(d,p) methods were used to investigate the structure and vibrational analysis of (2A3MP) and (2A4MP). Tautomerization of 2A4MP was investigated by Density Functional Theory (DFT/B3LYP) method in the gas phase. For the first time, all tautomers including NH → NH conversions as well as those usually omitted, NH → CH and CH → CH, were considered. The canonical structure (2A4MP1) is the most stable tautomer. It is 13.60 kcal/mole more stable than the next (2A4MP2). Transition state structures of pyramidal N inversion and proton transfer were computed at B3LYP/6-311++G(d,p). Barrier to transition state of hydrogen proton transfer is calculated as 44.81 kcal/mol. Transition state activation energy of pyramidal inversion at amino N is found to be 0.41 kcal/mol using the above method. Bond order and natural atomic charges were also calculated at the same level. The raman and FT-IR spectra of (2A3MP) and (2A4MP) were measured (4000-400 cm(-1)). The optimized molecular geometries, frequencies and vibrational bands intensity were calculated at ab initio (MP2) and DFT(B3LYP) levels of theory with 6-31G(d), 6-31++G(d,p) and 6-311++G(d,p) basis sets. The vibrational frequencies were compared with experimentally measured FT-IR and FT-Raman spectra. Reconsidering the vibrational analysis of (2A3MP) and (2A4MP) with more accurate FT-IR machine and highly accurate animation programs result in new improved vibrational assignments. Sophisticated quantum mechanics methods enable studying the transition state structure for different chemical systems.
Structural Insight into Nucleoprotein Conformation Change Chaperoned by VP35 Peptide in Marburg Virus.

PubMed

Liu, Baocheng; Dong, Shishang; Li, Guobang; Wang, Wenming; Liu, Xiang; Wang, Yantong; Yang, Cheng; Rao, Zihe; Guo, Yu

2017-08-15

Marburg virus (MARV) encodes a nucleoprotein (NP) to encapsidate its genome by oligomerization and form a ribonucleoprotein complex (RNP). According to previous investigation on nonsegmented negative-sense RNA viruses (nsNSV), the newly synthesized NPs must be prevented from indiscriminately binding to noncognate RNAs. During the viral RNA synthesis process, the RNPs undergo a transition from an RNA-bound form to a template-free form, to open access for the interaction between the viral polymerase and the RNA template. In filoviruses, this transition is regulated by VP35 peptide and other viral components. To further understand the dynamic process of filovirus RNP formation, we report here the structure of MARV NP core , both in the apo form and in the VP35 peptide-chaperoned form. These structures reveal a typical bilobed structure, with a positive-charged RNA binding groove between two lobes. In the apo form, the MARV NP exists in an interesting hexameric state formed by the hydrophobic interaction within the long helix of the NP core C-terminal region, which shows high structural flexibility among filoviruses and may imply critical function during RNP formation. Moreover, the VP35 peptide-chaperoned NP core remains in a monomeric state and completely loses its affinity for single-stranded RNA (ssRNA). The structural comparison reveals that the RNA binding groove undergoes a transition from closed state to open state, chaperoned by VP35 peptide, thus preventing the interaction for viral RNA. Our investigation provides considerable structural insight into the filovirus RNP working mechanism and may support the development of antiviral therapies targeting the RNP formation of filovirus. IMPORTANCE Marburg virus is one of the most dangerous viruses, with high morbidity and mortality. A recent outbreak in Angola in 2005 caused the deaths of 272 persons. NP is one of the most essential proteins, as it encapsidates and protects the whole virus genome simultaneously with self-assembly oligomerization. Here we report the structures of MARV NP core in two different forms. In the MARV NP apo form, we identify an interesting hexamer formed by hydrophobic interaction within a long helix, which is highly conserved and flexible among filoviruses and may indicate its critical function during the virus RNP formation. Moreover, the structural comparison with the NP-VP35 peptide complex reveals a structural transition chaperoned by VP35, in which the RNA binding groove undergoes a transition from closed state to open state. Finally, we discussed the high conservation and critical role of the VP35 binding pocket and its potential use for therapeutic development. Copyright © 2017 American Society for Microbiology.
Suppression of Structural Phase Transition in VO2 by Epitaxial Strain in Vicinity of Metal-insulator Transition

PubMed Central

Yang, Mengmeng; Yang, Yuanjun; Bin Hong; Wang, Liangxin; Hu, Kai; Dong, Yongqi; Xu, Han; Huang, Haoliang; Zhao, Jiangtao; Chen, Haiping; Song, Li; Ju, Huanxin; Zhu, Junfa; Bao, Jun; Li, Xiaoguang; Gu, Yueliang; Yang, Tieying; Gao, Xingyu; Luo, Zhenlin; Gao, Chen

2016-01-01

Mechanism of metal-insulator transition (MIT) in strained VO2 thin films is very complicated and incompletely understood despite three scenarios with potential explanations including electronic correlation (Mott mechanism), structural transformation (Peierls theory) and collaborative Mott-Peierls transition. Herein, we have decoupled coactions of structural and electronic phase transitions across the MIT by implementing epitaxial strain on 13-nm-thick (001)-VO2 films in comparison to thicker films. The structural evolution during MIT characterized by temperature-dependent synchrotron radiation high-resolution X-ray diffraction reciprocal space mapping and Raman spectroscopy suggested that the structural phase transition in the temperature range of vicinity of the MIT is suppressed by epitaxial strain. Furthermore, temperature-dependent Ultraviolet Photoelectron Spectroscopy (UPS) revealed the changes in electron occupancy near the Fermi energy EF of V 3d orbital, implying that the electronic transition triggers the MIT in the strained films. Thus the MIT in the bi-axially strained VO2 thin films should be only driven by electronic transition without assistance of structural phase transition. Density functional theoretical calculations further confirmed that the tetragonal phase across the MIT can be both in insulating and metallic states in the strained (001)-VO2/TiO2 thin films. This work offers a better understanding of the mechanism of MIT in the strained VO2 films. PMID:26975328
Analogous Gamow-Teller and M1 Transitions in Tz = ±½ Mirror Nuclei and in Tz = ±1, 0 Triplet Nuclei relevant to Low-energy Super GT state

NASA Astrophysics Data System (ADS)

Fujita, Yoshitaka; Fujita, Hirohiko; Tanumura, Yusuke

2018-05-01

Nuclei have spin- and isospin-degrees of freedom. Therefore, Gamow-Teller (GT) transitions caused by the στ operator (spin-isospin operator) are unique tools for the studies of nuclear structure as well as nuclear interactions. They can be studied in β decays as well as charge-exchange (CE) reactions. Similarly, M1 γ decays are mainly caused by the στ operator. Combined studies of these transitions caused by Weak, Strong, and Electro-Magnetic interactions provide us a deeper understanding of nuclear spin-isospin-type transitions. We first compare the strengths of analogous GT and M1 transitions in the A = 27, Tz = ±½ mirror nuclei 27Al and 27Si. The comparison is extended to the Tz = ±1, 0 nuclei. The strength of GT transition from the ground state (g.s.) of 42Ca to the 0.611 MeV first Jπ = 1+ state in 42Sc is compared with that of the analogous M1 transition from the 0.611 MeV state to the T = 1, 0+ g.s. (isobaric analog state: IAS) in 42Sc. The 0.611 MeV state has the property of Low-energy Super GT (LeSGT) state, because it carries the main part of the GT strength of all available transitions from the g.s. of 42Ca (and 42Ti) to the Jπ = 1+ GT states in 42Sc.

Laser photoelectron spectroscopy of CrH - , CoH - , and NiH - : Periodic trends in the electronic structure of the transition-metal hydrides

NASA Astrophysics Data System (ADS)

Stevens Miller, Amy E.; Feigerle, C. S.; Lineberger, W. C.

1987-08-01

The laser photoelectron spectra of CrH-, CoH-, and NiH- and the analogous deuterides are reported. The spectra are interpreted using a qualitative description of the electronic structure for the hydrides. This model is used to assign off-diagonal transitions in the photodetachment to low-spin states of the neutrals, and diagonal transitions to high-spin states of the neutrals. These data are used to identify the high-spin states of CoH and NiH; several other states of CrH, CoH, and NiH are also identified. Periodic trends in the bond lengths, vibrational frequencies, and electronic excitation energies for the MnH through NiH molecules are examined. Electron affinities are reported for CrH (0.563±0.010 eV), CoH (0.671±0.010 eV), and NiH (0.481±0.007 eV), and the corresponding deuterides.
Fine-structure resolved rotational transitions and database for CN+H2 collisions

NASA Astrophysics Data System (ADS)

Burton, Hannah; Mysliwiec, Ryan; Forrey, Robert C.; Yang, B. H.; Stancil, P. C.; Balakrishnan, N.

2018-06-01

Cross sections and rate coefficients for CN+H2 collisions are calculated using the coupled states (CS) approximation. The calculations are benchmarked against more accurate close-coupling (CC) calculations for transitions between low-lying rotational states. Comparisons are made between the two formulations for collision energies greater than 10 cm-1. The CS approximation is used to construct a database which includes highly excited rotational states that are beyond the practical limitations of the CC method. The database includes fine-structure resolved rotational quenching transitions for v = 0 and j ≤ 40, where v and j are the vibrational and rotational quantum numbers of the initial state of the CN molecule. Rate coefficients are computed for both para-H2 and ortho-H2 colliders. The results are shown to be in good agreement with previous calculations, however, the rates are substantially different from mass-scaled CN+He rates that are often used in astrophysical models.
DOE Office of Scientific and Technical Information (OSTI.GOV)

Dmowski, W.; Gierlotka, S.; Wang, Z.

Through high-energy x-ray diffraction and atomic pair density function analysis we find that Zr-based metallic alloy, heated to the supercooled liquid state under hydrostatic pressure and then quenched to room temperature, exhibits a distinct glassy structure. The PDF indicates that the Zr-Zr distances in this glass are significantly reduced compared to those quenched without pressure. Annealing at the glass transition temperature at ambient pressure reverses structural changes and the initial glassy state is recovered. This result suggests that pressure causes a liquid-to-liquid phase transition in this metallic alloy supercooled melt. Such a pressure induced transition is known for covalent liquids,more » but has not been observed for metallic liquids. The High Pressure Quenched glasses are stable in ambient conditions after decompression.« less
Mechanical properties of 4d transition metals in molten state

NASA Astrophysics Data System (ADS)

Singh, Deobrat; Sonvane, Yogesh; Thakor, P. B.

2016-05-01

Mechanical properties of 4d transition metals in molten state have been studied in the present study. We have calculated mechanical properties such as isothermal bulk modulus (B), modulus of rigidity (G), Young's modulus (Y) and Hardness have also been calculated from the elastic part of the Phonon dispersion curve (PDC). To describe the structural information, we have used different structure factor S(q) using Percus-Yevick hard sphere (PYHS) reference systems along with our newly constructed parameter free model potential.To see the influence of exchange and correlation effect on the above said properties of 3d liquid transition metals, we have used Sarkar et al (S)local field correction functions. Present results have been found good in agreement with available experimental data.
Static, dynamic and electronic properties of expanded fluid mercury in the metal-nonmetal transition range. An ab initio study.

PubMed

Calderín, L; González, L E; González, D J

2011-09-21

Fluid Hg undergoes a metal-nonmetal (M-NM) transition when expanded toward a density of around 9 g cm(-3). We have performed ab initio molecular dynamics simulations for several thermodynamic states around the M-NM transition range and the associated static, dynamic and electronic properties have been analyzed. The calculated static structure shows a good agreement with the available experimental data. It is found that the volume expansion decreases the number of nearest neighbors from 10 (near the triple point) to around 8 at the M-NM transition region. Moreover, these neighbors are arranged into two subshells and the decrease in the number of neighbors occurs in the inner subshell. The calculated dynamic structure factors agree fairly well with their experimental counterparts obtained by inelastic x-ray scattering experiments, which display inelastic side peaks. The derived dispersion relation exhibits some positive dispersion for all the states, although its value around the M-NM transition region is not as marked as suggested by the experiment. We have also calculated the electronic density of states, which shows the appearance of a gap at a density of around 8.3 g cm(-3).
Insights into the nature of DNA binding of AbrB-like transcription factors

PubMed Central

Sullivan, Daniel M.; Bobay, Benjamin G.; Kojetin, Douglas J.; Thompson, Richele J.; Rance, Mark; Strauch, Mark A.; Cavanagh, John

2008-01-01

Summary Understanding the DNA recognition and binding by the AbrB-like family of transcriptional regulators is of significant interest since these proteins enable bacteria to elicit the appropriate response to diverse environmental stimuli. Although these ‘transition-state regulator’ proteins have been well characterized at the genetic level, the general and specific mechanisms of DNA binding remain elusive. We present RDC-refined NMR solution structures and dynamic properties of the DNA-binding domains of three Bacillus subtilis transition-state regulators AbrB, Abh, and SpoVT. We combined previously investigated DNase I footprinting, DNA methylation, gel shift assays, mutagenic and NMR studies to generate a structural model of the complex between AbrBN55 and its cognate promoter, abrB8. These investigations have enabled us to generate the first model for the specific nature of the transition-state regulator-DNA interaction. PMID:19000822
Substituent effects on rates and torquoselectivities of electrocyclic ring-openings of N-substituted 2-azetines.

PubMed

Lopez, Steven A; Houk, K N

2014-07-03

Transition structures for the conrotatory electrocyclic ring-opening reactions of N-substituted 2-azetines were computed with the density functional M06-2X/6-31+G(d,p). A wide range of substituents from π acceptors (e.g., CHO, CN) to π donors (NMe2, OMe) was explored. Acceptor substituents delocalize the nitrogen lone pair and stabilize the reactant state of 2-azetines, while donors destabilize the 2-azetine reactant state. The conrotatory ring-opening is torquoselective, and the transition state for the outward rotation of the N-substituent and inward rotation of the nitrogen lone pair is preferred. This transition structure is stabilized by an interaction between the nitrogen lone pair and the vacant π* orbital. The activation free energies are linearly related to the reaction free energies and the Taft σR(0) parameter.
Transition state-finding strategies for use with the growing string method.

PubMed

Goodrow, Anthony; Bell, Alexis T; Head-Gordon, Martin

2009-06-28

Efficient identification of transition states is important for understanding reaction mechanisms. Most transition state search algorithms require long computational times and a good estimate of the transition state structure in order to converge, particularly for complex reaction systems. The growing string method (GSM) [B. Peters et al., J. Chem. Phys. 120, 7877 (2004)] does not require an initial guess of the transition state; however, the calculation is still computationally intensive due to repeated calls to the quantum mechanics code. Recent modifications to the GSM [A. Goodrow et al., J. Chem. Phys. 129, 174109 (2008)] have reduced the total computational time for converging to a transition state by a factor of 2 to 3. In this work, three transition state-finding strategies have been developed to complement the speedup of the modified-GSM: (1) a hybrid strategy, (2) an energy-weighted strategy, and (3) a substring strategy. The hybrid strategy initiates the string calculation at a low level of theory (HF/STO-3G), which is then refined at a higher level of theory (B3LYP/6-31G(*)). The energy-weighted strategy spaces points along the reaction pathway based on the energy at those points, leading to a higher density of points where the energy is highest and finer resolution of the transition state. The substring strategy is similar to the hybrid strategy, but only a portion of the low-level string is refined using a higher level of theory. These three strategies have been used with the modified-GSM and are compared in three reactions: alanine dipeptide isomerization, H-abstraction in methanol oxidation on VO(x)/SiO(2) catalysts, and C-H bond activation in the oxidative carbonylation of toluene to p-toluic acid on Rh(CO)(2)(TFA)(3) catalysts. In each of these examples, the substring strategy was proved most effective by obtaining a better estimate of the transition state structure and reducing the total computational time by a factor of 2 to 3 compared to the modified-GSM. The applicability of the substring strategy has been extended to three additional examples: cyclopropane rearrangement to propylene, isomerization of methylcyclopropane to four different stereoisomers, and the bimolecular Diels-Alder condensation of 1,3-butadiene and ethylene to cyclohexene. Thus, the substring strategy used in combination with the modified-GSM has been demonstrated to be an efficient transition state-finding strategy for a wide range of types of reactions.
Unfolding and melting of DNA (RNA) hairpins: the concept of structure-specific 2D dynamic landscapes.

PubMed

Lin, Milo M; Meinhold, Lars; Shorokhov, Dmitry; Zewail, Ahmed H

2008-08-07

A 2D free-energy landscape model is presented to describe the (un)folding transition of DNA/RNA hairpins, together with molecular dynamics simulations and experimental findings. The dependence of the (un)folding transition on the stem sequence and the loop length is shown in the enthalpic and entropic contributions to the free energy. Intermediate structures are well defined by the two coordinates of the landscape during (un)zipping. Both the free-energy landscape model and the extensive molecular dynamics simulations totaling over 10 mus predict the existence of temperature-dependent kinetic intermediate states during hairpin (un)zipping and provide the theoretical description of recent ultrafast temperature-jump studies which indicate that hairpin (un)zipping is, in general, not a two-state process. The model allows for lucid prediction of the collapsed state(s) in simple 2D space and we term it the kinetic intermediate structure (KIS) model.
Equilibrium and kinetics of DNA overstretching modeled with a quartic energy landscape.

PubMed

Argudo, David; Purohit, Prashant K

2014-11-04

It is well known that the dsDNA molecule undergoes a phase transition from B-DNA into an overstretched state at high forces. For some time, the structure of the overstretched state remained unknown and highly debated, but recent advances in experimental techniques have presented evidence of more than one possible phase (or even a mixed phase) depending on ionic conditions, temperature, and basepair sequence. Here, we present a theoretical model to study the overstretching transition with the possibility that the overstretched state is a mixture of two phases: a structure with portions of inner strand separation (melted or M-DNA), and an extended phase that retains the basepair structure (S-DNA). We model the double-stranded DNA as a chain composed of n segments of length l, where the transition is studied by means of a Landau quartic potential with statistical fluctuations. The length l is a measure of cooperativity of the transition and is key to characterizing the overstretched phase. By analyzing the different values of l corresponding to a wide spectrum of experiments, we find that for a range of temperatures and ionic conditions, the overstretched form is likely to be a mix of M-DNA and S-DNA. For a transition close to a pure S-DNA state, where the change in extension is close to 1.7 times the original B-DNA length, we find l ? 25 basepairs regardless of temperature and ionic concentration. Our model is fully analytical, yet it accurately reproduces the force-extension curves, as well as the transient kinetic behavior, seen in DNA overstretching experiments.
Temperature-triggered reversible dielectric and nonlinear optical switch based on the one-dimensional organic-inorganic hybrid phase transition compound [C6H11NH3]2CdCl4.

PubMed

Liao, Wei-Qiang; Ye, Heng-Yun; Fu, Da-Wei; Li, Peng-Fei; Chen, Li-Zhuang; Zhang, Yi

2014-10-20

The one-dimensional organic-inorganic hybrid compound bis(cyclohexylammonium) tetrachlorocadmate(II) (1), in which the adjacent infinite [CdCl4]n(-) chains are connected to each other though Cd···Cl weak interactions to form perovskite-type layers of corner-sharing CdCl6 octahedra separated by cyclohexylammonium cation bilayers, was synthesized. It undergoes two successive structural phase transitions, at 215 and 367 K, which were confirmed by systematic characterizations including differential scanning calorimetry (DSC) measurements, variable-temperature structural analyses, and dielectric and second harmonic generation (SHG) measurements. A precise structural analysis discloses that the phase transition at 215 K is induced by the disorder-order transition of cyclohexylammonium cations, while the phase transition at 367 K derives from changes in the relative location of Cd atoms. Emphatically, both the dielectric constant and SHG intensity of 1 show a striking change between low and high states at around 367 K, which reveals that 1 might be considered as a potential dielectric and nonlinear optical (NLO) switch with high-temperature response characterization, excellent reversibility, and obvious change of states.
The Effect of a Helix-Coil Transition on the Extension Elasticity

NASA Astrophysics Data System (ADS)

Buhot, Arnaud; Halperin, Avi

2000-03-01

The secondary structure of a polymer affects its deformation behavior in accordance with the Le Chatelier principle. An important example of such secondary structure is the alpha helix encountered in polypeptides. Similar structure was recently proposed for PEO in aqueous media. Our discussion concerns the coupling of the cooperative helix-coil transition and the extension elasticity. In particular, we analyze the extension of a long single chain by use of optical tweezers or AFM. We consider chains that exist in the coil-state when unperturbed. The transition nevertheless occurs because the extension favors the low entropy helical state. As a result, the corresponding force law exhibits a plateau. The analysis of this situation involves two ingredients: (I) the stretching free energy penalty for a rod-coil mutiblock copolymer (II) the entropy associated with the possible placements of the rod and coil blocks.
Formation of structural steady states in lamellar/sponge phase-separating fluids under shear flow

NASA Astrophysics Data System (ADS)

Panizza, P.; Courbin, L.; Cristobal, G.; Rouch, J.; Narayanan, T.

2003-05-01

We investigate the effect of shear flow on a lamellar-sponge phase-separating fluid when subjected to shear flow. We show the existence of two different steady states (droplets and ribbons structures) whose nature does not depend on the way to reach the two-phase unstable region of the phase diagram (temperature quench or stirring). The transition between ribbons and droplets is shear thickening and its nature strongly depends on what dynamical variable is imposed. If the stress is fixed, flow visualization shows the existence of shear bands at the transition, characteristic of coexistence in the cell between ribbons and droplets. In this shear-banding region, the viscosity oscillates. When the shear rate is fixed, no shear bands are observed. Instead, the transition exhibits a hysteretic behavior leading to a structural bi-stability of the phase-separating fluid under flow.
Structural signal of a dynamic glass transition

NASA Astrophysics Data System (ADS)

Chattopadhyay, Sudeshna; Uysal, Ahmet; Stripe, Benjamin; Evmenenko, Guennadi; Dutta, Pulak; Ehrlich, Steven; Karapetrova, Evguenia A.

2010-03-01

Conventional wisdom states that there is no significant difference between the static structures of the glass and liquid states of a given material. Using x-ray reflectivity, we have studied pentaphenyl trimethyl trisiloxane, an isotropic liquid at room temperature with a dynamic glass transition at 224K. Surface density oscillations (surface layers) develop below 285K, similar to those seen in other metallic and dielectric liquids and in computer simulations [1]. Upon cooling further, there is a sharp increase in the penetration of the surface layers into the bulk material, i.e. an apparently discontinuous change in the static structure, exactly at the glass transition (224K) [2]. [4pt] [1]. e.g. O. M. Magnussen et al., PRL 74, 4444 (1995); H. Mo et al. PRL 96, 096107 (2006); E. Chac'on et al., PRL 87, 166101 (2001) [0pt] [2] S. Chattopadhyay et al, PRL 103, 175701 (2009)
Atomic sulfur: Frequency measurement of the J = 0 left arrow 1 fine-structure transition at 56.3 microns by laser magnetic resonance

NASA Technical Reports Server (NTRS)

Brown, John M.; Evenson, Kenneth M.; Zink, Lyndon R.

1994-01-01

The J = 0 left arrow 1 fine-structure transition in atomic sulfur (S I) in its ground (3)P state has been detected in the laboratory by far-infrared laser magnetic resonance. The fine-structure interval has been measured accurately as 5,322,492.9 +/- 2.8 MHz which corresponds to a wavelength of 56.325572 +/- 0.000030 micrometers.
Use of state-and-transition simulation modeling in National Forest planning in the Pacific Northwest, U.S.A

Treesearch

Ayn J. Shlisky; Don Vandendriesche

2012-01-01

Effective national forest planning depends on scientifically sound analyses of land management alternatives relative to desired future conditions and environmental effects. The USDA Forest Service Pacific Northwest Region is currently using state-and-transition simulation models (STMs) to simulate changes in forest composition and structure for the revisions of five...
Urea-temperature phase diagrams capture the thermodynamics of denatured state expansion that accompany protein unfolding.

PubMed

Tischer, Alexander; Auton, Matthew

2013-09-01

We have analyzed the thermodynamic properties of the von Willebrand factor (VWF) A3 domain using urea-induced unfolding at variable temperature and thermal unfolding at variable urea concentrations to generate a phase diagram that quantitatively describes the equilibrium between native and denatured states. From this analysis, we were able to determine consistent thermodynamic parameters with various spectroscopic and calorimetric methods that define the urea-temperature parameter plane from cold denaturation to heat denaturation. Urea and thermal denaturation are experimentally reversible and independent of the thermal scan rate indicating that all transitions are at equilibrium and the van't Hoff and calorimetric enthalpies obtained from analysis of individual thermal transitions are equivalent demonstrating two-state character. Global analysis of the urea-temperature phase diagram results in a significantly higher enthalpy of unfolding than obtained from analysis of individual thermal transitions and significant cross correlations describing the urea dependence of ΔH0 and ΔCP0 that define a complex temperature dependence of the m-value. Circular dichroism (CD) spectroscopy illustrates a large increase in secondary structure content of the urea-denatured state as temperature increases and a loss of secondary structure in the thermally denatured state upon addition of urea. These structural changes in the denatured ensemble make up ∼40% of the total ellipticity change indicating a highly compact thermally denatured state. The difference between the thermodynamic parameters obtained from phase diagram analysis and those obtained from analysis of individual thermal transitions illustrates that phase diagrams capture both contributions to unfolding and denatured state expansion and by comparison are able to decipher these contributions. © 2013 The Protein Society.
Probing the free energy landscape of the FBP28WW domain using multiple techniques.

PubMed

Periole, Xavier; Allen, Lucy R; Tamiola, Kamil; Mark, Alan E; Paci, Emanuele

2009-05-01

The free-energy landscape of a small protein, the FBP 28 WW domain, has been explored using molecular dynamics (MD) simulations with alternative descriptions of the molecule. The molecular models used range from coarse-grained to all-atom with either an implicit or explicit treatment of the solvent. Sampling of conformation space was performed using both conventional and temperature-replica exchange MD simulations. Experimental chemical shifts and NOEs were used to validate the simulations, and experimental phi values both for validation and as restraints. This combination of different approaches has provided insight into the free energy landscape and barriers encountered by the protein during folding and enabled the characterization of native, denatured and transition states which are compatible with the available experimental data. All the molecular models used stabilize well defined native and denatured basins; however, the degree of agreement with the available experimental data varies. While the most detailed, explicit solvent model predicts the data reasonably accurately, it does not fold despite a simulation time 10 times that of the experimental folding time. The less detailed models performed poorly relative to the explicit solvent model: an implicit solvent model stabilizes a ground state which differs from the experimental native state, and a structure-based model underestimates the size of the barrier between the two states. The use of experimental phi values both as restraints, and to extract structures from unfolding simulations, result in conformations which, although not necessarily true transition states, appear to share the geometrical characteristics of transition state structures. In addition to characterizing the native, transition and denatured states of this particular system in this work, the advantages and limitations of using varying levels of representation are discussed. 2008 Wiley Periodicals, Inc.
Identity, Family, and Faith: U.S. Third Culture Kids Transition to College

ERIC Educational Resources Information Center

Kortegast, Carrie; Yount, Emily M.

2016-01-01

Recent trends in globalization have increased the number of U.S. children and adolescents being raised outside the United States. Using the framework of adults in transition, the authors sought to understand the structure of Third Culture Kids' (TCKs), specifically Missionary Kids', transition to college. Findings indicate that participants must…
Structure and physical properties of YCoO3 at temperatures up to 1000K

NASA Astrophysics Data System (ADS)

Knížek, K.; Jirák, Z.; Hejtmánek, J.; Veverka, M.; Maryško, M.; Hauback, B. C.; Fjellvåg, H.

2006-06-01

The crystal structure of perovskite YCoO3 has been studied by neutron powder diffraction up to high temperatures. The orthorhombic Pbnm symmetry is confirmed in the whole temperature range. A significant isotropic enlargement of CoO6 octahedra is evidenced above 600K leading to unit cell expansion and increased octahedral tilting. Supported by complementary physical measurements, the origin of anomalous expansion is identified with a gradual transition of Co3+ ions from the diamagnetic low-spin (S=0) ground state to excited magnetic states with spin S=1 or 2. The magnetic transition is closely followed by a broad resistivity transition of the insulator-metal type, centered at 750K . The changes in magnetic susceptibility, electric resistivity, thermopower and thermal conductivity associated with transitions in YCoO3 are discussed in comparison with similar data on related perovskite LaCoO3 .

Molecular dynamics studies of protein folding and aggregation

NASA Astrophysics Data System (ADS)

Ding, Feng

This thesis applies molecular dynamics simulations and statistical mechanics to study: (i) protein folding; and (ii) protein aggregation. Most small proteins fold into their native states via a first-order-like phase transition with a major free energy barrier between the folded and unfolded states. A set of protein conformations corresponding to the free energy barrier, Delta G >> kBT, are the folding transition state ensemble (TSE). Due to their evasive nature, TSE conformations are hard to capture (probability ∝ exp(-DeltaG/k BT)) and characterize. A coarse-grained discrete molecular dynamics model with realistic steric constraints is constructed to reproduce the experimentally observed two-state folding thermodynamics. A kinetic approach is proposed to identify the folding TSE. A specific set of contacts, common to the TSE conformations, is identified as the folding nuclei which are necessary to be formed in order for the protein to fold. Interestingly, the amino acids at the site of the identified folding nuclei are highly conserved for homologous proteins sharing the same structures. Such conservation suggests that amino acids that are important for folding kinetics are under selective pressure to be preserved during the course of molecular evolution. In addition, studies of the conformations close to the transition states uncover the importance of topology in the construction of order parameter for protein folding transition. Misfolded proteins often form insoluble aggregates, amyloid fibrils, that deposit in the extracellular space and lead to a type of disease known as amyloidosis. Due to its insoluble and non-crystalline nature, the aggregation structure and, thus the aggregation mechanism, has yet to be uncovered. Discrete molecular dynamics studies reveal an aggregate structure with the same structural signatures as in experimental observations and show a nucleation aggregation scenario. The simulations also suggest a generic aggregation mechanism that globular proteins under a denaturing environment partially unfold and aggregate by forming stabilizing hydrogen bonds between the backbones of the partial folded substructures. Proteins or peptides rich in alpha-helices also aggregate into beta-rich amyloid fibrils. Upon aggregation, the protein or peptide undergoes a conformational transition from alpha-helices to beta-sheets. The transition of alpha-helix to beta-hairpin (two-stranded beta-sheet) is studied in an all-heavy-atom discrete molecular dynamics model of a polyalanine chain. An entropical driving scenario for the alpha-helix to beta-hairpin transition is discovered.
Ultraviolet laser spectroscopy of jet-cooled CaNC and SrNC free radicals: Observation of bent excited electronic states

NASA Astrophysics Data System (ADS)

Greetham, Gregory M.; Ellis, Andrew M.

2000-11-01

New electronic transitions of the CaNC and SrNC free radicals have been identified in the near ultraviolet. For CaNC one new system, labeled the D˜-X˜ transition, was observed in the 31 500-33 400 cm-1 region. Two new transitions were found for SrNC, the D˜-X˜ and Ẽ-X˜ systems spanning 29 100-31 000 and 32 750-34 000 cm-1, respectively. Jet-cooled laser excitation spectra yield complex vibrational structure, much of which is attributed to excitation of the bending vibration. This has been used to infer that the molecule adopts a nonlinear equilibrium geometry in the upper electronic state in all three band systems, in contrast to the linear ground electronic state. This structural change is accounted for by the increased diffuseness of the unpaired electron in the excited states, which favors deviation from linearity. All three new excited states are assigned 2A' symmetry and correlate with 2Σ+ states in the linear molecule limit. Tentative estimates for the barriers to linearity in the D˜ 2A' states of CaNC and SrNC have been determined as ˜700 and ˜1050 cm-1, respectively.
A quantum chemical calculation of the potential energy surface in the formation of HOSO 2 from OH + SO 2

NASA Astrophysics Data System (ADS)

Sitha, Sanyasi; Jewell, Linda L.; Piketh, Stuart J.; Fourie, Gerhard

2011-01-01

The formation of HOSO 2 from OH and SO 2 has been thoroughly investigated using several different methods (MP2=Full, MP2=FC, B3LYP, HF and composite G∗ methods) and basis sets (6-31G(d,p), 6-31++G(d,p), 6-31++G(2d,2p), 6-31++G(2df,2p) and aug-cc-pVnZ). We have found two different possible transition state structures, one of which is a true transition state since it has a higher energy than the reactants and products (MP2=Full, MP2=FC and HF), while the other is not a true transition state since it has an energy which lies between that of the reactants and products (B3LYP and B3LYP based methods). The transition state structure (from MP2) has a twist angle of the OH fragment relative to the SO bond of the SO 2 fragment of -50.0°, whereas this angle is 26.7° in the product molecule. Examination of the displacement vectors confirms that this is a true transition state structure. The MP2=Full method with a larger basis set (MP2=Full/6-31++G(2df,2p)) predicts the enthalpy of reaction to be -112.8 kJ mol -1 which is close to the experimental value of -113.3 ± 6 kJ mol -1, and predicts a rather high barrier of 20.0 kJ mol -1. When the TS structure obtained by the MP2 method is used as the input for calculating the energetics using the QCISD/6-31++G(2df,2p) method, a barrier of 4.1 kJ mol -1 is obtained (ZPE corrected). The rate constant calculated from this barrier is 1.3 × 10 -13 cm 3 molecule -1 s -1. We conclude that while the MP2 methods correctly predict the TS from a structural point of view, higher level energy corrections are needed for estimation of exact barrier height.
Effective Collision Strengths for Fine-structure Transitions in Si VII

NASA Astrophysics Data System (ADS)

Sossah, A. M.; Tayal, S. S.

2014-05-01

The effective collision strengths for electron-impact excitation of fine-structure transitions in Si VII are calculated as a function of electron temperature in the range 5000-2,000,000 K. The B-spline Breit-Pauli R-matrix method has been used to calculate collision strengths by electron impact. The target wave functions have been obtained using the multi-configuration Hartree-Fock method with term-dependent non-orthogonal orbitals. The 92 fine-structure levels belonging to the 46 LS states of 2s 22p 4, 2s2p 5, 2p 6, 2s 22p 33s, 2s 22p 33p, 2s 22p 33d, and 2s2p 43s configurations are included in our calculations of oscillator strengths and collision strengths. There are 4186 possible fine-structure allowed and forbidden transitions among the 92 levels. The present excitation energies, oscillator strengths, and collision strengths have been compared with previous theoretical results and available experimental data. Generally, a good agreement is found with the 6 LS-state close-coupling approximation results of Butler & Zeippen and the 44 LS-state distorted wave calculation of Bhatia & Landi.
Determining the transition-state structure for different SN2 reactions using experimental nucleophile carbon and secondary alpha-deuterium kinetic isotope effects and theory.

PubMed

Westaway, Kenneth C; Fang, Yao-ren; MacMillar, Susanna; Matsson, Olle; Poirier, Raymond A; Islam, Shahidul M

2008-10-16

Nucleophile (11)C/ (14)C [ k (11)/ k (14)] and secondary alpha-deuterium [( k H/ k D) alpha] kinetic isotope effects (KIEs) were measured for the S N2 reactions between tetrabutylammonium cyanide and ethyl iodide, bromide, chloride, and tosylate in anhydrous DMSO at 20 degrees C to determine whether these isotope effects can be used to determine the structure of S N2 transition states. Interpreting the experimental KIEs in the usual fashion (i.e., that a smaller nucleophile KIE indicates the Nu-C alpha transition state bond is shorter and a smaller ( k H/ k D) alpha is found when the Nu-LG distance in the transition state is shorter) suggests that the transition state is tighter with a slightly shorter NC-C alpha bond and a much shorter C alpha-LG bond when the substrate has a poorer halogen leaving group. Theoretical calculations at the B3LYP/aug-cc-pVDZ level of theory support this conclusion. The results show that the experimental nucleophile (11)C/ (14)C KIEs can be used to determine transition-state structure in different reactions and that the usual method of interpreting these KIEs is correct. The magnitude of the experimental secondary alpha-deuterium KIE is related to the nucleophile-leaving group distance in the S N2 transition state ( R TS) for reactions with a halogen leaving group. Unfortunately, the calculated and experimental ( k H/ k D) alpha's change oppositely with leaving group ability. However, the calculated ( k H/ k D) alpha's duplicate both the trend in the KIE with leaving group ability and the magnitude of the ( k H/ k D) alpha's for the ethyl halide reactions when different scale factors are used for the high and the low energy vibrations. This suggests it is critical that different scaling factors for the low and high energy vibrations be used if one wishes to duplicate experimental ( k H/ k D) alpha's. Finally, neither the experimental nor the theoretical secondary alpha-deuterium KIEs for the ethyl tosylate reaction fit the trend found for the reactions with a halogen leaving group. This presumably is found because of the bulky (sterically hindered) leaving group in the tosylate reaction. From every prospective, the tosylate reaction is too different from the halogen reactions to be compared.
Laser photoelectron spectroscopy of MnH - and FeH - : Electronic structures of the metal hydrides, identification of a low-spin excited state of MnH, and evidence for a low-spin ground state of FeH

NASA Astrophysics Data System (ADS)

Stevens, Amy E.; Feigerle, C. S.; Lineberger, W. C.

1983-05-01

The laser photoelectron spectra of MnH- and MnD-, and FeH- and FeD- are reported. A qualitative description of the electronic structure of the low-spin and high-spin states of the metal hydrides is developed, and used to interpret the spectra. A diagonal transition in the photodetachment to the known high-spin, 7Σ+, ground state of MnH is observed. An intense off-diagonal transition to a state of MnH, at 1725±50 cm-1 excitation energy, is attributed to loss of an antibonding electron from MnH-, to yield a low-spin quintet state of MnH. For FeH- the photodetachment to the ground state is an off-diagonal transition, attributed to loss of the antibonding electron from FeH-, to yield a low-spin quartet ground state of FeH. A diagonal transition results in an FeH state at 1945±55 cm-1; this state of FeH is assigned as the lowest-lying high-spin sextet state of FeH. An additional excited state of MnH and two other excited states of FeH are observed. Excitation energies for all the states are reported; vibrational frequencies and bond lengths for the ions and several states of the neutrals are also determined from the spectra. The electron affinity of MnH is found to be 0.869±0.010 eV; and the electron affinity of FeH is determined to be 0.934±0.011 eV. Spectroscopic constants for the various deuterides are also reported.
Theoretical studies for the rates and kinetic isotope effects of the excited-state double proton transfer in the 1:1 7-azaindole:H2O complex using variational transition state theory including multidimensional tunneling.

PubMed

Duong, My Phu Thi; Kim, Yongho

2010-03-18

Variational transition state theory calculations including multidimensional tunneling (VTST/MT) for excited-state tautomerization in the 1:1 7-azaindole:H(2)O complex were performed. Electronic structures and energies for reactant, product, transition state, and potential energy curves along the reaction coordinate were computed at the CASSCF(10,9)/6-31G(d,p) level of theory. The potential energies were corrected by second-order multireference perturbation theory to take the dynamic electron correlation into consideration. The final potential energy curves along the reaction coordinate were generated at the MRPT2//CASSCF(10,9)/6-31G(d,p) level. Two protons in the excited-state tautomerization are transferred concertedly, albeit asynchronously. The position of the variational transition state is very different from the conventional transition state, and is highly dependent on isotopic substitution. Rate constants were calculated using VTST/MT, and were on the order of 10(-6) s(-1) at room temperature. The HH/DD kinetic isotope effects are consistent with experimental observations; consideration of both tunneling and variational effects was essential to predict the experimental values correctly.
Electronic and structural properties of Lu under pressure: Relation to structural phases of the rare-earth metals

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

Min, B.I.; Oguchi, T.; Jansen, H.J.F.

1986-07-15

Ground-state electronic and structural properties of Lu under pressure are investigated with use of the self-consistent all-electron total-energy linear muffin-tin orbital band-structure method within a local-density-functional approximation. Pressure-induced structural transitions are found to occur in the following sequence: hcp--(Sm-type)--dhcp--fcc, which is the same as that observed in the crystal structures of the trivalent rare-earth metals with decreasing atomic number. This structural transition is correlated with the increase in the number of d-italic electrons under pressure.
Phase transition of a DPPC bilayer induced by an external surface pressure: from bilayer to monolayer behavior. a molecular dynamics simulation study.

PubMed

López Cascales, J J; Otero, T F; Fernandez Romero, A J; Camacho, L

2006-06-20

Understanding the lipid phase transition of lipid bilayers is of great interest from biophysical, physicochemical, and technological points of view. With the aim of elucidating the structural changes that take place in a DPPC phospholipid bilayer induced by an external isotropic surface pressure, five computer simulations were carried out in a range from 0.1 to 40 mN/m. Molecular dynamics simulations provided insight into the structural changes that took place in the lipid structure. It was seen that low pressures ranging from 0.1 to 1 mN/m had hardly any effect on the structure, electrical properties, or hydration of the lipid bilayer. However, for pressures above 40 mN/m, there was a sharp change in the lipid-lipid interactions, hydrocarbon lipid fluidity, and electrostatic potential, corresponding to the mesomorphic transition from a liquid crystalline state (L(alpha)) to its gel state (P'(beta)). The head lipid orientation remained almost unaltered, parallel to the lipid layer, as the surface pressure was increased, although a noticeable change in its angular distribution function was evident with the phase transition.
First principles study of structural, electronic and optical properties of polymorphic forms of Rb 2Te

NASA Astrophysics Data System (ADS)

Alay-e-Abbas, S. M.; Shaukat, A.

2011-05-01

First-principles density functional theory calculations have been performed for structural, electronic and optical properties of three polymorphic forms of rubidium telluride. Our calculations show that the sequence of pressure induced phase transitions for Rb 2Te is Fm3¯m → Pnma → P6 3/mmc which is governed by the coordination numbers of the anions. From our calculated low transition pressure value for the Fm3¯m phase to the Pnma phase transition of Rb 2Te, the experimentally observed meta-stability of Fm3¯m phase at ambient conditions seems reasonable. The electronic band structure has been calculated for all the three phases and the change in the energy band gap is discussed for the transitioning phases. The energy band gaps obtained for the three phases of Rb 2Te decrease on going from the meta-stable phase to the high-pressure phases. Total and partial density of states for the polymorphs of Rb 2Te has been computed to elucidate the contribution of various atomic states on the electronic band structure. Furthermore, optical properties for all the polymorphic forms have been presented in form of the complex dielectric function.
Picosecond view of a martensitic transition and nucleation in the shape memory alloy M n50N i40S n10 by four-dimensional transmission electron microscopy

NASA Astrophysics Data System (ADS)

Zhang, Ming; Cao, Gaolong; Tian, Huanfang; Sun, Shuaishuai; Li, Zhongwen; Li, Xingyuan; Guo, Cong; Li, Zian; Yang, Huaixin; Li, Jianqi

2017-11-01

The photoinduced martensitic (MT) transition and reverse transition in a shape memory alloy M n50N i40S n10 have been examined by using high spatiotemporal resolution four-dimensional transmission electron microscopy (4D-TEM), and the experimental results clearly demonstrate that the MT transition and reverse transition in this Heusler alloy contain a variety of structural dynamic features at picosecond time scales. The 4D-TEM imaging and diffraction observations clearly show that MT transition and MT domain nucleation, which are related to cooperative atomic motions, occur at between 10 and 20 ps, depending on the thickness of the sample. Moreover, a strong coupling between the MT transition and lattice breathing mode is discovered in this system, which can result in a periodic structural oscillation between the MT phase and austenitic (AUS) phase. This allows us to directly observe the MT nucleation and domain wall motions in transient states using high spatiotemporal imaging. A careful analysis of the ultrafast images demonstrates the presence of remarkable transient states, which exhibit the essential features of MT nucleation, lattice symmetry breaking, and a rapid growth of MT plates. These results not only provide insights into the time-resolved structural dynamics and elementary mechanisms that govern the MT transition but also contribute to the development of a novel technique for future 4D-TEM investigations.
Superlattice formation lifting degeneracy protected by nonsymmorphic symmetry through a metal-insulator transition in RuAs

NASA Astrophysics Data System (ADS)

Kotegawa, Hisashi; Takeda, Keiki; Kuwata, Yoshiki; Hayashi, Junichi; Tou, Hideki; Sugawara, Hitoshi; Sakurai, Takahiro; Ohta, Hitoshi; Harima, Hisatomo

2018-05-01

A single crystal of RuAs obtained with the Bi-flux method shows obvious successive metal-insulator transitions at TMI 1˜255 K and TMI 2˜195 K. The x-ray diffraction measurement reveals the formation of a superlattice of 3 ×3 ×3 of the original unit cell below TMI 2, accompanied by a change of the crystal system from the orthorhombic structure to the monoclinic one. Simple dimerization of the Ru ions is not seen in the ground state. The multiple As sites observed in the nuclear quadrupole resonance spectrum also demonstrate the formation of the superlattice in the ground state, which is clarified to be nonmagnetic. The divergence in 1 /T1 at TMI 1 shows that a symmetry lowering by the metal-insulator transition is accompanied by strong critical fluctuations of some degrees of freedom. Using the structural parameters in the insulating state, the first-principles calculation reproduces successfully the reasonable size of nuclear quadrupole frequencies νQ for the multiple As sites, ensuring the high validity of the structural parameters. The calculation also gives a remarkable suppression in the density of states near the Fermi level, although the gap opening is insufficient. A coupled modulation of the calculated Ru d -electron numbers and the crystal structure proposes the formation of a charge density wave in RuAs. Some lacking factors remain, but it is shown that a lifting of degeneracy protected by the nonsymmorphic symmetry through the superlattice formation is a key ingredient for the metal-insulator transition in RuAs.
A Three-State System Based on Branched DNA Hybrids.

PubMed

He, Shiliang; Richert, Clemens

2018-03-26

There is a need for materials that respond to chemical or physical stimuli through a change in their structure. While a transition between water-soluble form and solid is not uncommon for DNA-based structures, systems that transition between three different states at room temperature and ambient pressure are rare. Here we report the preparation of branched DNA hybrids with eight oligodeoxycytidylate arms via solution-phase, H-phosphonate-based synthesis. Some hybrids assemble into hydrogels upon lowering the pH, acting as efficient gelators at pH 4-6, but can also transition into a more condensed solid state form upon exposure to divalent cations. Together with the homogeneous solutions that the i-motif-forming compounds give at neutral pH, three-state systems result. Each state has its own color, if chromophores are included in the system. The assembly and gelation properties can be tuned by choosing the chain length of the arms. Their responsive properties make the dC-rich DNA hybrids candidates for smart material applications. © 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.
Tetrahedral 4 α and 12C+α cluster structures in 16O

NASA Astrophysics Data System (ADS)

Kanada-En'yo, Yoshiko

2017-09-01

I have investigated structures of the ground and excited states of 16O with the method of variation after spin-parity projection in the antisymmetrized molecular dynamics model combined with the generator coordinate method of 12C+α cluster. The calculation reasonably reproduces the experimental energy spectra; E 2 , E 3 , E 4 , and I S 1 transitions; and α -decay properties. The formation of 4 α clusters has been confirmed from nucleon degrees of freedom in the AMD model without assuming the existence of any clusters. They form "tetrahedral" 4 α - and 12C+α cluster structures. The 12C+α structure constructs the Kπ=0+ band consisting of the 02+, 21+, and 41+ states and the Kπ=0- band of the 12-, 32-, and 51- states. The 01+, 31-, and 42+ states are assigned to the ground band constructed from the tetrahedral 4 α structure. The 01+ and 31- are approximately interpreted as Td band members with the ideal tetrahedral configuration. The ground-state 4 α correlation plays an important role in the enhancement of the E 3 transition strength to the 31-. The 42+ state is not the ideal Td member but constructed from a distorted tetrahedral 4 α structure. Moreover, significant state mixing of the tetrahedral 4 α and 12C+α cluster structures occurs between 41+ and 42+ states, indicating that the Td configuration of 4 α is rather fragile at Jπ=4+ .
Pressure-induced Td to 1T' structural phase transition in WTe 2

DOE PAGES

Zhou, Yonghui; Chen, Xuliang; Li, Nana; ...

2016-07-01

WTe 2 is provoking immense interest owing to its extraordinary properties, such as large positive magnetoresistance, pressure-driven superconductivity and possible type-II Weyl semimetal state. Here we report results of high-pressure synchrotron X-ray diffraction (XRD), Raman and electrical transport measurements on WTe 2. Both the XRD and Raman results reveal a structural transition upon compression, starting at 6.0 GPa and completing above 15.5 GPa. We have determined that the high-pressure lattice symmetry is monoclinic 1T' with space group of P21/m. This transition is related to a lateral sliding of adjacent Te-W-Te layers and results in a collapse of the unit cellmore » volume by ~20.5%. The structural transition also casts a pressure range with the broadened superconducting transition, where the zero resistance disappears.« less
Structural transitions in vortex systems with anisotropic interactions

DOE PAGES

Olszewski, Maciej W.; Eskildsen, M. R.; Reichhardt, Charles; ...

2017-12-29

We introduce a model of vortices in type-II superconductors with a four-fold anisotropy in the vortex–vortex interaction potential. Using numerical simulations we show that the vortex lattice undergoes structural transitions as the anisotropy is increased, with a triangular lattice at low anisotropy, a rhombic intermediate state, and a square lattice for high anisotropy. In some cases we observe a multi-q state consisting of an Archimedean tiling that combines square and triangular local ordering. At very high anisotropy, domains of vortex chain states appear. We discuss how this model can be generalized to higher order anisotropy as well as its applicabilitymore » to other particle-based systems with anisotropic particle–particle interactions.« less
Transition metal atoms absorbed on MoS2/h-BN heterostructure: stable geometries, band structures and magnetic properties.

PubMed

Wu, Yanbing; Huang, Zongyu; Liu, Huating; He, Chaoyu; Xue, Lin; Qi, Xiang; Zhong, Jianxin

2018-06-15

We have studied the stable geometries, band structures and magnetic properties of transition-metal (V, Cr, Mn, Fe, Co and Ni) atoms absorbed on MoS2/h-BN heterostructure systems by first-principles calculations. By comparing the adsorption energies, we find that the adsorbed transition metal (TM) atoms prefer to stay on the top of Mo atoms. The results of the band structure without spin-orbit coupling (SOC) interaction indicate that the Cr-absorbed systems behave in a similar manner to metals, and the Co-absorbed system exhibits a half-metallic state. We also deduce that the V-, Mn-, Fe-absorbed systems are semiconductors with 100% spin polarization at the HOMO level. The Ni-absorbed system is a nonmagnetic semiconductor. In contrast, the Co-absorbed system exhibits metallic state, and the bandgap of V-absorbed system decreases slightly according to the SOC calculations. In addition, the magnetic moments of all the six TM atoms absorbed on the MoS2/h-BN heterostructure systems decrease when compared with those of their free-standing states.
Ricin - inhibitor design. Annual report, 15 April 1994-14 April 1995

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

Schramm, V.L.

1995-05-14

Substrates for ricin A-chain include short RNA stem-loop structures which have been synthesized with radioactive labels for ease of catalytic assay and for kinetic isotope effects. Ricin A-chain from several sources is incapable of completing multiple catalytic cycles using these substrates. A family of ricin substrate analogue molecules have been synthesized and tested which are specific for transition states with oxycarbonium character or for enzymatic mechanisms involving protonation of the adenine leaving group. Formycin analogues were incorporated into RNA oligomeric structures and tested for binding to ricin A-chain or as inhibitors of the ricin-inactivation of in vitro translation using rabbitmore » reticulocyte lysates. Ribo-oxycarbonium ion analogues containing iminoribitol analogues of ribose were synthetically incorporated into RNA oligomeric structures. Neither formycin nor ribo-oxycarbonium analogues, either singly or in RNA oligomers caused significant inhibition of ricin A-chain when assayed in reticulocyte lysate translation assays. The results indicate a novel transition state mechanism for ricin A-chain, or a requirement for additional features of 28s rRNA to bind transition state analogues.« less
Lagrangian descriptors of driven chemical reaction manifolds.

PubMed

Craven, Galen T; Junginger, Andrej; Hernandez, Rigoberto

2017-08-01

The persistence of a transition state structure in systems driven by time-dependent environments allows the application of modern reaction rate theories to solution-phase and nonequilibrium chemical reactions. However, identifying this structure is problematic in driven systems and has been limited by theories built on series expansion about a saddle point. Recently, it has been shown that to obtain formally exact rates for reactions in thermal environments, a transition state trajectory must be constructed. Here, using optimized Lagrangian descriptors [G. T. Craven and R. Hernandez, Phys. Rev. Lett. 115, 148301 (2015)PRLTAO0031-900710.1103/PhysRevLett.115.148301], we obtain this so-called distinguished trajectory and the associated moving reaction manifolds on model energy surfaces subject to various driving and dissipative conditions. In particular, we demonstrate that this is exact for harmonic barriers in one dimension and this verification gives impetus to the application of Lagrangian descriptor-based methods in diverse classes of chemical reactions. The development of these objects is paramount in the theory of reaction dynamics as the transition state structure and its underlying network of manifolds directly dictate reactivity and selectivity.
Magneto-elastic coupling across the first-order transition in the distorted kagome lattice antiferromagnet Dy3Ru4Al12

PubMed Central

Henriques, M.S.; Gorbunov, D.I.; Kriegner, D.; Vališka, M.; Andreev, A.V.; Matěj, Z.

2018-01-01

Structural changes through the first-order paramagnetic-antiferromagnetic phase transition of Dy3Ru4Al12 at 7 K have been studied by means of X-ray diffraction and thermal expansion measurements. The compound crystallizes in a hexagonal crystal structure of Gd3Ru4Al12 type (P63/mmc space group), and no structural phase transition has been found in the temperature interval between 2.5 and 300 K. Nevertheless, due to the spin-lattice coupling the crystal volume undergoes a small orthorhombic distortion of the order of 2×10-5 as the compound enters the antiferromagnetic state. We propose that the first-order phase transition is not driven by the structural changes but rather by the exchange interactions present in the system. PMID:29445250

Localization-delocalization transition of electrons at the percolation threshold of semiconductor GaAs 1–xN x alloys: The appearance of a mobility edge

DOE PAGES

Alberi, K.; Fluegel, B.; Beaton, D. A.; ...

2012-07-09

Electrons in semiconductor alloys have generally been described in terms of Bloch states that evolve from constructive interference of electron waves scattering from perfectly periodic potentials, despite the loss of structural periodicity that occurs on alloying. Using the semiconductor alloy GaAs₁₋ xN x as a prototype, we demonstrate a localized to delocalized transition of the electronic states at a percolation threshold, the emergence of a mobility edge, and the onset of an abrupt perturbation to the host GaAs electronic structure, shedding light on the evolution of electronic structure in these abnormal alloys.
Strong cooperative coupling of pressure-induced magnetic order and nematicity in FeSe

DOE PAGES

Kothapalli, K.; Bohmer, A. E.; Jayasekara, W. T.; ...

2016-09-01

A hallmark of the iron-based superconductors is the strong coupling between magnetic, structural and electronic degrees of freedom. However, a universal picture of the normal state properties of these compounds has been confounded by recent investigations of FeSe where the nematic (structural) and magnetic transitions appear to be decoupled. Here, using synchrotron-based high-energy x-ray diffraction and time-domain Mossbauer spectroscopy, we show that nematicity and magnetism in FeSe under applied pressure are indeed strongly coupled. Distinct structural and magnetic transitions are observed for pressures between 1.0 and 1.7 GPa and merge into a single first-order transition for pressures ≳1.7 GPa, reminiscentmore » of what has been found for the evolution of these transitions in the prototypical system Ba(Fe 1–xCo x) 2As 2. Lastly, our results are consistent with a spin-driven mechanism for nematic order in FeSe and provide an important step towards a universal description of the normal state properties of the iron-based superconductors.« less
Effects of pressure on the magnetic properties of FeO: A diffusion Monte Carlo study

NASA Astrophysics Data System (ADS)

Townsend, Joshua; Shulenburger, Luke; Mattsson, Thomas; Esler, Ken; Cohen, Ronald

While simple in terms of structure and composition, both experimental and computational investigations have demonstrated that FeO has a rich phase diagram of structural phase transformations, electronic spin transitions, insulator-metal transitions, and magnetic ordering transitions, due to the open-shell occupation of the Fe 3d electrons. We investigated the magnetic and electronic structures of FeO under ambient and high pressure conditions using diffusion Quantum Monte Carlo (QMC) within the fixed-node approximation. QMC techniques are especially well suited to the study of strongly correlated systems because they explicitly include correlation into the ground-state wave function. Here we report on the effects of the choice of trial wave function on the ambient pressure lattice distortion due to AFM ordering, as well as the equation of state, spin collapse, and metal-insulator transitions. Sandia National Laboratories is a multi-mission laboratory managed and operated by Sandia Corporation, a wholly owned subsidiary of Lockheed Martin Corporation, for the U.S. Department of Energy's National Nuclear Security Administration under contract DE.
Structural phase transition and 5f-electrons localization of PuSe explored by ab initio calculations

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

Cui Shouxin, E-mail: shouxincui@yahoo.co; Feng Wenxia; Hu Haiquan

2010-04-15

An investigation into the structural phase transformation, electronic and optical properties of PuSe under high pressure was conducted by using the full potential linearized augmented plane wave plus local orbitals (FP-LAPW+lo) method, in the presence and in the absence of spin-orbit coupling (SOC). Our results demonstrate that there exists a structural phase transition from rocksalt (B 1) structure to CsCl-type (B 2) structure at the transition pressure of 36.3 GPa (without SOC) and 51.3 GPa (with SOC). The electronic density of states (DOS) for PuSe show that the f-electrons of Pu are more localized and concentrated in a narrow peakmore » near the Fermi level, which is consistent with the experimental studies. The band structure shows that B 1-PuSe is metallic. A pseudogap appears around the Fermi level of the total density of states of B 1 phase PuSe, which may contribute to its stability. The calculated reflectivity R(omega) shows agreement with the available experimental results. Furthermore, the absorption spectrum, refractive index, extinction coefficient, energy-loss spectrum and dielectric function were calculated. The origin of the spectral peaks was interpreted based on the electronic structures. - Abstract: Graphical Abstract Legend (TOC Figure): 5f-electrons are more localized by the analysis of the density of states (SOC). The origin spectra peaks was interpreted based on electronic structures.« less
Structural basis of urea-induced unfolding: Unraveling the folding pathway of hemochromatosis factor E.

PubMed

Khan, Parvez; Prakash, Amresh; Haque, Md Anzarul; Islam, Asimul; Hassan, Md Imtaiyaz; Ahmad, Faizan

2016-10-01

Hereditary hemochromatosis factor E (HFE) is a type 1 transmembrane protein, and acts as a negative regulator of iron-uptake. The equilibrium unfolding and conformational stability of the HFE protein was examined in the presence of urea. The folding and unfolding transitions were monitored with the help of circular dichroism (CD), intrinsic fluorescence and absorption spectroscopy. Analysis of transition curves revealed that the folding of HFE is not a two-state process. However, it involved stable intermediates. Transition curves (plot of fluorescence (F346) and CD signal at 222nm (θ222) versus [Urea], the molar urea concentration) revealed a biphasic transition with midpoint (Cm) values at 2.88M and 4.95M urea. Whereas, absorption analysis shows one two-state transition centered at 2.96M. To estimate the protein stability, denaturation curves were analyzed for Gibbs free energy change in the absence of urea (ΔGD(0)) associated with the equilibrium of denaturation exist between native state↔denatured state. The intermediate state was further characterized by hydrophobic probe, 1-anilinonaphthalene-8-sulfonic acid (ANS-binding). For seeing the effect of urea on the structure and dynamics of HFE, molecular dynamics simulation for 60ns was also performed. A clear correspondence was established between the in vitro and in silico studies. Copyright © 2016 Elsevier B.V. All rights reserved.
Structures and Binding Energies of the Naphthalene Dimer in Its Ground and Excited States.

PubMed

Dubinets, N O; Safonov, A A; Bagaturyants, A A

2016-05-05

Possible structures of the naphthalene dimer corresponding to local energy minima in the ground and excited (excimer) electronic states are comprehensively investigated using DFT-D and TDDFT-D methods with a special accent on the excimer structures. The corresponding binding and electronic transition energies are calculated, and the nature of the electronic states in different structures is analyzed. Several parallel (stacked) and T-shaped structures were found in both the ground and excited (excimer) states in a rather narrow energy range. The T-shaped structure with the lowest energy in the excited state exhibits a marked charge transfer from the upright molecule to the base one.
Transitions in U.S. Higher Education: Implications for Geography Learning

ERIC Educational Resources Information Center

Nellis, M. Duane

2017-01-01

In the United States, higher education institutions and structures governing higher education are going through dramatic change. The implications of new technology and changing modes of course structure, and evolving federal and state policies have the potential for significant impact on higher education. The historic federal mandates regarding…
In-Beam Studies of High-Spin States in Mercury -183 and MERCURY-181

NASA Astrophysics Data System (ADS)

Shi, Detang

The high-spin states of ^{183 }Hg were studied by using the reaction ^{155}Gd(^{32}S, 4n)^{183}Hg at a beam energy of 160 MeV with the tandem-linac accelerator system and the multi-element gamma-ray detection array at Florida State University. Two new bands, consisting of stretched E2 transitions and connected by M1 inter-band transitions, were identified in ^{183}Hg. Several new levels were added to the previously known bands at higher spin. The spins and parities to the levels in ^{183}Hg were determined from the analysis of their DCO ratios and B(M1)/B(E2) ratios. While the two pairs of previously known bands in ^ {183}Hg were proposed to 7/2^ -[514] and 9/2^+ [624], the two new bands are assigned as the 1/2^-[521] ground state configuration based upon the systematics of Nilsson orbitals in this mass region. The 354-keV transition previously was considered to be an E2 transition and assigned as the only transition from a band which is built on an oblate deformed i_{13/2} isomeric state. However, our DCO ratio analysis indicates that the 354-keV gamma-ray is an M1 transition. This changes the decay pattern of the 9/2^+[624 ] prolate structure in ^ {183}Hg, so it is seen to feed only into the i_{13/2} isomer band head. Our knowledge of the mercury nuclei far from stability was then extended through an in-beam study of the reaction ^{144}Sm(^{40 }Ar, 3n)^{181}Hg by using the Fragment Mass Analyzer (FMA) and the ten-Compton-suppressed -germanium-detector system at Argonne National Laboratory. Band structures to high-spin states are established for the first time in ^{181}Hg in the present experiment. The observed level structure of ^{181}Hg is midway between those in ^{185}Hg and in ^{183}Hg. The experimental results are analyzed in the framework of the cranking shell model (CSM). Alternative theoretical explanations are also presented and discussed. Systematics of neighboring mercury isotopes and N = 103 isotones is analyzed.
Magnetic layering transitions in a polyamidoamine (PAMAM) dendrimer nano-structure: Monte Carlo study

NASA Astrophysics Data System (ADS)

Ziti, S.; Aouini, S.; Labrim, H.; Bahmad, L.

2017-02-01

We study the magnetic layering transitions in a polyamidoamine (PAMAM) dendrimer nano-structure, under the effect of an external magnetic field. We examine the magnetic properties, of this model of the spin S=1 Ising ferromagnetic in real nanostructure used in several scientific domains. For T=0, we give and discuss the ground state phase diagrams. At non null temperatures, we applied the Monte Carlo simulations giving important results summarized in the form of the phase diagrams. We also analyzed the effect of varying the external magnetic field, and found the layering transitions in the polyamidoamine (PAMAM) dendrimer nano-structure.
TransQUAL Online User's Guide: Improving Student Transitions to Life after School. Version 3.0

ERIC Educational Resources Information Center

Brewer, David

2006-01-01

TransQUAL Online is designed to assist school districts collaborate with others and continuously improve their transition practices for youth. TransQUAL incorporates New York State Education Department Transition Quality Indicators (TQI), based on the work of Paula Kolher from Western Michigan University. The TQI assesses program structure,…
A Time Integration Algorithm Based on the State Transition Matrix for Structures with Time Varying and Nonlinear Properties

NASA Technical Reports Server (NTRS)

Bartels, Robert E.

2003-01-01

A variable order method of integrating the structural dynamics equations that is based on the state transition matrix has been developed. The method has been evaluated for linear time variant and nonlinear systems of equations. When the time variation of the system can be modeled exactly by a polynomial it produces nearly exact solutions for a wide range of time step sizes. Solutions of a model nonlinear dynamic response exhibiting chaotic behavior have been computed. Accuracy of the method has been demonstrated by comparison with solutions obtained by established methods.
Insights into the Effects of Zinc Doping on Structural Phase Transition of P2-Type Sodium Nickel Manganese Oxide Cathodes for High-Energy Sodium Ion Batteries.

PubMed

Wu, Xuehang; Xu, Gui-Liang; Zhong, Guiming; Gong, Zhengliang; McDonald, Matthew J; Zheng, Shiyao; Fu, Riqiang; Chen, Zonghai; Amine, Khalil; Yang, Yong

2016-08-31

P2-type sodium nickel manganese oxide-based cathode materials with higher energy densities are prime candidates for applications in rechargeable sodium ion batteries. A systematic study combining in situ high energy X-ray diffraction (HEXRD), ex situ X-ray absorption fine spectroscopy (XAFS), transmission electron microscopy (TEM), and solid-state nuclear magnetic resonance (SS-NMR) techniques was carried out to gain a deep insight into the structural evolution of P2-Na0.66Ni0.33-xZnxMn0.67O2 (x = 0, 0.07) during cycling. In situ HEXRD and ex situ TEM measurements indicate that an irreversible phase transition occurs upon sodium insertion-extraction of Na0.66Ni0.33Mn0.67O2. Zinc doping of this system results in a high structural reversibility. XAFS measurements indicate that both materials are almost completely dependent on the Ni(4+)/Ni(3+)/Ni(2+) redox couple to provide charge/discharge capacity. SS-NMR measurements indicate that both reversible and irreversible migration of transition metal ions into the sodium layer occurs in the material at the fully charged state. The irreversible migration of transition metal ions triggers a structural distortion, leading to the observed capacity and voltage fading. Our results allow a new understanding of the importance of improving the stability of transition metal layers.
Pressure-induced structural change in liquid GeI4.

PubMed

Fuchizaki, Kazuhiro; Nishimura, Hironori; Hase, Takaki; Saitoh, Hiroyuki

2017-12-27

The similarity in the shape of the melting curve of GeI 4 to that of SnI 4 suggests that a liquid-liquid transition as observed in liquid SnI 4 is also expected to occur in liquid GeI 4 . Because the slope of the melting curve of GeI 4 abruptly changes at around 3 GPa, in situ synchrotron diffraction measurements were conducted to examine closely the structural changes upon compression at around 3 GPa. The reduced radial distribution functions of the high- and low-pressure liquid states of GeI 4 share the same feature inherent in the high-pressure (high-density) and low-pressure (low-density) radial distribution functions of liquid SnI 4 . This feature allows us to introduce local order parameters that we may use to observe the transition. Unlike the transition in liquid SnI 4 , the transition from the low-pressure to the high-pressure structure seems sluggish. We speculate that the liquid-liquid critical point of GeI 4 is no longer a thermodynamically stable state and is slightly located below the melting curve. As a result, the structural change is said to be a crossover rather than a transition. The behavior of the local-order parameters implies a metastable extension of the liquid-liquid phase boundary with a negative slope.
Far-infrared laser magnetic resonance of vibrationally excited CD2

NASA Technical Reports Server (NTRS)

Evenson, K. M.; Sears, T. J.; Mckellar, A. R. W.

1984-01-01

The detection of 13 rotational transitions in the first excited bending state (010) of CD2 using the technique of far-infrared laser magnetic resonance spectroscopy is reported. Molecular parameters for this state are determined from these new data together with existing infrared observations of the v(2) band. Additional information on the ground vibrational state (000) is also provided by the observation of a new rotational transition, and this is combined with existing data to provide a refined set of molecular parameters for the CD2 ground state. One spectrum has been observed that is assigned as a rotational transition within the first excited symmetric stretching state (100) of CD2. These data will be of use in refining the structure and the potential function of the methylene radical.
First-principles study of the structural properties of Ge

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

Chang, K.J.; Cohen, M.L.

1986-12-15

With the use of an ab initio pseudopotential method, the structural properties of Ge are investigated at normal and high pressures. The pressure-induced structural phase transitions from cubic diamond to ..beta..-Sn, to simple hexagonal (sh), and to double hexagonal close packed (dhcp) are examined. With the possible exception of the dhcp structure, the calculated transition pressures, transition volumes, and axial ratios are in good agreement with experimental results. We find that sh Ge has characteristics similar to those of sh Si; the bonds between hexagonal layers are stronger than intralayer bonds and the transverse phonon modes become soft near themore » transitions from the sh to ..beta..-Sn and the sh to hcp structures. At normal pressures, we compare the crystal energies for the cubic diamond, hexagonal 2H, and hexagonal 4H structures. Because of the similar sp/sup 3/ bonds in these structures, the structural energy differences are less than about 14 meV, and the 2H and 4H phases are metastable with respect to the cubic diamond structure. The equation of state is also presented and compared with experiment.« less
X-ray diffraction study of elemental thulium to 86 GPa

NASA Astrophysics Data System (ADS)

Pravica, Michael; Romano, Edward; Quine, Zachary; Pravica, Walter

2006-03-01

We have studied the structures and equation of state of elemental thulium up to 86 GPa in a diamond anvil cell using angular-dispersive x-ray powder diffraction methods at the Advanced Photon Source. This is part of a study of phase transitions in the lanthanide-series metals using cyclohexane as a quasi-hydrostatic medium. We present evidence of a series of phase transitions that appear to follow the anticipated hcp ->Sm-type -> dhcp -> distorted fcc sequence of transitions and show the equation of state derived from the x-ray fit data.
Spectroscopy of Vibrational States in Diatomic Iodine Molecules

NASA Astrophysics Data System (ADS)

Mulholland, Mary; Harrill, Charles H.; Smith, R. Seth

2015-04-01

This project is focused on understanding the vibrational structure of iodine, which is a homonuclear diatomic molecule. A 20 mW, 532 nm cw diode laser was used to selectively excite neutral iodine molecules to a higher energy electronic state. By performing spectroscopy on the transitions from this state to a lower energy electronic state, the data only showed those vibrational bands which connect the two electronic states. Since a number of vibrational levels are populated in the higher energy electronic state, the transitions to all of the allowed vibrational levels in the lower energy electronic state provided sufficient data to determine the vibrational structures of both states. Emission spectra were collected with an Ocean Optics USB4000 Compact CCD Spectrometer. The spectrometer had a range of 500 - 770 nm with a resolution of approximately 0.5 nm and was sensitive enough to resolve the vibrational states in diatomic iodine molecules. The results were compared to a simple harmonic oscillator model.
Transitional circuitry for studying the properties of DNA

NASA Astrophysics Data System (ADS)

Trubochkina, N.

2018-01-01

The article is devoted to a new view of the structure of DNA as an intellectual scheme possessing the properties of logic and memory. The theory of transient circuitry, developed by the author for optimal computer circuits, revealed an amazing structural similarity between mathematical models of transition silicon elements and logic and memory circuits of solid state transient circuitry and atomic models of parts of DNA.
A molten globule-like intermediate state detected in the thermal transition of cytochrome c under low salt concentration.

PubMed

Nakamura, Shigeyoshi; Baba, Takayuki; Kidokoro, Shun-Ichi

2007-04-01

To understand the stabilization mechanism of the transient intermediate state in protein folding, it is very important to understand the structure and stability of the molten globule state under a native condition, in which the native state exists stably. The thermal transitions of horse cytochrome c were thermodynamically evaluated by highly precise differential scanning calorimetry (DSC) at pH 3.8-5.0. The heat capacity functions were analyzed using double deconvolution and the nonlinear least-squares method. An intermediate (I) state is clearly confirmed in the thermal native (N)-to-denatured (D) transition of horse cytochrome c. The mole fraction of the intermediate state shows the largest value, 0.4, at nearly 70 degrees C at pH 4.1. This intermediate state was also detected by the circular dichroism (CD) method and was found to have the properties of the molten globule-like structure by three-state analysis of the CD data. The Gibbs free-energy change between N and I, DeltaG(NI), and that between N and D, DeltaG(ND), were evaluated to be 9-22 kJ mol(-1) and 41-45 kJ mol(-1), respectively at 15( ) degrees C and pH 4.1.
DOE Office of Scientific and Technical Information (OSTI.GOV)

Yu, Liang; Abild-Pedersen, Frank

On the basis of an extensive set of density functional theory calculations, it is shown that a simple scheme provides a fundamental understanding of variations in the transition state energies and structures of reaction intermediates on transition metal surfaces across the periodic table. The scheme is built on the bond order conservation principle and requires a limited set of input data, still achieving transition state energies as a function of simple descriptors with an error smaller than those of approaches based on linear fits to a set of calculated transition state energies. Here, we have applied this approach together withmore » linear scaling of adsorption energies to obtain the energetics of the NH 3 decomposition reaction on a series of stepped fcc(211) transition metal surfaces. Moreover, this information is used to establish a microkinetic model for the formation of N 2 and H 2, thus providing insight into the components of the reaction that determines the activity.« less

Hydrogen-bonded intermediates and transition states during spontaneous and acid-catalyzed hydrolysis of the carcinogen (+)-anti-BPDE.

PubMed

Palenik, Mark C; Rodriguez, Jorge H

2014-07-07

Understanding mechanisms of (+)-anti-BPDE detoxification is crucial for combating its mutagenic and potent carcinogenic action. However, energetic-structural correlations of reaction intermediates and transition states during detoxification via hydrolysis are poorly understood. To gain mechanistic insight we have computationally characterized intermediate and transition species associated with spontaneous and general-acid catalyzed hydrolysis of (+)-anti-BPDE. We studied the role of cacodylic acid as a proton donor in the rate limiting step. The computed activation energy (ΔG‡) is in agreement with the experimental value for hydrolysis in a sodium cacodylate buffer. Both types of, spontaneous and acid catalyzed, BPDE hydrolysis can proceed through low-entropy hydrogen bonded intermediates prior to formation of transition states whose energies determine reaction activation barriers and rates.
Quantum transition state dynamics of the cyclooctatetraene unimolecular reaction on ab initio potential energy surfaces

NASA Astrophysics Data System (ADS)

Tokizaki, Chihiro; Yoshida, Takahiko; Takayanagi, Toshiyuki

2016-05-01

The cyclooctatetraene (COT) anion has a stable D4h structure that is similar to the transition state configurations of the neutral C-C bond-alternation (D4h ↔ D8h ↔ D4h) and ring-inversion (D2d ↔ D4h ↔ D2d) unimolecular reactions. The previously measured photodetachment spectrum of COT- revealed the reaction dynamics in the vicinity of the two transition states on the neutral potential energy surface. In this work, the photodetachment spectrum is calculated quantum mechanically on ab initio-level potential energy surfaces within a three degree-of-freedom reduced-dimensionality model. Very good agreement has been obtained between theory and experiment, providing reliable interpretations for the experimental spectrum. A detailed picture of the reactive molecular dynamics of the COT unimolecular reaction in the transition state region is also discussed.
Structural state diagram of concentrated suspensions of jammed soft particles in oscillatory shear flow

NASA Astrophysics Data System (ADS)

Khabaz, Fardin; Cloitre, Michel; Bonnecaze, Roger T.

2018-03-01

In a recent study [Khabaz et al., Phys. Rev. Fluids 2, 093301 (2017), 10.1103/PhysRevFluids.2.093301], we showed that jammed soft particle glasses (SPGs) crystallize and order in steady shear flow. Here we investigate the rheology and microstructures of these suspensions in oscillatory shear flow using particle-dynamics simulations. The microstructures in both types of flows are similar, but their evolutions are very different. In both cases the monodisperse and polydisperse suspensions form crystalline and layered structures, respectively, at high shear rates. The crystals obtained in the oscillatory shear flow show fewer defects compared to those in the steady shear. SPGs remain glassy for maximum oscillatory strains less than about the yield strain of the material. For maximum strains greater than the yield strain, microstructural and rheological transitions occur for SPGs. Polydisperse SPGs rearrange into a layered structure parallel to the flow-vorticity plane for sufficiently high maximum shear rates and maximum strains about 10 times greater than the yield strain. Monodisperse suspensions form a face-centered cubic (FCC) structure when the maximum shear rate is low and hexagonal close-packed (HCP) structure when the maximum shear rate is high. In steady shear, the transition from a glassy state to a layered one for polydisperse suspensions included a significant induction strain before the transformation. In oscillatory shear, the transformation begins to occur immediately and with different microstructural changes. A state diagram for suspensions in large amplitude oscillatory shear flow is found to be in close but not exact agreement with the state diagram for steady shear flow. For more modest amplitudes of around one to five times the yield strain, there is a transition from a glassy structure to FCC and HCP crystals, at low and high frequencies, respectively, for monodisperse suspensions. At moderate frequencies, the transition is from glassy to HCP via an intermediate FCC phase.
Thermopower analysis of the electronic structure around the metal-insulator transition in V1-xWxO2

NASA Astrophysics Data System (ADS)

Katase, Takayoshi; Endo, Kenji; Ohta, Hiromichi

2014-10-01

The electronic structure across the metal-insulator (MI) transition of electron-doped V1-xWxO2 epitaxial films (x =0-0.06) grown on α-Al2O3 substrates was studied by means of thermopower (S) measurements. Significant increase of |S | values accompanied by MI transition was observed, and the transition temperatures of S (TS) decreased with x in a good linear relation with MI transition temperatures. |S| values of V1-xWxO2 films at T>TS were constant at low values of 23μVK-1 independently of x, which reflects a metallic electronic structure, whereas those at T
Evolution of structural and transport properties in Y-doped double perovskite Sr2FeIrO6

NASA Astrophysics Data System (ADS)

Kharkwal, K. C.; Pramanik, A. K.

2018-05-01

The structural and transport properties of Yttrium doped double perovskite Sr2FeIrO6 have been investigated. Structural properties have been investigated by means of x-ray diffraction measurement and Rietveld analysis. Structural transition has not been observed although lattice parameters evolve with the Yttrium doping. All samples have been found to be insulating over the whole temperature range where the resistivity increases with doping. This increase in resistivity with doping may be due to the change in charge state of transition metal.
Reducing fatigue damage for ships in transit through structured decision making

USGS Publications Warehouse

Nichols, J.M.; Fackler, P.L.; Pacifici, K.; Murphy, K.D.; Nichols, J.D.

2014-01-01

Research in structural monitoring has focused primarily on drawing inference about the health of a structure from the structure’s response to ambient or applied excitation. Knowledge of the current state can then be used to predict structural integrity at a future time and, in principle, allows one to take action to improve safety, minimize ownership costs, and/or increase the operating envelope. While much time and effort has been devoted toward data collection and system identification, research to-date has largely avoided the question of how to choose an optimal maintenance plan. This work describes a structured decision making (SDM) process for taking available information (loading data, model output, etc.) and producing a plan of action for maintaining the structure. SDM allows the practitioner to specify his/her objectives and then solves for the decision that is optimal in the sense that it maximizes those objectives. To demonstrate, we consider the problem of a Naval vessel transiting a fixed distance in varying sea-state conditions. The physics of this problem are such that minimizing transit time increases the probability of fatigue failure in the structural supports. It is shown how SDM produces the optimal trip plan in the sense that it minimizes both transit time and probability of failure in the manner of our choosing (i.e., through a user-defined cost function). The example illustrates the benefit of SDM over heuristic approaches to maintaining the vessel.
Elucidating the ensemble of functionally-relevant transitions in protein systems with a robotics-inspired method.

PubMed

Molloy, Kevin; Shehu, Amarda

2013-01-01

Many proteins tune their biological function by transitioning between different functional states, effectively acting as dynamic molecular machines. Detailed structural characterization of transition trajectories is central to understanding the relationship between protein dynamics and function. Computational approaches that build on the Molecular Dynamics framework are in principle able to model transition trajectories at great detail but also at considerable computational cost. Methods that delay consideration of dynamics and focus instead on elucidating energetically-credible conformational paths connecting two functionally-relevant structures provide a complementary approach. Effective sampling-based path planning methods originating in robotics have been recently proposed to produce conformational paths. These methods largely model short peptides or address large proteins by simplifying conformational space. We propose a robotics-inspired method that connects two given structures of a protein by sampling conformational paths. The method focuses on small- to medium-size proteins, efficiently modeling structural deformations through the use of the molecular fragment replacement technique. In particular, the method grows a tree in conformational space rooted at the start structure, steering the tree to a goal region defined around the goal structure. We investigate various bias schemes over a progress coordinate for balance between coverage of conformational space and progress towards the goal. A geometric projection layer promotes path diversity. A reactive temperature scheme allows sampling of rare paths that cross energy barriers. Experiments are conducted on small- to medium-size proteins of length up to 214 amino acids and with multiple known functionally-relevant states, some of which are more than 13Å apart of each-other. Analysis reveals that the method effectively obtains conformational paths connecting structural states that are significantly different. A detailed analysis on the depth and breadth of the tree suggests that a soft global bias over the progress coordinate enhances sampling and results in higher path diversity. The explicit geometric projection layer that biases the exploration away from over-sampled regions further increases coverage, often improving proximity to the goal by forcing the exploration to find new paths. The reactive temperature scheme is shown effective in increasing path diversity, particularly in difficult structural transitions with known high-energy barriers.
Scan Rate Dependent Spin Crossover Iron(II) Complex with Two Different Relaxations and Thermal Hysteresis fac-[Fe(II)(HL(n-Pr))3]Cl·PF6 (HL(n-Pr) = 2-Methylimidazol-4-yl-methylideneamino-n-propyl).

PubMed

Fujinami, Takeshi; Nishi, Koshiro; Hamada, Daisuke; Murakami, Keishiro; Matsumoto, Naohide; Iijima, Seiichiro; Kojima, Masaaki; Sunatsuki, Yukinari

2015-08-03

Solvent-free spin crossover Fe(II) complex fac-[Fe(II)(HL(n-Pr))3]Cl·PF6 was prepared, where HL(n-Pr) denotes 2-methylimidazol-4-yl-methylideneamino-n-propyl. The magnetic susceptibility measurements at scan rate of 0.5 K min(-1) showed two successive spin transition processes consisting of the first spin transition T1 centered at 122 K (T1↑ = 127.1 K, T1↓ = 115.8 K) and the second spin transition T2 centered at ca. 105 K (T2↑ = 115.8 K, T2↓ = 97.2 K). The magnetic susceptibility measurements at the scan rate of 2.0, 1.0, 0.5, 0.25, and 0.1 K min(-1) showed two scan speed dependent spin transitions, while the Mössbauer spectra detected only the first spin transition T1. The crystal structures were determined at 160, 143, 120, 110, 95 K in the cooling mode, and 110, 120, and 130 K in the warming mode so as to follow the spin transition process of high-spin HS → HS(T1) → HS(T2) → low-spin LS → LS(T2) → LS(T1) → HS. The crystal structures at all temperatures have a triclinic space group P1̅ with Z = 2. The complex-cation has an octahedral N6 coordination geometry with three bidentate ligands and assume a facial-isomer with Δ- and Λ-enantimorphs. Three imidazole groups of fac-[Fe(II)(HL(n-Pr))3](2+) are hydrogen-bonded to three Cl(-) ions. The 3:3 NH(imidazole)···Cl(-) hydrogen-bonds form a stepwise ladder assembly structure, which is maintained during the spin transition process. The spin transition process is related to the structural changes of the FeN6 coordination environment, the order-disorder of PF6(-) anion, and the conformation change of n-propyl groups. The Fe-N bond distance in the HS state is longer by 0.2 Å than that in the LS state. Disorder of PF6(-) anion is not observed in the LS state but in the HS state. The conformational changes of n-propyl groups are found in the spin transition processes except for HS → HS(T1) → HS(T2).
The transition state structure for binding between TAZ1 of CBP and the disordered Hif-1α CAD.

PubMed

Lindström, Ida; Andersson, Eva; Dogan, Jakob

2018-05-18

Intrinsically disordered proteins (IDPs) are common in eukaryotes. However, relatively few experimental studies have addressed the nature of the rate-limiting transition state for the coupled binding and folding reactions involving IDPs. By using site-directed mutagenesis in combination with kinetics measurements we have here characterized the transition state for binding between the globular TAZ1 domain of CREB binding protein and the intrinsically disordered C-terminal activation domain of Hif-1α (Hif-1α CAD). A total of 17 Hif-1α CAD point-mutations were generated and a Φ-value binding analysis was carried out. We found that native hydrophobic binding interactions are not formed at the transition state. We also investigated the effect the biologically important Hif-1α CAD Asn-803 hydroxylation has on the binding kinetics, and found that the whole destabilization effect due the hydroxylation is within the dissociation rate constant. Thus, the rate-limiting transition state is "disordered-like", with native hydrophobic binding contacts being formed cooperatively after the rate-limiting barrier, which is clearly shown by linear free energy relationships. The same behavior was observed in a previously characterized TAZ1/IDP interaction, which may suggest common features for the rate-limiting transition state for TAZ1/IDP interactions.
Volume-wise destruction of the antiferromagnetic Mott insulating state through quantum tuning.

NASA Astrophysics Data System (ADS)

Uemura, Yasutomo

RENiO3 (RE = rare-earth element) and V2O3 are archetypal Mott insulator systems. When tuned by chemical substitution (RENiO3) or hydrostatic pressure (V2O3) , they exhibit a quantum phase transition (QPT) between an antiferromagnetic Mott insulating state and a paramagnetic metallic state. We demonstrate through muon spin relaxation/rotation (μSR) experiments that the QPT in RENiO3 and V2O3 is first order: the magnetically ordered volume fraction decreases to zero at the QPT, resulting in a broad region of intrinsic phase separation, while the ordered magnetic moment retains its full value until it is suddenly destroyed at the QPT. These two cases correspond to the band-width tuning of Mott transitions, and also associated with structural phase transitions, Volume evolutions of antiferromagnetic transition from μSR will be compared to those of structure by x-ray and metallicity by nano optics, in first-order thermal Mott transition in a V2O3 film at ambient pressure. These results will be compared to the process of destruction of magnetic order in another Mott transition system Ba(Co,Ni)S2 in ``filling control'' without structural transition, and in parent compounds of high-Tc cuprates and Fe-based superconductors. We will also discuss roles of first-order quantum transition in generating soft modes relevant to magnetic resonance mode in unconventional superconductors. Work performed in collaboration with the groups of: J.A. Alonso (Madrid), H. Kageyama (Kyoto). E. Morenzoni (PSI), G.M. Luke (McMaster), C.Q. Jin (IOP Beijing), F.L. Ning (Zhejian), S.J.L. Billinge (Columbia), S. Shamoto, W. Higemoto (JAEA), A. Fujimori (Tokyo), A. Gauzzi (Paris), R. de Renzi (Parma), G. Kotliar (Rutgers), M. Imada (Tokyo), D. Basov (UCSD), I, Schuller (UCSD). supported by NSF DMR-1610633 and DMR-1436095 (DMREF).
An Examination of the Mixing of Low-Lying Excited 0+ States in 116Sn

NASA Astrophysics Data System (ADS)

Pore, Jennifer Louise

The even-even tin isotopes are known to exhibit shape coexistence, the phenomenon where multiple shapes coexist in a narrow energy region at relatively lowlying levels of the nucleus. These nuclei have a 0+ spherical ground state and multiple excited 0+ states, one of which is a band head for a deformed rotational band, caused by the promotion of two protons across the Z=50 shell gap. Experimental and theoretical investigations have been performed on 116Sn to describe the nature of the mixing that occurs between the vibrational phonon levels and the deformed rotational band by probing the character of the excited 0+ states. At the time it was thought that the 0+ states showed almost equal mixing of rotational and vibrational character, but this result was based on an indirect observation and fit of the intensity of a weak 85 keV transition. The current work, a high-statistics 116Sn measurement, demonstrates unequal mixing of character between the two excited 0+ states based on a direct measurement of the intensity of the 85 keV transition. These new results might prompt a new interpretation of the structure of 116Sn. The experiment to investigate the low-lying structure of 116Sn was conducted at TRIUMF, Canada's National Laboratory for Nuclear and Particle Physics. A highintensity and high-purity beam of 116In was used to populate states in 116Sn via beta decay. The resulting gamma rays were observed with the 8th detector array, which consists of twenty high-purity Compton-suppressed germanium detectors coupled to a suite of ancillary detectors for beta particle detection and conversion electron spectroscopy. From this high-statistics measurement 57 gamma-ray transitions were observed, with 4 new transitions that depopulate the 3096 keV level observed for the first time with energies of 101 keV, 296 keV, 447 keV, and 871 keV. Branching ratios were determined for all of the observed transitions. For the 57 transitions observed, a relative intensity had not been reported for 17 of them, and a branching ratio had not been reported for 12 of them. Transition rates were determined for 25 transitions that depopulate levels with previously reported lifetimes, and 2 of these transition rates had not been previously observed.
High-resolution study of Gamow-Teller transitions in the 47Ti(3He,t)47V reaction

NASA Astrophysics Data System (ADS)

Ganioǧlu, E.; Fujita, H.; Fujita, Y.; Adachi, T.; Algora, A.; Csatlós, M.; Deaven, J. M.; Estevez-Aguado, E.; Guess, C. J.; Gulyás, J.; Hatanaka, K.; Hirota, K.; Honma, M.; Ishikawa, D.; Krasznahorkay, A.; Matsubara, H.; Meharchand, R.; Molina, F.; Okamura, H.; Ong, H. J.; Otsuka, T.; Perdikakis, G.; Rubio, B.; Scholl, C.; Shimbara, Y.; Susoy, G.; Suzuki, T.; Tamii, A.; Thies, J. H.; Zegers, R. G. T.; Zenihiro, J.

2013-01-01

Given the importance of Gamow-Teller (GT) transitions in nuclear structure and astrophysical nuclear processes, we have studied Tz=+3/2→+1/2, GT transitions starting from the 47Ti nucleus in the (3He,t) charge-exchange reaction at 0∘ and at an intermediate incident energy of 140 MeV/nucleon. The experiments were carried out at the Research Center for Nuclear Physics (RCNP), Osaka, using the high-resolution facility with a high-dispersion beam line and the Grand-Raiden spectrometer. With an energy resolution of 20 keV, individual GT transitions were observed and GT strength was derived for each state populated up to an excitation energy (Ex) of 12.5 MeV. The GT strength was widely distributed from low excitation energy up to 12.5 MeV, where we had to stop the analysis because of the high level density. The distribution of the GT strengths was compared with the results of shell model calculations using the GXPF1 interaction. The calculations could reproduce the experimental GT distributions well. The GT transitions from the ground state of 47Ti and the M1 transitions from the isobaric analog state in 47V to the same low-lying states in 47V are analogous. It was found that the ratios of GT transition strengths to the ground state, the 0.088-MeV state, and the 0.146-MeV state are similar to the ratios of the strengths of the analogous M1 transitions from the isobaric analog state (IAS) to these states. The measured distribution of the GT strengths was also compared with those starting from the Tz=+3/2 nucleus 41K to the Tz=+1/2 nucleus 41Ca.
Geometric structure and information change in phase transitions

NASA Astrophysics Data System (ADS)

Kim, Eun-jin; Hollerbach, Rainer

2017-06-01

We propose a toy model for a cyclic order-disorder transition and introduce a geometric methodology to understand stochastic processes involved in transitions. Specifically, our model consists of a pair of forward and backward processes (FPs and BPs) for the emergence and disappearance of a structure in a stochastic environment. We calculate time-dependent probability density functions (PDFs) and the information length L , which is the total number of different states that a system undergoes during the transition. Time-dependent PDFs during transient relaxation exhibit strikingly different behavior in FPs and BPs. In particular, FPs driven by instability undergo the broadening of the PDF with a large increase in fluctuations before the transition to the ordered state accompanied by narrowing the PDF width. During this stage, we identify an interesting geodesic solution accompanied by the self-regulation between the growth and nonlinear damping where the time scale τ of information change is constant in time, independent of the strength of the stochastic noise. In comparison, BPs are mainly driven by the macroscopic motion due to the movement of the PDF peak. The total information length L between initial and final states is much larger in BPs than in FPs, increasing linearly with the deviation γ of a control parameter from the critical state in BPs while increasing logarithmically with γ in FPs. L scales as |lnD | and D-1 /2 in FPs and BPs, respectively, where D measures the strength of the stochastic forcing. These differing scalings with γ and D suggest a great utility of L in capturing different underlying processes, specifically, diffusion vs advection in phase transition by geometry. We discuss physical origins of these scalings and comment on implications of our results for bistable systems undergoing repeated order-disorder transitions (e.g., fitness).
Geometric structure and information change in phase transitions.

PubMed

Kim, Eun-Jin; Hollerbach, Rainer

2017-06-01

We propose a toy model for a cyclic order-disorder transition and introduce a geometric methodology to understand stochastic processes involved in transitions. Specifically, our model consists of a pair of forward and backward processes (FPs and BPs) for the emergence and disappearance of a structure in a stochastic environment. We calculate time-dependent probability density functions (PDFs) and the information length L, which is the total number of different states that a system undergoes during the transition. Time-dependent PDFs during transient relaxation exhibit strikingly different behavior in FPs and BPs. In particular, FPs driven by instability undergo the broadening of the PDF with a large increase in fluctuations before the transition to the ordered state accompanied by narrowing the PDF width. During this stage, we identify an interesting geodesic solution accompanied by the self-regulation between the growth and nonlinear damping where the time scale τ of information change is constant in time, independent of the strength of the stochastic noise. In comparison, BPs are mainly driven by the macroscopic motion due to the movement of the PDF peak. The total information length L between initial and final states is much larger in BPs than in FPs, increasing linearly with the deviation γ of a control parameter from the critical state in BPs while increasing logarithmically with γ in FPs. L scales as |lnD| and D^{-1/2} in FPs and BPs, respectively, where D measures the strength of the stochastic forcing. These differing scalings with γ and D suggest a great utility of L in capturing different underlying processes, specifically, diffusion vs advection in phase transition by geometry. We discuss physical origins of these scalings and comment on implications of our results for bistable systems undergoing repeated order-disorder transitions (e.g., fitness).
Predicting a new phase (T'') of two-dimensional transition metal di-chalcogenides and strain-controlled topological phase transition

NASA Astrophysics Data System (ADS)

Ma, Fengxian; Gao, Guoping; Jiao, Yalong; Gu, Yuantong; Bilic, Ante; Zhang, Haijun; Chen, Zhongfang; Du, Aijun

2016-02-01

Single layered transition metal dichalcogenides have attracted tremendous research interest due to their structural phase diversities. By using a global optimization approach, we have discovered a new phase of transition metal dichalcogenides (labelled as T''), which is confirmed to be energetically, dynamically and kinetically stable by our first-principles calculations. The new T'' MoS2 phase exhibits an intrinsic quantum spin Hall (QSH) effect with a nontrivial gap as large as 0.42 eV, suggesting that a two-dimensional (2D) topological insulator can be achieved at room temperature. Most interestingly, there is a topological phase transition simply driven by a small tensile strain of up to 2%. Furthermore, all the known MX2 (M = Mo or W; X = S, Se or Te) monolayers in the new T'' phase unambiguously display similar band topologies and strain controlled topological phase transitions. Our findings greatly enrich the 2D families of transition metal dichalcogenides and offer a feasible way to control the electronic states of 2D topological insulators for the fabrication of high-speed spintronics devices.Single layered transition metal dichalcogenides have attracted tremendous research interest due to their structural phase diversities. By using a global optimization approach, we have discovered a new phase of transition metal dichalcogenides (labelled as T''), which is confirmed to be energetically, dynamically and kinetically stable by our first-principles calculations. The new T'' MoS2 phase exhibits an intrinsic quantum spin Hall (QSH) effect with a nontrivial gap as large as 0.42 eV, suggesting that a two-dimensional (2D) topological insulator can be achieved at room temperature. Most interestingly, there is a topological phase transition simply driven by a small tensile strain of up to 2%. Furthermore, all the known MX2 (M = Mo or W; X = S, Se or Te) monolayers in the new T'' phase unambiguously display similar band topologies and strain controlled topological phase transitions. Our findings greatly enrich the 2D families of transition metal dichalcogenides and offer a feasible way to control the electronic states of 2D topological insulators for the fabrication of high-speed spintronics devices. Electronic supplementary information (ESI) available: Detailed computational method; structural data of T'' MoS2; DOS of the T'' MoS2 phase under different strains; orbital energy of T'' MoS2 under different strains; electronic structures for all other five MX2 in the T'' phase; edge states of T'' MoS2. See DOI: 10.1039/c5nr07715j
Raman study of high temperature insulator-insulator transition in Ba2Co9O14

NASA Astrophysics Data System (ADS)

Zaghrioui, M.; Delorme, F.; Chen, C.; Camara, N. R.; Giovannelli, F.

2018-05-01

The insulator-insulator transition, at Tt = 570 K, in layered cobalt oxide Ba2Co9O14 was investigated using Raman scattering technique. High temperature (300-800 K) measurements have evidenced no structural transition occurring at Tt. The obtained results are rather consistent with low to high spin-state transition of Co3+ ions in the Co3O12 octahedral trimer. More precisely, only one cobalt ion located in the central octahedron of the trimer undergoes this transition.
Exploring the color of transition metal ions in irregular coordination geometries: new colored inorganic oxides based on the spiroffite structure, Zn(2-x)M(x)Te3O8 (M = Co, Ni, Cu).

PubMed

Tamilarasan, S; Sarma, Debajit; Bhattacharjee, S; Waghmare, U V; Natarajan, S; Gopalakrishnan, J

2013-05-20

We describe the synthesis, crystal structures, and optical absorption spectra of transition metal-substituted spiroffite derivatives, Zn(2-x)M(x)Te3O8 (M(II) = Co, Ni, Cu; 0 < x ≤ 1.0). The oxides are readily synthesized by solid state reaction of stoichiometric mixtures of the constituent binaries at 620 °C. Reitveld refinement of the crystal structures from powder X-ray diffraction (XRD) data shows that the Zn/MO6 octahedra are strongly distorted, as in the parent Zn2Te3O8 structure, consisting of five relatively short Zn/M(II)-O bonds (1.898-2.236 Å) and one longer Zn/M(II)-O bond (2.356-2.519 Å). We have interpreted the unique colors and the optical absorption/diffuse reflectance spectra of Zn(2-x)M(x)Te3O8 in the visible, in terms of the observed/irregular coordination geometry of the Zn/M(II)-O chromophores. We could not however prepare the fully substituted M2Te3O8 (M(II) = Co, Ni, Cu) by the direct solid state reaction method. Density Functional Theory (DFT) modeling of the electronic structure of both the parent and the transition metal substituted derivatives provides new insights into the bonding and the role of transition metals toward the origin of color in these materials. We believe that transition metal substituted spiroffites Zn(2-x)M(x)Te3O8 reported here suggest new directions for the development of colored inorganic materials/pigments featuring irregular/distorted oxygen coordination polyhedra around transition metal ions.
Decoding brain state transitions in the pedunculopontine nucleus: cooperative phasic and tonic mechanisms

PubMed Central

Petzold, Anne; Valencia, Miguel; Pál, Balázs; Mena-Segovia, Juan

2015-01-01

Cholinergic neurons of the pedunculopontine nucleus (PPN) are most active during the waking state. Their activation is deemed to cause a switch in the global brain activity from sleep to wakefulness, while their sustained discharge may contribute to upholding the waking state and enhancing arousal. Similarly, non-cholinergic PPN neurons are responsive to brain state transitions and their activation may influence some of the same targets of cholinergic neurons, suggesting that they operate in coordination. Yet, it is not clear how the discharge of distinct classes of PPN neurons organize during brain states. Here, we monitored the in vivo network activity of PPN neurons in the anesthetized rat across two distinct levels of cortical dynamics and their transitions. We identified a highly structured configuration in PPN network activity during slow-wave activity that was replaced by decorrelated activity during the activated state (AS). During the transition, neurons were predominantly excited (phasically or tonically), but some were inhibited. Identified cholinergic neurons displayed phasic and short latency responses to sensory stimulation, whereas the majority of non-cholinergic showed tonic responses and remained at high discharge rates beyond the state transition. In vitro recordings demonstrate that cholinergic neurons exhibit fast adaptation that prevents them from discharging at high rates over prolonged time periods. Our data shows that PPN neurons have distinct but complementary roles during brain state transitions, where cholinergic neurons provide a fast and transient response to sensory events that drive state transitions, whereas non-cholinergic neurons maintain an elevated firing rate during global activation. PMID:26582977
Atomically thin transition metal layers: Atomic layer stabilization and metal-semiconductor transition

NASA Astrophysics Data System (ADS)

Hwang, Jeongwoon; Oh, Young Jun; Kim, Jiyoung; Sung, Myung Mo; Cho, Kyeongjae

2018-04-01

We have performed first-principle calculations to explore the possibility of synthesizing atomically thin transition metal (TM) layers. Buckled structures as well as planar structures of elemental 2D TM layers result in significantly higher formation energies compared with sp-bonded elemental 2D materials with similar structures, such as silicene and phosphorene. It is shown that the TM layers can be stabilized by surface passivation with HS, C6H5S2, or O, and O passivation is most effective. The surface oxygen passivation can improve stability leading to thermodynamically stable TM monolayers except Au, which is the most non-reactive metal element. Such stabilized TM monolayers also show an electronic structure transition from metallic state of free-standing TM layer to semiconducting O-passivated Mo and W monolayers with band gaps of 0.20-1.38 eV.
Structural changes during a liquid-liquid transition in the deeply undercooled Z r58.5C u15.6N i12.8A l10.3N b2.8 bulk metallic glass forming melt

NASA Astrophysics Data System (ADS)

Stolpe, Moritz; Jonas, Isabell; Wei, Shuai; Evenson, Zach; Hembree, William; Yang, Fan; Meyer, Andreas; Busch, Ralf

2016-01-01

Using high energy synchrotron x-ray radiation combined with electrostatic levitation, in situ structural analysis of a bulk metallic glass forming liquid is performed from above the liquidus temperature down to the glass transition. The data indicate a liquid-liquid transition (LLT) in the deeply undercooled state at T /Tg˜1.2 which manifests as a maximum in the heat capacity and an abrupt shift in the first peak position of the total structure factor in the absence of a pronounced density change. Analysis of the corresponding real-space data shows that the LLT involves changes in short- and medium-range order. The structural changes on the length scale of medium-range order imply a fragile-strong transition in agreement with experimental viscosity data.

Recycling nicotinamide. The transition-state structure of human nicotinamide phosphoribosyltransferase

PubMed Central

Burgos, Emmanuel S.; Vetticatt, Mathew J.; Schramm, Vern L.

2013-01-01

Human nicotinamide phosphoribosyltransferase (NAMPT) replenishes the NAD pool and controls the activities of sirtuins (SIRT), mono- and poly-(ADP-ribose) polymerases (PARP) and NAD nucleosidase (CD38). The nature of the enzymatic transition-state (TS) is central to understanding the function of NAMPT. We determined the TS structure for pyrophosphorolysis of nicotinamide mononucleotide (NMN) by kinetic isotope effects (KIEs). With the natural substrates, NMN and pyrophosphate (PPi), the intrinsic KIEs of [1′-14C], [1-15N], [1′-3H] and [2′-3H] are 1.047, 1.029, 1.154 and 1.093, respectively. A unique quantum computational approach was used for TS analysis that included structural elements of the catalytic site. Without constraints (e.g. imposed torsion angles), the theoretical and experimental data are in good agreement. The quantum-mechanical calculations incorporated a crucial catalytic site residue (D313), two magnesium atoms and coordinated water molecules. The transition state model predicts primary 14C, α-secondary 3H, β-secondary 3H and primary 15N KIE close to the experimental values. The analysis reveals significant ribocation character at the TS. The attacking PPi nucleophile is weakly interacting (rC-O = 2.60 Å) and the N-ribosidic C1′-N bond is highly elongated at the TS (rC-N = 2.35 Å), consistent with an ANDN mechanism. Together with the crystal structure of the NMN•PPi•Mg2•enzyme complex, the reaction coordinate is defined. The enzyme holds the nucleophile and leaving group in relatively fixed positions to create a reaction coordinate with C1′-anomeric migration from nicotinamide to the PPi. The transition state is reached by a 0.85 Å migration of C1′. PMID:23373462
Identification of the protein folding transition state from molecular dynamics trajectories

NASA Astrophysics Data System (ADS)

Muff, S.; Caflisch, A.

2009-03-01

The rate of protein folding is governed by the transition state so that a detailed characterization of its structure is essential for understanding the folding process. In vitro experiments have provided a coarse-grained description of the folding transition state ensemble (TSE) of small proteins. Atomistic details could be obtained by molecular dynamics (MD) simulations but it is not straightforward to extract the TSE directly from the MD trajectories, even for small peptides. Here, the structures in the TSE are isolated by the cut-based free-energy profile (cFEP) using the network whose nodes and links are configurations sampled by MD and direct transitions among them, respectively. The cFEP is a barrier-preserving projection that does not require arbitrarily chosen progress variables. First, a simple two-dimensional free-energy surface is used to illustrate the successful determination of the TSE by the cFEP approach and to explain the difficulty in defining boundary conditions of the Markov state model for an entropically stabilized free-energy minimum. The cFEP is then used to extract the TSE of a β-sheet peptide with a complex free-energy surface containing multiple basins and an entropic region. In contrast, Markov state models with boundary conditions defined by projected variables and conventional histogram-based free-energy profiles are not able to identify the TSE of the β-sheet peptide.
Transition to subcritical turbulence in a tokamak plasma

NASA Astrophysics Data System (ADS)

van Wyk, F.; Highcock, E. G.; Schekochihin, A. A.; Roach, C. M.; Field, A. R.; Dorland, W.

2016-12-01

Tokamak turbulence, driven by the ion-temperature gradient and occurring in the presence of flow shear, is investigated by means of local, ion-scale, electrostatic gyrokinetic simulations (with both kinetic ions and electrons) of the conditions in the outer core of the Mega-Ampere Spherical Tokamak (MAST). A parameter scan in the local values of the ion-temperature gradient and flow shear is performed. It is demonstrated that the experimentally observed state is near the stability threshold and that this stability threshold is nonlinear: sheared turbulence is subcritical, i.e. the system is formally stable to small perturbations, but, given a large enough initial perturbation, it transitions to a turbulent state. A scenario for such a transition is proposed and supported by numerical results: close to threshold, the nonlinear saturated state and the associated anomalous heat transport are dominated by long-lived coherent structures, which drift across the domain, have finite amplitudes, but are not volume filling; as the system is taken away from the threshold into the more unstable regime, the number of these structures increases until they overlap and a more conventional chaotic state emerges. Whereas this appears to represent a new scenario for transition to turbulence in tokamak plasmas, it is reminiscent of the behaviour of other subcritically turbulent systems, e.g. pipe flows and Keplerian magnetorotational accretion flows.
Johari-Goldstein Relaxation Far Below Tg: Experimental Evidence for the Gardner Transition in Structural Glasses?

NASA Astrophysics Data System (ADS)

Geirhos, K.; Lunkenheimer, P.; Loidl, A.

2018-02-01

Experimental evidence for the Gardner transition, theoretically predicted to arise deep in the glassy state of matter, is scarce. At this transition, the energy landscape sensed by the particles forming the glass is expected to become more complex. In the present Letter, we report the dielectric response of two typical glass formers with well-pronounced Johari-Goldstein β relaxation, following this response down to unprecedented low temperatures, far below the glass transition. As the Johari-Goldstein process is believed to arise from the local structure of the energy landscape, its investigation seems an ideal tool to seek evidence for the Gardner transition. Indeed, we find an unusual broadening of the β relaxation below about 110 K for sorbitol and 100 K for xylitol, in excess of the expected broadening arising from a distribution of energy barriers. These results are well consistent with the presence of the Gardner transition in canonical structural glass formers.
Topotactic Metal-Insulator Transition in Epitaxial SrFeO x Thin Films

DOE PAGES

Khare, Amit; Shin, Dongwon; Yoo, Tae Sup; ...

2017-07-31

Multivalent transition metal oxides provide fascinating and rich physics related to oxygen stoichiometry. In particular, the adoptability of various valence states of transition metals enables perovskite oxides to display mixed (oxygen) ionic and electronic conduction and catalytic activity useful in many practical applications, including solid-oxide fuel cells (SOFCs), rechargeable batteries, gas sensors, and memristive devices. For proper realization of the ionic conduction and catalytic activity, it is essential to understand the reversible oxidation and reduction process, which is governed by oxygen storage/release steps in oxides. Topotactic phase transformation facilitates the redox process in perovskites with specific oxygen vacancy ordering bymore » largely varying the oxygen concentration of a material without losing the lattice framework. The concentration and diffusion of oxide ions (O 2–), the valence state of the transition metal cations, and the thermodynamic structural integrity together provide fundamental understanding and ways to explicitly control the redox reaction.[6] In addition, it offers an attractive route for tuning the emergent physical properties of transition metal oxides, via strong coupling between the crystal lattice and electronic structure.« less
Local electronic structure and ferromagnetic interaction in La(Co,Ni)O3

NASA Astrophysics Data System (ADS)

Schuppler, S.; Nagel, P.; Fuchs, D.; Löhneysen, H. V.; Merz, M.; Huang, M.-J.

Perovskite-related transition-metal oxides exhibit properties ranging from insulating to superconducting as well as unusual magnetic phases, and cobaltates, in particular, have been known for their propensity for spin-state transitions. Nonmagnetic LaCoO3 and paramagnetic LaNiO3 are parent compounds for the La(Co1-xNix) O3 (LCNO) family, which, for intermediate Ni content x, exhibits ferromagnetism. The local electronic structure and the ferromagnetic interaction in LCNO have been studied by x-ray absorption (XAS) and x-ray magnetic circular dichroism (XMCD). XAS indicates a mixed-valence state for both Co and Ni, with both valences changing systematically with increasing x. Simultaneously, a spin-state redistribution towards HS (Co site) and LS (Ni site) occurs, and temperature-dependent spin-state transitions are increasingly suppressed. XMCD identifies the element-specific contributions to the magnetic moment and interactions. A simple model based on a double-exchange-like mechanism between Co3+ HS and Ni3+HS can qualitatively account for the evolution of ferromagnetism in the LCNO series.
Infrared and far-infrared laser magnetic resonance spectroscopy of the GeH radical - Determination of ground state parameters

NASA Technical Reports Server (NTRS)

Brown, J. M.; Evenson, K. M.; Sears, T. J.

1985-01-01

The GeH radical has been detected in its ground 2 Pi state in the gas phase reaction of fluorine atoms with GeH4 by laser magnetic resonance techniques. Rotational transitions within both 2 Pi 1/2 and 2 Pi 3/2 manifolds have been observed at far-infrared wavelengths and rotational transitions between the two fine structure components have been detected at infrared wavelengths (10 microns). Signals have been observed for all five naturally occurring isotopes of germanium. Nuclear hyperfine structure for H-1 and Ge-73 has also been observed. The data for the dominant isotope (/Ge-74/H) have been fitted to within experimental error by an effective Hamiltonian to give a set of molecular parameters for the X 2 Pi state which is very nearly complete. In addition, the dipole moment of GeH in its ground state has been estimated from the relative intensities of electric and magnetic dipole transitions in the 10 micron spectrum to be 1.24(+ or - 0.10) D.
Spin textures on general surfaces of the correlated topological insulator SmB6

NASA Astrophysics Data System (ADS)

Baruselli, Pier Paolo; Vojta, Matthias

2016-05-01

Employing the k .p expansion for a family of tight-binding models for SmB6, we analytically compute topological surface states on a generic (l m n ) surface. We show how the Dirac-cone spin structure depends on model ingredients and on the angle θ between the surface normal and the main crystal axes. We apply the general theory to (001), (110), (111), and (210) surfaces, for which we provide concrete predictions for the spin pattern of surface states which we also compare with tight-binding results. As shown in previous work, the spin pattern on a (001 ) surface can be related to the value of mirror Chern numbers, and we explore the possibility of topological phase transitions between states with different mirror Chern numbers and the associated change of the spin structure of surface states. Such transitions may be accessed by varying either the hybridization between conduction and f electrons or the crystal-field splitting of the low-energy f multiplets, and we compute corresponding phase diagrams. Experimentally, chemical doping is a promising route to realize such transitions.
Rotational cross sections and rate coefficients of aluminium monoxide AlO(X2Σ+) induced by its collision with He(1 S) at low temperature

NASA Astrophysics Data System (ADS)

Tchakoua, Théophile; Nkot Nkot, Pierre René; Fifen, Jean Jules; Nsangou, Mama; Motapon, Ousmanou

2018-06-01

We present the first potential energy surface (PES) for the AlO(X2Σ+)-He(1 S) van der Waals complex. This PES has been calculated at the RCCSD(T) level of theory. The mixed Gaussian/Exponential Extrapolation Scheme of complete basis set [CBS(D,T,Q)] was employed. The PES was fitted using global analytical method. This fitted PES was used subsequently in the close-coupling approach for the computation of the state-to-state collisional excitation cross sections of the fine-structure levels of the AlO-He complex. Collision energies were taken up to 2500 cm-1 and they yield after thermal averaging, state-to-state rate coefficients up to 300 K. The propensity rules between the lowest fine-structure levels were studied. These rules show, on one hand, a strong propensity in favour of odd ΔN transitions, and on the other hand, that cross sections and collisional rate coefficients for Δj = ΔN transitions are larger than those for Δj ≠ ΔN transitions.
A reduced-amide inhibitor of Pin1 binds in a conformation resembling a twisted-amide transition state.

PubMed

Xu, Guoyan G; Zhang, Yan; Mercedes-Camacho, Ana Y; Etzkorn, Felicia A

2011-11-08

The mechanism of the cell cycle regulatory peptidyl prolyl isomerase (PPIase), Pin1, was investigated using reduced-amide inhibitors designed to mimic the twisted-amide transition state. Inhibitors, R-pSer-Ψ[CH(2)N]-Pro-2-(indol-3-yl)ethylamine, 1 [R = fluorenylmethoxycarbonyl (Fmoc)] and 2 (R = Ac), of Pin1 were synthesized and bioassayed. Inhibitor 1 had an IC(50) value of 6.3 μM, which is 4.5-fold better for Pin1 than our comparable ground-state analogue, a cis-amide alkene isostere-containing inhibitor. The change of Fmoc to Ac in 2 improved aqueous solubility for structural determination and resulted in an IC(50) value of 12 μM. The X-ray structure of the complex of 2 bound to Pin1 was determined to 1.76 Å resolution. The structure revealed that the reduced amide adopted a conformation similar to the proposed twisted-amide transition state of Pin1, with a trans-pyrrolidine conformation of the prolyl ring. A similar conformation of substrate would be destabilized relative to the planar amide conformation. Three additional reduced amides, with Thr replacing Ser and l- or d-pipecolate (Pip) replacing Pro, were slightly weaker inhibitors of Pin1.
Frequency metrology using highly charged ions

NASA Astrophysics Data System (ADS)

Crespo López-Urrutia, J. R.

2016-06-01

Due to the scaling laws of relativistic fine structure splitting, many forbidden optical transitions appear within the ground state configurations of highly charged ions (HCI). In some hydrogen-like ions, even the hyperfine splitting of the 1s ground state gives rise to optical transitions. Given the very low polarizability of HCI, such laser-accessible transitions are extremely impervious to external perturbations and systematics that limit optical clock performance and arise from AC and DC Stark effects, such as black-body radiation and light shifts. Moreover, AC and DC Zeeman splitting are symmetric due to the much larger relativistic spin-orbit coupling and corresponding fine-structure splitting. Appropriate choice of states or magnetic sub-states with suitable total angular momentum and magnetic quantum numbers can lead to a cancellation of residual quadrupolar shifts. All these properties are very advantageous for the proposed use of HCI forbidden lines as optical frequency standards. Extremely magnified relativistic, quantum electrodynamic, and nuclear size contributions to the binding energies of the optically active electrons make HCI ideal tools for fundamental research, as in proposed studies of a possible time variation of the fine structure constant. Beyond this, HCI that cannot be photoionized by vacuum-ultraviolet photons could also provide frequency standards for future lasers operating in that range.
A cavitation transition in the energy landscape of simple cohesive liquids and glasses

NASA Astrophysics Data System (ADS)

Altabet, Y. Elia; Stillinger, Frank H.; Debenedetti, Pablo G.

2016-12-01

In particle systems with cohesive interactions, the pressure-density relationship of the mechanically stable inherent structures sampled along a liquid isotherm (i.e., the equation of state of an energy landscape) will display a minimum at the Sastry density ρS. The tensile limit at ρS is due to cavitation that occurs upon energy minimization, and previous characterizations of this behavior suggested that ρS is a spinodal-like limit that separates all homogeneous and fractured inherent structures. Here, we revisit the phenomenology of Sastry behavior and find that it is subject to considerable finite-size effects, and the development of the inherent structure equation of state with system size is consistent with the finite-size rounding of an athermal phase transition. What appears to be a continuous spinodal-like point at finite system sizes becomes discontinuous in the thermodynamic limit, indicating behavior akin to a phase transition. We also study cavitation in glassy packings subjected to athermal expansion. Many individual expansion trajectories averaged together produce a smooth equation of state, which we find also exhibits features of finite-size rounding, and the examples studied in this work give rise to a larger limiting tension than for the corresponding landscape equation of state.
High-pressure phase transitions of Fe 3-xTi xO 4 solid solution up to 60 GPa correlated with electronic spin transition

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

Yamanaka, Takamitsu; Kyono, Atsushi; Nakamoto, Yuki

2013-06-12

The structural phase transition of the titanomagnetite (Fe 3–xTi xO 4) solid solution under pressures up to 60 GPa has been clarified by single-crystal and powder diffraction studies using synchrotron radiation and a diamond-anvil cell. Present Rietveld structure refinements of the solid solution prove that the prefered cation distribution is based on the crystal field preference rather than the magnetic spin ordering in the solid solution. The Ti-rich phases in 0.734 ≤ x ≤1.0 undergo a phase transformation from the cubic spinel of Fd3m to the tetragonal spinel structure of I4 1/amd with c/a < 1.0. The transition is drivenmore » by a Jahn-Teller effect of IVFe 2+ (3d 6) on the tetrahedral site. The c/a < 1 ratio is induced by lifting of the degeneracy of the e orbitals by raising the d x2-y2 orbital below the energy of the d z2 orbital. The distortion characterized by c/a < 1 is more pronounced with increasing Ti content in the Fe 3–xTi xO 4 solid solutions and with increasing pressure. An X-ray emission experiment of Fe 2TiO 4 at high pressures confirms the spin transition of FeKβ from high spin to intermediate spin (IS) state. The high spin (HS)-to-low spin (LS) transition starts at 14 GPa and the IS state gradually increases with compression. The VIFe 2+ in the octahedral site is more prone for the HS-to-LS transition, compared with Fe 2+ in the fourfold- or eightfold-coordinated site. The transition to the orthorhombic post-spinel structure with space group Cmcm has been confirmed in the whole compositional range of Fe 3–xTi xO 4. The transition pressure decreases from 25 GPa (x = 0.0) to 15 GPa (x = 1.0) with increasing Ti content. There are two cation sites in the orthorhombic phase: M1 and M2 sites of eightfold and sixfold coordination, respectively. Fe 2+ and Ti 4+ are disordered on the M2 site. This structural change is accelerated at higher pressures due to the spin transition of Fe 2+ in the octahedral site. This is because the ionic radius of VIFe 2+ becomes 20% shortened by the spin transition. At 53 GPa, the structure transforms to another high-pressure polymorph with Pmma symmetry with the ordered structure of Ti and Fe atoms in the octahedral site. This structure change results from the order-disorder transition.« less
Regulation of photochemical energy transfer accompanied by structural changes in thylakoid membranes of heat-stressed wheat.

PubMed

Marutani, Yoko; Yamauchi, Yasuo; Miyoshi, Akihito; Inoue, Kanako; Ikeda, Ken-ichi; Mizutani, Masaharu; Sugimoto, Yukihiro

2014-12-11

Photosystems of higher plants alleviate heat-induced damage in the presence of light under moderate stressed conditions; however, in the absence of light (i.e., in the dark), the same plants are damaged more easily. (Yamauchi and Kimura, 2011) We demonstrate that regulating photochemical energy transfer in heat-treated wheat at 40 °C with light contributed to heat tolerance of the photosystem. Chlorophyll fluorescence analysis using heat-stressed wheat seedlings in light showed increased non-photochemical quenching (NPQ) of chlorophyll fluorescence, which was due to thermal dissipation that was increased by state 1 to state 2 transition. Transmission electron microscopy revealed structural changes in thylakoid membranes, including unstacking of grana regions under heat stress in light. It was accompanied by the phosphorylation of thylakoid proteins such as D1 and D2 proteins and the light harvesting complex II proteins Lhcb1 and Lhcb2. These results suggest that heat stress at 40 °C in light induces state 1 to state 2 transition for the preferential excitation of photosystem I (PSI) by phosphorylating thylakoid proteins more strongly. Structural changes of thylakoid membrane also assist the remodeling of photosystems and regulation of energy distribution by transition toward state 2 probably contributes to plastoquione oxidation; thus, light-driven electrons flowing through PSI play a protective role against PSII damage under heat stress.
Ionic switch controls the DNA state in phage λ

PubMed Central

Li, Dong; Liu, Ting; Zuo, Xiaobing; Li, Tao; Qiu, Xiangyun; Evilevitch, Alex

2015-01-01

We have recently found that DNA packaged in phage λ undergoes a disordering transition triggered by temperature, which results in increased genome mobility. This solid-to-fluid like DNA transition markedly increases the number of infectious λ particles facilitating infection. However, the structural transition strongly depends on temperature and ionic conditions in the surrounding medium. Using titration microcalorimetry combined with solution X-ray scattering, we mapped both energetic and structural changes associated with transition of the encapsidated λ-DNA. Packaged DNA needs to reach a critical stress level in order for transition to occur. We varied the stress on DNA in the capsid by changing the temperature, packaged DNA length and ionic conditions. We found striking evidence that the intracapsid DNA transition is ‘switched on’ at the ionic conditions mimicking those in vivo and also at the physiologic temperature of infection at 37°C. This ion regulated on-off switch of packaged DNA mobility in turn affects viral replication. These results suggest a remarkable adaptation of phage λ to the environment of its host bacteria in the human gut. The metastable DNA state in the capsid provides a new paradigm for the physical evolution of viruses. PMID:26092697
Ionic switch controls the DNA state in phage λ

DOE PAGES

Li, Dong; Liu, Ting; Zuo, Xiaobing; ...

2015-06-19

We have recently found that DNA packaged in phage λ undergoes a disordering transition triggered by temperature, which results in increased genome mobility. This solid-to-fluid like DNA transition markedly increases the number of infectious λ particles facilitating infection. However, the structural transition strongly depends on temperature and ionic conditions in the surrounding medium. Using titration microcalorimetry combined with solution X-ray scattering, we mapped both energetic and structural changes associated with transition of the encapsidated λ-DNA. Packaged DNA needs to reach a critical stress level in order for transition to occur. We varied the stress on DNA in the capsid bymore » changing the temperature, packaged DNA length and ionic conditions. We found striking evidence that the intracapsid DNA transition is ‘switched on’ at the ionic conditions mimicking those in vivo and also at the physiologic temperature of infection at 37°C. This ion regulated on-off switch of packaged DNA mobility in turn affects viral replication. The results suggest a remarkable adaptation of phage λ to the environment of its host bacteria in the human gut. The metastable DNA state in the capsid provides a new paradigm for the physical evolution of viruses.« less
Ionic switch controls the DNA state in phage λ

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

Li, Dong; Liu, Ting; Zuo, Xiaobing

We have recently found that DNA packaged in phage λ undergoes a disordering transition triggered by temperature, which results in increased genome mobility. This solid-to-fluid like DNA transition markedly increases the number of infectious λ particles facilitating infection. However, the structural transition strongly depends on temperature and ionic conditions in the surrounding medium. Using titration microcalorimetry combined with solution X-ray scattering, we mapped both energetic and structural changes associated with transition of the encapsidated λ-DNA. Packaged DNA needs to reach a critical stress level in order for transition to occur. We varied the stress on DNA in the capsid bymore » changing the temperature, packaged DNA length and ionic conditions. We found striking evidence that the intracapsid DNA transition is ‘switched on’ at the ionic conditions mimicking those in vivo and also at the physiologic temperature of infection at 37°C. This ion regulated on-off switch of packaged DNA mobility in turn affects viral replication. The results suggest a remarkable adaptation of phage λ to the environment of its host bacteria in the human gut. The metastable DNA state in the capsid provides a new paradigm for the physical evolution of viruses.« less
Do state-and-transition models derived from vegetation succession also represent avian succession in restored mine pits?

PubMed

Craig, Michael D; Stokes, Vicki L; Fontaine, Joseph B; Hardy, Giles E StJ; Grigg, Andrew H; Hobbs, Richard J

2015-10-01

State-and-transition models are increasingly used as a tool to inform management of post-disturbance succession and effective conservation of biodiversity in production landscapes. However, if they are to do this effectively, they need to represent faunal, as well as vegetation, succession. We assessed the congruence between vegetation and avian succession by sampling avian communities in each state of a state-and-transition model used to inform management of post-mining restoration in a production landscape in southwestern Australia. While avian communities differed significantly among states classified as on a desirable successional pathway, they did not differ between desirable and deviated states of the same post-mining age. Overall, we concluded there was poor congruence between vegetation and avian succession in this state-and-transition model. We identified four factors that likely contributed to this lack of congruence, which were that long-term monitoring of succession in restored mine pits was not used to update and improve models, states were not defined based on ecological processes and thresholds, states were not defined by criteria that were important in structuring the avian community, and states were not based on criteria that related to values in the reference community. We believe that consideration of these four factors in the development of state-and-transition models should improve their ability to accurately represent faunal, as well as vegetation, succession. Developing state-and-transition models that better incorporate patterns of faunal succession should improve the ability to manage post-disturbance succession across a range of ecosystems for biodiversity conservation.
Allosteric Inhibition via R-state Destabilization in ATP Sulfurylase from Penicillium chrysogenum

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

MacRae, I. J.

2002-01-01

The structure of the cooperative hexameric enzyme ATP sulfurylase from Penicillium chrysogenum bound to its allosteric inhibitor, 3'-phosphoadenosine-5'-phosphosulfate (PAPS), was determined to 2.6 {angstrom} resolution. This structure represents the low substrate-affinity T-state conformation of the enzyme. Comparison with the high substrate-affinity R-state structure reveals that a large rotational rearrangement of domains occurs as a result of the R-to-T transition. The rearrangement is accompanied by the 17 {angstrom} movement of a 10-residue loop out of the active site region, resulting in an open, product release-like structure of the catalytic domain. Binding of PAPS is proposed to induce the allosteric transition bymore » destabilizing an R-state-specific salt linkage between Asp 111 in an N-terminal domain of one subunit and Arg 515 in the allosteric domain of a trans-triad subunit. Disrupting this salt linkage by site-directed mutagenesis induces cooperative inhibition behavior in the absence of an allosteric effector, confirming the role of these two residues.« less
Accurate determination of the fine-structure intervals in the 3P ground states of C-13 and C-12 by far-infrared laser magnetic resonance

NASA Technical Reports Server (NTRS)

Cooksy, A. L.; Saykally, R. J.; Brown, J. M.; Evenson, K. M.

1986-01-01

Accurate values are presented for the fine-structure intervals in the 3P ground state of neutral atomic C-12 and C-13 as obtained from laser magnetic resonance spectroscopy. The rigorous analysis of C-13 hyperfine structure, the measurement of resonant fields for C-12 transitions at several additional far-infrared laser frequencies, and the increased precision of the C-12 measurements, permit significant improvement in the evaluation of these energies relative to earlier work. These results will expedite the direct and precise measurement of these transitions in interstellar sources and should assist in the determination of the interstellar C-12/C-13 abundance ratio.

The special features of the crystal structure and properties of oxides with mixed conductivity based on lanthanum gallate

NASA Astrophysics Data System (ADS)

Politova, E. D.; Ivanov, S. A.; Kaleva, G. M.; Mosunov, A. V.; Rusakov, V. S.

2008-10-01

The paper presents a review of works on the synthesis, structural composition effects, phase transitions, and electrical conductivity properties of multicomponent solid solutions based on heterosubstituted lanthanum gallate (La,A)(Ga,M)O3 - y . High-temperature phase transitions and structural and charge ordering effects were studied. The presence of iron cations in different valence states was proved; the relative contents of these cations depended on the x parameter and nonstoichiometry parameter y of the base composition. For M = Fe, antiferromagnetic ordering was observed; its temperature interval was determined by the concentration of iron cations in the high-spin state. The total conductivity was found to increase as the concentration of transition metal cations grew because of an increase in the electronic conductivity component. The data on structural parameters and dc and ac conductivity substantiated the conclusion that the highest ionic conductivity and permeability to oxygen were characteristic of iron-containing oxides. The results obtained are evidence that crystal chemical factors play a determining role in the formation of the ion-conducting properties of anion-deficient perovskite-like oxides.
Pathways for Ethanol Dehydrogenation and Dehydration Catalyzed by Ceria (111) and (100) Surfaces

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

Beste, Ariana; Steven Overbury

2015-01-08

We have performed computations to better understand how surface structure affects selectivity in dehydrogenation and dehydration reactions of alcohols. Ethanol reactions on the (111) and (100) ceria surfaces were studied starting from the dominant surface species, ethoxy. We used DFT (PBE+U) to explore reaction pathways leading to ethylene and acetaldehyde and calculated estimates of rate constants employing transition state theory. To assess pathway contributions, we carried out kinetic analysis. Our results show that intermediate and transition state structures are stabilized on the (100) surface compared to the (111) surface. Formation of acetaldehyde over ethylene is kinetically and thermodynamically preferred onmore » both surfaces. Our results are consistent with temperature programmed surface reaction and steady-state experiments, where acetaldehyde was found as the main product and evidence was presented that ethylene formation at higher temperature originates from changes in adsorbate and surface structure.« less
The nature of photoinduced phase transition and metastable states in vanadium dioxide

DOE PAGES

Tao, Zhensheng; Zhou, Faran; Han, Tzong-Ru T.; ...

2016-12-16

Photoinduced threshold switching processes that lead to bistability and the formation of metastable phases in photoinduced phase transition of VO 2 are elucidated through ultrafast electron diffraction and diffusive scattering techniques with varying excitation wavelengths. We uncover two distinct regimes of the dynamical phase change: a nearly instantaneous crossover into an intermediate state and its decay led by lattice instabilities over 10 ps timescales. The structure of this intermediate state is identified to be monoclinic, but more akin to M 2 rather than M1 based on structure refinements. The extinction of all major monoclinic features within just a few picosecondsmore » at the above-threshold-level (~20%) photoexcitations and the distinct dynamics in diffusive scattering that represents medium-range atomic fluctuations at two photon wavelengths strongly suggest a density-driven and nonthermal pathway for the initial process of the photoinduced phase transition. These results highlight the critical roles of electron correlations and lattice instabilities in driving and controlling phase transformations far from equilibrium.« less
The nature of photoinduced phase transition and metastable states in vanadium dioxide

PubMed Central

Tao, Zhensheng; Zhou, Faran; Han, Tzong-Ru T.; Torres, David; Wang, Tongyu; Sepulveda, Nelson; Chang, Kiseok; Young, Margaret; Lunt, Richard R.; Ruan, Chong-Yu

2016-01-01

Photoinduced threshold switching processes that lead to bistability and the formation of metastable phases in photoinduced phase transition of VO2 are elucidated through ultrafast electron diffraction and diffusive scattering techniques with varying excitation wavelengths. We uncover two distinct regimes of the dynamical phase change: a nearly instantaneous crossover into an intermediate state and its decay led by lattice instabilities over 10 ps timescales. The structure of this intermediate state is identified to be monoclinic, but more akin to M2 rather than M1 based on structure refinements. The extinction of all major monoclinic features within just a few picoseconds at the above-threshold-level (~20%) photoexcitations and the distinct dynamics in diffusive scattering that represents medium-range atomic fluctuations at two photon wavelengths strongly suggest a density-driven and nonthermal pathway for the initial process of the photoinduced phase transition. These results highlight the critical roles of electron correlations and lattice instabilities in driving and controlling phase transformations far from equilibrium. PMID:27982066
The nature of photoinduced phase transition and metastable states in vanadium dioxide

NASA Astrophysics Data System (ADS)

Tao, Zhensheng; Zhou, Faran; Han, Tzong-Ru T.; Torres, David; Wang, Tongyu; Sepulveda, Nelson; Chang, Kiseok; Young, Margaret; Lunt, Richard R.; Ruan, Chong-Yu

2016-12-01

Photoinduced threshold switching processes that lead to bistability and the formation of metastable phases in photoinduced phase transition of VO2 are elucidated through ultrafast electron diffraction and diffusive scattering techniques with varying excitation wavelengths. We uncover two distinct regimes of the dynamical phase change: a nearly instantaneous crossover into an intermediate state and its decay led by lattice instabilities over 10 ps timescales. The structure of this intermediate state is identified to be monoclinic, but more akin to M2 rather than M1 based on structure refinements. The extinction of all major monoclinic features within just a few picoseconds at the above-threshold-level (~20%) photoexcitations and the distinct dynamics in diffusive scattering that represents medium-range atomic fluctuations at two photon wavelengths strongly suggest a density-driven and nonthermal pathway for the initial process of the photoinduced phase transition. These results highlight the critical roles of electron correlations and lattice instabilities in driving and controlling phase transformations far from equilibrium.
Amorphous to amorphous transition in particle rafts

NASA Astrophysics Data System (ADS)

Varshney, Atul; Sane, A.; Ghosh, Shankar; Bhattacharya, S.

2012-09-01

Space-filling assemblies of athermal hydrophobic particles floating at an air-water interface, called particle rafts, are shown to undergo an unusual phase transition between two amorphous states, i.e., a low density “less-rigid” state and a high density “more-rigid” state, as a function of particulate number density (Φ). The former is shown to be a capillary bridged solid and the latter is shown to be a frictionally coupled one. Simultaneous studies involving direct imaging as well as measuring its mechanical response to longitudinal and shear stresses show that the transition is marked by a subtle structural anomaly and a weakening of the shear response. The structural anomaly is identified from the variation of the mean coordination number, mean area of the Voronoi cells, and spatial profile of the displacement field with Φ. The weakened shear response is related to local plastic instabilities caused by the depinning of the contact line of the underlying fluid on the rough surfaces of the particles.
Memory-efficient RNA energy landscape exploration

PubMed Central

Mann, Martin; Kucharík, Marcel; Flamm, Christoph; Wolfinger, Michael T.

2014-01-01

Motivation: Energy landscapes provide a valuable means for studying the folding dynamics of short RNA molecules in detail by modeling all possible structures and their transitions. Higher abstraction levels based on a macro-state decomposition of the landscape enable the study of larger systems; however, they are still restricted by huge memory requirements of exact approaches. Results: We present a highly parallelizable local enumeration scheme that enables the computation of exact macro-state transition models with highly reduced memory requirements. The approach is evaluated on RNA secondary structure landscapes using a gradient basin definition for macro-states. Furthermore, we demonstrate the need for exact transition models by comparing two barrier-based approaches, and perform a detailed investigation of gradient basins in RNA energy landscapes. Availability and implementation: Source code is part of the C++ Energy Landscape Library available at http://www.bioinf.uni-freiburg.de/Software/. Contact: mmann@informatik.uni-freiburg.de Supplementary information: Supplementary data are available at Bioinformatics online. PMID:24833804
Computationally efficient characterization of potential energy surfaces based on fingerprint distances

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

Schaefer, Bastian; Goedecker, Stefan, E-mail: stefan.goedecker@unibas.ch

2016-07-21

An analysis of the network defined by the potential energy minima of multi-atomic systems and their connectivity via reaction pathways that go through transition states allows us to understand important characteristics like thermodynamic, dynamic, and structural properties. Unfortunately computing the transition states and reaction pathways in addition to the significant energetically low-lying local minima is a computationally demanding task. We here introduce a computationally efficient method that is based on a combination of the minima hopping global optimization method and the insight that uphill barriers tend to increase with increasing structural distances of the educt and product states. This methodmore » allows us to replace the exact connectivity information and transition state energies with alternative and approximate concepts. Without adding any significant additional cost to the minima hopping global optimization approach, this method allows us to generate an approximate network of the minima, their connectivity, and a rough measure for the energy needed for their interconversion. This can be used to obtain a first qualitative idea on important physical and chemical properties by means of a disconnectivity graph analysis. Besides the physical insight obtained by such an analysis, the gained knowledge can be used to make a decision if it is worthwhile or not to invest computational resources for an exact computation of the transition states and the reaction pathways. Furthermore it is demonstrated that the here presented method can be used for finding physically reasonable interconversion pathways that are promising input pathways for methods like transition path sampling or discrete path sampling.« less
Effective collision strengths for forbidden transitions among the 3s23p3 fine-structure levels of CL IIIIII

NASA Astrophysics Data System (ADS)

Ramsbottom, C. A.; Bell, K. L.; Keenan, F. P.

1999-08-01

Effective collision strengths for the 10 astrophysically important fine-structure forbidden transitions among the ^4S^o, ^2D^o and ^2P^o levels in the 3s^23p^3 configuration of Cliii are presented. The calculation employs the multichannel R-matrix method to compute the electron-impact excitation collision strengths in a close-coupling expansion, which incorporates the lowest 23 LS target eigenstates of Cliii. These states are formed from the 3s^23p^3, 3s3p^4, 3s^23p^23d and 3s^23p^24s configurations. The Maxwellian-averaged effective collision strengths are presented graphically for all 10 fine-structure transitions over a wide range of electron temperatures appropriate for astrophysical applications [logT(K)=3.3-logT(K)=5.9]. Comparisons are made with the earlier seven-state close-coupling calculation of Butler & Zeippen, and in general excellent agreement is found in the low-temperature region where a comparison is possible [logT(K)=3.3-logT(K)=4.7]. However, discrepancies of up to 30 per cent are found to occur for the forbidden transitions which involve the ^4S^o ground state level, particularly for the lowest temperatures considered. At the higher temperatures, the present data are the only reliable results currently available.
Experimental scaling law for the subcritical transition to turbulence in plane Poiseuille flow.

PubMed

Lemoult, Grégoire; Aider, Jean-Luc; Wesfreid, José Eduardo

2012-02-01

We present an experimental study of the transition to turbulence in a plane Poiseuille flow. Using a well-controlled perturbation, we analyze the flow by using extensive particle image velocimetry and flow visualization (using laser-induced fluorescence) measurements, and use the deformation of the mean velocity profile as a criterion to characterize the state of the flow. From a large parametric study, four different states are defined, depending on the values of the Reynolds number and the amplitude of the perturbation. We discuss the role of coherent structures, such as hairpin vortices, in the transition. We find that the minimal amplitude of the perturbation triggering transition scales asymptotically as Re(-1).
Geometrical Frustration in Interleukin-33 Decouples the Dynamics of the Functional Element from the Folding Transition State Ensemble

PubMed Central

Fisher, Kaitlin M.; Haglund, Ellinor; Noel, Jeffrey K.; Hailey, Kendra L.; Onuchic, José N.; Jennings, Patricia A.

2015-01-01

Interleukin-33 (IL-33) is currently the focus of multiple investigations into targeting pernicious inflammatory disorders. This mediator of inflammation plays a prevalent role in chronic disorders such as asthma, rheumatoid arthritis, and progressive heart disease. In order to better understand the possible link between the folding free energy landscape and functional regions in IL-33, a combined experimental and theoretical approach was applied. IL-33 is a pseudo- symmetrical protein composed of three distinct structural elements that complicate the folding mechanism due to competition for nucleation on the dominant folding route. Trefoil 1 constitutes the majority of the binding interface with the receptor whereas Trefoils 2 and 3 provide the stable scaffold to anchor Trefoil 1. We identified that IL-33 folds with a three-state mechanism, leading to a rollover in the refolding arm of its chevron plots in strongly native conditions. In addition, there is a second slower refolding phase that exhibits the same rollover suggesting similar limitations in folding along parallel routes. Characterization of the intermediate state and the rate limiting steps required for folding suggests that the rollover is attributable to a moving transition state, shifting from a post- to pre-intermediate transition state as you move from strongly native conditions to the midpoint of the transition. On a structural level, we found that initially, all independent Trefoil units fold equally well until a QCA of 0.35 when Trefoil 1 will backtrack in order to allow Trefoils 2 and 3 to fold in the intermediate state, creating a stable scaffold for Trefoil 1 to fold onto during the final folding transition. The formation of this intermediate state and subsequent moving transition state is a result of balancing the difficulty in folding the functionally important Trefoil 1 onto the remainder of the protein. Taken together our results indicate that the functional element of the protein is geometrically frustrated, requiring the more stable elements to fold first, acting as a scaffold for docking of the functional element to allow productive folding to the native state. PMID:26630011
A specific transition state for S-peptide combining with folded S-protein and then refolding

PubMed Central

Goldberg, Jonathan M.; Baldwin, Robert L.

1999-01-01

We measured the folding and unfolding kinetics of mutants for a simple protein folding reaction to characterize the structure of the transition state. Fluorescently labeled S-peptide analogues combine with S-protein to form ribonuclease S analogues: initially, S-peptide is disordered whereas S-protein is folded. The fluorescent probe provides a convenient spectroscopic probe for the reaction. The association rate constant, kon, and the dissociation rate constant, koff, were both determined for two sets of mutants. The dissociation rate constant is measured by adding an excess of unlabeled S-peptide analogue to a labeled complex (RNaseS*). This strategy allows kon and koff to be measured under identical conditions so that microscopic reversibility applies and the transition state is the same for unfolding and refolding. The first set of mutants tests the role of the α-helix in the transition state. Solvent-exposed residues Ala-6 and Gln-11 in the α-helix of native RNaseS were replaced by the helix destabilizing residues glycine or proline. A plot of log kon vs. log Kd for this series of mutants is linear over a very wide range, with a slope of −0.3, indicating that almost all of the molecules fold via a transition state involving the helix. A second set of mutants tests the role of side chains in the transition state. Three side chains were investigated: Phe-8, His-12, and Met-13, which are known to be important for binding S-peptide to S-protein and which also contribute strongly to the stability of RNaseS*. Only the side chain of Phe-8 contributes significantly, however, to the stability of the transition state. The results provide a remarkably clear description of a folding transition state. PMID:10051587
Transition State Analysis of Thymidine Hydrolysis by Human Thymidine Phosphorylase*

PubMed Central

Schwartz, Phillip A.; Vetticatt, Mathew; Schramm, Vern L.

2010-01-01

Human thymidine phosphorylase (hTP) is responsible for thymidine (dT) homeostasis and its action promotes angiogenesis. In the absence of phosphate, hTP catalyzes a slow hydrolytic depyrimidination of dT yielding thymine and 2-deoxyribose (dRib). Its transition state was characterized using multiple kinetic isotope effect (KIE) measurements. Isotopically enriched thymidines were synthesized enzymatically from glucose or (deoxy)ribose and intrinsic KIEs were used to interpret the transition state structure. KIEs from [1′-14C]-, [1-15N]-, [1′-3H]-, [2′R-3H]-, [2′S-3H]-, [4′-3H]-, [5′-3H]dTs provided values of 1.033 ± 0.002, 1.004 ± 0.002, 1.325 ± 0.003, 1.101 ± 0.004, 1.087 ± 0.005, 1.040 ± 0.003, and 1.033 ± 0.003, respectively. Transition state analysis revealed a stepwise mechanism with a 2-deoxyribocation formed early and a higher energetic barrier for nucleophilic attack of a water molecule on the high energy intermediate. An equilibrium exists between the deoxyribocation and reactants prior to the irreversible nucleophilic attack by water. The results establish activation of the thymine leaving group without requirement for phosphate. A transition state constrained to match the intrinsic KIEs was found using density functional theory. An active site histidine (His116) is implicated as the catalytic base for activation of the water nucleophile at the rate-limiting transition state. The distance between the water nucleophile and the anomeric carbon (rC-O) is predicted to be 2.3 Å at the transition state. The transition state model predicts that deoxyribose adopts a mild 3′-endo confirmation during nucleophilic capture. These results differ from the concerted bimolecular mechanism reported for the arsenolytic reaction PMID:20804144
The angular electronic band structure and free particle model of aromatic molecules: High-frequency photon-induced ring current

NASA Astrophysics Data System (ADS)

Öncan, Mehmet; Koç, Fatih; Şahin, Mehmet; Köksal, Koray

2017-05-01

This work introduces an analysis of the relationship of first-principles calculations based on DFT method with the results of free particle model for ring-shaped aromatic molecules. However, the main aim of the study is to reveal the angular electronic band structure of the ring-shaped molecules. As in the case of spherical molecules such as fullerene, it is possible to observe a parabolic dispersion of electronic states with the variation of angular quantum number in the planar ring-shaped molecules. This work also discusses the transition probabilities between the occupied and virtual states by analyzing the angular electronic band structure and the possibility of ring currents in the case of spin angular momentum (SAM) or orbital angular momentum (OAM) carrying light. Current study focuses on the benzene molecule to obtain its angular electronic band structure. The obtained electronic band structure can be considered as a useful tool to see the transition probabilities between the electronic states and possible contribution of the states to the ring currents. The photoinduced current due to the transfer of SAM into the benzene molecule has been investigated by using analytical calculations within the frame of time-dependent perturbation theory.
Pressure induced metallization with absence of structural transition in layered molybdenum diselenide

PubMed Central

Zhao, Zhao; Zhang, Haijun; Yuan, Hongtao; Wang, Shibing; Lin, Yu; Zeng, Qiaoshi; Xu, Gang; Liu, Zhenxian; Solanki, G. K.; Patel, K. D.; Cui, Yi; Hwang, Harold Y.; Mao, Wendy L.

2015-01-01

Layered transition-metal dichalcogenides have emerged as exciting material systems with atomically thin geometries and unique electronic properties. Pressure is a powerful tool for continuously tuning their crystal and electronic structures away from the pristine states. Here, we systematically investigated the pressurized behavior of MoSe2 up to ∼60 GPa using multiple experimental techniques and ab-initio calculations. MoSe2 evolves from an anisotropic two-dimensional layered network to a three-dimensional structure without a structural transition, which is a complete contrast to MoS2. The role of the chalcogenide anions in stabilizing different layered patterns is underscored by our layer sliding calculations. MoSe2 possesses highly tunable transport properties under pressure, determined by the gradual narrowing of its band-gap followed by metallization. The continuous tuning of its electronic structure and band-gap in the range of visible light to infrared suggest possible energy-variable optoelectronics applications in pressurized transition-metal dichalcogenides. PMID:26088416
Pressure induced metallization with absence of structural transition in layered molybdenum diselenide

DOE PAGES

Zhao, Zhao; Zhang, Haijun; Yuan, Hongtao; ...

2015-06-19

Layered transition-metal dichalcogenides have emerged as exciting material systems with atomically thin geometries and unique electronic properties. Pressure is a powerful tool for continuously tuning their crystal and electronic structures away from the pristine states. Here, we systematically investigated the pressurized behavior of MoSe 2 up to ~60 GPa using multiple experimental techniques and ab-initio calculations. MoSe 2 evolves from an anisotropic two-dimensional layered network to a three-dimensional structure without a structural transition, which is a complete contrast to MoS 2. The role of the chalcogenide anions in stabilizing different layered patterns is underscored by our layer sliding calculations. MoSemore » 2 possesses highly tunable transport properties under pressure, determined by the gradual narrowing of its band-gap followed by metallization. The continuous tuning of its electronic structure and band-gap in the range of visible light to infrared suggest possible energy-variable optoelectronics applications in pressurized transition-metal dichalcogenides.« less
Effect of pressure on the superconducting {ital T}{sub {ital c}} of lanthanum

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

Tissen, V.G.; Ponyatovskii, E.G.; Nefedova, M.V.

1996-04-01

The effect of pressure on the superconducting transition temperature {ital T}{sub {ital c}} of La was studied up to 50 GPa. {ital T}{sub {ital c}}({ital P}) shows a rather complicated variation with a discontinuous increase in {ital T}{sub {ital c}} at about 2.2 GPa due to the first-order phase transition from dhcp to fcc structure. At about 5.4 GPa a sharp peak is observed due to the soft-mode phase transition from fcc to the distorted fcc structure and two broad maxima are found within the stability region of the distorted fcc structure around 12 and 39 GPa. Some differences betweenmore » these and previous low-pressure data for metastable fcc La are noticed. The results are discussed in connection with pressure-induced structural phase transitions found in earlier x-ray-diffraction experiments and band-structure calculations giving evidences for van Hove singularities in the density of states. {copyright} {ital 1996 The American Physical Society.}« less
Hydrogen–Deuterium Exchange and Mass Spectrometry Reveal the pH-Dependent Conformational Changes of Diphtheria Toxin T Domain

PubMed Central

2015-01-01

The translocation (T) domain of diphtheria toxin plays a critical role in moving the catalytic domain across the endosomal membrane. Translocation/insertion is triggered by a decrease in pH in the endosome where conformational changes of T domain occur through several kinetic intermediates to yield a final trans-membrane form. High-resolution structural studies are only applicable to the static T-domain structure at physiological pH, and studies of the T-domain translocation pathway are hindered by the simultaneous presence of multiple conformations. Here, we report the application of hydrogen–deuterium exchange mass spectrometry (HDX-MS) for the study of the pH-dependent conformational changes of the T domain in solution. Effects of pH on intrinsic HDX rates were deconvolved by converting the on-exchange times at low pH into times under our “standard condition” (pH 7.5). pH-Dependent HDX kinetic analysis of T domain clearly reveals the conformational transition from the native state (W-state) to a membrane-competent state (W+-state). The initial transition occurs at pH 6 and includes the destabilization of N-terminal helices accompanied by the separation between N- and C-terminal segments. The structural rearrangements accompanying the formation of the membrane-competent state expose a hydrophobic hairpin (TH8–9) to solvent, prepare it to insert into the membrane. At pH 5.5, the transition is complete, and the protein further unfolds, resulting in the exposure of its C-terminal hydrophobic TH8–9, leading to subsequent aggregation in the absence of membranes. This solution-based study complements high resolution crystal structures and provides a detailed understanding of the pH-dependent structural rearrangement and acid-induced oligomerization of T domain. PMID:25290210
Hydrogen-deuterium exchange and mass spectrometry reveal the pH-dependent conformational changes of diphtheria toxin T domain.

PubMed

Li, Jing; Rodnin, Mykola V; Ladokhin, Alexey S; Gross, Michael L

2014-11-04

The translocation (T) domain of diphtheria toxin plays a critical role in moving the catalytic domain across the endosomal membrane. Translocation/insertion is triggered by a decrease in pH in the endosome where conformational changes of T domain occur through several kinetic intermediates to yield a final trans-membrane form. High-resolution structural studies are only applicable to the static T-domain structure at physiological pH, and studies of the T-domain translocation pathway are hindered by the simultaneous presence of multiple conformations. Here, we report the application of hydrogen-deuterium exchange mass spectrometry (HDX-MS) for the study of the pH-dependent conformational changes of the T domain in solution. Effects of pH on intrinsic HDX rates were deconvolved by converting the on-exchange times at low pH into times under our "standard condition" (pH 7.5). pH-Dependent HDX kinetic analysis of T domain clearly reveals the conformational transition from the native state (W-state) to a membrane-competent state (W(+)-state). The initial transition occurs at pH 6 and includes the destabilization of N-terminal helices accompanied by the separation between N- and C-terminal segments. The structural rearrangements accompanying the formation of the membrane-competent state expose a hydrophobic hairpin (TH8-9) to solvent, prepare it to insert into the membrane. At pH 5.5, the transition is complete, and the protein further unfolds, resulting in the exposure of its C-terminal hydrophobic TH8-9, leading to subsequent aggregation in the absence of membranes. This solution-based study complements high resolution crystal structures and provides a detailed understanding of the pH-dependent structural rearrangement and acid-induced oligomerization of T domain.
Two dimensional disorder in black phosphorus and layered monochalcogenides

NASA Astrophysics Data System (ADS)

Barraza-Lopez, Salvador; Mehboudi, Mehrshad; Kumar, Pradeep; Harriss, Edmund O.; Churchill, Hugh O. H.; Dorio, Alex M.; Zhu, Wenjuan; van der Zande, Arend; Pacheco Sanjuan, Alejandro A.

The degeneracies of the structural ground state of materials with a layered orthorhombic structure such as black phosphorus and layered monochalcogenides GeS, GeSe, SnS, and SnSe, lead to an order/disorder transition in two dimensions at finite temperature. This transition has consequences on applications based on these materials requiring a crystalline two-dimensional structure. Details including a Potts model that explains the two-dimensional transition, among other results, will be given in this talk. References: M. Mehboudi, A.M. Dorio, W. Zhu, A. van der Zande, H.O.H. Churchill, A.A. Pacheco Sanjuan, E.O.H. Harris, P. Kumar, and S. Barraza-Lopez. arXiv:1510.09153.

Electronic excitation induced amorphization in titanate pyrochlores: an ab initio molecular dynamics study

PubMed Central

Xiao, H. Y.; Weber, W. J.; Zhang, Y.; Zu, X. T.; Li, S.

2015-01-01

The response of titanate pyrochlores (A2Ti2O7, A = Y, Gd and Sm) to electronic excitation is investigated utilizing an ab initio molecular dynamics method. All the titanate pyrochlores are found to undergo a crystalline-to-amorphous structural transition under a low concentration of electronic excitations. The transition temperature at which structural amorphization starts to occur depends on the concentration of electronic excitations. During the structural transition, O2-like molecules are formed, and this anion disorder further drives cation disorder that leads to an amorphous state. This study provides new insights into the mechanisms of amorphization in titanate pyrochlores under laser, electron and ion irradiations. PMID:25660219
Electronic excitation induced amorphization in titanate pyrochlores: an ab initio molecular dynamics study.

PubMed

Xiao, H Y; Weber, W J; Zhang, Y; Zu, X T; Li, S

2015-02-09

The response of titanate pyrochlores (A2Ti2O7, A = Y, Gd and Sm) to electronic excitation is investigated utilizing an ab initio molecular dynamics method. All the titanate pyrochlores are found to undergo a crystalline-to-amorphous structural transition under a low concentration of electronic excitations. The transition temperature at which structural amorphization starts to occur depends on the concentration of electronic excitations. During the structural transition, O2-like molecules are formed, and this anion disorder further drives cation disorder that leads to an amorphous state. This study provides new insights into the mechanisms of amorphization in titanate pyrochlores under laser, electron and ion irradiations.
Glass transition of anhydrous starch by fast scanning calorimetry.

PubMed

Monnier, Xavier; Maigret, Jean-Eudes; Lourdin, Denis; Saiter, Allisson

2017-10-01

By means of fast scanning calorimetry, the glass transition of anhydrous amorphous starch has been measured. With a scanning rate of 2000Ks -1 , thermal degradation of starch prior to the glass transition has been inhibited. To certify the glass transition measurement, structural relaxation of the glassy state has been investigated through physical aging as well as the concept of limiting fictive temperature. In both cases, characteristic enthalpy recovery peaks related to the structural relaxation of the glass have been observed. Thermal lag corrections based on the comparison of glass transition temperatures measured by means of differential and fast scanning calorimetry have been proposed. The complementary investigations give an anhydrous amorphous starch glass transition temperature of 312±7°C. This estimation correlates with previous extrapolation performed on hydrated starches. Copyright © 2017 Elsevier Ltd. All rights reserved.
Magnetic and Structural Phase Transitions in Thulium under High Pressures and Low Temperatures

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

Vohra, Yogesh K.; Tsoi, Georgiy M.; Samudrala, Gopi K.

2017-10-01

The nature of 4f electrons in many rare earth metals and compounds may be broadly characterized as being either "localized" or "itinerant", and is held responsible for a wide range of physical and chemical properties. The pressure variable has a very dramatic effect on the electronic structure of rare earth metals which in turn drives a sequence of structural and magnetic transitions. We have carried out four-probe electrical resistance measurements on rare earth metal Thulium (Tm) under high pressures to 33 GPa and low temperatures to 10 K to monitor the magnetic ordering transition. These studies are complemented by anglemore » dispersive x-ray diffraction studies to monitor crystallographic phase transitions at high pressures and low temperatures. We observe an abrupt increase in magnetic ordering temperature in Tm at a pressure of 17 GPa on phase transition from ambient pressure hcp-phase to α-Sm phase transition. In addition, measured equation of state (EOS) at low temperatures show anomalously low thermal expansion coefficients likely linked to magnetic transitions.« less
End-effector microprocessor

NASA Technical Reports Server (NTRS)

Doggett, William R.

1992-01-01

The topics are presented in viewgraph form and include: automated structures assembly facility current control hierarchy; automated structures assembly facility purposed control hierarchy; end-effector software state transition diagram; block diagram for ideal install composite; and conclusions.
Ground-State Hyperfine Structure of Heavy Hydrogen-Like Ions

NASA Astrophysics Data System (ADS)

Kühl, T.; Borneis, S.; Dax, A.; Engel, T.; Faber, S.; Gerlach, M.; Holbrow, C.; Huber, G.; Marx, D.; Merz, P.; Quint, W.; Schmitt, F.; Seelig, P.; Tomaselli, M.; Winter, H.; Wuertz, M.; Beckert, K.; Franzke, B.; Nolden, F.; Reich, H.; Steck, M.

Contributions of quantum electrodynamics (QED) to the combined electric and magnetic interaction between the electron and the nucleus can be studied by optical spectroscopy in high-Z hydrogen-like heavy ions. The transition studied is the ground-state hyperfine structure transition, well known from the 21 cm line in atomic hydrogen. The hyperfine splitting of the is ground state of hydrogen-like systems constitutes the simplest and most basic magnetic interaction in atomic physics. The Z3-increase leads to a transition energy in the UV-region of the optical spectrum for the case of Bi82+. At the same time, the QED correction rises to nearly 1 fraction of higher order contributions. This situation is particularly useful for a comparison with non-perturbative QED calculations. The combination of exceptionally intense electric and magnetic fields electric and magnetic fields is unique. This transition has become accessible to precision laser spectroscopy at the high-energy heavy-ion storage ring at GSI-Darmstadt in the hydrogen-like 209Bi82+ and 207Pb81+. In the meantime, 165Ho66+ and 185,187Re74+ were also studied with reduced resolution by conventional optical spectroscopy at the SuperEBIT ion trap at Lawrence Livermore National Laboratory.
Coupling between crystal structure and magnetism in transition-metal oxides

NASA Astrophysics Data System (ADS)

Barton, Phillip Thomas

Transition-metal oxides exhibit a fascinating array of phenomena ranging from superconductivity to negative thermal expansion to catalysis. This dissertation focuses on magnetism, which is integral to engineering applications such as data storage, electric motors/generators, and transformers. The investigative approach follows structure-property relationships from materials science and draws on intuition from solid-state chemistry. The interplay between crystal structure and magnetic properties is studied experimentally in order to enhance the understanding of magnetostructural coupling mechanisms and provide insight into avenues for tuning behavior. A combination of diffraction and physical property measurements were used to study structural and magnetic phase transitions as a function of chemical composition, temperature, and magnetic field. The systems examined are of importance in Li-ion battery electrochemistry, condensed-matter physics, solid-state chemistry, and p-type transparent conducting oxides. The materials were prepared by solid-state reaction of powder reagents at high temperatures for periods lasting tens of hours. The first project discussed is of a solid solution between NiO, a correlated insulator, and LiNiO2, a layered battery cathode. Despite the deceptive structural and compositional simplicity of this system, a complete understanding of its complex magnetic properties has remained elusive. This study shows that nanoscale domains of chemical order form at intermediate compositions, creating interfaces between antiferromagnetism and ferrimagnetism that give rise to magnetic exchange bias. A simple model of the magnetism is presented along with a comprehensive phase diagram. The second set of investigations focus on the Ge-Co-O system where the spin-orbit coupling of Co(II) plays a significant role. GeCo2O 4 is reported to exhibit unusual magnetic behavior that arises from Ising spin in its spinel crystal structure. Studies by variable-temperature synchrotron X-ray diffraction reveal a magnetostructural transition and capacitance measurements show evidence for magnetodielectric behavior. The above work uncovered a Co10Ge3O16 phase that had a known structure but whose physical properties were largely uncharacterized. This project examined its metamagnetic properties using detailed magnetometry experiments. Upon the application of a magnetic field, this material goes through a first-order phase transition from a noncollinear antiferromagnet to an unknown ferrimagnetic state. Lastly, this thesis explored the chemical dilution of magnetism in some perovskite and delafossite solid solutions. In the perovskite structure, compositions intermediate to the endmembers SrRuO3, a ferromagnetic metal, and LaRhO3, a diamagnetic semiconductor, were investigated. While the magnetism of this system is poised between localized and itinerant behavior, a compositionally-driven metal to insulator transition, revealed by electrical resistivity measurements, did not strongly impact the magnetic properties. Instead, both octahedral tilting and magnetic dilution had strong effects, and comparison of this characterization to Sr1-- x CaxRuO3 reinforces the important role of structural distortions in determining magnetic ground state. The final materials studied were of composition CuAl1-- xCrxO2 (0 < x < 1) in the delafossite structure. The primary interest was the geometric frustration of antiferromagnetism in CuCrO 2 and significant short-range correlations were observed above TN. The analysis found that reducing the number of degenerate states through Al substitution did not enhance magnetic ordering because of the weakening of magnetic exchange.
Transition-state structure for the quintessential SN2 reaction of a carbohydrate: reaction of α-glucopyranosyl fluoride with azide ion in water.

PubMed

Chan, Jefferson; Sannikova, Natalia; Tang, Ariel; Bennet, Andrew J

2014-09-03

We report that the SN2 reaction of α-d-glucopyranosyl fluoride with azide ion proceeds through a loose (exploded) transition-state (TS) structure. We reached this conclusion by modeling the TS using a suite of five experimental kinetic isotope effects (KIEs) as constraints for the calculations. We also report that the anomeric (13)C-KIE is not abnormally large (k12/k13 = 1.024 ± 0.006), a finding which is at variance with the previous literature value (Zhang et al. J. Am. Chem. Soc. 1994, 116, 7557).
Reusable fast opening switch

DOEpatents

Van Devender, J.P.; Emin, D.

1983-12-21

A reusable fast opening switch for transferring energy, in the form of a high power pulse, from an electromagnetic storage device such as an inductor into a load. The switch is efficient, compact, fast and reusable. The switch comprises a ferromagnetic semiconductor which undergoes a fast transition between conductive and metallic states at a critical temperature and which undergoes the transition without a phase change in its crystal structure. A semiconductor such as europium rich europhous oxide, which undergoes a conductor to insulator transition when it is joule heated from its conductor state, can be used to form the switch.
Reusable fast opening switch

DOEpatents

Van Devender, John P.; Emin, David

1986-01-01

A reusable fast opening switch for transferring energy, in the form of a high power pulse, from an electromagnetic storage device such as an inductor into a load. The switch is efficient, compact, fast and reusable. The switch comprises a ferromagnetic semiconductor which undergoes a fast transition between conductive and insulating states at a critical temperature and which undergoes the transition without a phase change in its crystal structure. A semiconductor such as europium rich europhous oxide, which undergoes a conductor to insulator transition when it is joule heated from its conductor state, can be used to form the switch.
Structural transition and amorphization in compressed α - Sb 2 O 3

DOE PAGES

Zhao, Zhao; Zeng, Qiaoshi; Zhang, Haijun; ...

2015-05-27

Sb₂O₃-based materials are of broad interest in materials science and industry. High-pressure study using diamond anvil cells shows promise in obtaining new crystal and electronic structures different from their pristine states. Here, we conducted in situ angle dispersive synchrotron x-ray-diffraction and Raman spectroscopy experiments on α-Sb₂O₃ up to 50 GPa with neon as the pressure transmitting medium. A first-order structural transition was observed in between 15 and 20 GPa, where the cubic phase I gradually transformed into a layered tetragonal phase II through structural distortion and symmetry breaking. To explain the dramatic changes in sample color and transparency, we performedmore » first-principles calculations to track the evolution of its density of states and electronic structure under pressure. At higher pressure, a sluggish amorphization was observed. Our results highlight the structural connections among the sesquioxides, where the lone electron pair plays an important role in determining the local structures.« less
Effective collision strengths for fine-structure forbidden transitions among the 3s^23p^3 levels of AR IV

NASA Astrophysics Data System (ADS)

Ramsbottom, C. A.; Bell, K. L.; Keenan, F. P.

1997-01-01

The multichannel R-matrix method is used to compute electron impact excitation collision strengths in Ar iv for all fine-structure transitions among the ^4S^o, ^2D^o and ^2P^o levels in the 3s^23p^3 ground configuration. Included in the expansion of the total wavefunction are the lowest 13 LS target eigenstates of Ar iv formed from the 3s^23p^3, 3s3p^4 and 3s^23p^23d configurations. The effective collision strengths, obtained by averaging the electron collision strengths over a Maxwellian distribution of electron velocities, are presented for all 10 fine-structure transitions over a wide range of electron temperatures of astrophysical interest (T_e=2000-100 000K). Comparisons are made with an earlier 7-state close-coupling calculation by Zeippen, Butler & Le Bourlot, and significant differences are found to occur for many of the forbidden transitions considered, in particular those involving the ^4S^o ground state, where discrepancies of up to a factor of 3 are found in the low-temperature region.
Candidate Elastic Quantum Critical Point in LaCu 6 - x Au x

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

Poudel, Lekh; May, Andrew F.; Koehler, Michael R.

2016-11-30

In this paper, the structural properties of LaCu 6-xAu x are studied using neutron diffraction, x-ray diffraction, and heat capacity measurements. The continuous orthorhombic-monoclinic structural phase transition in LaCu 6 is suppressed linearly with Au substitution until a complete suppression of the structural phase transition occurs at the critical composition x c=0.3. Heat capacity measurements at low temperatures indicate residual structural instability at x c. The instability is ferroelastic in nature, with density functional theory calculations showing negligible coupling to electronic states near the Fermi level. Finally, the data and calculations presented here are consistent with the zero temperature terminationmore » of a continuous structural phase transition suggesting that the LaCu 6-xAu x series hosts an elastic quantum critical point.« less
Insights into the Effects of Zinc Doping on Structural Phase Transition of P2-Type Sodium Nickel Manganese Oxide Cathodes for High-Energy Sodium Ion Batteries

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

Wu, Xuehang; Xu, Gui-Liang; Zhong, Guiming

P2-type sodium nickel manganese oxide-based cathode materials with higher energy densities are prime candidates for applications in rechargeable sodium ion batteries. A systematic study combining in situ high energy X-ray diffraction (HEXRD), ex situ Xray absorption fine spectroscopy (XAFS), transmission electron microscopy (TEM), and solid-state nuclear magnetic resonance (SSNMR) techniques was carried out to gain a deep insight into the structural evolution of P2-Na 0.66Ni 0.33-xZn xMn 0.67O 2 (x = 0, 0.07) during cycling. In situ HEXRD and ex situ TEM measurements indicate that an irreversible phase transition occurs upon sodium insertion-extraction of Na 0.66Ni 0.33Mn 0.67O 2. Zincmore » doping of this system results in a high structural reversibility. XAFS measurements indicate that both materials are almost completely dependent on the Ni 4+/Ni 3+/ Ni 2+ redox couple to provide charge/discharge capacity. SS-NMR measurements indicate that both reversible and irreversible migration of transition metal ions into the sodium layer occurs in the material at the fully charged state. The irreversible migration of transition metal ions triggers a structural distortion, leading to the observed capacity and voltage fading. Our results allow a new understanding of the importance of improving the stability of transition metal layers.« less
First Principles Study on Topological-Phase Transition in Ferroelectric Oxides

NASA Astrophysics Data System (ADS)

Yamauchi, Kunihiko; Barone, Paolo; Picozzi, Silvia

Graphene is known as a 2D topological insulator with zero energy gap and Dirac cone. In this study, we theoretically designed a honeycomb structure of Au ions embedded in a ferroelectric host oxide, in order to exploit structural distortions to control topological properties. We show that the polar structural distortion induces the emergence of spin-valley coupling, together with a topological transition from a quantum spin-Hall insulating phase to a trivial band insulator. The phase transition also affects the Berry curvature and spin-valley selection rules. Analogously to graphene, the microscopic origin of this topological phase is ascribed to a spin-valley-sublattice coupling, which arises from the interplay between trigonal crystal field and an ``effective'' spin-orbit interaction due to virtual excitations between eg and t2g states of transition-metal ions.
Two distinct overstretched DNA structures revealed by single-molecule thermodynamics measurements

PubMed Central

Zhang, Xinghua; Chen, Hu; Fu, Hongxia; Doyle, Patrick S.; Yan, Jie

2012-01-01

Double-stranded DNA is a dynamic molecule whose structure can change depending on conditions. While there is consensus in the literature about many structures DNA can have, the state of highly-stretched DNA is still not clear. Several groups have shown that DNA in the torsion-unconstrained B-form undergoes an “overstretching” transition at a stretching force of around 65 pN, which leads to approximately 1.7-fold elongation of the DNA contour length. Recent experiments have revealed that two distinct structural transitions are involved in the overstretching process: (i) a hysteretic “peeling” off one strand from its complementary strand, and (ii) a nonhysteretic transition that leads to an undetermined DNA structure. We report the first simultaneous determination of the entropy (ΔS) and enthalpy changes (ΔH) pertaining to these respective transitions. For the hysteretic peeling transition, we determined ΔS ∼ 20 cal/(K.mol) and ΔH ∼ 7 kcal/mol. In the case of the nonhysteretic transition, ΔS ∼ -3 cal/(K.mol) and ΔH ∼ 1 kcal/mol. Furthermore, the response of the transition force to salt concentration implies that the two DNA strands are spatially separated after the hysteretic peeling transition. In contrast, the corresponding response after the nonhysteretic transition indicated that the strands remained in close proximity. The selection between the two transitions depends on DNA base-pair stability, and it can be illustrated by a multidimensional phase diagram. Our results provide important insights into the thermodynamics of DNA overstretching and conformational structures of overstretched DNA that may play an important role in vivo. PMID:22532662
Nuclear Structure of 124Xe Studied with β+/EC-Decay

NASA Astrophysics Data System (ADS)

Radich, A. J.; Garrett, P. E.; Allmond, J. M.; Andreoiu, C.; Ball, G. C.; Bianco, L.; Bildstein, V.; Chagnon-Lessard, S.; Cross, D. S.; Diaz Varela, A.; Dunlop, R.; Finlay, P.; Garnsworthy, A. B.; Hackman, G.; Hadinia, B.; Jigmeddorj, B.; Laffoley, A. T.; Leach, K. G.; Michetti-Wilson, J.; Orce, J. N.; Rajabali, M. M.; Rand, E.; Starosta, K.; Sumithrarachchi, C. S.; Svensson, C. E.; Triambak, S.; Wang, Z. M.; Wood, J. L.; Wong, J.; Williams, S. J.; Yates, S. W.

The nuclear structure of 124Xe was investigated using γ-ray spectroscopy following the β+/EC-decay of 124Cs. A very high-statistics data set was collected and γγ coincidence data was analyzed, greatly adding to the 124Xe level scheme. A new decay branch from the high-spin isomer of 124Cs was observed as well as weak E2 transitions into excited 0+ states in 124Xe. B(E2) transition strengths of such low-spin transitions are very important in determining collective properties, which are currently poorly characterized in the region of neutron-deficient xenon isotopes.
Statistical Mechanical Foundation for the Two-State Transition in Protein Folding of Small Globular Proteins

NASA Astrophysics Data System (ADS)

Iguchi, Kazumoto

We discuss the statistical mechanical foundation for the two-state transition in the protein folding of small globular proteins. In the standard arguments of protein folding, the statistical search for the ground state is carried out from astronomically many conformations in the configuration space. This leads us to the famous Levinthal's paradox. To resolve the paradox, Gō first postulated that the two-state transition - all-or-none type transition - is very crucial for the protein folding of small globular proteins and used the Gō's lattice model to show the two-state transition nature. Recently, there have been accumulated many experimental results that support the two-state transition for small globular proteins. Stimulated by such recent experiments, Zwanzig has introduced a minimal statistical mechanical model that exhibits the two-state transition. Also, Finkelstein and coworkers have discussed the solution of the paradox by considering the sequential folding of a small globular protein. On the other hand, recently Iguchi have introduced a toy model of protein folding using the Rubik's magic snake model, in which all folded structures are exactly known and mathematically represented in terms of the four types of conformations: cis-, trans-, left and right gauche-configurations between the unit polyhedrons. In this paper, we study the relationship between the Gō's two-state transition, the Zwanzig's statistical mechanics model and the Finkelsteinapos;s sequential folding model by applying them to the Rubik's magic snake models. We show that the foundation of the Gō's two-state transition model relies on the search within the equienergy surface that is labeled by the contact order of the hydrophobic condensation. This idea reproduces the Zwanzig's statistical model as a special case, realizes the Finkelstein's sequential folding model and fits together to understand the nature of the two-state transition of a small globular protein by calculating the physical quantities such as the free energy, the contact order and the specific heat. We point out the similarity between the liquid-gas transition in statistical mechanics and the two-state transition of protein folding. We also study morphology of the Rubik's magic snake models to give a prototype model for understanding the differences between α-helices proteins and β-sheets proteins.
Superconductivity in zirconium-rhodium alloys

NASA Technical Reports Server (NTRS)

Zegler, S. T.

1969-01-01

Metallographic studies and transition temperature measurements were made with isothermally annealed and water-quenched zirconium-rhodium alloys. The results clarify both the solid-state phase relations at the Zr-rich end of the Zr-Rh alloy system and the influence upon the superconducting transition temperature of structure and composition.
A DNA-based nanomechanical device with three robust states.

PubMed

Chakraborty, Banani; Sha, Ruojie; Seeman, Nadrian C

2008-11-11

DNA has been used to build a variety of devices, ranging from those that are controlled by DNA structural transitions to those that are controlled by the addition of specific DNA strands. These sequence-dependent devices fulfill the promise of DNA in nanotechnology because a variety of devices in the same physical environment can be controlled individually. Many such devices have been reported, but most of them contain one or two structurally robust end states, in addition to a floppy intermediate or even a floppy end state. We describe a system in which three different structurally robust end states can be obtained, all resulting from the addition of different set strands to a single floppy intermediate. This system is an extension of the PX-JX(2) DNA device. The three states are related to each other by three different motions, a twofold rotation, a translation of approximately 2.1-2.5 nm, and a twofold screw rotation, which combines these two motions. We demonstrate the transitions by gel electrophoresis, by fluorescence resonance energy transfer, and by atomic force microscopy. The control of this system by DNA strands opens the door to trinary logic and to systems containing N devices that are able to attain 3(N) structural states.

A DNA-based nanomechanical device with three robust states

PubMed Central

Chakraborty, Banani; Sha, Ruojie; Seeman, Nadrian C.

2008-01-01

DNA has been used to build a variety of devices, ranging from those that are controlled by DNA structural transitions to those that are controlled by the addition of specific DNA strands. These sequence-dependent devices fulfill the promise of DNA in nanotechnology because a variety of devices in the same physical environment can be controlled individually. Many such devices have been reported, but most of them contain one or two structurally robust end states, in addition to a floppy intermediate or even a floppy end state. We describe a system in which three different structurally robust end states can be obtained, all resulting from the addition of different set strands to a single floppy intermediate. This system is an extension of the PX-JX2 DNA device. The three states are related to each other by three different motions, a twofold rotation, a translation of ≈2.1–2.5 nm, and a twofold screw rotation, which combines these two motions. We demonstrate the transitions by gel electrophoresis, by fluorescence resonance energy transfer, and by atomic force microscopy. The control of this system by DNA strands opens the door to trinary logic and to systems containing N devices that are able to attain 3N structural states. PMID:18474862
Insight into the Structural and Biological Relevance of the T/R Transition of the N-Terminus of the B-Chain in Human Insulin

PubMed Central

2014-01-01

The N-terminus of the B-chain of insulin may adopt two alternative conformations designated as the T- and R-states. Despite the recent structural insight into insulin–insulin receptor (IR) complexes, the physiological relevance of the T/R transition is still unclear. Hence, this study focused on the rational design, synthesis, and characterization of human insulin analogues structurally locked in expected R- or T-states. Sites B3, B5, and B8, capable of affecting the conformation of the N-terminus of the B-chain, were subjects of rational substitutions with amino acids with specific allowed and disallowed dihedral φ and ψ main-chain angles. α-Aminoisobutyric acid was systematically incorporated into positions B3, B5, and B8 for stabilization of the R-state, and N-methylalanine and d-proline amino acids were introduced at position B8 for stabilization of the T-state. IR affinities of the analogues were compared and correlated with their T/R transition ability and analyzed against their crystal and nuclear magnetic resonance structures. Our data revealed that (i) the T-like state is indeed important for the folding efficiency of (pro)insulin, (ii) the R-state is most probably incompatible with an active form of insulin, (iii) the R-state cannot be induced or stabilized by a single substitution at a specific site, and (iv) the B1–B8 segment is capable of folding into a variety of low-affinity T-like states. Therefore, we conclude that the active conformation of the N-terminus of the B-chain must be different from the “classical” T-state and that a substantial flexibility of the B1–B8 segment, where GlyB8 plays a key role, is a crucial prerequisite for an efficient insulin–IR interaction. PMID:24819248
Spontaneous emission from radiative chiral nematic liquid crystals at the photonic band-gap edge: an investigation into the role of the density of photon states near resonance.

PubMed

Mavrogordatos, Th K; Morris, S M; Wood, S M; Coles, H J; Wilkinson, T D

2013-06-01

In this article, we investigate the spontaneous emission properties of radiating molecules embedded in a chiral nematic liquid crystal, under the assumption that the electronic transition frequency is close to the photonic edge mode of the structure, i.e., at resonance. We take into account the transition broadening and the decay of electromagnetic field modes supported by the so-called "mirrorless"cavity. We employ the Jaynes-Cummings Hamiltonian to describe the electron interaction with the electromagnetic field, focusing on the mode with the diffracting polarization in the chiral nematic layer. As known in these structures, the density of photon states, calculated via the Wigner method, has distinct peaks on either side of the photonic band gap, which manifests itself as a considerable modification of the emission spectrum. We demonstrate that, near resonance, there are notable differences between the behavior of the density of states and the spontaneous emission profile of these structures. In addition, we examine in some detail the case of the logarithmic peak exhibited in the density of states in two-dimensional photonic structures and obtain analytic relations for the Lamb shift and the broadening of the atomic transition in the emission spectrum. The dynamical behavior of the atom-field system is described by a system of two first-order differential equations, solved using the Green's-function method and the Fourier transform. The emission spectra are then calculated and compared with experimental data.
Thermal unfolding of tetrameric melittin: comparison with the molten globule state of cytochrome c.

PubMed Central

Hagihara, Y.; Oobatake, M.; Goto, Y.

1994-01-01

Whereas melittin at micromolar concentrations is unfolded under conditions of low salt at neutral pH, it transforms to a tetrameric alpha-helical structure under several conditions, such as high peptide concentration, high anion concentration, or alkaline pH. The anion- and pH-dependent stabilization of the tetrameric structure is similar to that of the molten globule state of several acid-denatured proteins, suggesting that tetrameric melittin might be a state similar to the molten globule state. To test this possibility, we studied the thermal unfolding of tetrameric melittin using far-UV CD and differential scanning calorimetry. The latter technique revealed a broad but distinct heat absorption peak. The heat absorption curves were consistent with the unfolding transition observed by CD and were explainable by a 2-state transition mechanism between the tetrameric alpha-helical state and the monomeric unfolded state. From the peptide or salt-concentration dependence of unfolding, the heat capacity change upon unfolding was estimated to be 5 kJ (mol of tetramer)-1 K-1 at 30 degrees C and decreased with increasing temperature. The observed change in heat capacity was much smaller than that predicted from the crystallographic structure (9.2 kJ (mol of tetramer)-1 K-1), suggesting that the hydrophobic residues of tetrameric melittin in solution are exposed in comparison with the crystallographic structure. However, the results also indicate that the structure is more ordered than that of a typical molten globule state. We consider that the conformation is intermediate between the molten globule state and the native state of globular proteins. PMID:7833804
Heterogeneous distribution of water in the mantle transition zone beneath United States inferred from seismic observations

NASA Astrophysics Data System (ADS)

Wang, Y.; Pavlis, G. L.; Li, M.

2017-12-01

The amount of water in the Earth's deep mantle is critical for the evolution of the solid Earth and the atmosphere. Mineral physics studies have revealed that Wadsleyite and Ringwoodite in the mantle transition zone could store several times the volume of water in the ocean. However, the water content and its distribution in the transition zone remain enigmatic due to lack of direct observations. Here we use seismic data from the full deployment of the Earthscope Transportable Array to produce 3D image of P to S scattering of the mantle transition zone beneath the United States. We compute the image volume from 141,080 pairs of high quality receiver functions defined by the Earthscope Automated Receiver Survey, reprocessed by the generalized iterative deconvolution method and imaged by the plane wave migration method. We find that the transition zone is filled with previously unrecognized small-scale heterogeneities that produce pervasive, negative polarity P to S conversions. Seismic synthetic modeling using a point source simulation method suggests two possible structures for these objects: 1) a set of randomly distributed blobs of slight difference in size, and 2) near vertical diapir structures from small scale convections. Combining with geodynamic simulations, we interpret the observation as compositional heterogeneity from small-scale, low-velocity bodies that are water enriched. Our results indicate there is a heterogeneous distribution of water through the entire mantle transition zone beneath the contiguous United States.
Structural basis for the mechanism and substrate specificity of glycocyamine kinase, a phosphagen kinase family member

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

Lim, Kap; Pullalarevu, Sadhana; Surabian, Karen Talin

2010-03-12

Glycocyamine kinase (GK), a member of the phosphagen kinase family, catalyzes the Mg{sup 2+}-dependent reversible phosphoryl group transfer of the N-phosphoryl group of phosphoglycocyamine to ADP to yield glycocyamine and ATP. This reaction helps to maintain the energy homeostasis of the cell in some multicelullar organisms that encounter high and variable energy turnover. GK from the marine worm Namalycastis sp. is heterodimeric, with two homologous polypeptide chains, {alpha} and {beta}, derived from a common pre-mRNA by mutually exclusive N-terminal alternative exons. The N-terminal exon of GK{beta} encodes a peptide that is different in sequence and is 16 amino acids longermore » than that encoded by the N-terminal exon of GK{alpha}. The crystal structures of recombinant GK{alpha}{beta} and GK{beta}{beta} from Namalycastis sp. were determined at 2.6 and 2.4 {angstrom} resolution, respectively. In addition, the structure of the GK{beta}{beta} was determined at 2.3 {angstrom} resolution in complex with a transition state analogue, Mg{sup 2+}-ADP-NO{sub 3}{sup -}-glycocyamine. Consistent with the sequence homology, the GK subunits adopt the same overall fold as that of other phosphagen kinases of known structure (the homodimeric creatine kinase (CK) and the monomeric arginine kinase (AK)). As with CK, the GK N-termini mediate the dimer interface. In both heterodimeric and homodimeric GK forms, the conformations of the two N-termini are asymmetric, and the asymmetry is different than that reported previously for the homodimeric CKs from several organisms. The entire polypeptide chains of GK{alpha}{beta} are structurally defined, and the longer N-terminus of the {beta} subunit is anchored at the dimer interface. In GK{beta}{beta} the 24 N-terminal residues of one subunit and 11 N-terminal residues of the second subunit are disordered. This observation is consistent with a proposal that the GK{alpha}{beta} amino acids involved in the interface formation were optimized once a heterodimer emerged as the physiological form of the enzyme. As a consequence, the homodimer interface (either solely {alpha} or solely {beta} chains) has been corrupted. In the unbound state, GK exhibits an open conformation analogous to that observed with ligand-free CK or AK. Upon binding the transition state analogue, both subunits of GK undergo the same closure motion that clasps the transition state analogue, in contrast to the transition state analogue complexes of CK, where the corresponding transition state analogue occupies only one subunit, which undergoes domain closure. The active site environments of the GK, CK, and AK at the bound states reveal the structural determinants of substrate specificity. Despite the equivalent binding in both active sites of the GK dimer, the conformational asymmetry of the N-termini is retained. Thus, the coupling between the structural asymmetry and negative cooperativity previously proposed for CK is not supported in the case of GK.« less
Ultrafast optical snapshots of hybrid perovskites reveal the origin of multiband electronic transitions

DOE PAGES

Appavoo, Kannatassen; Nie, Wanyi; Blancon, Jean -Christophe; ...

2017-11-15

In this paper, connecting the complex electronic excitations of hybrid perovskites to their intricate organic-inorganic lattice structure has critical implications for energy conversion and optoelectronic technologies. Here we detail the multiband, multivalley electronic structure of a halide hybrid perovskite by measuring the absorption transients of a millimeter-scale-grain thin film as it undergoes a thermally controlled reversible tetragonal-to-orthogonal phase transition. Probing nearly single grains of this hybrid perovskite, we observe an unreported energy splitting (degeneracy lifting) of the high-energy 2.6 eV band in the tetragonal phase that further splits as the rotational degrees of freedom of the disordered CH 3NH 3more » + molecules are reduced when the sample is cooled. This energy splitting drastically increases during an extended phase-transition coexistence region that persists from 160 to 120 K, becoming more pronounced in the orthorhombic phase. By tracking the temperature-dependent optical transition energies and using symmetry analysis that describes the evolution of electronic states from the tetragonal phase to the orthorhombic phase, we assign this energy splitting to the nearly degenerate transitions in the tetragonal phase from both the R- and M-point-derived states. Importantly, these assignments explain how momentum conservation effects lead to long hot-carrier lifetimes in the room-temperature tetragonal phase, with faster hot-carrier relaxation when the hybrid perovskite structurally transitions to the orthorhombic phase due to enhanced scattering at the Γ point.« less
Ultrafast optical snapshots of hybrid perovskites reveal the origin of multiband electronic transitions

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

Appavoo, Kannatassen; Nie, Wanyi; Blancon, Jean -Christophe

In this paper, connecting the complex electronic excitations of hybrid perovskites to their intricate organic-inorganic lattice structure has critical implications for energy conversion and optoelectronic technologies. Here we detail the multiband, multivalley electronic structure of a halide hybrid perovskite by measuring the absorption transients of a millimeter-scale-grain thin film as it undergoes a thermally controlled reversible tetragonal-to-orthogonal phase transition. Probing nearly single grains of this hybrid perovskite, we observe an unreported energy splitting (degeneracy lifting) of the high-energy 2.6 eV band in the tetragonal phase that further splits as the rotational degrees of freedom of the disordered CH 3NH 3more » + molecules are reduced when the sample is cooled. This energy splitting drastically increases during an extended phase-transition coexistence region that persists from 160 to 120 K, becoming more pronounced in the orthorhombic phase. By tracking the temperature-dependent optical transition energies and using symmetry analysis that describes the evolution of electronic states from the tetragonal phase to the orthorhombic phase, we assign this energy splitting to the nearly degenerate transitions in the tetragonal phase from both the R- and M-point-derived states. Importantly, these assignments explain how momentum conservation effects lead to long hot-carrier lifetimes in the room-temperature tetragonal phase, with faster hot-carrier relaxation when the hybrid perovskite structurally transitions to the orthorhombic phase due to enhanced scattering at the Γ point.« less
Ultrafast optical snapshots of hybrid perovskites reveal the origin of multiband electronic transitions

NASA Astrophysics Data System (ADS)

Appavoo, Kannatassen; Nie, Wanyi; Blancon, Jean-Christophe; Even, Jacky; Mohite, Aditya D.; Sfeir, Matthew Y.

2017-11-01

Connecting the complex electronic excitations of hybrid perovskites to their intricate organic-inorganic lattice structure has critical implications for energy conversion and optoelectronic technologies. Here we detail the multiband, multivalley electronic structure of a halide hybrid perovskite by measuring the absorption transients of a millimeter-scale-grain thin film as it undergoes a thermally controlled reversible tetragonal-to-orthogonal phase transition. Probing nearly single grains of this hybrid perovskite, we observe an unreported energy splitting (degeneracy lifting) of the high-energy 2.6 eV band in the tetragonal phase that further splits as the rotational degrees of freedom of the disordered C H3N H3 + molecules are reduced when the sample is cooled. This energy splitting drastically increases during an extended phase-transition coexistence region that persists from 160 to 120 K, becoming more pronounced in the orthorhombic phase. By tracking the temperature-dependent optical transition energies and using symmetry analysis that describes the evolution of electronic states from the tetragonal phase to the orthorhombic phase, we assign this energy splitting to the nearly degenerate transitions in the tetragonal phase from both the R - and M -point-derived states. Importantly, these assignments explain how momentum conservation effects lead to long hot-carrier lifetimes in the room-temperature tetragonal phase, with faster hot-carrier relaxation when the hybrid perovskite structurally transitions to the orthorhombic phase due to enhanced scattering at the Γ point.
Amorphous-amorphous transition in a porous coordination polymer.

PubMed

Ohtsu, Hiroyoshi; Bennett, Thomas D; Kojima, Tatsuhiro; Keen, David A; Niwa, Yasuhiro; Kawano, Masaki

2017-07-04

The amorphous state plays a key role in porous coordination polymer and metal-organic framework phase transitions. We investigate a crystalline-to-amorphous-to-amorphous-to-crystalline (CAAC) phase transition in a Zn based coordination polymer, by X-ray absorption fine structure (XAFS) and X-ray pair distribution function (PDF) analysis. We show that the system shows two distinct amorphous phases upon heating. The first involves a reversible transition to a desolvated form of the original network, followed by an irreversible transition to an intermediate phase which has elongated Zn-I bonds.
High-temperature magnetostructural transition in van der Waals-layered α - MoCl 3

DOE PAGES

McGuire, Michael A.; Yan, Jiaqiang; Lampen-Kelley, Paula; ...

2017-11-07

Here, the crystallographic and magnetic properties of the cleavable 4d 3 transition metal compound α–MoCl 3 are reported, with a focus on the behavior above room temperature. Crystals were grown by chemical vapor transport and characterized using temperature dependent x-ray diffraction, Raman spectroscopy, and magnetization measurements. A structural phase transition occurs near 585 K, at which the Mo-Mo dimers present at room temperature are broken. A nearly regular honeycomb net of Mo is observed above the transition, and an optical phonon associated with the dimerization instability is identified in the Raman data and in first-principles calculations. The crystals are diamagneticmore » at room temperature in the dimerized state, and the magnetic susceptibility increases sharply at the structural transition. Moderately strong paramagnetism in the high-temperature structure indicates the presence of local moments on Mo. This is consistent with results of spin-polarized density functional theory calculations using the low- and high-temperature structures. Above the magnetostructural phase transition the magnetic susceptibility continues to increase gradually up to the maximum measurement temperature of 780 K, with a temperature dependence that suggests two-dimensional antiferromagnetic correlations.« less
High-temperature magnetostructural transition in van der Waals-layered α -MoCl3

NASA Astrophysics Data System (ADS)

McGuire, Michael A.; Yan, Jiaqiang; Lampen-Kelley, Paula; May, Andrew F.; Cooper, Valentino R.; Lindsay, Lucas; Puretzky, Alexander; Liang, Liangbo; KC, Santosh; Cakmak, Ercan; Calder, Stuart; Sales, Brian C.

2017-11-01

The crystallographic and magnetic properties of the cleavable 4 d3 transition metal compound α -MoCl3 are reported, with a focus on the behavior above room temperature. Crystals were grown by chemical vapor transport and characterized using temperature dependent x-ray diffraction, Raman spectroscopy, and magnetization measurements. A structural phase transition occurs near 585 K, at which the Mo-Mo dimers present at room temperature are broken. A nearly regular honeycomb net of Mo is observed above the transition, and an optical phonon associated with the dimerization instability is identified in the Raman data and in first-principles calculations. The crystals are diamagnetic at room temperature in the dimerized state, and the magnetic susceptibility increases sharply at the structural transition. Moderately strong paramagnetism in the high-temperature structure indicates the presence of local moments on Mo. This is consistent with results of spin-polarized density functional theory calculations using the low- and high-temperature structures. Above the magnetostructural phase transition the magnetic susceptibility continues to increase gradually up to the maximum measurement temperature of 780 K, with a temperature dependence that suggests two-dimensional antiferromagnetic correlations.
Highly responsive ground state of PbTaSe 2 : Structural phase transition and evolution of superconductivity under pressure

DOE PAGES

Kaluarachchi, Udhara S.; Deng, Yuhang; Besser, Matthew F.; ...

2017-06-09

Transport and magnetic studies of PbTaSe 2 under pressure suggest the existence of two superconducting phases with the low temperature phase boundary at ~ 0.25 GPa that is defined by a very sharp, first order, phase transition. The first order phase transition line can be followed via pressure dependent resistivity measurements, and is found to be near 0.12 GPa near room temperature. Transmission electron microscopy and x-ray diffraction at elevated temperatures confirm that this first order phase transition is structural and occurs at ambient pressure near ~ 425 K. The new, high temperature/high pressure phase has a similar crystal structuremore » and slightly lower unit cell volume relative to the ambient pressure, room temperature structure. Based on first-principles calculations this structure is suggested to be obtained by shifting the Pb atoms from the 1 a to 1 e Wyckoff position without changing the positions of Ta and Se atoms. PbTaSe 2 has an exceptionally pressure sensitive, structural phase transition with Δ T s / Δ P ≈ -1400 K/GPa near room temperature, and ≈ -1700 K/GPa near 4 K. This first order transition causes a ~ 1 K (~ 25 % ) steplike decrease in T c as pressure is increased through 0.25 GPa.« less
Bond Order Conservation Strategies in Catalysis Applied to the NH 3 Decomposition Reaction

DOE PAGES

Yu, Liang; Abild-Pedersen, Frank

2016-12-14

On the basis of an extensive set of density functional theory calculations, it is shown that a simple scheme provides a fundamental understanding of variations in the transition state energies and structures of reaction intermediates on transition metal surfaces across the periodic table. The scheme is built on the bond order conservation principle and requires a limited set of input data, still achieving transition state energies as a function of simple descriptors with an error smaller than those of approaches based on linear fits to a set of calculated transition state energies. Here, we have applied this approach together withmore » linear scaling of adsorption energies to obtain the energetics of the NH 3 decomposition reaction on a series of stepped fcc(211) transition metal surfaces. Moreover, this information is used to establish a microkinetic model for the formation of N 2 and H 2, thus providing insight into the components of the reaction that determines the activity.« less
Hydrogenation-controlled phase transition on two-dimensional transition metal dichalcogenides and their unique physical and catalytic properties.

PubMed

Qu, Yuanju; Pan, Hui; Kwok, Chi Tat

2016-09-30

Two-dimensional (2D) transition metal dichalcogenides (TMDs) have been widely used from nanodevices to energy harvesting/storage because of their tunable physical and chemical properties. In this work, we systematically investigate the effects of hydrogenation on the structural, electronic, magnetic, and catalytic properties of 33 TMDs based on first-principles calculations. We find that the stable phases of TMD monolayers can transit from 1T to 2H phase or vice versa upon the hydrogenation. We show that the hydrogenation can switch their magnetic and electronic states accompanying with the phase transition. The hydrogenation can tune the magnetic states of TMDs among non-, ferro, para-, and antiferro-magnetism and their electronic states among semiconductor, metal, and half-metal. We further show that, out of 33 TMD monolayers, 2H-TiS 2 has impressive catalytic ability comparable to Pt in hydrogen evolution reaction in a wide range of hydrogen coverages. Our findings would shed the light on the multi-functional applications of TMDs.
Electron affinity and excited states of methylglyoxal

NASA Astrophysics Data System (ADS)

Dauletyarov, Yerbolat; Dixon, Andrew R.; Wallace, Adam A.; Sanov, Andrei

2017-07-01

Using photoelectron imaging spectroscopy, we characterized the anion of methylglyoxal (X2A″ electronic state) and three lowest electronic states of the neutral methylglyoxal molecule: the closed-shell singlet ground state (X1A'), the lowest triplet state (a3A″), and the open-shell singlet state (A1A″). The adiabatic electron affinity (EA) of the ground state, EA(X1A') = 0.87(1) eV, spectroscopically determined for the first time, compares to 1.10(2) eV for unsubstituted glyoxal. The EAs (adiabatic attachment energies) of two excited states of methylglyoxal were also determined: EA(a3A″) = 3.27(2) eV and EA(A1A″) = 3.614(9) eV. The photodetachment of the anion to each of these two states produces the neutral species near the respective structural equilibria; hence, the a3A″ ← X2A″ and A1A″ ← X2A″ photodetachment transitions are dominated by intense peaks at their respective origins. The lowest-energy photodetachment transition, on the other hand, involves significant geometry relaxation in the X1A' state, which corresponds to a 60° internal rotation of the methyl group, compared to the anion structure. Accordingly, the X1A' ← X2A″ transition is characterized as a broad, congested band, whose vertical detachment energy, VDE = 1.20(4) eV, significantly exceeds the adiabatic EA. The experimental results are in excellent agreement with the ab initio predictions using several equation-of-motion methodologies, combined with coupled-cluster theory.
Gamow-Teller transitions in the 64Ni(3He, t)64Cu reaction

NASA Astrophysics Data System (ADS)

Popescu, L.; Adachi, T.; Berg, G. P. A.; von Brentano, P.; De Frenne, D.; Fujita, K.; Fujita, Y.; Hatanaka, K.; Jacobs, E.; Negret, A.; Nakanishi, K.; Sakemi, Y.; Shimbara, Y.; Shimizu, Y.; Tameshige, Y.; Tamii, A.; Uchida, M.; Yosoi, M.

2005-10-01

In order to study the Gamow-Teller (GT) transitions in the fp-shell nucleus 64Cu, the 64Ni(3He, t)64Cu charge-exchange reaction was investigated at E3He= 140 MeV/nucleon [1]. The outgoing tritons were momentum analysed by the Grand Raiden spectrometer at 0°. The very high energy resolution of 35 keV (FWHM) allowed the separation of individual levels in the excitation energy region from 0 to 3.5 MeV. An angular distribution analysis was performed for the observed transitions to these states. In addition to the ground state (g.s.), known to be a Jπ = 1+ GT state, several excited states showed L = 0 nature, making them candidates of GT states. At higher excitation energies, the level density becomes very high and a bump-like structure, the so-called GT Giant Resonance, dominates the spectrum.
Estimation of electronegativity values of elements in different valence states.

PubMed

Li, Keyan; Xue, Dongfeng

2006-10-05

The electronegativities of 82 elements in different valence states and with the most common coordination numbers have been quantitatively calculated on the basis of an effective ionic potential defined by the ionization energy and ionic radius. It is found that for a given cation, the electronegativity increases with increasing oxidation state and decreases with increasing coordination number. For the transition-metal cations, the electronegativity of the low-spin state is higher than that of the high-spin state. The ligand field stabilization, the first filling of p orbitals, the transition-metal contraction, and especially the lanthanide contraction are well-reflected by the relative values of our proposed electronegativity. This new scale is useful for us to estimate some quantities (e.g., the Lewis acid strength for the main group elements and the hydration free energy for the first transition series) and predict the structure and property of materials.
Ultrafast dynamics of multi-exciton state coupled to coherent vibration in zinc chlorin aggregates for artificial photosynthesis.

PubMed

Shi, Tongchao; Liu, Zhengzheng; Miyatake, Tomohiro; Tamiaki, Hitoshi; Kobayashi, Takayoshi; Zhang, Zeyu; Du, Juan; Leng, Yuxin

2017-11-27

Ultrafast vibronic dynamics induced by the interaction of the Frenkel exciton with the coherent molecular vibrations in a layer-structured zinc chlorin aggregates prepared for artificial photosynthesis have been studied by 7.1 fs real-time vibrational spectroscopy with multi-spectrum detection. The fast decay of 100 ± 5fs is ascribed to the relaxation from the higher multi-exciton state (MES) to the one-exciton state, and the slow one of 863 ± 70fs is assigned to the relaxation from Q-exciton state to the dark nonfluorescent charge-transfer (CT) state, respectively. In addition, the wavelength dependences of the exciton-vibration coupling strength are found to follow the zeroth derivative of the transient absorption spectra of the exciton. It could be explained in term of the transition dipole moment modulated by dynamic intensity borrowing between the B transition and the Q transition through the vibronic interactions.
On the vibronic level structure in the NO3 radical. Part III. Observation of intensity borrowing via ground state mixing.

PubMed

Stanton, John F; Okumura, Mitchio

2009-06-21

The A(2)E''<-- X(2)A'(2) absorption spectrum exhibits vibronically allowed transitions from the ground state of NO(3) to upper state levels having a''(1) and e' vibronic symmetries. This paper explores the coupling mechanisms that lend intensities to these features. While transitions to e' vibronic levels borrow intensity from the very strong B(2)E'<-- X(2)A'(2) electronic transition, those to a''(1) levels involve only negligible upper-state borrowing effects. Rather, it is the vibronic mixing of the ground vibronic level of NO(3) with vibrational levels in the B(2)E' electronic state that permit the a''(1) levels to be seen in the spectrum. These ideas are supported by vibronic coupling calculations. The fact that the intensities of features corresponding to the two different vibronic symmetries are comparable is thus accidental.

How cooperative are protein folding and unfolding transitions?

PubMed Central

Malhotra, Pooja

2016-01-01

Abstract A thermodynamically and kinetically simple picture of protein folding envisages only two states, native (N) and unfolded (U), separated by a single activation free energy barrier, and interconverting by cooperative two‐state transitions. The folding/unfolding transitions of many proteins occur, however, in multiple discrete steps associated with the formation of intermediates, which is indicative of reduced cooperativity. Furthermore, much advancement in experimental and computational approaches has demonstrated entirely non‐cooperative (gradual) transitions via a continuum of states and a multitude of small energetic barriers between the N and U states of some proteins. These findings have been instrumental towards providing a structural rationale for cooperative versus noncooperative transitions, based on the coupling between interaction networks in proteins. The cooperativity inherent in a folding/unfolding reaction appears to be context dependent, and can be tuned via experimental conditions which change the stabilities of N and U. The evolution of cooperativity in protein folding transitions is linked closely to the evolution of function as well as the aggregation propensity of the protein. A large activation energy barrier in a fully cooperative transition can provide the kinetic control required to prevent the accumulation of partially unfolded forms, which may promote aggregation. Nevertheless, increasing evidence for barrier‐less “downhill” folding, as well as for continuous “uphill” unfolding transitions, indicate that gradual non‐cooperative processes may be ubiquitous features on the free energy landscape of protein folding. PMID:27522064
Uncertainty and Intelligence in Computational Stochastic Mechanics

NASA Technical Reports Server (NTRS)

Ayyub, Bilal M.

1996-01-01

Classical structural reliability assessment techniques are based on precise and crisp (sharp) definitions of failure and non-failure (survival) of a structure in meeting a set of strength, function and serviceability criteria. These definitions are provided in the form of performance functions and limit state equations. Thus, the criteria provide a dichotomous definition of what real physical situations represent, in the form of abrupt change from structural survival to failure. However, based on observing the failure and survival of real structures according to the serviceability and strength criteria, the transition from a survival state to a failure state and from serviceability criteria to strength criteria are continuous and gradual rather than crisp and abrupt. That is, an entire spectrum of damage or failure levels (grades) is observed during the transition to total collapse. In the process, serviceability criteria are gradually violated with monotonically increasing level of violation, and progressively lead into the strength criteria violation. Classical structural reliability methods correctly and adequately include the ambiguity sources of uncertainty (physical randomness, statistical and modeling uncertainty) by varying amounts. However, they are unable to adequately incorporate the presence of a damage spectrum, and do not consider in their mathematical framework any sources of uncertainty of the vagueness type. Vagueness can be attributed to sources of fuzziness, unclearness, indistinctiveness, sharplessness and grayness; whereas ambiguity can be attributed to nonspecificity, one-to-many relations, variety, generality, diversity and divergence. Using the nomenclature of structural reliability, vagueness and ambiguity can be accounted for in the form of realistic delineation of structural damage based on subjective judgment of engineers. For situations that require decisions under uncertainty with cost/benefit objectives, the risk of failure should depend on the underlying level of damage and the uncertainties associated with its definition. A mathematical model for structural reliability assessment that includes both ambiguity and vagueness types of uncertainty was suggested to result in the likelihood of failure over a damage spectrum. The resulting structural reliability estimates properly represent the continuous transition from serviceability to strength limit states over the ultimate time exposure of the structure. In this section, a structural reliability assessment method based on a fuzzy definition of failure is suggested to meet these practical needs. A failure definition can be developed to indicate the relationship between failure level and structural response. In this fuzzy model, a subjective index is introduced to represent all levels of damage (or failure). This index can be interpreted as either a measure of failure level or a measure of a degree of belief in the occurrence of some performance condition (e.g., failure). The index allows expressing the transition state between complete survival and complete failure for some structural response based on subjective evaluation and judgment.
Hysteresis, reentrance, and glassy dynamics in systems of self-propelled rods

NASA Astrophysics Data System (ADS)

Kuan, Hui-Shun; Blackwell, Robert; Hough, Loren E.; Glaser, Matthew A.; Betterton, M. D.

2015-12-01

Nonequilibrium active matter made up of self-driven particles with short-range repulsive interactions is a useful minimal system to study active matter as the system exhibits collective motion and nonequilibrium order-disorder transitions. We studied high-aspect-ratio self-propelled rods over a wide range of packing fractions and driving to determine the nonequilibrium state diagram and dynamic properties. Flocking and nematic-laning states occupy much of the parameter space. In the flocking state, the average internal pressure is high and structural and mechanical relaxation times are long, suggesting that rods in flocks are in a translating glassy state despite overall flock motion. In contrast, the nematic-laning state shows fluidlike behavior. The flocking state occupies regions of the state diagram at both low and high packing fraction separated by nematic-laning at low driving and a history-dependent region at higher driving; the nematic-laning state transitions to the flocking state for both compression and expansion. We propose that the laning-flocking transitions are a type of glass transition that, in contrast to other glass-forming systems, can show fluidization as density increases. The fluid internal dynamics and ballistic transport of the nematic-laning state may promote collective dynamics of rod-shaped micro-organisms.
Hysteresis, reentrance, and glassy dynamics in systems of self-propelled rods.

PubMed

Kuan, Hui-Shun; Blackwell, Robert; Hough, Loren E; Glaser, Matthew A; Betterton, M D

2015-01-01

Nonequilibrium active matter made up of self-driven particles with short-range repulsive interactions is a useful minimal system to study active matter as the system exhibits collective motion and nonequilibrium order-disorder transitions. We studied high-aspect-ratio self-propelled rods over a wide range of packing fractions and driving to determine the nonequilibrium state diagram and dynamic properties. Flocking and nematic-laning states occupy much of the parameter space. In the flocking state, the average internal pressure is high and structural and mechanical relaxation times are long, suggesting that rods in flocks are in a translating glassy state despite overall flock motion. In contrast, the nematic-laning state shows fluidlike behavior. The flocking state occupies regions of the state diagram at both low and high packing fraction separated by nematic-laning at low driving and a history-dependent region at higher driving; the nematic-laning state transitions to the flocking state for both compression and expansion. We propose that the laning-flocking transitions are a type of glass transition that, in contrast to other glass-forming systems, can show fluidization as density increases. The fluid internal dynamics and ballistic transport of the nematic-laning state may promote collective dynamics of rod-shaped micro-organisms.
Large enhancement of second harmonic generation from transition-metal dichalcogenide monolayer on grating near bound states in the continuum.

PubMed

Wang, Tiecheng; Zhang, Shihao

2018-01-08

Second harmonic generation from the two-layer structure where a transition-metal dichalcogenide monolayer is put on a one-dimensional grating has been studied. This grating supports bound states in the continuum which have no leakage lying within the continuum of radiation modes, we can enhance the second harmonic generation from the transition-metal dichalcogenide monolayer by more than four orders of magnitude based on the critical field enhancement near the bound states in the continuum. In order to complete this calculation, the scattering matrix theory has been extended to include the nonlinear effect and the scattering matrix of a two-dimensional material including nonlinear terms; furthermore, two methods to observe the bound states in the continuum are considered, where one is tuning the thickness of the grating and the other is changing the incident angle of the electromagnetic wave. We have also discussed various modulation of the second harmonic generation enhancement by adjusting the azimuthal angle of the transition-metal dichalcogenide monolayer.
On the ion-pair dissociation mechanisms in the small NaCl·(H2 O)6 cluster: A perspective from reaction path search calculations.

PubMed

Takayanagi, Toshiyuki; Nakatomi, Taiki; Yonetani, Yoshiteru

2018-04-20

We performed reaction path search calculations for the NaCl·(H 2 O) 6 cluster using the global reaction route mapping (GRRM) code to understand the atomic-level mechanisms of the NaCl → Na + + Cl - ionic dissociation induced by water solvents. Low-lying minima, transition states connecting two local minima and corresponding intrinsic reaction coordinates on the potential energy surface are explored. We found that the NaCl distances at the transitions states for the dissociation pathways were distributed in a relatively wide range of 2.7-3.7 Å and that the NaCl distance at the transition state did not correlate with the commonly used solvation coordinates. This suggests that the definition of the transition states with specific structures as well as good reaction coordinate is very difficult for the ionic dissociation process even in a small water cluster. © 2018 Wiley Periodicals, Inc. © 2018 Wiley Periodicals, Inc.
Magnetic properties and effect of pressure on the electronic state of EuCo2Ge2

NASA Astrophysics Data System (ADS)

Ashitomi, Y.; Kakihana, M.; Honda, F.; Nakamura, A.; Aoki, D.; Uwatoko, Y.; Nakashima, M.; Amako, Y.; Takeuchi, T.; Kida, T.; Tahara, T.; Hagiwara, M.; Haga, Y.; Hedo, M.; Nakama, T.; Ōnuki, Y.

2018-05-01

EuCo2Ge2 with the tetragonal structure is a Eu-divalent antiferromagnet with the Néel temperature TN = 23 K. The magnetic easy-axis corresponds to the [100] direction (a-axis), while the [001] direction (c-axis) is a hard-axis. The magnetization for H∥ [ 100 ] indicates a metamagnetic transition at 25 kOe and saturates above 75 kOe. On the other hand, the hard-axis magnetization increases approximately linearly and saturates above 110 kOe. The magnetic phase diagram was constructed. A characteristic feature in EuCo2Ge2 is known as a valence transition under pressure, from Eu 2+δ to Eu 3 - δ ‧(δ, δ ‧ < 1). We also clarified the valence transition by measuring the electrical resistivity under pressure. The valence transition occurs at 3 GPa, with a hysteresis, and terminates at about 4.5 GPa. Further increasing pressure, the electronic state is changed into a moderate heavy fermion state and approaches the nearly trivalent electronic state.
Structural properties of Sb 2S 3 under pressure: Evidence of an electronic topological transition

DOE PAGES

Efthimiopoulos, Ilias; Buchan, Cienna; Wang, Yuejian

2016-04-06

High-pressure Raman spectroscopy and x-ray diffraction of Sb 2S 3 up to 53 GPa reveals two phase transitions at 5 GPa and 15 GPa. The first transition is evidenced by noticeable compressibility changes in distinct Raman-active modes, in the lattice parameter axial ratios, the unit cell volume, as well as in specific interatomic bond lengths and bond angles. By taking into account relevant results from the literature, we assign these effects to a second-order isostructural transition arising from an electronic topological transition in Sb 2S 3 near 5 GPa. Close comparison between Sb 2S 3 and Sb 2S 3 upmore » to 10 GPa reveals a slightly diverse structural behavior for these two compounds after the isostructural transition pressure. This structural diversity appears to account for the different pressure-induced electronic behavior of Sb 2S 3 and Sb 2S 3 up to 10 GPa, i.e. the absence of an insulator-metal transition in Sb 2S 3 up to that pressure. Lastly, the second high-pressure modification appearing above 15 GPa appears to trigger a structural disorder at ~20 GPa; full decompression from 53 GPa leads to the recovery of an amorphous state.« less
Quantum trajectory phase transitions in the micromaser.

PubMed

Garrahan, Juan P; Armour, Andrew D; Lesanovsky, Igor

2011-08-01

We study the dynamics of the single-atom maser, or micromaser, by means of the recently introduced method of thermodynamics of quantum jump trajectories. We find that the dynamics of the micromaser displays multiple space-time phase transitions, i.e., phase transitions in ensembles of quantum jump trajectories. This rich dynamical phase structure becomes apparent when trajectories are classified by dynamical observables that quantify dynamical activity, such as the number of atoms that have changed state while traversing the cavity. The space-time transitions can be either first order or continuous, and are controlled not just by standard parameters of the micromaser but also by nonequilibrium "counting" fields. We discuss how the dynamical phase behavior relates to the better known stationary-state properties of the micromaser.
Electronic signatures of dimerization in IrTe2

NASA Astrophysics Data System (ADS)

Dai, Jixia; Wu, Weida; Oh, Yoon Seok; Cheong, S.-W.; Yang, J. J.

2014-03-01

Recently, the mysterious phase transition around Tc ~ 260 K in IrTe2 has been intensively studied. A structural supermodulation with q =1/5 was identified below Tc. A variety of microscopic mechanisms have been proposed to account for this transition, including charge-density wave due to Fermi surface nesting, Te p-orbital driven structure instability, anionic depolymerization, ionic dimerization, and so on. However, there has not been an unified picture on the nature of this transition. To address this issue, we have performed low-temperature scanning tunneling microscopy and spectroscopy (STM/STS) experiments on IrTe2 and IrTe2-xSex. Our STM data clearly shows a strong bias dependence in both topography and local density of states (STS) maps. High resolution spectroscopic data further confirms the stripe-like electronic states modulation, which provides insight to the ionic dimerization revealed by X-ray diffraction.
Modulation of inherent dynamical tendencies of the bisabolyl cation via preorganization in epi-isozizaene synthase.

PubMed

Pemberton, Ryan P; Ho, Krystina C; Tantillo, Dean J

2015-04-01

The relative importance of preorganization, selective transition state stabilization and inherent reactivity are assessed through quantum chemical and docking calculations for a sesquiterpene synthase ( epi -isozizaene synthase, EIZS). Inherent reactivity of the bisabolyl cation, both static and dynamic, appears to determine the pathway to product, although preorganization and selective binding of the final transition state structure in the multi-step carbocation cascade that forms epi -isozizaene appear to play important roles.
Electronic excitation induced amorphization in titanate pyrochlores: an ab initio molecular dynamics study

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

Xiao, Haiyan Y.; Weber, William J.; Zhang, Yanwen

2015-02-09

In this study, the response of titanate pyrochlores (A 2Ti 2O 7, A = Y, Gd and Sm) to electronic excitation is investigated utilizing an ab initio molecular dynamics method. All the titanate pyrochlores are found to undergo a crystalline-to-amorphous structural transition under a low concentration of electronic excitations. The transition temperature at which structural amorphization starts to occur depends on the concentration of electronic excitations. During the structural transition, O 2-like molecules are formed, and this anion disorder further drives cation disorder that leads to an amorphous state. This study provides new insights into the mechanisms of amorphization inmore » titanate pyrochlores under laser, electron and ion irradiations.« less
Pressure-driven insulator-metal transition in cubic phase UO 2

DOE PAGES

Huang, Li; Wang, Yilin; Werner, Philipp

2017-09-21

Understanding the electronic properties of actinide oxides under pressure poses a great challenge for experimental and theoretical studies. Here, we investigate the electronic structure of cubic phase uranium dioxide at different volumes using a combination of density functional theory and dynamical mean-field theory. The ab initio calculations predict an orbital-selective insulator-metal transition at a moderate pressure of ~45 GPa. At this pressure the uranium's 5f 5/2 state becomes metallic, while the 5f 7/2 state remains insulating up to about 60 GPa. In the metallic state, we observe a rapid decrease of the 5f occupation and total angular momentum with pressure.more » Simultaneously, the so-called "Zhang-Rice state", which is of predominantly 5f 5/2 character, quickly disappears after the transition into the metallic phase.« less
Denatured states of yeast cytochrome c induced by heat and guanidinium chloride are structurally and thermodynamically different.

PubMed

Zaidi, Sobia; Haque, Md Anzarul; Ubaid-Ullah, Shah; Prakash, Amresh; Hassan, Md Imtaiyaz; Islam, Asimul; Batra, Janendra K; Ahmad, Faizan

2017-05-01

A sequence alignment of mammalian cytochromes c with yeast iso-1-cytochrome c (y-cyt-c) shows that the yeast protein contains five extra N-terminal residues. We have been interested in understanding the question: What is the role of these five extra N-terminal residues in folding and stability of the protein? To answer this question we have prepared five deletants of y-cyt-c by sequentially removing these extra residues. During our studies on the wild type (WT) protein and its deletants, we observed that the amount of secondary structure in the guanidinium chloride (GdmCl)-induced denatured (D) state of each protein is different from that of the heat-induced denatured (H) state. This finding is confirmed by the observation of an additional cooperative transition curve of optical properties between H and D states on the addition of different concentrations of GdmCl to the already heat denatured WT y-cyt-c and its deletants at pH 6.0 and 68°C. For each protein, analysis of transition curves representing processes, native (N) state ↔ D state, N state ↔ H state, and H state ↔ D state, was done to obtain Gibbs free energy changes associated with all the three processes. This analysis showed that, for each protein, thermodynamic cycle accommodates Gibbs free energies associated with transitions between N and D states, N and H states, and H and D states, the characteristics required for a thermodynamic function. All these experimental observations have been supported by our molecular dynamics simulation studies.
Two Active Site Divalent Ions in the Crystal Structure of the Hammerhead Ribozyme Bound to a Transition State Analogue.

PubMed

Mir, Aamir; Golden, Barbara L

2016-02-02

The crystal structure of the hammerhead ribozyme bound to the pentavalent transition state analogue vanadate reveals significant rearrangements relative to the previously determined structures. The active site contracts, bringing G10.1 closer to the cleavage site and repositioning a divalent metal ion such that it could, ultimately, interact directly with the scissile phosphate. This ion could also position a water molecule to serve as a general acid in the cleavage reaction. A second divalent ion is observed coordinated to O6 of G12. This metal ion is well-placed to help tune the pKA of G12. On the basis of this crystal structure as well as a wealth of biochemical studies, we propose a mechanism in which G12 serves as the general base and a magnesium-bound water serves as a general acid.
Two active site divalent ions in the crystal structure of the hammerhead ribozyme bound to a transition state analogue

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

Mir, Aamir; Golden, Barbara L.

2015-11-09

The crystal structure of the hammerhead ribozyme bound to the pentavalent transition state analogue vanadate reveals significant rearrangements relative to the previously determined structures. The active site contracts, bringing G10.1 closer to the cleavage site and repositioning a divalent metal ion such that it could, ultimately, interact directly with the scissile phosphate. This ion could also position a water molecule to serve as a general acid in the cleavage reaction. A second divalent ion is observed coordinated to O6 of G12. This metal ion is well-placed to help tune the p K A of G12. Finally, on the basis ofmore » this crystal structure as well as a wealth of biochemical studies, in this paper we propose a mechanism in which G12 serves as the general base and a magnesium-bound water serves as a general acid.« less
Dielectric response to the low-temperature magnetic defect structure and spin state transition in polycrystalline LaCoO3

NASA Astrophysics Data System (ADS)

Schmidt, Rainer; Wu, J.; Leighton, C.; Terry, I.

2009-03-01

The dielectric and magnetic properties and their correlations were investigated in polycrystalline perovskite LaCoO3-δ . The intrinsic bulk and grain-boundary (GB) dielectric relaxation processes were deconvoluted using impedance spectroscopy between 20 and 120 K, and resistivity and capacitance were analyzed separately. A thermally induced magnetic transition from a Co3+ low-spin (LS) (S=0;t2g6eg0) to a higher spin state occurs at Ts1≈80K , which is controversial in nature and has been suggested to be an intermediate-spin (IS) state (S=1;t2g5eg1) or a high-spin (HS) state (S=2;t2g4eg2) transition. This spin state transition was confirmed by magnetic-susceptibility measurements and was reflected in the impedance by a split of the single GB relaxation process into two coexisting contributions. This apparent electronic phase coexistence at T>80K was interpreted as a reflection of the coexistence of magnetic LS and IS/HS states. At lower temperatures (T≤40K) perceptible variation in bulk dielectric permittivity with temperature appeared to be correlated with the magnetic susceptibility associated with a magnetic defect structure. At 40K
Kinetic and thermodynamic framework for P4-P6 RNA reveals tertiary motif modularity and modulation of the folding preferred pathway

PubMed Central

Bisaria, Namita; Greenfeld, Max; Limouse, Charles; Pavlichin, Dmitri S.; Mabuchi, Hideo; Herschlag, Daniel

2016-01-01

The past decade has seen a wealth of 3D structural information about complex structured RNAs and identification of functional intermediates. Nevertheless, developing a complete and predictive understanding of the folding and function of these RNAs in biology will require connection of individual rate and equilibrium constants to structural changes that occur in individual folding steps and further relating these steps to the properties and behavior of isolated, simplified systems. To accomplish these goals we used the considerable structural knowledge of the folded, unfolded, and intermediate states of P4-P6 RNA. We enumerated structural states and possible folding transitions and determined rate and equilibrium constants for the transitions between these states using single-molecule FRET with a series of mutant P4-P6 variants. Comparisons with simplified constructs containing an isolated tertiary contact suggest that a given tertiary interaction has a stereotyped rate for breaking that may help identify structural transitions within complex RNAs and simplify the prediction of folding kinetics and thermodynamics for structured RNAs from their parts. The preferred folding pathway involves initial formation of the proximal tertiary contact. However, this preference was only ∼10 fold and could be reversed by a single point mutation, indicating that a model akin to a protein-folding contact order model will not suffice to describe RNA folding. Instead, our results suggest a strong analogy with a modified RNA diffusion-collision model in which tertiary elements within preformed secondary structures collide, with the success of these collisions dependent on whether the tertiary elements are in their rare binding-competent conformations. PMID:27493222
DOE Office of Scientific and Technical Information (OSTI.GOV)

Larson, Amber M.; Wilfong, Brandon; Moetakef, Pouya

A metal–insulator transition tuned by application of an external magnetic field occurs in the quasi-one dimensional system Bi1.7V8O16, which contains a mix of S = 1 and S = 1/2 vanadium cations. Unlike all other known vanadates, the magnetic susceptibility of Bi1.7V8O16 diverges in its insulating state, although no long-range magnetic ordering is observed from neutron diffraction measurements, possibly due to the frustrated geometry of the triangular ladders. Magnetotransport measurements reveal that the transition temperature is suppressed upon application of an external magnetic field, from 62.5 K at zero field to 40 K at 8 T. This behavior is bothmore » hysteretic and anisotropic, suggesting t2g orbital ordering of the V3+ and V4+ cations drives a first-order structural transition. Single crystal X-ray diffraction reveals a charge density wave of Bi3+ cations with a propagation vector of 0.846c*, which runs parallel to the triangular chain direction. Neutron powder diffraction measurements show a first-order structural transition, characterized by the coexistence of two tetragonal phases near the metal–insulator transition. Finally, we discuss the likelihood that ferromagnetic V–V dimers coexist with a majority spin-singlet state below the transition in Bi1.7V8O16.« less
Evidence for a pressure-induced spin transition in olivine-type LiFePO4 triphylite

NASA Astrophysics Data System (ADS)

Núñez Valdez, Maribel; Efthimiopoulos, Ilias; Taran, Michail; Müller, Jan; Bykova, Elena; McCammon, Catherine; Koch-Müller, Monika; Wilke, Max

2018-05-01

We present a combination of first-principles and experimental results regarding the structural and magnetic properties of olivine-type LiFePO4 under pressure. Our investigations indicate that the starting P b n m phase of LiFePO4 persists up to 70 GPa. Further compression leads to an isostructural transition in the pressure range of 70-75 GPa, inconsistent with a former theoretical study. Considering our first-principles prediction for a high-spin to low-spin transition of Fe2 + close to 72 GPa, we attribute the experimentally observed isostructural transition to a change in the spin state of Fe2 + in LiFePO4. Compared to relevant Fe-bearing minerals, LiFePO4 exhibits the largest onset pressure for a pressure-induced spin state transition.

Role of 5f electrons in the structural stability of light actinide (Th-U) mononitrides under pressure.

PubMed

Modak, P; Verma, Ashok K

2016-03-28

Pressure induced structural sequences and their mechanism for light actinide (Th-U) mononitrides were studied as a function of 5f-electron number using first-principles total energy and electronic structure calculations. Zero pressure lattice constants, bulk module and C11 elastic module vary systematically with 5f-electron number implying its direct role on crystal binding. There is a critical 5f-electron number below which the system makes B1-B2 and above it B1-R3̄m-B2 structural sequence under pressure. Also, the B1-B2 transition pressure increases with increasing 5f-electron number whereas an opposite trend is obtained for the B1-R3̄m transition pressure. The ascending of N p anti-bonding states through the Fermi level at high pressure is responsible for the structural instability of the system. Above the critical 5f-electron number in the system a narrow 5f-band occurs very close to the Fermi level which allows the system to lower its symmetry via band Jahn-Teller type lattice distortion and the system undergoes a B1-R3̄m phase transition. However, below the critical 5f-electron number this mechanism is not favorable due to a lack of sufficient 5f-state occupancy and thus the system undergoes a B1-B2 phase transition like other ionic solids.
Direct real-time detection of the structural and biochemical events in the myosin power stroke.

PubMed

Muretta, Joseph M; Rohde, John A; Johnsrud, Daniel O; Cornea, Sinziana; Thomas, David D

2015-11-17

A principal goal of molecular biophysics is to show how protein structural transitions explain physiology. We have developed a strategic tool, transient time-resolved FRET [(TR)(2)FRET], for this purpose and use it here to measure directly, with millisecond resolution, the structural and biochemical kinetics of muscle myosin and to determine directly how myosin's power stroke is coupled to the thermodynamic drive for force generation, actin-activated phosphate release, and the weak-to-strong actin-binding transition. We find that actin initiates the power stroke before phosphate dissociation and not after, as many models propose. This result supports a model for muscle contraction in which power output and efficiency are tuned by the distribution of myosin structural states. This technology should have wide application to other systems in which questions about the temporal coupling of allosteric structural and biochemical transitions remain unanswered.
Discriminating binding mechanisms of an intrinsically disordered protein via a multi-state coarse-grained model

NASA Astrophysics Data System (ADS)

Knott, Michael; Best, Robert B.

2014-05-01

Many proteins undergo a conformational transition upon binding to their cognate binding partner, with intrinsically disordered proteins (IDPs) providing an extreme example in which a folding transition occurs. However, it is often not clear whether this occurs via an "induced fit" or "conformational selection" mechanism, or via some intermediate scenario. In the first case, transient encounters with the binding partner favour transitions to the bound structure before the two proteins dissociate, while in the second the bound structure must be selected from a subset of unbound structures which are in the correct state for binding, because transient encounters of the incorrect conformation with the binding partner are most likely to result in dissociation. A particularly interesting situation involves those intrinsically disordered proteins which can bind to different binding partners in different conformations. We have devised a multi-state coarse-grained simulation model which is able to capture the binding of IDPs in alternate conformations, and by applying it to the binding of nuclear coactivator binding domain (NCBD) to either ACTR or IRF-3 we are able to determine the binding mechanism. By all measures, the binding of NCBD to either binding partner appears to occur via an induced fit mechanism. Nonetheless, we also show how a scenario closer to conformational selection could arise by choosing an alternative non-binding structure for NCBD.
Structural and magnetic phase transitions in EuTi 1-xNb xO 3

DOE PAGES

Li, Ling; Morris, James R.; Koehler, Michael R.; ...

2015-07-30

Here, we investigate the structural and magnetic phase transitions in EuTi 1-xNb xO 3 (0≤x≤0.3) with synchrotron powder x-ray diffraction, resonant ultrasound spectroscopy, and magnetization measurements. Upon Nb doping, the Pmmore » $$\\bar{3}$$m ↔ I4/mcm structural transition shifts to higher temperatures and the room temperature lattice parameter increases while the magnitude of the octahedral tilting decreases. In addition, Nb substitution for Ti destabilizes the antiferromagnetic ground state of the parent compound and long-range ferromagnetic order is observed in the samples with x≥0.1. Moreover, the structural transition in pure and doped compounds is marked by a dramatic step-like softening of the elastic moduli near T S, which resembles that of SrTiO 3 and can be adequately modeled using the Landau free energy model employing the same coupling between strain and octahedral tilting order parameter as previously used to model SrTiO 3.« less
On entropy determination from magnetic and calorimetric experiments in conventional giant magnetocaloric materials

NASA Astrophysics Data System (ADS)

Chen, Jing-Han; Us Saleheen, Ahmad; Adams, Philip W.; Young, David P.; Ali, Naushad; Stadler, Shane

2018-04-01

In this work, we discuss measurement protocols for the determination of the magnetic entropy change associated with first-order magneto-structural transitions from both magnetization and calorimetric experiments. The Cu-doped Ni2MnGa Heusler alloy with a first-order magneto-structural phase transition is used as a case study to illustrate how commonly-used magnetization measurement protocols result in spurious entropy evaluations. Two magnetization measurement protocols which allow for the accurate assessment of the magnetic entropy change across first-order magneto-structural transitions are presented. In addition, calorimetric measurements were performed to validate the results from the magnetization measurements. Self-consistent results between the magnetization and calorimetric measurements were obtained when the non-equilibrium thermodynamic state was carefully handled. Such methods could be applicable to other systems displaying giant magnetocaloric effects caused by first-order phase transitions with magnetic and thermal hysteresis.
Nuclear Shell Structure and Beta Decay I. Odd A Nuclei II. Even A Nuclei

DOE R&D Accomplishments Database

Mayer, M.G.; Moszkowski, S.A.; Nordheim, L.W.

1951-05-01

In Part I a systematics is given of all transitions for odd A nuclei for which sufficiently reliable data are available. The allowed or forbidden characters of the transitions are correlated with the positions of the initial and final odd nucleon groups in the nuclear shell scheme. The nuclear shells show definite characteristics with respect to parity of the ground states. The latter is the same as the one obtained from known spins and magnetic moments in a one-particle interpretation. In Part II a systematics of the beta transitions of even-A nuclei is given. An interpretation of the character of the transitions in terms of nuclear shell structure is achieved on the hypothesis that the odd nucleon groups have the same structure as in odd-A nuclei, together with a simple coupling rule between the neutron and proton groups in odd-odd nuclei.
Elucidating the ensemble of functionally-relevant transitions in protein systems with a robotics-inspired method

PubMed Central

2013-01-01

Background Many proteins tune their biological function by transitioning between different functional states, effectively acting as dynamic molecular machines. Detailed structural characterization of transition trajectories is central to understanding the relationship between protein dynamics and function. Computational approaches that build on the Molecular Dynamics framework are in principle able to model transition trajectories at great detail but also at considerable computational cost. Methods that delay consideration of dynamics and focus instead on elucidating energetically-credible conformational paths connecting two functionally-relevant structures provide a complementary approach. Effective sampling-based path planning methods originating in robotics have been recently proposed to produce conformational paths. These methods largely model short peptides or address large proteins by simplifying conformational space. Methods We propose a robotics-inspired method that connects two given structures of a protein by sampling conformational paths. The method focuses on small- to medium-size proteins, efficiently modeling structural deformations through the use of the molecular fragment replacement technique. In particular, the method grows a tree in conformational space rooted at the start structure, steering the tree to a goal region defined around the goal structure. We investigate various bias schemes over a progress coordinate for balance between coverage of conformational space and progress towards the goal. A geometric projection layer promotes path diversity. A reactive temperature scheme allows sampling of rare paths that cross energy barriers. Results and conclusions Experiments are conducted on small- to medium-size proteins of length up to 214 amino acids and with multiple known functionally-relevant states, some of which are more than 13Å apart of each-other. Analysis reveals that the method effectively obtains conformational paths connecting structural states that are significantly different. A detailed analysis on the depth and breadth of the tree suggests that a soft global bias over the progress coordinate enhances sampling and results in higher path diversity. The explicit geometric projection layer that biases the exploration away from over-sampled regions further increases coverage, often improving proximity to the goal by forcing the exploration to find new paths. The reactive temperature scheme is shown effective in increasing path diversity, particularly in difficult structural transitions with known high-energy barriers. PMID:24565158
Research investigation directed toward extending the useful range of the electromagnetic spectrum

NASA Technical Reports Server (NTRS)

Hartmann, S. R.

1971-01-01

The lifetimes and fine structure of He(-) were studied using time-of-flight techniques and quenching by a static axial magnetic field. Using level-crossing spectroscopy the hyperfine constants A and B and the lifetime of the 3 2P3/2 state of Li-7 were measured. Polarization of the Ru 7S level was created as a first step in determining the hyperfine structure of the alkali excited S state. The parametric interaction between light and microwaves in optically pumped Rb-87 vapor were investigated. Measurements and analyses of transitions in formaldehyde and its isotopic species and in the lowest two excited vibrational states of H2CO were also made, as well as of transitions in furan, pyrrole, formic acid, and cyanoacetylene. The Hanle effect was studied in the NO molecule, and RF oscillators were developed with flat, wideband output to observe excited state hyperfine transitions at zero field. Data was generated on the time-dependent behavior of photon echoes in ruby. Stimulated Raman scattering was studied in atomic Tl vapor. A Q switched, temperature-tuned ruby laser was developed which operates between 6934 and 6938 A. The frequency shift due to resonant interaction between identical radiating atoms was calculated.
Phase transitions of sodium niobate powder and ceramics, prepared by solid state synthesis

NASA Astrophysics Data System (ADS)

Koruza, J.; Tellier, J.; Malič, B.; Bobnar, V.; Kosec, M.

2010-12-01

Phase transitions of sodium niobate, prepared by the solid state synthesis method, were examined using dielectric measurements, differential scanning calorimetry, and high temperature x-ray diffraction, in order to contribute to the clarification of its structural behavior below 400 °C. Four phase transitions were detected in the ceramic sample using dielectric measurements and differential scanning calorimetry and the obtained temperatures were in a good agreement with previous reports for the transitions of the P polymorph. The anomaly observed by dielectric measurements in the vicinity of 150 °C was frequency dependent and could be related to the dynamics of the ferroelectric nanoregions. The phase transitions of the as-synthesized NaNbO3 powder were investigated using differential scanning calorimetry and high temperature x-ray diffraction. The results show the existence of the Q polymorph at room temperature, not previously reported for the powder, which undergoes a transition to the R polymorph upon heating through a temperature region between 265 and 326.5 °C. This transition is mainly related to the displacement of Na into a more symmetric position and a minor change in the tilting system. The structures at room temperature, 250, 300, and 420 °C were refined by the Rietveld method and the evolution of the tilting system of the octahedral network and cationic displacement are reported.
Polarized two-photon photoselection in EGFP: Theory and experiment

NASA Astrophysics Data System (ADS)

Masters, T. A.; Marsh, R. J.; Blacker, T. S.; Armoogum, D. A.; Larijani, B.; Bain, A. J.

2018-04-01

In this work, we present a complete theoretical description of the excited state order created by two-photon photoselection from an isotropic ground state; this encompasses both the conventionally measured quadrupolar (K = 2) and the "hidden" degree of hexadecapolar (K = 4) transition dipole alignment, their dependence on the two-photon transition tensor and emission transition dipole moment orientation. Linearly and circularly polarized two-photon absorption (TPA) and time-resolved single- and two-photon fluorescence anisotropy measurements are used to determine the structure of the transition tensor in the deprotonated form of enhanced green fluorescent protein. For excitation wavelengths between 800 nm and 900 nm, TPA is best described by a single element, almost completely diagonal, two-dimensional (planar) transition tensor whose principal axis is collinear to that of the single-photon S0 → S1 transition moment. These observations are in accordance with assignments of the near-infrared two-photon absorption band in fluorescent proteins to a vibronically enhanced S0 → S1 transition.
Polarized two-photon photoselection in EGFP: Theory and experiment.

PubMed

Masters, T A; Marsh, R J; Blacker, T S; Armoogum, D A; Larijani, B; Bain, A J

2018-04-07

In this work, we present a complete theoretical description of the excited state order created by two-photon photoselection from an isotropic ground state; this encompasses both the conventionally measured quadrupolar (K = 2) and the "hidden" degree of hexadecapolar (K = 4) transition dipole alignment, their dependence on the two-photon transition tensor and emission transition dipole moment orientation. Linearly and circularly polarized two-photon absorption (TPA) and time-resolved single- and two-photon fluorescence anisotropy measurements are used to determine the structure of the transition tensor in the deprotonated form of enhanced green fluorescent protein. For excitation wavelengths between 800 nm and 900 nm, TPA is best described by a single element, almost completely diagonal, two-dimensional (planar) transition tensor whose principal axis is collinear to that of the single-photon S 0 → S 1 transition moment. These observations are in accordance with assignments of the near-infrared two-photon absorption band in fluorescent proteins to a vibronically enhanced S 0 → S 1 transition.
Sequencing chess

NASA Astrophysics Data System (ADS)

Atashpendar, Arshia; Schilling, Tanja; Voigtmann, Thomas

2016-10-01

We analyze the structure of the state space of chess by means of transition path sampling Monte Carlo simulations. Based on the typical number of moves required to transpose a given configuration of chess pieces into another, we conclude that the state space consists of several pockets between which transitions are rare. Skilled players explore an even smaller subset of positions that populate some of these pockets only very sparsely. These results suggest that the usual measures to estimate both the size of the state space and the size of the tree of legal moves are not unique indicators of the complexity of the game, but that considerations regarding the connectedness of states are equally important.
Electronic structure of Fe, Co, and Ni impurities in Pd

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

van Acker, J.F.; Weijs, P.W.J.; Fuggle, J.C.

1988-11-15

A photoemission study of the valence bands of the dilute alloys PdFe, PdCo, and PdNi is presented. We use the Cooper minimum effect to estimate the local density of states on the impurity site. The behavior of transition-metal impurities in a transition-metal matrix is shown to be very different from their behavior in s-p metals. Our conclusion is that the Fe and Co 3d states are mixed with states throughout the Pd 4d band, while the Ni contribution to the spectra is dominated by a peak of (minority) 3d states near the Fermi level.
Nanofocusing of structured light for quadrupolar light-matter interactions.

PubMed

Sakai, Kyosuke; Yamamoto, Takeaki; Sasaki, Keiji

2018-05-17

The spatial structure of an electromagnetic field can determine the characteristics of light-matter interactions. A strong gradient of light in the near field can excite dipole-forbidden atomic transitions, e.g., electric quadrupole transitions, which are rarely observed under plane-wave far-field illumination. Structured light with a higher-order orbital angular momentum state may also modulate the selection rules in which an atom can absorb two quanta of angular momentum: one from the spin and another from the spatial structure of the beam. Here, we numerically demonstrate a strong focusing of structured light with a higher-order orbital angular momentum state in the near field. A quadrupole field was confined within a gap region of several tens of nanometres in a plasmonic tetramer structure. A plasmonic crystal surrounding the tetramer structure provides a robust antenna effect, where the incident structured light can be strongly coupled to the quadrupole field in the gap region with a larger alignment tolerance. The proposed system is expected to provide a platform for light-matter interactions with strong multipolar effects.
The fine-structure intervals of (N-14)+ by far-infrared laser magnetic resonance

NASA Technical Reports Server (NTRS)

Brown, John M.; Varberg, Thomas D.; Evenson, Kenneth M.; Cooksy, Andrew L.

1994-01-01

The far-infrared laser magnetic resonance spectra associated with both fine-structure transitions in (N-14)+ in its ground P-3 state have been recorded. This is the first laboratory observation of the J = 1 left arrow 0 transition and its frequency has been determined two orders of magnitude more accurately than previously. The remeasurement of the J = 2 left arrow 1 spectrum revealed a small error in the previous laboratory measurements. The fine-structure splittings (free of hyperfine interactions) determined in this work are (delta)E(sub 10) = 1461.13190 (61) GHz, (delta)E(sub 21) = 2459.38006 (37) GHz. Zero-field transition frequencies which include the effects of hyperfine structure have also been calculated. Refined values for the hyperfine constants and the g(sub J) factors have been obtained.
Laser-stimulated electric quadrupole transitions in the molecular hydrogen ion H2+

NASA Astrophysics Data System (ADS)

Korobov, V. I.; Danev, P.; Bakalov, D.; Schiller, S.

2018-03-01

Molecular hydrogen ions are of metrological relevance due to the possibility of precise theoretical evaluation of their spectrum and of external-field-induced shifts. We report the results of the calculations of the rate of laser-induced electric quadrupole transitions between a large set of ro-vibrational states of H2+. The hyperfine and Zeeman structure of the E 2 transition spectrum and the effects of the laser polarization are treated in detail. The treatment is generally applicable to molecules in 2Σ states. We also present the nuclear spin-electron spin-coupling constants, computed with a precision ten times higher than previously obtained.
Optical transitions in two-dimensional topological insulators with point defects

NASA Astrophysics Data System (ADS)

Sablikov, Vladimir A.; Sukhanov, Aleksei A.

2016-12-01

Nontrivial properties of electronic states in topological insulators are inherent not only to the surface and boundary states, but to bound states localized at structure defects as well. We clarify how the unusual properties of the defect-induced bound states are manifested in optical absorption spectra in two-dimensional topological insulators. The calculations are carried out for defects with short-range potential. We find that the defects give rise to the appearance of specific features in the absorption spectrum, which are an inherent property of topological insulators. They have the form of two or three absorption peaks that are due to intracenter transitions between electron-like and hole-like bound states.
Spatial perspectives in state-and-transition models: A missing link to land management?

USDA-ARS?s Scientific Manuscript database

Conceptual models of alternative states and thresholds are based largely on observations of ecosystem processes at a few points in space. Because the distribution of alternative states in spatially-structured ecosystems is the result of variations in pattern-process interactions at different scales,...
Conventional empirical law reverses in the phase transitions of 122-type iron-based superconductors

DOE PAGES

Yu, Zhenhai; Wang, Lin; Wang, Luhong; ...

2014-11-24

Phase transition of solid-state materials is a fundamental research topic in condensed matter physics, materials science and geophysics. It has been well accepted and widely proven that isostructural compounds containing different cations undergo same pressure-induced phase transitions but at progressively lower pressures as the cation radii increases. However, we discovered that this conventional law reverses in the structural transitions in 122-type iron-based superconductors. In this report, a combined low temperature and high pressure X-ray diffraction (XRD) measurement has identified the phase transition curves among the tetragonal (T), orthorhombic (O) and the collapsed-tetragonal (cT) phases in the structural phase diagram ofmore » the iron-based superconductor AFe 2As 2 (A = Ca, Sr, Eu, and Ba). As a result, the cation radii dependence of the phase transition pressure (T → cT) shows an opposite trend in which the compounds with larger ambient radii cations have a higher transition pressure.« less
Enhancing pairwise state-transition weights: A new weighting scheme in simulated tempering that can minimize transition time between a pair of conformational states

NASA Astrophysics Data System (ADS)

Qiao, Qin; Zhang, Hou-Dao; Huang, Xuhui

2016-04-01

Simulated tempering (ST) is a widely used enhancing sampling method for Molecular Dynamics simulations. As one expanded ensemble method, ST is a combination of canonical ensembles at different temperatures and the acceptance probability of cross-temperature transitions is determined by both the temperature difference and the weights of each temperature. One popular way to obtain the weights is to adopt the free energy of each canonical ensemble, which achieves uniform sampling among temperature space. However, this uniform distribution in temperature space may not be optimal since high temperatures do not always speed up the conformational transitions of interest, as anti-Arrhenius kinetics are prevalent in protein and RNA folding. Here, we propose a new method: Enhancing Pairwise State-transition Weights (EPSW), to obtain the optimal weights by minimizing the round-trip time for transitions among different metastable states at the temperature of interest in ST. The novelty of the EPSW algorithm lies in explicitly considering the kinetics of conformation transitions when optimizing the weights of different temperatures. We further demonstrate the power of EPSW in three different systems: a simple two-temperature model, a two-dimensional model for protein folding with anti-Arrhenius kinetics, and the alanine dipeptide. The results from these three systems showed that the new algorithm can substantially accelerate the transitions between conformational states of interest in the ST expanded ensemble and further facilitate the convergence of thermodynamics compared to the widely used free energy weights. We anticipate that this algorithm is particularly useful for studying functional conformational changes of biological systems where the initial and final states are often known from structural biology experiments.

Enhancing pairwise state-transition weights: A new weighting scheme in simulated tempering that can minimize transition time between a pair of conformational states

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

Qiao, Qin, E-mail: qqiao@ust.hk; Zhang, Hou-Dao; Huang, Xuhui, E-mail: xuhuihuang@ust.hk

2016-04-21

Simulated tempering (ST) is a widely used enhancing sampling method for Molecular Dynamics simulations. As one expanded ensemble method, ST is a combination of canonical ensembles at different temperatures and the acceptance probability of cross-temperature transitions is determined by both the temperature difference and the weights of each temperature. One popular way to obtain the weights is to adopt the free energy of each canonical ensemble, which achieves uniform sampling among temperature space. However, this uniform distribution in temperature space may not be optimal since high temperatures do not always speed up the conformational transitions of interest, as anti-Arrhenius kineticsmore » are prevalent in protein and RNA folding. Here, we propose a new method: Enhancing Pairwise State-transition Weights (EPSW), to obtain the optimal weights by minimizing the round-trip time for transitions among different metastable states at the temperature of interest in ST. The novelty of the EPSW algorithm lies in explicitly considering the kinetics of conformation transitions when optimizing the weights of different temperatures. We further demonstrate the power of EPSW in three different systems: a simple two-temperature model, a two-dimensional model for protein folding with anti-Arrhenius kinetics, and the alanine dipeptide. The results from these three systems showed that the new algorithm can substantially accelerate the transitions between conformational states of interest in the ST expanded ensemble and further facilitate the convergence of thermodynamics compared to the widely used free energy weights. We anticipate that this algorithm is particularly useful for studying functional conformational changes of biological systems where the initial and final states are often known from structural biology experiments.« less
Limiting similarity and niche theory for structured populations.

PubMed

Szilágyi, András; Meszéna, Géza

2009-05-07

We develop the theory of limiting similarity and niche for structured populations with finite number of individual states (i-state). In line with a previously published theory for unstructured populations, the niche of a species is specified by the impact and sensitivity niche vectors. They describe the population's impact on and sensitivity towards the variables involved in the population regulation. Robust coexistence requires sufficient segregation of the impact, as well as of the sensitivity niche vectors. Connection between the population-level impact and sensitivity and the impact/sensitivity of the specific i-states is developed. Each i-state contributes to the impact of the population proportional to its frequency in the population. Sensitivity of the population is composed of the sensitivity of the rates of demographic transitions, weighted by the frequency and by the reproductive value of the initial and final i-states of the transition, respectively. Coexistence in a multi-patch environment is studied. This analysis is interpreted as spatial niche segregation.
A comparison between state-specific and linear-response formalisms for the calculation of vertical electronic transition energy in solution with the CCSD-PCM method.

PubMed

Caricato, Marco

2013-07-28

The calculation of vertical electronic transition energies of molecular systems in solution with accurate quantum mechanical methods requires the use of approximate and yet reliable models to describe the effect of the solvent on the electronic structure of the solute. The polarizable continuum model (PCM) of solvation represents a computationally efficient way to describe this effect, especially when combined with coupled cluster (CC) methods. Two formalisms are available to compute transition energies within the PCM framework: State-Specific (SS) and Linear-Response (LR). The former provides a more complete account of the solute-solvent polarization in the excited states, while the latter is computationally very efficient (i.e., comparable to gas phase) and transition properties are well defined. In this work, I review the theory for the two formalisms within CC theory with a focus on their computational requirements, and present the first implementation of the LR-PCM formalism with the coupled cluster singles and doubles method (CCSD). Transition energies computed with LR- and SS-CCSD-PCM are presented, as well as a comparison between solvation models in the LR approach. The numerical results show that the two formalisms provide different absolute values of transition energy, but similar relative solvatochromic shifts (from nonpolar to polar solvents). The LR formalism may then be used to explore the solvent effect on multiple states and evaluate transition probabilities, while the SS formalism may be used to refine the description of specific states and for the exploration of excited state potential energy surfaces of solvated systems.
Mechanistic investigations of the hydrolysis of amides, oxoesters and thioesters via kinetic isotope effects and positional isotope exchange.

PubMed

Robins, Lori I; Fogle, Emily J; Marlier, John F

2015-11-01

The hydrolysis of amides, oxoesters and thioesters is an important reaction in both organic chemistry and biochemistry. Kinetic isotope effects (KIEs) are one of the most important physical organic methods for determining the most likely transition state structure and rate-determining step of these reaction mechanisms. This method induces a very small change in reaction rates, which, in turn, results in a minimum disturbance of the natural mechanism. KIE studies were carried out on both the non-enzymatic and the enzyme-catalyzed reactions in an effort to compare both types of mechanisms. In these studies the amides and esters of formic acid were chosen because this molecular structure allowed development of methodology to determine heavy-atom solvent (nucleophile) KIEs. This type of isotope effect is difficult to measure, but is rich in mechanistic information. Results of these investigations point to transition states with varying degrees of tetrahedral character that fit a classical stepwise mechanism. This article is part of a special issue entitled: Enzyme Transition States from Theory and Experiment. Copyright © 2014 Elsevier B.V. All rights reserved.
Measurement of protein unfolding/refolding kinetics and structural characterization of hidden intermediates by NMR relaxation dispersion

PubMed Central

Meinhold, Derrick W.; Wright, Peter E.

2011-01-01

Detailed understanding of protein function and malfunction hinges on the ability to characterize transiently populated states and the transitions between them. Here, we use 15N, , and 13CO NMR R2 relaxation dispersion to investigate spontaneous unfolding and refolding events of native apomyoglobin. Above pH 5.0, dispersion is dominated by processes involving fluctuations of the F-helix region, which is invisible in NMR spectra. Measurements of R2 dispersion for residues contacted by the F-helix region in the native (N) structure reveal a transient state formed by local unfolding of helix F and undocking from the protein core. A similar state was detected at pH 4.75–4.95 and determined to be an on-pathway intermediate (I1) in a linear three-state unfolding scheme (N⇆I1⇆MG) leading to a transiently populated molten globule (MG) state. The slowest steps in unfolding and refolding are N → I1 (36 s-1) and MG → I1 (26 s-1), respectively. Differences in chemical shift between N and I1 are very small, except in regions adjacent to helix F, showing that their core structures are similar. Chemical shift changes between the N and MG states, obtained from R2 dispersion, reveal that the transient MG state is structurally similar to the equilibrium MG observed previously at high temperature and low pH. Analysis of MG state chemical shifts shows the location of residual helical structure in the transient intermediate and identifies regions that unfold or rearrange into nonnative structure during the N → MG transition. The experiments also identify regions of energetic frustration that “crack” during unfolding and impede the refolding process. PMID:21562212
Retinal Ligand Mobility Explains Internal Hydration and Reconciles Active Rhodopsin Structures

PubMed Central

Leioatts, Nicholas; Mertz, Blake; Martínez-Mayorga, Karina; Romo, Tod D.; Pitman, Michael C.; Feller, Scott E.; Grossfield, Alan; Brown, Michael F.

2014-01-01

Rhodopsin, the mammalian dim-light receptor, is one of the best-characterized G-protein-coupled receptors, a pharmaceutically important class of membrane proteins that has garnered a great deal of attention because of the recent availability of structural information. Yet the mechanism of rhodopsin activation is not fully understood. Here, we use microsecond-scale all-atom molecular dynamics simulations, validated by solid-state 2H nuclear magnetic resonance spectroscopy, to understand the transition between the dark and metarhodopsin I (Meta I) states. Our analysis of these simulations reveals striking differences in ligand flexibility between the two states. Retinal is much more dynamic in Meta I, adopting an elongated conformation similar to that seen in the recent activelike crystal structures. Surprisingly, this elongation corresponds to both a dramatic influx of bulk water into the hydrophobic core of the protein and a concerted transition in the highly conserved Trp2656.48 residue. In addition, enhanced ligand flexibility upon light activation provides an explanation for the different retinal orientations observed in X-ray crystal structures of active rhodopsin. PMID:24328554
Evolution of the Structural-Phase State of a Ti-Al- V-Mo Alloy During Severe Plastic Deformation and SubSequent Annealing

NASA Astrophysics Data System (ADS)

Grabovetskaya, G. P.; Ratochka, I. V.; Mishin, I. P.; Zabudchenko, O. V.; Lykova, O. N.

2016-05-01

The effect of the initial phase composition of a Ti-Al-V-Mo alloy (VT16 according to Russian classification) on the evolution of its structural-phase state during the formation of ultrafine-grained structure and subsequent annealing is investigated by methods of optical and transmission electron microscopy and x-ray diffraction analysis. The structure is produced by cyclic pressing with a change of the deformation axis in each cycle combined with a gradual decrease of the pressing temperature from 1073 to 723 K. As this takes place, α″ → α + β and β → α phase transitions are found to develop in the test alloy. The phase state of the ultrafinegrained material thus produced depends for the most part on its elemental composition and severe plastic deformation regime. Annealing below the recrystallization temperature is shown to give rise to a β→α phase transition and alloying element redistribution. The foregoing processes allow for retaining a high level of the strength properties of the alloy.
Zipping and Unzipping of Adenylate Kinase: Atomistic Insights into the Ensemble of Open ↔ Closed Transitions

PubMed Central

Beckstein, Oliver; Denning, Elizabeth J.; Perilla, Juan R.; Woolf, Thomas B.

2009-01-01

Adenylate kinase (AdK), a phosphotransferase enzyme, plays an important role in cellular energy homeostasis. It undergoes a large conformational change between an open and a closed state, even in the absence of substrate. We investigate the apo-AdK transition at the atomic level both with free energy calculations and our new dynamic importance sampling (DIMS) molecular dynamics (MD) method. DIMS is shown to sample biologically relevant conformations as verified by comparing an ensemble of hundreds of DIMS transitions to AdK crystal structure intermediates. The simulations reveal in atomic detail how hinge regions partially and intermittently unfold during the transition. Conserved salt bridges are seen to have important structural and dynamic roles; in particular four ionic bonds are identified that open in a sequential, zipper-like fashion and thus dominate the free energy landscape of the transition. Transitions between the closed and open conformations only have to overcome moderate free energy barriers. Unexpectedly, the closed and open state encompass broad free energy basins that contain conformations differing in domain hinge motions by up to 40°. The significance of these extended states is discussed in relation to recent experimental FRET measurements. Taken together, these results demonstrate how a small number of cooperative key interactions can shape the overall dynamics of an enzyme and suggest an “all-or-nothing” mechanism for the opening and closing of AdK. Our efficient DIMS-MD computer simulation approach can provide a detailed picture of a functionally important macromolecular transition and thus help to interpret and suggest experiments to probe the conformational landscape of dynamic proteins such as AdK. PMID:19751742
Structural phase transitions in SrTiO 3 nanoparticles

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

Zhang, Han; Liu, Sizhan; Scofield, Megan E.

2017-07-31

Pressure dependent structural measurements on monodispersed nanoscale SrTiO3 samples with average diameters of 10 to ~80 nm were conducted to enhance the understanding of the structural phase diagram of nanoscale SrTiO3. A robust pressure independent polar structure was found in the 10 nm sample for pressures up to 13 GPa, while a size dependent cubic to tetragonal transition occurs (at P = Pc) for larger particle sizes. The results suggest that the growth of ~10 nm STO particles on substrates with significant lattice mismatch may maintain a polar state for a large range of strain values, possibly enabling device use.
Group-III elements under high pressure.

NASA Astrophysics Data System (ADS)

Simak, S. I.; Haussermann, U.; Ahuja, R.; Johansson, B.

2000-03-01

At ambient conditions the Group-III elements Ga and In attain unusual open ground-state crystal structures. Recent experiments have discovered that Ga under high pressure transforms into the face-centered (fcc) cubic close-packed structure, while such a transition for In has so far not been observed. We offer a simple explanation for such different behavior based on results from first principles calculations. We predict a so far undiscovered transition of In to the fcc structure at extreme pressures and show that the structure determining mechanism originates from the degree of s-p mixing of the valence orbitals. A unified bonding picture for the Group-III elements is discussed.
Charge order-superfluidity transition in a two-dimensional system of hard-core bosons and emerging domain structures

NASA Astrophysics Data System (ADS)

Moskvin, A. S.; Panov, Yu. D.; Rybakov, F. N.; Borisov, A. B.

2017-11-01

We have used high-performance parallel computations by NVIDIA graphics cards applying the method of nonlinear conjugate gradients and Monte Carlo method to observe directly the developing ground state configuration of a two-dimensional hard-core boson system with decrease in temperature, and its evolution with deviation from a half-filling. This has allowed us to explore unconventional features of a charge order—superfluidity phase transition, specifically, formation of an irregular domain structure, emergence of a filamentary superfluid structure that condenses within of the charge-ordered phase domain antiphase boundaries, and formation and evolution of various topological structures.
Temperature dependent photoreflectance and photoluminescence characterization of GaInNAs /GaAs single quantum well structures

NASA Astrophysics Data System (ADS)

Chen, T. H.; Huang, Y. S.; Lin, D. Y.; Tiong, K. K.

2004-12-01

Ga0.69In0.31NxAs1-x/GaAs single quantum well (SQW) structures with three different nitrogen compositions ( x =0%, 0.6%, and 0.9%) have been characterized, as functions of temperature in the range 10-300K, by the techniques of photoreflectance (PR) and photoluminescence (PL). In PR spectra, clear Franz-Keldysh oscillations (FKOs) above the GaAs band edge and the various excitonic transitions originating from the QW region have been observed. The built-in electric field in the SQW has been determined from FKOs and found to increase with N concentration. The PR signal has been found to decrease for nitrogen incorporated samples when the temperature was lowered due to a weakening of the modulation efficiency induced by carrier localization. A careful analysis of PR and PL spectra has led to the identification of various excitonic transitions, mnH(L), between the mth conduction band state and the nth heavy (light)-hole band state. The anomalous temperature dependent 11H transition energy and linewidth observed in the PL spectra have been explained as originating from the localized states as a result of nitrogen incorporation. The temperature dependence analysis yields information on the parameters that describe the temperature variations of the interband transitions.
Probing many-body localization with neural networks

NASA Astrophysics Data System (ADS)

Schindler, Frank; Regnault, Nicolas; Neupert, Titus

2017-06-01

We show that a simple artificial neural network trained on entanglement spectra of individual states of a many-body quantum system can be used to determine the transition between a many-body localized and a thermalizing regime. Specifically, we study the Heisenberg spin-1/2 chain in a random external field. We employ a multilayer perceptron with a single hidden layer, which is trained on labeled entanglement spectra pertaining to the fully localized and fully thermal regimes. We then apply this network to classify spectra belonging to states in the transition region. For training, we use a cost function that contains, in addition to the usual error and regularization parts, a term that favors a confident classification of the transition region states. The resulting phase diagram is in good agreement with the one obtained by more conventional methods and can be computed for small systems. In particular, the neural network outperforms conventional methods in classifying individual eigenstates pertaining to a single disorder realization. It allows us to map out the structure of these eigenstates across the transition with spatial resolution. Furthermore, we analyze the network operation using the dreaming technique to show that the neural network correctly learns by itself the power-law structure of the entanglement spectra in the many-body localized regime.
Structural Transition and Antibody Binding of EBOV GP and ZIKV E Proteins from Pre-Fusion to Fusion-Initiation State.

PubMed

Lappala, Anna; Nishima, Wataru; Miner, Jacob; Fenimore, Paul; Fischer, Will; Hraber, Peter; Zhang, Ming; McMahon, Benjamin; Tung, Chang-Shung

2018-05-10

Membrane fusion proteins are responsible for viral entry into host cells—a crucial first step in viral infection. These proteins undergo large conformational changes from pre-fusion to fusion-initiation structures, and, despite differences in viral genomes and disease etiology, many fusion proteins are arranged as trimers. Structural information for both pre-fusion and fusion-initiation states is critical for understanding virus neutralization by the host immune system. In the case of Ebola virus glycoprotein (EBOV GP) and Zika virus envelope protein (ZIKV E), pre-fusion state structures have been identified experimentally, but only partial structures of fusion-initiation states have been described. While the fusion-initiation structure is in an energetically unfavorable state that is difficult to solve experimentally, the existing structural information combined with computational approaches enabled the modeling of fusion-initiation state structures of both proteins. These structural models provide an improved understanding of four different neutralizing antibodies in the prevention of viral host entry.
Women in Transition: A Qualitative Analysis of Definitions of Poverty and Success

ERIC Educational Resources Information Center

Marsh-McDonald, Crystale M.; Schroeder, Sybil

2012-01-01

A phenomenological approach examined the stories of ten women transitioning from childhood poverty to adult life. Women were chosen from a pool of participants in an Upward Bound program designed to assist low-income and/or first-generation college students in the Midwestern United States. Semi-structured interviews were conducted to…
Prediction and validation of protein intermediate states from structurally rich ensembles and coarse-grained simulations

NASA Astrophysics Data System (ADS)

Orellana, Laura; Yoluk, Ozge; Carrillo, Oliver; Orozco, Modesto; Lindahl, Erik

2016-08-01

Protein conformational changes are at the heart of cell functions, from signalling to ion transport. However, the transient nature of the intermediates along transition pathways hampers their experimental detection, making the underlying mechanisms elusive. Here we retrieve dynamic information on the actual transition routes from principal component analysis (PCA) of structurally-rich ensembles and, in combination with coarse-grained simulations, explore the conformational landscapes of five well-studied proteins. Modelling them as elastic networks in a hybrid elastic-network Brownian dynamics simulation (eBDIMS), we generate trajectories connecting stable end-states that spontaneously sample the crystallographic motions, predicting the structures of known intermediates along the paths. We also show that the explored non-linear routes can delimit the lowest energy passages between end-states sampled by atomistic molecular dynamics. The integrative methodology presented here provides a powerful framework to extract and expand dynamic pathway information from the Protein Data Bank, as well as to validate sampling methods in general.
The gas phase structure of transition metal dihydrides

NASA Astrophysics Data System (ADS)

Demuynck, Jean; Schaefer, Henry F.

1980-01-01

ESR and infrared spectroscopic measurements on matrix isolated MnH2 and CrH2 have recently suggested that these simple molecules may be bent. This result would be the opposite of that found experimentally for the transition metal dihalides MX2, known to be linear. Here the geometrical structure of MnH2 has been investigated by molecular electronic structure theory. A large contracted Gaussian basis set [Mn(14s11p6p/9s8p3d), H(5s1p/3s1p)] was used in conjunction with self-consistent field and configuration interaction methods. These suggest that the 6A1 ground state of MnH2 is linear. Further studies of the 3A1 state (one of several low-lying states) of TiH2 also favor linearity, although this potential energy surface is extremely flat with respect to bending. Thus it appears probable that most MH2 molecules, like the related MX2 family, are linear.
Coincident structural and magnetic order in BaFe 2 ( As 1 - x P x ) 2 revealed by high-resolution neutron diffraction

DOE PAGES

Allred, J. M.; Taddei, K. M.; Bugaris, D. E.; ...

2014-09-19

We present neutron dffraction analysis of BaFe 2(As 1-xP x) 2 over a wide temperature (10 to 300 K) and compositional (0.11 < x < 0.79) range, including the normal state, the magnetically ordered state, and the superconducting state. The paramagnetic to spin-density wave and orthorhombic to tetragonal transitions are first order and coincident within the sensitivity of our measurements (~ 0:5 K). Extrapolation of the orthorhombic order parameter down to zero suggests that structural quantum criticality cannot exist at compositions higher than x = 0.28, which is much lower than values determined using other methods, but in good agreementmore » with our observations of the actual phase stability range. Lastly, the onset of spin-density wave order shows a stronger structural anomaly than the charge-doped system in the form of an enhancement of the c/a ratio below the transition.« less
Quasiclassical analysis of vortex lattice states in Rashba noncentrosymmetric superconductors

NASA Astrophysics Data System (ADS)

Dan, Yuichiro; Ikeda, Ryusuke

2015-10-01

Vortex lattice states occurring in noncentrosymmetric superconductors with a spin-orbit coupling of Rashba type under a magnetic field parallel to the symmetry plane are examined by assuming the s -wave pairing case and in an approach combining the quasiclassical theory with the Landau level expansion of the superconducting order parameter. The resulting field-temperature phase diagrams include not only a discontinuous transition but a continuous crossover between different vortex lattice structures, and, further, a critical end point of a structural transition line is found at an intermediate field and a low temperature in the present approach. It is pointed out that the strange field dependence of the vortex lattice structure is a consequence of that of its anisotropy stemming from the Rashba spin-orbit coupling, and that the critical end point is related to the helical phase modulation peculiar to these materials in the ideal Pauli-limited case. Furthermore, calculation results on the local density of states detectable in STM experiments are also presented.
Reduced-Amide Inhibitor of Pin1 Binds in a Conformation Resembling a Twisted-Amide Transition State†

PubMed Central

Xu, Guoyan G.; Zhang, Yan; Mercedes-Camacho, Ana Y.; Etzkorn, Felicia A.

2011-01-01

The mechanism of the cell cycle regulatory peptidyl prolyl isomerase (PPIase), Pin1, was investigated using reduced-amide inhibitors designed to mimic the twisted-amide transition state. Inhibitors, R–pSer–Ψ[CH2N]–Pro–2-(indol-3-yl)-ethylamine, 1 (R = fluorenylmethoxycarbonyl, Fmoc), and 2 (R = Ac), of Pin1 were synthesized and bioassayed. Inhibitor 1 had an IC50 value of 6.3 μM, which is 4.5-fold better inhibition for Pin1 than our comparable ground state analogue, a cis-amide alkene isostere containing inhibitor. The change of Fmoc to Ac in 2 improved aqueous solubility for structural determination, and resulted in an IC50 value of 12 μM. The X-ray structure of the complex of 2 bound to Pin1 was determined to 1.76 Å resolution. The structure revealed that the reduced amide adopted a conformation similar to the proposed twisted-amide transition state of Pin1, with a trans-pyrrolidine conformation of the prolyl ring. A similar conformation of substrate would be destabilized relative to the planar amide conformation. Three additional reduced amides, with Thr replacing Ser, and l- or d-pipecolate (Pip) replacing Pro, were slightly weaker inhibitors of Pin1. PMID:21980916

Influence of molecular designs on polaronic and vibrational transitions in a conjugated push-pull copolymer

NASA Astrophysics Data System (ADS)

Cobet, Christoph; Gasiorowski, Jacek; Menon, Reghu; Hingerl, Kurt; Schlager, Stefanie; White, Matthew S.; Neugebauer, Helmut; Sariciftci, N. Serdar; Stadler, Philipp

2016-10-01

Electron-phonon interactions of free charge-carriers in doped pi-conjugated polymers are conceptually described by 1-dimensional (1D) delocalization. Thereby, polaronic transitions fit the 1D-Froehlich model in quasi-confined chains. However, recent developments in conjugated polymers have diversified the backbones to become elaborate heterocylcic macromolecules. Their complexity makes it difficult to investigate the electron-phonon coupling. In this work we resolve the electron-phonon interactions in the ground and doped state in a complex push-pull polymer. We focus on the polaronic transitions using in-situ spectroscopy to work out the differences between single-unit and push-pull systems to obtain the desired structural- electronic correlations in the doped state. We apply the classic 1D-Froehlich model to generate optical model fits. Interestingly, we find the 1D-approach in push-pull polarons in agreement to the model, pointing at the strong 1D-character and plain electronic structure of the push-pull structure. In contrast, polarons in the single-unit polymer emerge to a multi- dimensional problem difficult to resolve due to their anisotropy. Thus, we report an enhancement of the 1D-character by the push-pull concept in the doped state - an important view in light of the main purpose of push-pull polymers for photovoltaic devices.
Structural Plasticity and Conformational Transitions of HIV Envelope Glycoprotein gp120

PubMed Central

Korkut, Anil; Hendrickson, Wayne A.

2012-01-01

HIV envelope glycoproteins undergo large-scale conformational changes as they interact with cellular receptors to cause the fusion of viral and cellular membranes that permits viral entry to infect targeted cells. Conformational dynamics in HIV gp120 are also important in masking conserved receptor epitopes from being detected for effective neutralization by the human immune system. Crystal structures of HIV gp120 and its complexes with receptors and antibody fragments provide high-resolution pictures of selected conformational states accessible to gp120. Here we describe systematic computational analyses of HIV gp120 plasticity in such complexes with CD4 binding fragments, CD4 mimetic proteins, and various antibody fragments. We used three computational approaches: an isotropic elastic network analysis of conformational plasticity, a full atomic normal mode analysis, and simulation of conformational transitions with our coarse-grained virtual atom molecular mechanics (VAMM) potential function. We observe collective sub-domain motions about hinge points that coordinate those motions, correlated local fluctuations at the interfacial cavity formed when gp120 binds to CD4, and concerted changes in structural elements that form at the CD4 interface during large-scale conformational transitions to the CD4-bound state from the deformed states of gp120 in certain antibody complexes. PMID:23300605
Evaluating transition state structures of vanadium-phosphatase protein complexes using shape analysis.

PubMed

Sánchez-Lombardo, Irma; Alvarez, Santiago; McLauchlan, Craig C; Crans, Debbie C

2015-06-01

Shape analysis of coordination complexes is well-suited to evaluate the subtle distortions in the trigonal bipyramidal (TBPY-5) geometry of vanadium coordinated in the active site of phosphatases and characterized by X-ray crystallography. Recent studies using the tau (τ) analysis support the assertion that vanadium is best described as a trigonal bipyramid, because this geometry is the ideal transition state geometry of the phosphate ester substrate hydrolysis (C.C. McLauchlan, B.J. Peters, G.R. Willsky, D.C. Crans, Coord. Chem. Rev. http://dx.doi.org/10.1016/j.ccr.2014.12.012 ; D.C. Crans, M.L. Tarlton, C.C. McLauchlan, Eur. J. Inorg. Chem. 2014, 4450-4468). Here we use continuous shape measures (CShM) analysis to investigate the structural space of the five-coordinate vanadium-phosphatase complexes associated with mechanistic transformations between the tetrahedral geometry and the five-coordinate high energy TBPY-5 geometry was discussed focusing on the protein tyrosine phosphatase 1B (PTP1B) enzyme. No evidence for square pyramidal geometries was observed in any vanadium-protein complexes. The shape analysis positioned the metal ion and the ligands in the active site reflecting the mechanism of the cleavage of the organic phosphate in a phosphatase. We identified the umbrella distortions to be directly on the reaction path between tetrahedral phosphate and the TBPY-5-types of high-energy species. The umbrella distortions of the trigonal bipyramid are therefore identified as being the most relevant types of transition state structures for the phosphoryl group transfer reactions for phosphatases and this may be related to the possibility that vanadium is an inhibitor for enzymes that support both exploded and five-coordinate transition states. Copyright © 2015 Elsevier Inc. All rights reserved.
Recognition and Resistance in TEM [superscript beta]-Lactamase

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

Wang, Xiaojun; Minasov, George; Blazquez, Jesus

Developing antimicrobials that are less likely to engender resistance has become an important design criterion as more and more drugs fall victim to resistance mutations. One hypothesis is that the more closely an inhibitor resembles a substrate, the more difficult it will be to develop resistant mutations that can at once disfavor the inhibitor and still recognize the substrate. To investigate this hypothesis, 10 transition-state analogues, of greater or lesser similarity to substrates, were tested for inhibition of TEM-1 beta-lactamase, the most widespread resistance enzyme to penicillin antibiotics. The inhibitors were also tested against four characteristic mutant enzymes: TEM-30, TEM-32,more » TEM-52, and TEM-64. The inhibitor most similar to the substrate, compound 10, was the most potent inhibitor of the WT enzyme, with a K(i) value of 64 nM. Conversely, compound 10 was the most susceptible to the TEM-30 (R244S) mutant, for which inhibition dropped by over 100-fold. The other inhibitors were relatively impervious to the TEM-30 mutant enzyme. To understand recognition and resistance to these transition-state analogues, the structures of four of these inhibitors in complex with TEM-1 were determined by X-ray crystallography. These structures suggest a structural basis for distinguishing inhibitors that mimic the acylation transition state and those that mimic the deacylation transition state; they also suggest how TEM-30 reduces the affinity of compound 10. In cell culture, this inhibitor reversed the resistance of bacteria to ampicillin, reducing minimum inhibitory concentrations of this penicillin by between 4- and 64-fold, depending on the strain of bacteria. Notwithstanding this activity, the resistance of TEM-30, which is already extant in the clinic, suggests that there can be resistance liabilities with substrate-based design.« less
Viewing brain processes as Critical State Transitions across levels of organization: Neural events in Cognition and Consciousness, and general principles.

PubMed

Werner, Gerhard

2009-04-01

In this theoretical and speculative essay, I propose that insights into certain aspects of neural system functions can be gained from viewing brain function in terms of the branch of Statistical Mechanics currently referred to as "Modern Critical Theory" [Stanley, H.E., 1987. Introduction to Phase Transitions and Critical Phenomena. Oxford University Press; Marro, J., Dickman, R., 1999. Nonequilibrium Phase Transitions in Lattice Models. Cambridge University Press, Cambridge, UK]. The application of this framework is here explored in two stages: in the first place, its principles are applied to state transitions in global brain dynamics, with benchmarks of Cognitive Neuroscience providing the relevant empirical reference points. The second stage generalizes to suggest in more detail how the same principles could also apply to the relation between other levels of the structural-functional hierarchy of the nervous system and between neural assemblies. In this view, state transitions resulting from the processing at one level are the input to the next, in the image of a 'bucket brigade', with the content of each bucket being passed on along the chain, after having undergone a state transition. The unique features of a process of this kind will be discussed and illustrated.
Insights from the structure of a smallpox virus topoisomerase-DNA transition state mimic

PubMed Central

Perry, Kay; Hwang, Young; Bushman, Frederic D.; Van Duyne, Gregory D.

2010-01-01

Summary Poxviruses encode their own type IB topoisomerases (TopIBs) which release superhelical tension generated by replication and transcription of their genomes. To investigate the reaction catalyzed viral TopIBs, we have determined the structure of a variola virus topoisomerase-DNA complex trapped as a vanadate transition state mimic. The structure reveals how the viral TopIB enzymes are likely to position the DNA duplex for ligation following relaxation of supercoils and identifies the sources of friction observed in single molecule experiments that argue against free rotation. The structure also identifies a conformational change in the leaving group sugar that must occur prior to cleavage and reveals a mechanism for promoting ligation following relaxation of supercoils that involves a novel Asp-minor groove interaction. Overall, the new structural data support a common catalytic mechanism for the TopIB superfamily but indicate distinct methods for controlling duplex rotation in the small vs. large enzyme subfamilies. PMID:20152159
Conformational heterogeneity in closed and open states of the KcsA potassium channel in lipid bicelles

PubMed Central

Kim, Dorothy M.; Dikiy, Igor; Upadhyay, Vikrant; Posson, David J.

2016-01-01

The process of ion channel gating—opening and closing—involves local and global structural changes in the channel in response to external stimuli. Conformational changes depend on the energetic landscape that underlies the transition between closed and open states, which plays a key role in ion channel gating. For the prokaryotic, pH-gated potassium channel KcsA, closed and open states have been extensively studied using structural and functional methods, but the dynamics within each of these functional states as well as the transition between them is not as well understood. In this study, we used solution nuclear magnetic resonance (NMR) spectroscopy to investigate the conformational transitions within specific functional states of KcsA. We incorporated KcsA channels into lipid bicelles and stabilized them into a closed state by using either phosphatidylcholine lipids, known to favor the closed channel, or mutations designed to trap the channel shut by disulfide cross-linking. A distinct state, consistent with an open channel, was uncovered by the addition of cardiolipin lipids. Using selective amino acid labeling at locations within the channel that are known to move during gating, we observed at least two different slowly interconverting conformational states for both closed and open channels. The pH dependence of these conformations and the predictable disruptions to this dependence observed in mutant channels with altered pH sensing highlight the importance of conformational heterogeneity for KcsA gating. PMID:27432996
Modeling Temporal Behavior in Large Networks: A Dynamic Mixed-Membership Model

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

Rossi, R; Gallagher, B; Neville, J

Given a large time-evolving network, how can we model and characterize the temporal behaviors of individual nodes (and network states)? How can we model the behavioral transition patterns of nodes? We propose a temporal behavior model that captures the 'roles' of nodes in the graph and how they evolve over time. The proposed dynamic behavioral mixed-membership model (DBMM) is scalable, fully automatic (no user-defined parameters), non-parametric/data-driven (no specific functional form or parameterization), interpretable (identifies explainable patterns), and flexible (applicable to dynamic and streaming networks). Moreover, the interpretable behavioral roles are generalizable, computationally efficient, and natively supports attributes. We applied ourmore » model for (a) identifying patterns and trends of nodes and network states based on the temporal behavior, (b) predicting future structural changes, and (c) detecting unusual temporal behavior transitions. We use eight large real-world datasets from different time-evolving settings (dynamic and streaming). In particular, we model the evolving mixed-memberships and the corresponding behavioral transitions of Twitter, Facebook, IP-Traces, Email (University), Internet AS, Enron, Reality, and IMDB. The experiments demonstrate the scalability, flexibility, and effectiveness of our model for identifying interesting patterns, detecting unusual structural transitions, and predicting the future structural changes of the network and individual nodes.« less
Quantifying structural states of soft mudrocks

NASA Astrophysics Data System (ADS)

Li, B.; Wong, R. C. K.

2016-05-01

In this paper, a cm model is proposed to quantify structural states of soft mudrocks, which are dependent on clay fractions and porosities. Physical properties of natural and reconstituted soft mudrock samples are used to derive two parameters in the cm model. With the cm model, a simplified homogenization approach is proposed to estimate geomechanical properties and fabric orientation distributions of soft mudrocks based on the mixture theory. Soft mudrocks are treated as a mixture of nonclay minerals and clay-water composites. Nonclay minerals have a high stiffness and serve as a structural framework of mudrocks when they have a high volume fraction. Clay-water composites occupy the void space among nonclay minerals and serve as an in-fill matrix. With the increase of volume fraction of clay-water composites, there is a transition in the structural state from the state of framework supported to the state of matrix supported. The decreases in shear strength and pore size as well as increases in compressibility and anisotropy in fabric are quantitatively related to such transition. The new homogenization approach based on the proposed cm model yields better performance evaluation than common effective medium modeling approaches because the interactions among nonclay minerals and clay-water composites are considered. With wireline logging data, the cm model is applied to quantify the structural states of Colorado shale formations at different depths in the Cold Lake area, Alberta, Canada. Key geomechancial parameters are estimated based on the proposed homogenization approach and the critical intervals with low strength shale formations are identified.
Status in calculating electronic excited states in transition metal oxides from first principles.

PubMed

Bendavid, Leah Isseroff; Carter, Emily Ann

2014-01-01

Characterization of excitations in transition metal oxides is a crucial step in the development of these materials for photonic and optoelectronic applications. However, many transition metal oxides are considered to be strongly correlated materials, and their complex electronic structure is challenging to model with many established quantum mechanical techniques. We review state-of-the-art first-principles methods to calculate charged and neutral excited states in extended materials, and discuss their application to transition metal oxides. We briefly discuss developments in density functional theory (DFT) to calculate fundamental band gaps, and introduce time-dependent DFT, which can model neutral excitations. Charged excitations can be described within the framework of many-body perturbation theory based on Green's functions techniques, which predominantly employs the GW approximation to the self-energy to facilitate a feasible solution to the quasiparticle equations. We review the various implementations of the GW approximation and evaluate each approach in its calculation of fundamental band gaps of many transition metal oxides. We also briefly review the related Bethe-Salpeter equation (BSE), which introduces an electron-hole interaction between GW-derived quasiparticles to describe accurately neutral excitations. Embedded correlated wavefunction theory is another framework used to model localized neutral or charged excitations in extended materials. Here, the electronic structure of a small cluster is modeled within correlated wavefunction theory, while its coupling to its environment is represented by an embedding potential. We review a number of techniques to represent this background potential, including electrostatic representations and electron density-based methods, and evaluate their application to transition metal oxides.
Analysis of energy states in modulation doped multiquantum well heterostructures

NASA Technical Reports Server (NTRS)

Ji, G.; Henderson, T.; Peng, C. K.; Huang, D.; Morkoc, H.

1990-01-01

A precise and effective numerical procedure to model the band diagram of modulation doped multiquantum well heterostructures is presented. This method is based on a self-consistent iterative solution of the Schroedinger equation and the Poisson equation. It can be used rather easily in any arbitrary modulation-doped structure. In addition to confined energy subbands, the unconfined states can be calculated as well. Examples on realistic device structures are given to demonstrate capabilities of this procedure. The numerical results are in good agreement with experiments. With the aid of this method the transitions involving both the confined and unconfined conduction subbands in a modulation doped AlGaAs/GaAs superlattice, and in a strained layer InGaAs/GaAs superlattice are identified. These results represent the first observation of unconfined transitions in modulation doped multiquantum well structures.
Reconstruction of Band Structure Induced by Electronic Nematicity in an FeSe Superconductor

NASA Astrophysics Data System (ADS)

Nakayama, K.; Miyata, Y.; Phan, G. N.; Sato, T.; Tanabe, Y.; Urata, T.; Tanigaki, K.; Takahashi, T.

2014-12-01

We have performed high-resolution angle-resolved photoemission spectroscopy on an FeSe superconductor (Tc˜8 K ), which exhibits a tetragonal-to-orthorhombic structural transition at Ts˜90 K . At low temperature, we found splitting of the energy bands as large as 50 meV at the M point in the Brillouin zone, likely caused by the formation of electronically driven nematic states. This band splitting persists up to T ˜110 K , slightly above Ts, suggesting that the structural transition is triggered by the electronic nematicity. We have also revealed that at low temperature the band splitting gives rise to a van Hove singularity within 5 meV of the Fermi energy. The present result strongly suggests that this unusual electronic state is responsible for the unconventional superconductivity in FeSe.
Electronic structure reconstruction across the antiferromagnetic transition in TaFe₁̣₂₃Te₃ spin ladder

DOE PAGES

Xu, Min; Wang, Li -Min; Peng, Rui; ...

2015-02-01

With angle-resolved photoemission spectroscopy, we studied the electronic structure of TaFe₁̣₂₃Te₃, a two-leg spin ladder compound with a novel antiferromagnetic ground state. Quasi-two-dimensional Fermi surface is observed, with sizable inter-ladder hopping. Moreover, instead of observing an energy gap at the Fermi surface in the antiferromagnetic state, we observed the shifts of various bands. Combining these observations with density-functional-theory calculations, we propose that the large scale reconstruction of the electronic structure, caused by the interactions between coexisting itinerant electrons and local moments, is most likely the driving force of the magnetic transition. Thus TaFe₁̣₂₃Te₃ serves as a simpler platform that containsmore » similar ingredients as the parent compounds of iron-based superconductors.« less
Simulation studies of the fidelity of biomolecular structure ensemble recreation

NASA Astrophysics Data System (ADS)

Lätzer, Joachim; Eastwood, Michael P.; Wolynes, Peter G.

2006-12-01

We examine the ability of Bayesian methods to recreate structural ensembles for partially folded molecules from averaged data. Specifically we test the ability of various algorithms to recreate different transition state ensembles for folding proteins using a multiple replica simulation algorithm using input from "gold standard" reference ensembles that were first generated with a Gō-like Hamiltonian having nonpairwise additive terms. A set of low resolution data, which function as the "experimental" ϕ values, were first constructed from this reference ensemble. The resulting ϕ values were then treated as one would treat laboratory experimental data and were used as input in the replica reconstruction algorithm. The resulting ensembles of structures obtained by the replica algorithm were compared to the gold standard reference ensemble, from which those "data" were, in fact, obtained. It is found that for a unimodal transition state ensemble with a low barrier, the multiple replica algorithm does recreate the reference ensemble fairly successfully when no experimental error is assumed. The Kolmogorov-Smirnov test as well as principal component analysis show that the overlap of the recovered and reference ensembles is significantly enhanced when multiple replicas are used. Reduction of the multiple replica ensembles by clustering successfully yields subensembles with close similarity to the reference ensembles. On the other hand, for a high barrier transition state with two distinct transition state ensembles, the single replica algorithm only samples a few structures of one of the reference ensemble basins. This is due to the fact that the ϕ values are intrinsically ensemble averaged quantities. The replica algorithm with multiple copies does sample both reference ensemble basins. In contrast to the single replica case, the multiple replicas are constrained to reproduce the average ϕ values, but allow fluctuations in ϕ for each individual copy. These fluctuations facilitate a more faithful sampling of the reference ensemble basins. Finally, we test how robustly the reconstruction algorithm can function by introducing errors in ϕ comparable in magnitude to those suggested by some authors. In this circumstance we observe that the chances of ensemble recovery with the replica algorithm are poor using a single replica, but are improved when multiple copies are used. A multimodal transition state ensemble, however, turns out to be more sensitive to large errors in ϕ (if appropriately gauged) and attempts at successful recreation of the reference ensemble with simple replica algorithms can fall short.
Are rapid transitions between invasive and native species caused by alternative stable states, and does it matter?

PubMed

Hansen, Gretchen J A; Ives, Anthony R; Vander Zanden, M Jake; Carpenter, Stephen R

2013-10-01

Rapid transitions in ecosystem structure, or regime shifts, are a hallmark of alternative stable states (ASS). However, regime shifts can occur even when feedbacks are not strong enough to cause ASS. We investigated the potential for ASS to explain transitions between dominance of an invasive species, rusty crayfish (Orconectes rusticus), and native sunfishes (Lepomis spp.) in northern Wisconsin (USA) lakes. A rapid transition from Lepomis to rusty crayfish dominance occurred as rusty crayfish invaded Trout Lake, and the reverse transition resulted from an eight-year experimental removal of rusty crayfish from Sparkling Lake. We fit a stage-structured population model of species interactions to 31 years of time-series data from each lake. The model identified water level as an important driver, with drought conditions reducing rusty crayfish recruitment and allowing Lepomis dominance. The maximum-likelihood parameter estimates of the negative interaction between rusty crayfish and Lepomis led to ASS in the model, where each species was capable of excluding the other within a narrow range of environmental conditions. However, uncertainty in parameter estimates made it impossible to exclude the potential that rapid transitions were caused by a simpler threshold response lacking alternative equilibria. Simulated forward and backward transitions between species dominance occurred at different environmental conditions (i.e., hysteresis), even when the parameters used for simulation did not predict ASS as a result of slow species responses to environmental drivers. Thus, ASS are possible, but by no means certain, explanations for rapid transitions in this system, and our results highlight the difficulties associated with distinguishing ASS from other types of threshold responses. However, whether regime shifts are caused by ASS may be relatively unimportant in this system, as the range of conditions over which transitions occur is narrow, and under most conditions, the system is predicted to exist in only a single state.
Unfolding Kinetics of β-Lactoglobulin Induced by Surfactant and Denaturant: A Stopped-Flow/Fluorescence Study

PubMed Central

Viseu, Maria Isabel; Melo, Eduardo P.; Carvalho, Teresa Isabel; Correia, Raquel F.; Costa, Sílvia M. B.

2007-01-01

The β→α transition of β-lactoglobulin, a globular protein abundant in the milk of several mammals, is investigated in this work. This transition, induced by the cationic surfactant dodecyltrimethylammonium chloride (DTAC), is accompanied by partial unfolding of the protein. In this work, unfolding of bovine β-lactoglobulin in DTAC is compared with its unfolding induced by the chemical denaturant guanidine hydrochloride (GnHCl). The final protein states attained in the two media have quite different secondary structure: in DTAC the α-helical content increases, leading to the so-called α-state; in GnHCl the amount of ordered secondary-structure decreases, resulting in a random coil-rich final state (denatured, or D, state). To obtain information on both mechanistic routes, in DTAC and GnHCl, and to characterize intermediates, the kinetics of unfolding were investigated in the two media. Equilibrium and kinetic data show the partial accumulation of an on-pathway intermediate in each unfolding route: in DTAC, an intermediate (I1) with mostly native secondary structure but loose tertiary structure appears between the native (β) and α-states; in GnHCl, another intermediate (I2) appears between states β and D. Kinetic rate constants follow a linear Chevron-plot representation in GnHCl, but show a more complex mechanism in DTAC, which acts like a stronger binding species. PMID:17693475
ESTIMATION OF CARBOXYLIC ACID ESTER HYDROLYSIS RATE CONSTANTS

EPA Science Inventory

SPARC chemical reactivity models were extended to calculate hydrolysis rate constants for carboxylic acid esters from molecular structure. The energy differences between the initial state and the transition state for a molecule of interest are factored into internal and external...
{gamma}-vibrational states in superheavy nuclei

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

Sun Yang; Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou 730000; Joint Institute for Nuclear Astrophysics, University of Notre Dame, Notre Dame, Indiana 46556

2008-04-15

Recent experimental advances have made it possible to study excited structure in superheavy nuclei. The observed states have often been interpreted as quasiparticle excitations. We show that in superheavy nuclei collective vibrations systematically appear as low-energy excitation modes. By using the microscopic Triaxial Projected Shell Model, we make a detailed prediction on {gamma}-vibrational states and their E2 transition probabilities to the ground state band in fermium and nobelium isotopes where active structure research is going on, and in {sup 270}Ds, the heaviest isotope where decay data have been obtained for the ground-state and for an isomeric state.
A theoretical study of the structure and stability of borohydride on 3d transition metals

NASA Astrophysics Data System (ADS)

Arevalo, Ryan Lacdao; Escaño, Mary Clare Sison; Gyenge, Elod; Kasai, Hideaki

2012-12-01

The adsorption of borohydride on 3d transition metals (Cr, Mn, Fe, Co, Ni and Cu) was studied using first principles calculations within spin-polarized density functional theory. Magnetic effect on the stability of borohydride is noted. Molecular adsorption is favorable on Co, Ni and Cu, which is characterized by the strong s-dzz hybridization of the adsorbate-substrate states. Dissociated adsorption structure yielding one or two H adatom fragments on the surface is observed for Cr, Mn and Fe.
Experimental and theoretical studies of structural and photophysical properties of a novel heteroleptic cyclometalated iridium(III) complex with 8-hydroxyquinoline-phenylazo ligand

NASA Astrophysics Data System (ADS)

Maity, Amit; Sinha, Debopam; Rajak, Kajal Krishna

2018-04-01

One novel heteroleptic iridium(III) complex with cyclometalated 2-phenylquinoline(2-phq) was synthesized by the stoichiometric reaction of [Ir(2-phq)2Cl]2, i.e, Bis-[μ-chlorodi-(2-phenylquinoline)iridium(III)] and HL ligand, where L- is deprotonated form of azo ligand prepared from 8-hydroxyquinoline and aniline in a 1:1 proportion of dichloromethane and ethanol solvent at argon atmosphere in presence of mild base triethylamine in stoichiometric ratio. The prepared complex was characterized by 1H NMR, ESI-mass spectrometry, IR spectroscopy and most accurately by X-ray single crystallography. The photo physical properties like absorption and emission, i.e, photoluminescence in liquid state as well as solid state were studied exclusively. The experimental electrochemical study was also done with cyclic voltammetry. The theoretical investigations of the photo physical properties were done by DFT and TDDFT calculations. The ground state excitation transitions of the complex arise from 1ILCT and 1MLCT transition. The UV-Vis and photoluminescence transition was also investigated by NTO analysis. The triplet state emission transition was characterized by 3MLCT and some portion of 3ILCT transition.

First-principles study of configurational disorder in B4C using a superatom-special quasirandom structure method

NASA Astrophysics Data System (ADS)

Ektarawong, A.; Simak, S. I.; Hultman, L.; Birch, J.; Alling, B.

2014-07-01

Configurationally disordered crystalline boron carbide, with the composition B4C, is studied using first-principles calculations. We investigate both dilute and high concentrations of carbon-boron substitutional defects. For the latter purpose, we suggest a superatom's picture of the complex structure and combine it with a special quasirandom structure approach for disorder. In this way, we model a random distribution of high concentrations of the identified low-energy defects: (1) bipolar defects and (2) rotation of icosahedral carbon among the three polar-up sites. Additionally, the substitutional disorder of the icosahedral carbon at all six polar sites, as previously discussed in the literature, is also considered. Two configurational phase transitions from the ordered to the disordered configurations are predicted to take place upon an increase in temperature using a mean-field approximation for the entropy. The first transition, at 870 K, induces substitutional disorder of the icosahedral carbon atoms among the three polar-up sites; meanwhile the second transition, at 2325 K, reveals the random substitution of the icosahedral carbon atoms at all six polar sites coexisting with bipolar defects. Already the first transition removes the monoclinic distortion existing in the ordered ground-state configuration and restore the rhombohedral system (R3m). The restoration of inversion symmetry yielding the full rhombohedral symmetry (R3¯m ) on average, corresponding to what is reported in the literature, is achieved after the second transition. Investigating the effects of high pressure on the configurational stability of the disordered B4C phases reveals a tendency to stabilize the ordered ground-state configuration as the configurationally ordering/disordering transition temperature increases with pressure exerted on B4C. The electronic density of states, obtained from the disordered phases, indicates a sensitivity of the band gap to the degree of configurational disorder in B4C.
Hierarchical Modeling of Activation Mechanisms in the ABL and EGFR Kinase Domains: Thermodynamic and Mechanistic Catalysts of Kinase Activation by Cancer Mutations

PubMed Central

Dixit, Anshuman; Verkhivker, Gennady M.

2009-01-01

Structural and functional studies of the ABL and EGFR kinase domains have recently suggested a common mechanism of activation by cancer-causing mutations. However, dynamics and mechanistic aspects of kinase activation by cancer mutations that stimulate conformational transitions and thermodynamic stabilization of the constitutively active kinase form remain elusive. We present a large-scale computational investigation of activation mechanisms in the ABL and EGFR kinase domains by a panel of clinically important cancer mutants ABL-T315I, ABL-L387M, EGFR-T790M, and EGFR-L858R. We have also simulated the activating effect of the gatekeeper mutation on conformational dynamics and allosteric interactions in functional states of the ABL-SH2-SH3 regulatory complexes. A comprehensive analysis was conducted using a hierarchy of computational approaches that included homology modeling, molecular dynamics simulations, protein stability analysis, targeted molecular dynamics, and molecular docking. Collectively, the results of this study have revealed thermodynamic and mechanistic catalysts of kinase activation by major cancer-causing mutations in the ABL and EGFR kinase domains. By using multiple crystallographic states of ABL and EGFR, computer simulations have allowed one to map dynamics of conformational fluctuations and transitions in the normal (wild-type) and oncogenic kinase forms. A proposed multi-stage mechanistic model of activation involves a series of cooperative transitions between different conformational states, including assembly of the hydrophobic spine, the formation of the Src-like intermediate structure, and a cooperative breakage and formation of characteristic salt bridges, which signify transition to the active kinase form. We suggest that molecular mechanisms of activation by cancer mutations could mimic the activation process of the normal kinase, yet exploiting conserved structural catalysts to accelerate a conformational transition and the enhanced stabilization of the active kinase form. The results of this study reconcile current experimental data with insights from theoretical approaches, pointing to general mechanistic aspects of activating transitions in protein kinases. PMID:19714203
Switching dynamics of TaOx-based threshold switching devices

NASA Astrophysics Data System (ADS)

Goodwill, Jonathan M.; Gala, Darshil K.; Bain, James A.; Skowronski, Marek

2018-03-01

Bi-stable volatile switching devices are being used as access devices in solid-state memory arrays and as the active part of compact oscillators. Such structures exhibit two stable states of resistance and switch between them at a critical value of voltage or current. A typical resistance transient under a constant amplitude voltage pulse starts with a slow decrease followed by a rapid drop and leveling off at a low steady state value. This behavior prompted the interpretation of initial delay and fast transition as due to two different processes. Here, we show that the entire transient including incubation time, transition time, and the final resistance values in TaOx-based switching can be explained by one process, namely, Joule heating with the rapid transition due to the thermal runaway. The time, which is required for the device in the conducting state to relax back to the stable high resistance one, is also consistent with the proposed mechanism.
Hydrodynamic effects on phase transition in active matter

NASA Astrophysics Data System (ADS)

Gidituri, Harinadha; Akella, V. S.; Panchagnula, Mahesh; Vedantam, Srikanth; Multiphase flow physics lab Team

2017-11-01

Organized motion of active (self-propelled) objects are ubiquitous in nature. The objective of this study to investigate the effect of hydrodynamics on the coherent structures in active and passive particle mixtures. We use a mesoscopic method Dissipative Particle Dynamics (DPD). The system shows three different states viz. meso-turbulent (disordered state), polar flock and vortical (ordered state) for different values of activity and volume fraction of active particles. From our numerical simulations we construct a phase diagram between activity co-efficient, volume fraction and viscosity of the passive fluid. Transition from vortical to polar is triggered by increasing the viscosity of passive fluid which causes strong short-range hydrodynamic interactions. However, as the viscosity of the fluid decreases, both vortical and meso-turbulent states transition to polar flock phase. We also calculated the diffusion co-efficients via mean square displacement (MSD) for passive and active particles. We observe ballistic and diffusive regimes in the present system.
Order-disorder phase transition in the peroxidovanadium complex NH4[VO(O2)2(NH3)].

PubMed

Schwendt, Peter; Gyepes, Róbert; Chrappová, Jana; Němec, Ivan; Vaněk, Přemysl

2018-07-05

Complex NH 4 [VO(O 2 ) 2 (NH 3 )] (1) undergoes an order-disorder phase transition at T c ~258K. This transition is accompanied by change in the space group of the orthorhombic lattice and also by significant structural rearrangements of the constituent molecules, which are pertinent mostly to their NH 4 + ions and their ammonia ligands. The low-temperature solid state IR and Raman spectra of 1 were corroborated by solid-state computations that employed Gaussian functions as the basis set. Results of these computations yielded excellent agreement with experimental data. On the curves of temperature dependence of vibrational modes, the phase transition is expressed by an abrupt change of the slope above T c . Copyright © 2018 Elsevier B.V. All rights reserved.
Structural phase transition and phonon instability in Cu 12Sb 4S 13

DOE PAGES

May, Andrew F.; Delaire, Olivier A.; Niedziela, Jennifer L.; ...

2016-02-08

In this study, a structural phase transition has been discovered in the synthetic tetrahedrite Cu 12Sb 4S 13 at approximately 88 K. Upon cooling, the material transforms from its known cubic symmetry to a tetragonal unit cell that is characterized by an in-plane ordering that leads to a doubling of the unit cell volume. Specific heat capacity measurements demonstrate a hysteresis of more than two degrees in the associated anomaly. A similar hysteresis was observed in powder x-ray diffraction measurements, which also indicate a coexistence of the two phases, and together these results suggest a first-order transition. This structural transitionmore » coincides with a recently-reported metal-insulator transition, and the structural instability is related to the very low thermal conductivity κ in these materials. Inelastic neutron scattering was used to measure the phonon density of states in Cu 12Sb 4S 13 and Cu 10Zn 2Sb 4S 13, both of which possess a localized, low-energy phonon mode associated with strongly anharmonic copper displacements that suppress κ. In Cu 12Sb 4S 13, signatures of the phase transition are observed in the temperature dependence of the localized mode, which disappears at the structural transition. In contrast, in the cubic Zn-doped material, the mode is at slightly higher-energy but observable for all temperatures, though it softens upon cooling.« less
Transition structures and timing of transfer from paediatric to adult-based care after kidney transplantation in Germany: a qualitative study.

PubMed

Prüfe, Jenny; Dierks, Marie-Luise; Bethe, Dirk; Oldhafer, Martina; Müther, Silvia; Thumfart, Julia; Feldkötter, Markus; Büscher, Anja; Sauerstein, Katja; Hansen, Matthias; Pohl, Martin; Drube, Jens; Thiel, Florian; Rieger, Susanne; John, Ulrike; Taylan, Christina; Dittrich, Katalin; Hollenbach, Sabine; Klaus, Günter; Fehrenbach, Henry; Kranz, Birgitta; Montoya, Carmen; Lange-Sperandio, Bärbel; Ruckenbrod, Bettina; Billing, Heiko; Staude, Hagen; Brunkhorst, Reinhard; Rusai, Krisztina; Pape, Lars; Kreuzer, Martin

2017-06-12

It is known that transition, as a shift of care, marks a vulnerable phase in the adolescents' lives with an increased risk for non-adherence and allograft failure. Still, the transition process of adolescents and young adults living with a kidney transplant in Germany is not well defined. The present research aims to assess transition-relevant structures for this group of young people. Special attention is paid to the timing of the process. In an observational study, we visited 21 departments of paediatric nephrology in Germany. Participants were doctors (n=19), nurses (n=14) and psychosocial staff (n=16) who were responsible for transition in the relevant centres. Structural elements were surveyed using a short questionnaire. The experiential viewpoint was collected by interviews which were transcribedverbatim before thematic analysis was performed. This study highlights that professionals working within paediatric nephrology in Germany are well aware of the importance of successful transition. Key elements of transitional care are well understood and mutually agreed on. Nonetheless, implementation within daily routine seems challenging, and the absence of written, structured procedures may hamper successful transition. While professionals aim for an individual timing of transfer based on medical, social, emotional and structural aspects, rigid regulations on transfer age as given by the relevant health authorities add on to the challenge. ISRCTN Registry no 22988897; results (phase I) and pre-results (phase II). © Article author(s) (or their employer(s) unless otherwise stated in the text of the article) 2017. All rights reserved. No commercial use is permitted unless otherwise expressly granted.
Using instability to reconfigure smart structures in a spring-mass model

NASA Astrophysics Data System (ADS)

Zhang, Jiaying; McInnes, Colin R.

2017-07-01

Multistable phenomenon have long been used in mechanism design. In this paper a subset of unstable configurations of a smart structure model will be used to develop energy-efficient schemes to reconfigure the structure. This new concept for reconfiguration uses heteroclinic connections to transition the structure between different unstable equal-energy states. In an ideal structure model zero net energy input is required for the reconfiguration, compared to transitions between stable equilibria across a potential barrier. A simple smart structure model is firstly used to identify sets of equal-energy unstable configurations using dynamical systems theory. Dissipation is then added to be more representative of a practical structure. A range of strategies are then used to reconfigure the smart structure using heteroclinic connections with different approaches to handle dissipation.
Exchange interactions and magnetic properties of hexagonal rare-earth-cobalt compounds

NASA Astrophysics Data System (ADS)

Burzo, E.

2018-03-01

The magnetic properties of some GdxY1-xCo4A compounds with A = Co, Si or B are analysed including the pressure effects. Isomorphous structure transitions, parallelly with changes of cobalt moments from high spin states to low spin states, were shown as pressure increases. The magnetic data, obtained from band structures, were compared with those predicted by the mean field model.
Disorder-induced localization in crystalline phase-change materials.

PubMed

Siegrist, T; Jost, P; Volker, H; Woda, M; Merkelbach, P; Schlockermann, C; Wuttig, M

2011-03-01

Localization of charge carriers in crystalline solids has been the subject of numerous investigations over more than half a century. Materials that show a metal-insulator transition without a structural change are therefore of interest. Mechanisms leading to metal-insulator transition include electron correlation (Mott transition) or disorder (Anderson localization), but a clear distinction is difficult. Here we report on a metal-insulator transition on increasing annealing temperature for a group of crystalline phase-change materials, where the metal-insulator transition is due to strong disorder usually associated only with amorphous solids. With pronounced disorder but weak electron correlation, these phase-change materials form an unparalleled quantum state of matter. Their universal electronic behaviour seems to be at the origin of the remarkable reproducibility of the resistance switching that is crucial to their applications in non-volatile-memory devices. Controlling the degree of disorder in crystalline phase-change materials might enable multilevel resistance states in upcoming storage devices.
Influence of initial seed distribution on the pattern formation of the phase field crystals

NASA Astrophysics Data System (ADS)

Starodumov, Ilya; Galenko, Peter; Kropotin, Nikolai; Alexandrov, Dmitri V.

2017-11-01

The process of crystal growth can be expressed as a transition of atomic structure to a finally stable state or to a metastable state. In the Phase Field Crystal Model (PFC-model) these states are described by regular distributions of the atomic density. Getting the system into any metastable condition may be caused by the peculiarities of the computational domain, initial and boundary conditions. However, an important factor in the formation of the crystal structure can be the initial disturbance. In the report we show how different types of initial disturbance can change the finally stable state of crystal structure in equilibrium.
Structural and semiconductor-to-metal transitions of double-perovskite cobalt oxide Sr2-xLaxCoTiO6-δ with enhanced thermoelectric capability

NASA Astrophysics Data System (ADS)

Sugahara, Tohru; Ohtaki, Michitaka

2011-08-01

The thermoelectric properties of double-perovskite oxide Sr2-xLaxCoTiO6-δ were revealed to vary anomalously with the La concentration, plausibly due to a structural transition found in this study. Although the temperature dependence of the resistivity and thermopower of the present oxide showed a semiconductor-to-metal transition similar to those observed for other perovskite-related Co oxides such as Sr1-xYxCoO3-δ, the transition temperature was more than 350 K higher, implying considerable stabilization of the low-spin state of Co ions in the double-perovskite oxide. Consequently, the operating temperature range of the oxide for potential thermoelectric applications was significantly expanded toward higher temperatures.
Tuning the ferroelectric-to-paraelectric transition temperature and dipole orientation of group-IV monochalcogenide monolayers

NASA Astrophysics Data System (ADS)

Barraza-Lopez, Salvador; Kaloni, Thaneshwor P.; Poudel, Shiva P.; Kumar, Pradeep

2018-01-01

Coordination-related, two-dimensional (2D) structural phase transitions are a fascinating facet of two-dimensional materials with structural degeneracies. Nevertheless, a unified theoretical account of these transitions remains absent, and the following points are established through ab initio molecular dynamics and 2D discrete clock models here: Group-IV monochalcogenide (GeSe, SnSe, SnTe,...) monolayers have four degenerate structural ground states, and a phase transition from a threefold coordinated onto a fivefold coordinated structure takes place at finite temperature. On unstrained samples, this phase transition requires lattice parameters to evolve freely. A fundamental energy scale J permits understanding this transition, and numerical results indicate a transition temperature Tc of about 1.41 J . Numerical data provides a relation among the experimental (rhombic) parameter 〈Δ α 〉 [Chang et al., Science 353, 274 (2016), 10.1126/science.aad8609] and T of the form 〈Δ α 〉 =Δ α (T =0 ) (1-T /Tc)β , with a critical exponent β ≃1 /3 that coincides with experiment. It is also shown that 〈Δ α 〉 is temperature independent in another theoretical work [Fei et al., Phys. Rev. Lett. 117, 097601 (2016), 10.1103/PhysRevLett.117.097601], and thus incompatible with experiment. Tc and the orientation of the in-plane intrinsic electric dipole can be controlled by moderate uniaxial tensile strain, and a modified discrete clock model describes the transition on strained samples qualitatively. An analysis of out-of-plane fluctuations and a discussion of the need for van der Waals corrections to describe these materials are given too. These results provide an experimentally compatible framework to understand structural phase transitions in 2D materials and their effects on material properties.
Bulk and surface electronic structures of MgO

NASA Astrophysics Data System (ADS)

Schönberger, U.; Aryasetiawan, F.

1995-09-01

The bulk electronic structure of MgO is calculated from first principles including correlation effects within the GW approximation. The band gap, the position of the 2s O band, and the valence band width are in good agreement with experiment. From the quasiparticle band structure, optical transitions corresponding to the main optical absorption peaks are identified. The energy-loss spectrum is also calculated and compared with experiment. The surface electronic structure of MgO(100) is calculated self-consistently within the local-density approximation. It is found that states observed in a recent photoemission experiment outside the bulk allowed states are close to surface states.
Cavitation transition in the energy landscape: Distinct tensile yielding behavior in strongly and weakly attractive systems.

PubMed

Altabet, Y Elia; Fenley, Andreia L; Stillinger, Frank H; Debenedetti, Pablo G

2018-03-21

Particles with cohesive interactions display a tensile instability in the energy landscape at the Sastry density ρ S . The signature of this tensile limit is a minimum in the landscape equation of state, the pressure-density relationship of inherent structures sampled along a liquid isotherm. Our previous work [Y. E. Altabet, F. H. Stillinger, and P. G. Debenedetti, J. Chem. Phys. 145, 211905 (2016)] revisited the phenomenology of Sastry behavior and found that the evolution of the landscape equation of state with system size for particles with interactions typical of molecular liquids indicates the presence of an athermal first-order phase transition between homogeneous and fractured inherent structures, the latter containing several large voids. Here, we study how this tensile limit manifests itself for different interparticle cohesive strengths and identify two distinct regimes. Particles with sufficiently strong cohesion display an athermal first-order phase transition, consistent with our prior characterization. Weak cohesion also displays a tensile instability. However, the landscape equation of state for this regime is independent of system size, suggesting the absence of a first-order phase transition. An analysis of the voids suggests that yielding in the energy landscape of weakly cohesive systems is associated with the emergence of a highly interconnected network of small voids. While strongly cohesive systems transition from exclusively homogeneous to exclusively fractured configurations at ρ S in the thermodynamic limit, this interconnected network develops gradually, starting at ρ S , even at infinite system size.
Enhanced sampling by multiple molecular dynamics trajectories: carbonmonoxy myoglobin 10 micros A0-->A(1-3) transition from ten 400 picosecond simulations.

PubMed

Loccisano, Anne E; Acevedo, Orlando; DeChancie, Jason; Schulze, Brita G; Evanseck, Jeffrey D

2004-05-01

The utility of multiple trajectories to extend the time scale of molecular dynamics simulations is reported for the spectroscopic A-states of carbonmonoxy myoglobin (MbCO). Experimentally, the A0-->A(1-3) transition has been observed to be 10 micros at 300 K, which is beyond the time scale of standard molecular dynamics simulations. To simulate this transition, 10 short (400 ps) and two longer time (1.2 ns) molecular dynamics trajectories, starting from five different crystallographic and solution phase structures with random initial velocities centered in a 37 A radius sphere of water, have been used to sample the native-fold of MbCO. Analysis of the ensemble of structures gathered over the cumulative 5.6 ns reveals two biomolecular motions involving the side chains of His64 and Arg45 to explain the spectroscopic states of MbCO. The 10 micros A0-->A(1-3) transition involves the motion of His64, where distance between His64 and CO is found to vary up to 8.8 +/- 1.0 A during the transition of His64 from the ligand (A(1-3)) to bulk solvent (A0). The His64 motion occurs within a single trajectory only once, however the multiple trajectories populate the spectroscopic A-states fully. Consequently, multiple independent molecular dynamics simulations have been found to extend biomolecular motion from 5 ns of total simulation to experimental phenomena on the microsecond time scale.
Cavitation transition in the energy landscape: Distinct tensile yielding behavior in strongly and weakly attractive systems

NASA Astrophysics Data System (ADS)

Altabet, Y. Elia; Fenley, Andreia L.; Stillinger, Frank H.; Debenedetti, Pablo G.

2018-03-01

Particles with cohesive interactions display a tensile instability in the energy landscape at the Sastry density ρS. The signature of this tensile limit is a minimum in the landscape equation of state, the pressure-density relationship of inherent structures sampled along a liquid isotherm. Our previous work [Y. E. Altabet, F. H. Stillinger, and P. G. Debenedetti, J. Chem. Phys. 145, 211905 (2016)] revisited the phenomenology of Sastry behavior and found that the evolution of the landscape equation of state with system size for particles with interactions typical of molecular liquids indicates the presence of an athermal first-order phase transition between homogeneous and fractured inherent structures, the latter containing several large voids. Here, we study how this tensile limit manifests itself for different interparticle cohesive strengths and identify two distinct regimes. Particles with sufficiently strong cohesion display an athermal first-order phase transition, consistent with our prior characterization. Weak cohesion also displays a tensile instability. However, the landscape equation of state for this regime is independent of system size, suggesting the absence of a first-order phase transition. An analysis of the voids suggests that yielding in the energy landscape of weakly cohesive systems is associated with the emergence of a highly interconnected network of small voids. While strongly cohesive systems transition from exclusively homogeneous to exclusively fractured configurations at ρS in the thermodynamic limit, this interconnected network develops gradually, starting at ρS, even at infinite system size.
Stability limits and transformation pathways of α-quartz under high pressure

NASA Astrophysics Data System (ADS)

Hu, Q. Y.; Shu, J.-F.; Yang, W. G.; Park, C.; Chen, M. W.; Fujita, T.; Mao, H.-K.; Sheng, H. W.

2017-03-01

Ubiquitous on Earth, α-quartz plays an important role in modern science and technology. However, despite extensive research in the past, the mechanism of the polymorphic transitions of α-quartz at high pressures remains poorly understood. Here, combining in situ single-crystal x-ray diffraction experiment and advanced ab initio modeling, we report two stability limits and competing transition pathways of α-quartz under high pressure. Under near-equilibrium compression conditions at room temperature, α-quartz transits to a new P 2 /c silica phase via a structural intermediate. If the thermally activated transition is kinetically suppressed, the ultimate stability of α-quartz is controlled by its phonon instability and α-quartz collapses into a different crystalline phase. Our studies reveal that pressure-induced solid-state transformation of α-quartz undergoes a succession of structural stability limits, due to thermodynamic and mechanical catastrophes, and exhibits a hierarchy of transition pathways contingent upon kinetic conditions.
DOE Office of Scientific and Technical Information (OSTI.GOV)

Nigro, Valentina, E-mail: nigro@fis.uniroma3.it; Bruni, Fabio; Ricci, Maria Antonietta

The temperature dependence of the local intra-particle structure of colloidal microgel particles, composed of interpenetrated polymer networks, has been investigated by small-angle neutron scattering at different pH and concentrations, in the range (299÷315) K, where a volume phase transition from a swollen to a shrunken state takes place. Data are well described by a theoretical model that takes into account the presence of both interpenetrated polymer networks and cross-linkers. Two different behaviors are found across the volume phase transition. At neutral pH and T ≈ 307 K, a sharp change of the local structure from a water rich open inhomogeneousmore » interpenetrated polymer network to a homogeneous porous solid-like structure after expelling water is observed. Differently, at acidic pH, the local structure changes almost continuously. These findings demonstrate that a fine control of the pH of the system allows to tune the sharpness of the volume-phase transition.« less
Unique fluorophores in the dimeric archaeal histones hMfB and hPyA1 reveal the impact of nonnative structure in a monomeric kinetic intermediate

PubMed Central

Stump, Matthew R.; Gloss, Lisa M.

2008-01-01

Homodimeric archaeal histones and heterodimeric eukaryotic histones share a conserved structure but fold through different kinetic mechanisms, with a correlation between faster folding/association rates and the population of kinetic intermediates. Wild-type hMfB (from Methanothermus fervidus) has no intrinsic fluorophores; Met35, which is Tyr in hyperthermophilic archaeal histones such as hPyA1 (from Pyrococcus strain GB-3A), was mutated to Tyr and Trp. Two Tyr-to-Trp mutants of hPyA1 were also characterized. All fluorophores were introduced into the long, central α-helix of the histone fold. Far-UV circular dichroism (CD) indicated that the fluorophores did not significantly alter the helical content of the histones. The equilibrium unfolding transitions of the histone variants were two-state, reversible processes, with ΔG°(H2O) values within 1 kcal/mol of the wild-type dimers. The hPyA1 Trp variants fold by two-state kinetic mechanisms like wild-type hPyA1, but with increased folding and unfolding rates, suggesting that the mutated residues (Tyr-32 and Tyr-36) contribute to transition state structure. Like wild-type hMfB, M35Y and M35W hMfB fold by a three-state mechanism, with a stopped-flow CD burst-phase monomeric intermediate. The M35 mutants populate monomeric intermediates with increased secondary structure and stability but exhibit decreased folding rates; this suggests that nonnative interactions occur from burial of the hydrophobic Tyr and Trp residues in this kinetic intermediate. These results implicate the long central helix as a key component of the structure in the kinetic monomeric intermediates of hMfB as well as the dimerization transition state in the folding of hPyA1. PMID:18096639

Electronic Structure and Band Gap of Fullerenes on Tungsten Surfaces: Transition from a Semiconductor to a Metal Triggered by Annealing.

PubMed

Monazami, Ehsan; McClimon, John B; Rondinelli, James; Reinke, Petra

2016-12-21

The understanding and control of molecule-metal interfaces is critical to the performance of molecular electronics and photovoltaics devices. We present a study of the interface between C 60 and W, which is a carbide-forming transition metal. The complex solid-state reaction at the interface can be exploited to adjust the electronic properties of the molecule layer. Scanning tunneling microscopy/spectroscopy measurements demonstrate the progression of this reaction from wide band gap (>2.5 eV) to metallic molecular surface during annealing from 300 to 800 K. Differential conduction maps with 10 4 scanning tunneling spectra are used to quantify the transition in the density of states and the reduction of the band gap during annealing with nanometer spatial resolution. The electronic transition is spatially homogeneous, and the surface band gap can therefore be adjusted by a targeted annealing step. The modified molecules, which we call nanospheres, are quite resistant to ripening and coalescence, unlike any other metallic nanoparticle of the same size. Densely packed C 60 and isolated C 60 molecules show the same transition in electronic structure, which confirms that the transformation is controlled by the reaction at the C 60 -W interface. Density functional theory calculations are used to develop possible reaction pathways in agreement with experimentally observed electronic structure modulation. Control of the band gap by the choice of annealing temperature is a unique route to tailoring molecular-layer electronic properties.
pH dependent unfolding characteristics of DLC8 dimer: Residue level details from NMR.

PubMed

Mohan, P M Krishna; Hosur, Ramakrishna V

2008-11-01

Environment dependence of folding and unfolding of a protein is central to its function. In the same vein, knowledge of pH dependence of stability and folding/unfolding is crucial for many biophysical equilibrium and kinetic studies designed to understand protein folding mechanisms. In the present study we investigated the guanidine induced unfolding transition of dynein light chain protein (DLC8), a cargo adaptor of the dynein complex in the pH range 7-10. It is observed that while the protein remains a dimer in the entire pH range, its stability is somewhat reduced at alkaline pH. Global unfolding features monitored using fluorescence spectroscopy revealed that the unfolding transition of DLC8 at pH 7 is best described by a three-state model, whereas, that at pH 10 is best described by a two-state model. Chemical shift perturbations due to pH change provided insights into the corresponding residue level structural perturbations in the DLC8 dimer. Likewise, backbone (15)N relaxation measurements threw light on the corresponding motional changes in the dimeric protein. These observations have been rationalized on the basis of expected changes with increasing pH in the protonation states of the titratable residues on the structure of the protein. These, in turn provide an explanation for the change from three-state to two-state guanidine induced unfolding transition as the pH is increased from 7 to 10. All these results exemplify and highlight the role of environment vis-à-vis the sequence and structure of a given protein in dictating its folding/unfolding characteristics.
Widom Lines in Binary Mixtures of Supercritical Fluids.

PubMed

Raju, Muralikrishna; Banuti, Daniel T; Ma, Peter C; Ihme, Matthias

2017-06-08

Recent experiments on pure fluids have identified distinct liquid-like and gas-like regimes even under supercritical conditions. The supercritical liquid-gas transition is marked by maxima in response functions that define a line emanating from the critical point, referred to as Widom line. However, the structure of analogous state transitions in mixtures of supercritical fluids has not been determined, and it is not clear whether a Widom line can be identified for binary mixtures. Here, we present first evidence for the existence of multiple Widom lines in binary mixtures from molecular dynamics simulations. By considering mixtures of noble gases, we show that, depending on the phase behavior, mixtures transition from a liquid-like to a gas-like regime via distinctly different pathways, leading to phase relationships of surprising complexity and variety. Specifically, we show that miscible binary mixtures have behavior analogous to a pure fluid and the supercritical state space is characterized by a single liquid-gas transition. In contrast, immiscible binary mixture undergo a phase separation in which the clusters transition separately at different temperatures, resulting in multiple distinct Widom lines. The presence of this unique transition behavior emphasizes the complexity of the supercritical state to be expected in high-order mixtures of practical relevance.
Topological phase transitions of (BixSb1-x)2Se3 alloys by density functional theory.

PubMed

Abdalla, L B; Padilha José, E; Schmidt, T M; Miwa, R H; Fazzio, A

2015-07-01

We have performed an ab initio total energy investigation of the topological phase transition, and the electronic properties of topologically protected surface states of (BixSb1-x)2Se3 alloys. In order to provide an accurate alloy concentration for the phase transition, we have considered the special quasirandom structures to describe the alloy system. The trivial → topological transition concentration was obtained by (i) the calculation of the band gap closing as a function of Bi concentration (x), and (ii) the calculation of the Z2 topological invariant number. We show that there is a topological phase transition, for x around 0.4, verified for both procedures (i) and (ii). We also show that in the concentration range 0.4 < x < 0.7, the alloy does not present any other band at the Fermi level besides the Dirac cone, where the Dirac point is far from the bulk states. This indicates that a possible suppression of the scattering process due to bulk states will occur.
DOE Office of Scientific and Technical Information (OSTI.GOV)

Hirano, Kazumi; Van Kuppevelt, Toin H.; Nishihara, Shoko, E-mail: shoko@soka.ac.jp

Highlights: ► Fas transcript increases during the transition from the naïve to the primed state. ► 3OST-5 transcript, the HS4C3 epitope synthesis gene, increases during the transition. ► Fas signaling regulates the transition from the naïve to the primed state. ► HS4C3-binding epitope regulates the transition from the naïve to the primed state. ► Fas signaling is regulated by the HS4C3 epitope during the transition. -- Abstract: The characteristics of pluripotent embryonic stem cells of human and mouse are different. The properties of human embryonic stem cells (hESCs) are similar to those of mouse epiblast stem cells (mEpiSCs), which aremore » in a later developmental pluripotency state, the so-called “primed state” compared to mouse embryonic stem cells (mESCs) which are in a naïve state. As a result of the properties of the primed state, hESCs proliferate slowly, cannot survive as single cells, and can only be transfected with genes at low efficiency. Generating hESCs in the naïve state is necessary to overcome these problems and allow their application in regenerative medicine. Therefore, clarifying the mechanism of the transition between the naïve and primed states in pluripotent stem cells is important for the establishment of stable methods of generating naïve state hESCs. However, the signaling pathways which contribute to the transition between the naïve and primed states are still unclear. In this study, we carried out induction from mESCs to mEpiSC-like cells (mEpiSCLCs), and observed an increase in the activation of Fas signaling during the induction. The expression of Fgf5, an epiblast marker, was diminished by inhibition of Fas signaling using the caspase-8 and -3 blocking peptides, IETD and DEVD, respectively. Furthermore, during the induction, we observed increased expression of 3-O sulfated heparan sulfate (HS) structures synthesized by HS 3-O-sulfotransferase (3OST), which are recognized by the HS4C3 antibody (HS4C3-binding epitope). Knockdown of 3OST-5 reduced Fas signaling and the potential for the transition to mEpiSCLCs. This indicates that the HS4C3-binding epitope is necessary for the transition to the primed state. We propose that Fas signaling through the HS4C3-binding epitope contributes to the transition from the naïve state to the primed state.« less
Spectroscopy and high-spin structure of 210Fr: Isomerism and potential evidence for configuration mixing

NASA Astrophysics Data System (ADS)

Margerin, V.; Lane, G. J.; Dracoulis, G. D.; Palalani, N.; Smith, M. L.; Stuchbery, A. E.

2016-06-01

The structure of 210Fr has been established up to an excitation energy of ˜5.5 MeV and spins of ˜25 ℏ , via time-correlated γ -ray spectroscopy and using the 197Au(18O,5 n )210Fr reaction with pulsed beams at an energy of 97 MeV. A significantly different level scheme has been obtained compared to previous publications. Several isomers are reported here, including a Jπ=(23) +,τ =686 (9 ) -ns state at 4417 keV and a 10-, 29.8(11)-ns state at 1113 keV. The former isomer has been associated with the π (h9/2 3i13/2 2) ν (p1/2 -2f5/2 -1) configuration and decays via proposed E 3 transitions with strengths of 8.4(3) and 21.2(8) W.u. There are only very few known cases of a high-spin isomer decaying via two parallel E 3 transitions. Indeed, this is not seen in other Fr nuclei, and consequently these strengths differ from related decays in the neighboring isotopes. However, by examining the systematics of E 3 transitions in trans-lead nuclei, we suggest that the weaker of the two transitions decays to a mixed 20- state. Systematics of the 10- isomer are also discussed. Comparisons are made between the observed spectrum of states and those predicted from semiempirical shell-model calculations.
Structural Changes Fundamental to Gating of the Cystic Fibrosis Transmembrane Conductance Regulator Anion Channel Pore.

PubMed

Linsdell, Paul

2017-01-01

Cystic fibrosis is caused by mutations in the cystic fibrosis transmembrane conductance regulator (CFTR), an epithelial cell anion channel. Potentiator drugs used in the treatment of cystic fibrosis act on the channel to increase overall channel function, by increasing the stability of its open state and/or decreasing the stability of its closed state. The structure of the channel in either the open state or the closed state is not currently known. However, changes in the conformation of the protein as it transitions between these two states have been studied using functional investigation and molecular modeling techniques. This review summarizes our current understanding of the architecture of the transmembrane channel pore that controls the movement of chloride and other small anions, both in the open state and in the closed state. Evidence for different kinds of changes in the conformation of the pore as it transitions between open and closed states is described, as well as the mechanisms by which these conformational changes might be controlled to regulate normal channel gating. The ways that key conformational changes might be targeted by small compounds to influence overall CFTR activity are also discussed. Understanding the changes in pore structure that might be manipulated by such small compounds is key to the development of novel therapeutic strategies for the treatment of cystic fibrosis.
Laser Spectroscopy and AB Initio Calculations on the TaF Molecule

NASA Astrophysics Data System (ADS)

Ng, Kiu Fung; Zou, Wenli; Liu, Wenjian; Cheung, Allan S. C.

2016-06-01

Electronic transition spectrum of the tantalum monoflouride (TaF) molecule in the spectral region between 448 and 520 nm has been studied using the technique of laser-ablation/reaction free jet expansion and laser induced fluorescence spectroscopy. TaF molecule was produced by reacting laser-ablated tantalum atoms with sulfur hexafluoride gas seeded in argon. Sixteen vibrational bands with resolved rotational structure have been recorded and analyzed, which were organized into six electronic transition systems and the ground state has been identified to be the X3Σ-(0+) state with bond length, ro, and equilibrium vibrational frequency, ωe, determined to be 1.8209 Å and 700.1 wn respectively. In addition, four vibrational bands belong to another transition system involving lower state with Ω = 2 component has also been analyzed. All observed transitions are with ΔΩ = 0. Least-squares fit of the measured line positions yielded molecular constants for the electronic states involved. The Λ-S and Ω states of TaF were calculated at the state-averaged complete active space self-consistent field (SA-CASSCF) and the subsequent internally contracted multi-reference configuration interaction with singles and doubles and Davidson's cluster correction (MRCISD+Q) levels of theory with the active space of 4 electrons in 6 orbitals, that is, the molecular orbitals corresponding to Ta 5d6s are active. The spin-orbit coupling (SOC) is calculated by the state-interaction approach at the SA-CASSCF level via the relativistic effective core potentials (RECPs) spin-orbit operator, where the diagonal elements of the spin-orbit matrix are replaced by the above MRCISD+Q energies. The spectroscopic properties of the ground and many low-lying electronic states of the TaF molecule will be reported. With respect to the observed electronic states in this work, the calculated results are in good agreement with our experimental determinations. This work represents the first experimental investigation of the molecular structure of the TaF molecule.
High pressure and synchrotron radiation studies of solid state electronic instabilities

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

Pifer, J.H.; Croft, M.C.

This report discusses Eu and General Valence Instabilities; Ce Problem: L{sub 3} Spectroscopy Emphasis; Bulk Property Emphasis; Transition Metal Compound Electronic Structure; Electronic Structure-Phonon Coupling Studies; High Temperature Superconductivity and Oxide Materials; and Novel Materials Collaboration with Chemistry.
Public Policy Implications of the Transition to a Subscription-Based Economic Structure for the Television Industry.

ERIC Educational Resources Information Center

Baldwin, Thomas F.; Wirth, Michael O.

This paper argues that the United States television industry is in a transitional period between the dominance of an advertiser-supported system and an advertiser-subscription system, and that a "dual revenue stream" system of subscription and advertising will eventually relegate the advertiser-only support system to a secondary role.…
Education in Mongolia: The Difficulties and Achievements of the Period of Transition

ERIC Educational Resources Information Center

Suprunova, L. L.

2007-01-01

Since the early 1990s, the system of education in Mongolia has gone through radical changes that stem from the country's transition to the market economy and the democratic state structure. Favorable prerequisites were already in place to renovate education on democratic principles, because during the period of its socialist development Mongolia…
Spin-glass polyamorphism induced by a magnetic field in LaMnO3 single crystal

NASA Astrophysics Data System (ADS)

Eremenko, V. V.; Sirenko, V. A.; Baran, A.; Čižmár, E.; Feher, A.

2018-05-01

We present experimental evidence of field-driven transition in spin-glass state, similar to pressure-induced transition between amorphous phases in structural and metallic glasses, attributed to the polyamorphism phenomena. Cusp in temperature dependences of ac magnetic susceptibility of weakly disordered LaMnO3 single crystal is registered below the temperature of magnetic ordering. Frequency dependence of the cusp temperature proves its spin-glass origin. The transition induced by a magnetic field in spin-glass state, is manifested by peculiarity in dependence of cusp temperature on applied magnetic field. Field dependent maximum of heat capacity is observed in the same magnetic field and temperature range.
Investigation of ground state charge transfer complex between paracetamol and p-chloranil through DFT and UV-visible studies

NASA Astrophysics Data System (ADS)

Shukla, Madhulata; Srivastava, Nitin; Saha, Satyen

2012-08-01

The present report deals with the theoretical investigation on ground state structure and charge transfer (CT) transitions in paracetamol (PA)/p-chloranil (CA) complex using Density Functional Theory (DFT) and Time Dependent Density Functional Theory (TD-DFT) method. It is found that Cdbnd O bond length of p-chloranil increases on complexation with paracetamol along with considerable amount of charge transfer from PA to CA. TD-DFT calculations have been performed to analyse the observed UV-visible spectrum of PA-CA charge transferred complex. Interestingly, in addition to expected CT transition, a weak symmetry relieved π-π* transition in the chloranil is also observed.
A Liquid-Liquid Transition in an Undercooled Ti-Zr-Ni Liquid

NASA Technical Reports Server (NTRS)

Lee, G. W.; Gangopadhyay, A. K.; Kelton, K. F.; Hyers, R. W.; Rathz, T. J.; Rogers, J. R.

2003-01-01

If crystallization can be avoided, liquids enter a metastable (undercooled) state below their equilibrium liquidus temperatures, TI, finally freezing into a glass below a characteristic temperature called the glass transition temperature, T,. In rare cases, the undercooled liquid may undergo a liquid-liquid phase transition (liquid polymorphism) before entering the glassy state. This has been suggested from experimental studies of HzO and Si4. Such phase transitions have been predicted in some stable liquids, i.e. above TI at atmospheric pressure, for Si02 and BeF;, but these have not been verified experimentally. They have been observed in liquids of P7, Sis and C9, but only under high pressure. All of these transitions are driven by an anomalous density change, i.e. change in local structure, with temperature or pressure. In this letter we present the first experimental evidence for a phase transition in a low viscosity liquid that is not driven by an anomalous density change, but by an approach to a constant configuration state. A maximum in the specific heat at constant pressure, similar to what is normally observed near T,, is reported here for undercooled low viscosity liquids of quasicrystal- forming Ti-Zr-Ni alloys. that includes cooperativity, by incorporating a temperature dependent excitation energy fits the data well, signaling a phase transition.
Canted spin structure and the first order magnetic transition in CoFe2O4 nanoparticles coated by amorphous silica

NASA Astrophysics Data System (ADS)

Lyubutin, I. S.; Starchikov, S. S.; Gervits, N. E.; Korotkov, N. Yu.; Dmitrieva, T. V.; Lin, Chun-Rong; Tseng, Yaw-Teng; Shih, Kun-Yauh; Lee, Jiann-Shing; Wang, Cheng-Chien

2016-10-01

The functional polymer (PMA-co-MAA) latex microspheres were used as a core template to prepare magnetic hollow spheres consisting of CoFe2O4/SiO2 composites. The spinel type crystal structure of CoFe2O4 ferrite is formed under annealing, whereas the polymer cores are completely removed after annealing at 450 °C. Magnetic and Mössbauer spectroscopy measurements reveal very interesting magnetic properties of the CoFe2O4/SiO2 hollow spheres strongly dependent on the particle size which can be tuned by the annealing temperature. In the ground state of low temperatures, the CoFe2O4 nanoparticles are in antiferromagnetic state due to the canted magnetic structure. Under heating in the applied field, the magnetic structure gradually transforms from canted to collinear, which increases the magnetization. The Mössbauer data revealed that the small size CoFe2O4/SiO2 particles (2.2-4.3 nm) do not show superparamagnetic behavior but transit from the magnetic to the paramagnetic state by a jump-like magnetic transition of the first order This effect is a specific property of the magnetic nanoparticles isolated by inert material, and can be initiated by internal pressure creating at the particle surface. The suggested method of synthesis can be modified with various bio-ligands on the silane surface, and such materials can find many applications in diagnostics and bio-separation.
Dynamical transitions in large systems of mean field-coupled Landau-Stuart oscillators: Extensive chaos and cluster states.

PubMed

Ku, Wai Lim; Girvan, Michelle; Ott, Edward

2015-12-01

In this paper, we study dynamical systems in which a large number N of identical Landau-Stuart oscillators are globally coupled via a mean-field. Previously, it has been observed that this type of system can exhibit a variety of different dynamical behaviors. These behaviors include time periodic cluster states in which each oscillator is in one of a small number of groups for which all oscillators in each group have the same state which is different from group to group, as well as a behavior in which all oscillators have different states and the macroscopic dynamics of the mean field is chaotic. We argue that this second type of behavior is "extensive" in the sense that the chaotic attractor in the full phase space of the system has a fractal dimension that scales linearly with N and that the number of positive Lyapunov exponents of the attractor also scales linearly with N. An important focus of this paper is the transition between cluster states and extensive chaos as the system is subjected to slow adiabatic parameter change. We observe discontinuous transitions between the cluster states (which correspond to low dimensional dynamics) and the extensively chaotic states. Furthermore, examining the cluster state, as the system approaches the discontinuous transition to extensive chaos, we find that the oscillator population distribution between the clusters continually evolves so that the cluster state is always marginally stable. This behavior is used to reveal the mechanism of the discontinuous transition. We also apply the Kaplan-Yorke formula to study the fractal structure of the extensively chaotic attractors.
Dynamical transitions in large systems of mean field-coupled Landau-Stuart oscillators: Extensive chaos and cluster states

NASA Astrophysics Data System (ADS)

Ku, Wai Lim; Girvan, Michelle; Ott, Edward

2015-12-01

In this paper, we study dynamical systems in which a large number N of identical Landau-Stuart oscillators are globally coupled via a mean-field. Previously, it has been observed that this type of system can exhibit a variety of different dynamical behaviors. These behaviors include time periodic cluster states in which each oscillator is in one of a small number of groups for which all oscillators in each group have the same state which is different from group to group, as well as a behavior in which all oscillators have different states and the macroscopic dynamics of the mean field is chaotic. We argue that this second type of behavior is "extensive" in the sense that the chaotic attractor in the full phase space of the system has a fractal dimension that scales linearly with N and that the number of positive Lyapunov exponents of the attractor also scales linearly with N. An important focus of this paper is the transition between cluster states and extensive chaos as the system is subjected to slow adiabatic parameter change. We observe discontinuous transitions between the cluster states (which correspond to low dimensional dynamics) and the extensively chaotic states. Furthermore, examining the cluster state, as the system approaches the discontinuous transition to extensive chaos, we find that the oscillator population distribution between the clusters continually evolves so that the cluster state is always marginally stable. This behavior is used to reveal the mechanism of the discontinuous transition. We also apply the Kaplan-Yorke formula to study the fractal structure of the extensively chaotic attractors.
DOE Office of Scientific and Technical Information (OSTI.GOV)

Kozlov, D. V., E-mail: dvkoz@ipmras.ru; Rumyantsev, V. V.; Morozov, S. V.

A long-wavelength band caused by transitions between states related to the valence band is detected in the photoconductivity spectra of Hg{sub y}Te{sub 1–y}/Cd{sub x}Hg{sub 1–x}Te (CMT) structures with quantum wells. The energy states of mercury vacancies in quantum wells of CMT structures is calculated taking into account a chemical shift. It is shown that the long-wavelength band observed in the photoconductivity spectra of these structures is associated with the ionization of divalent acceptor centers which are such vacancies.
Thermal and urea-induced unfolding in T7 RNA polymerase: Calorimetry, circular dichroism and fluorescence study

PubMed Central

Griko, Yuri; Sreerama, Narasimha; Osumi-Davis, Patricia; Woody, Robert W.; Woody, A-Young Moon

2001-01-01

Structural changes in T7 RNA polymerase (T7RNAP) induced by temperature and urea have been studied over a wide range of conditions to obtain information about the structural organization and the stability of the enzyme. T7RNAP is a large monomeric enzyme (99 kD). Calorimetric studies of the thermal transitions in T7RNAP show that the enzyme consists of three cooperative units that may be regarded as structural domains. Interactions between these structural domains and their stability strongly depend on solvent conditions. The unfolding of T7RNAP under different solvent conditions induces a highly stable intermediate state that lacks specific tertiary interactions, contains a significant amount of residual secondary structure, and undergoes further cooperative unfolding at high urea concentrations. Circular dichroism (CD) studies show that thermal unfolding leads to an intermediate state that has increased β-sheet and reduced α-helix content relative to the native state. Urea-induced unfolding at 25°C reveals a two-step process. The first transition centered near 3 M urea leads to a plateau from 3.5 to 5.0 M urea, followed by a second transition centered near 6.5 M urea. The CD spectrum of the enzyme in the plateau region, which is similar to that of the enzyme thermally unfolded in the absence of urea, shows little temperature dependence from 15° to 60°C. The second transition leads to a mixture of poly(Pro)II and unordered conformations. As the temperature increases, the ellipticity at 222 nm becomes more negative because of conversion of poly(Pro)II to the unordered conformation. Near-ultraviolet CD spectra at 25°C at varying concentrations of urea are consistent with this picture. Both thermal and urea denaturation are irreversible, presumably because of processes that follow unfolding. PMID:11274475
Analysis of the Isolated SecA DEAD Motor Suggests a Mechanism for Chemical-Mechanical Coupling

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

Nithianantham, Stanley; Shilton, Brian H

The preprotein cross-linking domain and C-terminal domains of Escherichia coli SecA were removed to create a minimal DEAD motor, SecA-DM. SecA-DM hydrolyzes ATP and has the same affinity for ADP as full-length SecA. The crystal structure of SecA-DM in complex with ADP was solved and shows the DEAD motor in a closed conformation. Comparison with the structure of the E. coli DEAD motor in an open conformation (Protein Data Bank ID 2FSI) indicates main-chain conformational changes in two critical sequences corresponding to Motif III and Motif V of the DEAD helicase family. The structures that the Motif III and Motifmore » V sequences adopt in the DEAD motor open conformation are incompatible with the closed conformation. Therefore, when the DEAD motor makes the transition from open to closed, Motif III and Motif V are forced to change their conformations, which likely functions to regulate passage through the transition state for ATP hydrolysis. The transition state for ATP hydrolysis for the SecA DEAD motor was modeled based on the conformation of the Vasa helicase in complex with adenylyl imidodiphosphate and RNA (Protein Data Bank ID 2DB3). A mechanism for chemical-mechanical coupling emerges, where passage through the transition state for ATP hydrolysis is hindered by the conformational changes required in Motif III and Motif V, and may be promoted by binding interactions with the preprotein substrate and/or other translocase domains and subunits.« less

Analysis of the Isolated SecA DEAD Motor Suggests a Mechanism for Chemical-Mechanical Coupling

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

Nithianantham, Stanley; Shilton, Brian H

2011-09-28

The preprotein cross-linking domain and C-terminal domains of Escherichia coli SecA were removed to create a minimal DEAD motor, SecA-DM. SecA-DM hydrolyzes ATP and has the same affinity for ADP as full-length SecA. The crystal structure of SecA-DM in complex with ADP was solved and shows the DEAD motor in a closed conformation. Comparison with the structure of the E. coli DEAD motor in an open conformation (Protein Data Bank ID 2FSI) indicates main-chain conformational changes in two critical sequences corresponding to Motif III and Motif V of the DEAD helicase family. The structures that the Motif III and Motifmore » V sequences adopt in the DEAD motor open conformation are incompatible with the closed conformation. Therefore, when the DEAD motor makes the transition from open to closed, Motif III and Motif V are forced to change their conformations, which likely functions to regulate passage through the transition state for ATP hydrolysis. The transition state for ATP hydrolysis for the SecA DEAD motor was modeled based on the conformation of the Vasa helicase in complex with adenylyl imidodiphosphate and RNA (Protein Data Bank ID 2DB3). A mechanism for chemical-mechanical coupling emerges, where passage through the transition state for ATP hydrolysis is hindered by the conformational changes required in Motif III and Motif V, and may be promoted by binding interactions with the preprotein substrate and/or other translocase domains and subunits.« less
Probing the connections between superconductivity, stripe order, and structure in La₁.₉₀₅Ba₀.₀₉₅Cu 1-yZn yO₄

DOE PAGES

Wen, Jinsheng; Xu, Zhijun; Xu, Guangyong; ...

2012-04-12

The superconducting system La 2-xBa xCuO₄ is known to show a minimum in the transition temperature T c at x=1/8 where maximal stripe order is pinned by the anisotropy within the CuO₂ planes that occurs in the low-temperature-tetragonal (LTT) crystal structure. For x=0.095, where T c reaches its maximum value of 32 K, there is a roughly coincident structural transition to a phase that is very close to LTT. Here, we present a neutron scattering study of the structural transition, and demonstrate how features of it correlate with anomalies in the magnetic susceptibility, electrical resistivity, thermal conductivity, and thermoelectric power.more » We also present measurements on a crystal with 1% Zn substituted for Cu, which reduces T c to 17 K, enhances the spin stripe order, but has much less effect on the structural transition. We make the case that the structural transition correlates with a reduction of the Josephson coupling between the CuO₂ layers, which interrupts the growth of the superconducting order. We also discuss evidence for two-dimensional superconducting fluctuations in the normal state, analyze the effective magnetic moment per Zn impurity, and consider the significance of the anomalous thermopower often reported in the stripe-ordered phase.« less
Visualization of the ultrafast structural phase transitions in warm dense matter

NASA Astrophysics Data System (ADS)

Mo, Mianzhen

2017-10-01

It is still a great challenge to obtain real-time atomistic-scale information on the structural phase transitions that lead to warm dense matter state. Recent advances in ultrafast electron diffraction (UED) techniques have opened up exciting prospects to unravel the mechanisms of solid-liquid phase transitions under these extreme non-equilibrium conditions. Here we report on precise measurements of melt time dependency on laser excitation energy density that resolve for the first time the transition from heterogeneous to homogeneous melting. This transition appears in both polycrystalline and single-crystal gold nanofilms with distinct measurable differences. These results test predictions from molecular-dynamics simulations with different interatomic potential models. These data further deliver accurate structure factor data to large wavenumbers that allow us to constrain electron-ion equilibration constants. Our results demonstrate electron-phonon coupling strength much weaker than DFT calculations, and contrary to previous results, provide evidence for bond softening. This work is supported by DOE Office of Science, Fusion Energy Science under FWP 100182, and the DOE BES Accelerator and Detector R&D program.
Shear-induced structural transitions in Newtonian non-Newtonian two-phase flow

NASA Astrophysics Data System (ADS)

Cristobal, G.; Rouch, J.; Colin, A.; Panizza, P.

2000-09-01

We show the existence under shear flow of steady states in a two-phase region of a brine-surfactant system in which lyotropic dilute lamellar (non-Newtonian) and sponge (Newtonian) phases are coexisting. At high shear rates and low sponge phase-volume fractions, we report on the existence of a dynamic transition corresponding to the formation of a colloidal crystal of multilamellar vesicles (or ``onions'') immersed in the sponge matrix. As the sponge phase-volume fraction increases, this transition exhibits a hysteresis loop leading to a structural bistability of the two-phase flow. Contrary to single phase lamellar systems where it is always 100%, the onion volume fraction can be monitored continuously from 0 to 100 %.
Phonon-induced ultrafast band gap control in LaTiO3

NASA Astrophysics Data System (ADS)

Gu, Mingqiang; Rondinelli, James M.

We propose a route for ultrafast band gap engineering in correlated transition metal oxides by using optically driven phonons. We show that the ∖Gamma-point electron band energies can be deterministically tuned in the nonequilibrium state. Taking the Mott insulator LaTiO3 as an example, we show that such phonon-assisted processes dynamically induce an indirect-to-direct band gap transition or even a metal-to-insulator transition, depending on the electron correlation strength. We explain the origin of the dynamical band structure control and also establish its generality by examining related oxides. Lastly, we describe experimental routes to realize the band structure control with impulsive stimulated Raman scattering.
Fermi Surface as a Driver for the Shape-Memory Effect in AuZn

NASA Astrophysics Data System (ADS)

Lashley, Jason

2005-03-01

Martensites are materials that undergo diffusionless, solid-state transitions. The martensitic transition yields properties that depend on the history of the material and if reversible can allow it to recover its previous shape after plastic deformation. This is known as the shape-memory effect (SME). We have succeeded in identifying the operative electronic mechanism responsible for the martensitic transition in the shape-memory alloy AuZn by using Fermi-surface measurements (de Haas-van Alphen oscillations) and band-structure calculations. Our findings suggest that electronic band structure gives rise to special features on the Fermi surface that is important to consider in the design of SME alloys.
Transition to spatiotemporal chaos in a two-dimensional hydrodynamic system.

PubMed

Pirat, Christophe; Naso, Aurore; Meunier, Jean-Louis; Maïssa, Philippe; Mathis, Christian

2005-04-08

We study the transition to spatiotemporal chaos in a two-dimensional hydrodynamic experiment where liquid columns take place in the gravity induced instability of a liquid film. The film is formed below a plane grid which is used as a porous media and is continuously supplied with a controlled flow rate. This system can be either ordered (on a hexagonal structure) or disordered depending on the flow rate. We observe, for the first time in an initially structured state, a subcritical transition to spatiotemporal disorder which arises through spatiotemporal intermittency. Statistics of numbers, creations, and fusions of columns are investigated. We exhibit a critical behavior close to the directed percolation one.
Elastic Model Transitions: A Hybrid Approach Utilizing Quadratic Inequality Constrained Least Squares (LSQI) and Direct Shape Mapping (DSM)

NASA Technical Reports Server (NTRS)

Hannan, Mike R.; Jurenko, Robert J.; Bush, Jason; Ottander, John

2014-01-01

A method for transitioning linear time invariant (LTI) models in time varying simulation is proposed that utilizes a hybrid approach for determining physical displacements by augmenting the original quadratically constrained least squares (LSQI) algorithm with Direct Shape Mapping (DSM) and modifying the energy constraints. The approach presented is applicable to simulation of the elastic behavior of launch vehicles and other structures that utilize discrete LTI finite element model (FEM) derived mode sets (eigenvalues and eigenvectors) that are propagated throughout time. The time invariant nature of the elastic data presents a problem of how to properly transition elastic states from the prior to the new model while preserving motion across the transition and ensuring there is no truncation or excitation of the system. A previous approach utilizes a LSQI algorithm with an energy constraint to effect smooth transitions between eigenvector sets with no requirement that the models be of similar dimension or have any correlation. This approach assumes energy is conserved across the transition, which results in significant non-physical transients due to changing quasi-steady state energy between mode sets, a phenomenon seen when utilizing a truncated mode set. The computational burden of simulating a full mode set is significant so a subset of modes is often selected to reduce run time. As a result of this truncation, energy between mode sets may not be constant and solutions across transitions could produce non-physical transients. In an effort to abate these transients an improved methodology was developed based on the aforementioned approach, but this new approach can handle significant changes in energy across mode set transitions. It is proposed that physical velocities due to elastic behavior be solved for using the LSQI algorithm, but solve for displacements using a two-step process that independently addresses the quasi-steady-state and non-steady-state contributions to the elastic displacement. For structures subject to large external forces, such as thrust or atmospheric drag, it is imperative to capture these forces when solving for elastic displacement. To simplify the mathematical formulation, assumptions are made regarding mass matrix normalization, constant external forcing, and constant viscous damping. These simplifications allow for direct solutions to the quasi-steady-state displacements through a process titled Direct Shape Mapping. DSM solves for the displacements using the eigenvalues of the elastic modes and the external forcing and returns a set of elastic displacements dictated by the eigenvectors of the post-transition mode set. For the non-steady-state contributions to displacement we formulate a LSQI problem that is constrained by energy of the non-steady state terms. The contributions from the quasi-steady-state and non-steady state solutions are then combined to obtain the physical displacements associated with the new set of eigenvectors. Results for the LSQI-DSM approach show significant reduction/complete removal of transients across mode set transitions while maintaining elastic motion from the prior state. For time propagation applications employing discrete elastic models that need to be transitioned in time and where running with full a full mode set is not feasible, the method developed offers a practical solution to simulating vehicle elasticity.
Boron monosulfide: Equation of state and pressure-induced phase transition

NASA Astrophysics Data System (ADS)

Cherednichenko, K. A.; Kruglov, I. A.; Oganov, A. R.; Le Godec, Y.; Mezouar, M.; Solozhenko, V. L.

2018-04-01

Quasi-hydrostatic compression of rhombohedral boron monosulfide (r-BS) has been studied up to 50 GPa at room temperature using diamond-anvil cells and angle-dispersive synchrotron X-ray diffraction. A fit of the experimental P-V data to the Vinet equation of state yields the bulk modulus B0 of 42.2(1.4) GPa and its first pressure derivative B0' of 7.6(2) that are in excellent agreement with our ab initio calculations. Formation of a new high-pressure phase of boron monosulfide (hp-BS) has been observed above 35 GPa. According to ab initio evolutionary crystal structure predictions combined with Rietveld refinement of high-pressure X-ray diffraction data, the structure of hp-BS has trigonal symmetry and belongs to the space group P-3m1. As it follows from the electron density of state calculations, the phase transformation is accompanied by an insulator-metal transition.
Band dependence of charge density wave in quasi-one-dimensional Ta2NiSe7 probed by orbital magnetoresistance

NASA Astrophysics Data System (ADS)

He, Jiaming; Zhang, Yiran; Wen, Libin; Yang, Yusen; Liu, Jinyu; Wu, Yueshen; Lian, Hailong; Xing, Hui; Wang, Shun; Mao, Zhiqiang; Liu, Ying

2017-07-01

Ta2NiSe7 is a quasi-one-dimensional (quasi-1D) transition-metal chalcogenide with Ta and Ni chain structures. An incommensurate charge-density wave (CDW) in this quasi-1D structure was well studied previously using tunnelling spectrum, X-ray, and electron diffraction, whereas its transport property and the relation to the underlying electronic states remain to be explored. Here, we report our results of the magnetoresistance (MR) on Ta2NiSe7. A breakdown of Kohler's rule is found upon entering the CDW state. Concomitantly, a clear change in curvature in the field dependence of MR is observed. We show that the curvature change is well described by the two-band orbital MR, with the hole density being strongly suppressed in the CDW state, indicating that the p orbitals from Se atoms dominate the change in transport through CDW transition.
Upper critical field reaches 90 tesla near the Mott transition in fulleride superconductors

DOE PAGES

Kasahara, Y.; Takeuchi, Y.; Zadik, R. H.; ...

2017-02-17

Controlled access to the border of the Mott insulating state by variation of control parameters offers exotic electronic states such as anomalous and possibly high-transition-temperature (T c) superconductivity. The alkali-doped fullerides show a transition from a Mott insulator to a superconductor for the first time in three-dimensional materials, but the impact of dimensionality and electron correlation on superconducting properties has remained unclear. Here we show that, near the Mott insulating phase, the upper critical field H c2 of the fulleride superconductors reaches values as high as ~90 T—the highest among cubic crystals. This is accompanied by a crossover from weak-more » to strong-coupling superconductivity and appears upon entering the metallic state with the dynamical Jahn–Teller effect as the Mott transition is approached. Lastly, these results suggest that the cooperative interplay between molecular electronic structure and strong electron correlations plays a key role in realizing robust superconductivity with high-T c and high-H c2.« less
Upper critical field reaches 90 tesla near the Mott transition in fulleride superconductors

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

Kasahara, Y.; Takeuchi, Y.; Zadik, R. H.

Controlled access to the border of the Mott insulating state by variation of control parameters offers exotic electronic states such as anomalous and possibly high-transition-temperature (T c) superconductivity. The alkali-doped fullerides show a transition from a Mott insulator to a superconductor for the first time in three-dimensional materials, but the impact of dimensionality and electron correlation on superconducting properties has remained unclear. Here we show that, near the Mott insulating phase, the upper critical field H c2 of the fulleride superconductors reaches values as high as ~90 T—the highest among cubic crystals. This is accompanied by a crossover from weak-more » to strong-coupling superconductivity and appears upon entering the metallic state with the dynamical Jahn–Teller effect as the Mott transition is approached. Lastly, these results suggest that the cooperative interplay between molecular electronic structure and strong electron correlations plays a key role in realizing robust superconductivity with high-T c and high-H c2.« less
First-order metal-insulator transitions in vanadates from first principles

NASA Astrophysics Data System (ADS)

Kumar, Anil; Rabe, Karin

2013-03-01

Materials that exhibit first-order metal-insulator transitions, with the accompanying abrupt change in the conductivity, have potential applications as switches in future electronic devices. Identification of materials and exploration of the atomic-scale mechanisms for switching between the two electronic states is a focus of current research. In this work, we search for first-order metal-insulator transitions in transition metal compounds, with a particular focus on d1 and d2 systems, by using first principles calculations to screen for an alternative low-energy state having not only a electronic character opposite to that of the ground state, but a distinct structure and/or magnetic ordering which would permit switching by an applied field or stress. We will present the results of our investigation of the perovskite compounds SrVO3, LaVO3, CaVO3, YVO3, LaTiO3 and related layered phase, including superlattices and Ruddlesden-Popper phases. While the pure compounds do not satisfy the search criteria, the layered phases show promising results.
Classical Spin Nematic Transition in LiGa0.95In0.05Cr4O8

NASA Astrophysics Data System (ADS)

Wawrzyńczak, R.; Tanaka, Y.; Yoshida, M.; Okamoto, Y.; Manuel, P.; Casati, N.; Hiroi, Z.; Takigawa, M.; Nilsen, G. J.

2017-08-01

We present the results of a combined 7Li -NMR and diffraction study on LiGa0.95In0.05Cr4O8, a member of the LiGa1 -xInxCr4O8 "breathing" pyrochlore family. Via specific heat and NMR measurements, we find that the complex sequence of first-order transitions observed for LiGaCr4O8 is replaced by a single second-order transition at Tf=11 K . Neutron and x-ray diffraction rule out both structural symmetry lowering and magnetic long-range order as the origin of this transition. Instead, reverse Monte Carlo fitting of the magnetic diffuse scattering indicates that the low-temperature phase may be described as a collinear spin nematic state, characterized by a quadrupolar order parameter. This state also shows signs of short-range order between collinear spin arrangements on tetrahedra, revealed by mapping the reverse Monte Carlo spin configurations onto a three-state color model.
Phase transition in a spatial Lotka-Volterra model

NASA Astrophysics Data System (ADS)

Szabó, György; Czárán, Tamás

2001-06-01

Spatial evolution is investigated in a simulated system of nine competing and mutating bacterium strains, which mimics the biochemical war among bacteria capable of producing two different bacteriocins (toxins) at most. Random sequential dynamics on a square lattice is governed by very symmetrical transition rules for neighborhood invasions of sensitive strains by killers, killers by resistants, and resistants by sensitives. The community of the nine possible toxicity/resistance types undergoes a critical phase transition as the uniform transmutation rates between the types decreases below a critical value Pc above that all the nine types of strains coexist with equal frequencies. Passing the critical mutation rate from above, the system collapses into one of three topologically identical (degenerated) states, each consisting of three strain types. Of the three possible final states each accrues with equal probability and all three maintain themselves in a self-organizing polydomain structure via cyclic invasions. Our Monte Carlo simulations support that this symmetry-breaking transition belongs to the universality class of the three-state Potts model.
Slow transition of the Osborne Reynolds pipe flow: A direct numerical simulation study.

NASA Astrophysics Data System (ADS)

Wu, Xiaohua; Moin, Parviz; Adrian, Ronald J.; Baltzer, Jon R.

2015-11-01

Osborne Reynolds' pipe transition experiment marked the onset of fundamental turbulence research, yet the precise dynamics carrying the laminar state to fully-developed turbulence has been quite elusive. Our spatially-developing direct numerical simulation of this problem reveals interesting connections with theory and experiments. In particular, during transition the energy norms of localized, weakly finite inlet perturbations grow exponentially, rather than algebraically, with axial distance, in agreement with the edge-state based temporal results of Schneider et al. (PRL, 034502, 2007). When inlet disturbance is the core region, helical vortex filaments evolve into large-scale reverse hairpin vortices. The interaction of these reverse hairpins among themselves or with the near-wall flow produces small-scale hairpin packets. When inlet disturbance is near the wall, optimally positioned quasi-spanwise structure is stretched into a Lambda vortex, which grows into a turbulent spot of concentrated small-scale hairpin vortices. Waves of hairpin-like structures were observed by Mullin (Ann. Rev. Fluid Mech., Vol.43, 2011) in their experiment with very weak blowing and suction. This vortex dynamics is broadly analogous to that in the boundary layer bypass transition and in the secondary instability and breakdown stage of natural transition. Further details of our simulation are reported in Wu et al. (PNAS, 1509451112, 2015).
Pressure-induced structural change in liquid GeI₄.

PubMed

Fuchizaki, Kazuhiro; Nishimura, Hironori; Hase, Takaki; Saitoh, Hiroyuki

2017-12-13

The similarity in the shape of the melting curve of GeI4 to that of SnI4 suggests that a liquid-liquid transition as observed in liquid SnI4 is also expected to occur in liquid GeI4. Because the slope of the melting curve of GeI4 abruptly changes at around 3 GPa, in situ synchrotron diffraction measurements were conducted to examine closely the structural changes upon compression at around 3 GPa. The reduced radial distribution functions of the high- and low-pressure liquid states of GeI4 share the same feature inherent in the high-pressure (high-density) and low-pressure (low-density) radial distribution functions of liquid SnI4. This feature allows us to introduce local order parameters that we may use to observe the transition. Unlike the transition in liquid SnI4, the transition from the low-pressure to the high-pressure structure seems sluggish. We speculate that the liquid-liquid critical point of GeI4 is no longer a thermodynamically stable state and is slightly located below the melting curve. As a result, the structural change is said to be a crossover rather than a transition. The behavior of the local-order parameters implies a metastable extension of the liquid-liquid phase boundary with a negative slope. . © 2017 IOP Publishing Ltd.
Structural phase transitions in SrTiO 3 nanoparticles

DOE PAGES

Zhang, Han; Liu, Sizhan; Scofield, Megan E.; ...

2017-08-04

We present that pressure dependent structural measurements on monodispersed nanoscale SrTiO 3 samples with average diameters of 10 to ~80 nm were conducted to enhance the understanding of the structural phase diagram of nanoscale SrTiO 3. A robust pressure independent polar structure was found in the 10 nm sample for pressures up to 13 GPa, while a size dependent cubic to tetragonal transition occurs (at P = P c) for larger particle sizes. In conclusion, the results suggest that the growth of ~10 nm STO particles on substrates with significant lattice mismatch may maintain a polar state for a largemore » range of strain values, possibly enabling device use.« less
Ground State Structure Search of Fluoroperovskites through Lattice Instability

NASA Astrophysics Data System (ADS)

Mei, W. N.; Hatch, D. M.; Stokes, H. T.; Boyer, L. L.

2002-03-01

Many Fluoroperovskite are capable of a ferroelectric transition from a cubic to a tetragonal and even lower-symmetry structures. In this work, we studied systematically the structural phase transitions of several fluoroperovskites ABF3 where A= Na, K and B= Ca, Sr. Combining the Self-Consistent Atom Deformation (SCAD) -- a density-functional method using localized densities -- and the frozen-phonon method which utilizes the isotropy subgroup operations, we calculate the phonon energies and find instabilities which lower the symmetry of the crystal. Following this scheme, we work down to lower symmetry structures until we no longer find instabilities. The final results are used to compare with those obtained from molecular dynamics based on Gordon-Kim potentials.
Defect states of complexes involving a vacancy on the boron site in boronitrene

NASA Astrophysics Data System (ADS)

Ngwenya, T. B.; Ukpong, A. M.; Chetty, N.

2011-12-01

First principles calculations have been performed to investigate the ground state properties of freestanding monolayer hexagonal boronitrene (h-BN). We have considered monolayers that contain native point defects and their complexes, which form when the point defects bind with the boron vacancy on the nearest-neighbor position. The changes in the electronic structure are analyzed to show the extent of localization of the defect-induced midgap states. The variations in formation energies suggest that defective h-BN monolayers that contain carbon substitutional impurities are the most stable structures, irrespective of the changes in growth conditions. The high energies of formation of the boron vacancy complexes suggest that they are less stable, and their creation by ion bombardment would require high-energy ions compared to point defects. Using the relative positions of the derived midgap levels for the double vacancy complex, it is shown that the quasi-donor-acceptor pair interpretation of optical transitions is consistent with stimulated transitions between electron and hole states in boronitrene.

Novel Electronic Structures of Ru-pnictides RuPn (Pn = P, As, Sb)

NASA Astrophysics Data System (ADS)

Goto, H.; Toriyama, T.; Konishi, T.; Ohta, Y.

Density-functional-theory-based electronic structure calculations are made to consider the novel electronic states of Ru-pnictides RuP and RuAs where the intriguing phase transitions and superconductivity under doping of Rh have been reported. We find that there appear nearly degenerate flat bands just at the Fermi level in the high-temperature metallic phase of RuP and RuAs; the flat-band states come mainly from the 4dxy orbitals of Ru ions and the Rh doping shifts the Fermi level just above the flat bands. The splitting of the flat bands caused by their electronic instability may then be responsible for the observed phase transition to the nonmagnetic insulating phase at low temperatures. We also find that the band structure calculated for RuSb resembles that of the doped RuP and RuAs, which is consistent with experiment where superconductivity occurs in RuSb without Rh doping.
Theoretical study of some nitrososulfamide compounds with antitumor activity.

PubMed

Djameleddine, Khatmi; Soumeya, Seridi; Fatiha, Madi

2004-09-30

The lowest-energy conformations of four 2-chloroethylnitrososulfamides were determined using the MM+ molecular mechanics method as implemented in Hyperchem 6.0. Some of the calculated structural parameters, angles and bonds lengths were compared with the crystal structure data of N-nitroso-N-(2-chloroethyl)-N'-sulfamoyl- proline. Using MM+, AM1 and PM3 the anti conformation was predicted to be more stable than the syn conformation in each of these compounds. With these methods we found that the relative energy of the transition state (TS) was considerably higher, but with the ab initio method using RHF with minimal basic function STO-3G we found that the syn conformation is predicted to be slightly more stable. The determination of some atomic charges of a selection of atoms on the syn, anti and TS structures of the various compounds provided some details about the nature of the transition state.
Structural Transitions in Elemental Tin at Ultra High Pressures up to 230 GPa

NASA Astrophysics Data System (ADS)

Gavriliuk, A. G.; Troyan, I. A.; Ivanova, A. G.; Aksenov, S. N.; Starchikov, S. S.; Lyubutin, I. S.; Morgenroth, W.; Glazyrin, K. V.; Mezouar, M.

2017-12-01

The crystal structure of elemental Sn was investigated by synchrotron X-ray diffraction at ultra high pressures up to ˜230 GPa creating in diamond anvil cells. Above 70 GPa, a pure bcc structure of Sn was observed, which is stable up to 160GPa, until an occurrence of the hcp phase was revealed. At the onset of the bcc- hcp transition at pressure of about 160GPa, the drop of the unit cell volume is about 1%. A mixture of the bcc- hcp states was observed at least up to 230GPa, and it seems that this state could exist even up to higher pressures. The fractions of the bcc and hcp phases were evaluated in the pressure range of the phase coexistence 160-230 GPa. The difference between static and dynamic compression and its effect on the V- P phase diagram of Sn are discussed.
Pressure-driven insulator-metal transition in cubic phase UO2

NASA Astrophysics Data System (ADS)

Huang, Li; Wang, Yilin; Werner, Philipp

2017-09-01

Understanding the electronic properties of actinide oxides under pressure poses a great challenge for experimental and theoretical studies. Here, we investigate the electronic structure of cubic phase uranium dioxide at different volumes using a combination of density functional theory and dynamical mean-field theory. The ab initio calculations predict an orbital-selective insulator-metal transition at a moderate pressure of ∼45 GPa. At this pressure the uranium's 5f 5/2 state becomes metallic, while the 5f 7/2 state remains insulating up to about 60 GPa. In the metallic state, we observe a rapid decrease of the 5f occupation and total angular momentum with pressure. Simultaneously, the so-called “Zhang-Rice state”, which is of predominantly 5f 5/2 character, quickly disappears after the transition into the metallic phase.
Exploring telicity and transitivity in primordial thought language and body boundary imagery.

PubMed

Cariola, Laura A

2014-12-01

Linguistics research on 'unconscious knowledge' related to the right brain-hemisphere represents a shift from the prevalent scientific investigation of the linguistic processes of grammatical structures associated with the dominant 'verbal' left brain-hemisphere. This study explores the relationship among primordial thought language, body boundary awareness and syntactic features--i.e., telicity, perfectivity and transitivity-in autobiographical narratives of everyday and dream memories. The results showed that event descriptions with atelic predicates and intransitive structures were more frequent in dream recall than in narratives of everyday memories. Primordial thought language and body boundary awareness, however, decreased with atelic predicates and transitive structures, which might indicate both the tendency of events to describe result states, such as achievements and accomplishments, as a means to bring about an unconscious wish fulfilment and the emphasis on event arguments to be realised without the inclusion of an external object. In narratives of everyday memories, penetration imagery increased with imperfective verb forms and decreased with perfective verb forms, and emotion lexis increased with atelic predicates and transitive structures, but not in dream memories.
Magnetostructural Properties of Colossal Magnetoresistance Manganites Under External Magnetic Fields and Uniaxial Pressure

NASA Astrophysics Data System (ADS)

Kaplan, Michael; Zimmerman, George

2002-03-01

In the colossal magnetoresistance manganites the transport and magnetostructural properties are tightly connected [1,2]. Many magnetic field induced structural phase transitions and anomalous magnetoacoustical properties continue to be discovered in various manganite derivatives. Nevertheless the mechanism of structural transitions and microscopic theory of corresponding anomalous properties are still to be completely understood. Here we present a microscopic model of magnetic field and uniaxial pressure induced structural phase transitions in lightly doped manganites. The model is based on the cooperative Jahn-Teller effect which takes into account the Mn3+-ground doublet and excited triplet electronic states. Numerous calculations for different orientation magnetic field suggest the explanations of the origin of the structural transitions and of the measured magnetostriction data. The calculations for the two-sublattice antiferrodistortive crystals under uniaxial pressure support the idea of metaelasticity - a property typical for Jahn-Teller antiferroelastics. 1.Y. Tokura, ed. Colossal Magnetoresistance Oxides. Gordon & Breach, London, 2000. 2.M. Kaplan, G. Zimmerman, eds. Vibronic Interactions: Jahn-Teller Effect in Crystal and Molecules. NATO Science Series, Dordrecht/Boston/London, 2001
Exotic Structure of Carbon Isotopes

NASA Astrophysics Data System (ADS)

Suzuki, Toshio; Sagawa, Hiroyuki; Hagino, Kouichi

2003-12-01

Ground state properties of C isotopes, deformation and elecromagnetic moments, as well as electric dipole transition strength are investigated. We first study the ground state properties of C isotopes using a deformed Hartree-Fock (HF) + BCS model with Skyrme interactions. Isotope dependence of the deformation properties is investigated. Shallow deformation minima are found in several neutron-rich C isotopes. It is also shown that the deformation minima appear in both the oblate and the prolate sides in 17C and 19C having almost the same binding energies. Next, we carry out shell model calculations to study electromagnetic moments and electric dipole transitions of C isotopes. We point out the clear configuration dependence of the quadrupole and magnetic moments in the odd C isotopes, which will be useful to find out the deformation and spin-parities of the ground states of these nuclei. Electric dipole states of C isotopes are studied focusing on the interplay between low energy Pigmy strength and giant dipole resonances. Low peak energies, two-peak structure and large widths of the giant resonances show deformation effects. Calculated transition strength below dipole giant resonance in heavier C isotopes than 15C is found to exhaust 12 ~ 15% of the Thomas-Reiche-Kuhn sum rule value and 50 ~ 80% of the cluster sum rule value.
The nuclear magnetic moment of 208Bi and its relevance for a test of bound-state strong-field QED

NASA Astrophysics Data System (ADS)

Schmidt, S.; Billowes, J.; Bissell, M. L.; Blaum, K.; Garcia Ruiz, R. F.; Heylen, H.; Malbrunot-Ettenauer, S.; Neyens, G.; Nörtershäuser, W.; Plunien, G.; Sailer, S.; Shabaev, V. M.; Skripnikov, L. V.; Tupitsyn, I. I.; Volotka, A. V.; Yang, X. F.

2018-04-01

The hyperfine structure splitting in the 6p3 3/2 4S → 6p2 7 s 1/2 4P transition at 307 nm in atomic 208Bi was measured with collinear laser spectroscopy at ISOLDE, CERN. The hyperfine A and B factors of both states were determined with an order of magnitude improved accuracy. Based on these measurements, theoretical input for the hyperfine structure anomaly, and results from hyperfine measurements on hydrogen-like and lithium-like 209Bi80+,82+, the nuclear magnetic moment of 208Bi has been determined to μ (208Bi) = + 4.570 (10)μN. Using this value, the transition energy of the ground-state hyperfine splitting in hydrogen-like and lithium-like 208Bi80+,82+ and their specific difference of -67.491(5)(148) meV are predicted. This provides a means for an experimental confirmation of the cancellation of nuclear structure effects in the specific difference in order to exclude such contributions as the cause of the hyperfine puzzle, the recently reported 7-σ discrepancy between experiment and bound-state strong-field QED calculations of the specific difference in the hyperfine structure splitting of 209Bi80+,82+.
Human γ-Glutamyl Transpeptidase 1: STRUCTURES OF THE FREE ENZYME, INHIBITOR-BOUND TETRAHEDRAL TRANSITION STATES, AND GLUTAMATE-BOUND ENZYME REVEAL NOVEL MOVEMENT WITHIN THE ACTIVE SITE DURING CATALYSIS.

PubMed

Terzyan, Simon S; Burgett, Anthony W G; Heroux, Annie; Smith, Clyde A; Mooers, Blaine H M; Hanigan, Marie H

2015-07-10

γ-Glutamyl transpeptidase 1 (GGT1) is a cell surface, N-terminal nucleophile hydrolase that cleaves glutathione and other γ-glutamyl compounds. GGT1 expression is essential in cysteine homeostasis, and its induction has been implicated in the pathology of asthma, reperfusion injury, and cancer. In this study, we report four new crystal structures of human GGT1 (hGGT1) that show conformational changes within the active site as the enzyme progresses from the free enzyme to inhibitor-bound tetrahedral transition states and finally to the glutamate-bound structure prior to the release of this final product of the reaction. The structure of the apoenzyme shows flexibility within the active site. The serine-borate-bound hGGT1 crystal structure demonstrates that serine-borate occupies the active site of the enzyme, resulting in an enzyme-inhibitor complex that replicates the enzyme's tetrahedral intermediate/transition state. The structure of GGsTop-bound hGGT1 reveals its interactions with the enzyme and why neutral phosphonate diesters are more potent inhibitors than monoanionic phosphonates. These structures are the first structures for any eukaryotic GGT that include a molecule in the active site covalently bound to the catalytic Thr-381. The glutamate-bound structure shows the conformation of the enzyme prior to release of the final product and reveals novel information regarding the displacement of the main chain atoms that form the oxyanion hole and movement of the lid loop region when the active site is occupied. These data provide new insights into the mechanism of hGGT1-catalyzed reactions and will be invaluable in the development of new classes of hGGT1 inhibitors for therapeutic use. © 2015 by The American Society for Biochemistry and Molecular Biology, Inc.
Human γ-glutamyl transpeptidase 1: Structures of the free enzyme, inhibitor-bound tetrahedral transition states, and glutamate-bound enzyme reveal novel movement within the active site during catalysis [Human gamma-glutamyl transpeptidase: Inhibitor binding and movement within the active site

DOE PAGES

Terzyan, Simon S.; Burgett, Anthony W. G.; Heroux, Annie; ...

2015-05-26

γ-Glutamyl transpeptidase 1 (GGT1) is a cell surface, N-terminal nucleophile hydrolase that cleaves glutathione and other γ-glutamyl compounds. GGT1 expression is essential in cysteine homeostasis, and its induction has been implicated in the pathology of asthma, reperfusion injury, and cancer. In this study, we report four new crystal structures of human GGT1 (hGGT1) that show conformational changes within the active site as the enzyme progresses from the free enzyme to inhibitor-bound tetrahedral transition states and finally to the glutamate-bound structure prior to the release of this final product of the reaction. The structure of the apoenzyme shows flexibility within themore » active site. The serine-borate-bound hGGT1 crystal structure demonstrates that serine-borate occupies the active site of the enzyme, resulting in an enzyme-inhibitor complex that replicates the enzyme's tetrahedral intermediate/transition state. The structure of GGsTop-bound hGGT1 reveals its interactions with the enzyme and why neutral phosphonate diesters are more potent inhibitors than monoanionic phosphonates. These structures are the first structures for any eukaryotic GGT that include a molecule in the active site covalently bound to the catalytic Thr-381. The glutamate-bound structure shows the conformation of the enzyme prior to release of the final product and reveals novel information regarding the displacement of the main chain atoms that form the oxyanion hole and movement of the lid loop region when the active site is occupied. Lastly,tThese data provide new insights into the mechanism of hGGT1-catalyzed reactions and will be invaluable in the development of new classes of hGGT1 inhibitors for therapeutic use.« less
Human γ-glutamyl transpeptidase 1: Structures of the free enzyme, inhibitor-bound tetrahedral transition states, and glutamate-bound enzyme reveal novel movement within the active site during catalysis [Human gamma-glutamyl transpeptidase: Inhibitor binding and movement within the active site

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

Terzyan, Simon S.; Burgett, Anthony W. G.; Heroux, Annie

γ-Glutamyl transpeptidase 1 (GGT1) is a cell surface, N-terminal nucleophile hydrolase that cleaves glutathione and other γ-glutamyl compounds. GGT1 expression is essential in cysteine homeostasis, and its induction has been implicated in the pathology of asthma, reperfusion injury, and cancer. In this study, we report four new crystal structures of human GGT1 (hGGT1) that show conformational changes within the active site as the enzyme progresses from the free enzyme to inhibitor-bound tetrahedral transition states and finally to the glutamate-bound structure prior to the release of this final product of the reaction. The structure of the apoenzyme shows flexibility within themore » active site. The serine-borate-bound hGGT1 crystal structure demonstrates that serine-borate occupies the active site of the enzyme, resulting in an enzyme-inhibitor complex that replicates the enzyme's tetrahedral intermediate/transition state. The structure of GGsTop-bound hGGT1 reveals its interactions with the enzyme and why neutral phosphonate diesters are more potent inhibitors than monoanionic phosphonates. These structures are the first structures for any eukaryotic GGT that include a molecule in the active site covalently bound to the catalytic Thr-381. The glutamate-bound structure shows the conformation of the enzyme prior to release of the final product and reveals novel information regarding the displacement of the main chain atoms that form the oxyanion hole and movement of the lid loop region when the active site is occupied. Lastly,tThese data provide new insights into the mechanism of hGGT1-catalyzed reactions and will be invaluable in the development of new classes of hGGT1 inhibitors for therapeutic use.« less
Optical properties of InAs/GaAs quantum dot superlattice structures

NASA Astrophysics Data System (ADS)

Imran, Ali; Jiang, Jianliang; Eric, Deborah; Zahid, M. Noaman; Yousaf, M.; Shah, Z. H.

2018-06-01

Quantum dot (QD) structure has potential applications in modern highly efficient optoelectronic devices due to their band-tuning. The device dimensions have been miniatured with increased efficiencies by virtue of this discovery. In this research, we have presented modified analytical and simulation results of InAs/GaAs QD superlattice (QDSL). We have applied tight binding model for the investigation of ground state energies using timeindependent Schrödinger equation (SE) with effective mass approximation. It has been investigated that the electron energies are confined due to wave function delocalization in closely coupled QD structures. The minimum ground state energy can be obtained by increasing the periodicity and decreasing the barrier layer thickness. We have calculated electronics and optical properties which includes ground state energies, transition energies, density of states (DOS), absorption coefficient and refractive index, which can be tuned by structure modification. In our results, the minimum ground state energy of QDSL is achieved to be 0.25 eV with a maximum period of 10 QDs. The minimum band to band and band to continuum transition energies are 63 meV and 130 meV with 2 nm barrier layer thickness respectively. The absorption coefficient of our proposed QDSL model is found to be maximum 1.2 × 104 cm-1 and can be used for highly sensitive infrared detector and high efficiency solar cells.
Ionic and Covalent Stabilization of Intermediates and Transition States in Catalysis by Solid Acids

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

Deshlahra, Prashant; Carr, Robert T.; Iglesia, Enrique

Reactivity descriptors describe catalyst properties that determine the stability of kinetically relevant transition states and adsorbed intermediates. Theoretical descriptors, such as deprotonation energies (DPE), rigorously account for Brønsted acid strength for catalytic solids with known structure. Here, mechanistic interpretations of methanol dehydration turnover rates are used to assess how charge reorganization (covalency) and electrostatic interactions determine DPE and how such interactions are recovered when intermediates and transition states interact with the conjugate anion in W and Mo polyoxometalate (POM) clusters and gaseous mineral acids. Turnover rates are lower and kinetically relevant species are less stable on Mo than W POMmore » clusters with similar acid strength, and such species are more stable on mineral acids than that predicted from W-POM DPE–reactivity trends, indicating that DPE and acid strength are essential but incomplete reactivity descriptors. Born–Haber thermochemical cycles indicate that these differences reflect more effective charge reorganization upon deprotonation of Mo than W POM clusters and the much weaker reorganization in mineral acids. Such covalency is disrupted upon deprotonation but cannot be recovered fully upon formation of ion pairs at transition states. Predictive descriptors of reactivity for general classes of acids thus require separate assessments of the covalent and ionic DPE components. Here, we describe methods to estimate electrostatic interactions, which, taken together with energies derived from density functional theory, give the covalent and ionic energy components of protons, intermediates, and transition states. In doing so, we provide a framework to predict the reactive properties of protons for chemical reactions mediated by ion-pair transition states.« less
Sampling the multiple folding mechanisms of Trp-cage in explicit solvent

PubMed Central

Juraszek, J.; Bolhuis, P. G.

2006-01-01

We investigate the kinetic pathways of folding and unfolding of the designed miniprotein Trp- cage in explicit solvent. Straightforward molecular dynamics and replica exchange methods both have severe convergence problems, whereas transition path sampling allows us to sample unbiased dynamical pathways between folded and unfolded states and leads to deeper understanding of the mechanisms of (un)folding. In contrast to previous predictions employing an implicit solvent, we find that Trp-cage folds primarily (80% of the paths) via a pathway forming the tertiary contacts and the salt bridge, before helix formation. The remaining 20% of the paths occur in the opposite order, by first forming the helix. The transition states of the rate-limiting steps are solvated native-like structures. Water expulsion is found to be the last step upon folding for each route. Committor analysis suggests that the dynamics of the solvent is not part of the reaction coordinate. Nevertheless, during the transition, specific water molecules are strongly bound and can play a structural role in the folding. PMID:17035504
The Effect of SiC Polytypes on the Heat Distribution Efficiency of a Phase Change Memory.

NASA Astrophysics Data System (ADS)

Aziz, M. S.; Mohammed, Z.; Alip, R. I.

2018-03-01

The amorphous to crystalline transition of germanium-antimony-tellurium (GST) using three types of silicon carbide’s structure as a heating element was investigated. Simulation was done using COMSOL Multiphysic 5.0 software with separate heater structure. Silicon carbide (SiC) has three types of structure; 3C-SiC, 4H-SiC and 6H-SiC. These structures have a different thermal conductivity. The temperature of GST and phase transition of GST can be obtained from the simulation. The temperature of GST when using 3C-SiC, 4H-SiC and 6H-SiC are 467K, 466K and 460K, respectively. The phase transition of GST from amorphous to crystalline state for three type of SiC’s structure can be determined in this simulation. Based on the result, the thermal conductivity of SiC can affecting the temperature of GST and changed of phase change memory (PCM).
Enhanced doping effect on tuning structural phases of monolayer antimony

NASA Astrophysics Data System (ADS)

Wang, Jizhang; Yang, Teng; Zhang, Zhidong; Yang, Li

2018-05-01

Doping is capable to control the atomistic structure, electronic structure, and even to dynamically realize a semiconductor-metal transition in two-dimensional (2D) transition metal dichalcogenides (TMDs). However, the high critical doping density (˜1014 electron/cm2), compound nature, and relatively low carrier mobility of TMDs limits broader applications. Using first-principles calculations, we predict that, via a small transition potential, a substantially lower hole doping density (˜6 × 1012 hole/cm2) can switch the ground-state structure of monolayer antimony from the hexagonal β-phase, a 2D semiconductor with excellent transport performance and air stability but an indirect bandgap, to the orthorhombic α phase with a direct bandgap and potentially better carrier mobility. We further show that this structural engineering can be achieved by the established electrostatic doping, surface functional adsorption, or directly using graphene substrate. This gives hope to dynamically tuning and large-scale production of 2D single-element semiconductors that simultaneously exhibit remarkable transport and optical performance.
Quantum Engineering of States in Heterostructure-based Detectors for Enhance Performance

DTIC Science & Technology

2017-05-26

excited carrier contribution in these heterostructure- based photodetectors has been reduced by using phonon-assisted transitions to design structures ...experimental investigations of nanostructure- based electronic and optoelectronic structures with the goal of facilitating major improvements in the performance...nanostructures. Quantum engineering of nano- structures is emphasized. Related quantum- based structures – including those with spontaneous polarizations are
A thermodynamic equation of jamming

NASA Astrophysics Data System (ADS)

Lu, Kevin; Pirouz Kavehpour, H.

2008-03-01

Materials ranging from sand to fire-retardant to toothpaste are considered fragile, able to exhibit both solid and fluid-like properties across the jamming transition. Guided by granular flow experiments, our equation of jammed states is path-dependent, definable at different athermal equilibrium states. The non-equilibrium thermodynamics based on a structural temperature incorporate physical ageing to address the non-exponential, non-Arrhenious relaxation of granular flows. In short, jamming is simply viewed as a thermodynamic transition that occurs to preserve a positive configurational entropy above absolute zero. Without any free parameters, the proposed equation-of-state governs the mechanism of shear-banding and the associated features of shear-softening and thickness-invariance.
Magnetic order and electronic structure of 5d 3 double perovskite Sr 2ScOsO 6

DOE PAGES

Taylor, A. E.; Morrow, R.; Singh, D. J.; ...

2015-03-01

The magnetic susceptibility, crystal and magnetic structures, and electronic structure of double perovskite Sr 2ScOsO 6 are reported. Using both neutron and x-ray powder diffraction we find that the crystal structure is monoclinic P21/n from 3.5 to 300 K. Magnetization measurements indicate an antiferromagnetic transition at TN=92 K, one of the highest transition temperatures of any double perovskite hosting only one magnetic ion. Type I antiferromagnetic order is determined by neutron powder diffraction, with an Os moment of only 1.6(1) muB, close to half the spin-only value for a crystal field split 5d electron state with t2g^3 ground state. Densitymore » functional calculations show that this reduction is largely the result of strong Os-O hybridization, with spin-orbit coupling responsible for only a ~0.1 muB reduction in the moment.« less
Weyl Semimetal to Metal Phase Transitions Driven by Quasiperiodic Potentials

NASA Astrophysics Data System (ADS)

Pixley, J. H.; Wilson, Justin H.; Huse, David A.; Gopalakrishnan, Sarang

2018-05-01

We explore the stability of three-dimensional Weyl and Dirac semimetals subject to quasiperiodic potentials. We present numerical evidence that the semimetal is stable for weak quasiperiodic potentials, despite being unstable for weak random potentials. As the quasiperiodic potential strength increases, the semimetal transitions to a metal, then to an "inverted" semimetal, and then finally to a metal again. The semimetal and metal are distinguished by the density of states at the Weyl point, as well as by level statistics, transport, and the momentum-space structure of eigenstates near the Weyl point. The critical properties of the transitions in quasiperiodic systems differ from those in random systems: we do not find a clear critical scaling regime in energy; instead, at the quasiperiodic transitions, the density of states appears to jump abruptly (and discontinuously to within our resolution).

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