phase transition pathways: Topics by Science.gov

Sample records for phase transition pathways

Mechanism and microstructures in Ga2O3 pseudomartensitic solid phase transition.

PubMed

Zhu, Sheng-Cai; Guan, Shu-Hui; Liu, Zhi-Pan

2016-07-21

Solid-to-solid phase transition, although widely exploited in making new materials, challenges persistently our current theory for predicting its complex kinetics and rich microstructures in transition. The Ga2O3α-β phase transformation represents such a common but complex reaction with marked change in cation coordination and crystal density, which was known to yield either amorphous or crystalline products under different synthetic conditions. Here we, via recently developed stochastic surface walking (SSW) method, resolve for the first time the atomistic mechanism of Ga2O3α-β phase transformation, the pathway of which turns out to be the first reaction pathway ever determined for a new type of diffusionless solid phase transition, namely, pseudomartensitic phase transition. We demonstrate that the sensitivity of product crystallinity is caused by its multi-step, multi-type reaction pathway, which bypasses seven intermediate phases and involves all types of elementary solid phase transition steps, i.e. the shearing of O layers (martensitic type), the local diffusion of Ga atoms (reconstructive type) and the significant lattice dilation (dilation type). While the migration of Ga atoms across the close-packed O layers is the rate-determining step and yields "amorphous-like" high energy intermediates, the shearing of O layers contributes to the formation of coherent biphase junctions and the presence of a crystallographic orientation relation, (001)α//(201[combining macron])β + [120]α//[13[combining macron]2]β. Our experiment using high-resolution transmission electron microscopy further confirms the theoretical predictions on the atomic structure of biphase junction and the formation of (201[combining macron])β twin, and also discovers the late occurrence of lattice expansion in the nascent β phase that grows out from the parent α phase. By distinguishing pseudomartensitic transition from other types of mechanisms, we propose general rules to predict the product crystallinity of solid phase transition. The new knowledge on the kinetics of pseudomartensitic transition complements the theory of diffusionless solid phase transition.
Growth Substrate- and Phase-Specific Expression of Biphenyl, Benzoate, and C1 Metabolic Pathways in Burkholderia xenovorans LB400

PubMed Central

Denef, V. J.; Patrauchan, M. A.; Florizone, C.; Park, J.; Tsoi, T. V.; Verstraete, W.; Tiedje, J. M.; Eltis, L. D.

2005-01-01

Recent microarray experiments suggested that Burkholderia xenovorans LB400, a potent polychlorinated biphenyl (PCB)-degrading bacterium, utilizes up to three apparently redundant benzoate pathways and a C1 metabolic pathway during biphenyl and benzoate metabolism. To better characterize the roles of these pathways, we performed quantitative proteome profiling of cells grown on succinate, benzoate, or biphenyl and harvested during either mid-logarithmic growth or the transition between the logarithmic and stationary growth phases. The Bph enzymes, catabolizing biphenyl, were ∼16-fold more abundant in biphenyl- versus succinate-grown cells. Moreover, the upper and lower bph pathways were independently regulated. Expression of each benzoate pathway depended on growth substrate and phase. Proteins specifying catabolism via benzoate dihydroxylation and catechol ortho-cleavage (ben-cat pathway) were approximately an order of magnitude more abundant in benzoate- versus biphenyl-grown cells at the same growth phase. The chromosomal copy of the benzoyl-coenzyme A (CoA) (boxC) pathway was also expressed during growth on biphenyl: BoxC proteins were approximately twice as abundant as Ben and Cat proteins under these conditions. By contrast, proteins of the megaplasmid copy of the benzoyl-CoA (boxM) pathway were only detected in transition-phase benzoate-grown cells. Other proteins detected at increased levels in benzoate- and biphenyl-grown cells included general stress response proteins potentially induced by reactive oxygen species formed during aerobic aromatic catabolism. Finally, C1 metabolic enzymes were present in biphenyl-grown cells during transition phase. This study provides insights into the physiological roles and integration of apparently redundant catabolic pathways in large-genome bacteria and establishes a basis for investigating the PCB-degrading abilities of this strain. PMID:16291673
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.
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.
Order parameter aided efficient phase space exploration under extreme conditions

NASA Astrophysics Data System (ADS)

Samanta, Amit

Physical processes in nature exhibit disparate time-scales, for example time scales associated with processes like phase transitions, various manifestations of creep, sintering of particles etc. are often much higher than time the system spends in the metastable states. The transition times associated with such events are also orders of magnitude higher than time-scales associated with vibration of atoms. Thus, an atomistic simulation of such transition events is a challenging task. Consequently, efficient exploration of configuration space and identification of metastable structures in condensed phase systems is challenging. In this talk I will illustrate how we can define a set of coarse-grained variables or order parameters and use these to systematically and efficiently steer a system containing thousands or millions of atoms over different parts of the configuration. This order parameter aided sampling can be used to identify metastable states, transition pathways and understand the mechanistic details of complex transition processes. I will illustrate how this sampling scheme can be used to study phase transition pathways and phase boundaries in prototypical materials, like SiO2 and Cu under high-pressure conditions. This work was performed under the auspices of the U.S. Department of Energy by Lawrence Livermore National Laboratory under Contract DE-AC52-07NA27344.
Phase Transition between Black and Blue Phosphorenes: A Quantum Monte Carlo Study

NASA Astrophysics Data System (ADS)

Li, Lesheng; Yao, Yi; Reeves, Kyle; Kanai, Yosuke

Phase transition of the more common black phosphorene to blue phosphorene is of great interest because they are predicted to exhibit unique electronic and optical properties. However, these two phases are predicted to be separated by a rather large energy barrier. In this work, we study the transition pathway between black and blue phosphorenes by using the variable cell nudge elastic band method combined with density functional theory calculation. We show how diffusion quantum Monte Carlo method can be used for determining the energetics of the phase transition and demonstrate the use of two approaches for removing finite-size errors. Finally, we predict how applied stress can be used to control the energetic balance between these two different phases of phosphorene.
Beyond "NEET" and "Tidy" Pathways: Considering the "Missing Middle" of Youth Transition Studies

ERIC Educational Resources Information Center

Roberts, Steven

2011-01-01

Jones' (2002) discussion of polarised transitions and the "fast and slow lanes to adulthood" espoused by Bynner "et al." (2002) are good examples of how dualistic language often permeates youth transitions discourses. This often results in transitions research concentrating on a dichotomy of experience during the youth phase.…
Nonequilibrium Phase Transitions in Supercooled Water

NASA Astrophysics Data System (ADS)

Limmer, David; Chandler, David

2012-02-01

We present results of a simulation study of water driven out of equilibrium. Using transition path sampling, we can probe stationary path distributions parameterize by order parameters that are extensive in space and time. We find that by coupling external fields to these parameters, we can drive water through a first order dynamical phase transition into amorphous ice. By varying the initial equilibrium distributions we can probe pathways for the creation of amorphous ices of low and high densities.
Reversible structure manipulation by tuning carrier concentration in metastable Cu2S

PubMed Central

Tao, Jing; Chen, Jingyi; Li, Jun; Mathurin, Leanne; Zheng, Jin-Cheng; Li, Yan; Lu, Deyu; Cao, Yue; Wu, Lijun; Cava, Robert Joseph; Zhu, Yimei

2017-01-01

The optimal functionalities of materials often appear at phase transitions involving simultaneous changes in the electronic structure and the symmetry of the underlying lattice. It is experimentally challenging to disentangle which of the two effects––electronic or structural––is the driving force for the phase transition and to use the mechanism to control material properties. Here we report the concurrent pumping and probing of Cu2S nanoplates using an electron beam to directly manipulate the transition between two phases with distinctly different crystal symmetries and charge-carrier concentrations, and show that the transition is the result of charge generation for one phase and charge depletion for the other. We demonstrate that this manipulation is fully reversible and nonthermal in nature. Our observations reveal a phase-transition pathway in materials, where electron-induced changes in the electronic structure can lead to a macroscopic reconstruction of the crystal structure. PMID:28855335
Metastable phase transformation and hcp-ω transformation pathways in Ti and Zr under high hydrostatic pressures

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

Gao, Lei; Ding, Xiangdong, E-mail: dingxd@mail.xjtu.edu.cn, E-mail: ekhard@esc.cam.ac.uk; Sun, Jun

2016-07-18

The energy landscape of Zr at high hydrostatic pressure suggests that its transformation behavior is strongly pressure dependent. This is in contrast to the known transition mechanism in Ti, which is essentially independent of hydrostatic pressure. Generalized solid-state nudged elastic band calculations at constant pressure shows that α-Zr transforms like Ti only at the lowest pressure inside the stability field of ω-phase. Different pathways apply at higher pressures where the energy landscape contains several high barriers so that metastable states are expected, including the appearance of a transient bcc phase at ca. 23 GPa. The global driving force for the hcp-ωmore » transition increases strongly with increasing pressure and reaches 23.7 meV/atom at 23 GPa. Much of this energy relates to the excess volume of the hcp phase compared with its ω phase.« less
Imaging Nanometer Phase Coexistence at Defects During the Insulator-Metal Phase Transformation in VO2 Thin Films by Resonant Soft X-ray Holography.

PubMed

Vidas, Luciana; Günther, Christian M; Miller, Timothy A; Pfau, Bastian; Perez-Salinas, Daniel; Martínez, Elías; Schneider, Michael; Gührs, Erik; Gargiani, Pierluigi; Valvidares, Manuel; Marvel, Robert E; Hallman, Kent A; Haglund, Richard F; Eisebitt, Stefan; Wall, Simon

2018-05-18

We use resonant soft X-ray holography to image the insulator-metal phase transition in vanadium dioxide with element and polarization specificity and nanometer spatial resolution. We observe that nanoscale inhomogeneity in the film results in spatial-dependent transition pathways between the insulating and metallic states. Additional nanoscale phases form in the vicinity of defects which are not apparent in the initial or final states of the system, which would be missed in area-integrated X-ray absorption measurements. These intermediate phases are vital to understand the phase transition in VO 2 , and our results demonstrate how resonant imaging can be used to understand the electronic properties of phase-separated correlated materials obtained by X-ray absorption.
Identification of pathways directly regulated by SHORT VEGETATIVE PHASE during vegetative and reproductive development in Arabidopsis

PubMed Central

2013-01-01

Background MADS-domain transcription factors play important roles during plant development. The Arabidopsis MADS-box gene SHORT VEGETATIVE PHASE (SVP) is a key regulator of two developmental phases. It functions as a repressor of the floral transition during the vegetative phase and later it contributes to the specification of floral meristems. How these distinct activities are conferred by a single transcription factor is unclear, but interactions with other MADS domain proteins which specify binding to different genomic regions is likely one mechanism. Results To compare the genome-wide DNA binding profile of SVP during vegetative and reproductive development we performed ChIP-seq analyses. These ChIP-seq data were combined with tiling array expression analysis, induction experiments and qRT-PCR to identify biologically relevant binding sites. In addition, we compared genome-wide target genes of SVP with those published for the MADS domain transcription factors FLC and AP1, which interact with SVP during the vegetative and reproductive phases, respectively. Conclusions Our analyses resulted in the identification of pathways that are regulated by SVP including those controlling meristem development during vegetative growth and flower development whereas floral transition pathways and hormonal signaling were regulated predominantly during the vegetative phase. Thus, SVP regulates many developmental pathways, some of which are common to both of its developmental roles whereas others are specific to only one of them. PMID:23759218
Digital gene expression analysis of male and female bud transition in Metasequoia reveals high activity of MADS-box transcription factors and hormone-mediated sugar pathways.

PubMed

Zhao, Ying; Liang, Haiying; Li, Lan; Tang, Sha; Han, Xiao; Wang, Congpeng; Xia, Xinli; Yin, Weilun

2015-01-01

Metasequoia glyptostroboides is a famous redwood tree of ecological and economic importance, and requires more than 20 years of juvenile-to-adult transition before producing female and male cones. Previously, we induced reproductive buds using a hormone solution in juvenile Metasequoia trees as young as 5-to-7 years old. In the current study, hormone-treated shoots found in female and male buds were used to identify candidate genes involved in reproductive bud transition in Metasequoia. Samples from hormone-treated cone reproductive shoots and naturally occurring non-cone setting shoots were analyzed using 24 digital gene expression (DGE) tag profiles using Illumina, generating a total of 69,520 putative transcripts. Next, 32 differentially and specifically expressed transcripts were determined using quantitative real-time polymerase chain reaction, including the upregulation of MADS-box transcription factors involved in male bud transition and flowering time control proteins involved in female bud transition. These differentially expressed transcripts were associated with 243 KEGG pathways. Among the significantly changed pathways, sugar pathways were mediated by hormone signals during the vegetative-to-reproductive phase transition, including glycolysis/gluconeogenesis and sucrose and starch metabolism pathways. Key enzymes were identified in these pathways, including alcohol dehydrogenase (NAD) and glutathione dehydrogenase for the glycolysis/gluconeogenesis pathway, and glucanphosphorylase for sucrose and starch metabolism pathways. Our results increase our understanding of the reproductive bud transition in gymnosperms. In addition, these studies on hormone-mediated sugar pathways increase our understanding of the relationship between sugar and hormone signaling during female and male bud initiation in Metasequoia.
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.
New pathway for the formation of metallic cubic phase Ge-Sb-Te compounds induced by an electric current

PubMed Central

Park, Yong-Jin; Cho, Ju-Young; Jeong, Min-Woo; Na, Sekwon; Joo, Young-Chang

2016-01-01

The novel discovery of a current-induced transition from insulator to metal in the crystalline phase of Ge2Sb2Te5 and GeSb4Te7 have been studied by means of a model using line-patterned samples. The resistivity of cubic phase Ge-Sb-Te compound was reduced by an electrical current (~1 MA/cm2), and the final resistivity was determined based on the stress current density, regardless of the initial resistivity and temperature, which indicates that the conductivity of Ge-Sb-Te compound can be modulated by an electrical current. The minimum resistivity of Ge-Sb-Te materials can be achieved at high kinetic rates by applying an electrical current, and the material properties change from insulating to metallic behavior without a phase transition. The current-induced metal transition is more effective in GeSb4Te7 than Ge2Sb2Te5, which depends on the intrinsic vacancy of materials. Electromigration, which is the migration of atoms induced by a momentum transfer from charge carriers, can easily promote the rearrangement of vacancies in the cubic phase of Ge-Sb-Te compound. This behavior differs significantly from thermal annealing, which accompanies a phase transition to the hexagonal phase. This result suggests a new pathway for modulating the electrical conductivity and material properties of chalcogenide materials by applying an electrical current. PMID:26902593
Digital gene expression analysis of male and female bud transition in Metasequoia reveals high activity of MADS-box transcription factors and hormone-mediated sugar pathways

PubMed Central

Zhao, Ying; Liang, Haiying; Li, Lan; Tang, Sha; Han, Xiao; Wang, Congpeng; Xia, Xinli; Yin, Weilun

2015-01-01

Metasequoia glyptostroboides is a famous redwood tree of ecological and economic importance, and requires more than 20 years of juvenile-to-adult transition before producing female and male cones. Previously, we induced reproductive buds using a hormone solution in juvenile Metasequoia trees as young as 5-to-7 years old. In the current study, hormone-treated shoots found in female and male buds were used to identify candidate genes involved in reproductive bud transition in Metasequoia. Samples from hormone-treated cone reproductive shoots and naturally occurring non-cone setting shoots were analyzed using 24 digital gene expression (DGE) tag profiles using Illumina, generating a total of 69,520 putative transcripts. Next, 32 differentially and specifically expressed transcripts were determined using quantitative real-time polymerase chain reaction, including the upregulation of MADS-box transcription factors involved in male bud transition and flowering time control proteins involved in female bud transition. These differentially expressed transcripts were associated with 243 KEGG pathways. Among the significantly changed pathways, sugar pathways were mediated by hormone signals during the vegetative-to-reproductive phase transition, including glycolysis/gluconeogenesis and sucrose and starch metabolism pathways. Key enzymes were identified in these pathways, including alcohol dehydrogenase (NAD) and glutathione dehydrogenase for the glycolysis/gluconeogenesis pathway, and glucanphosphorylase for sucrose and starch metabolism pathways. Our results increase our understanding of the reproductive bud transition in gymnosperms. In addition, these studies on hormone-mediated sugar pathways increase our understanding of the relationship between sugar and hormone signaling during female and male bud initiation in Metasequoia. PMID:26157452
Application of the string method to the study of critical nuclei in capillary condensation.

PubMed

Qiu, Chunyin; Qian, Tiezheng; Ren, Weiqing

2008-10-21

We adopt a continuum description for liquid-vapor phase transition in the framework of mean-field theory and use the string method to numerically investigate the critical nuclei for capillary condensation in a slit pore. This numerical approach allows us to determine the critical nuclei corresponding to saddle points of the grand potential function in which the chemical potential is given in the beginning. The string method locates the minimal energy path (MEP), which is the most probable transition pathway connecting two metastable/stable states in configuration space. From the MEP, the saddle point is determined and the corresponding energy barrier also obtained (for grand potential). Moreover, the MEP shows how the new phase (liquid) grows out of the old phase (vapor) along the most probable transition pathway, from the birth of a critical nucleus to its consequent expansion. Our calculations run from partial wetting to complete wetting with a variable strength of attractive wall potential. In the latter case, the string method presents a unified way for computing the critical nuclei, from film formation at solid surface to bulk condensation via liquid bridge. The present application of the string method to the numerical study of capillary condensation shows the great power of this method in evaluating the critical nuclei in various liquid-vapor phase transitions.
B1-B2 phase transition mechanism and pathway of PbS under pressure

NASA Astrophysics Data System (ADS)

Adeleke, Adebayo A.; Yao, Yansun

2018-03-01

Experimental studies at finite Pressure-Temperature (P-T) conditions and a theoretical study at 0 K of the phase transition in lead sulphide (PbS) have been inconclusive. Many studies that have been done to understand structural transformation in PbS can broadly be classified into two main ideological streams—one with Pnma and another with Cmcm orthorhombic intermediate phase. To foster better understanding of this phenomenon, we present the result of the first-principles study of phase transition in PbS at finite temperature. We employed the particle swarm-intelligence optimization algorithm for the 0 K structure search and first-principles metadynamics simulations to study the phase transition pathway of PbS from the ambient pressure, 0 K Fm-3m structure to the high-pressure Pm-3m phase under experimentally achievable P-T conditions. Significantly, our calculation shows that both streams are achievable under specific P-T conditions. We further uncover new tetragonal and monoclinic structures of PbS with space group P21/c and I41/amd, respectively. We propose the P21/c and I41/amd as a precursor phase to the Pnma and Cmcm phases, respectively. We investigated the stability of the new structures and found them to be dynamically stable at their stability pressure range. Electronic structure calculations reveal that both P21/c and I41/amd phases are semiconducting with direct and indirect bandgap energies of 0.69(5) eV and 0.97(3) eV, respectively. In general, both P21/c and I41/amd phases were found to be energetically competitive with their respective orthorhombic successors.
Induction of DREB2A pathway with repression of E2F, Jasmonic acid biosynthetic and photosynthesis pathways in cold acclimation specific freeze resistant wheat crown

USDA-ARS?s Scientific Manuscript database

Winter wheat lines can achieve cold acclimation (development of tolerance to freezing temperatures) and vernalization (delay in transition from vegetative to reproductive phase) in response to low non-freezing temperatures. To describe cold acclimation specific processes and pathways, we utilized co...
Structures of two intermediate phases between the B1 and B2 phases of PbS under high pressure

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

Li, Yanchun, E-mail: liyc@ihep.ac.cn, E-mail: liuj@ihep.ac.cn; Lin, Chuanlong; Li, Xiaodong

2014-12-15

The structural transitions of PbS were investigated at pressures up to 50 GPa using synchrotron powder and single crystal X-ray diffraction (XRD) methods in diamond anvil cells. We found two intermediate phases between the B1 phase under atmospheric pressure and the B2 phase at 21.1 GPa, which is different to previous reports. The structures of these two intermediate phases were indexed as B27 and B33, respectively. Their structural parameters were investigated using density functional theory (DFT) calculations. Our results provide a new insight into understanding the transition pathway between the B1 and B2 phases in PbS.

Self-catalyzed growth of S layers via an amorphous-to-crystalline transition limited by folding kinetics.

PubMed

Chung, Sungwook; Shin, Seong-Ho; Bertozzi, Carolyn R; De Yoreo, James J

2010-09-21

The importance of nonclassical, multistage crystallization pathways is increasingly evident from theoretical studies on colloidal systems and experimental investigations of proteins and biomineral phases. Although theoretical predictions suggest that proteins follow these pathways as a result of fluctuations that create unstable dense-liquid states, microscopic studies indicate these states are long-lived. Using in situ atomic force microscopy to follow 2D assembly of S-layer proteins on supported lipid bilayers, we have obtained a molecular-scale picture of multistage protein crystallization that reveals the importance of conformational transformations in directing the pathway of assembly. We find that monomers with an extended conformation first form a mobile adsorbed phase, from which they condense into amorphous clusters. These clusters undergo a phase transition through S-layer folding into crystalline clusters composed of compact tetramers. Growth then proceeds by formation of new tetramers exclusively at cluster edges, implying tetramer formation is autocatalytic. Analysis of the growth kinetics leads to a quantitative model in which tetramer creation is rate limiting. However, the estimated barrier is much smaller than expected for folding of isolated S-layer proteins, suggesting an energetic rationale for this multistage pathway.
Imaging metal-like monoclinic phase stabilized by surface coordination effect in vanadium dioxide nanobeam

PubMed Central

Li, Zejun; Wu, Jiajing; Hu, Zhenpeng; Lin, Yue; Chen, Qi; Guo, Yuqiao; Liu, Yuhua; Zhao, Yingcheng; Peng, Jing; Chu, Wangsheng; Wu, Changzheng; Xie, Yi

2017-01-01

In correlated systems, intermediate states usually appear transiently across phase transitions even at the femtosecond scale. It therefore remains an open question how to determine these intermediate states—a critical issue for understanding the origin of their correlated behaviour. Here we report a surface coordination route to successfully stabilize and directly image an intermediate state in the metal-insulator transition of vanadium dioxide. As a prototype metal-insulator transition material, we capture an unusual metal-like monoclinic phase at room temperature that has long been predicted. Coordinate bonding of L-ascorbic acid molecules with vanadium dioxide nanobeams induces charge-carrier density reorganization and stabilizes metallic monoclinic vanadium dioxide, unravelling orbital-selective Mott correlation for gap opening of the vanadium dioxide metal–insulator transition. Our study contributes to completing phase-evolution pathways in the metal-insulator transition process, and we anticipate that coordination chemistry may be a powerful tool for engineering properties of low-dimensional correlated solids. PMID:28613281
Kinetically-Driven Phase Transformation during Lithiation in Copper Sulfide Nanoflakes

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

He, Kai; Yao, Zhenpeng; Hwang, Sooyeon

Two-dimensional (2D) transition metal chalcogenides have been widely studied and utilized as electrode materials for lithium ion batteries due to their unique layered structures to accommodate reversible lithium insertion. Real-time observation and mechanistic understanding of the phase transformations during lithiation of these materials are critically important for improving battery performance by controlling structures and reaction pathways. Here, we use in situ transmission electron microscopy methods to study the structural, morphological, and chemical evolutions in individual copper sulfide (CuS) nanoflakes during lithiation. We report a highly kinetically driven phase transformation in which lithium ions rapidly intercalate into the 2D van dermore » Waals-stacked interlayers in the initial stage, and further lithiation induces the Cu extrusion via a displacement reaction mechanism that is different from the typical conversion reactions. Density functional theory calculations have confirmed both the thermodynamically favored and the kinetically driven reaction pathways. Lastly, our findings elucidate the reaction pathways of the Li/CuS system under nonequilibrium conditions and provide valuable insight into the atomistic lithiation mechanisms of transition metal sulfides in general.« less
Kinetically-Driven Phase Transformation during Lithiation in Copper Sulfide Nanoflakes

DOE PAGES

He, Kai; Yao, Zhenpeng; Hwang, Sooyeon; ...

2017-08-11

Two-dimensional (2D) transition metal chalcogenides have been widely studied and utilized as electrode materials for lithium ion batteries due to their unique layered structures to accommodate reversible lithium insertion. Real-time observation and mechanistic understanding of the phase transformations during lithiation of these materials are critically important for improving battery performance by controlling structures and reaction pathways. Here, we use in situ transmission electron microscopy methods to study the structural, morphological, and chemical evolutions in individual copper sulfide (CuS) nanoflakes during lithiation. We report a highly kinetically driven phase transformation in which lithium ions rapidly intercalate into the 2D van dermore » Waals-stacked interlayers in the initial stage, and further lithiation induces the Cu extrusion via a displacement reaction mechanism that is different from the typical conversion reactions. Density functional theory calculations have confirmed both the thermodynamically favored and the kinetically driven reaction pathways. Lastly, our findings elucidate the reaction pathways of the Li/CuS system under nonequilibrium conditions and provide valuable insight into the atomistic lithiation mechanisms of transition metal sulfides in general.« less
Innovative Pathways from School: The Case Studies. Phase 1 Report 2002.

ERIC Educational Resources Information Center

Boyd, Sally; McDowall, Sue; Cooper, Garrick

This report documents the Innovative Pathways study of nonconventional year 12 and 13 programs at 7 schools, considered successful in assisting "at risk" students in their transition from school to the work force or further education and training. Elements of good practice are documented that contributed to and assisted students'…
Ubiquitin control of S phase: a new role for the ubiquitin conjugating enzyme, UbcH7

USDA-ARS?s Scientific Manuscript database

Events within and transitions between the phases of the eukaryotic cell cycle are tightly controlled by transcriptional and post-translational processes. Prominent among them is a profound role for the ubiquitin proteasome proteolytic pathway. The timely degradation of proteins balances the increase...
On the P 21/m and Pmmn pathways of the B1 B2 phase transition in NaCl: a quantum-mechanical study

NASA Astrophysics Data System (ADS)

Catti, Michele

2004-06-01

The monoclinic P 21/m and orthorhombic Pmmn (Watanabe et al' s-type) mechanisms of the high-pressure phase transition of NaCl between the B1 (rocksalt, Fm\\overline 3 m ) and B2 (CsCl-like, Pm\\overline 3 m ) cubic phases were investigated by ab initio DFT techniques with all-electron localized basis sets. Enthalpy profiles versus the order parameter were computed at constant pressures of 15, 26.3 (equilibrium) and 35 GPa for each pathway. The monoclinic path shows a lower activation enthalpy at the equilibrium pressure, but at different p values (hysteresis effects) the other mechanism becomes competitive. In the P 21/m case, sharp jumps of structural parameters are observed along the transformation coordinate, which can be explained by a mechanism based on discontinuous sliding of alternating pairs of (100) atomic layers. This accounts also for the predicted formation of a metastable intermediate Cmcm phase with TlI-like structure, similar to that observed experimentally at high pressure in AgCl, and the relations with the KOH structure are discussed, too. On the other hand, along the Pmmn pathway the structural parameters vary quite smoothly, indicating a continuous motion of neighbouring atomic planes within the constraint of the additional mirror symmetry.
Femtosecond resolution of soft mode dynamics in structural phase transitions

NASA Technical Reports Server (NTRS)

Dougherty, Thomas P.; Wiederrecht, Gary P.; Nelson, Keith A.; Garrett, Mark H.; Jensen, Hans P.; Warde, Cardinal

1992-01-01

The microscopic pathway along which ions or molecules in a crystal move during structural phase transition can often be described in terms of a collective vibrational mode of the lattice. In many cases, this mode, called a 'soft' phonon mode because of its characteristically low frequency near the phase transition temperature, is difficult to characterize through conventional frequency-domain spectroscopies such as light or neutron scattering. A femtosecond time-domain analog of light-scattering spectroscopy called impulsive stimulated Raman scattering (ISRS) has been used to examine the soft modes of two perovskite ferroelectric crystals. The low-frequency lattice dynamics of KNbO3 and BaTiO3 are clarified in a manner that permits critical evaluation of microscopic models for their ferroelectric transitions. The results illustrate the advantages of ISRS over conventional Raman spectroscopy of low-frequency, heavily damped soft modes.
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.
Multiple pathways in pressure-induced phase transition of coesite

NASA Astrophysics Data System (ADS)

Liu, Wei; Wu, Xuebang; Liang, Yunfeng; Liu, Changsong; Miranda, Caetano R.; Scandolo, Sandro

2017-12-01

High-pressure single-crystal X-ray diffraction method with precise control of hydrostatic conditions, typically with helium or neon as the pressure-transmitting medium, has significantly changed our view on what happens with low-density silica phases under pressure. Coesite is a prototype material for pressure-induced amorphization. However, it was found to transform into a high-pressure octahedral (HPO) phase, or coesite-II and coesite-III. Given that the pressure is believed to be hydrostatic in two recent experiments, the different transformation pathways are striking. Based on molecular dynamic simulations with an ab initio parameterized potential, we reproduced all of the above experiments in three transformation pathways, including the one leading to an HPO phase. This octahedral phase has an oxygen hcp sublattice featuring 2 × 2 zigzag octahedral edge-sharing chains, however with some broken points (i.e., point defects). It transforms into α-PbO2 phase when it is relaxed under further compression. We show that the HPO phase forms through a continuous rearrangement of the oxygen sublattice toward hcp arrangement. The high-pressure amorphous phases can be described by an fcc and hcp sublattice mixture.
Exploration of metastability and hidden phases in correlated electron crystals visualized by femtosecond optical doping and electron crystallography

PubMed Central

Han, Tzong-Ru T.; Zhou, Faran; Malliakas, Christos D.; Duxbury, Phillip M.; Mahanti, Subhendra D.; Kanatzidis, Mercouri G.; Ruan, Chong-Yu

2015-01-01

Characterizing and understanding the emergence of multiple macroscopically ordered electronic phases through subtle tuning of temperature, pressure, and chemical doping has been a long-standing central issue for complex materials research. We report the first comprehensive studies of optical doping–induced emergence of stable phases and metastable hidden phases visualized in situ by femtosecond electron crystallography. The electronic phase transitions are triggered by femtosecond infrared pulses, and a temperature–optical density phase diagram is constructed and substantiated with the dynamics of metastable states, highlighting the cooperation and competition through which the macroscopic quantum orders emerge. These results elucidate key pathways of femtosecond electronic switching phenomena and provide an important new avenue to comprehensively investigate optical doping–induced transition states and phase diagrams of complex materials with wide-ranging applications. PMID:26601190
A molecular dynamic investigation for shock induced phase transition of water

NASA Astrophysics Data System (ADS)

Mitra, Nilanjan; Neogi, Anupam

2015-06-01

Atomistic equilibrium molecular dynamics (EMD) was carried out to investigate shock induced phase transition of bulk liquid water. Multi-scale shock technique (MSST) was utilized to investigate low (US = 2 . 5km /s) to strong (US = 6 . 5km /s) intensity shock response on an extended flexible three point model up to 100 ns. The thermodynamic pathway of phase transition from liquid water to ice VII was investigated using temporal variation of thermodynamic state variables, power spectrum analyses of O-H bond vibration along with temporal evolution of pair correlation function between O-O, O-H and H-H atoms. Static structure factor along with pair-distribution function extended up to 20 Å was calculated and compared against the ideal ice VII to get information regarding long range ordering. Bragg reflection at different crystal planes were evaluated to investigate percentage of crystallinity of the shocked sample. Specific questions answered in this work involves: What is the exact time frame after the passage of shock at certain intensity in which nucleation of solid phase can be observed? Is it a complete or partial phase transition? Are external nucleators essential for this transformation? What is the percentage of crystallinity of the nucleated phase?
MicroRNA-132 enhances transition from inflammation to proliferation during wound healing

PubMed Central

Li, Dongqing; Wang, Aoxue; Liu, Xi; Meisgen, Florian; Grünler, Jacob; Botusan, Ileana R.; Narayanan, Sampath; Erikci, Erdem; Li, Xi; Blomqvist, Lennart; Du, Lei; Pivarcsi, Andor; Sonkoly, Enikö; Chowdhury, Kamal; Catrina, Sergiu-Bogdan; Ståhle, Mona; Landén, Ning Xu

2015-01-01

Wound healing is a complex process that is characterized by an initial inflammatory phase followed by a proliferative phase. This transition is a critical regulatory point; however, the factors that mediate this process are not fully understood. Here, we evaluated microRNAs (miRs) in skin wound healing and characterized the dynamic change of the miRNome in human skin wounds. miR-132 was highly upregulated during the inflammatory phase of wound repair, predominantly expressed in epidermal keratinocytes, and peaked in the subsequent proliferative phase. TGF-β1 and TGF-β2 induced miR-132 expression in keratinocytes, and transcriptome analysis of these cells revealed that miR-132 regulates a large number of immune response– and cell cycle–related genes. In keratinocytes, miR-132 decreased the production of chemokines and the capability to attract leukocytes by suppressing the NF-κB pathway. Conversely, miR-132 increased activity of the STAT3 and ERK pathways, thereby promoting keratinocyte growth. Silencing of the miR-132 target heparin-binding EGF-like growth factor (HB-EGF) phenocopied miR-132 overexpression in keratinocytes. Using mouse and human ex vivo wound models, we found that miR-132 blockade delayed healing, which was accompanied by severe inflammation and deficient keratinocyte proliferation. Together, our results indicate that miR-132 is a critical regulator of skin wound healing that facilitates the transition from the inflammatory to the proliferative phase. PMID:26121747
Reordering transitions during annealing of block copolymer cylinder phases

DOE PAGES

Majewski, Pawel W.; Yager, Kevin G.

2015-10-06

While equilibrium block-copolymer morphologies are dictated by energy-minimization effects, the semi-ordered states observed experimentally often depend on the details of ordering pathways and kinetics. In this study, we explore reordering transitions in thin films of block-copolymer cylinder-forming polystyrene- block-poly(methyl methacrylate). We observe several transient states as films order towards horizontally-aligned cylinders. In particular, there is an early-stage reorganization from randomly-packed cylinders into hexagonally-packed vertically-aligned cylinders; followed by a reorientation transition from vertical to horizontal cylinder states. These transitions are thermally activated. The growth of horizontal grains within an otherwise vertical morphology proceeds anisotropically, resulting in anisotropic grains in the finalmore » horizontal state. The size, shape, and anisotropy of grains are influenced by ordering history; for instance, faster heating rates reduce grain anisotropy. These results help elucidate aspects of pathway-dependent ordering in block-copolymer thin films.« less
Multiple pathways in pressure-induced phase transition of coesite

PubMed Central

Liu, Wei; Wu, Xuebang; Liu, Changsong; Miranda, Caetano R.; Scandolo, Sandro

2017-01-01

High-pressure single-crystal X-ray diffraction method with precise control of hydrostatic conditions, typically with helium or neon as the pressure-transmitting medium, has significantly changed our view on what happens with low-density silica phases under pressure. Coesite is a prototype material for pressure-induced amorphization. However, it was found to transform into a high-pressure octahedral (HPO) phase, or coesite-II and coesite-III. Given that the pressure is believed to be hydrostatic in two recent experiments, the different transformation pathways are striking. Based on molecular dynamic simulations with an ab initio parameterized potential, we reproduced all of the above experiments in three transformation pathways, including the one leading to an HPO phase. This octahedral phase has an oxygen hcp sublattice featuring 2 × 2 zigzag octahedral edge-sharing chains, however with some broken points (i.e., point defects). It transforms into α-PbO2 phase when it is relaxed under further compression. We show that the HPO phase forms through a continuous rearrangement of the oxygen sublattice toward hcp arrangement. The high-pressure amorphous phases can be described by an fcc and hcp sublattice mixture. PMID:29162690
Water freezing and ice melting

DOE PAGES

Malolepsza, Edyta; Keyes, Tom

2015-10-12

The generalized replica exchange method (gREM) is designed to sample states with coexisting phases and thereby to describe strong first order phase transitions. The isobaric MD version of the gREM is presented and applied to freezing of liquid water, and melting of hexagonal and cubic ice. It is confirmed that coexisting states are well sampled. The statistical temperature as a function of enthalpy, T S(H), is obtained. Hysteresis between freezing and melting is observed and discussed. The entropic analysis of phase transitions is applied and equilibrium transition temperatures, latent heats, and surface tensions are obtained for hexagonal ice↔liquid and cubicmore » ice↔liquid, with excellent agreement with published values. A new method is given to assign water molecules among various symmetry types. As a result, pathways for water freezing, ultimately leading to hexagonal ice, are found to contain intermediate layered structures built from hexagonal and cubic ice.« less
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.
ENSO Transition Asymmetry: Internal and External Causes and Intermodel Diversity

NASA Astrophysics Data System (ADS)

An, Soon-Il; Kim, Ji-Won

2018-05-01

El Niño is frequently followed by La Niña, but the opposite case rarely happens. Here we explore a mechanism for such an asymmetrical transition and its future changes. Internally, the asymmetrical response of upper ocean waves against surface wind stress anomaly exerts a primary cause of El Niño-Southern Oscillation (ENSO) transition asymmetry. Externally, the asymmetrical capacitor effects of both Indian and Atlantic Oceans play some roles in driving the ENSO transition asymmetry via the interbasin interactions. The historical runs of Coupled Model Intercomparison Project Phase 5 show that the intermodel transition asymmetry is significantly correlated with the intermodel asymmetry in ocean wave response to surface wind forcing but not with that in the interbasin interactions. In addition, the El Niño-to-La Niña transition tendency was weaker in moderate global warming scenario runs (Representative Concentration Pathway 4.5) while slightly enhanced in strong warming scenario runs (Representative Concentration Pathway 8.5). Similar changes also appeared in the asymmetrical response of ocean waves against the surface wind forcing.

Structural phase transition of BeTe: an ab initio molecular dynamics study.

PubMed

Alptekin, Sebahaddin

2017-08-11

Beryllium telluride (BeTe) with cubic zinc-blende (ZB) structure was studied using ab initio constant pressure method under high pressure. The ab initio molecular dynamics (MD) approach for constant pressure was studied and it was found that the first order phase transition occurs from the ZB structure to the nickel arsenide (NiAs) structure. It has been shown that the MD simulation predicts the transition pressure P T more than the value obtained by the static enthalpy and experimental data. The structural pathway reveals MD simulation such as cubic → tetragonal → orthorhombic → monoclinic → orthorhombic → hexagonal, leading the ZB to NiAs phase. The phase transformation is accompanied by a 10% volume drop and at 80 GPa is likely to be around 35 GPa in the experiment. In the present study, our obtained values can be compared with the experimental and theoretical results. Graphical abstract The energy-volume relation and ZB phase for the BeTe.
Arginine pathways and the inflammatory response: interregulation of nitric oxide and polyamines: review article.

PubMed

Satriano, J

2004-07-01

An early response to an acute inflammatory insult, such as wound healing or experimental glomerulonephritis, is the conversion of arginine to the cytostatic molecule nitric oxide (NO). This 'anti-bacterial' phase is followed by the conversion of arginine to ornithine, which is the precursor for the pro-proliferative polyamines as well as proline for the production of extracellular matrix. This latter, pro-growth phase constitutes a 'repair' phase response. The temporal switch of arginine as a substrate for the cytostatic iNOS/NO axis to the pro-growth arginase/ ornithine/polyamine and proline axis is subject to regulation by inflammatory cytokines as well as interregulation by the arginine metabolites themselves. Arginine is also the precursor for another biogenic amine, agmatine. Here we describe the capacity of these three arginine pathways to interregulate, and propose a model whereby agmatine has the potential to serve in the coordination of the early and repair phase pathways of arginine in the inflammatory response by acting as a gating mechanism at the transition from the iNOS/NO axis to the arginase/ODC/polyamine axis. Due to the pathophysiologic and therapeutic potential, we will further examine the antiproliferative effects of agmatine on the polyamine pathway.
Kinetically Controlled Two-Step Amorphization and Amorphous-Amorphous Transition in Ice.

PubMed

Lin, Chuanlong; Yong, Xue; Tse, John S; Smith, Jesse S; Sinogeikin, Stanislav V; Kenney-Benson, Curtis; Shen, Guoyin

2017-09-29

We report the results of in situ structural characterization of the amorphization of crystalline ice Ih under compression and the relaxation of high-density amorphous (HDA) ice under decompression at temperatures between 96 and 160 K by synchrotron x-ray diffraction. The results show that ice Ih transforms to an intermediate crystalline phase at 100 K prior to complete amorphization, which is supported by molecular dynamics calculations. The phase transition pathways show clear temperature dependence: direct amorphization without an intermediate phase is observed at 133 K, while at 145 K a direct Ih-to-IX transformation is observed; decompression of HDA shows a transition to low-density amorphous ice at 96 K and ∼1 Pa, to ice Ic at 135 K and to ice IX at 145 K. These observations show that the amorphization of compressed ice Ih and the recrystallization of decompressed HDA are strongly dependent on temperature and controlled by kinetic barriers. Pressure-induced amorphous ice is an intermediate state in the phase transition from the connected H-bond water network in low pressure ices to the independent and interpenetrating H-bond network of high-pressure ices.
Kinetically Controlled Two-Step Amorphization and Amorphous-Amorphous Transition in Ice

NASA Astrophysics Data System (ADS)

Lin, Chuanlong; Yong, Xue; Tse, John S.; Smith, Jesse S.; Sinogeikin, Stanislav V.; Kenney-Benson, Curtis; Shen, Guoyin

2017-09-01

We report the results of in situ structural characterization of the amorphization of crystalline ice Ih under compression and the relaxation of high-density amorphous (HDA) ice under decompression at temperatures between 96 and 160 K by synchrotron x-ray diffraction. The results show that ice Ih transforms to an intermediate crystalline phase at 100 K prior to complete amorphization, which is supported by molecular dynamics calculations. The phase transition pathways show clear temperature dependence: direct amorphization without an intermediate phase is observed at 133 K, while at 145 K a direct Ih-to-IX transformation is observed; decompression of HDA shows a transition to low-density amorphous ice at 96 K and ˜1 Pa , to ice Ic at 135 K and to ice IX at 145 K. These observations show that the amorphization of compressed ice Ih and the recrystallization of decompressed HDA are strongly dependent on temperature and controlled by kinetic barriers. Pressure-induced amorphous ice is an intermediate state in the phase transition from the connected H-bond water network in low pressure ices to the independent and interpenetrating H-bond network of high-pressure ices.
Analysis of the tomato leaf transcriptome during successive hemibiotrophic stages of a compatible interaction with the oomycete pathogen Phytophthora infestans.

PubMed

Zuluaga, Andrea P; Vega-Arreguín, Julio C; Fei, Zhangjun; Matas, Antonio J; Patev, Sean; Fry, William E; Rose, Jocelyn K C

2016-01-01

The infection of plants by hemibiotrophic pathogens involves a complex and highly regulated transition from an initial biotrophic, asymptomatic stage to a later necrotrophic state, characterized by cell death. Little is known about how this transition is regulated, and there are conflicting views regarding the significance of the plant hormones jasmonic acid (JA) and salicylic acid (SA) in the different phases of infection. To provide a broad view of the hemibiotrophic infection process from the plant perspective, we surveyed the transcriptome of tomato (Solanum lycopersicum) during a compatible interaction with the hemibiotrophic oomycete Phytophthora infestans during three infection stages: biotrophic, the transition from biotrophy to necrotrophy, and the necrotrophic phase. Nearly 10 000 genes corresponding to proteins in approximately 400 biochemical pathways showed differential transcript abundance during the three infection stages, revealing a major reorganization of plant metabolism, including major changes in source-sink relations, as well as secondary metabolites. In addition, more than 100 putative resistance genes and pattern recognition receptor genes were induced, and both JA and SA levels and associated signalling pathways showed dynamic changes during the infection time course. The biotrophic phase was characterized by the induction of many defence systems, which were either insufficient, evaded or suppressed by the pathogen. © 2015 BSPP AND JOHN WILEY & SONS LTD.
Gas-Phase Reaction Pathways and Rate Coefficients for the Dichlorosilane-Hydrogen and Trichlorosilane-Hydrogen Systems

NASA Technical Reports Server (NTRS)

Dateo, Christopher E.; Walch, Stephen P.

2002-01-01

As part of NASA Ames Research Center's Integrated Process Team on Device/Process Modeling and Nanotechnology our goal is to create/contribute to a gas-phase chemical database for use in modeling microelectronics devices. In particular, we use ab initio methods to determine chemical reaction pathways and to evaluate reaction rate coefficients. Our initial studies concern reactions involved in the dichlorosilane-hydrogen (SiCl2H2--H2) and trichlorosilane-hydrogen (SiCl2H-H2) systems. Reactant, saddle point (transition state), and product geometries and their vibrational harmonic frequencies are determined using the complete-active-space self-consistent-field (CASSCF) electronic structure method with the correlation consistent polarized valence double-zeta basis set (cc-pVDZ). Reaction pathways are constructed by following the imaginary frequency mode of the saddle point to both the reactant and product. Accurate energetics are determined using the singles and doubles coupled-cluster method that includes a perturbational estimate of the effects of connected triple excitations (CCSD(T)) extrapolated to the complete basis set limit. Using the data from the electronic structure calculations, reaction rate coefficients are obtained using conventional and variational transition state and RRKM theories.
Pathways for tailoring the magnetostructural behavior of FeRh-based systems

NASA Astrophysics Data System (ADS)

Barua, Radhika

2014-03-01

The prediction of phase transition temperatures in functional materials provides dual benefits of supplying insight into fundamental drivers underlying the phase transition, as well as enabling new and improved technological applications that employ the material. In this work, studies focused on understanding the magnetostructural phase transition of FeRh as a function of elemental substitution, provides guidance for tailoring phase transitions in this compound, with possible extensions to other intermetallic-based magnetostructural compounds. Clear trends in the magnetostructural temperatures (Tt) of alloys of composition Fe(Rh1-xMx) or (Fe1-xMx) Rh (M = 3 d, 4 d or 5 d transition metals), as reported in literature since 1961, were identified and confirmed as a function of the valence band electron concentration ((s + d) electrons/atom) of the system. It is observed that substitution of 3 dor 4 delements (x <= 6.5 at%) into B2-ordered FeRh compounds causes Ttto increase to a maximum around a critical valence band electron concentration (ev *) of 8.50 electrons/atom and then decrease. Substitution of 5 delements echoes this trend but with an overall increase in Ttand a shift in ev * to 8.52 electrons/atom. For ev>8.65 electrons/atom, FeRh-based alloys cease to adopt the B2-ordered crystallographic structure in favor of the chemically disordered A1-type structure or the ordered L10-type structure. This phenomenological model has been confirmed through synthesis and characterization of FeRh alloys with Cu, Ni and Au additions. The success of this model in confirming existing data trends in chemically-substituted FeRh and predicting new composition-transition temperature correlations emphasizes the strong interplay between the electronic spin configuration, the electronic band structure, and crystal lattice of this system. Further these results provide pathways for tailoring the magnetostructural behavior and the associated functional response of FeRh-based systems for potential technological applications. Research was performed under the auspices of the U.S. Department of Energy (Contract No. DE-SC0005250).
Exploring the free energy surface using ab initio molecular dynamics

DOE PAGES

Samanta, Amit; Morales, Miguel A.; Schwegler, Eric

2016-04-22

Efficient exploration of the configuration space and identification of metastable structures are challenging from both computational as well as algorithmic perspectives. Here, we extend the recently proposed orderparameter aided temperature accelerated sampling schemes to efficiently and systematically explore free energy surfaces, and search for metastable states and reaction pathways within the framework of density functional theory based molecular dynamics. The sampling method is applied to explore the relevant parts of the configuration space in prototypical materials SiO 2 and Ti to identify the different metastable structures corresponding to different phases in these materials. In addition, we use the string methodmore » in collective variables to study the melting pathways in the high pressure cotunnite phase of SiO 2 and the hcp to fcc phase transition in Ti.« less
Coherent control of the formation of cold heteronuclear molecules by photoassociation

NASA Astrophysics Data System (ADS)

de Lima, Emanuel F.

2017-01-01

We consider the formation of cold diatomic molecules in the electronic ground state by photoassociation of atoms of dissimilar species. A combination of two transition pathways from the free colliding pair of atoms to a bound vibrational level of the electronic molecular ground state is envisioned. The first pathway consists of a pump-dump scheme with two time-delayed laser pulses in the near-infrared frequency domain. The pump pulse drives the transition to a bound vibrational level of an excited electronic state, while the dump pulse transfers the population to a bound vibrational level of the electronic ground state. The second pathway takes advantage of the existing permanent dipole moment and employs a single pulse in the far-infrared domain to drive the transition from the unbound atoms directly to a bound vibrational level in the electronic ground state. We show that this scheme offers the possibility to coherently control the photoassociation yield by manipulating the relative phase and timing of the pulses. The photoassociation mechanism is illustrated for the formation of cold LiCs molecules.
A steep-slope transistor based on abrupt electronic phase transition

NASA Astrophysics Data System (ADS)

Shukla, Nikhil; Thathachary, Arun V.; Agrawal, Ashish; Paik, Hanjong; Aziz, Ahmedullah; Schlom, Darrell G.; Gupta, Sumeet Kumar; Engel-Herbert, Roman; Datta, Suman

2015-08-01

Collective interactions in functional materials can enable novel macroscopic properties like insulator-to-metal transitions. While implementing such materials into field-effect-transistor technology can potentially augment current state-of-the-art devices by providing unique routes to overcome their conventional limits, attempts to harness the insulator-to-metal transition for high-performance transistors have experienced little success. Here, we demonstrate a pathway for harnessing the abrupt resistivity transformation across the insulator-to-metal transition in vanadium dioxide (VO2), to design a hybrid-phase-transition field-effect transistor that exhibits gate controlled steep (`sub-kT/q') and reversible switching at room temperature. The transistor design, wherein VO2 is implemented in series with the field-effect transistor's source rather than into the channel, exploits negative differential resistance induced across the VO2 to create an internal amplifier that facilitates enhanced performance over a conventional field-effect transistor. Our approach enables low-voltage complementary n-type and p-type transistor operation as demonstrated here, and is applicable to other insulator-to-metal transition materials, offering tantalizing possibilities for energy-efficient logic and memory applications.
A steep-slope transistor based on abrupt electronic phase transition.

PubMed

Shukla, Nikhil; Thathachary, Arun V; Agrawal, Ashish; Paik, Hanjong; Aziz, Ahmedullah; Schlom, Darrell G; Gupta, Sumeet Kumar; Engel-Herbert, Roman; Datta, Suman

2015-08-07

Collective interactions in functional materials can enable novel macroscopic properties like insulator-to-metal transitions. While implementing such materials into field-effect-transistor technology can potentially augment current state-of-the-art devices by providing unique routes to overcome their conventional limits, attempts to harness the insulator-to-metal transition for high-performance transistors have experienced little success. Here, we demonstrate a pathway for harnessing the abrupt resistivity transformation across the insulator-to-metal transition in vanadium dioxide (VO2), to design a hybrid-phase-transition field-effect transistor that exhibits gate controlled steep ('sub-kT/q') and reversible switching at room temperature. The transistor design, wherein VO2 is implemented in series with the field-effect transistor's source rather than into the channel, exploits negative differential resistance induced across the VO2 to create an internal amplifier that facilitates enhanced performance over a conventional field-effect transistor. Our approach enables low-voltage complementary n-type and p-type transistor operation as demonstrated here, and is applicable to other insulator-to-metal transition materials, offering tantalizing possibilities for energy-efficient logic and memory applications.
Signaling molecules involved in the transition of growth to development of Dictyostelium discoideum.

PubMed

Mir, Hina A; Rajawat, Jyotika; Pradhan, Shalmali; Begum, Rasheedunnisa

2007-03-01

The social amoeba Dictyostelium discoideum, a powerful paradigm provides clear insights into the regulation of growth and development. In addition to possessing complex individual cellular functions like a unicellular eukaryote, D. discoideum cells face the challenge of multicellular development. D. discoideum undergoes a relatively simple differentiation process mainly by cAMP mediated pathway. Despite this relative simplicity, the regulatory signaling pathways are as complex as those seen in metazoan development. However, the introduction of restriction-enzyme-mediated integration (REMI) technique to produce developmental gene knockouts has provided novel insights into the discovery of signaling molecules and their role in D. discoideum development. Cell cycle phase is an important aspect for differentiation of D. discoideum, as cells must reach a specific stage to enter into developmental phase and specific cell cycle regulators are involved in arresting growth phase genes and inducing the developmental genes. In this review, we present an overview of the signaling molecules involved in the regulation of growth to differentiation transition (GDT), molecular mechanism of early developmental events leading to generation of cAMP signal and components of cAMP relay system that operate in this paradigm.
Construction of a biodynamic model for Cry protein production studies.

PubMed

Navarro-Mtz, Ana Karin; Pérez-Guevara, Fermín

2014-12-01

Mathematical models have been used from growth kinetic simulation to gen regulatory networks prediction for B. thuringiensis culture. However, this culture is a time dependent dynamic process where cells physiology suffers several changes depending on the changes in the cell environment. Therefore, through its culture, B. thuringiensis presents three phases related with the predominance of three major metabolic pathways: vegetative growth (Embded-Meyerhof-Parnas pathway), transition (γ-aminobutiric cycle) and sporulation (tricarboxylic acid cycle). There is not available a mathematical model that relates the different stages of cultivation with the metabolic pathway active on each one of them. Therefore, in the present study, and based on published data, a biodynamic model was generated to describe the dynamic of the three different phases based on their major metabolic pathways. The biodynamic model is used to study the interrelation between the different culture phases and their relationship with the Cry protein production. The model consists of three interconnected modules where each module represents one culture phase and its principal metabolic pathway. For model validation four new fermentations were done showing that the model constructed describes reasonably well the dynamic of the three phases. The main results of this model imply that poly-β-hydroxybutyrate is crucial for endospore and Cry protein production. According to the yields of dipicolinic acid and Cry from poly-β-hydroxybutyrate, calculated with the model, the endospore and Cry protein production are not just simultaneous and parallel processes they are also competitive processes.
Golf-course and funnel energy landscapes: Protein folding concepts in martensites

NASA Astrophysics Data System (ADS)

Shankaraiah, N.

2017-06-01

We use protein folding energy landscape concepts such as golf course and funnel to study re-equilibration in athermal martensites under systematic temperature quench Monte Carlo simulations. On quenching below a transition temperature, the seeded high-symmetry parent-phase austenite that converts to the low-symmetry product-phase martensite, through autocatalytic twinning or elastic photocopying, has both rapid conversions and incubation delays in the temperature-time-transformation phase diagram. We find the rapid (incubation delays) conversions at low (high) temperatures arises from the presence of large (small) size of golf-course edge that has the funnel inside for negative energy states. In the incubating state, the strain structure factor enters into the Brillouin-zone golf course through searches for finite transitional pathways which close off at the transition temperature with Vogel-Fulcher divergences that are insensitive to Hamiltonian energy scales and log-normal distributions, as signatures of dominant entropy barriers. The crossing of the entropy barrier is identified through energy occupancy distributions, Monte Carlo acceptance fractions, heat emission, and internal work.
DOE Office of Scientific and Technical Information (OSTI.GOV)

Hsu, Chih-Hao; Yue, Kan; Wang, Jing

Controlling self-assembled nanostructures in thin films allows the bottom-up fabrication of ordered nanoscale patterns. Here we report the unique thickness-dependent phase behavior in thin films of a bolaform-like giant surfactant, which consists of butyl- and hydroxyl-functionalized polyhedral oligomeric silsesquioxane (BPOSS and DPOSS) cages telechelically located at the chain ends of a polystyrene (PS) chain with 28 repeating monomers on average. In the bulk, BPOSS-PS28-DPOSS forms a double gyroid (DG) phase. Both grazing incidence small angle X-ray scattering and transmission electron microscopy techniques are combined to elucidate the thin film structures. Interestingly, films with thicknesses thinner than 200 nm exhibit anmore » irreversible phase transition from hexagonal perforated layer (HPL) to compressed hexagonally packed cylinders (c-HEX) at 130 °C, while films with thickness larger than 200 nm show an irreversible transition from HPL to DG at 200 °C. The thickness-controlled transition pathway suggests possibilities to obtain diverse patterns via thin film self-assembly.« less
Sensitive frequency dependence of the carrier-envelope phase effect on bound-bound transitions: An interference perspective

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

Peng Dian; Fu Panming; Wang Bingbing

2010-11-15

We investigate numerically with Hylleraas coordinates the frequency dependence of the carrier-envelope phase (CEP) effect on bound-bound transitions of helium induced by an ultrashort laser pulse of a few cycles. We find that the CEP effect is very sensitive to the carrier frequency of the laser pulse, occurring regularly even at far-off-resonance frequencies. By analyzing a two-level model, we find that the CEP effect can be attributed to the quantum interference between neighboring multiphoton transition pathways, which is made possible by the broadened spectrum of the ultrashort laser pulse. A general picture is developed along this line to understand themore » sensitivity of the CEP effect to the laser's carrier frequency. Multilevel influence on the CEP effect is also discussed.« less
Proline 54 trans-cis isomerization is responsible for the kinetic partitioning at the last-step photocycle of photoactive yellow protein

PubMed Central

Lee, Byoung-Chul; Hoff, Wouter D.

2008-01-01

Photoactive yellow protein (PYP), a blue-light photoreceptor for Ectothiorhodospira halophila, has provided a unique system for studying protein folding that is coupled with a photocycle. Upon receptor activation by blue light, PYP proceeds through a photocycle that includes a partially folded signaling state. The last-step photocycle is a thermal recovery reaction from the signaling state to the native state. Bi-exponential kinetics had been observed for the last-step photocycle; however, the slow phase of the bi-exponential kinetics has not been extensively studied. Here we analyzed both fast and slow phases of the last-step photocycle in PYP. From the analysis of the denaturant dependence of the fast and slow phases, we found that the last-step photocycle proceeds through parallel channels of the folding pathway. The burial of the solvent-accessible area was responsible for the transition state of the fast phase, while structural rearrangement from the compact state to the native state was responsible for the transition state of the slow phase. The photocycle of PYP was linked to the thermodynamic cycle that includes both unfolding and refolding of the fast- and slow-phase intermediates. In order to test the hypothesis of proline-limited folding for the slow phase, we constructed two proline mutants: P54A and P68A. We found that only a single phase of the last-step photocycle was observed in P54A. This suggests that there is a low energy barrier between trans to cis conformation in P54 in the light-induced state of PYP, and the resulting cis conformation of P54 generates a slow-phase kinetic trap during the photocycle-coupled folding pathway of PYP. PMID:18794212
Nonclassical nucleation pathways in protein crystallization

NASA Astrophysics Data System (ADS)

Zhang, Fajun

2017-11-01

Classical nucleation theory (CNT), which was established about 90 years ago, has been very successful in many research fields, and continues to be the most commonly used theory in describing the nucleation process. For a fluid-to-solid phase transition, CNT states that the solute molecules in a supersaturated solution reversibly form small clusters. Once the cluster size reaches a critical value, it becomes thermodynamically stable and favored for further growth. One of the most important assumptions of CNT is that the nucleation process is described by one reaction coordinate and all order parameters proceed simultaneously. Recent studies in experiments, computer simulations and theory have revealed nonclassical features in the early stage of nucleation. In particular, the decoupling of order parameters involved during a fluid-to-solid transition leads to the so-called two-step nucleation mechanism, in which a metastable intermediate phase (MIP) exists between the initial supersaturated solution and the final crystals. Depending on the exact free energy landscapes, the MIPs can be a high density liquid phase, mesoscopic clusters, or a pre-ordered state. In this review, we focus on the studies of nonclassical pathways in protein crystallization and discuss the applications of the various scenarios of two-step nucleation theory. In particular, we focus on protein solutions in the presence of multivalent salts, which serve as a model protein system to study the nucleation pathways. We wish to point out the unique features of proteins as model systems for further studies.
Nonclassical nucleation pathways in protein crystallization.

PubMed

Zhang, Fajun

2017-11-08

Classical nucleation theory (CNT), which was established about 90 years ago, has been very successful in many research fields, and continues to be the most commonly used theory in describing the nucleation process. For a fluid-to-solid phase transition, CNT states that the solute molecules in a supersaturated solution reversibly form small clusters. Once the cluster size reaches a critical value, it becomes thermodynamically stable and favored for further growth. One of the most important assumptions of CNT is that the nucleation process is described by one reaction coordinate and all order parameters proceed simultaneously. Recent studies in experiments, computer simulations and theory have revealed nonclassical features in the early stage of nucleation. In particular, the decoupling of order parameters involved during a fluid-to-solid transition leads to the so-called two-step nucleation mechanism, in which a metastable intermediate phase (MIP) exists between the initial supersaturated solution and the final crystals. Depending on the exact free energy landscapes, the MIPs can be a high density liquid phase, mesoscopic clusters, or a pre-ordered state. In this review, we focus on the studies of nonclassical pathways in protein crystallization and discuss the applications of the various scenarios of two-step nucleation theory. In particular, we focus on protein solutions in the presence of multivalent salts, which serve as a model protein system to study the nucleation pathways. We wish to point out the unique features of proteins as model systems for further studies.
Interplay between sugar and hormone signaling pathways modulate floral signal transduction

PubMed Central

Matsoukas, Ianis G.

2014-01-01

NOMENCLATURE The following nomenclature will be used in this article: Names of genes are written in italicized upper-case letters, e.g., ABI4.Names of proteins are written in non-italicized upper-case letters, e.g., ABI4.Names of mutants are written in italicized lower-case letters, e.g., abi4. The juvenile-to-adult and vegetative-to-reproductive phase transitions are major determinants of plant reproductive success and adaptation to the local environment. Understanding the intricate molecular genetic and physiological machinery by which environment regulates juvenility and floral signal transduction has significant scientific and economic implications. Sugars are recognized as important regulatory molecules that regulate cellular activity at multiple levels, from transcription and translation to protein stability and activity. Molecular genetic and physiological approaches have demonstrated different aspects of carbohydrate involvement and its interactions with other signal transduction pathways in regulation of the juvenile-to-adult and vegetative-to-reproductive phase transitions. Sugars regulate juvenility and floral signal transduction through their function as energy sources, osmotic regulators and signaling molecules. Interestingly, sugar signaling has been shown to involve extensive connections with phytohormone signaling. This includes interactions with phytohormones that are also important for the orchestration of developmental phase transitions, including gibberellins, abscisic acid, ethylene, and brassinosteroids. This article highlights the potential roles of sugar-hormone interactions in regulation of floral signal transduction, with particular emphasis on Arabidopsis thaliana mutant phenotypes, and suggests possible directions for future research. PMID:25165468

Interplay between sugar and hormone signaling pathways modulate floral signal transduction.

PubMed

Matsoukas, Ianis G

2014-01-01

NOMENCLATURE The following nomenclature will be used in this article: Names of genes are written in italicized upper-case letters, e.g., ABI4.Names of proteins are written in non-italicized upper-case letters, e.g., ABI4.Names of mutants are written in italicized lower-case letters, e.g., abi4. The juvenile-to-adult and vegetative-to-reproductive phase transitions are major determinants of plant reproductive success and adaptation to the local environment. Understanding the intricate molecular genetic and physiological machinery by which environment regulates juvenility and floral signal transduction has significant scientific and economic implications. Sugars are recognized as important regulatory molecules that regulate cellular activity at multiple levels, from transcription and translation to protein stability and activity. Molecular genetic and physiological approaches have demonstrated different aspects of carbohydrate involvement and its interactions with other signal transduction pathways in regulation of the juvenile-to-adult and vegetative-to-reproductive phase transitions. Sugars regulate juvenility and floral signal transduction through their function as energy sources, osmotic regulators and signaling molecules. Interestingly, sugar signaling has been shown to involve extensive connections with phytohormone signaling. This includes interactions with phytohormones that are also important for the orchestration of developmental phase transitions, including gibberellins, abscisic acid, ethylene, and brassinosteroids. This article highlights the potential roles of sugar-hormone interactions in regulation of floral signal transduction, with particular emphasis on Arabidopsis thaliana mutant phenotypes, and suggests possible directions for future research.
DOE Office of Scientific and Technical Information (OSTI.GOV)

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

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
Formation of porous crystals via viscoelastic phase separation

NASA Astrophysics Data System (ADS)

Tsurusawa, Hideyo; Russo, John; Leocmach, Mathieu; Tanaka, Hajime

2017-10-01

Viscoelastic phase separation of colloidal suspensions can be interrupted to form gels either by glass transition or by crystallization. With a new confocal microscopy protocol, we follow the entire kinetics of phase separation, from homogeneous phase to different arrested states. For the first time in experiments, our results unveil a novel crystallization pathway to sponge-like porous crystal structures. In the early stages, we show that nucleation requires a structural reorganization of the liquid phase, called stress-driven ageing. Once nucleation starts, we observe that crystallization follows three different routes: direct crystallization of the liquid phase, the Bergeron process, and Ostwald ripening. Nucleation starts inside the reorganized network, but crystals grow past it by direct condensation of the gas phase on their surface, driving liquid evaporation, and producing a network structure different from the original phase separation pattern. We argue that similar crystal-gel states can be formed in monatomic and molecular systems if the liquid phase is slow enough to induce viscoelastic phase separation, but fast enough to prevent immediate vitrification. This provides a novel pathway to form nanoporous crystals of metals and semiconductors without dealloying, which may be important for catalytic, optical, sensing, and filtration applications.
On the dosimetric effect and reduction of inverse consistency and transitivity errors in deformable image registration for dose accumulation

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

Bender, Edward T.; Hardcastle, Nicholas; Tome, Wolfgang A.

2012-01-15

Purpose: Deformable image registration (DIR) is necessary for accurate dose accumulation between multiple radiotherapy image sets. DIR algorithms can suffer from inverse and transitivity inconsistencies. When using deformation vector fields (DVFs) that exhibit inverse-inconsistency and are nontransitive, dose accumulation on a given image set via different image pathways will lead to different accumulated doses. The purpose of this study was to investigate the dosimetric effect of and propose a postprocessing solution to reduce inverse consistency and transitivity errors. Methods: Four MVCT images and four phases of a lung 4DCT, each with an associated calculated dose, were selected for analysis. DVFsmore » between all four images in each data set were created using the Fast Symmetric Demons algorithm. Dose was accumulated on the fourth image in each set using DIR via two different image pathways. The two accumulated doses on the fourth image were compared. The inverse consistency and transitivity errors in the DVFs were then reduced. The dose accumulation was repeated using the processed DVFs, the results of which were compared with the accumulated dose from the original DVFs. To evaluate the influence of the postprocessing technique on DVF accuracy, the original and processed DVF accuracy was evaluated on the lung 4DCT data on which anatomical landmarks had been identified by an expert. Results: Dose accumulation to the same image via different image pathways resulted in two different accumulated dose results. After the inverse consistency errors were reduced, the difference between the accumulated doses diminished. The difference was further reduced after reducing the transitivity errors. The postprocessing technique had minimal effect on the accuracy of the DVF for the lung 4DCT images. Conclusions: This study shows that inverse consistency and transitivity errors in DIR have a significant dosimetric effect in dose accumulation; Depending on the image pathway taken to accumulate the dose, different results may be obtained. A postprocessing technique that reduces inverse consistency and transitivity error is presented, which allows for consistent dose accumulation regardless of the image pathway followed.« less
Ultrafast dynamics during the photoinduced phase transition in VO2

NASA Astrophysics Data System (ADS)

Wegkamp, Daniel; Stähler, Julia

2015-12-01

The phase transition of VO2 from a monoclinic insulator to a rutile metal, which occurs thermally at TC = 340 K, can also be driven by strong photoexcitation. The ultrafast dynamics during this photoinduced phase transition (PIPT) have attracted great scientific attention for decades, as this approach promises to answer the question of whether the insulator-to-metal (IMT) transition is caused by electronic or crystallographic processes through disentanglement of the different contributions in the time domain. We review our recent results achieved by femtosecond time-resolved photoelectron, optical, and coherent phonon spectroscopy and discuss them within the framework of a selection of latest, complementary studies of the ultrafast PIPT in VO2. We show that the population change of electrons and holes caused by photoexcitation launches a highly non-equilibrium plasma phase characterized by enhanced screening due to quasi-free carriers and followed by two branches of non-equilibrium dynamics: (i) an instantaneous (within the time resolution) collapse of the insulating gap that precedes charge carrier relaxation and significant ionic motion and (ii) an instantaneous lattice potential symmetry change that represents the onset of the crystallographic phase transition through ionic motion on longer timescales. We discuss the interconnection between these two non-thermal pathways with particular focus on the meaning of the critical fluence of the PIPT in different types of experiments. Based on this, we conclude that the PIPT threshold identified in optical experiments is most probably determined by the excitation density required to drive the lattice potential change rather than the IMT. These considerations suggest that the IMT can be driven by weaker excitation, predicting a transiently metallic, monoclinic state of VO2 that is not stabilized by the non-thermal structural transition and, thus, decays on ultrafast timescales.
Parallel Allostery by cAMP and PDE Coordinates Activation and Termination Phases in cAMP Signaling.

PubMed

Krishnamurthy, Srinath; Tulsian, Nikhil Kumar; Chandramohan, Arun; Anand, Ganesh S

2015-09-15

The second messenger molecule cAMP regulates the activation phase of the cAMP signaling pathway through high-affinity interactions with the cytosolic cAMP receptor, the protein kinase A regulatory subunit (PKAR). Phosphodiesterases (PDEs) are enzymes responsible for catalyzing hydrolysis of cAMP to 5' AMP. It was recently shown that PDEs interact with PKAR to initiate the termination phase of the cAMP signaling pathway. While the steps in the activation phase are well understood, steps in the termination pathway are unknown. Specifically, the binding and allosteric networks that regulate the dynamic interplay between PKAR, PDE, and cAMP are unclear. In this study, PKAR and PDE from Dictyostelium discoideum (RD and RegA, respectively) were used as a model system to monitor complex formation in the presence and absence of cAMP. Amide hydrogen/deuterium exchange mass spectrometry was used to monitor slow conformational transitions in RD, using disordered regions as conformational probes. Our results reveal that RD regulates its interactions with cAMP and RegA at distinct loci by undergoing slow conformational transitions between two metastable states. In the presence of cAMP, RD and RegA form a stable ternary complex, while in the absence of cAMP they maintain transient interactions. RegA and cAMP each bind at orthogonal sites on RD with resultant contrasting effects on its dynamics through parallel allosteric relays at multiple important loci. RD thus serves as an integrative node in cAMP termination by coordinating multiple allosteric relays and governing the output signal response. Copyright © 2015 Biophysical Society. Published by Elsevier Inc. All rights reserved.
APC/C and retinoblastoma interaction: cross-talk of retinoblastoma protein with the ubiquitin proteasome pathway.

PubMed

Ramanujan, Ajeena; Tiwari, Swati

2016-10-01

The ubiquitin (Ub) ligase anaphase promoting complex/cyclosome (APC/C) and the tumour suppressor retinoblastoma protein (pRB) play key roles in cell cycle regulation. APC/C is a critical regulator of mitosis and G1-phase of the cell cycle whereas pRB keeps a check on proliferation by inhibiting transition to the S-phase. APC/C and pRB interact with each other via the co-activator of APC/C, FZR1, providing an alternative pathway of regulation of G1 to S transition by pRB using a post-translational mechanism. Both pRB and FZR1 have complex roles and are implicated not only in regulation of cell proliferation but also in differentiation, quiescence, apoptosis, maintenance of chromosomal integrity and metabolism. Both are also targeted by transforming viruses. We discuss recent advances in our understanding of the involvement of APC/C and pRB in cell cycle based decisions and how these insights will be useful for development of anti-cancer and anti-viral drugs. © 2016 The Author(s).
APC/C and retinoblastoma interaction: cross-talk of retinoblastoma protein with the ubiquitin proteasome pathway

PubMed Central

Ramanujan, Ajeena; Tiwari, Swati

2016-01-01

The ubiquitin (Ub) ligase anaphase promoting complex/cyclosome (APC/C) and the tumour suppressor retinoblastoma protein (pRB) play key roles in cell cycle regulation. APC/C is a critical regulator of mitosis and G1-phase of the cell cycle whereas pRB keeps a check on proliferation by inhibiting transition to the S-phase. APC/C and pRB interact with each other via the co-activator of APC/C, FZR1, providing an alternative pathway of regulation of G1 to S transition by pRB using a post-translational mechanism. Both pRB and FZR1 have complex roles and are implicated not only in regulation of cell proliferation but also in differentiation, quiescence, apoptosis, maintenance of chromosomal integrity and metabolism. Both are also targeted by transforming viruses. We discuss recent advances in our understanding of the involvement of APC/C and pRB in cell cycle based decisions and how these insights will be useful for development of anti-cancer and anti-viral drugs. PMID:27402801
Pressure-temperature phase behavior of mixtures of natural sphingomyelin and ceramide extracts.

PubMed

Barriga, Hanna M G; Parsons, Edward S; McCarthy, Nicola L C; Ces, Oscar; Seddon, John M; Law, Robert V; Brooks, Nicholas J

2015-03-31

Ceramides are a group of sphingolipids that act as highly important signaling molecules in a variety of cellular processes including differentiation and apoptosis. The predominant in vivo synthetic pathway for ceramide formation is via sphingomyelinase catalyzed hydrolysis of sphingomyelin. The biochemistry of this essential pathway has been studied in detail; however, there is currently a lack of information on the structural behavior of sphingomyelin- and ceramide-rich model membrane systems, which is essential for developing a bottom-up understanding of ceramide signaling and platform formation. We have studied the lyotropic phase behavior of sphingomyelin-ceramide mixtures in excess water as a function of temperature (30-70 °C) and pressure (1-200 MPa) by small- and wide-angle X-ray scattering. At low ceramide concentrations the mixtures form the ripple gel phase (P(β)') below the gel transition temperature for sphingomyelin, and this observation has been confirmed by atomic force microscopy. Formation of the ripple gel phase can also be induced at higher temperatures via the application of hydrostatic pressure. At high ceramide concentration an inverse hexagonal phase (HII) is formed coexisting with a cubic phase.
Kinetically Controlled Two-Step Amorphization and Amorphous-Amorphous Transition in Ice

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

Lin, Chuanlong; Yong, Xue; Tse, John S.

We report the results of in situ structural characterization of the amorphization of crystalline ice Ih under compression and the relaxation of high-density amorphous (HDA) ice under decompression at temperatures between 96 and 160 K by synchrotron x-ray diffraction. The results show that ice Ih transforms to an intermediate crystalline phase at 100 K prior to complete amorphization, which is supported by molecular dynamics calculations. The phase transition pathways show clear temperature dependence: direct amorphization without an intermediate phase is observed at 133 K, while at 145 K a direct Ih-to-IX transformation is observed; decompression of HDA shows a transitionmore » to low-density amorphous ice at 96 K and ~ 1 Pa , to ice Ic at 135 K and to ice IX at 145 K. These observations show that the amorphization of compressed ice Ih and the recrystallization of decompressed HDA are strongly dependent on temperature and controlled by kinetic barriers. Pressure-induced amorphous ice is an intermediate state in the phase transition from the connected H-bond water network in low pressure ices to the independent and interpenetrating H-bond network of high-pressure ices.« less
Poplar FT2 Shortens the Juvenile Phase and Promotes Seasonal Flowering[W

PubMed Central

Hsu, Chuan-Yu; Liu, Yunxia; Luthe, Dawn S.; Yuceer, Cetin

2006-01-01

Many woody perennials, such as poplar (Populus deltoides), are not able to form flower buds during the first several years of their life cycle. They must undergo a transition from the juvenile phase to the reproductive phase to be competent to produce flower buds. After this transition, trees begin to form flower buds in the spring of each growing season. The genetic factors that control flower initiation, ending the juvenile phase, are unknown in poplar. The factors that regulate seasonal flower bud formation are also unknown. Here, we report that poplar FLOWERING LOCUS T2 (FT2), a relative of the Arabidopsis thaliana flowering-time gene FT, controls first-time and seasonal flowering in poplar. The FT2 transcript is rare during the juvenile phase of poplar. When juvenile poplar is transformed with FT2 and transcript levels are increased, flowering is induced within 1 year. During the transition between vegetative and reproductive growth in mature trees, FT2 transcripts are abundant during reproductive growth under long days. Subsequently, floral meristems emerge on flanks of the axillary inflorescence shoots. These findings suggest that FT2 is part of the flower initiation pathway in poplar and plays an additional role in regulating seasonal flower initiation that is integrated with the poplar perennial growth habit. PMID:16844908
Communication: Direct evidence for sequential dissociation of gas-phase Fe(CO)5 via a singlet pathway upon excitation at 266 nm

PubMed Central

Leitner, T.; Mazza, T.; Schröder, H.; Kunnus, K.; Schreck, S.; Radcliffe, P.; Düsterer, S.; Meyer, M.; Föhlisch, A.

2017-01-01

We prove the hitherto hypothesized sequential dissociation of Fe(CO)5 in the gas phase upon photoexcitation at 266 nm via a singlet pathway with time-resolved valence and core-level photoelectron spectroscopy with an x-ray free-electron laser. Valence photoelectron spectra are used to identify free CO molecules and to determine the time constants of stepwise dissociation to Fe(CO)4 within the temporal resolution of the experiment and further to Fe(CO)3 within 3 ps. Fe 3p core-level photoelectron spectra directly reflect the singlet spin state of the Fe center in Fe(CO)5, Fe(CO)4, and Fe(CO)3 showing that the dissociation exclusively occurs along a singlet pathway without triplet-state contribution. Our results are important for assessing intra- and intermolecular relaxation processes in the photodissociation dynamics of the prototypical Fe(CO)5 complex in the gas phase and in solution, and they establish time-resolved core-level photoelectron spectroscopy as a powerful tool for determining the multiplicity of transition metals in photochemical reactions of coordination complexes. PMID:28595420
Pathways through equilibrated states with coexisting phases for gas hydrate formation

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

Malolepsza, Edyta; Keyes, Tom

Under ambient conditions, water freezes to either hexagonal ice or a hexagonal/cubic composite ice. The presence of hydrophobic guest molecules introduces a competing pathway: gas hydrate formation, with the guests in clathrate cages. Here, the pathways of the phase transitions are sought as sequences of states with coexisting phases, using a generalized replica exchange algorithm designed to sample them in equilibrium, avoiding nonequilibrium processes. For a dilute solution of methane in water under 200 atm, initializing the simulation with the full set of replicas leads to methane trapped in hexagonal/cubic ice, while gradually adding replicas with decreasing enthalpy produces themore » initial steps of hydrate growth. Once a small amount of hydrate is formed, water rearranges to form empty cages, eventually transforming the remainder of the system to metastable β ice, a scaffolding for hydrates. It is suggested that configurations with empty cages are reaction intermediates in hydrate formation when more guest molecules are available. Furthermore, free energy profiles show that methane acts as a catalyst reducing the barrier for β ice versus hexagonal/cubic ice formation.« less
Pathways through equilibrated states with coexisting phases for gas hydrate formation

DOE PAGES

Malolepsza, Edyta; Keyes, Tom

2015-12-01

Under ambient conditions, water freezes to either hexagonal ice or a hexagonal/cubic composite ice. The presence of hydrophobic guest molecules introduces a competing pathway: gas hydrate formation, with the guests in clathrate cages. Here, the pathways of the phase transitions are sought as sequences of states with coexisting phases, using a generalized replica exchange algorithm designed to sample them in equilibrium, avoiding nonequilibrium processes. For a dilute solution of methane in water under 200 atm, initializing the simulation with the full set of replicas leads to methane trapped in hexagonal/cubic ice, while gradually adding replicas with decreasing enthalpy produces themore » initial steps of hydrate growth. Once a small amount of hydrate is formed, water rearranges to form empty cages, eventually transforming the remainder of the system to metastable β ice, a scaffolding for hydrates. It is suggested that configurations with empty cages are reaction intermediates in hydrate formation when more guest molecules are available. Furthermore, free energy profiles show that methane acts as a catalyst reducing the barrier for β ice versus hexagonal/cubic ice formation.« less
NiTi shape memory via solid-state nudge-elastic band

NASA Astrophysics Data System (ADS)

Zarkevich, Nikolai A.; Johnson, Duane D.

2014-03-01

We determine atomic mechanisms of the shape memory effect in NiTi from a generalized solid-state nudge elastic band (SSNEB) method. We consider transformation between the austenite B2 and the ground-state base-centered orthorhombic (BCO) structures. In these pathways we obtain the R-phase and discuss its structure. We confirm that BCO is the ground state, and determine the pathways to BCO martensite, which dictate transition barriers. While ideal B2 is unstable, we find a B2-like NiTi high-temperature solid phase with significant local displacement disorder, which is B2 on average. This B2-like phase appears to be entropically stabilized. This work is supported by the U.S. Department of Energy, Office of Basic Energy Science, Division of Materials Science and Engineering. Ames Laboratory is operated for the U.S. DOE by Iowa State University under contract DE-AC02-07CH11358.
First-principles analysis of ferroelectric transition in MnSnO3 and MnTiO3 perovskites

NASA Astrophysics Data System (ADS)

Kang, Sung Gu

2018-06-01

The ferroelectric instabilities of an artificially adopted Pnma structure in low tolerance perovskites have been explored (Kang et al., 2017) [4], where an unstable A-site environment was reported to be the major driving source for the low tolerance perovskites to exhibit ferroelectric instability. This study examined the ferroelectric transition of two magnetic perovskite materials, MnSnO3 and MnTiO3, in Pnma phase. Phase transitions to the Pnma phase at elevated pressures were observed. MnSnO3, which has a lower (larger) tolerance factor (B-site cation radius), showed a higher ferroelectric mode amplitude than MnTiO3. The distribution of the bond length of Mn-O and the mean quadratic elongation (QE) of octahedra (SnO6 or TiO6) were investigated for structural analysis. However, MnTiO3 showed a larger spontaneous polarization than MnSnO3 due to high Born effective charges of titanium. This study is useful because it provides a valuable pathway to the design of promising multiferroic materials.
Doppler-free spectroscopy of the atomic rubidium fine structure using ultrafast spatial coherent control method

NASA Astrophysics Data System (ADS)

Kim, Minhyuk; Kim, Kyungtae; Lee, Woojun; Kim, Hyosub; Ahn, Jaewook

2017-04-01

Spectral programming solutions for the ultrafast spatial coherent control (USCC) method to resolve the fine-structure energy levels of atomic rubidium are reported. In USCC, a pair of counter-propagating ultrashort laser pulses are programmed to make a two-photon excitation pattern specific to particular transition pathways and atom species, thus allowing the involved transitions resolvable in space simultaneously. With a proper spectral phase and amplitude modulation, USCC has been also demonstrated for the systems with many intermediate energy levels. Pushing the limit of system complexity even further, we show here an experimental demonstration of the rubidium fine-structure excitation pattern resolvable by USCC. The spectral programming solution for the given USCC is achieved by combining a double-V-shape spectral phase function and a set of phase steps, where the former distinguishes the fine structure and the latter prevents resonant transitions. The experimental results will be presented along with its application in conjunction with the Doppler-free frequency-comb spectroscopy for rubidium hyperfine structure measurements. Samsung Science and Technology Foundation [SSTFBA1301-12].
Visualizing non-equilibrium lithiation of spinel oxide via in situ transmission electron microscopy

PubMed Central

He, Kai; Zhang, Sen; Li, Jing; Yu, Xiqian; Meng, Qingping; Zhu, Yizhou; Hu, Enyuan; Sun, Ke; Yun, Hongseok; Yang, Xiao-Qing; Zhu, Yimei; Gan, Hong; Mo, Yifei; Stach, Eric A.; Murray, Christopher B.; Su, Dong

2016-01-01

Spinel transition metal oxides are important electrode materials for lithium-ion batteries, whose lithiation undergoes a two-step reaction, whereby intercalation and conversion occur in a sequential manner. These two reactions are known to have distinct reaction dynamics, but it is unclear how their kinetics affects the overall electrochemical response. Here we explore the lithiation of nanosized magnetite by employing a strain-sensitive, bright-field scanning transmission electron microscopy approach. This method allows direct, real-time, high-resolution visualization of how lithiation proceeds along specific reaction pathways. We find that the initial intercalation process follows a two-phase reaction sequence, whereas further lithiation leads to the coexistence of three distinct phases within single nanoparticles, which has not been previously reported to the best of our knowledge. We use phase-field theory to model and describe these non-equilibrium reaction pathways, and to directly correlate the observed phase evolution with the battery's discharge performance. PMID:27157119
Phase diagram and decomposition of 1,1-diamino-2,2-dinitroethene single crystals at high pressures and temperatures

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

Dreger, Zbigniew A.; Tao, Yuchuan; Gupta, Yogendra M.

The high pressure-high temperature (HP-HT) phase diagram and decomposition of FOX-7, central to understanding its stability and reactivity, were determined using optical spectroscopy and imaging measurements in hydrostatically compressed and heated single crystals. Boundaries between various FOX-7 phases (α, α’, β, γ, and ε) and melting/decomposition curves were established up to 10 GPa and 750 K. Main findings are: (i) a triple point is observed between α, β, and γ phases ~ 0.6 GPa and ~ 535 K, (ii) previously suggested δ phase is not a new phase but is partly decomposed γ phase, (iii) the α-α’ transition takes placemore » along an isobar, whereas the α’-ε transition pressure decreases with increasing temperature, and (iv) melting/decomposition temperatures increase rapidly with pressure, with an increase in the slope at the onset of the α’-ε transition. Our results differ from the recently reported HP-HT phase diagram for nonhydrostatically compressed polycrystalline FOX-7. In addition, the observed interplay between melting and decomposition suggests the suppression of melting with pressure. Our FTIR measurements at different pressures to 3.5 GPa showed similar decomposition products, suggesting similar decomposition pathways irrespective of the pressure. Lastly, the present results provide new insights into the structural and chemical stability of an important insensitive high explosive (IHE) crystal under well-defined HP-HT conditions.« less
Phase diagram and decomposition of 1,1-diamino-2,2-dinitroethene single crystals at high pressures and temperatures

DOE PAGES

Dreger, Zbigniew A.; Tao, Yuchuan; Gupta, Yogendra M.

2016-05-10

The high pressure-high temperature (HP-HT) phase diagram and decomposition of FOX-7, central to understanding its stability and reactivity, were determined using optical spectroscopy and imaging measurements in hydrostatically compressed and heated single crystals. Boundaries between various FOX-7 phases (α, α’, β, γ, and ε) and melting/decomposition curves were established up to 10 GPa and 750 K. Main findings are: (i) a triple point is observed between α, β, and γ phases ~ 0.6 GPa and ~ 535 K, (ii) previously suggested δ phase is not a new phase but is partly decomposed γ phase, (iii) the α-α’ transition takes placemore » along an isobar, whereas the α’-ε transition pressure decreases with increasing temperature, and (iv) melting/decomposition temperatures increase rapidly with pressure, with an increase in the slope at the onset of the α’-ε transition. Our results differ from the recently reported HP-HT phase diagram for nonhydrostatically compressed polycrystalline FOX-7. In addition, the observed interplay between melting and decomposition suggests the suppression of melting with pressure. Our FTIR measurements at different pressures to 3.5 GPa showed similar decomposition products, suggesting similar decomposition pathways irrespective of the pressure. Lastly, the present results provide new insights into the structural and chemical stability of an important insensitive high explosive (IHE) crystal under well-defined HP-HT conditions.« less

High-Pressure Behavior of Difluorides: The Case of SrF2

NASA Astrophysics Data System (ADS)

Swadba, K. E.; Stan, C. V.; Dutta, R.; Prakapenka, V.; Duffy, T. S.

2016-12-01

The high-pressure behavior of compounds in the AX2 family has attracted much attention due to their extensive polymorphism, highly coordinated structures, and diverse transformation pathways. The canonical transformation sequence for alkaline earth difluorides is from the fluorite-type structure (8 coordinated) to cotunnite (9 coordinated) to Ni2In (11 coordinated). Lead Fluoride, on the other hand, undergoes an unusual isosymmetric transition from cotunnite to a Co2Si-type structure (10 coordinated) at high pressures, during which it exhibits highly anisotropic lattice parameter trends (Haines et al, 1998; Stan et al 2016). Sr has a similar ionic radius as Pb, and is thus a good candidate for further exploring the compressional anisotropy in alkaline earth fluorides. In this study, we report a detailed examination of the compressional behavior of SrF2 to identify whether an intermediate phase occurs in this system prior to transformation to the Ni2In structure. Raman spectroscopy and x-ray diffraction experiments, performed at Princeton University and the Advanced Photon Source GSECARS beamline, respectively, were carried out on SrF2 up to 63 GPa using a diamond anvil cell. From Raman spectroscopy, we observed evidence for a high-pressure phase transition between 38.9 and 51.0 GPa. The x-ray diffraction data in this region show evidence for highly anisotropic compression, most notably a strong negative compressibility in the b direction, in the pressure region from 45.2 to 51.6 GPa. Comparison of our data with lattice parameter systematics for AX2 phases indicates that our results are consistent with the formation of the Co2Si phase in this region, along with a sluggish transformation to the Ni2In-type structure. Our findings contribute to a broader understanding of AX2 compounds and their phase transition pathways.
Kinetic studies of the folding of heterodimeric monellin: evidence for switching between alternative parallel pathways.

PubMed

Aghera, Nilesh; Udgaonkar, Jayant B

2012-07-13

Determining whether or not a protein uses multiple pathways to fold is an important goal in protein folding studies. When multiple pathways are present, defined by transition states that differ in their compactness and structure but not significantly in energy, they may manifest themselves by causing the dependence on denaturant concentration of the logarithm of the observed rate constant of folding to have an upward curvature. In this study, the folding mechanism of heterodimeric monellin [double-chain monellin (dcMN)] has been studied over a range of protein and guanidine hydrochloride (GdnHCl) concentrations, using the intrinsic tryptophan fluorescence of the protein as the probe for the folding reaction. Refolding is shown to occur in multiple kinetic phases. In the first stage of refolding, which is silent to any change in intrinsic fluorescence, the two chains of monellin bind to one another to form an encounter complex. Interrupted folding experiments show that the initial encounter complex folds to native dcMN via two folding routes. A productive folding intermediate population is identified on one route but not on both of these routes. Two intermediate subpopulations appear to form in a fast kinetic phase, and native dcMN forms in a slow kinetic phase. The chevron arms for both the fast and slow phases of refolding are shown to have upward curvatures, suggesting that at least two pathways each defined by a different intermediate are operational during these kinetic phases of structure formation. Refolding switches from one pathway to the other as the GdnHCl concentration is increased. Copyright © 2012 Elsevier Ltd. All rights reserved.
Poplar Wood Rays Are Involved in Seasonal Remodeling of Tree Physiology1[C][W

PubMed Central

Larisch, Christina; Dittrich, Marcus; Wildhagen, Henning; Lautner, Silke; Fromm, Jörg; Polle, Andrea; Hedrich, Rainer; Rennenberg, Heinz; Müller, Tobias; Ache, Peter

2012-01-01

Understanding seasonality and longevity is a major challenge in tree biology. In woody species, growth phases and dormancy follow one another consecutively. In the oldest living individuals, the annual cycle may run for more than 1,000 years. So far, however, not much is known about the processes triggering reactivation from dormancy. In this study, we focused on wood rays, which are known to play an important role in tree development. The transition phase from dormancy to flowering in early spring was compared with the phase of active growth in summer. Rays from wood samples of poplar (Populus × canescens) were enriched by laser microdissection, and transcripts were monitored by poplar whole-genome microarrays. The resulting seasonally varying complex expression and metabolite patterns were subjected to pathway analyses. In February, the metabolic pathways related to flower induction were high, indicating that reactivation from dormancy was already taking place at this time of the year. In July, the pathways related to active growth, like lignin biosynthesis, nitrogen assimilation, and defense, were enriched. Based on “marker” genes identified in our pathway analyses, we were able to validate periodical changes in wood samples by quantitative polymerase chain reaction. These studies, and the resulting ray database, provide new insights into the steps underlying the seasonality of poplar trees. PMID:22992511
Topological Phase Transitions in the Photonic Spin Hall Effect

DOE PAGES

Kort-Kamp, Wilton Junior de Melo

2017-10-04

The recent synthesis of two-dimensional staggered materials opens up burgeoning opportunities to study optical spin-orbit interactions in semiconducting Dirac-like systems. In this work, we unveil topological phase transitions in the photonic spin Hall effect in the graphene family materials. It is shown that an external static electric field and a high frequency circularly polarized laser allow for active on-demand manipulation of electromagnetic beam shifts. The spin Hall effect of light presents a rich dependence with radiation degrees of freedom, and material properties, and features nontrivial topological properties. Finally, we discover that photonic Hall shifts are sensitive to spin and valleymore » properties of the charge carriers, providing an unprecedented pathway to investigate spintronics and valleytronics in staggered 2D semiconductors.« less
Roles of GasderminA3 in Catagen-Telogen Transition During Hair Cycling.

PubMed

Bai, Xiufeng; Lei, Mingxing; Shi, Jiazhong; Yu, Yu; Qiu, Weiming; Lai, Xiangdong; Liu, Yingxin; Yang, Tian; Yang, Li; Widelitz, Randall B; Chuong, Cheng-Ming; Lian, Xiaohua

2015-09-01

Hair follicles undergo cyclic behavior through regression (catagen), rest (telogen), and regeneration (anagen) during postnatal life. The hair cycle transition is strictly regulated by the autonomous and extrinsic molecular environment. However, whether there is a switch controlling catagen-telogen transition remains largely unknown. Here we show that hair follicles cycle from catagen to the next anagen without transitioning through a morphologically typical telogen after Gsdma3 mutation. This leaves an ESLS (epithelial strand-like structure) during the time period corresponding to telogen phase in WT mice. Molecularly, Wnt10b is upregulated in Gsdma3 mutant mice. Restoration of Gsdma3 expression in AE (alopecia and excoriation) mouse skin rescues hair follicle telogen entry and significantly decreases the Wnt10b-mediated Wnt/β-catenin signaling pathway. Overexpression of Wnt10b inhibits telogen entry by increasing epithelial strand cell proliferation. Subsequently, hair follicles with a Gsdma3 mutation enter the second anagen simultaneously as WT mice. Hair follicles cannot enter the second anagen with ectopic WT Gsdma3 overexpression. A luciferase reporter assay proves that Gsdma3 directly suppresses Wnt signaling. Our findings suggest that Gsdma3 has an important role in catagen-telogen transition by balancing the Wnt signaling pathway and that morphologically typical telogen is not essential for the initiation of a new hair cycle.
Roles of GasderminA3 in catagen- telogen transition during hair cycling

PubMed Central

Bai, Xiufeng; Lei, Mingxing; Shi, Jiazhong; Yu, Yu; Qiu, Weiming; Lai, Xiangdong; Liu, Yingxin; Yang, Tian; Yang, Li; Widelitz, Randall Bruce; Chuong, Cheng-Ming; Lian, Xiaohua

2015-01-01

Hair follicles undergo cyclic behavior through regression (catagen), rest (telogen) and regeneration (anagen) during postnatal life. The hair cycle transition is strictly regulated by the autonomous and extrinsic molecular environment. However, whether there is a switch controlling catagen-telogen transition remains largely unknown. Here we show that hair follicles cycle from catagen to the next anagen without transitioning through a morphologically typical telogen after Gsdma3 mutation. This leaves an ESLS (epithelial strand-like structure) during the time period corresponding to telogen phase in WT mice. Molecularly, Wnt10b is upregulated in Gsdma3 mutant mice. Restoration of Gsdma3 expression in AE (alopecia and excoriation) mouse skin rescues hair follicle telogen entry and significantly decreases the Wnt10b-mediated Wnt/β-catenin signaling pathway. Overexpression of Wnt10b inhibits telogen entry by increasing epithelial strand cell proliferation. Subsequently, hair follicles with a Gsdma3 mutation enter the second anagen simultaneously as WT mice. Hair follicles cannot enter the second anagen with ectopic WT Gsdma3 overexpression. A luciferase reporter assay proves Gsdma3 directly suppresses Wnt signaling. Our findings suggest Gsdma3 plays an important role in catagen-telogen transition by balancing the Wnt signaling pathway, and that morphologically typical telogen is not essential for the initiation of a new hair cycle. PMID:25860385
Experimental and first-principles calculation study of the pressure-induced transitions to a metastable phase in GaP O4 and in the solid solution AlP O4-GaP O4

NASA Astrophysics Data System (ADS)

Angot, E.; Huang, B.; Levelut, C.; Le Parc, R.; Hermet, P.; Pereira, A. S.; Aquilanti, G.; Frapper, G.; Cambon, O.; Haines, J.

2017-08-01

α -Quartz-type gallium phosphate and representative compositions in the AlP O4-GaP O4 solid solution were studied by x-ray powder diffraction and absorption spectroscopy, Raman scattering, and by first-principles calculations up to pressures of close to 30 GPa. A phase transition to a metastable orthorhombic high-pressure phase along with some of the stable orthorhombic C m c m CrV O4 -type material is found to occur beginning at 9 GPa at 320 ∘C in GaP O4 . In the case of the AlP O4-GaP O4 solid solution at room temperature, only the metastable orthorhombic phase was obtained above 10 GPa. The possible crystal structures of the high-pressure forms of GaP O4 were predicted from first-principles calculations and the evolutionary algorithm USPEX. A predicted orthorhombic structure with a P m n 21 space group with the gallium in sixfold and phosphorus in fourfold coordination was found to be in the best agreement with the combined experimental data from x-ray diffraction and absorption and Raman spectroscopy. This method is found to very powerful to better understand competition between different phase transition pathways at high pressure.
MicroRNA-133 Inhibits Behavioral Aggregation by Controlling Dopamine Synthesis in Locusts

PubMed Central

Wang, Yanli; Guo, Xiaojiao; He, Jing; Kang, Le

2014-01-01

Phenotypic plasticity is ubiquitous and primarily controlled by interactions between environmental and genetic factors. The migratory locust, a worldwide pest, exhibits pronounced phenotypic plasticity, which is a population density-dependent transition that occurs between the gregarious and solitary phases. Genes involved in dopamine synthesis have been shown to regulate the phase transition of locusts. However, the function of microRNAs in this process remains unknown. In this study, we report the participation of miR-133 in dopamine production and the behavioral transition by negatively regulating two critical genes, henna and pale, in the dopamine pathway. miR-133 participated in the post-transcriptional regulation of henna and pale by binding to their coding region and 3′ untranslated region, respectively. miR-133 displayed cellular co-localization with henna/pale in the protocerebrum, and its expression in the protocerebrum was negatively correlated with henna and pale expression. Moreover, miR-133 agomir delivery suppressed henna and pale expression, which consequently decreased dopamine production, thus resulting in the behavioral shift of the locusts from the gregarious phase to the solitary phase. Increasing the dopamine content could rescue the solitary phenotype, which was induced by miR-133 agomir delivery. Conversely, miR-133 inhibition increased the expression of henna and pale, resulting in the gregarious-like behavior of solitary locusts; this gregarious phenotype could be rescued by RNA interference of henna and pale. This study shows the novel function and modulation pattern of a miRNA in phenotypic plasticity and provides insight into the underlying molecular mechanisms of the phase transition of locusts. PMID:24586212
MicroRNA-133 inhibits behavioral aggregation by controlling dopamine synthesis in locusts.

PubMed

Yang, Meiling; Wei, Yuanyuan; Jiang, Feng; Wang, Yanli; Guo, Xiaojiao; He, Jing; Kang, Le

2014-02-01

Phenotypic plasticity is ubiquitous and primarily controlled by interactions between environmental and genetic factors. The migratory locust, a worldwide pest, exhibits pronounced phenotypic plasticity, which is a population density-dependent transition that occurs between the gregarious and solitary phases. Genes involved in dopamine synthesis have been shown to regulate the phase transition of locusts. However, the function of microRNAs in this process remains unknown. In this study, we report the participation of miR-133 in dopamine production and the behavioral transition by negatively regulating two critical genes, henna and pale, in the dopamine pathway. miR-133 participated in the post-transcriptional regulation of henna and pale by binding to their coding region and 3' untranslated region, respectively. miR-133 displayed cellular co-localization with henna/pale in the protocerebrum, and its expression in the protocerebrum was negatively correlated with henna and pale expression. Moreover, miR-133 agomir delivery suppressed henna and pale expression, which consequently decreased dopamine production, thus resulting in the behavioral shift of the locusts from the gregarious phase to the solitary phase. Increasing the dopamine content could rescue the solitary phenotype, which was induced by miR-133 agomir delivery. Conversely, miR-133 inhibition increased the expression of henna and pale, resulting in the gregarious-like behavior of solitary locusts; this gregarious phenotype could be rescued by RNA interference of henna and pale. This study shows the novel function and modulation pattern of a miRNA in phenotypic plasticity and provides insight into the underlying molecular mechanisms of the phase transition of locusts.
Effects of HRAS oncogene on cell cycle progression in a cervical cancer-derived cell line.

PubMed

Córdova-Alarcón, Emilio; Centeno, Federico; Reyes-Esparza, Jorge; García-Carrancá, Alejandro; Garrido, Efraín

2005-01-01

Human papillomavirus (HPV) infection is the most prevalent factor in anogenital cancers. However, epidemiological surveys and molecular data indicate that viral presence is not enough to induce cervical cancer, suggesting that cellular factors could play a key role. One of the most important genes involved in cancer development is the RAS oncogene, and activating mutations in this gene have been associated with HPV infection and cervical neoplasia. Thus, we determined the effect of HRAS oncogene expression on cell proliferation in a cell line immortalized by E6 and E7 oncogenes. HPV positive human cervical carcinoma-derived cell lines (HeLa), previously transfected with the HRAS oncogene or the empty vector, were used. We first determined the proliferation rate and cell cycle profile of these cells by using flow cytometry and BrdU incorporation assays. In order to determine the signaling pathway regulated by HRAS and implicated in the alteration of proliferation of these cells, we used specific chemical inhibitors to inactivate the Raf and PI3K pathways. We observed that HeLa cells stably transfected with oncogenic HRAS progressed faster than control cells on the cell cycle by reducing their G1 phase. Additionally, HRAS overexpression accelerated the G1/S transition. Specific chemical inhibitors for PI3K and MEK activities indicated that both PI3K/AKT and RAF/MEK/ERK pathways are involved in the HRAS oncogene-induced reduction of the G1 phase. Our results suggest that the HRAS oncogene could play an important role in the development of cervical cancer, in addition to the presence of HPV, by reducing the G1 phase and accelerating the G1/S transition of infected cells.
Ultrafast electron crystallography of the cooperative reaction path in vanadium dioxide

PubMed Central

Yang, Ding-Shyue; Baum, Peter; Zewail, Ahmed H.

2016-01-01

Time-resolved electron diffraction with atomic-scale spatial and temporal resolution was used to unravel the transformation pathway in the photoinduced structural phase transition of vanadium dioxide. Results from bulk crystals and single-crystalline thin-films reveal a common, stepwise mechanism: First, there is a femtosecond V−V bond dilation within 300 fs, second, an intracell adjustment in picoseconds and, third, a nanoscale shear motion within tens of picoseconds. Experiments at different ambient temperatures and pump laser fluences reveal a temperature-dependent excitation threshold required to trigger the transitional reaction path of the atomic motions. PMID:27376103
Exploring the free energy surface using ab initio molecular dynamics

NASA Astrophysics Data System (ADS)

Samanta, Amit; Morales, Miguel A.; Schwegler, Eric

2016-04-01

Efficient exploration of configuration space and identification of metastable structures in condensed phase systems are challenging from both computational and algorithmic perspectives. In this regard, schemes that utilize a set of pre-defined order parameters to sample the relevant parts of the configuration space [L. Maragliano and E. Vanden-Eijnden, Chem. Phys. Lett. 426, 168 (2006); J. B. Abrams and M. E. Tuckerman, J. Phys. Chem. B 112, 15742 (2008)] have proved useful. Here, we demonstrate how these order-parameter aided temperature accelerated sampling schemes can be used within the Born-Oppenheimer and the Car-Parrinello frameworks of ab initio molecular dynamics to efficiently and systematically explore free energy surfaces, and search for metastable states and reaction pathways. We have used these methods to identify the metastable structures and reaction pathways in SiO2 and Ti. In addition, we have used the string method [W. E, W. Ren, and E. Vanden-Eijnden, Phys. Rev. B 66, 052301 (2002); L. Maragliano et al., J. Chem. Phys. 125, 024106 (2006)] within the density functional theory to study the melting pathways in the high pressure cotunnite phase of SiO2 and the hexagonal closed packed to face centered cubic phase transition in Ti.
Agmatine: at the crossroads of the arginine pathways.

PubMed

Satriano, Joseph

2003-12-01

In acute inflammatory responses, such as wound healing and glomerulonephritis, arginine is the precursor for production of the cytostatic molecule nitric oxide (NO) and the pro-proliferative polyamines. NO is an early phase response whereas increased generation of polyamines is requisite for the later, repair phase response. The temporal switch of arginine as a substrate for the inducible nitric oxide synthase (iNOS)/NO axis to arginase/ornithine decarboxylase (ODC)/polyamine axis is subject to regulation by inflammatory cytokines as well as interregulation by the arginine metabolites themselves. Herein we describe the capacity of another arginine pathway, the metabolism of arginine to agmatine by arginine decarboxylase (ADC), to aid in this interregulation. Agmatine is an antiproliferative molecule due to its suppressive effects on intracellular polyamine levels, whereas the aldehyde metabolite of agmatine is a potent inhibitor of iNOS. We propose that the catabolism of agmatine to its aldehyde metabolite may act as a gating mechanism at the transition from the iNOS/NO axis to the arginase/ODC/polyamine axis. Thus, agmatine has the potential to serve in the coordination of the early and repair phase pathways of arginine in inflammation.
The mechanism for water exchange in [UO(2)(H(2)O)(5)](2+) and [UO(2)(oxalate)(2)(H(2)O)](2-), as studied by quantum chemical methods.

PubMed

Vallet, V; Wahlgren, U; Schimmelpfennig, B; Szabó, Z; Grenthe, I

2001-12-05

The mechanisms for the exchange of water between [UO(2)(H(2)O)(5)](2+), [UO(2)(oxalate)(2)(H(2)O)](2)(-)(,) and water solvent along dissociative (D), associative (A) and interchange (I) pathways have been investigated with quantum chemical methods. The choice of exchange mechanism is based on the computed activation energy and the geometry of the identified transition states and intermediates. These quantities were calculated both in the gas phase and with a polarizable continuum model for the solvent. There is a significant and predictable difference between the activation energy of the gas phase and solvent models: the energy barrier for the D-mechanism increases in the solvent as compared to the gas phase, while it decreases for the A- and I-mechanisms. The calculated activation energy, Delta U(++), for the water exchange in [UO(2)(H(2)O)(5)](2+) is 74, 19, and 21 kJ/mol, respectively, for the D-, A-, and I-mechanisms in the solvent, as compared to the experimental value Delta H(++) = 26 +/- 1 kJ/mol. This indicates that the D-mechanism for this system can be ruled out. The energy barrier between the intermediates and the transition states is small, indicating a lifetime for the intermediate approximately 10(-10) s, making it very difficult to distinguish between the A- and I-mechanisms experimentally. There is no direct experimental information on the rate and mechanism of water exchange in [UO(2)(oxalate)(2)(H(2)O)](2-) containing two bidentate oxalate ions. The activation energy and the geometry of transition states and intermediates along the D-, A-, and I-pathways were calculated both in the gas phase and in a water solvent model, using a single-point MP2 calculation with the gas phase geometry. The activation energy, Delta U(++), in the solvent for the D-, A-, and I-mechanisms is 56, 12, and 53 kJ/mol, respectively. This indicates that the water exchange follows an associative reaction mechanism. The geometry of the A- and I-transition states for both [UO(2)(H(2)O)(5)](2+) and [UO(2)(oxalate)(2)(H(2)O)](2-) indicates that the entering/leaving water molecules are located outside the plane formed by the spectator ligands.
Transient Structures and Possible Limits of Data Recording in Phase-Change Materials.

PubMed

Hu, Jianbo; Vanacore, Giovanni M; Yang, Zhe; Miao, Xiangshui; Zewail, Ahmed H

2015-07-28

Phase-change materials (PCMs) represent the leading candidates for universal data storage devices, which exploit the large difference in the physical properties of their transitional lattice structures. On a nanoscale, it is fundamental to determine their performance, which is ultimately controlled by the speed limit of transformation among the different structures involved. Here, we report observation with atomic-scale resolution of transient structures of nanofilms of crystalline germanium telluride, a prototypical PCM, using ultrafast electron crystallography. A nonthermal transformation from the initial rhombohedral phase to the cubic structure was found to occur in 12 ps. On a much longer time scale, hundreds of picoseconds, equilibrium heating of the nanofilm is reached, driving the system toward amorphization, provided that high excitation energy is invoked. These results elucidate the elementary steps defining the structural pathway in the transformation of crystalline-to-amorphous phase transitions and describe the essential atomic motions involved when driven by an ultrafast excitation. The establishment of the time scales of the different transient structures, as reported here, permits determination of the possible limit of performance, which is crucial for high-speed recording applications of PCMs.
MR-1 blocks the megakaryocytic differentiation and transition of CML from chronic phase to blast crisis through MEK dephosphorylation

PubMed Central

Zhao, W; He, H; Ren, K; Li, B; Zhang, H; Lin, Y; Shao, R-g

2013-01-01

Chronic myelogenous leukemia (CML) evolves from a chronic phase characterized by the Philadelphia chromosome as the sole genetic abnormality and the accumulation of mature cells in peripheral blood into blast crisis, which is characterized by the rapid expansion of myeloid- or lymphoid-differentiation-arrested blast cells. Although ample studies have been conducted on the disease progress mechanisms, the underlying molecular mechanisms of the malignant phenotype transition are still unclear. In this study, we have shown that myofibrillogenesis regulator-1 (MR-1) was overexpressed in blast crisis patients and leukemic cells, but there was little trace expressed in healthy individuals and in most patients in CML chronic phase. MR-1 could inhibit the differentiation of myeloid cells into megakaryocytic lineages and accelerate cell proliferation. The molecular mechanism responsible for these effects was the interaction of MR-1 with MEK, which blocked the MEK/ERK signaling pathway by dephosphorylating MEK. Our results provide compelling and important evidence that MR-1 might act as a diagnostic marker and potential target of CML progression from chronic phase to blast crisis. PMID:23542180
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.
Aromatic sulfonation with sulfur trioxide: mechanism and kinetic model.

PubMed

Moors, Samuel L C; Deraet, Xavier; Van Assche, Guy; Geerlings, Paul; De Proft, Frank

2017-01-01

Electrophilic aromatic sulfonation of benzene with sulfur trioxide is studied with ab initio molecular dynamics simulations in gas phase, and in explicit noncomplexing (CCl 3 F) and complexing (CH 3 NO 2 ) solvent models. We investigate different possible reaction pathways, the number of SO 3 molecules participating in the reaction, and the influence of the solvent. Our simulations confirm the existence of a low-energy concerted pathway with formation of a cyclic transition state with two SO 3 molecules. Based on the simulation results, we propose a sequence of elementary reaction steps and a kinetic model compatible with experimental data. Furthermore, a new alternative reaction pathway is proposed in complexing solvent, involving two SO 3 and one CH 3 NO 2 .
Activation of the yeast Hippo pathway by phosphorylation-dependent assembly of signaling complexes.

PubMed

Rock, Jeremy M; Lim, Daniel; Stach, Lasse; Ogrodowicz, Roksana W; Keck, Jamie M; Jones, Michele H; Wong, Catherine C L; Yates, John R; Winey, Mark; Smerdon, Stephen J; Yaffe, Michael B; Amon, Angelika

2013-05-17

Scaffold-assisted signaling cascades guide cellular decision-making. In budding yeast, one such signal transduction pathway called the mitotic exit network (MEN) governs the transition from mitosis to the G1 phase of the cell cycle. The MEN is conserved and in metazoans is known as the Hippo tumor-suppressor pathway. We found that signaling through the MEN kinase cascade was mediated by an unusual two-step process. The MEN kinase Cdc15 first phosphorylated the scaffold Nud1. This created a phospho-docking site on Nud1, to which the effector kinase complex Dbf2-Mob1 bound through a phosphoserine-threonine binding domain, in order to be activated by Cdc15. This mechanism of pathway activation has implications for signal transmission through other kinase cascades and might represent a general principle in scaffold-assisted signaling.
Phase transitions in colloidal fluids: Kinetically or thermodynamically controlled?

NASA Astrophysics Data System (ADS)

Duran-Olivencia, Miguel A.; Yatsyshin, Peter; Lutsko, James F.; Kalliadasis, Serafim

2017-11-01

In recent years, a flurry of experimental observations suggests that most phase transitions occur in a multistage manner and via intermediate phases. These precursors to the final phase are commonly understood as the local minima of the free energy of the system. Inherently, the classical paradigm of nucleation has no capacity to describe neither the origin nor the role played by these precursors in the nucleation pathway. Here we present a systematic theoretical framework capable of describing the precursor phases in a self-consistent way. We demonstrate that nucleation precursors can appear even in situations involving a single free-energy barrier. This contradicts previous phenomenological approaches, which always characterise intermediate phases as the minima of a complex free-energy landscape. We show that a kinetically-induced mechanism temporarily stabilises an intermediate phase, which thus is not the result of a local minimum of the free energy but a consequence of the entropic cost of cluster formation. Moreover, the appearance of precursors does not seem to influence the overall nucleation time, which is governed by the free-energy barrier. The mechanism uncovered in this study can be used to explain recently reported experimental findings in crystallisation. European Research Council - Advanced Grant No. 247031; Engineering and Physical Sciences Research Council - Grant Nos. EP/L020564 and EP/L025159.

The influence of age on gait parameters during the transition from a wide to a narrow pathway.

PubMed

Shkuratova, Nataliya; Taylor, Nicholas

2008-06-01

The ability to negotiate pathways of different widths is a prerequisite of daily living. However, only a few studies have investigated changes in gait parameters in response to walking on narrow pathways. The aim of this study is to examine the influence of age on gait adjustments during the transition from a wide to a narrow pathway. Two-group repeated measures design. Gait Laboratory. Twenty healthy older participants (mean [M] = 74.3 years, Standard deviation [SD] = 7.2 years); 20 healthy young participants (M = 26.6 years, SD = 6.1 years). Making the transition from walking on a wide pathway (68 cm) to walking on a narrow pathway (15 cm). Step length, step time, step width, double support time and base of support. Healthy older participants were able to make the transition from a wide to a narrow pathway successfully. There was only one significant interaction, between age and base of support (p < 0.003). Older adults decreased their base of support only when negotiating the transition step, while young participants started decreasing their base of support prior to the negotiation of transition step (p < 0.01). Adjustments to the transition from a wide to a narrow pathway are largely unaffected by normal ageing. Difficulties in making the transition to a narrow pathway during walking should not be attributed to normal age-related changes. (c) 2008 John Wiley & Sons, Ltd.
Dynamic Stacking Pathway of Perylene Dimers in Aromatic and Nonaromatic Solvents.

PubMed

Hollfelder, Manuel; Gekle, Stephan

2015-08-13

Using molecular dynamics simulations, we elucidate in detail the dynamics of the π-π stacking process of a perylene bisimide (PBI) dimer solvated in toluene. Our calculations show that the transition from the open (unstacked) to the stacked configuration is hindered by a small free energy barrier of approximately 1kBT in toluene but not in the nonaromatic solvent hexane. A similar effect is observed tor two non-covalently linked monomers. The origin of this barrier is traced back to π-π interactions between perylene and the aromatic solvent which are very similar in nature to those between two PBI monomers. The stacking process proceeds in three phases via two well-defined transition states: (i) in the first phase, the two PBI molecules share part of their respective solvation shells forming the first transition state. Further approach needs to squeeze out the shared solvent layer, thus creating the energy barrier. (ii) After removal of the separating solvent, the two PBIs form a second transition state with one monomer located at a random position in the other's solvation shell. (iii) Finally, the two PBIs slide on top of each other into their final stacked position.
Metallic hydrogen

NASA Astrophysics Data System (ADS)

Silvera, Isaac F.; Dias, Ranga

2018-06-01

Hydrogen is the simplest and most abundant element in the Universe. There are two pathways for creating metallic hydrogen under high pressures. Over 80 years ago Wigner and Huntington predicted that if solid molecular hydrogen was sufficiently compressed in the T = 0 K limit, molecules would dissociate to form atomic metallic hydrogen (MH). We have observed this transition at a pressure of 4.95 megabars. MH in this form has probably never existed on Earth or in the Universe; it may be a room temperature superconductor and is predicted to be metastable. If metastable it will have an important technological impact. Liquid metallic hydrogen can also be produced at intermediate pressures and high temperatures and is believed to make up ~90% of the planet Jupiter. We have observed this liquid–liquid transition, also known as the plasma phase transition, at pressures of ~1–2 megabar and temperatures ~1000–2000 K. However, in this paper we shall focus on the Wigner–Huntington transition. We shall discuss the methods used to observe metallic hydrogen at extreme conditions of static pressure in the laboratory, extending our understanding of the phase diagram of the simplest atom in the periodic table.
Small RNA-Sequencing Links Physiological Changes and RdDM Process to Vegetative-to-Floral Transition in Apple.

PubMed

Guo, Xinwei; Ma, Zeyang; Zhang, Zhonghui; Cheng, Lailiang; Zhang, Xiuren; Li, Tianhong

2017-01-01

Transition from vegetative to floral buds is a critical physiological change during flower induction that determines fruit productivity. Small non-coding RNAs (sRNAs) including microRNAs (miRNAs) and small interfering RNAs (siRNAs) are pivotal regulators of plant growth and development. Although the key role of sRNAs in flowering regulation has been well-described in Arabidopsis and some other annual plants, their relevance to vegetative-to-floral transition (hereafter, referred to floral transition) in perennial woody trees remains under defined. Here, we performed Illumina sequencing of sRNA libraries prepared from vegetative and floral bud during flower induction of the apple trees. A large number of sRNAs exemplified by 33 previously annotated miRNAs and six novel members display significant differential expression (DE) patterns. Notably, most of these DE-miRNAs in floral transition displayed opposite expression changes in reported phase transition in apple trees. Bioinformatics analysis suggests most of the DE-miRNAs targeted transcripts involved in SQUAMOSA PROMOTER BINDING PROTEIN-LIKE ( SPL ) gene regulation, stress responses, and auxin and gibberellin (GA) pathways, with further suggestion that there is an inherent link between physiological stress response and metabolism reprogramming during floral transition. We also observed significant changes in 24 nucleotide (nt) sRNAs that are hallmarks for RNA-dependent DNA methylation (RdDM) pathway, suggestive of the correlation between epigenetic modifications and the floral transition. The study not only provides new insight into our understanding of fundamental mechanism of poorly studied floral transition in apple and other woody plants, but also presents important sRNA resource for future in-depth research in the apple flowering physiology.
Small RNA-Sequencing Links Physiological Changes and RdDM Process to Vegetative-to-Floral Transition in Apple

PubMed Central

Guo, Xinwei; Ma, Zeyang; Zhang, Zhonghui; Cheng, Lailiang; Zhang, Xiuren; Li, Tianhong

2017-01-01

Transition from vegetative to floral buds is a critical physiological change during flower induction that determines fruit productivity. Small non-coding RNAs (sRNAs) including microRNAs (miRNAs) and small interfering RNAs (siRNAs) are pivotal regulators of plant growth and development. Although the key role of sRNAs in flowering regulation has been well-described in Arabidopsis and some other annual plants, their relevance to vegetative-to-floral transition (hereafter, referred to floral transition) in perennial woody trees remains under defined. Here, we performed Illumina sequencing of sRNA libraries prepared from vegetative and floral bud during flower induction of the apple trees. A large number of sRNAs exemplified by 33 previously annotated miRNAs and six novel members display significant differential expression (DE) patterns. Notably, most of these DE-miRNAs in floral transition displayed opposite expression changes in reported phase transition in apple trees. Bioinformatics analysis suggests most of the DE-miRNAs targeted transcripts involved in SQUAMOSA PROMOTER BINDING PROTEIN-LIKE (SPL) gene regulation, stress responses, and auxin and gibberellin (GA) pathways, with further suggestion that there is an inherent link between physiological stress response and metabolism reprogramming during floral transition. We also observed significant changes in 24 nucleotide (nt) sRNAs that are hallmarks for RNA-dependent DNA methylation (RdDM) pathway, suggestive of the correlation between epigenetic modifications and the floral transition. The study not only provides new insight into our understanding of fundamental mechanism of poorly studied floral transition in apple and other woody plants, but also presents important sRNA resource for future in-depth research in the apple flowering physiology. PMID:28611800
Spontaneous recovery of superhydrophobicity on nanotextured surfaces

PubMed Central

Prakash, Suruchi; Xi, Erte; Patel, Amish J.

2016-01-01

Rough or textured hydrophobic surfaces are dubbed “superhydrophobic” due to their numerous desirable properties, such as water repellency and interfacial slip. Superhydrophobicity stems from an aversion of water for the hydrophobic surface texture, so that a water droplet in the superhydrophobic “Cassie state” contacts only the tips of the rough surface. However, superhydrophobicity is remarkably fragile and can break down due to the wetting of the surface texture to yield the “Wenzel state” under various conditions, such as elevated pressures or droplet impact. Moreover, due to large energetic barriers that impede the reverse transition (dewetting), this breakdown in superhydrophobicity is widely believed to be irreversible. Using molecular simulations in conjunction with enhanced sampling techniques, here we show that on surfaces with nanoscale texture, water density fluctuations can lead to a reduction in the free energetic barriers to dewetting by circumventing the classical dewetting pathways. In particular, the fluctuation-mediated dewetting pathway involves a number of transitions between distinct dewetted morphologies, with each transition lowering the resistance to dewetting. Importantly, an understanding of the mechanistic pathways to dewetting and their dependence on pressure allows us to augment the surface texture design, so that the barriers to dewetting are eliminated altogether and the Wenzel state becomes unstable at ambient conditions. Such robust surfaces, which defy classical expectations and can spontaneously recover their superhydrophobicity, could have widespread importance, from underwater operation to phase-change heat transfer applications. PMID:27140619
Field-induced polarization rotation and phase transitions in 0.70 Pb ( M g 1 / 3 N b 2 / 3 ) O 3 – 0.30 PbTi O 3 piezoceramics observed by in situ high-energy x-ray scattering

DOE PAGES

Hou, Dong; Usher, Tedi -Marie; Fulanovic, Lovro; ...

2018-06-12

Changes to the crystal structure of 0.70Pb(Mg 1/3Nb 2/3)O 3–0.30PbTiO 3 (PMN-0.30PT) piezoceramic under application of electric fields at the long-range and local scale are revealed by in situ high-energy x-ray diffraction (XRD) and pair-distribution function (PDF) analyses, respectively. The crystal structure of unpoled samples is identified as monoclinic Cm at both the long-range and local scale. In situ XRD results suggest that field-induced polarization rotation and phase transitions occur at specific field strengths. A polarization rotation pathway is proposed based on the Bragg-peak behaviors and the Le Bail fitting results of the in situ XRD patterns. The PDF resultsmore » show systematic changes to the structures at the local scale, which is in agreement with the changes inferred from the in situ XRD study. More importantly, our results prove that polarization rotation can be detected and determined in a polycrystalline relaxor ferroelectric. Furthermore, this study supports the idea that multiple contributions, specifically ferroelectric-ferroelectric phase transition and polarization rotation, are responsible for the high piezoelectric properties at the morphotropic phase boundary of PMN-xPT piezoceramics.« less
Field-induced polarization rotation and phase transitions in 0.70 Pb ( M g 1 / 3 N b 2 / 3 ) O 3 – 0.30 PbTi O 3 piezoceramics observed by in situ high-energy x-ray scattering

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

Hou, Dong; Usher, Tedi -Marie; Fulanovic, Lovro

Changes to the crystal structure of 0.70Pb(Mg 1/3Nb 2/3)O 3–0.30PbTiO 3 (PMN-0.30PT) piezoceramic under application of electric fields at the long-range and local scale are revealed by in situ high-energy x-ray diffraction (XRD) and pair-distribution function (PDF) analyses, respectively. The crystal structure of unpoled samples is identified as monoclinic Cm at both the long-range and local scale. In situ XRD results suggest that field-induced polarization rotation and phase transitions occur at specific field strengths. A polarization rotation pathway is proposed based on the Bragg-peak behaviors and the Le Bail fitting results of the in situ XRD patterns. The PDF resultsmore » show systematic changes to the structures at the local scale, which is in agreement with the changes inferred from the in situ XRD study. More importantly, our results prove that polarization rotation can be detected and determined in a polycrystalline relaxor ferroelectric. Furthermore, this study supports the idea that multiple contributions, specifically ferroelectric-ferroelectric phase transition and polarization rotation, are responsible for the high piezoelectric properties at the morphotropic phase boundary of PMN-xPT piezoceramics.« less
Field-induced polarization rotation and phase transitions in 0.70 Pb (M g1 /3N b2 /3 ) O3-0.30 PbTi O3 piezoceramics observed by in situ high-energy x-ray scattering

NASA Astrophysics Data System (ADS)

Hou, Dong; Usher, Tedi-Marie; Fulanovic, Lovro; Vrabelj, Marko; Otonicar, Mojca; Ursic, Hana; Malic, Barbara; Levin, Igor; Jones, Jacob L.

2018-06-01

Changes to the crystal structure of 0.70 Pb (M g1 /3N b2 /3 ) O3-0.30 PbTi O3 (PMN-0.30PT) piezoceramic under application of electric fields at the long-range and local scale are revealed by in situ high-energy x-ray diffraction (XRD) and pair-distribution function (PDF) analyses, respectively. The crystal structure of unpoled samples is identified as monoclinic C m at both the long-range and local scale. In situ XRD results suggest that field-induced polarization rotation and phase transitions occur at specific field strengths. A polarization rotation pathway is proposed based on the Bragg-peak behaviors and the Le Bail fitting results of the in situ XRD patterns. The PDF results show systematic changes to the structures at the local scale, which is in agreement with the changes inferred from the in situ XRD study. More importantly, our results prove that polarization rotation can be detected and determined in a polycrystalline relaxor ferroelectric. This study supports the idea that multiple contributions, specifically ferroelectric-ferroelectric phase transition and polarization rotation, are responsible for the high piezoelectric properties at the morphotropic phase boundary of PMN-x PT piezoceramics.
Nucleation via an unstable intermediate phase.

PubMed

Sear, Richard P

2009-08-21

The pathway for crystallization from dilute vapors and solutions is often observed to take a detour via a liquid or concentrated-solution phase. For example, in moist subzero air, droplets of liquid water form, which then freeze. In this example and in many others, an intermediate phase (here liquid water) is dramatically accelerating the kinetics of a phase transition between two other phases (water vapor and ice). Here we study this phenomenon via exact computer simulations of a simple lattice model. Surprisingly, we find that the rate of nucleation of the new equilibrium phase is actually fastest when the intermediate phase is slightly unstable in the bulk, i.e., has a slightly higher free energy than the phase we start in. Nucleation occurs at a concave part of the surface and microscopic amounts of the intermediate phase can form there even before the phase is stable in the bulk. As the nucleus of the equilibrium phase is microscopic, this allows nucleation to occur effectively in the intermediate phase before it is stable in the bulk.
New pathways for formation of acids and carbonyl products in low-temperature oxidation: the Korcek decomposition of γ-ketohydroperoxides.

PubMed

Jalan, Amrit; Alecu, Ionut M; Meana-Pañeda, Rubén; Aguilera-Iparraguirre, Jorge; Yang, Ke R; Merchant, Shamel S; Truhlar, Donald G; Green, William H

2013-07-31

We present new reaction pathways relevant to low-temperature oxidation in gaseous and condensed phases. The new pathways originate from γ-ketohydroperoxides (KHP), which are well-known products in low-temperature oxidation and are assumed to react only via homolytic O-O dissociation in existing kinetic models. Our ab initio calculations identify new exothermic reactions of KHP forming a cyclic peroxide isomer, which decomposes via novel concerted reactions into carbonyl and carboxylic acid products. Geometries and frequencies of all stationary points are obtained using the M06-2X/MG3S DFT model chemistry, and energies are refined using RCCSD(T)-F12a/cc-pVTZ-F12 single-point calculations. Thermal rate coefficients are computed using variational transition-state theory (VTST) calculations with multidimensional tunneling contributions based on small-curvature tunneling (SCT). These are combined with multistructural partition functions (Q(MS-T)) to obtain direct dynamics multipath (MP-VTST/SCT) gas-phase rate coefficients. For comparison with liquid-phase measurements, solvent effects are included using continuum dielectric solvation models. The predicted rate coefficients are found to be in excellent agreement with experiment when due consideration is made for acid-catalyzed isomerization. This work provides theoretical confirmation of the 30-year-old hypothesis of Korcek and co-workers that KHPs are precursors to carboxylic acid formation, resolving an open problem in the kinetics of liquid-phase autoxidation. The significance of the new pathways in atmospheric chemistry, low-temperature combustion, and oxidation of biological lipids are discussed.
New Pathways for Formation of Acids and Carbonyl Products in Low-Temperature Oxidation: The Korcek Decomposition of γ-Ketohydroperoxides

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

Jalan, Amrit; Alecu, Ionut M.; Meana-Pañeda, Rubén

2013-07-31

We present new reaction pathways relevant to low-temperature oxidation in gaseous and condensed phases. The new pathways originate from γ-ketohydroperoxides (KHP), which are well-known products in low-temperature oxidation and are assumed to react only via homolytic O-O dissociation in existing kinetic models. Our ab initio calculations identify new exothermic reactions of KHP forming a cyclic peroxide isomer, which decomposes via novel concerted reactions into carbonyl and carboxylic acid products. Geometries and frequencies of all stationary points are obtained using the M06-2X/MG3S DFT model chemistry, and energies are refined using RCCSD(T)-F12a/cc-pVTZ-F12 single-point calculations. Thermal rate coefficients are computed using variational transition-statemore » theory (VTST) calculations with multidimensional tunneling contributions based on small-curvature tunneling (SCT). These are combined with multistructural partition functions (QMS-T) to obtain direct dynamics multipath (MP-VTST/ SCT) gas-phase rate coefficients. For comparison with liquid-phase measurements, solvent effects are included using continuum dielectric solvation models. The predicted rate coefficients are found to be in excellent agreement with experiment when due consideration is made for acid-catalyzed isomerization. This work provides theoretical confirmation of the 30-year-old hypothesis of Korcek and co-workers that KHPs are precursors to carboxylic acid formation, resolving an open problem in the kinetics of liquid-phase autoxidation. The significance of the new pathways in atmospheric chemistry, low-temperature combustion, and oxidation of biological lipids are discussed.« less
Formation of Silicate Grains in Circumstellar Environments: Experiment, Theory and Observations

NASA Technical Reports Server (NTRS)

Castleman, A., Jr.; Reber, A.; Clayborne, P.; Reveles, J.; Khanna, S.; Ali, A.

2006-01-01

Amongst chemical reactions (1) in the molecular universe (2), condensation reaction is probably the most poorly understood. The condensation of a solid from its components in the gas phase occurs in many parts of our galaxy such as stellar mass outflows, the terrestrial region of protoplanetary disks and in primordial solar nebula (3). But how does the transition occur from molecules to intermediate clusters to macroscopic grains? The major focus of the present work is the identification of chemical condensation reaction pathways that lead to the formation of stoichiometry, composition and crystallinity of cosmic silicates from vapor phase species.
Pressure-induced silica quartz amorphization studied by iterative stochastic surface walking reaction sampling.

PubMed

Zhang, Xiao-Jie; Shang, Cheng; Liu, Zhi-Pan

2017-02-08

The crystal to amorphous transformation is a common phenomenon in Nature and has important impacts on material properties. Our current knowledge on such complex solid transformation processes is, however, limited because of their slow kinetics and the lack of long-range ordering in amorphous structures. To reveal the kinetics in the amorphization of solids, this work, by developing iterative reaction sampling based on the stochastic surface walking global optimization method, investigates the well-known crystal to amorphous transformation of silica (SiO 2 ) under external pressures, the mechanism of which has long been debated for its non-equilibrium, pressure-sensitive kinetics and complex product components. Here we report for the first time the global potential energy surface (PES) and the lowest energy pathways for α-quartz amorphization from first principles. We show that the pressurization at 15 GPa, the reaction condition, can lift the quartz phase energetically close to the amorphous zone, which thermodynamically initializes the amorphization. More importantly, the large flexibility of Si cation coordination (including four, five and six coordination) results in many kinetically competing routes to more stable dense forms, including the known MI, stishovite, newly-identified MII and TI phases. All these pathways have high barriers due to the local Si-O bond breaking and are mediated by amorphous structures with five-fold Si. This causes simultaneous crystal-to-crystal and crystal-to-amorphous transitions. The high barrier and the reconstructive nature of the phase transition are the key kinetics origin for silica amorphization under pressures.
Microscopic and histochemical manifestations of hyaline cartilage dynamics.

PubMed

Malinin, G I; Malinin, T I

1999-01-01

Structure and function of hyaline cartilages has been the focus of many correlative studies for over a hundred years. Much of what is known regarding dynamics and function of cartilage constituents has been derived or inferred from biochemical and electron microscopic investigations. Here we show that in conjunction with ultrastructural, and high-magnification transmission light and polarization microscopy, the well-developed histochemical methods are indispensable for the analysis of cartilage dynamics. Microscopically demonstrable aspects of cartilage dynamics include, but are not limited to, formation of the intracellular liquid crystals, phase transitions of the extracellular matrix and tubular connections between chondrocytes. The role of the interchondrocytic liquid crystals is considered in terms of the tensegrity hypothesis and non-apoptotic cell death. Phase transitions of the extracellular matrix are discussed in terms of self-alignment of chondrons, matrix guidance pathways and cartilage growth in the absence of mitosis. The possible role of nonenzymatic glycation reactions in cartilage dynamics is also reviewed.
Amorphous ices explained in terms of nonequilibrium phase transitions in supercooled water

NASA Astrophysics Data System (ADS)

Limmer, David; Chandler, David

2013-03-01

We analyze the phase diagram of supercooled water out-of-equilibrium using concepts from space-time thermodynamics and the dynamic facilitation theory of the glass transition, together with molecular dynamics simulations. We find that when water is driven out-of-equilibrium, it can exist in multiple amorphous states. In contrast, we find that when water is at equilibrium, it can exist in only one liquid state. The amorphous non-equilibrium states are solids, distinguished from the liquid by their lack of mobility, and distinguished from each other by their different densities and local structure. This finding explains the experimentally observed polyamorphism of water as a class of nonequilibrium phenomena involving glasses of different densities. While the amorphous solids can be long lived, they are thermodynamically unstable. When allowed to relax to equilibrium, they crystallize with pathways that pass first through liquid state configurations and then to ordered ice.
Probing the thermal stability and the decomposition mechanism of a magnesium-fullerene polymer via X-ray Raman spectroscopy, X-ray diffraction and molecular dynamics simulations.

PubMed

Aramini, Matteo; Niskanen, Johannes; Cavallari, Chiara; Pontiroli, Daniele; Musazay, Abdurrahman; Krisch, Michael; Hakala, Mikko; Huotari, Simo

2016-02-21

We report the microscopic view of the thermal structural stability of the magnesium intercalated fullerene polymer Mg2C60. With the application of X-ray Raman spectroscopy and X-ray diffraction, we study in detail the decomposition pathways of the polymer system upon annealing at temperatures between 300 and 700 °C. We show that there are at least two energy scales involved in the decomposition reaction. Intermolecular carbon bonds, which are responsible for the formation of a 2D fullerene polymer, are broken with a relatively modest thermal energy, while the long-range order of the original polymer remains intact. With an increased thermal energy, the crystal structure in turn is found to undergo a transition to a novel intercalated cubic phase that is stable up to the highest temperature studied here. The local structure surrounding magnesium ions gets severely modified close to, possibly at, the phase transition. We used density functional theory based calculations to study the thermodynamic and kinetic aspects of the collapse of the fullerene network, and to explain the intermediate steps as well as the reaction pathways in the break-up of this peculiar C60 intermolecular bonding architecture.
Combined Effects of Feedforward Inhibition and Excitation in Thalamocortical Circuit on the Transitions of Epileptic Seizures

PubMed Central

Fan, Denggui; Duan, Lixia; Wang, Qian; Luan, Guoming

2017-01-01

The mechanisms underlying electrophysiologically observed two-way transitions between absence and tonic-clonic epileptic seizures in cerebral cortex remain unknown. The interplay within thalamocortical network is believed to give rise to these epileptic multiple modes of activity and transitions between them. In particular, it is thought that in some areas of cortex there exists feedforward inhibition from specific relay nucleus of thalamus (TC) to inhibitory neuronal population (IN) which has even more stronger functions on cortical activities than the known feedforward excitation from TC to excitatory neuronal population (EX). Inspired by this, we proposed a modified computational model by introducing feedforward inhibitory connectivity within thalamocortical circuit, to systematically investigate the combined effects of feedforward inhibition and excitation on transitions of epileptic seizures. We first found that the feedforward excitation can induce the transition from tonic oscillation to spike and wave discharges (SWD) in cortex, i.e., the epileptic tonic-absence seizures, with the fixed weak feedforward inhibition. Thereinto, the phase of absence seizures corresponding to strong feedforward excitation can be further transformed into the clonic oscillations with the increasing of feedforward inhibition, representing the epileptic absence-clonic seizures. We also observed the other fascinating dynamical states, such as periodic 2/3/4-spike and wave discharges, reversed SWD and clonic oscillations, as well as saturated firings. More importantly, we can identify the stable parameter regions representing the tonic-clonic oscillations and SWD discharges of epileptic seizures on the 2-D plane composed of feedforward inhibition and excitation, where the physiologically plausible transition pathways between tonic-clonic and absence seizures can be figured out. These results indicate the functional role of feedforward pathways in controlling epileptic seizures and the modified thalamocortical model may provide a guide for future efforts to mechanistically link feedforward pathways in the pathogenesis of epileptic seizures. PMID:28736520
On structural transitions, thermodynamic equilibrium, and the phase diagram of DNA and RNA duplexes under torque and tension.

PubMed

Wereszczynski, Jeff; Andricioaei, Ioan

2006-10-31

A precise understanding of the flexibility of double stranded nucleic acids and the nature of their deformed conformations induced by external forces is important for a wide range of biological processes including transcriptional regulation, supercoil and catenane removal, and site-specific recombination. We present, at atomic resolution, a simulation of the dynamics involved in the transitions from B-DNA and A-RNA to Pauling (P) forms and to denatured states driven by application of external torque and tension. We then calculate the free energy profile along a B- to P-transition coordinate and from it, compute a reversible pathway, i.e., an isotherm of tension and torque pairs required to maintain P-DNA in equilibrium. The reversible isotherm maps correctly onto a phase diagram derived from single molecule experiments, and yields values of elongation, twist, and twist-stretch coupling in agreement with measured values. We also show that configurational entropy compensates significantly for the large electrostatic energy increase due to closer-packed P backbones. A similar set of simulations applied to RNA are used to predict a novel structure, P-RNA, with its associated free energy, equilibrium tension, torque and structural parameters, and to assign the location, on the phase-diagram, of a putative force-torque-dependent RNA "triple point."
Coherent Control of Nanoscale Ballistic Currents in Transition Metal Dichalcogenide ReS2.

PubMed

Cui, Qiannan; Zhao, Hui

2015-04-28

Transition metal dichalcogenides are predicted to outperform traditional semiconductors in ballistic devices with nanoscale channel lengths. So far, experimental studies on charge transport in transition metal dichalcogenides are limited to the diffusive regime. Here we show, using ReS2 as an example, all-optical injection, detection, and coherent control of ballistic currents. By utilizing quantum interference between one-photon and two-photon interband transition pathways, ballistic currents are injected in ReS2 thin film samples by a pair of femtosecond laser pulses. We find that the current decays on an ultrafast time scale, resulting in an electron transport of only a fraction of one nanometer. Following the relaxation of the initially injected momentum, backward motion of the electrons for about 1 ps is observed, driven by the Coulomb force from the oppositely moved holes. We also show that the injected current can be controlled by the phase of the laser pulses. These results demonstrate a new platform to study ballistic transport of nonequilibrium carriers in transition metal dichalcogenides.

Protein Folding Mechanism of the Dimeric AmphiphysinII/Bin1 N-BAR Domain

PubMed Central

Gruber, Tobias; Balbach, Jochen

2015-01-01

The human AmphyphisinII/Bin1 N-BAR domain belongs to the BAR domain superfamily, whose members sense and generate membrane curvatures. The N-BAR domain is a 57 kDa homodimeric protein comprising a six helix bundle. Here we report the protein folding mechanism of this protein as a representative of this protein superfamily. The concentration dependent thermodynamic stability was studied by urea equilibrium transition curves followed by fluorescence and far-UV CD spectroscopy. Kinetic unfolding and refolding experiments, including rapid double and triple mixing techniques, allowed to unravel the complex folding behavior of N-BAR. The equilibrium unfolding transition curve can be described by a two-state process, while the folding kinetics show four refolding phases, an additional burst reaction and two unfolding phases. All fast refolding phases show a rollover in the chevron plot but only one of these phases depends on the protein concentration reporting the dimerization step. Secondary structure formation occurs during the three fast refolding phases. The slowest phase can be assigned to a proline isomerization. All kinetic experiments were also followed by fluorescence anisotropy detection to verify the assignment of the dimerization step to the respective folding phase. Based on these experiments we propose for N-BAR two parallel folding pathways towards the homodimeric native state depending on the proline conformation in the unfolded state. PMID:26368922
Sulforaphane inhibits TGF-β-induced epithelial-mesenchymal transition of hepatocellular carcinoma cells via the reactive oxygen species-dependent pathway.

PubMed

Wu, Jinsheng; Han, Jingli; Hou, Benxin; Deng, Chengwei; Wu, Huanliang; Shen, Liangfang

2016-05-01

Sulforaphane is recognized as a safe antitumor agent derived from various cruciferous vegetables, including broccoli. It has been demonstrated that sulforaphase is a potent antitumor agent in diverse cancers. However, its effect on hepatocellular carcinoma remains largely unknown. Here, we show that sulforaphane inhibits TGF-β-induced epithelial-mesenchymal transition of hepatocellular carcinoma cell via the reactive oxygen species-dependent pathway. We found sulforaphane inhibited hepatocellular carcinoma cell proliferation in a dose- and time-dependent manner. Sulforaphane induced G0/G1 phase cell cycle arrest and promoted cell apoptosis. A set of experiments showed that sulforaphase inhibited hepatocellular carcinoma cell migration and invasion, inhibited the formation of fibroblast like mesenchymal cells and the expression of Vimentin, but increased the expression of E-cadherin, suggesting sulforaphane suppresses epithelial-mesenchymal transition (EMT) process. Cotreatment with N-acetyl-L-cysteine inhibited sulforaphane-inhibited invasion and upregulation of E-cadherin and almost completely abolished the sulforaphane-induced expression of Vimentin. The effect of sulforaphane on the growth of hepatocellular carcinoma cells was confirmed by a xenograft tumor growth model. All our finding indicated that sulforaphane is a promising and safe strategy for treating hepatocellular carcinoma.
Multiple-probe analysis of folding and unfolding pathways of human serum albumin. Evidence for a framework mechanism of folding.

PubMed

Santra, Manas Kumar; Banerjee, Abhijit; Krishnakumar, Shyam Sundar; Rahaman, Obaidur; Panda, Dulal

2004-05-01

The changes in the far-UV CD signal, intrinsic tryptophan fluorescence and bilirubin absorbance showed that the guanidine hydrochloride (GdnHCl)-induced unfolding of a multidomain protein, human serum albumin (HSA), followed a two-state process. However, using environment sensitive Nile red fluorescence, the unfolding and folding pathways of HSA were found to follow a three-state process and an intermediate was detected in the range 0.25-1.5 m GdnHCl. The intermediate state displayed 45% higher fluorescence intensity than that of the native state. The increase in the Nile red fluorescence was found to be due to an increase in the quantum yield of the HSA-bound Nile red. Low concentrations of GdnHCl neither altered the binding affinity of Nile red to HSA nor induced the aggregation of HSA. In addition, the secondary structure of HSA was not perturbed during the first unfolding transition (<1.5 m GdnHCl); however, the secondary structure was completely lost during the second transition. The data together showed that the half maximal loss of the tertiary structure occurred at a lower GdnHCl concentration than the loss of the secondary structure. Further kinetic studies of the refolding process of HSA using multiple spectroscopic techniques showed that the folding occurred in two phases, a burst phase followed by a slow phase. An intermediate with native-like secondary structure but only a partial tertiary structure was found to form in the burst phase of refolding. Then, the intermediate slowly folded into the native state. An analysis of the refolding data suggested that the folding of HSA could be best explained by the framework model.
Two Bistable Switches Govern M Phase Entry.

PubMed

Mochida, Satoru; Rata, Scott; Hino, Hirotsugu; Nagai, Takeharu; Novák, Béla

2016-12-19

The abrupt and irreversible transition from interphase to M phase is essential to separate DNA replication from chromosome segregation. This transition requires the switch-like phosphorylation of hundreds of proteins by the cyclin-dependent kinase 1 (Cdk1):cyclin B (CycB) complex. Previous studies have ascribed these switch-like phosphorylations to the auto-activation of Cdk1:CycB through the removal of inhibitory phosphorylations on Cdk1-Tyr15 [1, 2]. The positive feedback in Cdk1 activation creates a bistable switch that makes mitotic commitment irreversible [2-4]. Here, we surprisingly find that Cdk1 auto-activation is dispensable for irreversible, switch-like mitotic entry due to a second mechanism, whereby Cdk1:CycB inhibits its counteracting phosphatase (PP2A:B55). We show that the PP2A:B55-inhibiting Greatwall (Gwl)-endosulfine (ENSA) pathway is both necessary and sufficient for switch-like phosphorylations of mitotic substrates. Using purified components of the Gwl-ENSA pathway in a reconstituted system, we found a sharp Cdk1 threshold for phosphorylation of a luminescent mitotic substrate. The Cdk1 threshold to induce mitotic phosphorylation is distinctly higher than the Cdk1 threshold required to maintain these phosphorylations-evidence for bistability. A combination of mathematical modeling and biochemical reconstitution show that the bistable behavior of the Gwl-ENSA pathway emerges from its mutual antagonism with PP2A:B55. Our results demonstrate that two interlinked bistable mechanisms provide a robust solution for irreversible and switch-like mitotic entry. Copyright © 2016 Elsevier Ltd. All rights reserved.
Unimolecular Reaction Pathways of a γ-Ketohydroperoxide from Combined Application of Automated Reaction Discovery Methods

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

Grambow, Colin A.; Jamal, Adeel; Li, Yi -Pei

Ketohydroperoxides are important in liquid-phase autoxidation and in gas-phase partial oxidation and pre-ignition chemistry, but because of their low concentration, instability, and various analytical chemistry limitations, it has been challenging to experimentally determine their reactivity, and only a few pathways are known. In the present work, 75 elementary-step unimolecular reactions of the simplest γ-ketohydroperoxide, 3-hydroperoxypropanal, were discovered by a combination of density functional theory with several automated transition-state search algorithms: the Berny algorithm coupled with the freezing string method, single- and double-ended growing string methods, the heuristic KinBot algorithm, and the single-component artificial force induced reaction method (SC-AFIR). The presentmore » joint approach significantly outperforms previous manual and automated transition-state searches – 68 of the reactions of γ-ketohydroperoxide discovered here were previously unknown and completely unexpected. All of the methods found the lowest-energy transition state, which corresponds to the first step of the Korcek mechanism, but each algorithm except for SC-AFIR detected several reactions not found by any of the other methods. We show that the low-barrier chemical reactions involve promising new chemistry that may be relevant in atmospheric and combustion systems. Our study highlights the complexity of chemical space exploration and the advantage of combined application of several approaches. Altogether, the present work demonstrates both the power and the weaknesses of existing fully automated approaches for reaction discovery which suggest possible directions for further method development and assessment in order to enable reliable discovery of all important reactions of any specified reactant(s).« less
Unimolecular Reaction Pathways of a γ-Ketohydroperoxide from Combined Application of Automated Reaction Discovery Methods

DOE PAGES

Grambow, Colin A.; Jamal, Adeel; Li, Yi -Pei; ...

2017-12-22

Ketohydroperoxides are important in liquid-phase autoxidation and in gas-phase partial oxidation and pre-ignition chemistry, but because of their low concentration, instability, and various analytical chemistry limitations, it has been challenging to experimentally determine their reactivity, and only a few pathways are known. In the present work, 75 elementary-step unimolecular reactions of the simplest γ-ketohydroperoxide, 3-hydroperoxypropanal, were discovered by a combination of density functional theory with several automated transition-state search algorithms: the Berny algorithm coupled with the freezing string method, single- and double-ended growing string methods, the heuristic KinBot algorithm, and the single-component artificial force induced reaction method (SC-AFIR). The presentmore » joint approach significantly outperforms previous manual and automated transition-state searches – 68 of the reactions of γ-ketohydroperoxide discovered here were previously unknown and completely unexpected. All of the methods found the lowest-energy transition state, which corresponds to the first step of the Korcek mechanism, but each algorithm except for SC-AFIR detected several reactions not found by any of the other methods. We show that the low-barrier chemical reactions involve promising new chemistry that may be relevant in atmospheric and combustion systems. Our study highlights the complexity of chemical space exploration and the advantage of combined application of several approaches. Altogether, the present work demonstrates both the power and the weaknesses of existing fully automated approaches for reaction discovery which suggest possible directions for further method development and assessment in order to enable reliable discovery of all important reactions of any specified reactant(s).« less
Weak values, 'negative probability', and the uncertainty principle

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

Sokolovski, D.

2007-10-15

A quantum transition can be seen as a result of interference between various pathways (e.g., Feynman paths), which can be labeled by a variable f. An attempt to determine the value of f without destroying the coherence between the pathways produces a weak value of f. We show f to be an average obtained with an amplitude distribution which can, in general, take negative values, which, in accordance with the uncertainty principle, need not contain information about the actual range of f which contributes to the transition. It is also demonstrated that the moments of such alternating distributions have amore » number of unusual properties which may lead to a misinterpretation of the weak-measurement results. We provide a detailed analysis of weak measurements with and without post-selection. Examples include the double-slit diffraction experiment, weak von Neumann and von Neumann-like measurements, traversal time for an elastic collision, phase time, and local angular momentum.« less
SMZ/SNZ and gibberellin signaling are required for nitrate-elicited delay of flowering time in Arabidopsis thaliana.

PubMed

Gras, Diana E; Vidal, Elena A; Undurraga, Soledad F; Riveras, Eleodoro; Moreno, Sebastián; Dominguez-Figueroa, José; Alabadi, David; Blázquez, Miguel A; Medina, Joaquín; Gutiérrez, Rodrigo A

2018-01-23

The reproductive success of plants largely depends on the correct programming of developmental phase transitions, particularly the shift from vegetative to reproductive growth. The timing of this transition is finely regulated by the integration of an array of environmental and endogenous factors. Nitrogen is the mineral macronutrient that plants require in the largest amount, and as such its availability greatly impacts on many aspects of plant growth and development, including flowering time. We found that nitrate signaling interacts with the age-related and gibberellic acid pathways to control flowering time in Arabidopsis thaliana. We revealed that repressors of flowering time belonging to the AP2-type transcription factor family including SCHLAFMUTZE (SMZ) and SCHNARCHZAPFEN (SNZ) are important regulators of flowering time in response to nitrate. Our results support a model whereby nitrate activates SMZ and SNZ via the gibberellin pathway to repress flowering time in Arabidopsis thaliana. © The Author(s) 2017. Published by Oxford University Press on behalf of the Society for Experimental Biology.
Transition model for ricin-aptamer interactions with multiple pathways and energy barriers

NASA Astrophysics Data System (ADS)

Wang, Bin; Xu, Bingqian

2014-02-01

We develop a transition model to interpret single-molecule ricin-aptamer interactions with multiple unbinding pathways and energy barriers measured by atomic force microscopy dynamic force spectroscopy. Molecular simulations establish the relationship between binding conformations and the corresponding unbinding pathways. Each unbinding pathway follows a Bell-Evans multiple-barrier model. Markov-type transition matrices are developed to analyze the redistribution of unbinding events among the pathways under different loading rates. Our study provides detailed information about complex behaviors in ricin-aptamer unbinding events.
Photodissociation Spectroscopy of Anionic Transition Metal Complexes

NASA Astrophysics Data System (ADS)

Kaufman, Sydney Hamilton

Transition metal complexes play an important role in many aspects of chemistry; whether in supporting biological functions, as catalysts for organic reactions, in the environment, or in industry. This thesis is comprised of gas-phase spectroscopic studies of four transition metal species with implications for many different chemical applications. Most knowledge of the target molecules in this thesis are derived from studies in the condensed phase, where the chemical environment can change molecular properties. As a result, it is difficult to gain an understanding of the intrinsic properties in solution as well as a molecular-level picture of chemical reactions that take place where many oxidation states, molecular species, and solvent interactions occur. By isolating one particular species in the gas phase, we are able to observe how each species interacts with light independent of perturbing effects of solvent and counter ions. In this thesis, we perform spectroscopic experiments on mass-selected ions in the gas phase, where we are able to gain information on intrinsic molecular properties without the influence of a condensed phase chemical environment. We employ photodissociation spectroscopy, where we mass-select a particular ionic species from solution and irradiate that molecular ion with the output of a tunable laser in the ultraviolet and visible regions. By monitoring the fragments produced, we can obtain an electronic absorption spectrum of the isolated species as well as gain insight into the photochemistry of the ions under study from the fragmentation pathways observed. We combine this method with solution absorption spectra as well as electronic structure calculations.
Unimolecular dissociation of protonated trans-1,4-diphenyl-2-butene-1,4-dione in the gas phase: rearrangement versus simple cleavage.

PubMed

Wu, Lianming; Liu, David Q; Vogt, Frederick G

2006-01-01

Fragmentation mechanisms of trans-1,4-diphenyl-2-butene-1,4-dione were studied using a variety of mass spectrometric techniques. The major fragmentation pathways occur by various rearrangements by loss of H(2)O, CO, H(2)O and CO, and CO(2). The other fragmentation pathways via simple alpha cleavages were also observed but accounted for the minor dissociation channels in both a two-dimensional (2-D) linear ion trap and a quadrupole time-of-flight (Q-TOF) mass spectrometer. The elimination of CO(2) (rather than CH(3)CHO or C(3)H(8)), which was confirmed by an exact mass measurement using the Q-TOF instrument, represented a major fragmentation pathway in the 2-D linear ion trap mass spectrometer. However, the elimination of H(2)O and CO becomes more competitive in the beam-type Q-TOF instrument. The loss of CO is observed in both the MS(2) experiment of m/z 237 and the MS(3) experiment of m/z 219 but via the different transition states. The data suggest that the olefinic double bond in protonated trans-1,4-diphenyl-2-butene-1,4-dione plays a key role in stabilizing the rearrangement transition states and increasing the bond dissociation (cleavage) energy to give favorable rearrangement fragmentation pathways. Copyright (c) 2006 John Wiley & Sons, Ltd.
Inhibition of Rac1 activity induces G1/S phase arrest through the GSK3/cyclin D1 pathway in human cancer cells.

PubMed

Liu, Linna; Zhang, Hongmei; Shi, Lei; Zhang, Wenjuan; Yuan, Juanli; Chen, Xiang; Liu, Juanjuan; Zhang, Yan; Wang, Zhipeng

2014-10-01

Rac1 has been shown to regulate the cell cycle in cancer cells. Yet, the related mechanism remains unclear. Thus, the present study aimed to investigate the mechanism involved in the regulation of G1/S phase transition by Rac1 in cancer cells. Inhibition of Rac1 by inhibitor NSC23766 induced G1/S phase arrest and inhibited the proliferation of A431, SW480 and U2-OS cells. Suppression of GSK3 by shRNA partially rescued G1/S phase arrest and inhibition of proliferation. Incubation of cells with NSC23766 reduced p-AKT and inactivated p-GSK3α and p-GSK3β, increased p-cyclin D1 expression and decreased the level of cyclin D1 protein. Consequently, cyclin D1 targeting transcriptional factor E2F1 expression, which promotes G1 to S phase transition, was also reduced. In contrast, constitutive active Rac1 resulted in increased p-AKT and inactivated p-GSK3α and p-GSK3β, decreased p-cyclin D1 expression and enhanced levels of cyclin D1 and E2F1 expression. Moreover, suppression of GSK3 did not alter p-AKT or Rac1 activity, but decreased p-cyclin D1 and increased total cyclin D1 protein. However, neither Rac1 nor GSK3 inhibition altered cyclin D1 at the RNA level. Moreover, after inhibition of Rac1 or GSK3 following proteasome inhibitor MG132 treatment, cyclin D1 expression at the protein level remained constant, indicating that Rac1 and GSK3 may regulate cyclin D1 turnover through phosphorylation and degradation. Therefore, our findings suggest that inhibition of Rac1 induces cell cycle G1/S arrest in cancer cells by regulation of the GSK3/cyclin D1 pathway.
An integrated framework for the optimisation of sport and athlete development: a practitioner approach.

PubMed

Gulbin, Jason P; Croser, Morag J; Morley, Elissa J; Weissensteiner, Juanita R

2013-01-01

This paper introduces a new sport and athlete development framework that has been generated by multidisciplinary sport practitioners. By combining current theoretical research perspectives with extensive empirical observations from one of the world's leading sport agencies, the proposed FTEM (Foundations, Talent, Elite, Mastery) framework offers broad utility to researchers and sporting stakeholders alike. FTEM is unique in comparison with alternative models and frameworks, because it: integrates general and specialised phases of development for participants within the active lifestyle, sport participation and sport excellence pathways; typically doubles the number of developmental phases (n = 10) in order to better understand athlete transition; avoids chronological and training prescriptions; more optimally establishes a continuum between participation and elite; and allows full inclusion of many developmental support drivers at the sport and system levels. The FTEM framework offers a viable and more flexible alternative for those sporting stakeholders interested in managing, optimising, and researching sport and athlete development pathways.
Confinement and low adhesion induce fast amoeboid migration of slow mesenchymal cells.

PubMed

Liu, Yan-Jun; Le Berre, Maël; Lautenschlaeger, Franziska; Maiuri, Paolo; Callan-Jones, Andrew; Heuzé, Mélina; Takaki, Tohru; Voituriez, Raphaël; Piel, Matthieu

2015-02-12

The mesenchymal-amoeboid transition (MAT) was proposed as a mechanism for cancer cells to adapt their migration mode to their environment. While the molecular pathways involved in this transition are well documented, the role of the microenvironment in the MAT is still poorly understood. Here, we investigated how confinement and adhesion affect this transition. We report that, in the absence of focal adhesions and under conditions of confinement, mesenchymal cells can spontaneously switch to a fast amoeboid migration phenotype. We identified two main types of fast migration--one involving a local protrusion and a second involving a myosin-II-dependent mechanical instability of the cell cortex that leads to a global cortical flow. Interestingly, transformed cells are more prone to adopt this fast migration mode. Finally, we propose a generic model that explains migration transitions and predicts a phase diagram of migration phenotypes based on three main control parameters: confinement, adhesion, and contractility. Copyright © 2015 Elsevier Inc. All rights reserved.
A Comparison of Photocatalytic Activities of Gold Nanoparticles Following Plasmonic and Interband Excitation and a Strategy for Harnessing Interband Hot Carriers for Solution Phase Photocatalysis

PubMed Central

2017-01-01

Light driven excitation of gold nanoparticles (GNPs) has emerged as a potential strategy to generate hot carriers for photocatalysis through excitation of localized surface plasmon resonance (LSPR). In contrast, carrier generation through excitation of interband transitions remains a less explored and underestimated pathway for photocatalytic activity. Photoinduced oxidative etching of GNPs with FeCl3 was investigated as a model reaction in order to elucidate the effects of both types of transitions. The quantitative results show that interband transitions more efficiently generate hot carriers and that those carriers exhibit higher reactivity as compared to those generated solely by LSPR. Further, leveraging the strong π-acidic character of the resulting photogenerated Au+ hole, an interband transition induced cyclization reaction of alkynylphenols was developed. Notably, alkyne coordination to the Au+ hole intercepts the classic oxidation event and leads to the formation of the catalytically active gold clusters on subnanometer scale. PMID:28573211
Does It Really Matter Where You Look When Walking on Stairs? Insights from a Dual-Task Study

PubMed Central

Miyasike-daSilva, Veronica; McIlroy, William E.

2012-01-01

Although the visual system is known to provide relevant information to guide stair locomotion, there is less understanding of the specific contributions of foveal and peripheral visual field information. The present study investigated the specific role of foveal vision during stair locomotion and ground-stairs transitions by using a dual-task paradigm to influence the ability to rely on foveal vision. Fifteen healthy adults (26.9±3.3 years; 8 females) ascended a 7-step staircase under four conditions: no secondary tasks (CONTROL); gaze fixation on a fixed target located at the end of the pathway (TARGET); visual reaction time task (VRT); and auditory reaction time task (ART). Gaze fixations towards stair features were significantly reduced in TARGET and VRT compared to CONTROL and ART. Despite the reduced fixations, participants were able to successfully ascend stairs and rarely used the handrail. Step time was increased during VRT compared to CONTROL in most stair steps. Navigating on the transition steps did not require more gaze fixations than the middle steps. However, reaction time tended to increase during locomotion on transitions suggesting additional executive demands during this phase. These findings suggest that foveal vision may not be an essential source of visual information regarding stair features to guide stair walking, despite the unique control challenges at transition phases as highlighted by phase-specific challenges in dual-tasking. Instead, the tendency to look at the steps in usual conditions likely provides a stable reference frame for extraction of visual information regarding step features from the entire visual field. PMID:22970297
A p53-independent damage-sensing mechanism that functions as a checkpoint at the G1/S transition in Chinese hamster ovary cells

PubMed Central

Lee, Hoyun; Larner, James M.; Hamlin, Joyce L.

1997-01-01

In response to a moderate dose of radiation, asynchronous mammalian cell populations rapidly and transiently down-regulate the rate of DNA synthesis to ≈50% of preirradiation values. We show here that only half of the reduction in overall replication rate can be accounted for by direct inhibition of initiation at origins in S-phase cells. The other half results from the operation of a newly defined cell cycle checkpoint that functions at the G1/S transition. This checkpoint senses damage incurred at any time during the last 2 hr of G1 and effectively prevents entry into the S period. The G1/S and S-phase checkpoints are both p53-independent and, unlike the p53-mediated G1 checkpoint, respond rapidly to radiation, suggesting that they may represent major damage-sensing mechanisms connecting the replication machinery with DNA repair pathways. PMID:9012817
Re-equilibration after quenches in athermal martensites: Conversion delays for vapor-to-liquid domain-wall phases

NASA Astrophysics Data System (ADS)

Shankaraiah, N.; Murthy, K. P. N.; Lookman, T.; Shenoy, S. R.

2015-06-01

Entropy barriers and aging states appear in martensitic structural-transition models, slowly re-equilibrating after temperature quenches, under Monte Carlo dynamics. Concepts from protein folding and aging harmonic oscillators turn out to be useful in understanding these nonequilibrium evolutions. We show how the athermal, nonactivated delay time for seeded parent-phase austenite to convert to product-phase martensite arises from an identified entropy barrier in Fourier space. In an aging state of low Monte Carlo acceptances, the strain structure factor makes constant-energy searches for rare pathways to enter a Brillouin zone "golf hole" enclosing negative-energy states, and to suddenly release entropically trapped stresses. In this context, a stress-dependent effective temperature can be defined, that re-equilibrates to the quenched bath temperature.
Normal mode-guided transition pathway generation in proteins

PubMed Central

Lee, Byung Ho; Seo, Sangjae; Kim, Min Hyeok; Kim, Youngjin; Jo, Soojin; Choi, Moon-ki; Lee, Hoomin; Choi, Jae Boong

2017-01-01

The biological function of proteins is closely related to its structural motion. For instance, structurally misfolded proteins do not function properly. Although we are able to experimentally obtain structural information on proteins, it is still challenging to capture their dynamics, such as transition processes. Therefore, we need a simulation method to predict the transition pathways of a protein in order to understand and study large functional deformations. Here, we present a new simulation method called normal mode-guided elastic network interpolation (NGENI) that performs normal modes analysis iteratively to predict transition pathways of proteins. To be more specific, NGENI obtains displacement vectors that determine intermediate structures by interpolating the distance between two end-point conformations, similar to a morphing method called elastic network interpolation. However, the displacement vector is regarded as a linear combination of the normal mode vectors of each intermediate structure, in order to enhance the physical sense of the proposed pathways. As a result, we can generate more reasonable transition pathways geometrically and thermodynamically. By using not only all normal modes, but also in part using only the lowest normal modes, NGENI can still generate reasonable pathways for large deformations in proteins. This study shows that global protein transitions are dominated by collective motion, which means that a few lowest normal modes play an important role in this process. NGENI has considerable merit in terms of computational cost because it is possible to generate transition pathways by partial degrees of freedom, while conventional methods are not capable of this. PMID:29020017
Transitions from near-surface to interior redox upon lithiation in conversion electrode materials.

PubMed

He, Kai; Xin, Huolin L; Zhao, Kejie; Yu, Xiqian; Nordlund, Dennis; Weng, Tsu-Chien; Li, Jing; Jiang, Yi; Cadigan, Christopher A; Richards, Ryan M; Doeff, Marca M; Yang, Xiao-Qing; Stach, Eric A; Li, Ju; Lin, Feng; Su, Dong

2015-02-11

Nanoparticle electrodes in lithium-ion batteries have both near-surface and interior contributions to their redox capacity, each with distinct rate capabilities. Using combined electron microscopy, synchrotron X-ray methods and ab initio calculations, we have investigated the lithiation pathways that occur in NiO electrodes. We find that the near-surface electroactive (Ni(2+) → Ni(0)) sites saturated very quickly, and then encounter unexpected difficulty in propagating the phase transition into the electrode (referred to as a "shrinking-core" mode). However, the interior capacity for Ni(2+) → Ni(0) can be accessed efficiently following the nucleation of lithiation "fingers" that propagate into the sample bulk, but only after a certain incubation time. Our microstructural observations of the transition from a slow shrinking-core mode to a faster lithiation finger mode corroborate with synchrotron characterization of large-format batteries and can be rationalized by stress effects on transport at high-rate discharge. The finite incubation time of the lithiation fingers sets the intrinsic limitation for the rate capability (and thus the power) of NiO for electrochemical energy storage devices. The present work unravels the link between the nanoscale reaction pathways and the C-rate-dependent capacity loss and provides guidance for the further design of battery materials that favors high C-rate charging.

Chemical Conversion Pathways and Kinetic Modeling for the OH-Initiated Reaction of Triclosan in Gas-Phase

PubMed Central

Zhang, Xue; Zhang, Chenxi; Sun, Xiaomin; Kang, Lingyan; Zhao, Yan

2015-01-01

As a widely used antimicrobial additive in daily consumption, attention has been paid to the degradation and conversion of triclosan for a long time. The quantum chemistry calculation and the canonical variational transition state theory are employed to investigate the mechanism and kinetic property. Besides addition and abstraction, oxidation pathways and further conversion pathways are also considered. The OH radicals could degrade triclosan to phenols, aldehydes, and other easily degradable substances. The conversion mechanisms of triclosan to the polychlorinated dibenzopdioxin and furan (PCDD/Fs) and polychlorinated biphenyls (PCBs) are clearly illustrated and the toxicity would be strengthened in such pathways. Single radical and diradical pathways are compared to study the conversion mechanism of dichlorodibenzo dioxin (DCDD). Furthermore, thermochemistry is discussed in detail. Kinetic property is calculated and the consequent ratio of kadd/ktotal and kabs/ktotal at 298.15 K are 0.955 and 0.045, respectively. Thus, the OH radical addition reactions are predominant, the substitute position of OH radical on triclosan is very important to generate PCDD and furan, and biradical is also a vital intermediate to produce dioxin. PMID:25867482
The mid-developmental transition and the evolution of animal body plans

PubMed Central

Cole, Alison G.; Winter, Eitan; Mostov, Natalia; Khair, Sally; Senderovich, Naftalie; Kovalev, Ekaterina; Silver, David H.; Feder, Martin; Fernandez-Valverde, Selene L.; Nakanishi, Nagayasu; Simmons, David; Simakov, Oleg; Larsson, Tomas; Liu, Shang-Yun; Jerafi-Vider, Ayelet; Yaniv, Karina; Ryan, Joseph F.; Martindale, Mark Q.; Rink, Jochen C.; Arendt, Detlev; Degnan, Sandie M.; Degnan, Bernard M.; Hashimshony, Tamar; Yanai, Itai

2016-01-01

Animals are grouped into ~35 ‘phyla’ based upon the notion of distinct body plans1–4. Morphological and molecular analyses have revealed that a stage in the middle of development—known as the phylotypic period—is conserved among species within some phyla5–9. Although these analyses provide evidence for their existence, phyla have also been criticized as lacking an objective definition, and consequently based on arbitrary groupings of animals10. Here we compare the developmental transcriptomes of ten species, each annotated to a different phylum, with a wide range of life histories and embryonic forms. We find that in all ten species, development comprises the coupling of early and late phases of conserved gene expression. These phases are linked by a divergent ‘mid-developmental transition’ that uses species-specific suites of signalling pathways and transcription factors. This mid-developmental transition overlaps with the phylotypic period that has been defined previously for three of the ten phyla, suggesting that transcriptional circuits and signalling mechanisms active during this transition are crucial for defining the phyletic body plan and that the mid-developmental transition may be used to define phylotypic periods in other phyla. Placing these observations alongside the reported conservation of mid-development within phyla, we propose that a phylum may be defined as a collection of species whose gene expression at the mid-developmental transition is both highly conserved among them, yet divergent relative to other species. PMID:26886793
Modeling the Transition From Predominantly Gas- to Predominantly Aerosol-Phase Products From OH Reactions With the Homologous Series of C10 to C15 n- Alkanes

NASA Astrophysics Data System (ADS)

Jordan, C. E.; Ziemann, P. J.; Griffin, R. J.; Lim, Y. B.; Atkinson, R.; Arey, J.

2006-12-01

Recent laboratory studies have shown significant formation of secondary organic aerosol (SOA) from OH reactions with a homologous series of n-alkanes. SOA mass yields of 56% were observed for pentadecane (C15), while only 0.5% yield was observed from octane (C8, the smallest alkane in the series). A rapid transition in SOA yield is observed from C10 to C13, with SOA yields increasing from 4% to 49%. In standard gas-aerosol partitioning theory, the vapor pressure controls the amount of material that can condense into the particle phase. However, the rapid transition observed here suggests there may also be a shift in the predominant reaction pathways for longer chain alkanes, leading to greater production of lower vapor pressure products. Here we present an investigation of the role of vapor pressure versus the role of shifting branching ratios to test the influence of each of these on SOA mass yields. We have added each of the alkanes in this series to the Caltech Atmospheric Chemistry Mechanism (CACM). This mechanism was developed in part to predict explicitly concentrations of secondary and tertiary semivolatile oxidation products that potentially form SOA. Although it is has been developed to lump similar compounds together for computational efficiency, it is nonetheless easily adapted and ideally suited for a detailed zero-dimensional modeling study of this kind. This gas-phase mechanism is linked to the aerosol partitioning module MPMPO (Model to Predict the Multi- phase Partitioning of Organics). MPMPO is a fully coupled module that allows the simultaneous partitioning of semi-volatile species to both an aqueous and an organic aerosol phase.
Grass meristems I: shoot apical meristem maintenance, axillary meristem determinacy and the floral transition.

PubMed

Pautler, Michael; Tanaka, Wakana; Hirano, Hiro-Yuki; Jackson, David

2013-03-01

The vegetative and reproductive shoot architectures displayed by members of the grass family are critical to reproductive success, and thus agronomic yield. Variation in shoot architecture is explained by the maintenance, activity and determinacy of meristems, pools of pluripotent stem cells responsible for post-embryonic plant growth. This review summarizes recent progress in understanding the major properties of grass shoot meristems, focusing on vegetative phase meristems and the floral transition, primarily in rice and maize. Major areas of interest include: the control of meristem homeostasis by the CLAVATA-WUSCHEL pathway and by hormones such as cytokinin; the initiation of axillary meristems and the control of axillary meristem dormancy; and the environmental and endogenous cues that regulate flowering time. In an accompanying paper, Tanaka et al. review subsequent stages of shoot development, including current knowledge of reproductive meristem determinacy and the fate transitions associated with these meristems.
Simulation studies of GST phase change alloys

NASA Astrophysics Data System (ADS)

Martyna, Glenn

2008-03-01

In order to help drive post-Moore's Law technology development, switching processes involving novel materials, in particular, GeSbTe (GST) alloys are being investigated for use in memory and eFuse applications. An anneal/quench thermal process crystallizes/amorphosizes a GST alloy which then has a low/high resistance and thereby forms a readable/writeable bit; for example, a ``one'' might be the low resistance, conducting crystalline state and a ``zero'' might be the high resistance, glassy state. There are many open questions about the precise nature of the structural transitions and the coupling to electronic structure changes. Computational and experimental studies of the effect of pressure on the GST materials were initiated in order to probe the physics behind the thermal switching process. A new pathway to reversible phase change involving pressure-induced structural metal insulator transitions was discovered. In a binary GS system, a room-temperature, direct, pressure-induced transformation from the high resistance amorphous phase to the low resistance crystalline phase was observed experimentally while the reverse process under tensile load was demonstrated via ab initio MD simulations performed on IBM's Blue Gene/L enabled by massively parallel software. Pressure induced transformations of the ternary material GST-225 (Ge2Sb2Te5) were, also, examined In the talk, the behavior of the two systems will be compared and insight into the nature of the phase change given.
Coherent control of optical absorption and the energy transfer pathway of an infrared quantum dot hybridized with a VO2 nanoparticle

NASA Astrophysics Data System (ADS)

Hatef, Ali; Zamani, Naser; Johnston, William

2017-04-01

We systematically investigate the optical response of a semiconductor quantum dot (QD) hybridized with a vanadium dioxide nanoparticle (VO2NP) in the infrared (IR) region. The VO2NP features a semiconductor to metal phase change characteristic below and above a critical temperature that leads to an abrupt change in the particle’s optical properties. This feature means that the QD-VO2NP hybrid system can support the coherent coupling of exciton-polaritons and exciton-plasmon polaritons in the semiconductor and metal phases of the VO2NP, respectively. In our calculations, the VO2NP phase transition is modelled with a filling fraction (f), representing the fraction of the VO2NP in the metallic phase. The phase transition is driven by the hybrid system’s interaction with a continuous wave (CW) IR laser field. In this paper, we show how control over the filling fraction results in the enhancement or suppression of the QD’s linear absorption. These variations in the QD absorption is due to dramatic changes in the effective local field experienced by the QD and the non-radiative energy transfer from the QD to the VO2NP. The presented results have the potential to be applied to the design of thermal sensors at the nanoscale.
Use of a Bacterial Luciferase Monitoring System To Estimate Real-Time Dynamics of Intracellular Metabolism in Escherichia coli.

PubMed

Shimada, Tomohiro; Tanaka, Kan

2016-10-01

Regulation of central carbon metabolism has long been an important research subject in every organism. While the dynamics of metabolic flows during changes in available carbon sources have been estimated based on changes in metabolism-related gene expression, as well as on changes in the metabolome, the flux change itself has scarcely been measured because of technical difficulty, which has made conclusions elusive in many cases. Here, we used a monitoring system employing Vibrio fischeri luciferase to probe the intracellular metabolic condition in Escherichia coli Using a batch culture provided with a limited amount of glucose, we performed a time course analysis, where the predominant carbon source shifts from glucose to acetate, and identified a series of sequential peaks in the luciferase activity (peaks 1 to 4). Two major peaks, peaks 1 and 3, were considered to correspond to the glucose and acetate consuming phases, respectively, based on the glucose, acetate, and dissolved oxygen concentrations in the medium. The pattern of these peaks was changed by the addition of a different carbon source or by an increasing concentration of glucose, which was consistent with the present model. Genetically, mutations involved in glycolysis or the tricarboxylic acid (TCA) cycle/gluconeogenesis specifically affected peak 1 or peak 3, respectively, as expected from the corresponding metabolic phase. Intriguingly, mutants for the acetate excretion pathway showed a phenotype of extended peak 2 and delayed transition to the TCA cycle/gluconeogenesis phase, which suggests that peak 2 represents the metabolic transition phase. These results indicate that the bacterial luciferase monitoring system is useful to understand the real-time dynamics of metabolism in living bacterial cells. Intracellular metabolic flows dynamically change during shifts in available carbon sources. However, because of technical difficulty, the flux change has scarcely been measured in living cells. Here, we used a Vibrio fischeri luciferase monitoring system to probe the intracellular metabolic condition in Escherichia coli Using a limited amount of glucose batch culture, a series of sequential peaks (peaks 1 to 4) in the luciferase activity was observed. Changes in the pattern of these peaks by the addition of extra carbon sources and in mutant strains involved in glycolysis or the TCA cycle/gluconeogenesis gene assigned the metabolic phase corresponding to peak 1 as the glycolysis phase and peak 3 as the TCA cycle/gluconeogenesis phase. Intriguingly, the acetate excretion pathway engaged in peak 2 represents the metabolic transition phase. These results indicate that the bacterial luciferase monitoring system is useful to understand the real-time dynamics of metabolism in living bacterial cells. Copyright © 2016, American Society for Microbiology. All Rights Reserved.
Ferric sulfates on Mars: Surface Explorations and Laboratory Experiments

NASA Astrophysics Data System (ADS)

Wang, A.; Ling, Z.; Freeman, J. J.

2008-12-01

Recent results from missions to Mars have reinforced the importance of sulfates for Mars science. They are the hosts of water, the sinks of acidity, and maybe the most active species in the past and current surface/near-surface processes on Mars. Fe-sulfate was found frequently by Spirit and Opportunity rovers: jarosite in Meridiani Planum outcrops and a less specific "ferric sulfate" in the salty soils excavated by Spirit at Gusev Crater. Pancam spectral analysis suggests a variety of ferric sulfates in these soils, i.e. ferricopiapite, jarosite, fibroferrite, and rhomboclase. A change in the Pancam spectral features occurred in Tyrone soils after ~ 190 sols of exposure to surface conditions. Dehydration of ferric sulfate is a possible cause. We synthesized eight ferric sulfates and conducted a series of hydration/dehydration experiments. Our goal was to establish the stability fields and phase transition pathways of these ferric sulfates. In our experiments, water activity, temperature, and starting structure are the variables. No redox state change was observed. Acidic, neutral, and basic salts were used. Ferric sulfate sample containers were placed into relative humidity buffer solutions that maintain static relative humidity levels at three temperatures. The five starting phases were ferricopiapite (Fe4.67(SO4)6(OH)2.20H2O), kornelite (Fe2(SO4)3.7H2O), rhomboclase (FeH(SO4)2.4H2O), pentahydrite (Fe2(SO4)3.5H2O), and an amorphous phase (Fe2(SO4)3.5H2O). A total of one hundred fifty experiments have been running for nearly ten months. Thousands of coupled Raman and gravimetric measurements were made at intermediate steps to monitor the phase transitions. The first order discovery from these experiments is the extremely large stability field of ferricopiapite. Ferricopiapite is the major ferric sulfate to precipitate from a Fe3+-S-rich aqueous solution at mid-low temperature, and it has the highest H2O/Fe ratio (~ 4.3). However, unlike the Mg-sulfate with highest hydration state (epsomite, at mid-low temperature), which would dehydrate readily at low relative humidity, ferricopiapite remains unchanged over ten months under extremely dry conditions. On the other hand, amorphous ferric sulfate which forms easily from solutions at dry conditions, is similar to the amorphous magnesium sulfate in stability field, thus can potentially be a very important phase in the phase transition pathways of ferric sulfates on Mars.
PATHWAYS OF GLUCOSE CATABOLISM IN BACILLUS CEREUS1

PubMed Central

Goldman, Manuel; Blumenthal, Harold J.

1964-01-01

Goldman, Manuel (The University of Michigan, Ann Arbor), and Harold J. Blumenthal. Pathways of glucose catabolism in Bacillus cereus. J. Bacteriol. 87:377–386. 1964.—Estimates by a radiorespirometric method of the pathways of glucose catabolism of resting-cell suspensions of Bacillus cereus strain terminalis indicate that the Embden-Meyerhof pathway predominates at every stage of development, including the sporogenic and germinative phases. At the filamentous, granular, forespore, and transitional stages, 98% of the glucose was catabolized by the Embden-Meyerhof pathway, and the remainder by the hexose monophosphate oxidative pathway. Estimates of the pathways in resting spore-suspensions arrested at defined stages of development indicate that 20% of the glucose was catabolized through the hexose monophosphate pathway in germinated spores, and 10% in the swollen and elongated stages of postgermination. In cells which had completed the first cell division, the figure fell to about 2%, a level similar to that found for vegetative cells at later stages of development. The key Embden-Meyerhof enzymes, hexokinase, phosphohexoisomerase, phosphofructokinase, and aldolase, as well as several other enzymes, were present at all stages of germination and postgerminative development, supporting the radioisotopic data obtained with whole cells. As indicated by the release of C14O2 from glucose-6-C14, terminal respiration of resting-cell suspensions operates maximally in vegetative cells at the granular, fore-spore, and transitional stages. There was marked inhibition of terminal respiration during the development of spores into vegetative cells. Only slight activity occurred in the earliest vegetative stages, and maximal operation developed after about ten cell divisions. Fumarase was absent in spores until sometime late in the elongation stage. At this point, a weak but definite activity appeared which increased during later stages of development so that, by the end of about the sixth cell division, fumarase had a specific activity about 80 times that observed at elongation. PMID:14151060
Improving pathways to transit for persons with disabilities.

DOT National Transportation Integrated Search

2016-08-01

Persons with disabilities can achieve a greater degree of freedom when they have full access to a variety of transit modes, but this : can only be achieved when the pathways to transit the infrastructure and conditions in the built environment ...
The perspectives of young adults on recovery from repeated suicide-related behavior.

PubMed

Bergmans, Yvonne; Langley, John; Links, Paul; Lavery, James V

2009-01-01

This qualitative study sought to develop an understanding of how young adults between the ages of 18-25 years, who have a history of two or more suicide attempts, transition away from high-risk suicide-related behaviors. To understand the transition to safer behaviors and to provide clinical suggestions for those who provide care to this population. Sixteen young adults under the age of 25 years, who had completed at least one cycle of intervention for people with repeated suicide attempts, participated in this qualitative, grounded theory study. The young adults described a pathway that included three major elements: (a) "living to die", (b) ambivalence and tipping/turning points, and (c) a process of recovery that included small steps or phases (pockets of recovery) toward life. The journey was not always experienced as steady movement forward, and the potential for relapse either in the young people's behavior or their wish to engage in their relationship with death could ebb and flow. Clinicians need to be aware that the struggle to live is a process involving a fluid pathway moving between three key elements.
Phase transformations during the growth of paracetamol crystals from the vapor phase

NASA Astrophysics Data System (ADS)

Belyaev, A. P.; Rubets, V. P.; Antipov, V. V.; Bordei, N. S.

2014-07-01

Phase transformations during the growth of paracetamol crystals from the vapor phase are studied by differential scanning calorimetry. It is found that the vapor-crystal phase transition is actually a superposition of two phase transitions: a first-order phase transition with variable density and a second-order phase transition with variable ordering. The latter, being a diffuse phase transition, results in the formation of a new, "pretransition," phase irreversibly spent in the course of the transition, which ends in the appearance of orthorhombic crystals. X-ray diffraction data and micrograph are presented.
Neighbouring group processes in the deamination of protonated phenylalanine derivatives.

PubMed

Lioe, Hadi; O'Hair, Richard A J

2005-10-21

The gas-phase fragmentation of protonated phenylalanine and a series of its derivatives (tyrosine, 4-methylphenylalanine, 4-aminophenylalanine, 4-methoxyphenylalanine, 4-tert-butylphenylalanine, 4-fluorophenylalanine, 4-chlorophenylalanine, 4-bromophenylalanine, 4-iodophenylalanine, 4-cyanophenylalanine, 4-nitrophenylalanine, 3-fluorophenylalanine, and 3,4-dichlorophenylalanine) were examined using a combination of low energy CID in a quadrupole ion trap mass spectrometer as well as DFT calculations and RRKM modelling. In particular, the relationship between the electron-donating ability of the substituent and the competitive losses of H2O + CO and NH3 were explored through the application of the Hammett equation. It was found that electron-donating substituents promote the loss of NH3, while electron-withdrawing substituents suppress the loss of NH3 and favour the H2O + CO loss fragmentation channel instead. These observations are consistent with a neighbouring group pathway operating for the loss of NH3. Molecular orbital calculation (at the B3LYP/6-31+G(d,p) level of theory) were also performed for a range of derivatives to compare the relative transition state energy barriers for three competing mechanisms: (i) the combined loss of H2O + CO, which is triggered by an initial intramolecular proton transfer from the ammonium group to hydroxyl OH, followed by the combined loss of H2O and CO to form an immonium ion; (ii) loss of NH3 via an aryl assisted neighbouring group pathway to yield a phenonium ion; (iii) loss of NH3 via a 1,2-hydride migration process, which results in the formation of a benzyl cation. The relative energy barriers for H2O + CO loss remain nearly constant, while that for both NH3 pathways increase as the substituent moves from electron-donating to electron-withdrawing. The relative transition state energy for loss of NH3 via the aryl assisted neighbouring group pathway is always lower than that of the 1,2-hydride migration process. RRKM modelling of the DFT predicted barrier heights suggest that the rate constants for H2O + CO loss are insensitive to the substituent on the ring, while the NH3 loss channels are greatly affected by the substituent. These theoretical results are consistent with the experimental observation of the relative yields of the competing fragmentation channels. Finally, comparisons with published gas phase and condensed phase studies on related systems are made.
Puzzling calcite-III dimorphism: crystallography, high-pressure behavior, and pathway of single-crystal transitions

NASA Astrophysics Data System (ADS)

Pippinger, T.; Miletich, R.; Merlini, M.; Lotti, P.; Schouwink, P.; Yagi, T.; Crichton, W. A.; Hanfland, M.

2015-01-01

High-pressure phase transformations between the polymorphic forms I, II, III, and IIIb of CaCO3 were investigated by analytical in situ high-pressure high-temperature experiments on oriented single-crystal samples. All experiments at non-ambient conditions were carried out by means of Raman scattering, X-ray, and synchrotron diffraction techniques using diamond-anvil cells in the pressure range up to 6.5 GPa. The composite-gasket resistive heating technique was applied for all high-pressure investigations at temperatures up to 550 K. High-pressure Raman spectra reveal distinguishable characteristic spectral differences located in the wave number range of external modes with the occurrence of band splitting and shoulders due to subtle symmetry changes. Constraints from in situ observations suggest a stability field of CaCO3-IIIb at relatively low temperatures adjacent to the calcite-II field. Isothermal compression of calcite provides the sequence from I to II, IIIb, and finally, III, with all transformations showing volume discontinuities. Re-transformation at decreasing pressure from III oversteps the stability field of IIIb and demonstrates the pathway of pressure changes to determine the transition sequence. Clausius-Clapeyron slopes of the phase boundary lines were determined as: Δ P/Δ T = -2.79 ± 0.28 × 10-3 GPa K-1 (I-II); +1.87 ± 0.31 × 10-3 GPa K-1 (II/III); +4.01 ± 0.5 × 10-3 GPa K-1 (II/IIIb); -33.9 ± 0.4 × 10-3 GPa K-1 (IIIb/III). The triple point between phases II, IIIb, and III was determined by intersection and is located at 2.01(7) GPa/338(5) K. The pathway of transition from I over II to IIIb can be interpreted by displacement with small shear involved (by 2.9° on I/II and by 8.2° on II/IIIb). The former triad of calcite-I corresponds to the [20-1] direction in the P21/ c unit cell of phase II and to [101] in the pseudomonoclinic C setting of phase IIIb. Crystal structure investigations of triclinic CaCO3-III at non-ambient pressure-temperature conditions confirm the reported structure, and the small changes associated with the variation in P and T explain the broad stability of this structure with respect to variations in P and T. PVT equation of state parameters was determined from experimental data points in the range of 2.20-6.50 GPa at 298-405 K providing = 87.5(5.1) GPa, ( δK T/ δT) P = -0.21(0.23) GPa K-1, α 0 = 0.8(21.4) × 10-5 K-1, and α 1 = 1.0(3.7) × 10-7 K-1 using a second-order Birch-Murnaghan equation of state formalism.
Uranium redox transition pathways in acetate-amended sediments

USGS Publications Warehouse

Bargar, John R.; Williams, Kenneth H.; Campbell, Kate M.; Long, Philip E.; Stubbs, Joanne E.; Suvorova, Elenal I.; Lezama-Pacheco, Juan S.; Alessi, Daniel S.; Stylo, Malgorzata; Webb, Samuel M.; Davis, James A.; Giammar, Daniel E.; Blue, Lisa Y.; Bernier-Latmani, Rizlan

2013-01-01

Redox transitions of uranium [from U(VI) to U(IV)] in low-temperature sediments govern the mobility of uranium in the environment and the accumulation of uranium in ore bodies, and inform our understanding of Earth’s geochemical history. The molecular-scale mechanistic pathways of these transitions determine the U(IV) products formed, thus influencing uranium isotope fractionation, reoxidation, and transport in sediments. Studies that improve our understanding of these pathways have the potential to substantially advance process understanding across a number of earth sciences disciplines. Detailed mechanistic information regarding uranium redox transitions in field sediments is largely nonexistent, owing to the difficulty of directly observing molecular-scale processes in the subsurface and the compositional/physical complexity of subsurface systems. Here, we present results from an in situ study of uranium redox transitions occurring in aquifer sediments under sulfate-reducing conditions. Based on molecular-scale spectroscopic, pore-scale geochemical, and macroscale aqueous evidence, we propose a biotic–abiotic transition pathway in which biomass-hosted mackinawite (FeS) is an electron source to reduce U(VI) to U(IV), which subsequently reacts with biomass to produce monomeric U(IV) species. A species resembling nanoscale uraninite is also present, implying the operation of at least two redox transition pathways. The presence of multiple pathways in low-temperature sediments unifies apparently contrasting prior observations and helps to explain sustained uranium reduction under disparate biogeochemical conditions. These findings have direct implications for our understanding of uranium bioremediation, ore formation, and global geochemical processes.
AMPKα1 controls hepatocyte proliferation independently of energy balance by regulating Cyclin A2 expression.

PubMed

Merlen, Grégory; Gentric, Géraldine; Celton-Morizur, Séverine; Foretz, Marc; Guidotti, Jacques-Emmanuel; Fauveau, Véronique; Leclerc, Jocelyne; Viollet, Benoit; Desdouets, Chantal

2014-01-01

AMP-activated protein kinase (AMPK) is an evolutionarily conserved sensor of cellular energy status that contributes to restoration of energy homeostasis by slowing down ATP-consuming pathways and activating ATP-producing pathways. Unexpectedly, in different systems, AMPK is also required for proper cell division. In the current study, we evaluated the potential effect of the AMPK catalytic subunit, AMPKα1, on hepatocyte proliferation. Hepatocyte proliferation was determined in AMPKα1 knockout and wild-type mice in vivo after two thirds partial hepatectomy, and in vitro in primary hepatocyte cultures. The activities of metabolic and cell cycle-related signaling pathways were measured. After partial hepatectomy, hepatocytes proliferated rapidly, correlating with increased AMPK phosphorylation. Deletion of AMPKα1 delayed liver regeneration by impacting on G1/S transition phase. The proliferative defect of AMPKα1-deficient hepatocytes was cell autonomous, and independent of energy balance. The priming phase, lipid droplet accumulation, protein anabolic responses and growth factor activation after partial hepatectomy occurred normally in the absence of AMPKα1 activity. By contrast, mRNA and protein expression of cyclin A2, a key driver of S phase progression, were compromised in the absence of AMPK activity. Importantly, AMPKα1 controlled cyclin A2 transcription mainly through the ATF/CREB element. Our study highlights a novel role for AMPKα1 as a positive regulator of hepatocyte division occurring independently of energy balance. Copyright © 2013 European Association for the Study of the Liver. Published by Elsevier B.V. All rights reserved.
Wilson loop's phase transition probed by non-local observable

NASA Astrophysics Data System (ADS)

Li, Hui-Ling; Feng, Zhong-Wen; Yang, Shu-Zheng; Zu, Xiao-Tao

2018-04-01

In order to give further insights into the holographic Van der Waals phase transition, it would be of great interest to investigate the behavior of Wilson loop across the holographic phase transition for a higher dimensional hairy black hole. We offer a possibility to proceed with a numerical calculation in order to discussion on the hairy black hole's phase transition, and show that Wilson loop can serve as a probe to detect a phase structure of the black hole. Furthermore, for a first order phase transition, we calculate numerically the Maxwell's equal area construction; and for a second order phase transition, we also study the critical exponent in order to characterize the Wilson loop's phase transition.
Pressure dependence of band-gap and phase transitions in bulk CuX (X = Cl, Br, I)

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

Azhikodan, Dilna; Nautiyal, Tashi; Sharma, S.

2016-05-06

Usually a phase transition, in theoretical studies, is explored or verified by studying the total energy as a function of the volume considering various plausible phases. The intersection point, if any, of the free energy vs. volume curves for the different phases is then the indicator of the phase transition(s). The question is, can the theoretical study of a single phase alone indicate a phase transition? i.e. can we look beyond the phase under consideration through such a study? Using density-functional theory, we report a novel approach to suggest phase transition(s) through theoretical study of a single phase. Copper halidesmore » have been engaged for this study. These are direct band-gap semiconductors, with zinc blende structure at ambient conditions, and are reported to exhibit many phase transitions. We show that the study of volume dependence of energy band-gap in a single phase facilitates looking beyond the phase under consideration. This, when translated to pressures, reflects the phase transition pressures for CuX (X = Cl, Br, I) with an encouraging accuracy. This work thus offers a simple, yet reliable, approach based on electronic structure calculations to investigate new semiconducting materials for phase changes under pressure.« less
Eigenstate Phase Transitions

NASA Astrophysics Data System (ADS)

Zhao, Bo

Phase transitions are one of the most exciting physical phenomena ever discovered. The understanding of phase transitions has long been of interest. Recently eigenstate phase transitions have been discovered and studied; they are drastically different from traditional thermal phase transitions. In eigenstate phase transitions, a sharp change is exhibited in properties of the many-body eigenstates of the Hamiltonian of a quantum system, but not the thermal equilibrium properties of the same system. In this thesis, we study two different types of eigenstate phase transitions. The first is the eigenstate phase transition within the ferromagnetic phase of an infinite-range spin model. By studying the interplay of the eigenstate thermalization hypothesis and Ising symmetry breaking, we find two eigenstate phase transitions within the ferromagnetic phase: In the lowest-temperature phase the magnetization can macroscopically oscillate by quantum tunneling between up and down. The relaxation of the magnetization is always overdamped in the remainder of the ferromagnetic phase, which is further divided into phases where the system thermally activates itself over the barrier between the up and down states, and where it quantum tunnels. The second is the many-body localization phase transition. The eigenstates on one side of the transition obey the eigenstate thermalization hypothesis; the eigenstates on the other side are many-body localized, and thus thermal equilibrium need not be achieved for an initial state even after evolving for an arbitrary long time. We study this many-body localization phase transition in the strong disorder renormalization group framework. After setting up a set of coarse-graining rules for a general one dimensional chain, we get a simple "toy model'' and obtain an almost purely analytical solution to the infinite-randomness critical fixed point renormalization group equation. We also get an estimate of the correlation length critical exponent nu ≈ 2.5.
Parallel cascade selection molecular dynamics (PaCS-MD) to generate conformational transition pathway

NASA Astrophysics Data System (ADS)

Harada, Ryuhei; Kitao, Akio

2013-07-01

Parallel Cascade Selection Molecular Dynamics (PaCS-MD) is proposed as a molecular simulation method to generate conformational transition pathway under the condition that a set of "reactant" and "product" structures is known a priori. In PaCS-MD, the cycle of short multiple independent molecular dynamics simulations and selection of the structures close to the product structure for the next cycle are repeated until the simulated structures move sufficiently close to the product. Folding of 10-residue mini-protein chignolin from the extended to native structures and open-close conformational transition of T4 lysozyme were investigated by PaCS-MD. In both cases, tens of cycles of 100-ps MD were sufficient to reach the product structures, indicating the efficient generation of conformational transition pathway in PaCS-MD with a series of conventional MD without additional external biases. Using the snapshots along the pathway as the initial coordinates, free energy landscapes were calculated by the combination with multiple independent umbrella samplings to statistically elucidate the conformational transition pathways.

Reaction between hydrous wadsleyite and iron: Implication for water distribution in Earth's transition zone

NASA Astrophysics Data System (ADS)

Zhu, F.; Li, J.; Liu, J.; Dong, J.

2017-12-01

The mantle transition zone (TZ) is considered as a potential water reservoir due to large capacities of wadsleyite and ringwoodite to store water in the structures. Whether it is a hydrous layer or an empty reservoir, however, is still under debate. Because the TZ may contain metallic iron1, 2 and water is an oxidizing agent at > 5 GPa, the stability of coexisting iron and TZ hydrous phases needs to be examined. In this study, we conducted multi-anvil experiments on iron with synthetic hydrous wadsleyite or forsterite and water under TZ pressure-temperature conditions. Similar rapid reactions were observed for both types of starting materials, producing ferropericlase, iron-bearing wadsleyite or ringwoodite, and iron hydride. The results imply that a hydrous TZ is incompatible with a reduced state, and that water distribution of TZ is confined to subducting slabs and slab-mantle boundaries, where water or hydrous phases in slab must oxidize the adjacent mantle before they can hydrate the silicates. In contrast, the bulk transition zone may be mostly dry. The iron hydride produced from this slab-mantle interaction may sink to greater depths due to their low melting temperature3, thus providing a pathway for hydrogen to enter the lower mantle and core. References 1. O'Neill HSC, McCammon C, Canil D, Rubie D, Ross C, Seifert F. Mossbauer spectroscopy of mantle transition zone phases and determination of minimum Fe3+ content. American Mineralogist 1993, 78(3-4): 456-460. 2. Rohrbach A, Ballhaus C, Golla-Schindler U, Ulmer P, Kamenetsky VS, Kuzmin DV. Metal saturation in the upper mantle. Nature 2007, 449(7161): 456-458. 3. Sakamaki K, Takahashi E, Nakajima Y, Nishihara Y, Funakoshi K, Suzuki T, et al. Melting phase relation of FeH x up to 20GPa: Implication for the temperature of the Earth's core. Physics of the Earth and Planetary Interiors 2009, 174(1): 192-201.
Folding mechanism of an extremely thermostable (βα)(8)-barrel enzyme: a high kinetic barrier protects the protein from denaturation.

PubMed

Carstensen, Linn; Zoldák, Gabriel; Schmid, Franz-Xaver; Sterner, Reinhard

2012-04-24

HisF, the cyclase subunit of imidazole glycerol phosphate synthase (ImGPS) from Thermotoga maritima, is an extremely thermostable (βα)(8)-barrel protein. We elucidated the unfolding and refolding mechanism of HisF. Its unfolding transition is reversible and adequately described by the two-state model, but 6 weeks is necessary to reach equilibrium (at 25 °C). During refolding, initially a burst-phase off-pathway intermediate is formed. The subsequent productive folding occurs in two kinetic phases with time constants of ~3 and ~20 s. They reflect a sequential process via an on-pathway intermediate, as revealed by stopped-flow double-mixing experiments. The final step leads to native HisF, which associates with the glutaminase subunit HisH to form the functional ImGPS complex. The conversion of the on-pathway intermediate to the native protein results in a 10(6)-fold increase of the time constant for unfolding from 89 ms to 35 h (at 4.0 M GdmCl) and thus establishes a high energy barrier to denaturation. We conclude that the extra stability of HisF is used for kinetic protection against unfolding. In its refolding mechanism, HisF resembles other (βα)(8)-barrel proteins.
Third Space Strategists: International Students Negotiating the Transition from Pathway Program to Postgraduate Coursework Degree

ERIC Educational Resources Information Center

Benzie, Helen

2015-01-01

Pathway programs exist to prepare students for progression into university degrees but the transition experience for many students may not be as smooth as is suggested by the notion of the pathway. While attending a pathway program and at the beginning of their university degree, students may be in a third space, a liminal space where they engage…
Vapor-crystal phase transition in synthesis of paracetamol films by vacuum evaporation and condensation

NASA Astrophysics Data System (ADS)

Belyaev, A. P.; Rubets, V. P.; Antipov, V. V.; Bordei, N. S.; Zarembo, V. I.

2014-03-01

We report on the structural and technological investigations of the vapor-crystal phase transition during synthesis of paracetamol films of the monoclinic system by vacuum evaporation and condensation in the temperature range 220-320 K. The complex nature of the transformation accompanied by the formation of a gel-like phase is revealed. The results are interpreted using a model according to which the vapor-crystal phase transition is not a simple first-order phase transition, but is a nonlinear superposition of two phase transitions: a first-order transition with a change in density and a second-order phase transition with a change in ordering. Micrographs of the surface of the films are obtained at different phases of formation.
Phase transitions in a multistate majority-vote model on complex networks

NASA Astrophysics Data System (ADS)

Chen, Hanshuang; Li, Guofeng

2018-06-01

We generalize the original majority-vote (MV) model from two states to arbitrary p states and study the order-disorder phase transitions in such a p -state MV model on complex networks. By extensive Monte Carlo simulations and a mean-field theory, we show that for p ≥3 the order of phase transition is essentially different from a continuous second-order phase transition in the original two-state MV model. Instead, for p ≥3 the model displays a discontinuous first-order phase transition, which is manifested by the appearance of the hysteresis phenomenon near the phase transition. Within the hysteresis loop, the ordered phase and disordered phase are coexisting, and rare flips between the two phases can be observed due to the finite-size fluctuation. Moreover, we investigate the type of phase transition under a slightly modified dynamics [Melo et al., J. Stat. Mech. (2010) P11032, 10.1088/1742-5468/2010/11/P11032]. We find that the order of phase transition in the three-state MV model depends on the degree heterogeneity of networks. For p ≥4 , both dynamics produce the first-order phase transitions.
The phase transitions between Z n × Z n bosonic topological phases in 1 + 1D, and a constraint on the central charge for the critical points between bosonic symmetry protected topological phases

DOE PAGES

Tsui, Lokman; Huang, Yen-Ta; Jiang, Hong-Chen; ...

2017-03-27

The study of continuous phase transitions triggered by spontaneous symmetry breaking has brought revolutionary ideas to physics. Recently, through the discovery of symmetry protected topological phases, it is realized that continuous quantum phase transition can also occur between states with the same symmetry but different topology. Here in this paper we study a specific class of such phase transitions in 1+1 dimensions – the phase transition between bosonic topological phases protected by Z n × Z n. We find in all cases the critical point possesses two gap opening relevant operators: one leads to a Landau-forbidden symmetry breaking phase transitionmore » and the other to the topological phase transition. We also obtained a constraint on the central charge for general phase transitions between symmetry protected bosonic topological phases in 1+1D.« less
The phase transitions between Z n × Z n bosonic topological phases in 1 + 1D, and a constraint on the central charge for the critical points between bosonic symmetry protected topological phases

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

Tsui, Lokman; Huang, Yen-Ta; Jiang, Hong-Chen

The study of continuous phase transitions triggered by spontaneous symmetry breaking has brought revolutionary ideas to physics. Recently, through the discovery of symmetry protected topological phases, it is realized that continuous quantum phase transition can also occur between states with the same symmetry but different topology. Here in this paper we study a specific class of such phase transitions in 1+1 dimensions – the phase transition between bosonic topological phases protected by Z n × Z n. We find in all cases the critical point possesses two gap opening relevant operators: one leads to a Landau-forbidden symmetry breaking phase transitionmore » and the other to the topological phase transition. We also obtained a constraint on the central charge for general phase transitions between symmetry protected bosonic topological phases in 1+1D.« less
Study of a structural phase transition by two dimensional Fourier transform NMR method

NASA Astrophysics Data System (ADS)

Trokiner, A.; Man, P. P.; Théveneau, H.; Papon, P.

1985-09-01

The fluoroperovskite RbCaF 3 undergoes a structural phase transition at 195.5 K, from a cubic phase where the 87Rb nuclei have no quadrupolar interaction ( ωQ= 0) to a tetragonal phase where ω Q ≠ O. The transition is weakly first-order. A two-dimensional FT NMR experiment has been performed on 87Rb ( I = {3}/{2}) in a single crystal in both phases and in the vicinity of the phase transition. Our results show the coexistence of the two phases at the phase transition.
Structural, magnetic, and ferroelectric properties of T-like cobalt-doped BiFeO3 thin films

NASA Astrophysics Data System (ADS)

Young, T.; Sharma, P.; Kim, D. H.; Ha, Thai Duy; Juang, Jenh-Yih; Chu, Y.-H.; Seidel, J.; Nagarajan, V.; Yasui, S.; Itoh, M.; Sando, D.

2018-02-01

We present a comprehensive study of the physical properties of epitaxial cobalt-doped BiFeO3 films ˜50 nm thick grown on (001) LaAlO3 substrates. X-ray diffraction and magnetic characterization demonstrate high quality purely tetragonal-like (T') phase films with no parasitic impurities. Remarkably, the step-and-terrace film surface morphology can be fully recovered following a local electric-field-induced rhombohedral-like to T' phase transformation. Local switching spectroscopy experiments confirm the ferroelectric switching to follow previously reported transition pathways. Critically, we show unequivocal evidence for conduction at domain walls between polarization variants in T'-like BFO, making this material system an attractive candidate for domain wall-based nanoelectronics.
Transitions from near-surface to interior redox upon lithiation in conversion electrode materials

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

He, Kai; Xin, Huolin L.; Zhao, Kejie

Nanoparticle electrodes in lithium-ion batteries have both near-surface and interior contributions to their redox capacity, each with distinct rate capabilities. Using combined electron microscopy, synchrotron X-ray methods and ab initio calculations, we have investigated the lithiation pathways that occur in NiO electrodes. We find that the near-surface electroactive (Ni²⁺→Ni⁰) sites saturated very quickly, and then encounter unexpected difficulty in propagating the phase transition into the electrode (referred to as a “shrinking-core” mode). However, the interior capacity for Ni²⁺→Ni⁰ can be accessed efficiently following the nucleation of lithiation “fingers” which propagate into the sample bulk, but only after a certain incubationmore » time. Our microstructural observations of the transition from a slow shrinking-core mode to a faster lithiation finger mode corroborate with synchrotron characterization of large-format batteries, and can be rationalized by stress effects on transport at high-rate discharge. The finite incubation time of the lithiation fingers sets the intrinsic limitation for the rate capability (and thus the power) of NiO for electrochemical energy storage devices. The present work unravels the link between the nanoscale reaction pathways and the C-rate-dependent capacity loss, and provides guidance for the further design of battery materials that favors high C-rate charging.« less
Transitions from near-surface to interior redox upon lithiation in conversion electrode materials

DOE PAGES

He, Kai; Xin, Huolin L.; Zhao, Kejie; ...

2015-01-29

Nanoparticle electrodes in lithium-ion batteries have both near-surface and interior contributions to their redox capacity, each with distinct rate capabilities. Using combined electron microscopy, synchrotron X-ray methods and ab initio calculations, we have investigated the lithiation pathways that occur in NiO electrodes. We find that the near-surface electroactive (Ni²⁺→Ni⁰) sites saturated very quickly, and then encounter unexpected difficulty in propagating the phase transition into the electrode (referred to as a “shrinking-core” mode). However, the interior capacity for Ni²⁺→Ni⁰ can be accessed efficiently following the nucleation of lithiation “fingers” which propagate into the sample bulk, but only after a certain incubationmore » time. Our microstructural observations of the transition from a slow shrinking-core mode to a faster lithiation finger mode corroborate with synchrotron characterization of large-format batteries, and can be rationalized by stress effects on transport at high-rate discharge. The finite incubation time of the lithiation fingers sets the intrinsic limitation for the rate capability (and thus the power) of NiO for electrochemical energy storage devices. The present work unravels the link between the nanoscale reaction pathways and the C-rate-dependent capacity loss, and provides guidance for the further design of battery materials that favors high C-rate charging.« less
Molecular nucleation mechanisms and control strategies for crystal polymorph selection.

PubMed

Van Driessche, Alexander E S; Van Gerven, Nani; Bomans, Paul H H; Joosten, Rick R M; Friedrich, Heiner; Gil-Carton, David; Sommerdijk, Nico A J M; Sleutel, Mike

2018-04-04

The formation of condensed (compacted) protein phases is associated with a wide range of human disorders, such as eye cataracts, amyotrophic lateral sclerosis, sickle cell anaemia and Alzheimer's disease. However, condensed protein phases have their uses: as crystals, they are harnessed by structural biologists to elucidate protein structures, or are used as delivery vehicles for pharmaceutical applications. The physiochemical properties of crystals can vary substantially between different forms or structures ('polymorphs') of the same macromolecule, and dictate their usability in a scientific or industrial context. To gain control over an emerging polymorph, one needs a molecular-level understanding of the pathways that lead to the various macroscopic states and of the mechanisms that govern pathway selection. However, it is still not clear how the embryonic seeds of a macromolecular phase are formed, or how these nuclei affect polymorph selection. Here we use time-resolved cryo-transmission electron microscopy to image the nucleation of crystals of the protein glucose isomerase, and to uncover at molecular resolution the nucleation pathways that lead to two crystalline states and one gelled state. We show that polymorph selection takes place at the earliest stages of structure formation and is based on specific building blocks for each space group. Moreover, we demonstrate control over the system by selectively forming desired polymorphs through site-directed mutagenesis, specifically tuning intermolecular bonding or gel seeding. Our results differ from the present picture of protein nucleation, in that we do not identify a metastable dense liquid as the precursor to the crystalline state. Rather, we observe nucleation events that are driven by oriented attachments between subcritical clusters that already exhibit a degree of crystallinity. These insights suggest ways of controlling macromolecular phase transitions, aiding the development of protein-based drug-delivery systems and macromolecular crystallography.
Molecular nucleation mechanisms and control strategies for crystal polymorph selection

NASA Astrophysics Data System (ADS)

van Driessche, Alexander E. S.; van Gerven, Nani; Bomans, Paul H. H.; Joosten, Rick R. M.; Friedrich, Heiner; Gil-Carton, David; Sommerdijk, Nico A. J. M.; Sleutel, Mike

2018-04-01

The formation of condensed (compacted) protein phases is associated with a wide range of human disorders, such as eye cataracts, amyotrophic lateral sclerosis, sickle cell anaemia and Alzheimer’s disease. However, condensed protein phases have their uses: as crystals, they are harnessed by structural biologists to elucidate protein structures, or are used as delivery vehicles for pharmaceutical applications. The physiochemical properties of crystals can vary substantially between different forms or structures (‘polymorphs’) of the same macromolecule, and dictate their usability in a scientific or industrial context. To gain control over an emerging polymorph, one needs a molecular-level understanding of the pathways that lead to the various macroscopic states and of the mechanisms that govern pathway selection. However, it is still not clear how the embryonic seeds of a macromolecular phase are formed, or how these nuclei affect polymorph selection. Here we use time-resolved cryo-transmission electron microscopy to image the nucleation of crystals of the protein glucose isomerase, and to uncover at molecular resolution the nucleation pathways that lead to two crystalline states and one gelled state. We show that polymorph selection takes place at the earliest stages of structure formation and is based on specific building blocks for each space group. Moreover, we demonstrate control over the system by selectively forming desired polymorphs through site-directed mutagenesis, specifically tuning intermolecular bonding or gel seeding. Our results differ from the present picture of protein nucleation, in that we do not identify a metastable dense liquid as the precursor to the crystalline state. Rather, we observe nucleation events that are driven by oriented attachments between subcritical clusters that already exhibit a degree of crystallinity. These insights suggest ways of controlling macromolecular phase transitions, aiding the development of protein-based drug-delivery systems and macromolecular crystallography.
Hydrogen-bond symmetrization breakdown and dehydrogenation mechanism in FeO2H at high pressure

NASA Astrophysics Data System (ADS)

Hu, Q.; Zhu, S.; Mao, H. K.; Mao, W. L.; Sheng, H.

2017-12-01

The cycling of hydrogen plays an important role in the geochemical evolution of our planet. In Earth's interiors, hydrogen cycling is mainly carried out by hydrous minerals. Under high-pressure conditions, asymmetric hydroxyl bonds in hydrous minerals tend to form a symmetric O-H-O configuration that improves their thermal stability. Therefore it is possible to transport water into the deeper part of the Earth's lower mantle. Here, we employ first-principles free-energy landscape sampling methods based on a recently developed stochastic surface walking algorithm to reveal the transition mechanism of a water-bearing mineral, FeO2H, at deep mantle conditions. By resolving the lowest-energy transition pathway from ɛ-FeO2H to the high-pressure Py-phase, we demonstrate that half of the O-H bonds in the mineral rupture during the structural transition, leading toward the breakdown of symmetrized hydrogen bonds and eventual dehydrogenation. Our study sheds new light on the stability of symmetric hydrogen bonds in hydrous minerals during structural transitions and suggests a dehydrogenation mechanism from water in the deep mantle.
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.
A Comparison of Photocatalytic Activities of Gold Nanoparticles Following Plasmonic and Interband Excitation and a Strategy for Harnessing Interband Hot Carriers for Solution Phase Photocatalysis

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

Zhao, Jie; Nguyen, Son C.; Ye, Rong

Light driven excitation of gold nanoparticles (GNPs) has emerged as a potential strategy to generate hot carriers for photocatalysis through excitation of localized surface plasmon resonance (LSPR). In contrast, carrier generation through excitation of interband transitions remains a less explored and underestimated pathway for photocatalytic activity. Photoinduced oxidative etching of GNPs with FeCl3 was investigated as a model reaction in order to elucidate the effects of both types of transitions. Our quantitative results show that interband transitions more efficiently generate hot carriers and that those carriers exhibit higher reactivity as compared to those generated solely by LSPR. Furthermore, by leveragingmore » the strong π-acidic character of the resulting photogenerated Au+ hole, an interband transition induced cyclization reaction of alkynylphenols was developed. One thing of note is that the, alkyne coordination to the Au+ hole intercepts the classic oxidation event and leads to the formation of the catalytically active gold clusters on subnanometer scale.« less
A Comparison of Photocatalytic Activities of Gold Nanoparticles Following Plasmonic and Interband Excitation and a Strategy for Harnessing Interband Hot Carriers for Solution Phase Photocatalysis

DOE PAGES

Zhao, Jie; Nguyen, Son C.; Ye, Rong; ...

2017-05-10

Light driven excitation of gold nanoparticles (GNPs) has emerged as a potential strategy to generate hot carriers for photocatalysis through excitation of localized surface plasmon resonance (LSPR). In contrast, carrier generation through excitation of interband transitions remains a less explored and underestimated pathway for photocatalytic activity. Photoinduced oxidative etching of GNPs with FeCl3 was investigated as a model reaction in order to elucidate the effects of both types of transitions. Our quantitative results show that interband transitions more efficiently generate hot carriers and that those carriers exhibit higher reactivity as compared to those generated solely by LSPR. Furthermore, by leveragingmore » the strong π-acidic character of the resulting photogenerated Au+ hole, an interband transition induced cyclization reaction of alkynylphenols was developed. One thing of note is that the, alkyne coordination to the Au+ hole intercepts the classic oxidation event and leads to the formation of the catalytically active gold clusters on subnanometer scale.« less
The c-Jun N-terminal kinase pathway is critical for cell transformation by the latent membrane protein 1 of Epstein-Barr virus

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

Kutz, Helmut; Reisbach, Gilbert; Schultheiss, Ute

The latent membrane protein 1 (LMP1) of Epstein-Barr virus (EBV) transforms cells activating signal transduction pathways such as NF-{kappa}B, PI3-kinase, or c-Jun N-terminal kinase (JNK). Here, we investigated the functional role of the LMP1-induced JNK pathway in cell transformation. Expression of a novel dominant-negative JNK1 allele caused a block of proliferation in LMP1-transformed Rat1 fibroblasts. The JNK-specific inhibitor SP600125 reproduced this effect in Rat1-LMP1 cells and efficiently interfered with proliferation of EBV-transformed lymphoblastoid cells (LCLs). Inhibition of the LMP1-induced JNK pathway in LCLs caused the downregulation of c-Jun and Cdc2, the essential G2/M cell cycle kinase, which was accompanied bymore » a cell cycle arrest of LCLs at G2/M phase transition. Moreover, SP600125 retarded tumor growth of LCLs in a xenograft model in SCID mice. Our data support a critical role of the LMP1-induced JNK pathway for proliferation of LMP1-transformed cells and characterize JNK as a potential target for intervention against EBV-induced malignancies.« less
Chemical conversion pathways and kinetic modeling for the OH-initiated reaction of triclosan in gas-phase.

PubMed

Zhang, Xue; Zhang, Chenxi; Sun, Xiaomin; Kang, Lingyan; Zhao, Yan

2015-04-10

As a widely used antimicrobial additive in daily consumption, attention has been paid to the degradation and conversion of triclosan for a long time. The quantum chemistry calculation and the canonical variational transition state theory are employed to investigate the mechanism and kinetic property. Besides addition and abstraction, oxidation pathways and further conversion pathways are also considered. The OH radicals could degrade triclosan to phenols, aldehydes, and other easily degradable substances. The conversion mechanisms of triclosan to the polychlorinated dibenzopdioxin and furan (PCDD/Fs) and polychlorinated biphenyls (PCBs) are clearly illustrated and the toxicity would be strengthened in such pathways. Single radical and diradical pathways are compared to study the conversion mechanism of dichlorodibenzo dioxin (DCDD). Furthermore, thermochemistry is discussed in detail. Kinetic property is calculated and the consequent ratio of k add/k total and k abs/k total at 298.15 K are 0.955 and 0.045, respectively. Thus, the OH radical addition reactions are predominant, the substitute position of OH radical on triclosan is very important to generate PCDD and furan, and biradical is also a vital intermediate to produce dioxin.
Aurora kinase A revives dormant laryngeal squamous cell carcinoma cells via FAK/PI3K/Akt pathway activation

PubMed Central

Yang, Li-yun; He, Chang-yu; Chen, Xue-hua; Su, Li-ping; Liu, Bing-ya; Zhang, Hao

2016-01-01

Revival of dormant tumor cells may be an important tumor metastasis mechanism. We hypothesized that aurora kinase A (AURKA), a cell cycle control kinase, promotes the transition of laryngeal squamous cell carcinoma (LSCC) cells from G0 phase to active division. We therefore investigated whether AURKA could revive dormant tumor cells to promote metastasis. Western blotting revealed that AURKA expression was persistently low in dormant laryngeal cancer Hep2 (D-Hep2) cells and high in non-dormant (T-Hep2) cells. Decreasing AURKA expression in T-Hep2 cells induced dormancy and reduced FAK/PI3K/Akt pathway activity. Increasing AURKA expression in D-Hep2 cells increased FAK/PI3K/Akt pathway activity and enhanced cellular proliferation, migration, invasion and metastasis. In addition, FAK/PI3K/Akt pathway inhibition caused dormancy-like behavior and reduced cellular mobility, migration and invasion. We conclude that AURKA may revive dormant tumor cells via FAK/PI3K/Akt pathway activation, thereby promoting migration and invasion in laryngeal cancer. AURKA/FAK/PI3K/Akt inhibitors may thus represent potential targets for clinical LSCC treatment. PMID:27356739

Probabilistic physical characteristics of phase transitions at highway bottlenecks: incommensurability of three-phase and two-phase traffic-flow theories.

PubMed

Kerner, Boris S; Klenov, Sergey L; Schreckenberg, Michael

2014-05-01

Physical features of induced phase transitions in a metastable free flow at an on-ramp bottleneck in three-phase and two-phase cellular automaton (CA) traffic-flow models have been revealed. It turns out that at given flow rates at the bottleneck, to induce a moving jam (F → J transition) in the metastable free flow through the application of a time-limited on-ramp inflow impulse, in both two-phase and three-phase CA models the same critical amplitude of the impulse is required. If a smaller impulse than this critical one is applied, neither F → J transition nor other phase transitions can occur in the two-phase CA model. We have found that in contrast with the two-phase CA model, in the three-phase CA model, if the same smaller impulse is applied, then a phase transition from free flow to synchronized flow (F → S transition) can be induced at the bottleneck. This explains why rather than the F → J transition, in the three-phase theory traffic breakdown at a highway bottleneck is governed by an F → S transition, as observed in real measured traffic data. None of two-phase traffic-flow theories incorporates an F → S transition in a metastable free flow at the bottleneck that is the main feature of the three-phase theory. On the one hand, this shows the incommensurability of three-phase and two-phase traffic-flow theories. On the other hand, this clarifies why none of the two-phase traffic-flow theories can explain the set of fundamental empirical features of traffic breakdown at highway bottlenecks.
Investigation of phase transitions in LiK 1- x(NH 4) xSO 4 mixed crystal

NASA Astrophysics Data System (ADS)

Freire, P. T. C.; Paraguassu, W.; Silva, A. P.; Pilla, O.; Teixeira, A. M. R.; Sasaki, J. M.; Mendes Filho, J.; Guedes, I.; Melo, F. E. A.

1999-02-01

We present Raman scattering results on LiK 1- x(NH 4) xSO 4 mixed crystal for temperatures between 100 and 300 K. We observed that in this temperature range the crystal undergoes two different phase transitions, which we call Bansal and Tomaszewski phase transitions. The introduction of ammonium ions in the potassium sites increases the C 66→C 3v4 (Bansal) phase transition temperature and decreases the Tomaszewski phase transition temperature. Finally, the most impressive effect of the presence of ammonium impurity in the LiKSO 4 structure is the decrease in the temperature hysteresis of Bansal phase transition and the almost complete destruction of hysteresis in the Tomaszewski phase transition, leading to a high temperature range of stability of the trigonal phase.
Transitions to Middle-Skill Jobs: Pathways into the New Racio-Economic Structure of the 21st Century

ERIC Educational Resources Information Center

Vafai, Maliheh Mansuripur

2016-01-01

"College and Career Pathways" is an educational policy initiative widely acclaimed as a commonsensical and effective measure to ease students' transitions between secondary and postsecondary education and into the middle-skill jobs. This article investigates the internal dynamics of the "Pathways'" curricular model as well as…
Structural phase transition in monolayer MoTe2 driven by electrostatic doping

NASA Astrophysics Data System (ADS)

Wang, Ying; Xiao, Jun; Zhu, Hanyu; Li, Yao; Alsaid, Yousif; Fong, King Yan; Zhou, Yao; Wang, Siqi; Shi, Wu; Wang, Yuan; Zettl, Alex; Reed, Evan J.; Zhang, Xiang

2017-10-01

Monolayers of transition-metal dichalcogenides (TMDs) exhibit numerous crystal phases with distinct structures, symmetries and physical properties. Exploring the physics of transitions between these different structural phases in two dimensions may provide a means of switching material properties, with implications for potential applications. Structural phase transitions in TMDs have so far been induced by thermal or chemical means; purely electrostatic control over crystal phases through electrostatic doping was recently proposed as a theoretical possibility, but has not yet been realized. Here we report the experimental demonstration of an electrostatic-doping-driven phase transition between the hexagonal and monoclinic phases of monolayer molybdenum ditelluride (MoTe2). We find that the phase transition shows a hysteretic loop in Raman spectra, and can be reversed by increasing or decreasing the gate voltage. We also combine second-harmonic generation spectroscopy with polarization-resolved Raman spectroscopy to show that the induced monoclinic phase preserves the crystal orientation of the original hexagonal phase. Moreover, this structural phase transition occurs simultaneously across the whole sample. This electrostatic-doping control of structural phase transition opens up new possibilities for developing phase-change devices based on atomically thin membranes.
Gas phase hydrolysis of formaldehyde to form methanediol: impact of formic acid catalysis.

PubMed

Hazra, Montu K; Francisco, Joseph S; Sinha, Amitabha

2013-11-21

We find that formic acid (FA) is very effective at facilitating diol formation through its ability to reduce the barrier for the formaldehyde (HCHO) hydrolysis reaction. The rate limiting step in the mechanism involves the isomerization of a prereactive collision complex formed through either the HCHO···H2O + FA and/or HCHO + FA···H2O pathways. The present study finds that the effective barrier height, defined as the difference between the zero-point vibrational energy (ZPE) corrected energy of the transition state (TS) and the HCHO···H2O + FA and HCHO + FA···H2O starting reagents, are respectively only ∼1 and ∼4 kcal/mol. These barriers are substantially lower than the ∼17 kcal/mol barrier associated with the corresponding step in the hydrolysis of HCHO catalyzed by a single water molecule (HCHO + H2O + H2O). The significantly lower barrier heights for the formic acid catalyzed pathway reveal a new important role that organic acids play in the gas phase hydrolysis of atmospheric carbonyl compounds.
Higher order genomic organization and regulatory compartmentalization for cell cycle control at the G1/S-phase transition.

PubMed

Ghule, Prachi N; Seward, David J; Fritz, Andrew J; Boyd, Joseph R; van Wijnen, Andre J; Lian, Jane B; Stein, Janet L; Stein, Gary S

2018-05-10

Fidelity of histone gene regulation, and ultimately of histone protein biosynthesis, is obligatory for packaging of newly replicated DNA into chromatin. Control of histone gene expression within the 3-dimensional context of nuclear organization is reflected by two well documented observations. DNA replication-dependent histone mRNAs are synthesized at specialized subnuclear domains designated histone locus bodies (HLBs), in response to activation of the growth factor dependent Cyclin E/CDK2/HINFP/NPAT pathway at the G1/S transition in mammalian cells. Complete loss of the histone gene regulatory factors HINFP or NPAT disrupts HLB integrity that is necessary for coordinate control of DNA replication and histone gene transcription. Here we review the molecular histone-related requirements for G1/S-phase progression during the cell cycle. Recently developed experimental strategies, now enable us to explore mechanisms involved in dynamic control of histone gene expression in the context of the temporal (cell cycle) and spatial (HLBs) remodeling of the histone gene loci. © 2018 Wiley Periodicals, Inc.
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.
Epithelial Mesenchymal Transition in Cancer Progression: Prev entive Phytochemicals.

PubMed

Illam, Soorya P; Narayanankutty, Arunaksharan; Mathew, Shaji E; Valsalakumari, Remya; Jacob, Rosemol M; Raghavamenon, Achuthan C

2017-01-01

Epithelial-Mesenchymal Transition (EMT) is the conversion of epithelial cells into mesenchymal phenotype generally observed during embryogenesis and wound healing as well as in malignant transformation. Several signaling pathways and transcription factors associated with EMT have been explored. Dietary phytochemicals that are multi-targeted agents which interfere with these pathways, assume preventive potential against pathologic EMT. The present review aims to provide a detailed description of the nature and characteristics of EMT in physiological and pathophysiological conditions and the scope of phytochemicals in its prevention. Details regarding the initiation, progression as well as prevention of pathologic EMT and metastasis and recent patents on preventive phytochemicals were obtained from PubMed literatures and patent databases. The phenotypic changes during EMT are regulated by transcription factors like Snail, Slug, Twist and Zeb, which are activated through diverse signaling pathways of TGF-β, NF-kB, Wnt and Notch. s phytocompounds that are potent enough to interfere with these signaling pathways, which in turn prevent pathological implications of EMT. Present review also discusses 28 recent patents on those phytocompounds. EMT is a significant pharmacological target for developing preventive agents to combat pathological conditions like malignancy. Many of the phytochemicals cited in this review are being enrolled for different phases of clinical trials for their efficacy. In spite of the major limitations regarding bioavailability, sensitivity and tolerance of these compounds, their synthetic analogs, formulations and efficient drug delivery systems are also being attempted which will hopefully generate productive and promising results in near future. Copyright© Bentham Science Publishers; For any queries, please email at epub@benthamscience.org.
A stress-induced phase transition model for semi-crystallize shape memory polymer

NASA Astrophysics Data System (ADS)

Guo, Xiaogang; Zhou, Bo; Liu, Liwu; Liu, Yanju; Leng, Jinsong

2014-03-01

The developments of constitutive models for shape memory polymer (SMP) have been motivated by its increasing applications. During cooling or heating process, the phase transition which is a continuous time-dependent process happens in semi-crystallize SMP and the various individual phases form at different temperature and in different configuration. Then, the transformation between these phases occurred and shape memory effect will emerge. In addition, stress applied on SMP is an important factor for crystal melting during phase transition. In this theory, an ideal phase transition model considering stress or pre-strain is the key to describe the behaviors of shape memory effect. So a normal distributed model was established in this research to characterize the volume fraction of each phase in SMP during phase transition. Generally, the experiment results are partly backward (in heating process) or forward (in cooling process) compared with the ideal situation considering delay effect during phase transition. So, a correction on the normal distributed model is needed. Furthermore, a nonlinear relationship between stress and phase transition temperature Tg is also taken into account for establishing an accurately normal distributed phase transition model. Finally, the constitutive model which taking the stress as an influence factor on phase transition was also established. Compared with the other expressions, this new-type model possesses less parameter and is more accurate. For the sake of verifying the rationality and accuracy of new phase transition and constitutive model, the comparisons between the simulated and experimental results were carried out.
DOE Office of Scientific and Technical Information (OSTI.GOV)

Renlund, Anita Mariana; Tappan, Alexander Smith; Miller, Jill C.

The HMX {beta}-{delta} solid-solid phase transition, which occurs as HMX is heated near 170 C, is linked to increased reactivity and sensitivity to initiation. Thermally damaged energetic materials (EMs) containing HMX therefore may present a safety concern. Information about the phase transition is vital to predictive safety models for HMX and HMX-containing EMs. We report work on monitoring the phase transition with real-time Raman spectroscopy aimed towards obtaining a better understanding of physical properties of HMX through the phase transition. HMX samples were confined in a cell of minimal free volume in a displacement-controlled or load-controlled arrangement. The cell wasmore » heated and then cooled at controlled rates while real-time Raman spectroscopic measurements were performed. Raman spectroscopy provides a clear distinction between the phases of HMX because the vibrational transitions of the molecule change with conformational changes associated with the phase transition. Temperature of phase transition versus load data are presented for both the heating and cooling cycles in the load-controlled apparatus, and general trends are discussed. A weak dependence of the temperature of phase transition on load was discovered during the heating cycle, with higher loads causing the phase transition to occur at a higher temperature. This was especially true in the temperature of completion of phase transition data as opposed to the temperature of onset of phase transition data. A stronger dependence on load was observed in the cooling cycle, with higher loads causing the reverse phase transitions to occur at a higher cooling temperature. Also, higher loads tended to cause the phase transition to occur over a longer period of time in the heating cycle and over a shorter period of time in the cooling cycle. All three of the pure HMX phases ({alpha}, {beta} and {delta}) were detected on cooling of the heated samples, either in pure form or as a mixture.« less
Molecular dissection of transcriptional reprogramming of steviol glycosides synthesis in leaf tissue during developmental phase transitions in Stevia rebaudiana Bert.

PubMed

Singh, Gopal; Singh, Gagandeep; Singh, Pradeep; Parmar, Rajni; Paul, Navgeet; Vashist, Radhika; Swarnkar, Mohit Kumar; Kumar, Ashok; Singh, Sanatsujat; Singh, Anil Kumar; Kumar, Sanjay; Sharma, Ram Kumar

2017-09-19

Stevia is a natural source of commercially important steviol glycosides (SGs), which share biosynthesis route with gibberellic acids (GAs) through plastidal MEP and cytosolic MVA pathways. Ontogeny-dependent deviation in SGs biosynthesis is one of the key factor for global cultivation of Stevia, has not been studied at transcriptional level. To dissect underlying molecular mechanism, we followed a global transcriptome sequencing approach and generated more than 100 million reads. Annotation of 41,262 de novo assembled transcripts identified all the genes required for SGs and GAs biosynthesis. Differential gene expression and quantitative analysis of important pathway genes (DXS, HMGR, KA13H) and gene regulators (WRKY, MYB, NAC TFs) indicated developmental phase dependent utilization of metabolic flux between SGs and GAs synthesis. Further, identification of 124 CYPs and 45 UGTs enrich the genomic resources, and their PPI network analysis with SGs/GAs biosynthesis proteins identifies putative candidates involved in metabolic changes, as supported by their developmental phase-dependent expression. These putative targets can expedite molecular breeding and genetic engineering efforts to enhance SGs content, biomass and yield. Futuristically, the generated dataset will be a useful resource for development of functional molecular markers for diversity characterization, genome mapping and evolutionary studies in Stevia.
Molecular processes from the AGB to the PN stage

NASA Astrophysics Data System (ADS)

García-Hernández, D. Anibal

2012-08-01

Many complex organic molecules and inorganic solid-state compounds have been observed in the circumstellar shell of stars (both C-rich and O-rich) in the transition phase between Asymptotic Giant Branch (AGB) stars and Planetary Nebulae (PNe). This short (~102-104 years) phase of stellar evolution represents a wonderful laboratory for astrochemistry and provides severe constraints on any model of gas-phase and solid-state chemistry. One of the major challenges of present day astrophysics and astrochemistry is to understand the formation pathways of these complex organic molecules and inorganic solid-state compounds (e.g., polycyclic aromatic hydrocarbons, fullerenes, and graphene in the case of a C-rich chemistry and oxides and crystalline silicates in O-rich environments) in space. In this review, I present an observational review of the molecular processes in the late stages of stellar evolution with a special emphasis on the first detections of fullerenes and graphene in PNe.
DOE Office of Scientific and Technical Information (OSTI.GOV)

Hintermeier, Peter H.; Eckstein, Sebastian; Mei, Donghai

Hydronium ions in the pores of zeolite H-ZSM5 show high catalytic activity in the elimination of water from cyclohexanol in aqueous phase. Substitution induces subtle changes in rates and reaction pathways, which are concluded to be related to steric effects. Exploring the reaction pathways of 2-, 3-, and 4-methylcyclohexanol (2-McyOH, 3-McyOH, and 4-McyOH), 2- and 4-ethylcyclohexanol (2-EcyOH and 4-EcyOH), 2- n-propylcyclohexanol (2-PcyOH), and cyclohexanol (CyOH) it is shown that the E2 character increases with closer positioning of the alkyl and hydroxyl groups. Thus, 4-McyOH dehydration proceeds via an E1-type elimination, while cis-2-McyOH preferentially reacts via an E2 pathway. The entropymore » of activation decreased with increasing alkyl chain length (ca. 20 J mol -1 K -1 per CH 2 unit) for 2-substituted alcohols, which is concluded to result from constraints influencing the configurational entropy of the transition states.« less
Methanol steam reforming over Ni-CeO 2 model and powder catalysts: Pathways to high stability and selectivity for H 2/CO 2 production

DOE PAGES

Liu, Zongyuan; Yao, Siyu; Johnston-Peck, Aaron; ...

2017-08-25

Here, nickel-ceria has been reported as a very good catalysts for the reforming of methane. Here, the methanol steam reforming reaction on both powder (Ni-CeO 2) and model (Ni-CeO 2-x(111)) catalysts was investigated. The active phase evolution and surface species transformation on powder catalysts were studied via in situ X-ray diffraction (XRD) and diffuse reflectance infrared transform spectroscopy (DRIFTS). Phase transitions of NiO → NiC → Ni and CeO 2 → CeO 2-x were observed during the reaction. The simultaneous production of H 2/CO 2 demonstrates that the active phase of the catalysts contains metallic Ni supported over partially reducedmore » ceria. The DRIFTS experiments indicate that a methoxy to formate transition is associated with the reduction of ceria whereas the formation of carbonate species results from the presence of metallic Ni. A study of the reaction of methanol with Ni-CeO 2-x(111) by X-ray photoelectron spectroscopy (XPS) points to the essential role of metal-support interactions in an oxygen transfer from ceria to Ni that contributes to the high selectivity of the catalysts.« less
Methanol steam reforming over Ni-CeO 2 model and powder catalysts: Pathways to high stability and selectivity for H 2/CO 2 production

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

Liu, Zongyuan; Yao, Siyu; Johnston-Peck, Aaron

Here, nickel-ceria has been reported as a very good catalysts for the reforming of methane. Here, the methanol steam reforming reaction on both powder (Ni-CeO 2) and model (Ni-CeO 2-x(111)) catalysts was investigated. The active phase evolution and surface species transformation on powder catalysts were studied via in situ X-ray diffraction (XRD) and diffuse reflectance infrared transform spectroscopy (DRIFTS). Phase transitions of NiO → NiC → Ni and CeO 2 → CeO 2-x were observed during the reaction. The simultaneous production of H 2/CO 2 demonstrates that the active phase of the catalysts contains metallic Ni supported over partially reducedmore » ceria. The DRIFTS experiments indicate that a methoxy to formate transition is associated with the reduction of ceria whereas the formation of carbonate species results from the presence of metallic Ni. A study of the reaction of methanol with Ni-CeO 2-x(111) by X-ray photoelectron spectroscopy (XPS) points to the essential role of metal-support interactions in an oxygen transfer from ceria to Ni that contributes to the high selectivity of the catalysts.« less
Students' Learning Performance and Transitions in Different Learning Pathways to Higher Vocational Education

ERIC Educational Resources Information Center

Biemans, Harm; Mariën, Hans; Fleur, Erik; Tobi, Hilde; Nieuwenhuis, Loek; Runhaar, Piety

2016-01-01

To improve students' transitions between successive educational levels, continuing learning pathways are being designed and implemented in many countries. This study was carried out to examine the effects of the Green Lycea (GL) as critical cases of continuing learning pathways in vocational education in The Netherlands. The GL were compared with…
Controlling the Temperature and Speed of the Phase Transition of VO 2 Microcrystals

DOE PAGES

Yoon, Joonseok; Kim, Howon; Chen, Xian; ...

2015-12-29

Here, we investigated the control of two important parameters of vanadium dioxide (VO 2 ) microcrystals, the phase transition temperature and speed, by varying microcrystal width. By using the reflectivity change between insulating and metallic phases, phase transition temperature is measured by optical microscopy. As the width of square cylinder-shaped microcrystals decreases from ~70 to ~1 μm, the phase transition temperature (67 °C for bulk) varied as much as 26.1 °C (19.7 °C) during heating (cooling). In addition, the propagation speed of phase boundary in the microcrystal, i.e., phase transition speed, is monitored at the onset of phase transition bymore » using the high-speed resistance measurement. The phase transition speed increases from 4.6 × 10 2 to 1.7 × 10 4 μm/s as the width decreases from ~50 to ~2 μm. While the statistical description for a heterogeneous nucleation process explains the size dependence on phase transition temperature of VO 2 , the increase of effective thermal exchange process is responsible for the enhancement of phase transition speed of small VO 2 microcrystals. These findings not only enhance the understanding of VO 2 intrinsic properties but also contribute to the development of innovative electronic devices.« less
Controlling the Temperature and Speed of the Phase Transition of VO 2 Microcrystals

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

Yoon, Joonseok; Kim, Howon; Chen, Xian

Here, we investigated the control of two important parameters of vanadium dioxide (VO 2 ) microcrystals, the phase transition temperature and speed, by varying microcrystal width. By using the reflectivity change between insulating and metallic phases, phase transition temperature is measured by optical microscopy. As the width of square cylinder-shaped microcrystals decreases from ~70 to ~1 μm, the phase transition temperature (67 °C for bulk) varied as much as 26.1 °C (19.7 °C) during heating (cooling). In addition, the propagation speed of phase boundary in the microcrystal, i.e., phase transition speed, is monitored at the onset of phase transition bymore » using the high-speed resistance measurement. The phase transition speed increases from 4.6 × 10 2 to 1.7 × 10 4 μm/s as the width decreases from ~50 to ~2 μm. While the statistical description for a heterogeneous nucleation process explains the size dependence on phase transition temperature of VO 2 , the increase of effective thermal exchange process is responsible for the enhancement of phase transition speed of small VO 2 microcrystals. These findings not only enhance the understanding of VO 2 intrinsic properties but also contribute to the development of innovative electronic devices.« less
Origin of phase transition in VO2

NASA Astrophysics Data System (ADS)

Basu, Raktima; Sardar, Manas; Dhara, Sandip

2018-04-01

Vanadium dioxide (VO2) exhibits a reversible first-order metal to insulator transition (MIT) along with a structural phase transition (SPT) from monoclinic M1 to rutile tetragonal R via another two intermediate phases of monoclinic M2 and triclinic T at a technologically important temperature of 340K. In the present work, besides synthesizing M1 phase of VO2, we also stabilized M2 and T phases at room temperature by introducing native defects in the system and observed an increase in transition temperature with increase in native defects. Raman spectroscopic measurements were carried out to confirm the pure VO2 phases. Since the MIT is accompanied by SPT in these systems, the origin of the phase transition is still under debate. The controversy between MIT and SPT, whether electron-phonon coupling or strong electron-electron correlation triggers the phase transition in VO2 is also resolved by examining the presence of intermediate phase M2 during phase transition.
Interstitial effects of B and Li on the magnetic phase transition and magnetocaloric effects in Gd2In alloy

NASA Astrophysics Data System (ADS)

Yang, Yang; Xie, Yigao; Zhou, Xiaoqian; Zhong, Hui; Jiang, Qingzheng; Ma, Shengcan; Zhong, Zhenchen; Cui, Weibin; Wang, Qiang

2018-05-01

Interstitial effects of B and Li on the phase transition and magnetocaloric effect in Gd2In alloys had been studied. The antiferromagnetic (AFM) - ferromagnetic (FM) phase transition was found to be of first-order nature while ferromagnetic - paramagnetic (PM) phase transition was of second-order nature in B- or Li-doped Gd2In alloys. AFM-FM phase transition temperature was increased while FM-PM phase transition was decreased with more doping concentrations. During AFM-FM phase transition, the slope of temperature-dependent critical field (μ0Hcr) was increased by increased doping amounts. The magnetic entropy changes under small field change were enhanced by B and Li addition, which showed the beneficial effects of B and Li additions.

Interactions between coherent twin boundaries and phase transition of iron under dynamic loading and unloading

NASA Astrophysics Data System (ADS)

Wang, Kun; Chen, Jun; Zhang, Xueyang; Zhu, Wenjun

2017-09-01

Phase transitions and deformation twins are constantly reported in many BCC metals under high pressure, whose interactions are of fundamental importance to understand the strengthening mechanism of these metals under extreme conditions. However, the interactions between twins and phase transition in BCC metals remain largely unexplored. In this work, interactions between coherent twin boundaries and α ↔ ɛ phase transition of iron are investigated using both non-equilibrium molecular dynamics simulations and the nudged elastic band method. Mechanisms of both twin-assisted phase transition and reverse phase transition are studied, and orientation relationships between BCC and HCP phases are found to be ⟨"separators="|11 1 ¯ ⟩ B C C||⟨"separators="|1 ¯2 1 ¯ 0 ⟩ H C P and ⟨"separators="|1 1 ¯ 0 ⟩ B C C||⟨"separators="|0001 ⟩ H C P for both cases. The twin boundary corresponds to {"separators="|10 1 ¯ 0 } H C P after the phase transition. It is amazing that the reverse transition seems to be able to "memorize" and recover the initial BCC twins. The memory would be partly lost when plastic slips take place in the HCP phase before the reverse transition. In the recovered initial BCC twins, three major twin spacings are observed, which are well explained in terms of energy barriers of transition from the HCP phase to the BCC twin. Besides, the variant selection rule of the twin assisted phase transition is also discussed. The results of present work could be expected to give some clues for producing ultra-fine grain structures in materials exhibiting martensitic phase transition.
How to quantify the transition phase during golf swing performance: Torsional load affects low back complaints during the transition phase.

PubMed

Sim, Taeyong; Choi, Ahnryul; Lee, Soeun; Mun, Joung Hwan

2017-10-01

The transition phase of a golf swing is considered to be a decisive instant required for a powerful swing. However, at the same time, the low back torsional loads during this phase can have a considerable effect on golf-related low back pain (LBP). Previous efforts to quantify the transition phase were hampered by problems with accuracy due to methodological limitations. In this study, vector-coding technique (VCT) method was proposed as a comprehensive methodology to quantify the precise transition phase and examine low back torsional load. Towards this end, transition phases were assessed using three different methods (VCT, lead hand speed and X-factor stretch) and compared; then, low back torsional load during the transition phase was examined. As a result, the importance of accurate transition phase quantification has been documented. The largest torsional loads were observed in healthy professional golfers (10.23 ± 1.69 N · kg -1 ), followed by professional golfers with a history of LBP (7.93 ± 1.79 N · kg -1 ), healthy amateur golfers (1.79 ± 1.05 N · kg -1 ) and amateur golfers with a history of LBP (0.99 ± 0.87 N · kg -1 ), which order was equal to that of the transition phase magnitudes of each group. These results indicate the relationship between the transition phase and LBP history and the dependency of the torsional load magnitude on the transition phase.
Structural hierarchy as a key to complex phase selection in Al-Sm

NASA Astrophysics Data System (ADS)

Ye, Z.; Zhang, F.; Sun, Y.; Nguyen, M. C.; Zhou, S. H.; Zhou, L.; Meng, F.; Ott, R. T.; Park, E.; Besser, M. F.; Kramer, M. J.; Ding, Z. J.; Mendelev, M. I.; Wang, C. Z.; Napolitano, R. E.; Ho, K. M.

2017-10-01

Investigating the unknown structure of the complex cubic phase, previously observed to crystallize from melt-spun amorphous Al-10 at.% Sm alloy, we determine the structure in full site-occupancy detail, highlighting several critical structural features that govern the far-from-equilibrium phase selection pathway. Using an efficient genetic algorithm combining molecular dynamics, density functional theory, and x-ray diffraction, the structure is clearly identified as body-centered cubic I m 3 ¯m (No. 229) with ˜140 atoms per cubic unit cell and a lattice parameter of 1.4 nm. The complex structure is further refined to elucidate the detailed site occupancy, revealing full Sm occupancy on 6b sites and split Sm/Al occupancy on 16f sites. Based on the refined site occupancy associated with the experimentally observed phase, we term this phase ɛ -A l60S m11 (bcc), corresponding to the limiting situation when all 16f sites are occupied by Sm. However, it should be recognized that the range of solubility enabled by split occupancy at Sm sites is an important feature in phase selection under experimental conditions, permitting an avenue for transition with little or no chemical partitioning. Our analysis shows that the ɛ -A l60S m11 (bcc) exhibits a "3-6-6-1" first-shell packing around Sm centers on 16f sites, the same dominant motif exhibited by the undercooled liquid. The coincident motif supports the notion that liquid/glass ordering at high undercooling may give rise to topological invariants between the noncrystalline and crystalline states that provide kinetic pathways to metastable phases that are not accessible during near-equilibrium processing.
Structural hierarchy as a key to complex phase selection in Al-Sm

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

Ye, Z.; Zhang, F.; Sun, Y.

Investigating the unknown structure of the complex cubic phase, previously observed to crystallize from melt-spun amorphous Al–10 at.% Sm alloy, we determine the structure in full site-occupancy detail, highlighting several critical structural features that govern the far-from-equilibrium phase selection pathway. Using an efficient genetic algorithm combining molecular dynamics, density functional theory, and x-ray diffraction, the structure is clearly identified as body-centered cubic Im¯3m (No. 229) with ~140 atoms per cubic unit cell and a lattice parameter of 1.4 nm. The complex structure is further refined to elucidate the detailed site occupancy, revealing full Sm occupancy on 6b sites and splitmore » Sm/Al occupancy on 16f sites. Based on the refined site occupancy associated with the experimentally observed phase, we term this phase ε–Al 60Sm 11(bcc), corresponding to the limiting situation when all 16f sites are occupied by Sm. However, it should be recognized that the range of solubility enabled by split occupancy at Sm sites is an important feature in phase selection under experimental conditions, permitting an avenue for transition with little or no chemical partitioning. Our analysis shows that the ε–Al 60Sm 11(bcc) exhibits a “3-6-6-1” first-shell packing around Sm centers on 16f sites, the same dominant motif exhibited by the undercooled liquid. Here, the coincident motif supports the notion that liquid/glass ordering at high undercooling may give rise to topological invariants between the noncrystalline and crystalline states that provide kinetic pathways to metastable phases that are not accessible during near-equilibrium processing.« less
Structural hierarchy as a key to complex phase selection in Al-Sm

DOE PAGES

Ye, Z.; Zhang, F.; Sun, Y.; ...

2017-10-12

Investigating the unknown structure of the complex cubic phase, previously observed to crystallize from melt-spun amorphous Al–10 at.% Sm alloy, we determine the structure in full site-occupancy detail, highlighting several critical structural features that govern the far-from-equilibrium phase selection pathway. Using an efficient genetic algorithm combining molecular dynamics, density functional theory, and x-ray diffraction, the structure is clearly identified as body-centered cubic Im¯3m (No. 229) with ~140 atoms per cubic unit cell and a lattice parameter of 1.4 nm. The complex structure is further refined to elucidate the detailed site occupancy, revealing full Sm occupancy on 6b sites and splitmore » Sm/Al occupancy on 16f sites. Based on the refined site occupancy associated with the experimentally observed phase, we term this phase ε–Al 60Sm 11(bcc), corresponding to the limiting situation when all 16f sites are occupied by Sm. However, it should be recognized that the range of solubility enabled by split occupancy at Sm sites is an important feature in phase selection under experimental conditions, permitting an avenue for transition with little or no chemical partitioning. Our analysis shows that the ε–Al 60Sm 11(bcc) exhibits a “3-6-6-1” first-shell packing around Sm centers on 16f sites, the same dominant motif exhibited by the undercooled liquid. Here, the coincident motif supports the notion that liquid/glass ordering at high undercooling may give rise to topological invariants between the noncrystalline and crystalline states that provide kinetic pathways to metastable phases that are not accessible during near-equilibrium processing.« less
CUX1/Wnt signaling regulates Epithelial Mesenchymal Transition in EBV infected epithelial cells

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

Malizia, Andrea P.; Lacey, Noreen; Walls, Dermot

Idiopathic pulmonary fibrosis (IPF) is a refractory and lethal interstitial lung disease characterized by alveolar epithelial cells apoptosis, fibroblast proliferation and extra-cellular matrix protein deposition. EBV, localised to alveolar epithelial cells of pulmonary fibrosis patients is associated with a poor prognosis. A strategy based on microarray-differential gene expression analysis to identify molecular drivers of EBV-associated lung fibrosis was utilized. Alveolar epithelial cells were infected with EBV to identify genes whose expression was altered following TGF{beta}1-mediated lytic phase. EBV lytic reactivation by TGF{beta}1 drives a selective alteration in CUX1 variant (a) (NCBI accession number NM{sub 1}81552) expression, inducing activation of non-canonicalmore » Wnt pathway mediators, implicating it in Epithelial Mesenchymal Transition (EMT), the molecular event underpinning scar production in tissue fibrosis. The role of EBV in EMT can be attenuated by antiviral strategies and inhibition of Wnt signaling by using All-Trans Retinoic Acids (ATRA). Activation of non-canonical Wnt signaling pathway by EBV in epithelial cells suggests a novel mechanism of EMT via CUX1 signaling. These data present a framework for further description of the link between infectious agents and fibrosis, a significant disease burden.« less
New force replica exchange method and protein folding pathways probed by force-clamp technique.

PubMed

Kouza, Maksim; Hu, Chin-Kun; Li, Mai Suan

2008-01-28

We have developed a new extended replica exchange method to study thermodynamics of a system in the presence of external force. Our idea is based on the exchange between different force replicas to accelerate the equilibrium process. This new approach was applied to obtain the force-temperature phase diagram and other thermodynamical quantities of the three-domain ubiquitin. Using the C(alpha)-Go model and the Langevin dynamics, we have shown that the refolding pathways of single ubiquitin depend on which terminus is fixed. If the N end is fixed then the folding pathways are different compared to the case when both termini are free, but fixing the C terminal does not change them. Surprisingly, we have found that the anchoring terminal does not affect the pathways of individual secondary structures of three-domain ubiquitin, indicating the important role of the multidomain construction. Therefore, force-clamp experiments, in which one end of a protein is kept fixed, can probe the refolding pathways of a single free-end ubiquitin if one uses either the polyubiquitin or a single domain with the C terminus anchored. However, it is shown that anchoring one end does not affect refolding pathways of the titin domain I27, and the force-clamp spectroscopy is always capable to predict folding sequencing of this protein. We have obtained the reasonable estimate for unfolding barrier of ubiquitin, using the microscopic theory for the dependence of unfolding time on the external force. The linkage between residue Lys48 and the C terminal of ubiquitin is found to have the dramatic effect on the location of the transition state along the end-to-end distance reaction coordinate, but the multidomain construction leaves the transition state almost unchanged. We have found that the maximum force in the force-extension profile from constant velocity force pulling simulations depends on temperature nonlinearly. However, for some narrow temperature interval this dependence becomes linear, as have been observed in recent experiments.
Modeling the global distribution of the oxygen isotopic composition of sulfate aerosols: Importance of transition metal catalyzed S(IV) oxidation chemistry

NASA Astrophysics Data System (ADS)

Alexander, B.; Park, R. J.

2006-12-01

The oxygen isotopic composition of sulfate aerosols (Δ17O ~ δ&&17O 0.5*δ18O) reflects the relative importance of different photochemical oxidation pathways in the atmosphere. Simulated isotopic variability in a global chemical transport model (GEOS-Chem) shows good agreement with observations in oceanic [Alexander et al., 2005] and some continental sites. However, a large discrepancy exists between modeled and measured isotopic composition in the high northern latitudes, reflecting an incomplete understanding of the sulfur budget in this region. Recent oxygen isotope measurements of sulfate aerosols collected at Alert, Canada suggest that transition metal catalyzed oxidation of SO2 by O2 in the aqueous-phase is significant during winter [Mc Cabe et al.,2006]. Global chemistry models ignore this oxidation pathway because it is believed to be important only regionally, and because of the large uncertainties in atmospheric metal concentrations and oxidation states. We have incorporated Fe(III) and Mn(II) catalyzed oxidation of S(IV) (S(IV) = SO2·H2O + HSO3- + SO32-) by O2 into the GEOS-Chem model using the McCabe et al. [2006] isotope measurements as a constraint. We will examine the importance of this oxidation pathway for the sulfur budget in the Arctic, and on the global scale. Preliminary results suggest that, during winter, up to 75% of aerosol sulfate at Alert forms via the metal catalysis pathway. The addition of this chemical pathway decreases the SO2 burden in the Arctic (north of 60°N) by 40% due to an increase in the oxidation rate. The comparison of large-scale sulfate aerosol models study (COSAM) showed that on average, models over-predict SO2 mixing ratios by factors of 2 or more [Barrie et al., 2001]. This "missing" S(IV) oxidation pathway can partially explain this discrepancy.
Distinguishing Signatures of Multipathway Conformational Transitions

NASA Astrophysics Data System (ADS)

Pierse, Christopher A.; Dudko, Olga K.

2017-02-01

The folding and binding of biomolecules into functional conformations are thought to be commonly mediated by multiple pathways rather than a unique route. Yet even in experiments where one can "see" individual conformational transitions, their stochastic nature generally precludes one from determining whether the transitions occurred through one or multiple pathways. We establish model-free, observable signatures in the response of macromolecules to force that unambiguously identify multiple pathways—even when the pathways themselves cannot be resolved. The unified analytical description reveals that, through multiple pathways, the response of molecules to external forces can be shaped in diverse ways, resulting in a rich design space for a tailored biological function already at the single-molecule level.
Microscopic origin of black hole reentrant phase transitions

NASA Astrophysics Data System (ADS)

Zangeneh, M. Kord; Dehyadegari, A.; Sheykhi, A.; Mann, R. B.

2018-04-01

Understanding the microscopic behavior of the black hole ingredients has been one of the important challenges in black hole physics during the past decades. In order to shed some light on the microscopic structure of black holes, in this paper, we explore a recently observed phenomenon for black holes namely reentrant phase transition, by employing the Ruppeiner geometry. Interestingly enough, we observe two properties for the phase behavior of small black holes that leads to reentrant phase transition. They are correlated and they are of the interaction type. For the range of pressure in which the system underlies reentrant phase transition, it transits from the large black holes phase to the small one which possesses higher correlation than the other ranges of pressures. On the other hand, the type of interaction between small black holes near the large/small transition line differs for usual and reentrant phase transitions. Indeed, for the usual case, the dominant interaction is repulsive whereas for the reentrant case we encounter an attractive interaction. We show that in the reentrant phase transition case, the small black holes behave like a bosonic gas whereas in the usual phase transition case, they behave like a quantum anyon gas.
5 CFR 362.110 - Transition.

Code of Federal Regulations, 2014 CFR

2014-01-01

... 5 Administrative Personnel 1 2014-01-01 2014-01-01 false Transition. 362.110 Section 362.110 Administrative Personnel OFFICE OF PERSONNEL MANAGEMENT CIVIL SERVICE REGULATIONS PATHWAYS PROGRAMS General... applicable Pathways Program and may revise that guidance as necessary. ...
5 CFR 362.110 - Transition.

Code of Federal Regulations, 2013 CFR

2013-01-01

... 5 Administrative Personnel 1 2013-01-01 2013-01-01 false Transition. 362.110 Section 362.110 Administrative Personnel OFFICE OF PERSONNEL MANAGEMENT CIVIL SERVICE REGULATIONS PATHWAYS PROGRAMS General... applicable Pathways Program and may revise that guidance as necessary. ...
Structures, Phase Transitions and Tricritical Behavior of the Hybrid Perovskite Methyl Ammonium Lead Iodide

DOE PAGES

Whitfield, P. S.; Herron, N.; Guise, W. E.; ...

2016-10-21

Here, we examine the crystal structures and structural phase transitions of the deuterated, partially deuterated and hydrogenous organic-inorganic hybrid perovskite methyl ammonium lead iodide (MAPbI 3) using time-of-flight neutron and synchrotron X-ray powder diffraction. Near 330 K the high temperature cubic phases transformed to a body-centered tetragonal phase. The variation of the order parameter Q for this transition scaled with temperature T as Q (T c-T) , where T c is the critical temperature and the exponent was close to , as predicted for a tricritical phase transition. We also observed coexistence of the cubic and tetragonal phases over amore » range of temperature in all cases, demonstrating that the phase transition was in fact first-order, although still very close to tricritical. Upon cooling further, all the tetragonal phases transformed into a low temperature orthorhombic phase around 160 K, again via a first-order phase transition. Finally, based upon these results, we discuss the impact of the structural phase transitions upon photovoltaic performance of MAPbI 3 based solar cells.« less
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
Metabolic and transcriptional transitions in barley glumes reveal a role as transitory resource buffers during endosperm filling.

PubMed

Kohl, Stefan; Hollmann, Julien; Erban, Alexander; Kopka, Joachim; Riewe, David; Weschke, Winfriede; Weber, Hans

2015-03-01

During grain filling in barley (Hordeum vulgare L. cv. Barke) reserves are remobilized from vegetative organs. Glumes represent the vegetative tissues closest to grains, senesce late, and are involved in the conversion of assimilates. To analyse glume development and metabolism related to grain filling, parallel transcript and metabolite profiling in glumes and endosperm were performed, showing that glume metabolism and development adjusts to changing grain demands, reflected by specific signatures of metabolite and transcript abundances. Before high endosperm sink strength is established by storage product accumulation, glumes form early, intermediary sink organs, shifting then to remobilizing and exporting source organs. Metabolic and transcriptional transitions occur at two phases: first, at the onset of endosperm filling, as a consequence of endosperm sink activity and assimilate depletion in endosperm and vascular tissues; second, at late grain filling, by developmental ageing and senescence. Regulation of and transition between phases are probably governed by specific NAC and WRKY transcription factors, and both abscisic and jasmonic acid, and are accompanied by changed expression of specific nitrogen transporters. Expression and metabolite profiling suggest glume-specific mechanisms of assimilate conversion and translocation. In summary, grain filling and endosperm sink strength coordinate phase changes in glumes via metabolic, hormonal, and transcriptional control. This study provides a comprehensive view of barley glume development and metabolism, and identifies candidate genes and associated pathways, potentially important for breeding improved grain traits. © The Author 2015. Published by Oxford University Press on behalf of the Society for Experimental Biology.
Conformational Transition Pathways of Epidermal Growth Factor Receptor Kinase Domain from Multiple Molecular Dynamics Simulations and Bayesian Clustering.

PubMed

Li, Yan; Li, Xiang; Ma, Weiya; Dong, Zigang

2014-08-12

The epidermal growth factor receptor (EGFR) is aberrantly activated in various cancer cells and an important target for cancer treatment. Deep understanding of EGFR conformational changes between the active and inactive states is of pharmaceutical interest. Here we present a strategy combining multiply targeted molecular dynamics simulations, unbiased molecular dynamics simulations, and Bayesian clustering to investigate transition pathways during the activation/inactivation process of EGFR kinase domain. Two distinct pathways between the active and inactive forms are designed, explored, and compared. Based on Bayesian clustering and rough two-dimensional free energy surfaces, the energy-favorable pathway is recognized, though DFG-flip happens in both pathways. In addition, another pathway with different intermediate states appears in our simulations. Comparison of distinct pathways also indicates that disruption of the Lys745-Glu762 interaction is critically important in DFG-flip while movement of the A-loop significantly facilitates the conformational change. Our simulations yield new insights into EGFR conformational transitions. Moreover, our results verify that this approach is valid and efficient in sampling of protein conformational changes and comparison of distinct pathways.
Computational studies of thermal and quantum phase transitions approached through non-equilibrium quenching

NASA Astrophysics Data System (ADS)

Liu, Cheng-Wei

Phase transitions and their associated critical phenomena are of fundamental importance and play a crucial role in the development of statistical physics for both classical and quantum systems. Phase transitions embody diverse aspects of physics and also have numerous applications outside physics, e.g., in chemistry, biology, and combinatorial optimization problems in computer science. Many problems can be reduced to a system consisting of a large number of interacting agents, which under some circumstances (e.g., changes of external parameters) exhibit collective behavior; this type of scenario also underlies phase transitions. The theoretical understanding of equilibrium phase transitions was put on a solid footing with the establishment of the renormalization group. In contrast, non-equilibrium phase transition are relatively less understood and currently a very active research topic. One important milestone here is the Kibble-Zurek (KZ) mechanism, which provides a useful framework for describing a system with a transition point approached through a non-equilibrium quench process. I developed two efficient Monte Carlo techniques for studying phase transitions, one is for classical phase transition and the other is for quantum phase transitions, both are under the framework of KZ scaling. For classical phase transition, I develop a non-equilibrium quench (NEQ) simulation that can completely avoid the critical slowing down problem. For quantum phase transitions, I develop a new algorithm, named quasi-adiabatic quantum Monte Carlo (QAQMC) algorithm for studying quantum quenches. I demonstrate the utility of QAQMC quantum Ising model and obtain high-precision results at the transition point, in particular showing generalized dynamic scaling in the quantum system. To further extend the methods, I study more complex systems such as spin-glasses and random graphs. The techniques allow us to investigate the problems efficiently. From the classical perspective, using the NEQ approach I verify the universality class of the 3D Ising spin-glasses. I also investigate the random 3-regular graphs in terms of both classical and quantum phase transitions. I demonstrate that under this simulation scheme, one can extract information associated with the classical and quantum spin-glass transitions without any knowledge prior to the simulation.
Temperature-Controlled High-Speed AFM: Real-Time Observation of Ripple Phase Transitions.

PubMed

Takahashi, Hirohide; Miyagi, Atsushi; Redondo-Morata, Lorena; Scheuring, Simon

2016-11-01

With nanometer lateral and Angstrom vertical resolution, atomic force microscopy (AFM) has contributed unique data improving the understanding of lipid bilayers. Lipid bilayers are found in several different temperature-dependent states, termed phases; the main phases are solid and fluid phases. The transition temperature between solid and fluid phases is lipid composition specific. Under certain conditions some lipid bilayers adopt a so-called ripple phase, a structure where solid and fluid phase domains alternate with constant periodicity. Because of its narrow regime of existence and heterogeneity ripple phase and its transition dynamics remain poorly understood. Here, a temperature control device to high-speed atomic force microscopy (HS-AFM) to observe dynamics of phase transition from ripple phase to fluid phase reversibly in real time is developed and integrated. Based on HS-AFM imaging, the phase transition processes from ripple phase to fluid phase and from ripple phase to metastable ripple phase to fluid phase could be reversibly, phenomenologically, and quantitatively studied. The results here show phase transition hysteresis in fast cooling and heating processes, while both melting and condensation occur at 24.15 °C in quasi-steady state situation. A second metastable ripple phase with larger periodicity is formed at the ripple phase to fluid phase transition when the buffer contains Ca 2+ . The presented temperature-controlled HS-AFM is a new unique experimental system to observe dynamics of temperature-sensitive processes at the nanoscopic level. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.
Method for identifying and probing phase transitions in materials

DOEpatents

Asay, Blaine W.; Henson, Bryan F.; Sander, Robert K.; Robinson, Jeanne M.; Son, Steven F.; Dickson, Peter M.

2002-01-01

The present invention includes a method for identifying and probing phase transitions in materials. A polymorphic material capable of existing in at least one non-centrosymmetric phase is interrogated with a beam of laser light at a chosen wavelength and frequency. A phase transition is induced in the material while it is interrogated. The intensity of light scattered by the material and having a wavelength equal to one half the wavelength of the interrogating laser light is detected. If the phase transition results in the production of a non-centrosymmetric phase, the intensity of this scattered light increases; if the phase transition results in the disappearance of a non-centrosymmetric phase, the intensity of this scattered light decreases.
Spontaneous Symmetry Breaking of Domain Walls in Phase-Competing Regions

NASA Astrophysics Data System (ADS)

Ishizuka, Hiroaki; Yamada, Yasusada; Nagaosa, Naoto

2018-05-01

In this study, we investigate the nature of domain walls in an ordered phase in the phase-competing region of two Ising-type order parameters. We consider a two-component ϕ4 theory and show that the domain wall of the ground-state (primary) order parameter shows a second-order phase transition associated with the secondary order parameter of the competing phase; the effective theory of the phase transition is given by the Landau theory of an Ising-type phase transition. We find that the phase boundary of this phase transition is different from the spinodal line of the competing order. The phase transition is detected experimentally by the divergence of the susceptibility corresponding to the secondary order when the temperature is quenched to introduce the domain walls.

Tautomers of Gas-Phase Erythrose and Their Interconversion Reactions: Insights from High-Level ab Initio Study.

PubMed

Szczepaniak, Marek; Moc, Jerzy

2015-11-05

D-Erythrose is a C4 monosaccharide with a biological and potential astrobiological relevance. We have investigated low-energy structures of d-erythrose and their interconversion in the gas phase with the highest-level calculations up-to-date. We have identified a number of structurally distinct furanose and open-chain isomers and predicted α ↔ α and β ↔ β furanose interconversion pathways involving the O-H rotamers. We have estimated relative Gibbs free energies of the erythrose species based on the CCSD(T)/aug-cc-pVTZ electronic energies and MP2/aug-cc-pVTZ vibrational frequencies. By using natural bond orbital theory we have also quantified a stabilization of erythrose conformers and interconversion transition states by intramolecular H-bonds.
The infinite limit as an eliminable approximation for phase transitions

NASA Astrophysics Data System (ADS)

Ardourel, Vincent

2018-05-01

It is generally claimed that infinite idealizations are required for explaining phase transitions within statistical mechanics (e.g. Batterman 2011). Nevertheless, Menon and Callender (2013) have outlined theoretical approaches that describe phase transitions without using the infinite limit. This paper closely investigates one of these approaches, which consists of studying the complex zeros of the partition function (Borrmann et al., 2000). Based on this theory, I argue for the plausibility for eliminating the infinite limit for studying phase transitions. I offer a new account for phase transitions in finite systems, and I argue for the use of the infinite limit as an approximation for studying phase transitions in large systems.
Anisotropy of Earth's D'' layer and stacking faults in the MgSiO3 post-perovskite phase.

PubMed

Oganov, Artem R; Martonák, Roman; Laio, Alessandro; Raiteri, Paolo; Parrinello, Michele

2005-12-22

The post-perovskite phase of (Mg,Fe)SiO3 is believed to be the main mineral phase of the Earth's lowermost mantle (the D'' layer). Its properties explain numerous geophysical observations associated with this layer-for example, the D'' discontinuity, its topography and seismic anisotropy within the layer. Here we use a novel simulation technique, first-principles metadynamics, to identify a family of low-energy polytypic stacking-fault structures intermediate between the perovskite and post-perovskite phases. Metadynamics trajectories identify plane sliding involving the formation of stacking faults as the most favourable pathway for the phase transition, and as a likely mechanism for plastic deformation of perovskite and post-perovskite. In particular, the predicted slip planes are {010} for perovskite (consistent with experiment) and {110} for post-perovskite (in contrast to the previously expected {010} slip planes). Dominant slip planes define the lattice preferred orientation and elastic anisotropy of the texture. The {110} slip planes in post-perovskite require a much smaller degree of lattice preferred orientation to explain geophysical observations of shear-wave anisotropy in the D'' layer.
fcc-bcc phase transition in plasma crystals using time-resolved measurements

NASA Astrophysics Data System (ADS)

Dietz, C.; Bergert, R.; Steinmüller, B.; Kretschmer, M.; Mitic, S.; Thoma, M. H.

2018-04-01

Three-dimensional plasma crystals are often described as Yukawa systems for which a phase transition between the crystal structures fcc and bcc has been predicted. However, experimental investigations of this transition are missing. We use a fast scanning video camera to record the crystallization process of 70 000 microparticles and investigate the existence of the fcc-bcc phase transition at neutral gas pressures of 30, 40, and 50 Pa. To analyze the crystal, robust phase diagrams with the help of a machine learning algorithm are calculated. This work shows that the phase transition can be investigated experimentally and makes a comparison with numerical results of Yukawa systems. The phase transition is analyzed in dependence on the screening parameter and structural order. We suggest that the transition is an effect of gravitational compression of the plasma crystal. Experimental investigations of the fcc-bcc phase transition will provide an opportunity to estimate the coupling strength Γ by comparison with numerical results of Yukawa systems.
Learning phase transitions by confusion

NASA Astrophysics Data System (ADS)

van Nieuwenburg, Evert P. L.; Liu, Ye-Hua; Huber, Sebastian D.

2017-02-01

Classifying phases of matter is key to our understanding of many problems in physics. For quantum-mechanical systems in particular, the task can be daunting due to the exponentially large Hilbert space. With modern computing power and access to ever-larger data sets, classification problems are now routinely solved using machine-learning techniques. Here, we propose a neural-network approach to finding phase transitions, based on the performance of a neural network after it is trained with data that are deliberately labelled incorrectly. We demonstrate the success of this method on the topological phase transition in the Kitaev chain, the thermal phase transition in the classical Ising model, and the many-body-localization transition in a disordered quantum spin chain. Our method does not depend on order parameters, knowledge of the topological content of the phases, or any other specifics of the transition at hand. It therefore paves the way to the development of a generic tool for identifying unexplored phase transitions.
Two kinds of phase transitions in a voting model

NASA Astrophysics Data System (ADS)

Hisakado, M.; Mori, S.

2012-08-01

In this paper, we discuss a voting model with two candidates, C0 and C1. We consider two types of voters—herders and independents. The voting of independents is based on their fundamental values, while the voting of herders is based on the number of previous votes. We can identify two kinds of phase transitions. One is an information cascade transition similar to a phase transition seen in the Ising model. The other is a transition of super and normal diffusions. These phase transitions coexist. We compared our results to the conclusions of experiments and identified the phase transitions in the upper limit of the time t by using the analysis of human behavior obtained from experiments.
Detecting phase transitions in a neural network and its application to classification of syndromes in traditional Chinese medicine

NASA Astrophysics Data System (ADS)

Chen, J.; Xi, G.; Wang, W.

2008-02-01

Detecting phase transitions in neural networks (determined or random) presents a challenging subject for phase transitions play a key role in human brain activity. In this paper, we detect numerically phase transitions in two types of random neural network(RNN) under proper parameters.
Free energy landscape and transition pathways from Watson–Crick to Hoogsteen base pairing in free duplex DNA

PubMed Central

Yang, Changwon; Kim, Eunae; Pak, Youngshang

2015-01-01

Houghton (HG) base pairing plays a central role in the DNA binding of proteins and small ligands. Probing detailed transition mechanism from Watson–Crick (WC) to HG base pair (bp) formation in duplex DNAs is of fundamental importance in terms of revealing intrinsic functions of double helical DNAs beyond their sequence determined functions. We investigated a free energy landscape of a free B-DNA with an adenosine–thymine (A–T) rich sequence to probe its conformational transition pathways from WC to HG base pairing. The free energy landscape was computed with a state-of-art two-dimensional umbrella molecular dynamics simulation at the all-atom level. The present simulation showed that in an isolated duplex DNA, the spontaneous transition from WC to HG bp takes place via multiple pathways. Notably, base flipping into the major and minor grooves was found to play an important role in forming these multiple transition pathways. This finding suggests that naked B-DNA under normal conditions has an inherent ability to form HG bps via spontaneous base opening events. PMID:26250116
Universal phase transition in community detectability under a stochastic block model.

PubMed

Chen, Pin-Yu; Hero, Alfred O

2015-03-01

We prove the existence of an asymptotic phase-transition threshold on community detectability for the spectral modularity method [M. E. J. Newman, Phys. Rev. E 74, 036104 (2006) and Proc. Natl. Acad. Sci. (USA) 103, 8577 (2006)] under a stochastic block model. The phase transition on community detectability occurs as the intercommunity edge connection probability p grows. This phase transition separates a subcritical regime of small p, where modularity-based community detection successfully identifies the communities, from a supercritical regime of large p where successful community detection is impossible. We show that, as the community sizes become large, the asymptotic phase-transition threshold p* is equal to √[p1p2], where pi(i=1,2) is the within-community edge connection probability. Thus the phase-transition threshold is universal in the sense that it does not depend on the ratio of community sizes. The universal phase-transition phenomenon is validated by simulations for moderately sized communities. Using the derived expression for the phase-transition threshold, we propose an empirical method for estimating this threshold from real-world data.
Intramolecular fluorine migration via four-member cyclic transition states

PubMed

Nguyen; Mayer; Morton

2000-11-17

Gaseous CF(3)(+) interchanges F(+) for O with simple carbonyl compounds. CF(3)(+) reacts with propionaldehyde in the gas phase to produce (CH(3))(2)CF(+) via two competing pathways. Starting with 1-(13)C-propionaldehyde, the major pathway (80%) produces (CH(3))(2)CF(+) with the carbon label in one of the methyl groups. The minor pathway (20%) produces (CH(3))(2)CF(+) with the carbon label in the central position. The relative proportions of these two pathways are measured by (19)F NMR analysis of the neutral CH(3)CF=CH(2) produced by deprotonation of (CH(3))(2)CF(+) at <10(-)(3) Torr in an electron bombardment flow (EBFlow) reactor. Formation of alkene in which carbon is directly bonded to fluorine means that (in the minor product, at least) an F(+) for O transposition occurs via adduct formation followed by 1,3-atom transfer and then isomerization of CH(3)CH(2)CHF(+) to the more stable (CH(3))(2)CF(+). Use of CF(4) as a chemical ionization (CI) reagent gas leads to CF(3)(+) adduct ions for a variety of ketones, in addition to isoelectronic transposition of F(+) for O. Metastable ion decompositions of the adduct ions yield the metathesis products. Decompositions of fluorocycloalkyl cations formed in this manner give evidence for the same kinds of rearrangements as take place in CH(3)CH(2)CHF(+). Density functional calculations confirm that F(+) for O metathesis takes place via addition of CF(3)(+) to the carbonyl oxygen followed by transposition via a four-member cyclic transition state. A computational survey of the effects of different substituents in a series of aldehydes and acyclic ketones reveals no systematic variation of the energy of the transition state as a function of thermochemistry, but the Hammond postulate does appear to be obeyed in terms of progress along the reaction coordinate. Bond lengths corresponding to the central barrier correlate with overall thermochemistry of the F(+) for O interchange, but in a sense opposite to what might have been expected: the transition state becomes more product-like as the metathesis becomes increasingly exothermic. This reversal of the naive interpretation of the Hammond postulate is accounted for by the relative positions of the potential energy wells that precede and follow the central barrier.
Materials science of the gel to fluid phase transition in a supported phospholipid bilayer.

PubMed

Xie, Anne Feng; Yamada, Ryo; Gewirth, Andrew A; Granick, Steve

2002-12-09

We report the results of in situ AFM measurements examining the phase transition of bilayers formed from the zwitterionic phospholipid, DMPC, 1,2-dimyristoyl-sn-glycero-3-phosphocholine, supported on mica. The images show that the fluid to gel phase transition process features substantial tearing of the bilayer due to the density change between the two phases. The gel to fluid transition is strongly affected by the resultant stress introduced into the gel phase, which changes the degree of cooperativity, the shape of developing fluid phase regions, and the course of the transition.
Isothermal lipid phase transitions.

PubMed

Cevc, G

1991-03-01

In liotropic lipid systems phase transitions can be induced isothermally by changing the solvent concentration or composition; alternatively, lipid composition can be modified by (bio)chemical means. The probability for isothermal phase transitions increases with the decreasing transition entropy; it is proportional to the magnitude of the transition temperature shift caused by transformation-inducing system variation. Manipulations causing large thermodynamic effects, such as lipid (de)hydration, binding of protons or divalent ions and macromolecular adsorption, but also close bilayer approach are, therefore, likely to cause structural lipid change(s) at a constant temperature. Net lipid charges enhance the membrane susceptibility to salt-induced isothermal phase transitions; a large proportion of this effect is due to the bilayer dehydration, however, rather than being a consequence of the decreased Coulombic electrostatic interactions. Membrane propensity for isothermal phase transitions, consequently, always increases with the hydrophilicity of the lipid heads, as well as with the desaturation and shortening of the lipid chains. Upon a phase change at a constant temperature, some of the interfacially bound solutes (e.g. protons or calcium) are released in the solution. Membrane permeability and fusogenicity simultaneously increase. In mixed systems, isothermal phase transitions, moreover, may result in lateral phase separation. All this opens up ways for the involvement of isothermal phase transitions in the regulation of biological processes.
A Global Analysis of Kinase Function in Candida albicans Hyphal Morphogenesis Reveals a Role for the Endocytosis Regulator Akl1

PubMed Central

Bar-Yosef, Hagit; Gildor, Tsvia; Ramírez-Zavala, Bernardo; Schmauch, Christian; Weissman, Ziva; Pinsky, Mariel; Naddaf, Rawi; Morschhäuser, Joachim; Arkowitz, Robert A.; Kornitzer, Daniel

2018-01-01

The human pathogenic fungus Candida albicans can switch between yeast and hyphal morphologies as a function of environmental conditions and cellular physiology. The yeast-to-hyphae morphogenetic switch is activated by well-established, kinase-based signal transduction pathways that are induced by extracellular stimuli. In order to identify possible inhibitory pathways of the yeast-to-hyphae transition, we interrogated a collection of C. albicans protein kinases and phosphatases ectopically expressed under the regulation of the TETon promoter. Proportionately more phosphatases than kinases were identified that inhibited hyphal morphogenesis, consistent with the known role of protein phosphorylation in hyphal induction. Among the kinases, we identified AKL1 as a gene that significantly suppressed hyphal morphogenesis in serum. Akl1 specifically affected hyphal elongation rather than initiation: overexpression of AKL1 repressed hyphal growth, and deletion of AKL1 resulted in acceleration of the rate of hyphal elongation. Akl1 suppressed fluid-phase endocytosis, probably via Pan1, a putative clathrin-mediated endocytosis scaffolding protein. In the absence of Akl1, the Pan1 patches were delocalized from the sub-apical region, and fluid-phase endocytosis was intensified. These results underscore the requirement of an active endocytic pathway for hyphal morphogenesis. Furthermore, these results suggest that under standard conditions, endocytosis is rate-limiting for hyphal elongation. PMID:29473018
A Global Analysis of Kinase Function in Candida albicans Hyphal Morphogenesis Reveals a Role for the Endocytosis Regulator Akl1.

PubMed

Bar-Yosef, Hagit; Gildor, Tsvia; Ramírez-Zavala, Bernardo; Schmauch, Christian; Weissman, Ziva; Pinsky, Mariel; Naddaf, Rawi; Morschhäuser, Joachim; Arkowitz, Robert A; Kornitzer, Daniel

2018-01-01

The human pathogenic fungus Candida albicans can switch between yeast and hyphal morphologies as a function of environmental conditions and cellular physiology. The yeast-to-hyphae morphogenetic switch is activated by well-established, kinase-based signal transduction pathways that are induced by extracellular stimuli. In order to identify possible inhibitory pathways of the yeast-to-hyphae transition, we interrogated a collection of C. albicans protein kinases and phosphatases ectopically expressed under the regulation of the TETon promoter. Proportionately more phosphatases than kinases were identified that inhibited hyphal morphogenesis, consistent with the known role of protein phosphorylation in hyphal induction. Among the kinases, we identified AKL1 as a gene that significantly suppressed hyphal morphogenesis in serum. Akl1 specifically affected hyphal elongation rather than initiation: overexpression of AKL1 repressed hyphal growth, and deletion of AKL1 resulted in acceleration of the rate of hyphal elongation. Akl1 suppressed fluid-phase endocytosis, probably via Pan1, a putative clathrin-mediated endocytosis scaffolding protein. In the absence of Akl1, the Pan1 patches were delocalized from the sub-apical region, and fluid-phase endocytosis was intensified. These results underscore the requirement of an active endocytic pathway for hyphal morphogenesis. Furthermore, these results suggest that under standard conditions, endocytosis is rate-limiting for hyphal elongation.
Gas-phase structure and fragmentation pathways of singly protonated peptides with N-terminal arginine.

PubMed

Bythell, Benjamin J; Csonka, István P; Suhai, Sándor; Barofsky, Douglas F; Paizs, Béla

2010-11-25

The gas-phase structures and fragmentation pathways of the singly protonated peptide arginylglycylaspartic acid (RGD) are investigated by means of collision-induced-dissociation (CID) and detailed molecular mechanics and density functional theory (DFT) calculations. It is demonstrated that despite the ionizing proton being strongly sequestered at the guanidine group, protonated RGD can easily be fragmented on charge directed fragmentation pathways. This is due to facile mobilization of the C-terminal or aspartic acid COOH protons thereby generating salt-bridge (SB) stabilized structures. These SB intermediates can directly fragment to generate b(2) ions or facilely rearrange to form anhydrides from which both b(2) and b(2)+H(2)O fragments can be formed. The salt-bridge stabilized and anhydride transition structures (TSs) necessary to form b(2) and b(2)+H(2)O are much lower in energy than their traditional charge solvated counterparts. These mechanisms provide compelling evidence of the role of SB and anhydride structures in protonated peptide fragmentation which complements and supports our recent findings for tryptic systems (Bythell, B. J.; Suhai, S.; Somogyi, A.; Paizs, B. J. Am. Chem. Soc. 2009, 131, 14057-14065.). In addition to these findings we also report on the mechanisms for the formation of the b(1) ion, neutral loss (H(2)O, NH(3), guanidine) fragment ions, and the d(3) ion.
Ultrafast Dynamics in Vanadium Dioxide: Separating Spatially Segregated Mixed Phase Dynamics in the Time-domain

NASA Astrophysics Data System (ADS)

Hilton, David

2011-10-01

In correlated electronic systems, observed electronic and structural behavior results from the complex interplay between multiple, sometimes competing degrees-of- freedom. One such material used to study insulator-to-metal transitions is vanadium dioxide, which undergoes a phase transition from a monoclinic-insulating phase to a rutile-metallic phase when the sample is heated to 340 K. The major open question with this material is the relative influence of this structural phase transition (Peirels transition) and the effects of electronic correlations (Mott transition) on the observed insulator-to-metal transition. Answers to these major questions are complicated by vanadium dioxide's sensitivity to perturbations in the chemical structure in VO2. For example, related VxOy oxides with nearly a 2:1 ratio do not demonstrate the insulator-to- metal transition, while recent work has demonstrated that W:VO2 has demonstrated a tunable transition temperature controllable with tungsten doping. All of these preexisting results suggest that the observed electronic properties are exquisitely sensitive to the sample disorder. Using ultrafast spectroscopic techniques, it is now possible to impulsively excite this transition and investigate the photoinduced counterpart to this thermal phase transition in a strongly nonequilibrium regime. I will discuss our recent results studying the terahertz-frequency conductivity dynamics of this photoinduced phase transition in the poorly understood near threshold temperature range. We find a dramatic softening of the transition near the critical temperature, which results primarily from the mixed phase coexistence near the transition temperature. To directly study this mixed phase behavior, we directly study the nucleation and growth rates of the metallic phase in the parent insulator using non-degenerate optical pump-probe spectroscopy. These experiments measure, in the time- domain, the coexistent phase separation in VO2 (spatially separated insulator and metal islands) and, more importantly, their dynamic evolution in response to optical excitation.
The role of upper mantle mineral phase transitions on the current structure of large-scale Earth's mantle convection.

NASA Astrophysics Data System (ADS)

Thoraval, C.

2017-12-01

Describing the large-scale structures of mantle convection and quantifying the mass transfer between upper and lower mantle request to account for the role played by mineral phase transitions in the transition zone. We build a density distribution within the Earth mantle from velocity anomalies described by global seismic tomographic models. The density distribution includes thermal anomalies and topographies of the phase transitions at depths of 410 and 660 km. We compute the flow driven by this density distribution using a 3D spherical circulation model, which account for depth-dependent viscosity. The dynamic topographies at the surface and at the CMB and the geoid are calculated as well. Within the range of viscosity profiles allowing for a satisfying restitution of the long wavelength geoid, we perform a parametric study to decipher the role of the characteristics of phase diagrams - mainly the Clapeyron's slopes - and of the kinetics of phase transitions, which may modify phase transition topographies. Indeed, when a phase transition is delayed, the boundary between two mineral phases is both dragged by the flow and interfere with it. The results are compared to recent estimations of surface dynamic topography and to the phase transition topographies as revealed by seismic studies. The consequences are then discussed in terms of structure of mantle flow. Comparisons between various tomographic models allow us to enlighten the most robust features. At last, the role played by the phase transitions on the lateral variations of mass transfer between upper and lower mantle are quantified by comparison to cases with no phase transitions and confronted to regional tomographic models, which reflect the variability of the behaviors of the descending slabs in the transition zone.
Asymmetry and basic pathways in sleep-stage transitions

NASA Astrophysics Data System (ADS)

Lo, Chung-Chuan; Bartsch, Ronny P.; Ivanov, Plamen Ch.

2013-04-01

We study dynamical aspects of sleep micro-architecture. We find that sleep dynamics exhibits a high degree of asymmetry, and that the entire class of sleep-stage transition pathways underlying the complexity of sleep dynamics throughout the night can be characterized by two independent asymmetric transition paths. These basic pathways remain stable under sleep disorders, even though the degree of asymmetry is significantly reduced. Our findings demonstrate an intriguing temporal organization in sleep micro-architecture at short time scales that is typical for physical systems exhibiting self-organized criticality (SOC), and indicates nonequilibrium critical dynamics in brain activity during sleep.
Defect-induced local variation of crystal phase transition temperature in metal-halide perovskites.

PubMed

Dobrovolsky, Alexander; Merdasa, Aboma; Unger, Eva L; Yartsev, Arkady; Scheblykin, Ivan G

2017-06-26

Solution-processed organometal halide perovskites are hybrid crystalline semiconductors highly interesting for low-cost and efficient optoelectronics. Their properties are dependent on the crystal structure. Literature shows a variety of crystal phase transition temperatures and often a spread of the transition over tens of degrees Kelvin. We explain this inconsistency by demonstrating that the temperature of the tetragonal-to-orthorhombic phase transition in methylammonium lead triiodide depends on the concentration and nature of local defects. Phase transition in individual nanowires was studied by photoluminescence microspectroscopy and super-resolution imaging. We propose that upon cooling from 160 to 140 K, domains of the crystal containing fewer defects stay in the tetragonal phase longer than highly defected domains that readily transform to the high bandgap orthorhombic phase at higher temperatures. The existence of relatively pure tetragonal domains during the phase transition leads to drastic photoluminescence enhancement, which is inhomogeneously distributed across perovskite microcrystals.Understanding crystal phase transition in materials is of fundamental importance. Using luminescence spectroscopy and super-resolution imaging, Dobrovolsky et al. study the transition from the tetragonal to orthorhombic crystal phase in methylammonium lead triiodide nanowires at low temperature.
Ab Initio Simulations of Temperature Dependent Phase Stability and Martensitic Transitions in NiTi

NASA Technical Reports Server (NTRS)

Haskins, Justin B.; Thompson, Alexander E.; Lawson, John W.

2016-01-01

For NiTi based alloys, the shape memory effect is governed by a transition from a low-temperature martensite phase to a high-temperature austenite phase. Despite considerable experimental and computational work, basic questions regarding the stability of the phases and the martensitic phase transition remain unclear even for the simple case of binary, equiatomic NiTi. We perform ab initio molecular dynamics simulations to describe the temperature-dependent behavior of NiTi and resolve several of these outstanding issues. Structural correlation functions and finite temperature phonon spectra are evaluated to determine phase stability. In particular, we show that finite temperature, entropic effects stabilize the experimentally observed martensite (B19') and austenite (B2) phases while destabilizing the theoretically predicted (B33) phase. Free energy computations based on ab initio thermodynamic integration confirm these results and permit estimates of the transition temperature between the phases. In addition to the martensitic phase transition, we predict a new transition between the B33 and B19' phases. The role of defects in suppressing these phase transformations is discussed.

Anatase-rutile phase transformation of titanium dioxide bulk material: a DFT + U approach

NASA Astrophysics Data System (ADS)

Vu, Nam H.; Le, Hieu V.; Cao, Thi M.; Pham, Viet V.; Le, Hung M.; Nguyen-Manh, Duc

2012-10-01

The anatase-rutile phase transformation of TiO2 bulk material is investigated using a density functional theory (DFT) approach in this study. According to the calculations employing the Perdew-Burke-Ernzerhof (PBE) exchange-correlation functional with the Vanderbilt ultrasoft pseudopotential, it is suggested that the anatase phase is more energetically stable than rutile, which is in variance with the experimental observations. Consequently, the DFT + U method is employed in order to predict the correct structural stability in titania from electronic-structure-based total energy calculations. The Hubbard U term is determined by examining the band structure of rutile with various values of U from 3 to 10 eV. At U = 5 eV, a theoretical bandgap for rutile is obtained as 3.12 eV, which is in very good agreement with the reported experimental bandgap. Hence, we choose the DFT + U method (with U = 5 eV) to investigate the transformation pathway using the newly-developed solid-state nudged elastic band (ss-NEB) method, and consequently obtain an intermediate transition structure that is 9.794 eV per four-TiO2 above the anatase phase. When the Ti-O bonds in the transition state are examined using charge density analysis, seven Ti-O bonds (out of 24 bonds in the anatase unit cell) are broken, and this result is in excellent agreement with a previous experimental study (Penn and Banfield 1999 Am. Miner. 84 871-6).
Formation of the molecular crystal structure during the vacuum sublimation of paracetamol

NASA Astrophysics Data System (ADS)

Belyaev, A. P.; Rubets, V. P.; Antipov, V. V.; Bordei, N. S.

2015-04-01

The results from structural and thermal studies on the formation of molecular crystals during the vacuum sublimation of paracetamol from its vapor phase are given. It is established that the vapor-crystal phase transition proceeds in a complicated way as the superposition of two phase transitions: a first-order phase transition with a change in density, and a second-order phase transition with a change in ordering. It is shown that the latter is a smeared phase transition that proceeds with the formation of a pretransitional phase that is irreversibly dissipated during phase transformation, leading to the formation of crystals of the rhombic syngony. Data from differential scanning calorimetry and X-ray diffraction analysis are presented along with microphotographs.
Key feature of the catalytic cycle of TNF-α converting enzyme involves communication between distal protein sites and the enzyme catalytic core

PubMed Central

Solomon, Ariel; Akabayov, Barak; Frenkel, Anatoly; Milla, Marcos E.; Sagi, Irit

2007-01-01

Despite their key roles in many normal and pathological processes, the molecular details by which zinc-dependent proteases hydrolyze their physiological substrates remain elusive. Advanced theoretical analyses have suggested reaction models for which there is limited and controversial experimental evidence. Here we report the structure, chemistry and lifetime of transient metal–protein reaction intermediates evolving during the substrate turnover reaction of a metalloproteinase, the tumor necrosis factor-α converting enzyme (TACE). TACE controls multiple signal transduction pathways through the proteolytic release of the extracellular domain of a host of membrane-bound factors and receptors. Using stopped-flow x-ray spectroscopy methods together with transient kinetic analyses, we demonstrate that TACE's catalytic zinc ion undergoes dynamic charge transitions before substrate binding to the metal ion. This indicates previously undescribed communication pathways taking place between distal protein sites and the enzyme catalytic core. The observed charge transitions are synchronized with distinct phases in the reaction kinetics and changes in metal coordination chemistry mediated by the binding of the peptide substrate to the catalytic metal ion and product release. Here we report key local charge transitions critical for proteolysis as well as long sought evidence for the proposed reaction model of peptide hydrolysis. This study provides a general approach for gaining critical insights into the molecular basis of substrate recognition and turnover by zinc metalloproteinases that may be used for drug design. PMID:17360351
Phase transitions in (NH4)2MoO2F4 crystal

NASA Astrophysics Data System (ADS)

Krylov, Alexander; Laptash, Natalia; Vtyurin, Alexander; Krylova, Svetlana

2016-11-01

The mechanisms of temperature and high pressure phase transitions have been studied by Raman spectroscopy. Room temperature (295 K) experiments under high hydrostatic pressure up to 3.6 GPa for (NH4)2 MoO2 F4 have been carried out. Experimental data indicates a phase transition into a new high-pressure phase for (NH4)2 MoO2 F4 at 1.2 GPa. This phase transition is related to the ordering anion octahedron groups [MoO2 F4]2- and is not associated with ammonium group. Raman spectra of small non-oriented crystals ranging from 10 to 350 K have been observed. The experiment shows anion groups [MoO2 F4]2- and ammonium in high temperature phase are disordered. The phase transition at T1 = 269.8 K is of the first-order, close to the tricritical point. The first temperature phase transition is related to the ordering anion octahedron groups [MoO2 F4]2-. Second phase transitions T2 = 180 K are associated with the ordering of ammonium. The data presented within this study demonstrate that 2D correlation analysis combined with traditional Raman spectroscopy are powerful tool to study phase transitions in the crystals.
Unconventional phase transitions in liquid crystals

NASA Astrophysics Data System (ADS)

Kats, E. I.

2017-12-01

According to classical textbooks on thermodynamics or statistical physics, there are only two types of phase transitions: continuous, or second-order, in which the latent heat L is zero, and first-order, in which L ≠ 0. Present-day textbooks and monographs also mention another, stand-alone type—the Berezinskii-Kosterlitz-Thouless transition, which exists only in two dimensions and shares some features with first- and second-order phase transitions. We discuss examples of non-conventional thermodynamic behavior (i.e., which is inconsistent with the theoretical phase transition paradigm now universally accepted). For phase transitions in smectic liquid crystals, mechanisms for nonconventional behavior are proposed and the predictions they imply are examined.
Superradiant phase transition with graphene embedded in one dimensional optical cavity

NASA Astrophysics Data System (ADS)

Li, Benliang; Liu, Tao; Hewak, Daniel W.; Wang, Qi Jie

2018-01-01

We theoretically investigate the cavity QED of graphene embedded in an optical cavity under perpendicular magnetic field. We consider the coupling of cyclotron transition and a multimode cavity described by a multimode Dicke model. This model exhibits a superradiant quantum phase transition, which we describe exactly in an effective Hamiltonian approach. The complete excitation spectrum in both the normal phase and superradiant phase regimes is given. In contrast to the single mode case, multimode coupling of cavity photon and cyclotron transition can greatly reduce the critical vacuum Rabi frequency required for quantum phase transition, and dramatically enhance the superradiant emission by fast modulating the Hamiltonian. Our work paves a way to experimental explorations of quantum phase transitions in solid state systems.
Interference of interchromophoric energy-transfer pathways in π-conjugated macrocycles

DOE PAGES

Alfonso Hernandez, Laura; Nelson, Tammie Renee; Gelin, Maxim F.; ...

2016-11-10

The interchromophoric energy-transfer pathways between weakly coupled units in a π-conjugated phenylene–ethynylene macrocycle and its half-ring analogue have been investigated using the nonadiabatic excited-state molecular dynamics approach. To track the flow of electronic transition density between macrocycle units, we formulate a transition density flux analysis adapted from the statistical minimum flow method previously developed to investigate vibrational energy flow. Following photoexcitation, transition density is primarily delocalized on two chromophore units and the system undergoes ultrafast energy transfer, creating a localized excited state on a single unit. In the macrocycle, distinct chromophore units donate transition density to a single acceptor unitmore » but do not interchange transition density among each other. We find that energy transfer in the macrocycle is slower than in the corresponding half ring because of the presence of multiple interfering energy-transfer pathways. Finally, simulation results are validated by modeling the fluorescence anisotropy decay.« less
Analyzing milestoning networks for molecular kinetics: definitions, algorithms, and examples.

PubMed

Viswanath, Shruthi; Kreuzer, Steven M; Cardenas, Alfredo E; Elber, Ron

2013-11-07

Network representations are becoming increasingly popular for analyzing kinetic data from techniques like Milestoning, Markov State Models, and Transition Path Theory. Mapping continuous phase space trajectories into a relatively small number of discrete states helps in visualization of the data and in dissecting complex dynamics to concrete mechanisms. However, not only are molecular networks derived from molecular dynamics simulations growing in number, they are also getting increasingly complex, owing partly to the growth in computer power that allows us to generate longer and better converged trajectories. The increased complexity of the networks makes simple interpretation and qualitative insight of the molecular systems more difficult to achieve. In this paper, we focus on various network representations of kinetic data and algorithms to identify important edges and pathways in these networks. The kinetic data can be local and partial (such as the value of rate coefficients between states) or an exact solution to kinetic equations for the entire system (such as the stationary flux between vertices). In particular, we focus on the Milestoning method that provides fluxes as the main output. We proposed Global Maximum Weight Pathways as a useful tool for analyzing molecular mechanism in Milestoning networks. A closely related definition was made in the context of Transition Path Theory. We consider three algorithms to find Global Maximum Weight Pathways: Recursive Dijkstra's, Edge-Elimination, and Edge-List Bisection. The asymptotic efficiency of the algorithms is analyzed and numerical tests on finite networks show that Edge-List Bisection and Recursive Dijkstra's algorithms are most efficient for sparse and dense networks, respectively. Pathways are illustrated for two examples: helix unfolding and membrane permeation. Finally, we illustrate that networks based on local kinetic information can lead to incorrect interpretation of molecular mechanisms.
Dehydration pathways of 1-propanol on HZSM-5 in the presence and absence of water

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

Zhi, Yuchun; Shi, Hui; Mu, Linyu

The Brønsted acid-catalyzed gas-phase dehydration of 1-propanol (0.075-4 kPa) was studied on zeolite H-MFI (Si/Al = 26, containing minimal amounts of extraframework Al moieties) in the absence and presence of co-fed water (0-2.5 kPa) at 413-443 K. It is shown that propene can be formed from monomeric and dimeric adsorbed 1-propanol. The stronger adsorption of 1-propanol relative to water indicates that the reduced dehydration rates in the presence of water are not a consequence of the competitive adsorption between 1-propanol and water. Instead, the deleterious effect is related to the different extents of stabilization of adsorbed intermediates and the relevantmore » elimination/substitution transition states by water. Water stabilizes the adsorbed 1-propanol monomer significantly more than the elimination transition state, leading to a higher activation barrier and a greater entropy gain for the rate-limiting step, which eventually leads to propene. In a similar manner, an excess of 1-propanol stabilizes the adsorbed state of 1-propanol more than the elimination transition state. In comparison with the monomer-mediated pathway, adsorbed dimer and the relevant transition states for propene and ether formation are similarly, while less effectively, stabilized by intrazeolite water molecules. This work was supported by the US Department of Energy, Office of Science, Office of Basic Energy Sciences, Division of Chemical Sciences, Geosciences, and Biosciences, and was performed in part using the Molecular Sciences Computing Facility (MSCF) in the William R. Wiley Environmental Molecular Sciences Laboratory, a DOE national scientific user facility sponsored by the DOE’s Office of Biological and Environmental Research and located and the Pacific Northwest National Laboratory (PNNL). PNNL is operated by Battelle for DOE.« less
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.
Induction of DREB2A pathway with repression of E2F, jasmonic acid biosynthetic and photosynthesis pathways in cold acclimation-specific freeze-resistant wheat crown.

PubMed

Karki, Amrit; Horvath, David P; Sutton, Fedora

2013-03-01

Winter wheat lines can achieve cold acclimation (development of tolerance to freezing temperatures) and vernalization (delay in transition from vegetative to reproductive phase) in response to low non-freezing temperatures. To describe cold-acclimation-specific processes and pathways, we utilized cold acclimation transcriptomic data from two lines varying in freeze survival but not vernalization. These lines, designated freeze-resistant (FR) and freeze-susceptible (FS), were the source of crown tissue RNA. Well-annotated differentially expressed genes (p ≤ 0.005 and fold change ≥ 2 in response to 4 weeks cold acclimation) were used for gene ontology and pathway analysis. "Abiotic stimuli" was identified as the most enriched and unique for FR. Unique to FS was "cytoplasmic components." Pathway analysis revealed the "triacylglycerol degradation" pathway as significantly downregulated and common to both FR and FS. The most enriched of FR pathways was "neighbors of DREB2A," with the highest positive median fold change. The "13-LOX and 13-HPL" and the "E2F" pathways were enriched in FR only with a negative median fold change. The "jasmonic acid biosynthesis" pathway and four "photosynthetic-associated" pathways were enriched in both FR and FS but with a more negative median fold change in FR than in FS. A pathway unique to FS was "binding partners of LHCA1," which was enriched only in FS with a significant negative median fold change. We propose that the DREB2A, E2F, jasmonic acid biosynthesis, and photosynthetic pathways are critical for discrimination between cold-acclimated lines varying in freeze survival.
A density functional theory study of the decomposition mechanism of nitroglycerin.

PubMed

Pei, Liguan; Dong, Kehai; Tang, Yanhui; Zhang, Bo; Yu, Chang; Li, Wenzuo

2017-08-21

The detailed decomposition mechanism of nitroglycerin (NG) in the gas phase was studied by examining reaction pathways using density functional theory (DFT) and canonical variational transition state theory combined with a small-curvature tunneling correction (CVT/SCT). The mechanism of NG autocatalytic decomposition was investigated at the B3LYP/6-31G(d,p) level of theory. Five possible decomposition pathways involving NG were identified and the rate constants for the pathways at temperatures ranging from 200 to 1000 K were calculated using CVT/SCT. There was found to be a lower energy barrier to the β-H abstraction reaction than to the α-H abstraction reaction during the initial step in the autocatalytic decomposition of NG. The decomposition pathways for CHOCOCHONO 2 (a product obtained following the abstraction of three H atoms from NG by NO 2 ) include O-NO 2 cleavage or isomer production, meaning that the autocatalytic decomposition of NG has two reaction pathways, both of which are exothermic. The rate constants for these two reaction pathways are greater than the rate constants for the three pathways corresponding to unimolecular NG decomposition. The overall process of NG decomposition can be divided into two stages based on the NO 2 concentration, which affects the decomposition products and reactions. In the first stage, the reaction pathway corresponding to O-NO 2 cleavage is the main pathway, but the rates of the two autocatalytic decomposition pathways increase with increasing NO 2 concentration. However, when a threshold NO 2 concentration is reached, the NG decomposition process enters its second stage, with the two pathways for NG autocatalytic decomposition becoming the main and secondary reaction pathways.
Boron-tuning transition temperature of vanadium dioxide from rutile to monoclinic phase

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

Zhang, J. J.; He, H. Y.; Xie, Y.

2014-11-21

The effect of the doped boron on the phase transition temperature between the monoclinic phase and the rutile phase of VO{sub 2} has been studied by performing first-principles calculations. It is found that the phase transition temperature decreases linearly with increasing the doping level of B in each system, no matter where the B atom is in the crystal. More importantly, the descent of the transition temperature is predicted to be as large as 83 K/at. % B, indicating that the boron concentration of only 0.5% can cause the phase transition at room temperature. These findings provide a new routinemore » of modulating the phase transition of VO{sub 2} and pave a way for the practicality of VO{sub 2} as an energy-efficient green material.« less
New Insights into the Compositional Dependence of Li-Ion Transport in Polymer-Ceramic Composite Electrolytes.

PubMed

Zheng, Jin; Hu, Yan-Yan

2018-01-31

Composite electrolytes are widely studied for their potential in realizing improved ionic conductivity and electrochemical stability. Understanding the complex mechanisms of ion transport within composites is critical for effectively designing high-performance solid electrolytes. This study examines the compositional dependence of the three determining factors for ionic conductivity, including ion mobility, ion transport pathways, and active ion concentration. The results show that with increase in the fraction of ceramic Li 7 La 3 Zr 2 O 12 (LLZO) phase in the LLZO-poly(ethylene oxide) composites, ion mobility decreases, ion transport pathways transit from polymer to ceramic routes, and the active ion concentration increases. These changes in ion mobility, transport pathways, and concentration collectively explain the observed trend of ionic conductivity in composite electrolytes. Liquid additives alter ion transport pathways and increase ion mobility, thus enhancing ionic conductivity significantly. It is also found that a higher content of LLZO leads to improved electrochemical stability of composite electrolytes. This study provides insight into the recurring observations of compositional dependence of ionic conductivity in current composite electrolytes and pinpoints the intrinsic limitations of composite electrolytes in achieving fast ion conduction.
Study of anyon condensation and topological phase transitions from a Z4 topological phase using the projected entangled pair states approach

NASA Astrophysics Data System (ADS)

Iqbal, Mohsin; Duivenvoorden, Kasper; Schuch, Norbert

2018-05-01

We use projected entangled pair states (PEPS) to study topological quantum phase transitions. The local description of topological order in the PEPS formalism allows us to set up order parameters which measure condensation and deconfinement of anyons and serve as substitutes for conventional order parameters. We apply these order parameters, together with anyon-anyon correlation functions and some further probes, to characterize topological phases and phase transitions within a family of models based on a Z4 symmetry, which contains Z4 quantum double, toric code, double semion, and trivial phases. We find a diverse phase diagram which exhibits a variety of different phase transitions of both first and second order which we comprehensively characterize, including direct transitions between the toric code and the double semion phase.
The growth mechanism of grain boundary carbide in Alloy 690

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

Li, Hui, E-mail: huili@shu.edu.cn; Institute of Materials, Shanghai University, Shanghai 200072; Xia, Shuang

2013-07-15

The growth mechanism of grain boundary M{sub 23}C{sub 6} carbides in nickel base Alloy 690 after aging at 715 °C was investigated by high resolution transmission electron microscopy. The grain boundary carbides have coherent orientation relationship with only one side of the matrix. The incoherent phase interface between M{sub 23}C{sub 6} and matrix was curved, and did not lie on any specific crystal plane. The M{sub 23}C{sub 6} carbide transforms from the matrix phase directly at the incoherent interface. The flat coherent phase interface generally lies on low index crystal planes, such as (011) and (111) planes. The M{sub 23}C{submore » 6} carbide transforms from a transition phase found at curved coherent phase interface. The transition phase has a complex hexagonal crystal structure, and has coherent orientation relationship with matrix and M{sub 23}C{sub 6}: (111){sub matrix}//(0001){sub transition}//(111){sub carbide}, <112{sup ¯}>{sub matrix}//<21{sup ¯}10>{sub transition}//<112{sup ¯}>{sub carbide}. The crystal lattice constants of transition phase are c{sub transition}=√(3)×a{sub matrix} and a{sub transition}=√(6)/2×a{sub matrix}. Based on the experimental results, the growth mechanism of M{sub 23}C{sub 6} and the formation mechanism of transition phase are discussed. - Highlights: • A transition phase was observed at the coherent interfaces of M{sub 23}C{sub 6} and matrix. • The transition phase has hexagonal structure, and is coherent with matrix and M{sub 23}C{sub 6}. • The M{sub 23}C{sub 6} transforms from the matrix directly at the incoherent phase interface.« less
Detecting critical state before phase transition of complex systems by hidden Markov model

NASA Astrophysics Data System (ADS)

Liu, Rui; Chen, Pei; Li, Yongjun; Chen, Luonan

Identifying the critical state or pre-transition state just before the occurrence of a phase transition is a challenging task, because the state of the system may show little apparent change before this critical transition during the gradual parameter variations. Such dynamics of phase transition is generally composed of three stages, i.e., before-transition state, pre-transition state, and after-transition state, which can be considered as three different Markov processes. Thus, based on this dynamical feature, we present a novel computational method, i.e., hidden Markov model (HMM), to detect the switching point of the two Markov processes from the before-transition state (a stationary Markov process) to the pre-transition state (a time-varying Markov process), thereby identifying the pre-transition state or early-warning signals of the phase transition. To validate the effectiveness, we apply this method to detect the signals of the imminent phase transitions of complex systems based on the simulated datasets, and further identify the pre-transition states as well as their critical modules for three real datasets, i.e., the acute lung injury triggered by phosgene inhalation, MCF-7 human breast cancer caused by heregulin, and HCV-induced dysplasia and hepatocellular carcinoma.
Boundary-field-driven control of discontinuous phase transitions on hyperbolic lattices

NASA Astrophysics Data System (ADS)

Lee, Yoju; Verstraete, Frank; Gendiar, Andrej

2016-08-01

The multistate Potts models on two-dimensional hyperbolic lattices are studied with respect to various boundary effects. The free energy is numerically calculated using the corner transfer matrix renormalization group method. We analyze phase transitions of the Potts models in the thermodynamic limit with respect to contracted boundary layers. A false phase transition is present even if a couple of the boundary layers are contracted. Its significance weakens, as the number of the contracted boundary layers increases, until the correct phase transition (deep inside the bulk) prevails over the false one. For this purpose, we derive a thermodynamic quantity, the so-called bulk excess free energy, which depends on the contracted boundary layers and memorizes additional boundary effects. In particular, the magnetic field is imposed on the outermost boundary layer. While the boundary magnetic field does not affect the second-order phase transition in the bulk if suppressing all the boundary effects on the hyperbolic lattices, the first-order (discontinuous) phase transition is significantly sensitive to the boundary magnetic field. Contrary to the phase transition on the Euclidean lattices, the discontinuous phase transition on the hyperbolic lattices can be continuously controlled (within a certain temperature coexistence region) by varying the boundary magnetic field.
Correlation and nonlocality measures as indicators of quantum phase transitions in several critical systems

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

Altintas, Ferdi, E-mail: ferdialtintas@ibu.edu.tr; Eryigit, Resul, E-mail: resul@ibu.edu.tr

2012-12-15

We have investigated the quantum phase transitions in the ground states of several critical systems, including transverse field Ising and XY models as well as XY with multiple spin interactions, XXZ and the collective system Lipkin-Meshkov-Glick models, by using different quantumness measures, such as entanglement of formation, quantum discord, as well as its classical counterpart, measurement-induced disturbance and the Clauser-Horne-Shimony-Holt-Bell function. Measurement-induced disturbance is found to detect the first and second order phase transitions present in these critical systems, while, surprisingly, it is found to fail to signal the infinite-order phase transition present in the XXZ model. Remarkably, the Clauser-Horne-Shimony-Holt-Bellmore » function is found to detect all the phase transitions, even when quantum and classical correlations are zero for the relevant ground state. - Highlights: Black-Right-Pointing-Pointer The ability of correlation measures to detect quantum phase transitions has been studied. Black-Right-Pointing-Pointer Measurement induced disturbance fails to detect the infinite order phase transition. Black-Right-Pointing-Pointer CHSH-Bell function detects all phase transitions even when the bipartite density matrix is uncorrelated.« less
Strain and defect engineering on phase transition of monolayer black phosphorene

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

Chen, Yan; Shi, Xiaoyang; Li, Mingjia

Under biaxial strain, SW-2 defect can move inward the phase boundary of α-P and β-P remarkably and promote the phase transition from α-P to β-P, serving as an excellent ‘phase transition catalyzer’.

Strain and defect engineering on phase transition of monolayer black phosphorene

DOE PAGES

Chen, Yan; Shi, Xiaoyang; Li, Mingjia; ...

2018-01-01

Under biaxial strain, SW-2 defect can move inward the phase boundary of α-P and β-P remarkably and promote the phase transition from α-P to β-P, serving as an excellent ‘phase transition catalyzer’.
Quantum phase transitions between a class of symmetry protected topological states

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

Tsui, Lokman; Jiang, Hong-Chen; Lu, Yuan-Ming

2015-07-01

The subject of this paper is the phase transition between symmetry protected topological states (SPTs). We consider spatial dimension d and symmetry group G so that the cohomology group, Hd+1(G,U(1)), contains at least one Z2n or Z factor. We show that the phase transition between the trivial SPT and the root states that generate the Z2n or Z groups can be induced on the boundary of a (d+1)-dimensional View the MathML source-symmetric SPT by a View the MathML source symmetry breaking field. Moreover we show these boundary phase transitions can be “transplanted” to d dimensions and realized in lattice modelsmore » as a function of a tuning parameter. The price one pays is for the critical value of the tuning parameter there is an extra non-local (duality-like) symmetry. In the case where the phase transition is continuous, our theory predicts the presence of unusual (sometimes fractionalized) excitations corresponding to delocalized boundary excitations of the non-trivial SPT on one side of the transition. This theory also predicts other phase transition scenarios including first order transition and transition via an intermediate symmetry breaking phase.« less
Quantum phase transitions between a class of symmetry protected topological states

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

Tsui, Lokman; Jiang, Hong -Chen; Lu, Yuan -Ming

2015-04-30

The subject of this paper is the phase transition between symmetry protected topological states (SPTs). We consider spatial dimension d and symmetry group G so that the cohomology group, H d+1(G,U(1)), contains at least one Z 2n or Z factor. We show that the phase transition between the trivial SPT and the root states that generate the Z 2n or Z groups can be induced on the boundary of a (d+1)-dimensional G x Z T 2-symmetric SPT by a Z T 2 symmetry breaking field. Moreover we show these boundary phase transitions can be “transplanted” to d dimensions and realizedmore » in lattice models as a function of a tuning parameter. The price one pays is for the critical value of the tuning parameter there is an extra non-local (duality-like) symmetry. In the case where the phase transition is continuous, our theory predicts the presence of unusual (sometimes fractionalized) excitations corresponding to delocalized boundary excitations of the non-trivial SPT on one side of the transition. This theory also predicts other phase transition scenarios including first order transition and transition via an intermediate symmetry breaking phase.« less
Size-dependent phase transition in methylammonium lead iodide perovskite microplate crystals

PubMed Central

Li, Dehui; Wang, Gongming; Cheng, Hung-Chieh; Chen, Chih-Yen; Wu, Hao; Liu, Yuan; Huang, Yu; Duan, Xiangfeng

2016-01-01

Methylammonium lead iodide perovskite has attracted considerable recent interest for solution processable solar cells and other optoelectronic applications. The orthorhombic-to-tetragonal phase transition in perovskite can significantly alter its optical, electrical properties and impact the corresponding applications. Here, we report a systematic investigation of the size-dependent orthorhombic-to-tetragonal phase transition using a combined temperature-dependent optical, electrical transport and transmission electron microscopy study. Our studies of individual perovskite microplates with variable thicknesses demonstrate that the phase transition temperature decreases with reducing microplate thickness. The sudden decrease of mobility around phase transition temperature and the presence of hysteresis loops in the temperature-dependent mobility confirm that the orthorhombic-to-tetragonal phase transition is a first-order phase transition. Our findings offer significant fundamental insight on the temperature- and size-dependent structural, optical and charge transport properties of perovskite materials, and can greatly impact future exploration of novel electronic and optoelectronic devices from these materials. PMID:27098114
Size-dependent phase transition in methylammonium lead iodide perovskite microplate crystals

DOE PAGES

Li, Dehui; Wang, Gongming; Cheng, Hung -Chieh; ...

2016-04-21

Methylammonium lead iodide perovskite has attracted considerable recent interest for solution processable solar cells and other optoelectronic applications. The orthorhombic-to-tetragonal phase transition in perovskite can significantly alter its optical, electrical properties and impact the corresponding applications. Here, we report a systematic investigation of the size-dependent orthorhombic-to-tetragonal phase transition using a combined temperature-dependent optical, electrical transport and transmission electron microscopy study. Our studies of individual perovskite microplates with variable thicknesses demonstrate that the phase transition temperature decreases with reducing microplate thickness. The sudden decrease of mobility around phase transition temperature and the presence of hysteresis loops in the temperature-dependent mobility confirmmore » that the orthorhombic-to-tetragonal phase transition is a first-order phase transition. Lastly, our findings offer significant fundamental insight on the temperature-and size-dependent structural, optical and charge transport properties of perovskite materials, and can greatly impact future exploration of novel electronic and optoelectronic devices from these materials.« less
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
Quasi-phases and pseudo-transitions in one-dimensional models with nearest neighbor interactions

NASA Astrophysics Data System (ADS)

de Souza, S. M.; Rojas, Onofre

2018-01-01

There are some particular one-dimensional models, such as the Ising-Heisenberg spin models with a variety of chain structures, which exhibit unexpected behaviors quite similar to the first and second order phase transition, which could be confused naively with an authentic phase transition. Through the analysis of the first derivative of free energy, such as entropy, magnetization, and internal energy, a "sudden" jump that closely resembles a first-order phase transition at finite temperature occurs. However, by analyzing the second derivative of free energy, such as specific heat and magnetic susceptibility at finite temperature, it behaves quite similarly to a second-order phase transition exhibiting an astonishingly sharp and fine peak. The correlation length also confirms the evidence of this pseudo-transition temperature, where a sharp peak occurs at the pseudo-critical temperature. We also present the necessary conditions for the emergence of these quasi-phases and pseudo-transitions.
Pressure-induced Lifshitz and structural transitions in NbAs and TaAs: experiments and theory

NASA Astrophysics Data System (ADS)

Nath Gupta, Satyendra; Singh, Anjali; Pal, Koushik; Muthu, D. V. S.; Shekhar, C.; Elghazali, Moaz A.; Naumov, Pavel G.; Medvedev, Sergey A.; Felser, C.; Waghmare, U. V.; Sood, A. K.

2018-05-01

High pressure Raman, resistivity and synchrotron x-ray diffraction studies on Weyl semimetals NbAs and TaAs have been carried out along with density functional theoretical (DFT) analysis to explain pressure induced structural and electronic topological phase transitions. The frequencies of first order Raman modes harden with increasing pressure, exhibiting a slope change at GPa for NbAs and GPa for TaAs. The resistivities of NbAs and TaAs exhibit a minimum at pressures close to these transition pressures and also a change in the bulk modulus is observed. Our first-principles calculations reveal that the transition is associated with an electronic Lifshitz transition at for NbAs while it is a structural phase transition from body centered tetragonal to hexagonal phase at for TaAs. Further, our DFT calculations show a structural phase transition at 24 GPa from body centered tetragonal phase to hexagonal phase.
A Networks Approach to Modeling Enzymatic Reactions.

PubMed

Imhof, P

2016-01-01

Modeling enzymatic reactions is a demanding task due to the complexity of the system, the many degrees of freedom involved and the complex, chemical, and conformational transitions associated with the reaction. Consequently, enzymatic reactions are not determined by precisely one reaction pathway. Hence, it is beneficial to obtain a comprehensive picture of possible reaction paths and competing mechanisms. By combining individually generated intermediate states and chemical transition steps a network of such pathways can be constructed. Transition networks are a discretized representation of a potential energy landscape consisting of a multitude of reaction pathways connecting the end states of the reaction. The graph structure of the network allows an easy identification of the energetically most favorable pathways as well as a number of alternative routes. © 2016 Elsevier Inc. All rights reserved.
The transition to the metallic state in low density hydrogen

DOE PAGES

McMinis, Jeremy; Morales, Miguel A.; Ceperley, David M.; ...

2015-11-18

Solid atomic hydrogen is one of the simplest systems to undergo a metal-insulator transition. Near the transition, the electronic degrees of freedom become strongly correlated and their description provides a difficult challenge for theoretical methods. As a result, the order and density of the phase transition are still subject to debate. In this work we use diffusion quantum Monte Carlo to benchmark the transition between the paramagnetic and anti-ferromagnetic phases of ground state body centered cubic atomic hydrogen. We locate the density of the transition by computing the equation of state for these two phases and identify the phase transitionmore » order by computing the band gap near the phase transition. These benchmark results show that the phase transition is continuous and occurs at a Wigner-Seitz radius of r s = 2.27(3)a 0. As a result, we compare our results to previously reported density functional theory, Hedin s GW approximation, and dynamical mean field theory results.« less
Phase transformation mechanism in lithium manganese nickel oxide revealed by single-crystal hard X-ray microscopy

DOE PAGES

Kuppan, Saravanan; Xu, Yahong; Liu, Yijin; ...

2017-02-01

Understanding the reaction pathway and kinetics of solid-state phase transformation is critical in designing advanced electrode materials with better performance and stability. Despite the first-order phase transition with a large lattice mismatch between the involved phases, spinel LiMn 1.5Ni 0.5O 4 is capable of fast rate even at large particle size, presenting an enigma yet to be understood. The present study uses advanced two-dimensional and three-dimensional nano-tomography on a series of well-formed LixMn 1.5Ni 0.5O 4 (0 ≤ x ≤ 1) crystals to visualize the mesoscale phase distribution, as a function of Li content at the sub-particle level. Inhomogeneity alongmore » with the coexistence of Li-rich and Li-poor phases are broadly observed on partially delithiated crystals, providing direct evidence for a concurrent nucleation and growth process instead of a shrinking-core or a particle-by-particle process. As a result, superior kinetics of (100) facets at the vertices of truncated octahedral particles promote preferential delithiation, whereas the observation of strain-induced cracking suggests mechanical degradation in the material.« less
Visualization of a stable intermediate phase in photoinduced metal-to-insulator transition in manganites

NASA Astrophysics Data System (ADS)

Lin, Hanxuan; Liu, Hao; Bai, Yu; Miao, Tian; Yu, Yang; Zhu, Yinyan; Chen, Hongyan; Kou, Yunfang; Niu, Jiebin; Wang, Wenbin; Yin, Lifeng; Shen, Jian

First order metal-insulator transition, accounting for various intriguing phenomena, is one of the most important phase transitions in condensed matter systems. Aside from the initial and final states, i.e. the metallic and insulating phases, no stable intermediate phase has been experimentally identified in such first order phase transition, though some transient phases do exist at the ultrafast time scale. Here, using our unique low-temperature, high-field magnetic force microscopy with photoexcitation, we directly observed a stable intermediate phase emerging and mediating the photoinduced first order metal-insulator transition in manganites. This phase is characteristic of low net magnetization and high resistivity. Our observations unveil the microscopic details of the photoinduced metal-insulator transition in manganites, which may be insightful to study first order metal-insulator transition in other condensed matter systems. This work was supported by National Key Research Program of China (2016YFA0300702), National Basic Research Program of China (973 Program) under the Grant No. 2013CB932901 and 2014CB921104; National Natural Science Foundation of China (11274071, 11504053).
Carbon Chemistry in Transitional Clouds from the GOT C+ Survey of CII 158 micron Emission in the Galactic Plane

NASA Astrophysics Data System (ADS)

Langer, W. D.; Velusamy, T.; Pineda, J.; Willacy, K.; Goldsmith, P. F.

2011-05-01

In understanding the lifecycle and chemistry of the interstellar gas, the transition from diffuse atomic to molecular gas clouds is a very important stage. The evolution of carbon from C+ to C0 and CO is a fundamental part of this transition, and C+ along with its carbon chemistry is a key diagnostic. Until now our knowledge of interstellar gas has been limited primarily to the diffuse atomic phase traced by HI and the dense molecular H2 phase traced by CO. However, we have generally been missing an important layer in diffuse and transition clouds, which is denoted by the warm "dark gas'', that is mostly H2 and little HI and CO, and is best traced with C+. Here, we discuss the chemistry in the transition from C+ to C0 and CO in these clouds as understood by a survey of the CII 1.9 THz (158 micron) line from a sparse survey of the inner galaxy over about 40 degrees in longitude as part of the Galactic Observations of Terahertz C+ (GOT C+) program, a Herschel Space Observatory Open Time Key Program to study interstellar clouds by sampling ionized carbon. Using the first results from GOT C+ along 11 LOSs, in a sample of 53 transition clouds, Velusamy, Langer et al. (A&A 521, L18, 2010) detected an excess of CII intensities indicative of a thick H2 layer (a significant warm H2, "dark gas'' component) around the 12CO core. Here we present a much larger, statistically significant sample of a few hundred diffuse and transition clouds traced by CII, along with auxiliary HI and CO data in the inner Galaxy between l=-30° and +30°. Our new and more extensive sample of transition clouds is used to elucidate the time dependent physical and carbon chemical evolution of diffuse to transition clouds, and transition layers. We consider the C+ to CO conversion pathways such as H++ O and C+ + H2 chemistry for CO production to constrain the physical parameters such as the FUV intensity and cosmic ray ionization rate that drive the CO chemistry in the diffuse transition clouds.
Rho-associated Kinase Connects a Cell Cycle-controlling Anchorage Signal to the Mammalian Target of Rapamycin Pathway*

PubMed Central

Park, Jung-ha; Arakawa-Takeuchi, Shiho; Jinno, Shigeki; Okayama, Hiroto

2011-01-01

When deprived of anchorage to the extracellular matrix, fibroblasts arrest in G1 phase at least in part due to inactivation of G1 cyclin-dependent kinases. Despite great effort, how anchorage signals control the G1-S transition of fibroblasts remains highly elusive. We recently found that the mammalian target of rapamycin (mTOR) cascade might convey an anchorage signal that regulates S phase entry. Here, we show that Rho-associated kinase connects this signal to the TSC1/TSC2-RHEB-mTOR pathway. Expression of a constitutively active form of ROCK1 suppressed all of the anchorage deprivation effects suppressible by tsc2 mutation in rat embryonic fibroblasts. TSC2 contains one evolutionarily conserved ROCK target-like sequence, and an alanine substitution for Thr1203 in this sequence severely impaired the ability of ROCK1 to counteract the anchorage loss-imposed down-regulation of both G1 cell cycle factors and mTORC1 activity. Moreover, TSC2 Thr1203 underwent ROCK-dependent phosphorylation in vivo and could be phosphorylated by bacterially expressed active ROCK1 in vitro, providing biochemical evidence for a direct physical interaction between ROCK and TSC2. PMID:21561859
High-Resolution Tracking Asymmetric Lithium Insertion and Extraction and Local Structure Ordering in SnS2.

PubMed

Gao, Peng; Wang, Liping; Zhang, Yu-Yang; Huang, Yuan; Liao, Lei; Sutter, Peter; Liu, Kaihui; Yu, Dapeng; Wang, En-Ge

2016-09-14

In the rechargeable lithium ion batteries, the rate capability and energy efficiency are largely governed by the lithium ion transport dynamics and phase transition pathways in electrodes. Real-time and atomic-scale tracking of fully reversible lithium insertion and extraction processes in electrodes, which would ultimately lead to mechanistic understanding of how the electrodes function and why they fail, is highly desirable but very challenging. Here, we track lithium insertion and extraction in the van der Waals interactions dominated SnS2 by in situ high-resolution TEM method. We find that the lithium insertion occurs via a fast two-phase reaction to form expanded and defective LiSnS2, while the lithium extraction initially involves heterogeneous nucleation of intermediate superstructure Li0.5SnS2 domains with a 1-4 nm size. Density functional theory calculations indicate that the Li0.5SnS2 is kinetically favored and structurally stable. The asymmetric reaction pathways may supply enlightening insights into the mechanistic understanding of the underlying electrochemistry in the layered electrode materials and also suggest possible alternatives to the accepted explanation of the origins of voltage hysteresis in the intercalation electrode materials.
Berezinskii-Kosterlitz-Thouless phase transition for the dilute planar rotator model on a triangular lattice

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

Sun Yunzhou; Yi Lin; Wysin, G. M.

2008-10-15

The Berezinskii-Kosterlitz-Thouless (BKT) phase transition for the dilute planar rotator model on a triangular lattice is studied by using a hybrid Monte Carlo method. The phase-transition temperatures for different nonmagnetic impurity densities are obtained by three approaches: finite-size scaling of plane magnetic susceptibility, helicity modulus, and Binder's fourth cumulant. It is found that the phase-transition temperature decreases with increasing impurity density {rho} and the BKT phase transition vanishes when the magnetic occupancy falls to the site percolation threshold: 1-{rho}{sub c}=p{sub c}=0.5.
Local bias-induced phase transitions

DOE PAGES

Seal, Katyayani; Baddorf, Arthur P.; Jesse, Stephen; ...

2008-11-27

Electrical bias-induced phase transitions underpin a wide range of applications from data storage to energy generation and conversion. The mechanisms behind these transitions are often quite complex and in many cases are extremely sensitive to local defects that act as centers for local transformations or pinning. Furthermore, using ferroelectrics as an example, we review methods for probing bias-induced phase transitions and discuss the current limitations and challenges for extending the methods to field-induced phase transitions and electrochemical reactions in energy storage, biological and molecular systems.
Mixed-order phase transition in a colloidal crystal.

PubMed

Alert, Ricard; Tierno, Pietro; Casademunt, Jaume

2017-12-05

Mixed-order phase transitions display a discontinuity in the order parameter like first-order transitions yet feature critical behavior like second-order transitions. Such transitions have been predicted for a broad range of equilibrium and nonequilibrium systems, but their experimental observation has remained elusive. Here, we analytically predict and experimentally realize a mixed-order equilibrium phase transition. Specifically, a discontinuous solid-solid transition in a 2D crystal of paramagnetic colloidal particles is induced by a magnetic field [Formula: see text] At the transition field [Formula: see text], the energy landscape of the system becomes completely flat, which causes diverging fluctuations and correlation length [Formula: see text] Mean-field critical exponents are predicted, since the upper critical dimension of the transition is [Formula: see text] Our colloidal system provides an experimental test bed to probe the unconventional properties of mixed-order phase transitions.
Mixed-order phase transition in a colloidal crystal

NASA Astrophysics Data System (ADS)

Alert, Ricard; Tierno, Pietro; Casademunt, Jaume

2017-12-01

Mixed-order phase transitions display a discontinuity in the order parameter like first-order transitions yet feature critical behavior like second-order transitions. Such transitions have been predicted for a broad range of equilibrium and nonequilibrium systems, but their experimental observation has remained elusive. Here, we analytically predict and experimentally realize a mixed-order equilibrium phase transition. Specifically, a discontinuous solid-solid transition in a 2D crystal of paramagnetic colloidal particles is induced by a magnetic field H. At the transition field Hs, the energy landscape of the system becomes completely flat, which causes diverging fluctuations and correlation length ξ∝|H2-Hs2|-1/2. Mean-field critical exponents are predicted, since the upper critical dimension of the transition is du=2. Our colloidal system provides an experimental test bed to probe the unconventional properties of mixed-order phase transitions.
The Cancer-Related Transcription Factor Runx2 Modulates Cell Proliferation in Human Osteosarcoma Cell Lines

PubMed Central

Lucero, Claudia M.J.; Vega, Oscar A.; Osorio, Mariana M.; Tapia, Julio C.; Antonelli, Marcelo; Stein, Gary S.; Van Wijnen, Andre J.; Galindo, Mario A.

2013-01-01

Runx2 regulates osteogenic differentiation and bone formation, but also suppresses pre-osteoblast proliferation by affecting cell cycle progression in the G1 phase. The growth suppressive potential of Runx2 is normally inactivated in part by protein destabilization, which permits cell cycle progression beyond the G1/S phase transition, and Runx2 is again up-regulated after mitosis. Runx2 expression also correlates with metastasis and poor chemotherapy response in osteosarcoma. Here we show that six human osteosarcoma cell lines (SaOS, MG63, U2OS, HOS, G292, and 143B) have different growth rates, which is consistent with differences in the lengths of the cell cycle. Runx2 protein levels are cell cycle-regulated with respect to the G1/S phase transition in U2OS, HOS, G292, and 143B cells. In contrast, Runx2 protein levels are constitutively expressed during the cell cycle in SaOS and MG63 cells. Forced expression of Runx2 suppresses growth in all cell lines indicating that accumulation of Runx2 in excess of its pre-established levels in a given cell type triggers one or more anti-proliferative pathways in osteosarcoma cells. Thus, regulatory mechanisms controlling Runx2 expression in osteosarcoma cells must balance Runx2 protein levels to promote its putative oncogenic functions, while avoiding suppression of bone tumor growth. PMID:22949168

GLABROUS INFLORESCENCE STEMS modulates the regulation by gibberellins of epidermal differentiation and shoot maturation in Arabidopsis.

PubMed

Gan, Yinbo; Kumimoto, Rod; Liu, Chang; Ratcliffe, Oliver; Yu, Hao; Broun, Pierre

2006-06-01

As a plant shoot matures, it transitions through a series of growth phases in which successive aerial organs undergo distinct developmental changes. This process of phase change is known to be influenced by gibberellins (GAs). We report the identification of a putative transcription factor, GLABROUS INFLORESCENCE STEMS (GIS), which regulates aspects of shoot maturation in Arabidopsis thaliana. GIS loss-of-function mutations affect the epidermal differentiation of inflorescence organs, causing a premature decrease in trichome production on successive leaves, stem internodes, and branches. Overexpression has the opposite effect on trichome initiation and causes other heterochronic phenotypes, affecting flowering and juvenile-adult leaf transition and inducing the formation of rosette leaves on inflorescence stems. Genetic and gene expression analyses suggest that GIS acts in a GA-responsive pathway upstream of the trichome initiation regulator GLABROUS1 (GL1) and downstream of the GA signaling repressor SPINDLY (SPY). GIS mediates the induction of GL1 expression by GA in inflorescence organs and is antagonized in its action by the DELLA repressor GAI. The implication of GIS in the broader regulation of phase change is further suggested by the delay in flowering caused by GIS loss of function in the spy background. The discovery of GIS reveals a novel mechanism in the control of shoot maturation, through which GAs regulate cellular differentiation in plants.
Adolescents with Type 1 Diabetes: transition between diabetes services.

PubMed

Visentin, Kate; Koch, Tina; Kralik, Debbie

2006-06-01

The research aimed to develop a sustainable and coordinated approach to facilitating the transition between diabetes services for adolescents. The objectives were to: (1) involve key diabetes health delivery stakeholders in expressing their concerns and issues about current service delivery and ways to improve same, and (2) reveal from the perspective of the adolescents living with Type 1 Diabetes their experiences surrounding the process of transition. This paper presents research that sought to identify the major concerns and issues that stakeholders had about transition and to reveal the experience of transition for the adolescent with Type 1 Diabetes. Key representatives from seven public diabetes services in Adelaide, South Australia worked collaboratively to answer the objectives of this inquiry. Approach. Interview data were generated and analysed using a response focus framework provided by fourth generation evaluation research. In this study, the focus was on common concerns, claims and issues raised by health care professionals (n = 21) and adolescents (n = 10) aged between 15 and 18 years about transferring from children's to adult diabetes services. Data revealed education and dietetic advice was reactive rather than proactive and that the paediatric model of care is philosophically and practically different to the adult model of diabetes care. Three phases of transition were identified: preparation, formal transition and evaluation. Our findings indicated that these stages of transition were not being fully implemented in health units. The project findings have set the scene to establish a multidisciplinary working party to work collaboratively across agencies to develop effective transition pathways. The role of diabetes nurse educators and dietitians in South Australia is under-used throughout the transition process. Diabetes nurse educators are in an ideal position to prepare, coordinate and evaluate transitional processes.
Global quantum discord and quantum phase transition in XY model

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

Liu, Si-Yuan; Beijing National Laboratory for Condensed Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing 100190; Zhang, Yu-Ran, E-mail: yrzhang@iphy.ac.cn

We study the relationship between the behavior of global quantum correlations and quantum phase transitions in XY model. We find that the two kinds of phase transitions in the studied model can be characterized by the features of global quantum discord (GQD) and the corresponding quantum correlations. We demonstrate that the maximum of the sum of all the nearest neighbor bipartite GQDs is effective and accurate for signaling the Ising quantum phase transition, in contrast, the sudden change of GQD is very suitable for characterizing another phase transition in the XY model. This may shed lights on the study ofmore » properties of quantum correlations in different quantum phases.« less
The Mitotic and Metabolic Effects of Phosphatidic Acid in the Primary Muscle Cells of Turbot (Scophthalmus maximus).

PubMed

Wang, Tingting; Wang, Xuan; Zhou, Huihui; Jiang, Haowen; Mai, Kangsen; He, Gen

2018-01-01

Searching for nutraceuticals and understanding the underlying mechanism that promote fish growth is at high demand for aquaculture industry. In this study, the modulatory effects of soy phosphatidic acids (PA) on cell proliferation, nutrient sensing, and metabolic pathways were systematically examined in primary muscle cells of turbot ( Scophthalmus maximus ). PA was found to stimulate cell proliferation and promote G1/S phase transition through activation of target of rapamycin signaling pathway. The expression of myogenic regulatory factors, including myoD and follistatin , was upregulated, while that of myogenin and myostatin was downregulated by PA. Furthermore, PA increased intracellular free amino acid levels and enhanced protein synthesis, lipogenesis, and glycolysis, while suppressed amino acid degradation and lipolysis. PA also was found to increased cellular energy production through stimulated tricarboxylic acid cycle and oxidative phosphorylation. Our results identified PA as a potential nutraceutical that stimulates muscle cell proliferation and anabolism in fish.
Hugoniot curve calculation of nitromethane decomposition mixtures: A reactive force field molecular dynamics approach

NASA Astrophysics Data System (ADS)

Guo, Feng; Zhang, Hong; Hu, Hai-Quan; Cheng, Xin-Lu; Zhang, Li-Yan

2015-11-01

We investigate the Hugoniot curve, shock-particle velocity relations, and Chapman-Jouguet conditions of the hot dense system through molecular dynamics (MD) simulations. The detailed pathways from crystal nitromethane to reacted state by shock compression are simulated. The phase transition of N2 and CO mixture is found at about 10 GPa, and the main reason is that the dissociation of the C-O bond and the formation of C-C bond start at 10.0-11.0 GPa. The unreacted state simulations of nitromethane are consistent with shock Hugoniot data. The complete pathway from unreacted to reacted state is discussed. Through chemical species analysis, we find that the C-N bond breaking is the main event of the shock-induced nitromethane decomposition. Project supported by the National Natural Science Foundation of China (Grant No. 11374217) and the Shandong Provincial Natural Science Foundation, China (Grant No. ZR2014BQ008).
Growth phase-dependent proteomes of the Malaysian isolated Lactococcus lactis dairy strain M4 using label-free qualitative shotgun proteomics analysis.

PubMed

Yap, Theresa Wan Chen; Rabu, Amir; Abu Bakar, Farah Diba; Rahim, Raha Abdul; Mahadi, Nor Muhammad; Illias, Rosli Md; Murad, Abdul Munir Abdul

2014-01-01

Lactococcus lactis is the most studied mesophilic fermentative lactic acid bacterium. It is used extensively in the food industry and plays a pivotal role as a cell factory and also as vaccine delivery platforms. The proteome of the Malaysian isolated L. lactis M4 dairy strain, obtained from the milk of locally bred cows, was studied to elucidate the physiological changes occurring between the growth phases of this bacterium. In this study, ultraperformance liquid chromatography nanoflow electrospray ionization tandem mass spectrometry (UPLC- nano-ESI-MS(E)) approach was used for qualitative proteomic analysis. A total of 100 and 121 proteins were identified from the midexponential and early stationary growth phases, respectively, of the L. lactis strain M4. During the exponential phase, the most important reaction was the generation of sufficient energy, whereas, in the early stationary phase, the metabolic energy pathways decreased and the biosynthesis of proteins became more important. Thus, the metabolism of the cells shifted from energy production in the exponential phase to the synthesis of macromolecules in the stationary phase. The resultant proteomes are essential in providing an improved view of the cellular machinery of L. lactis during the transition of growth phases and hence provide insight into various biotechnological applications.
First-order reversal curve of the magnetostructural phase transition in FeTe

DOE PAGES

Frampton, M. K.; Crocker, J.; Gilbert, D. A.; ...

2017-06-05

We apply the first-order reversal curve (FORC) method, adapted from studies of ferromagnetic materials, to the magnetostructural phase transition of Fe 1+yTe. FORC measurements reveal two features in the hysteretic phase transition, even in samples where traditional temperature measurements display only a single transition. For Fe 1.13Te, the influence of magnetic field suggests that the main feature is primarily structural while a smaller, slightly higher-temperature transition is magnetic in origin. By contrast, Fe 1.03Te has a single transition which shows a uniform response to magnetic field, indicating a stronger coupling of the magnetic and structural phase transitions. We also introducemore » uniaxial stress, which spreads the distribution width without changing the underlying energy barrier of the transformation. Finally, the work shows how FORC can help disentangle the roles of the magnetic and structural phase transitions in FeTe.« less
Understanding mechanisms of solid-state phase transformations by probing nuclear materials

NASA Astrophysics Data System (ADS)

Banerjee, Srikumar; Donthula, Harish

2018-04-01

In this review a few examples will be cited to illustrate that a study on a specific nuclear material sometimes lead to a better understanding of scientific phenomena of broader interests. Zirconium alloys offer some unique opportunities in addressing fundamental issues such as (i) distinctive features between displacive and diffusional transformations, (ii) characteristics of shuffle and shear dominated displacive transformations and (iii) nature of mixed-mode transformations. Whether a transformation is of first or higher order?" is often raised while classifying it. There are rare examples, such as Ni-Mo alloys, in which during early stages of ordering the system experiences tendencies for both first order and second order transitions. Studies on the order-disorder transitions under a radiation environment have established the pathway for the evolution of ordering. These studies have also identified the temperature range over which the chemically ordered state remains stable in steady state under radiation.
Msn2p and Msn4p Control a Large Number of Genes Induced at the Diauxic Transition Which Are Repressed by Cyclic AMP in Saccharomyces cerevisiae

PubMed Central

Boy-Marcotte, Emmanuelle; Perrot, Michel; Bussereau, Françoise; Boucherie, Hélian; Jacquet, Michel

1998-01-01

The multicopy suppressors of the snf1 defect, Msn2p and Msn4p transcription factors (Msn2/4p), activate genes through the stress-responsive cis element (CCCCT) in response to various stresses. This cis element is also the target for repression by the cyclic AMP (cAMP)-signaling pathway. We analyzed the two-dimensional gel electrophoresis pattern of protein synthesis of the msn2 msn4 double mutant and compared it with that of the wild-type strain during exponential growth phase and at the diauxic transition. Thirty-nine gene products (including those of ALD3, GDH3, GLK1, GPP2, HSP104, HXK1, PGM2, SOD2, SSA3, SSA4, TKL2, TPS1, and YBR149W) are dependent upon Msn2/4p for their induction at the diauxic transition. The expression of all these genes is repressed by cAMP. Thirty other genes identified during this study are still inducible in the mutant. A subset of these genes were found to be superinduced at the diauxic transition, and others were subject to cAMP repression (including ACH1, ADH2, ALD6, ATP2, GPD1, ICL1, and KGD2). We conclude from this analysis that Msn2/4p control a large number of genes induced at the diauxic transition but that other, as-yet-uncharacterized regulators, also contribute to this response. In addition, we show here that cAMP repression applies to both Msn2/4p-dependent and -independent control of gene expression at the diauxic shift. Furthermore, the fact that all the Msn2/4p gene targets are subject to cAMP repression suggests that these regulators could be targets for the cAMP-signaling pathway. PMID:9495741
Effect of Molecular Flexibility on the Nematic-to-Isotropic Phase Transition for Highly Biaxial Molecular Non-Symmetric Liquid Crystal Dimers

PubMed Central

Sebastián, Nerea; López, David Orencio; Diez-Berart, Sergio; de la Fuente, María Rosario; Salud, Josep; Pérez-Jubindo, Miguel Angel; Ros, María Blanca

2011-01-01

In this work, a study of the nematic (N)–isotropic (I) phase transition has been made in a series of odd non-symmetric liquid crystal dimers, the α-(4-cyanobiphenyl-4’-yloxy)-ω-(1-pyrenimine-benzylidene-4’-oxy) alkanes, by means of accurate calorimetric and dielectric measurements. These materials are potential candidates to present the elusive biaxial nematic (NB) phase, as they exhibit both molecular biaxiality and flexibility. According to the theory, the uniaxial nematic (NU)–isotropic (I) phase transition is first-order in nature, whereas the NB–I phase transition is second-order. Thus, a fine analysis of the critical behavior of the N–I phase transition would allow us to determine the presence or not of the biaxial nematic phase and understand how the molecular biaxiality and flexibility of these compounds influences the critical behavior of the N–I phase transition. PMID:28824100
Free energy landscape and transition pathways from Watson-Crick to Hoogsteen base pairing in free duplex DNA.

PubMed

Yang, Changwon; Kim, Eunae; Pak, Youngshang

2015-09-18

Houghton (HG) base pairing plays a central role in the DNA binding of proteins and small ligands. Probing detailed transition mechanism from Watson-Crick (WC) to HG base pair (bp) formation in duplex DNAs is of fundamental importance in terms of revealing intrinsic functions of double helical DNAs beyond their sequence determined functions. We investigated a free energy landscape of a free B-DNA with an adenosine-thymine (A-T) rich sequence to probe its conformational transition pathways from WC to HG base pairing. The free energy landscape was computed with a state-of-art two-dimensional umbrella molecular dynamics simulation at the all-atom level. The present simulation showed that in an isolated duplex DNA, the spontaneous transition from WC to HG bp takes place via multiple pathways. Notably, base flipping into the major and minor grooves was found to play an important role in forming these multiple transition pathways. This finding suggests that naked B-DNA under normal conditions has an inherent ability to form HG bps via spontaneous base opening events. © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.
Cristobalite X-I: A bridge between low and high density silica polymorphs

NASA Astrophysics Data System (ADS)

Shelton, H.; Tiange, B.; Zurek, E.; Smith, J.; Dera, P.

2017-12-01

SiO2 is one of the most common compounds found on Earth. Despite its chemical simplicity, and because of its crystal chemical characteristics, SiO2 exhibits a complex phase diagram. SiO2 has a wide variety of thermodynamically stable crystalline phases, as well as numerous metastable crystalline and amorphous polymorphs. Many of the phase transition sequences that produce metastable phases of SiO2 are strongly path-dependent, where the rate of change controls the transition just as much as the final conditions. The elusive metastable polymorphs of SiO2 may provide a better understanding of the factors controlling its densification. On compression of α-cristobalite (the high temperature tetrahedral phase of SiO2) to pressures above 12 GPa, a new polymorph known as cristobalite X-I forms. Existence of cristobalite X-I has been known for several decades, however, consensus regarding the exact atomic arrangement has not yet been reached. The X-I phase constitutes an important step in the silica densification process, separating low-density tetrahedral framework structures from high-density octahedral polymorphs. It is unique in being the only non-quenchable high-density SiO2 phase, which reverts back to the tetrahedral low-density form on decompression at ambient temperature. Our new single crystal synchrotron X-ray diffraction experiments, with quasihydrostatic neon as the pressure medium, revealed the structure of this enigmatic phase to consist of octahedral silicate chains with 4-60°-2 zigzag chain geometry. This geometry has not been considered before, but is closely related to post-quartz, stishovite and seifertite. Density functional theory calculations support this observation, confirming the dynamic stability of the X-I arrangement and reasonably reproducing the pressure at which the transformation takes place. The enthalpy of cristobalite X-I is higher than stishovite and seifertite, but it is favored as a high-pressure successor of cristobalite due to a unique transformation pathway.
Thermodynamic phase transition of a black hole in rainbow gravity

NASA Astrophysics Data System (ADS)

Feng, Zhong-Wen; Yang, Shu-Zheng

2017-09-01

In this letter, using the rainbow functions that were proposed by Magueijo and Smolin, we investigate the thermodynamics and the phase transition of rainbow Schwarzschild black hole. First, we calculate the rainbow gravity corrected Hawking temperature. From this modification, we then derive the local temperature, free energy, and other thermodynamic quantities in an isothermal cavity. Finally, we analyze the critical behavior, thermodynamic stability, and phase transition of the rainbow Schwarzschild black hole. The results show that the rainbow gravity can stop the Hawking radiation in the final stages of black holes' evolution and lead to the remnants of black holes. Furthermore, one can observe that the rainbow Schwarzschild black hole has one first-order phase transition, two second-order phase transitions, and three Hawking-Page-type phase transitions in the framework of rainbow gravity theory.
Ashkin-Teller criticality and weak first-order behavior of the phase transition to a fourfold degenerate state in two-dimensional frustrated Ising antiferromagnets

NASA Astrophysics Data System (ADS)

Liu, R. M.; Zhuo, W. Z.; Chen, J.; Qin, M. H.; Zeng, M.; Lu, X. B.; Gao, X. S.; Liu, J.-M.

2017-07-01

We study the thermal phase transition of the fourfold degenerate phases (the plaquette and single-stripe states) in the two-dimensional frustrated Ising model on the Shastry-Sutherland lattice using Monte Carlo simulations. The critical Ashkin-Teller-like behavior is identified both in the plaquette phase region and the single-stripe phase region. The four-state Potts critical end points differentiating the continuous transitions from the first-order ones are estimated based on finite-size-scaling analyses. Furthermore, a similar behavior of the transition to the fourfold single-stripe phase is also observed in the anisotropic triangular Ising model. Thus, this work clearly demonstrates that the transitions to the fourfold degenerate states of two-dimensional Ising antiferromagnets exhibit similar transition behavior.
Investigating rare events with nonequilibrium work measurements. I. Nonequilibrium transition path probabilities

NASA Astrophysics Data System (ADS)

Moradi, Mahmoud; Sagui, Celeste; Roland, Christopher

2014-01-01

We have developed a formalism for investigating transition pathways and transition probabilities for rare events in biomolecular systems. In this paper, we set the theoretical framework for employing nonequilibrium work relations to estimate the relative reaction rates associated with different classes of transition pathways. Particularly, we derive an extension of Crook's transient fluctuation theorem, which relates the relative transition rates of driven systems in the forward and reverse directions, and allows for the calculation of these relative rates using work measurements (e.g., in Steered Molecular Dynamics). The formalism presented here can be combined with Transition Path Theory to relate the equilibrium and driven transition rates. The usefulness of this framework is illustrated by means of a Gaussian model and a driven proline dimer.
Prolyl hydroxylase domain 2 deficiency promotes skeletal muscle fiber-type transition via a calcineurin/NFATc1-dependent pathway.

PubMed

Shin, Junchul; Nunomiya, Aki; Kitajima, Yasuo; Dan, Takashi; Miyata, Toshio; Nagatomi, Ryoichi

2016-01-01

Hypoxia exposure is known to induce an alteration in skeletal muscle fiber-type distribution mediated by hypoxia-inducible factor (HIF)-α. The downstream pathway of HIF-α leading to fiber-type shift, however, has not been elucidated. The calcineurin pathway is one of the pathways responsible for slow muscle fiber transition. Because calcineurin pathway is activated by vascular endothelial growth factor (VEGF), one of the factors induced by HIF-1α, we hypothesized that the stabilization of HIF-1α may lead to slow muscle fiber transition via the activation of calcineurin pathway in skeletal muscles. To induce HIF-1α stabilization, we used a loss of function strategy to abrogate Prolyl hydroxylase domain protein (PHD) 2 responsible for HIF-1α hydroxylation making HIF-1α susceptible to ubiquitin dependent degradation by proteasome. The purpose of this study was therefore to examine the effect of HIF-1α stabilization in PHD2 conditional knockout mouse on skeletal muscle fiber-type transition and to elucidate the involvement of calcineurin pathway on muscle fiber-type transition. PHD2 deficiency resulted in an increased capillary density in skeletal muscles due to the induction of vascular endothelial growth factor. It also elicited an alteration of skeletal muscle phenotype toward the type I fibers in both of the soleus (35.8 % in the control mice vs. 46.7 % in the PHD2-deficient mice, p < 0.01) and the gastrocnemius muscle (0.94 vs. 1.89 %, p < 0.01), and the increased proportion of type I fibers appeared to correspond to the area of increased capillary density. In addition, calcineurin and nuclear factor of activated T cell (NFATc1) protein levels were increased in both the gastrocnemius and soleus muscles, suggesting that the calcineurin/NFATc1 pathway was responsible for the type I fiber transition regardless of PGC-1α, which responded minimally to PHD2 deficiency. Indeed, we found that tacrolimus (FK-506), a calcineurin inhibitor, successfully suppressed slow fiber-type formation in PHD2-deficient mice. Taken together, stabilized HIF-1α induced by PHD2 conditional knockout resulted in the transition of muscle fibers toward a slow fiber type via a calcineurin/NFATc1 signaling pathway. PHD2 conditional knockout mice may serve as a model for chronic HIF-1α stabilization as in mice exposed to low oxygen concentration.
Structural phase transition in d-benzil characterised by capacitance measurements and neutron powder diffraction

NASA Astrophysics Data System (ADS)

Goossens, D. J.; Wu, Xiaodong; Prior, M.

2005-12-01

The ferroelectric phase transition in deuterated benzil, C 14H 10O 2, has been studied using capacitance measurements and neutron powder diffraction. Hydrogenous benzil shows a phase transition at 83.5 K from a high temperature P3 121 phase to a cell-doubled P2 1 phase. The phase transition in d-benzil occurs at 88.1 K, a small isotope effect. Neutron powder diffraction was consistent with a low temperature phase of space group P2 1. Upon deuteration the transition remained first-order and the dynamics of the phenyl ring dominated the behaviour. The isotope effect can be attributed to the difference in mass and moment of inertia between C 6H 5 and C 6D 5.
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
Working Together for Children: Strengthening Transition Pathways

ERIC Educational Resources Information Center

Collie, Louise; Willis, Felicity; Paine, Crystal; Windsor, Corina

2007-01-01

The "Working Together for Children: Strengthening Transition Pathways" Team has identified that there is a gap between the Early Childhood settings and schools within the Dubbo area. Through meetings with early childhood professionals within Dubbo the authors have identified that the current landscape of care and education within their community…
PTEN modulates cell cycle progression and cell survival by regulating phosphatidylinositol 3,4,5,-trisphosphate and Akt/protein kinase B signaling pathway.

PubMed

Sun, H; Lesche, R; Li, D M; Liliental, J; Zhang, H; Gao, J; Gavrilova, N; Mueller, B; Liu, X; Wu, H

1999-05-25

To investigate the molecular basis of PTEN-mediated tumor suppression, we introduced a null mutation into the mouse Pten gene by homologous recombination in embryonic stem (ES) cells. Pten-/- ES cells exhibited an increased growth rate and proliferated even in the absence of serum. ES cells lacking PTEN function also displayed advanced entry into S phase. This accelerated G1/S transition was accompanied by down-regulation of p27(KIP1), a major inhibitor for G1 cyclin-dependent kinases. Inactivation of PTEN in ES cells and in embryonic fibroblasts resulted in elevated levels of phosphatidylinositol 3,4,5,-trisphosphate, a product of phosphatidylinositol 3 kinase. Consequently, PTEN deficiency led to dosage-dependent increases in phosphorylation and activation of Akt/protein kinase B, a well-characterized target of the phosphatidylinositol 3 kinase signaling pathway. Akt activation increased Bad phosphorylation and promoted Pten-/- cell survival. Our studies suggest that PTEN regulates the phosphatidylinositol 3,4, 5,-trisphosphate and Akt signaling pathway and consequently modulates two critical cellular processes: cell cycle progression and cell survival.

Apparent critical phenomena in the superionic phase transition of Cu 2-xSe

DOE PAGES

Kang, Stephen Dongmin; Danilkin, Sergey A.; Aydemir, Umut; ...

2016-01-11

The superionic phase transition ofmore » $${\\mathrm{Cu}}_{2-x}\\mathrm{Se}$$ accompanies drastic changes in transport properties. The Seebeck coefficient increases sharply while the electrical conductivity and thermal diffusivity drops. Such behavior has previously been attributed to critical phenomena under the assumption of a continuous phase transition. However, applying Landau's criteria suggests that the transition should be first order. Using the phase diagram that is consistent with a first order transition, we show that the observed transport properties and heat capacity curves can be accounted for and modeled with good agreement. The apparent critical phenomena is shown to be a result of compositional degree-of-freedom. In conclusion, understanding of the phase transition allows to explain the enhancement in the thermoelectric figure-of-merit that is accompanied with the transition.« less
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
Deviatoric stress-induced phase transitions in diamantane

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

Yang, Fan; Lin, Yu; Dahl, Jeremy E. P.

2014-10-21

The high-pressure behavior of diamantane was investigated using angle-dispersive synchrotron x-ray diffraction (XRD) and Raman spectroscopy in diamond anvil cells. Our experiments revealed that the structural transitions in diamantane were extremely sensitive to deviatoric stress. Under non-hydrostatic conditions, diamantane underwent a cubic (space group Pa3) to a monoclinic phase transition at below 0.15 GPa, the lowest pressure we were able to measure. Upon further compression to 3.5 GPa, this monoclinic phase transformed into another high-pressure monoclinic phase which persisted to 32 GPa, the highest pressure studied in our experiments. However, under more hydrostatic conditions using silicone oil as a pressuremore » medium, the transition pressure to the first high-pressure monoclinic phase was elevated to 7–10 GPa, which coincided with the hydrostatic limit of silicone oil. In another experiment using helium as a pressure medium, no phase transitions were observed to the highest pressure we reached (13 GPa). In addition, large hysteresis and sluggish transition kinetics were observed upon decompression. Over the pressure range where phase transitions were confirmed by XRD, only continuous changes in the Raman spectra were observed. This suggests that these phase transitions are associated with unit cell distortions and modifications in molecular packing rather than the formation of new carbon-carbon bonds under pressure.« less
Local structural effects in Sr 3NiRhO 6 across magnetic transitions

DOE PAGES

Singh, Navneet; Khalid, S.; Bindu, R.

2016-04-06

Here, we investigate the temperature dependence of the structural parameters of quasi-one-dimensional Sr 3NiRhO 6 across the region of magnetic phase transitions using Ni K-edge and Sr K-edge x-ray absorption spectroscopy (XAS). The features in the x-ray absorption near-edge region are identified using multiple scattering calculations. The temperature-dependent extended x-ray absorption fine structure (EXAFS) studies show that the setting of the intra-chain super exchange interaction starts at ~200 K, which is well above the first transition temperature (45 K) revealed by magnetic susceptibility studies. The onset of the inter-chain super–super exchange interaction appears to be at ~125 K. Interestingly, themore » role played by direct exchange interaction between the Ni 3d and Rh 4d states in stabilising the magnetic interaction is less significant. The present results shed light on the generic features exhibited by isostructural compounds and may help in identifying the magnetic exchange pathways useful for understanding the unusual properties exhibited by such compounds.« less
Studies on phase transition temperature of rare earth niobates Ln3NbO7 (Ln = Pr, Sm, Eu) with orthorhombic fluorite-related structure

NASA Astrophysics Data System (ADS)

Hinatsu, Yukio; Doi, Yoshihiro

2017-06-01

The phase transition of ternary rare earth niobates Ln3NbO7 (Ln = Pr, Sm, Eu) was investigated by the measurements of high-temperature and low-temperature X-ray diffraction, differential scanning calorimetry (DSC) and differential thermal analysis (DTA). These compounds crystallize in an orthorhombic superstructure derived from the structure of cubic fluorite (space group Pnma for Ln = Pr; C2221 for Ln = Sm, Eu). Sm3NbO7 undergoes the phase transition when the temperature is increased through ca. 1080 K and above the transition temperature, its structure is well described with space group Pnma. For Eu3NbO7, the phase transition was not observed up to 1273 K Pr3NbO7 indicates the phase transition when the temperature is increased through ca. 370 K. The change of the phase transition temperature against the Ln ionic radius for Ln3NbO7 is quite different from those for Ln3MO7 (M = Mo, Ru, Re, Os, or Ir), i.e., no systematic relationship between the phase transition temperature and the Ln ionic radius has been observed for Ln3NbO7 compounds.
Order parameter free enhanced sampling of the vapor-liquid transition using the generalized replica exchange method.

PubMed

Lu, Qing; Kim, Jaegil; Straub, John E

2013-03-14

The generalized Replica Exchange Method (gREM) is extended into the isobaric-isothermal ensemble, and applied to simulate a vapor-liquid phase transition in Lennard-Jones fluids. Merging an optimally designed generalized ensemble sampling with replica exchange, gREM is particularly well suited for the effective simulation of first-order phase transitions characterized by "backbending" in the statistical temperature. While the metastable and unstable states in the vicinity of the first-order phase transition are masked by the enthalpy gap in temperature replica exchange method simulations, they are transformed into stable states through the parameterized effective sampling weights in gREM simulations, and join vapor and liquid phases with a succession of unimodal enthalpy distributions. The enhanced sampling across metastable and unstable states is achieved without the need to identify a "good" order parameter for biased sampling. We performed gREM simulations at various pressures below and near the critical pressure to examine the change in behavior of the vapor-liquid phase transition at different pressures. We observed a crossover from the first-order phase transition at low pressure, characterized by the backbending in the statistical temperature and the "kink" in the Gibbs free energy, to a continuous second-order phase transition near the critical pressure. The controlling mechanisms of nucleation and continuous phase transition are evident and the coexistence properties and phase diagram are found in agreement with literature results.
Mixed-order phase transition in a colloidal crystal

PubMed Central

Tierno, Pietro; Casademunt, Jaume

2017-01-01

Mixed-order phase transitions display a discontinuity in the order parameter like first-order transitions yet feature critical behavior like second-order transitions. Such transitions have been predicted for a broad range of equilibrium and nonequilibrium systems, but their experimental observation has remained elusive. Here, we analytically predict and experimentally realize a mixed-order equilibrium phase transition. Specifically, a discontinuous solid–solid transition in a 2D crystal of paramagnetic colloidal particles is induced by a magnetic field H. At the transition field Hs, the energy landscape of the system becomes completely flat, which causes diverging fluctuations and correlation length ξ∝|H2−Hs2|−1/2. Mean-field critical exponents are predicted, since the upper critical dimension of the transition is du=2. Our colloidal system provides an experimental test bed to probe the unconventional properties of mixed-order phase transitions. PMID:29158388
Pirfenidone Induces G1 Arrest in Human Tenon's Fibroblasts In Vitro Involving AKT and MAPK Signaling Pathways.

PubMed

Guo, Xiujuan; Yang, Yangfan; Liu, Liling; Liu, Xiaoan; Xu, Jiangang; Wu, Kaili; Yu, Minbin

2017-06-01

To investigate the underlying mechanism by which pirfenidone blocks the transition from the G1 to S phase in primary human Tenon's fibroblasts. Primary human Tenon's fibroblasts were characterized by immunocytofluorescence staining with vimentin, fibroblast surface protein, and cytokeratin. After treating Tenon's fibroblasts with pirfenidone under proliferation conditions (10% fetal bovine serum), cell proliferation was measured using a WST-1 assay. Progression through the cell cycle was analyzed by flow cytometry. The expression of CDK2, CDK6, cyclinD1, cyclinD3, and cyclinE and the phosphorylation of AKT, ERK1/2/MAPK, JNK/MAPK, and p38 MAPK were estimated using western blot analysis. Under proliferative conditions, pirfenidone inhibited Tenon's fibroblasts proliferation and arrested the cell cycle at the G1 phase; decreased the phosphorylation of AKT, GSK3β, ERK1/2/MAPK, and JNK/MAPK; increased the phosphorylation of p38 MAPK; and inhibited CDK2, CDK6, cyclin D1, cyclin D3, and cyclin E in a dose-dependent manner. Inhibitors of AKT (LY294002), ERK1/2 (U0126), and JNK (SP600125) arrested the G1/S transition, similar to the effect of pirfenidone. The p38 inhibitor (SB202190) decreased the G1-blocking effect of pirfenidone. The expression of CDK2, CDK6, cyclin D1, and cyclin D3 were inhibited by LY294002, U0126, and SP600125. SB202190 attenuated the pirfenidone-induced reduction of CDK2, CDK6, cyclin D1, cyclin D3, and cyclin E. Pirfenidone inhibited HTFs proliferation and induced G1 arrest by downregulating CDKs and cyclins involving the AKT/GSK3β and MAPK signaling pathways.
Ferroelectric to paraelectric phase transition mechanism in poled PVDF-TrFE copolymer films

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

Pramanick, A.; T. Misture, Scott; Osti, Naresh C.

2017-11-01

Direct experimental insights into the structural and dynamical mechanisms for ferroelectric β to paraelectric α phase transition in a poled PVDF-TrFE copolymer is obtained from in situ x-ray diffraction and quasielastic neutron scattering measurements at high temperatures. It is observed that the β-to-α phase transition proceeds through two energetically distinct processes, which are identified here as the nucleation and growth of an intermediate γ phase with random skew linkages followed by a γ-to-α transition. The two energetically distinct microscopic processes can explain the stages of evolution for β-to-α phase transition observed from heat flow measurements.
Dehydration-induced amorphous phases of calcium carbonate.

PubMed

Saharay, Moumita; Yazaydin, A Ozgur; Kirkpatrick, R James

2013-03-28

Amorphous calcium carbonate (ACC) is a critical transient phase in the inorganic precipitation of CaCO3 and in biomineralization. The calcium carbonate crystallization pathway is thought to involve dehydration of more hydrated ACC to less hydrated ACC followed by the formation of anhydrous ACC. We present here computational studies of the transition of a hydrated ACC with a H2O/CaCO3 ratio of 1.0 to anhydrous ACC. During dehydration, ACC undergoes reorganization to a more ordered structure with a significant increase in density. The computed density of anhydrous ACC is similar to that of calcite, the stable crystalline phase. Compared to the crystalline CaCO3 phases, calcite, vaterite, and aragonite, the computed local structure of anhydrous ACC is most-similar to those of calcite and vaterite, but the overall structure is not well described by either. The strong hydrogen bond interaction between the carbonate ions and water molecules plays a crucial role in stabilizing the less hydrated ACC compositions compared to the more hydrated ones, leading to a progressively increasing hydration energy with decreasing water content.
In situ observation of shear-driven amorphization in silicon crystals.

PubMed

He, Yang; Zhong, Li; Fan, Feifei; Wang, Chongmin; Zhu, Ting; Mao, Scott X

2016-10-01

Amorphous materials are used for both structural and functional applications. An amorphous solid usually forms under driven conditions such as melt quenching, irradiation, shock loading or severe mechanical deformation. Such extreme conditions impose significant challenges on the direct observation of the amorphization process. Various experimental techniques have been used to detect how the amorphous phases form, including synchrotron X-ray diffraction, transmission electron microscopy (TEM) and Raman spectroscopy, but a dynamic, atomistic characterization has remained elusive. Here, by using in situ high-resolution TEM (HRTEM), we show the dynamic amorphization process in silicon nanocrystals during mechanical straining on the atomic scale. We find that shear-driven amorphization occurs in a dominant shear band starting with the diamond-cubic (dc) to diamond-hexagonal (dh) phase transition and then proceeds by dislocation nucleation and accumulation in the newly formed dh-Si phase. This process leads to the formation of an amorphous Si (a-Si) band, embedded with dh-Si nanodomains. The amorphization of dc-Si via an intermediate dh-Si phase is a previously unknown pathway of solid-state amorphization.
Magnetocaloric effects and electrical resistivity of Ni2Mn0.55CoxCr0.45-xGa - A Heusler alloy system exhibiting a partially-decoupled first-order phase transition

NASA Astrophysics Data System (ADS)

Brock, Jeffrey; Khan, Mahmud

2018-05-01

The phase transitions and associated magnetocaloric properties of the Ni2Mn0.55CoxCr0.45-xGa (0 ≤ x ≤ 0.25) Heusler alloy system have been investigated. All samples exhibit a first-order martensitic phase transition, evidenced by a sharp drop in the resistivity versus temperature data and a thermomagnetic irreversibility in the dc magnetization data of the respective samples. Large magnetic entropy changes have also been observed near the phase transitions. The martensitic transformation temperature increases as Cr is partially replaced with Co. Additionally, this substitution leads to a partial decoupling of the magnetic and structural phase transitions, dramatically suppressing any magnetic hysteresis losses. Furthermore, the change in electrical resistivity during the phase transition remains relatively constant across the system, despite major changes in the degree of structural disorder and magnetostructural phase transition coupling. Detailed experimental results and conjectures as to the origin of these behaviors have been provided.
Microscopic Description of Thermodynamics of Lipid Membrane at Liquid-Gel Phase Transition

NASA Astrophysics Data System (ADS)

Kheyfets, B.; Galimzyanov, T.; Mukhin, S.

2018-05-01

A microscopic model of the lipid membrane is constructed that provides analytically tractable description of the physical mechanism of the first order liquid-gel phase transition. We demonstrate that liquid-gel phase transition is cooperative effect of the three major interactions: inter-lipid van der Waals attraction, steric repulsion and hydrophobic tension. The model explicitly shows that temperature-dependent inter-lipid steric repulsion switches the system from liquid to gel phase when the temperature decreases. The switching manifests itself in the increase of lateral compressibility of the lipids as the temperature decreases, making phase with smaller area more preferable below the transition temperature. The model gives qualitatively correct picture of abrupt change at transition temperature of the area per lipid, membrane thickness and volume per hydrocarbon group in the lipid chains. The calculated dependence of phase transition temperature on lipid chain length is in quantitative agreement with experimental data. Steric repulsion between the lipid molecules is shown to be the only driver of the phase transition, as van der Waals attraction and hydrophobic tension are weakly temperature dependent.
Lattice parameters and structural phase transition of lanthanum titanate perovskite, La0.68(Ti0.95,Al0.05)O3.

PubMed

Ali, Roushown; Yashima, Masatomo

2003-05-01

Lattice parameters and the structural phase transition of La(0.68)(Ti(0.95),Al(0.05))O(3) have been investigated in situ in the temperature range 301-689 K by the synchrotron radiation powder diffraction (SR-PD) technique. High-angular-resolution SR-PD is confirmed to be a powerful technique for determining precise lattice parameters around a phase-transition temperature. The title compound exhibits a reversible phase transition between orthorhombic and tetragonal phases at 622.3 +/- 0.6 K. The following results were obtained: (i) the lattice parameters increased continuously with temperature, while the b/a ratio decreased continuously with temperature and became unity at the orthorhombic-tetragonal transition point; (ii) no hysteresis was observed between the lattice-parameter values measured on heating and on cooling. Results (i) and (ii) indicate that the orthorhombic-tetragonal phase transition is continuous and reversible. The b/a ratio is found to exhibit a more continuous temperature evolution than does the order parameter for a typical second-order phase transition based on Landau theory.
Gravitation waves from QCD and electroweak phase transitions

NASA Astrophysics Data System (ADS)

Chen, Yidian; Huang, Mei; Yan, Qi-Shu

2018-05-01

We investigate the gravitation waves produced from QCD and electroweak phase transitions in the early universe by using a 5-dimension holographic QCD model and a holographic technicolor model. The dynamical holographic QCD model is to describe the pure gluon system, where a first order confinement-deconfinement phase transition can happen at the critical temperature around 250 MeV. The minimal holographic technicolor model is introduced to model the strong dynamics of electroweak, it can give a first order electroweak phase transition at the critical temperature around 100-360 GeV. We find that for both GW signals produced from QCD and EW phase transitions, in the peak frequency region, the dominant contribution comes from the sound waves, while away from the peak frequency region the contribution from the bubble collision is dominant. The peak frequency of gravitation wave determined by the QCD phase transition is located around 10-7 Hz which is within the detectability of FAST and SKA, and the peak frequency of gravitational wave predicted by EW phase transition is located at 0.002 - 0.007 Hz, which might be detectable by BBO, DECIGO, LISA and ELISA.
Tet1 is required for Rb phosphorylation during G1/S phase transition

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

Huang, Shengsong; Zhu, Ziqi; Wang, Yiqin

2013-05-03

Highlights: •Tet1 was required for NIT3T3 proliferation. •Tet1 depletion inhibited G1-S entry. •Cyclin D1 accumulation and Rb phosphorylation was blocked by Tet1 knockdown. -- Abstract: DNA methylation plays an important role in many biological processes, including regulation of gene expression, maintenance of chromatin conformation and genomic stability. TET-family proteins convert 5-methylcytosine (5mC) to 5-hydroxymethylcytosine (5hmC), which indicates that these enzymes may participate in DNA demethylation. The function of TET1 has not yet been well characterized in somatic cells. Here, we show that depletion of Tet1 in NIH3T3 cells inhibits cell growth. Furthermore, Tet1 knockdown blocks cyclin D1 accumulation in G1more » phase, inhibits Rb phosphorylation and consequently delays entrance to G1/S phase. Taken together, this study demonstrates that Tet1 is required for cell proliferation and that this process is mediated through the Rb pathway.« less
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.
Calorimetric and spectroscopic studies of the thermotropic phase behavior of lipid bilayer model membranes composed of a homologous series of linear saturated phosphatidylserines.

PubMed Central

Lewis, R N; McElhaney, R N

2000-01-01

The thermotropic phase behavior of lipid bilayer model membranes composed of the even-numbered, N-saturated 1,2-diacyl phosphatidylserines was studied by differential scanning calorimetry and by Fourier-transform infrared and (31)P-nuclear magnetic resonance spectroscopy. At pH 7.0, 0.1 M NaCl and in the absence of divalent cations, aqueous dispersions of these lipids, which have not been incubated at low temperature, exhibit a single calorimetrically detectable phase transition that is fully reversible, highly cooperative, and relatively energetic, and the transition temperatures and enthalpies increase progressively with increases in hydrocarbon chain length. Our spectroscopic observations confirm that this thermal event is a lamellar gel (L(beta))-to-lamellar liquid crystalline (L(alpha)) phase transition. However, after low temperature incubation, the L(beta)/L(alpha) phase transition of dilauroyl phosphatidylserine is replaced by a higher temperature, more enthalpic, and less cooperative phase transition, and an additional lower temperature, less enthalpic, and less cooperative phase transition appears in the longer chain phosphatidylserines. Our spectroscopic results indicate that this change in thermotropic phase behavior when incubated at low temperatures results from the conversion of the L(beta) phase to a highly ordered lamellar crystalline (L(c)) phase. Upon heating, the L(c) phase of dilauroyl phosphatidylserine converts directly to the L(alpha) phase at a temperature slightly higher than that of its original L(beta)/L(alpha) phase transition. Calorimetrically, this process is manifested by a less cooperative but considerably more energetic, higher-temperature phase transition, which replaces the weaker L(beta)/L(alpha) phase transition alluded to above. However, with the longer chain compounds, the L(c) phase first converts to the L(beta) phase at temperatures some 10-25 degrees C below that at which the L(beta) phase converts to the L(alpha) phase. Our results also suggest that shorter chain homologues form L(c) phases that are structurally related to, but more ordered than, those formed by the longer chain homologues, but that these L(c) phases are less ordered than those formed by other phospholipids. These studies also suggest that polar/apolar interfaces of the phosphatidylserine bilayers are more hydrated than those of other glycerolipid bilayers, possibly because of interactions between the polar headgroup and carbonyl groups of the fatty acyl chains. PMID:11023908
Two-order parameters theory of the metal-insulator phase transition kinetics in the magnetic field

NASA Astrophysics Data System (ADS)

Dubovskii, L. B.

2018-05-01

The metal-insulator phase transition is considered within the framework of the Ginzburg-Landau approach for the phase transition described with two coupled order parameters. One of the order parameters is the mass density which variation is responsible for the origin of nonzero overlapping of the two different electron bands and the appearance of free electron carriers. This transition is assumed to be a first-order phase one. The free electron carriers are described with the vector-function representing the second-order parameter responsible for the continuous phase transition. This order parameter determines mostly the physical properties of the metal-insulator transition and leads to a singularity of the surface tension at the metal-insulator interface. The magnetic field is involved into the consideration of the system. The magnetic field leads to new singularities of the surface tension at the metal-insulator interface and results in a drastic variation of the phase transition kinetics. A strong singularity in the surface tension results from the Landau diamagnetism and determines anomalous features of the metal-insulator transition kinetics.
Boundaries for martensitic transition of 7Li under pressure

DOE PAGES

Schaeffer, Anne Marie; Cai, Weizhao; Olejnik, Ella; ...

2015-08-14

We report that physical properties of lithium under extreme pressures continuously reveal unexpected features. These include a sequence of structural transitions to lower symmetry phases, metal-insulator-metal transition, superconductivity with one of the highest elemental transition temperatures, and a maximum followed by a minimum in its melting line. The instability of the bcc structure of lithium is well established by the presence of a temperature-driven martensitic phase transition. The boundaries of this phase, however, have not been previously explored above 3 GPa. All higher pressure phase boundaries are either extrapolations or inferred based on indirect evidence. Here we explore the pressuremore » dependence of the martensitic transition of lithium up to 7 GPa using a combination of neutron and X-ray scattering. We find a rather unexpected deviation from the extrapolated boundaries of the hR3 phase of lithium. Furthermore, there is evidence that, above ~3 GPa, once in fcc phase, lithium does not undergo a martensitic transition.« less

Pressure induced phase transitions in ceramic compounds containing tetragonal zirconia

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

Sparks, R.G.; Pfeiffer, G.; Paesler, M.A.

Stabilized tetragonal zirconia compounds exhibit a transformation toughening process in which stress applied to the material induces a crystallographic phase transition. The phase transition is accompanied by a volume expansion in the stressed region thereby dissipating stress and increasing the fracture strength of the material. The hydrostatic component of the stress required to induce the phase transition can be investigated by the use of a high pressure technique in combination with Micro-Raman spectroscopy. The intensity of Raman lines characteristic for the crystallographic phases can be used to calculate the amount of material that has undergone the transition as a functionmore » of pressure. It was found that pressures on the order of 2-5 kBar were sufficient to produce an almost complete transition from the original tetragonal to the less dense monoclinic phase; while a further increase in pressure caused a gradual reversal of the transition back to the original tetragonal structure.« less
Tunable phase transition in single-layer TiSe2 via electric field

NASA Astrophysics Data System (ADS)

Liu, Lei; Zhuang, Houlong L.

2018-06-01

Phase transition represents an intriguing physical phenomenon that exists in a number of single-layer transition-metal dichalcogenides. This phenomenon often occurs below a critical temperature and breaks the long-range crystalline order leading to a reconstructed superstructure called the charge-density wave (CDW) structure, which can therefore be recovered by external stimuli such as temperature. Alternatively, we show here that another external stimulation, electric field can also result in the phase transition between the regular and CDW structures of a single-layer transition-metal dichalcogenide. We used single-layer TiSe2 as an example to elucidate the mechanism of the CDW followed by calculations of the electronic structure using a hybrid density functional. We found that applying electric field can tune the phase transition between the 1T and CDW phases of single-layer TiSe2. Our work opens up a route of tuning the phase transition of single-layer materials via electric field.
Pressure-induced Lifshitz and structural transitions in NbAs and TaAs: experiments and theory.

PubMed

Gupta, Satyendra Nath; Singh, Anjali; Pal, Koushik; Muthu, D V S; Shekhar, C; Elghazali, Moaz A; Naumov, Pavel G; Medvedev, Sergey A; Felser, C; Waghmare, U V; Sood, A K

2018-05-10

High pressure Raman, resistivity and synchrotron x-ray diffraction studies on Weyl semimetals NbAs and TaAs have been carried out along with density functional theoretical (DFT) analysis to explain pressure induced structural and electronic topological phase transitions. The frequencies of first order Raman modes harden with increasing pressure, exhibiting a slope change at [Formula: see text] GPa for NbAs and [Formula: see text] GPa for TaAs. The resistivities of NbAs and TaAs exhibit a minimum at pressures close to these transition pressures and also a change in the bulk modulus is observed. Our first-principles calculations reveal that the transition is associated with an electronic Lifshitz transition at [Formula: see text] for NbAs while it is a structural phase transition from body centered tetragonal to hexagonal phase at [Formula: see text] for TaAs. Further, our DFT calculations show a structural phase transition at 24 GPa from body centered tetragonal phase to hexagonal phase.
The α-γ-ɛ triple point and phase boundaries of iron under shock compression

NASA Astrophysics Data System (ADS)

Li, Jun; Wu, Qiang; Xue, Tao; Geng, Huayun; Yu, Jidong; Jin, Ke; Li, Jiabo; Tan, Ye; Xi, Feng

2017-07-01

The phase transition of iron under shock compression has attracted much attention in recent decades because of its importance in fields such as condensed matter physics, geophysics, and metallurgy. At room temperature, the transition of iron from the α-phase (bcc) to the ɛ-phase (hpc) occurs at a stress of 13 GPa. At high temperature, a triple point followed by transformation to the γ-phase (fcc) is expected. However, the details of the high-temperature phase transitions of iron are still under debate. Here, we investigate the phase-transition behavior of polycrystalline iron under compression from room temperature to 820 K. The results show that the shock-induced phase transition is determined unequivocally from the measured three-wave-structure profiles, which clearly consist of an elastic wave, a plastic wave, and a phase-transition wave. The phase transition is temperature-dependent, with an average rate Δσtr/ΔT of -6.91 MPa/K below 700 K and -34.7 MPa/K at higher temperatures. The shock α-ɛ and α-γ phase boundaries intersect at 10.6 ± 0.53 GPa and 763 K, which agrees with the α-ɛ-γ triple point from early shock wave experiments and recent laser-heated diamond-anvil cell resistivity and in situ X-ray diffraction data but disagrees with the shock pressure-temperature phase diagram reported in 2009 by Zaretsky [J. Appl. Phys. 106, 023510 (2009)].
Exploring the transition from registered nurse to family nurse practitioner.

PubMed

Poronsky, Cathlin Buckingham

2013-01-01

There is limited information available regarding the transition from registered nurse (RN) to family nurse practitioner (FNP). Several authors described this transition as taking place in 4 stages, and others described it as a 2-phase process. However, there is a lack of consensus about the definition of these stages and phases and at what point they occur for nurses who are making the transition from an RN to an FNP. From what is known, this multistage/2-phase transition is accompanied by feelings of anxiety, stress, role confusion, and emotional turmoil. As a nurse faculty member, the author theorized that nurse faculty might be in a position to provide support for graduate students making this transition in role. However, there was little information available about the transition phases, stages, and needs of students during graduate school. The search for a framework to explore transition yielded transition theory, which is described and applied to FNP transition in this article. Transition theory may be useful for examining more fully the phases and stages of RN-to-FNP transition. In this time of increased need for qualified primary care providers, it is essential that graduates of FNP programs transition into practice following graduation. Copyright © 2013 Elsevier Inc. All rights reserved.
The Kibble-Zurek mechanism in phase transitions of non-equilibrium systems

NASA Astrophysics Data System (ADS)

Cheung, Hil F. H.; Patil, Yogesh S.; Date, Aditya G.; Vengalattore, Mukund

2017-04-01

We experimentally realize a driven-dissipative phase transition using a mechanical parametric amplifier to demonstrate key signatures of a second order phase transition, including a point where the susceptibilities and relaxation time scales diverge, and where the system exhibits a spontaneous breaking of symmetry. Though reminiscent of conventional equilibrium phase transitions, it is unclear if such driven-dissipative phase transitions are amenable to the conventional Landau-Ginsburg-Wilson paradigm, which relies on concepts of scale invariance and universality, and recent work has shown that such phase transitions can indeed lie beyond such conventional universality classes. By quenching the system past the critical point, we investigate the dynamics of the emergent ordered phase and find that our measurements are in excellent agreement with the Kibble-Zurek mechanism. In addition to verifying the Kibble-Zurek hypothesis in driven-dissipative phase transitions for the first time, we also demonstrate that the measured critical exponents accurately reflect the interplay between intrinsic coherent dynamics and environmental correlations, showing a clear departure from mean field exponents in the case of non-Markovian system-bath interactions. We further discuss how reservoir engineering and the imposition of artificial environmental correlations can result in the stabilization of novel many-body quantum phases and aid in the creation of exotic non-equilibrium states of matter.
High pressure ferroelastic phase transition in SrTiO3

NASA Astrophysics Data System (ADS)

Salje, E. K. H.; Guennou, M.; Bouvier, P.; Carpenter, M. A.; Kreisel, J.

2011-07-01

High pressure measurements of the ferroelastic phase transition of SrTiO3 (Guennou et al 2010 Phys. Rev. B 81 054115) showed a linear pressure dependence of the transition temperature between the cubic and tetragonal phase. Furthermore, the pressure induced transition becomes second order while the temperature dependent transition is near a tricritical point. The phase transition mechanism is characterized by the elongation and tilt of the TiO6 octahedra in the tetragonal phase, which leads to strongly nonlinear couplings between the structural order parameter, the volume strain and the applied pressure. The phase diagram is derived from the Clausius-Clapeyron relationship and is directly related to a pressure dependent Landau potential. The nonlinearities of the pressure dependent strains lead to an increase of the fourth order Landau coefficient with increasing pressure and, hence, to a tricritical-second order crossover. This behaviour is reminiscent of the doping related crossover in isostructural KMnF3.
Continuous Easy-Plane Deconfined Phase Transition on the Kagome Lattice

NASA Astrophysics Data System (ADS)

Zhang, Xue-Feng; He, Yin-Chen; Eggert, Sebastian; Moessner, Roderich; Pollmann, Frank

2018-03-01

We use large scale quantum Monte Carlo simulations to study an extended Hubbard model of hard core bosons on the kagome lattice. In the limit of strong nearest-neighbor interactions at 1 /3 filling, the interplay between frustration and quantum fluctuations leads to a valence bond solid ground state. The system undergoes a quantum phase transition to a superfluid phase as the interaction strength is decreased. It is still under debate whether the transition is weakly first order or represents an unconventional continuous phase transition. We present a theory in terms of an easy plane noncompact C P1 gauge theory describing the phase transition at 1 /3 filling. Utilizing large scale quantum Monte Carlo simulations with parallel tempering in the canonical ensemble up to 15552 spins, we provide evidence that the phase transition is continuous at exactly 1 /3 filling. A careful finite size scaling analysis reveals an unconventional scaling behavior hinting at deconfined quantum criticality.
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.
Thermodynamics and glassy phase transition of regular black holes

NASA Astrophysics Data System (ADS)

Javed, Wajiha; Yousaf, Z.; Akhtar, Zunaira

2018-05-01

This paper is aimed to study thermodynamical properties of phase transition for regular charged black holes (BHs). In this context, we have considered two different forms of BH metrics supplemented with exponential and logistic distribution functions and investigated the recent expansion of phase transition through grand canonical ensemble. After exploring the corresponding Ehrenfest’s equation, we found the second-order background of phase transition at critical points. In order to check the critical behavior of regular BHs, we have evaluated some corresponding explicit relations for the critical temperature, pressure and volume and draw certain graphs with constant values of Smarr’s mass. We found that for the BH metric with exponential configuration function, the phase transition curves are divergent near the critical points, while glassy phase transition has been observed for the Ayón-Beato-García-Bronnikov (ABGB) BH in n = 5 dimensions.
Weak arrest-like and field-driven first order magnetic phase transitions of itinerant Fe3Ga4 revealed by magnetization and magnetoresistance isotherms

NASA Astrophysics Data System (ADS)

Samatham, S. Shanmukharao; Suresh, K. G.

2017-01-01

The detailed magnetic study of complex 3d-electron based Fe3Ga4 is reported. It undergoes paramagnetic to antiferromagnetic (TN) and antiferromagnetic to ferromagnetic (TC) transitions respectively around 380 and 70 K. The thermal hysteresis of field-cooled cooling (FCC) and field-cooled warming (FCW) hints at first order phase transition below Curie temperature. A weak phase coexistence of ferro and antiferromagnetic phases is suggested by exploring the arrest-like first-order phenomenon. In the intermediate temperature range, field-driven metamagnetic transition from antiferro to ferromagnetic phase is confirmed. Further bringing the system very near to TN, field-induced transitions disappear and above TN predominant paramagnetic contribution is evident. The magnetic H-T phase diagram distinguishing different magnetic phases of Fe3Ga4 is obtained.
Nonequilibrium Phase Precursors during a Photoexcited Insulator-to-Metal Transition in V2O3

NASA Astrophysics Data System (ADS)

Singer, Andrej; Ramirez, Juan Gabriel; Valmianski, Ilya; Cela, Devin; Hua, Nelson; Kukreja, Roopali; Wingert, James; Kovalchuk, Olesya; Glownia, James M.; Sikorski, Marcin; Chollet, Matthieu; Holt, Martin; Schuller, Ivan K.; Shpyrko, Oleg G.

2018-05-01

Here, we photoinduce and directly observe with x-ray scattering an ultrafast enhancement of the structural long-range order in the archetypal Mott system V2O3 . Despite the ultrafast increase in crystal symmetry, the change of unit cell volume occurs an order of magnitude slower and coincides with the insulator-to-metal transition. The decoupling between the two structural responses in the time domain highlights the existence of a transient photoinduced precursor phase, which is distinct from the two structural phases present in equilibrium. X-ray nanoscopy reveals that acoustic phonons trapped in nanoscale twin domains govern the dynamics of the ultrafast transition into the precursor phase, while nucleation and growth of metallic domains dictate the duration of the slower transition into the metallic phase. The enhancement of the long-range order before completion of the electronic transition demonstrates the critical role the nonequilibrium structural phases play during electronic phase transitions in correlated electrons systems.
Thermodynamic, crystallographic, and dielectric study of the nature of glass transitions in cyclo-octanol

NASA Astrophysics Data System (ADS)

Puertas, Ricardo; Rute, Maria A.; Salud, Josep; López, David O.; Diez, Sergio; van Miltenburg, J. Kees; Pardo, Luis C.; Tamarit, Josep Ll.; Barrio, Maria; Pérez-Jubindo, Miguel A.; de La Fuente, Maria R.

2004-06-01

The stable solid polymorphism of cyclooctanol (C8H16O, for short C8 OH) is revealed to be a complex problem and only two stable solid phases, denoted on cooling from the liquid as phases I and II, are found using static (thermodynamic and x-ray diffraction) as well as dynamic (dielectric spectroscopy) experimental techniques. Both solid phases are known to exhibit glass transitions if they are cooled down fast enough to prevent transition to ordered crystalline states. Although glass transitions corresponding to both phases had been well documented by means of specific heat measurements, x-ray measurements constitute, as far as we know, the first evidence from the structural point of view. In addition, a great amount of dielectric works devoted to phase I and its glass transition, were published in the past but next to nothing relating to the dielectric properties of phase II and its glass transition. The nature of the disorder of phase II will be discussed.
Phase diagram of two-dimensional hard ellipses.

PubMed

Bautista-Carbajal, Gustavo; Odriozola, Gerardo

2014-05-28

We report the phase diagram of two-dimensional hard ellipses as obtained from replica exchange Monte Carlo simulations. The replica exchange is implemented by expanding the isobaric ensemble in pressure. The phase diagram shows four regions: isotropic, nematic, plastic, and solid (letting aside the hexatic phase at the isotropic-plastic two-step transition [E. P. Bernard and W. Krauth, Phys. Rev. Lett. 107, 155704 (2011)]). At low anisotropies, the isotropic fluid turns into a plastic phase which in turn yields a solid for increasing pressure (area fraction). Intermediate anisotropies lead to a single first order transition (isotropic-solid). Finally, large anisotropies yield an isotropic-nematic transition at low pressures and a high-pressure nematic-solid transition. We obtain continuous isotropic-nematic transitions. For the transitions involving quasi-long-range positional ordering, i.e., isotropic-plastic, isotropic-solid, and nematic-solid, we observe bimodal probability density functions. This supports first order transition scenarios.
Learning phase transitions by confusion

NASA Astrophysics Data System (ADS)

van Nieuwenburg, Evert; Liu, Ye-Hua; Huber, Sebastian

Classifying phases of matter is a central problem in physics. For quantum mechanical systems, this task can be daunting owing to the exponentially large Hilbert space. Thanks to the available computing power and access to ever larger data sets, classification problems are now routinely solved using machine learning techniques. Here, we propose to use a neural network based approach to find transitions depending on the performance of the neural network after training it with deliberately incorrectly labelled data. We demonstrate the success of this method on the topological phase transition in the Kitaev chain, the thermal phase transition in the classical Ising model, and the many-body-localization transition in a disordered quantum spin chain. Our method does not depend on order parameters, knowledge of the topological content of the phases, or any other specifics of the transition at hand. It therefore paves the way to a generic tool to identify unexplored transitions.
Phase transition in the (Li 0.5-( x/2) K 0.5-( x/2) Cs x) 2SO 4 system

NASA Astrophysics Data System (ADS)

Hamed, A. E.; El-Aziz, Y. M. Abd.; Madi, N. K.; Kassem, M. E.

1995-12-01

Phase transition in the (Li 0.5-( x/2) K 0.5-( x/2) Cs x) 2SO 4 system was studied by measuring the specific heat at constant pressure, C p, as a function of temperature in the temperature range 300-800 K. For non-zero values of X ( X = 0.2%, 0.5%, 1% and 2%) the critical behaviour of the phase transition was found to change considerably compared with that of X = 0 or pure LiKSO 4. The observed change in the phase transition with increase of Cs 2SO 4 content ( X) was accompanied by a decrease in the thermodynamic parameters: the value of the specific heat at the transition point (Δ C P) max, the transition temperature, T1, and the value of the energy of ordering. The results were interpreted within the Landau thermodynamic theory of the phase transition.
Pressure induced phase transition and elastic properties of cerium mono-nitride (CeN)

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

Yaduvanshi, Namrata, E-mail: namrata-yaduvanshi@yahoo.com; Singh, Sadhna

2016-05-23

In the present paper, we have investigated the high-pressure structural phase transition and elastic properties of cerium mono-nitride. We studied theoretically the structural properties of this compound (CeN) by using the improved interaction potential model (IIPM) approach. This compound exhibits first order crystallographic phase transition from NaCl (B{sub 1}) to tetragonal (BCT) phase at 37 GPa. The phase transition pressures and associated volume collapse obtained from present potential model (IIPM) show a good agreement with available theoretical data.
Nonequilibrium Phase Transition in a Model for Social Influence

NASA Astrophysics Data System (ADS)

Castellano, Claudio; Marsili, Matteo; Vespignani, Alessandro

2000-10-01

We present extensive numerical simulations of the Axelrod's model for social influence, aimed at understanding the formation of cultural domains. This is a nonequilibrium model with short range interactions and a remarkably rich dynamical behavior. We study the phase diagram of the model and uncover a nonequilibrium phase transition separating an ordered (culturally polarized) phase from a disordered (culturally fragmented) one. The nature of the phase transition can be continuous or discontinuous depending on the model parameters. At the transition, the size of cultural regions is power-law distributed.
Electrical conduction mechanism and phase transition studies using dielectric properties and Raman spectroscopy in ferroelectric Pb0.76Ca0.24TiO3 thin films

NASA Astrophysics Data System (ADS)

Pontes, F. M.; Pontes, D. S. L.; Leite, E. R.; Longo, E.; Chiquito, A. J.; Pizani, P. S.; Varela, J. A.

2003-12-01

We have studied the phase transition behavior of Pb0.76Ca0.24TiO3 thin films using Raman scattering and dielectric measurement techniques. We also have studied the leakage current conduction mechanism as a function of temperature for these thin films on platinized silicon substrates. A Pb0.76Ca0.24TiO3 thin film was prepared using a soft chemical process, called the polymeric precursor method. The results showed that the dependence of the dielectric constant upon the frequency does not reveal any relaxor behavior. However, a diffuse character-type phase transition was observed upon transformation from a cubic paraelectric phase to a tetragonal ferroelectric phase. The temperature dependency of Raman scattering spectra was investigated through the ferroelectric phase transition. The soft mode showed a marked dependence on temperature and its disappearance at about 598 K. On the other hand, Raman modes persist above the tetragonal to cubic phase transition temperature, although all optical modes should be Raman inactive above the phase transition temperature. The origin of these modes must be interpreted in terms of a local breakdown of cubic symmetry by some kind of disorder. The lack of a well-defined transition temperature suggested a diffuse-type phase transition. This result corroborate the dielectric constant versus temperature data, which showed a broad ferroelectric phase transition in the thin film. The leakage current density of the PCT24 thin film was studied at elevated temperatures, and the data were well fitted by the Schottky emission model. The Schottky barrier height of the PCT24 thin film was estimated to be 1.49 eV.
Phased models for evaluating the performability of computing systems

NASA Technical Reports Server (NTRS)

Wu, L. T.; Meyer, J. F.

1979-01-01

A phase-by-phase modelling technique is introduced to evaluate a fault tolerant system's ability to execute different sets of computational tasks during different phases of the control process. Intraphase processes are allowed to differ from phase to phase. The probabilities of interphase state transitions are specified by interphase transition matrices. Based on constraints imposed on the intraphase and interphase transition probabilities, various iterative solution methods are developed for calculating system performability.

Non-equilibrium phase transitions in a driven-dissipative system of interacting bosons

NASA Astrophysics Data System (ADS)

Young, Jeremy T.; Foss-Feig, Michael; Gorshkov, Alexey V.; Maghrebi, Mohammad F.

2017-04-01

Atomic, molecular, and optical systems provide unique opportunities to study simple models of driven-dissipative many-body quantum systems. Typically, one is interested in the resultant steady state, but the non-equilibrium nature of the physics involved presents several problems in understanding its behavior theoretically. Recently, it has been shown that in many of these models, it is possible to map the steady-state phase transitions onto classical equilibrium phase transitions. In the language of Keldysh field theory, this relation typically only becomes apparent after integrating out massive fields near the critical point, leaving behind a single massless field undergoing near-equilibrium dynamics. In this talk, we study a driven-dissipative XXZ bosonic model and discover critical points at which two fields become gapless. Each critical point separates three different possible phases: a uniform phase, an anti-ferromagnetic phase, and a limit cycle phase. Furthermore, a description in terms of an equilibrium phase transition does not seem possible, so the associated phase transitions appear to be inherently non-equilibrium.
The journey from precontemplation to action: Transitioning between electronic medical record systems.

PubMed

Bentley, Thomas; Rizer, Milisa; McAlearney, Ann Scheck; Mekhjian, Hagop; Siedler, Monica; Sharp, Karen; Teater, Phyllis; Huerta, Timothy

2016-01-01

Health care organizations, in response to federal programs, have sought to identify electronic medical record (EMR) strategies that align well with their visions for success. Little exists in the literature discussing the transition from one EMR strategy to another. The analysis and planning process used by a major academic medical center in its journey to adopt a new strategy was described in this study. We use the transtheoretical model of change to frame the five phases through which the organization transitioned from a best-of-breed system to an enterprise system. We explore the five phases of change from the perspective of a maturing approach to new technology adoption. Data collection included archival retrieval and review as well as interviews with key stakeholders. Although there was always a focus on some enterprise capabilities such as computerized physician order entry, the emphasis on EMR selection tended to be driven by specialty requirements. Focusing on the patient across the continuum of care, as opposed to focusing on excessive requirements by clinical specialties, was essential in forming and deploying a vision for the new EMR. This research outlines a successful pathway used by an organization that had invested heavily in EMR technology and was faced with evaluating whether to continue that investment or start with a new platform. Rather than focusing on the technology alone, efforts to reframe the discussion to one that focused on the patient resulted in less resistance to change.
Phase transition phenomenon: A compound measure analysis

NASA Astrophysics Data System (ADS)

Kang, Bo Soo; Park, Chanhi; Ryu, Doojin; Song, Wonho

2015-06-01

This study investigates the well-documented phenomenon of phase transition in financial markets using combined information from both return and volume changes within short time intervals. We suggest a new measure for the phase transition behaviour of markets, calculated as a return distribution conditional on local variance in volume imbalance, and show that this measure successfully captures phase transition behaviour under various conditions. We analyse the intraday trade and quote dataset from the KOSPI 200 index futures, which includes detailed information on the original order size and the type of each initiating investor. We find that among these two competing factors, the submitted order size yields more explanatory power on the phenomenon of market phase transition than the investor type.
Bismuth doping strategies in GeTe nanowires to promote high-temperature phase transition from rhombohedral to face-centered cubic structure

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

Zhang, Jie; Huang, Rong; Wei, Fenfen

2014-11-17

The phase transition of Bi-doped (∼3 at. %) GeTe nanowires from a rhombohedral (R) to a face-centered cubic (C) structure was observed in in situ high-temperature X-ray diffraction. The promotion of high-temperature R-C phase transition by a doping approach was revealed. Ab initio energy calculations of doped GeTe at various Bi doping concentrations were performed to interpret the promoted temperature-induced phase transitions. Those results indicated that the total energy differences between R and C structures of doped GeTe decreased as Bi doping concentrations increased, which facilitated R-C phase transitions.
Dynamic pathway of the photoinduced phase transition of TbMnO3

NASA Astrophysics Data System (ADS)

Bothschafter, Elisabeth M.; Abreu, Elsa; Rettig, Laurenz; Kubacka, Teresa; Parchenko, Sergii; Porer, Michael; Dornes, Christian; Windsor, Yoav William; Ramakrishnan, Mahesh; Alberca, Aurora; Manz, Sebastian; Saari, Jonathan; Koohpayeh, Seyed M.; Fiebig, Manfred; Forrest, Thomas; Werner, Philipp; Dhesi, Sarnjeet S.; Johnson, Steven L.; Staub, Urs

2017-11-01

We investigate the demagnetization dynamics of the cycloidal and sinusoidal phases of multiferroic TbMnO3 by means of time-resolved resonant soft x-ray diffraction following excitation by an optical pump. The use of orthogonal linear x-ray polarizations provides information on the contribution from the different magnetic moment directions, which can be interpreted as signatures from multiferroic cycloidal spin order and sinusoidal spin order. Tracking these signatures in the time domain enables us to identify the transient magnetic phase created by intense photoexcitation of the electrons and subsequent heating of the spin system on a picosecond time scale. The transient phase is shown to exhibit mostly spin density wave character, as in the adiabatic case, while nevertheless retaining the wave vector of the cycloidal long-range order. Two different pump photon energies, 1.55 and 3.1 eV, lead to population of the conduction band predominantly via intersite d -d or intrasite p -d transitions, respectively. We find that the nature of the optical excitation does not play an important role in determining the dynamics of magnetic order melting. Further, we observe that the orbital reconstruction, which is induced by the spin ordering, disappears on a time scale comparable to that of the cycloidal order, attesting to a direct coupling between magnetic order and orbital reconstruction. Our observations are discussed in the context of recent theoretical models of demagnetization dynamics in strongly correlated systems, revealing the potential of this type of measurement as a benchmark for such theoretical studies.
Influence of Pressure on Physical Property of Ammonia Borane and its Re-hydrogenation

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

Chen, Jiuhua

The project systematically studied the high pressure behavior of ammonia borane and its derivative lithium amidoborane. Phase transitions in these materials are investigated in the pressure range up to 20 GPa and temperature range from 80 K to 400K. A number of new phase transitions are discovered in this pressure and temperature range including a second order transformation at 5 GPa and a first order transformation at 12 GPa at room temperature, and four new transitions at high pressure and low temperatures. The Clapeyron slopes for both pressure-induce tetragonal (I4mm) phase to orthorhombic (Cmc21) phase and temperature-induce tetragonal (I4mm) phasemore » to orthorhombic (Pmn21) phase are determined to be positive, indicating these phase transitions are exothermic. This result demonstrates that the high pressure orthorhombic phase of ammonia borane has lower enthalpy than that of tetragonal phase at ambient conditions. If we assume decomposition from the orthorhombic phase yields the same products as that from the tetragonal phase, the decomposition of the orthorhombic phase will be less exothermic. Therefore rehydrogenation from the decomposed product into the orthorhombic phase at high pressure may become easier. The project also studied the influences of nanoconfinement on the phase transitions. Comparative study using Raman spectroscopy indicates that the temperature induced I4mm to Pmn21 transition is suppressed from 217 K to 195 K when the sample is confined in SBA15 (7-9 nm pore size). When the pore size is reduced from 7-9 nm to 3-4 nm, this transition is totally suppressed in the temperature down to 80 K. A similar influence of the nanoconfiement on pressure induced phase transitions is also observed using Raman spectroscopy. The phase boundary between the I4mm phase and high pressure Cmc21 phase at ambient temperature shifts from 0.9 GPa to 0.5 GPa; and that between the Cmc21 phase and higher pressure P21 phase shifts from 10.2 GPa to 9.7 GPa.« less
Post-Starburst Galaxies At The End of The E+A Phase

NASA Astrophysics Data System (ADS)

Liu, Charles; Marinelli, Mariarosa; Chang, Madeleine; Lyczko, Camilla; Vega Orozco, Cecilia; SDSS-IV Collaboration

2018-06-01

Post-starburst galaxies, once thought to be rare curiosities, are now recognized to represent a key phase in the galaxy evolution. The post-starburst, or E+A phase, should however not be considered as a single, short-lived phenomenon; rather, it is an extended evolutionary process that occurs a galaxy transitions from an actively star-forming system into a quiescent one. We present a study of nearby galaxies at or near the end of the E+A phase, wherein all star formation has been quenched, the fossilized stellar population of the most recent starburst is highly localized, and the remainder of the galaxy's stellar population is old and quiescent. The luminosity and stellar age distribution of these "end-phase E+As" can provide insights into the evolution of galaxies onto and within the red sequence, from active to passive systems. This work is supported by National Science Foundation grants to CUNY College of Staten Island and the American Museum of Natural History; the College of Staten Island Office of Academic Affairs; the Sherman Fairchild Science Pathways Scholars Program (SP^2) at Barnard College; and the Alfred P. Sloan Foundation.
Evolution of Government and Industrial Partnerships to Open the Space Frontier

NASA Technical Reports Server (NTRS)

Martin, Gary L.

2008-01-01

If the logical extension of the current exploration program is to develop self-sustaining settlements on the Moon and Mars over the next few centuries, then there is a path that takes civilization from its current one planet existence to a multi-world future. By considering the far term goal of space settlements as a desired endpoint and using the current state as a starting point, the policy drivers and potential pathways to the goal of sustainable space settlements can be explored. This paper describes a three-phased evolution of government and industrial partnerships from current day relationships to a time when there are sustainable settlements in space. Phase I details the current state government-led exploration while Phase III describes a desired endpoint of self-sufficient settlements in space. Phase II is an important transition phase, which acts as a bridge between now and the future. This paper discusses the critical evolution that must take place in two key areas to ensure a thriving future in space; space transportation and the right to use space property and resources. This paper focuses on the enabling role of government necessary to achieve United States (U.S.) goals for space exploration and open the frontier.
Micellar-shape anisometry near isotropic-liquid-crystal phase transitions

NASA Astrophysics Data System (ADS)

Itri, R.; Amaral, L. Q.

1993-04-01

Micellar phases of the sodium dodecyl (lauryl) sulfate (SLS)-water-decanol system have been studied by x-ray scattering in the isotropic (I) phase, with emphasis on the I-->hexagonal (Hα) and I-->nematic-cylindrical (Nc) lyotropic liquid-crystal phase transitions. Analysis of the scattering curves is made through modeling of the product P(q)S(q), where P(q) is the micellar form factor and S(q) is the intermicellar interference function, calculated from screened Coulombic repulsion in a mean spherical approximation. Results show that micelles grow more by decanol addition near the I-->Nc transition (anisometry ν~=3) than by increased amphiphile concentration in the binary system near the I-->Hα phase transition (ν~=2.4). These results compare well with recent theories for isotropic-liquid-crystal phase transitions.
Tentacle extract from the jellyfish Cyanea capillata increases proliferation and migration of human umbilical vein endothelial cells through the ERK1/2 signaling pathway

PubMed Central

Wang, Qianqian; Zhang, Hui; Liu, Guoyan; He, Qian; Zhang, Liming

2017-01-01

Wound healing is a complex biological process, and current research finds that jellyfish have a great capacity for promoting growth and healing. However, the underlying mechanisms remain unclear. Thus, this study was conducted to investigate the molecular mechanisms and effects of a tentacle extract (TE) from the jellyfish Cyanea capillata (C. capillata) on cell proliferation and migration in human umbilical vein endothelial cells (HUVECs). First, our results showed that TE at the concentration of 1 μg/ml could promote cell proliferation over various durations, induce a transition of the cells from the G1-phase to the S/G2-phase of the cell cycle, and increase the expression of cell cycle proteins (CyclinB1 and CyclinD1). Second, we found that TE could activate the PI3K/Akt, ERK1/2 and JNK MAPK signaling pathways but not the NF-κB signaling pathway or the apoptosis signaling cascade. Finally, we demonstrated that the TE-induced expression of cell cycle proteins was decreased by ERK1/2 inhibitor PD98059 but not by PI3K inhibitor LY294002 or JNK inhibitor SP600125. Similarly, the TE-enhanced migration ability of HUVECs was also markedly attenuated by PD98059. Taken together, our findings indicate that TE-induced proliferation and migration in HUVECs mainly occurred through the ERK1/2 MAPK signaling pathway. These results are instructively important for further research on the isolation and purification of growth-promoting factors from C. capillata and are hopeful as a means to improve human wound repair in unfavorable conditions. PMID:29261770
Tentacle extract from the jellyfish Cyanea capillata increases proliferation and migration of human umbilical vein endothelial cells through the ERK1/2 signaling pathway.

PubMed

Wang, Beilei; Liu, Dan; Wang, Chao; Wang, Qianqian; Zhang, Hui; Liu, Guoyan; He, Qian; Zhang, Liming

2017-01-01

Wound healing is a complex biological process, and current research finds that jellyfish have a great capacity for promoting growth and healing. However, the underlying mechanisms remain unclear. Thus, this study was conducted to investigate the molecular mechanisms and effects of a tentacle extract (TE) from the jellyfish Cyanea capillata (C. capillata) on cell proliferation and migration in human umbilical vein endothelial cells (HUVECs). First, our results showed that TE at the concentration of 1 μg/ml could promote cell proliferation over various durations, induce a transition of the cells from the G1-phase to the S/G2-phase of the cell cycle, and increase the expression of cell cycle proteins (CyclinB1 and CyclinD1). Second, we found that TE could activate the PI3K/Akt, ERK1/2 and JNK MAPK signaling pathways but not the NF-κB signaling pathway or the apoptosis signaling cascade. Finally, we demonstrated that the TE-induced expression of cell cycle proteins was decreased by ERK1/2 inhibitor PD98059 but not by PI3K inhibitor LY294002 or JNK inhibitor SP600125. Similarly, the TE-enhanced migration ability of HUVECs was also markedly attenuated by PD98059. Taken together, our findings indicate that TE-induced proliferation and migration in HUVECs mainly occurred through the ERK1/2 MAPK signaling pathway. These results are instructively important for further research on the isolation and purification of growth-promoting factors from C. capillata and are hopeful as a means to improve human wound repair in unfavorable conditions.
Raman spectra and phase transitions in Rb{sub 2}KInF{sub 6} elpasolite

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

Krylov, A. S.; Krylova, S. N., E-mail: slanky@iph.krasn.ru; Vtyurin, A. N.

2011-01-15

The Raman spectra of Rb{sub 2}KInF{sub 6} elpasolite crystal have been studied in a wide temperature range, including two phase transitions: from the cubic phase to the tetragonal phase and then to the monoclinic phase. Several anomalies of internal modes of InF{sub 6} octahedra and low-frequency lattice vibrations, which are related to the structural changes at the transition points, have been found and quantitatively analyzed. The results of a quantitative analysis of the temperature dependences of the parameters of spectral lines are in good agreement with the thermodynamic data on the phase transitions.
Role of relativity in high-pressure phase transitions of thallium.

PubMed

Kotmool, Komsilp; Chakraborty, Sudip; Bovornratanaraks, Thiti; Ahuja, Rajeev

2017-02-20

We demonstrate the relativistic effects in high-pressure phase transitions of heavy element thallium. The known first phase transition from h.c.p. to f.c.c. is initially investigated by various relativistic levels and exchange-correlation functionals as implemented in FPLO method, as well as scalar relativistic scheme within PAW formalism. The electronic structure calculations are interpreted from the perspective of energetic stability and electronic density of states. The full relativistic scheme (FR) within L(S)DA performs to be the scheme that resembles mostly with experimental results with a transition pressure of 3 GPa. The s-p hybridization and the valence-core overlapping of 6s and 5d states are the primary reasons behind the f.c.c. phase occurrence. A recent proposed phase, i.e., a body-centered tetragonal (b.c.t.) phase, is confirmed with a small distortion from the f.c.c. phase. We have also predicted a reversible b.c.t. → f.c.c. phase transition at 800 GPa. This finding has been suggested that almost all the III-A elements (Ga, In and Tl) exhibit the b.c.t. → f.c.c. phase transition at extremely high pressure.
Phase transitions in high magnetic fields

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

Arko, A.J.; Beers, C.J.; van Deursen, A.P.J.

1982-08-01

The purpose of this paper is to summarize some of the research activities recently performed at the Laboratorium voor Hoge Magneetvelden at the University of Nijmegen. The scope here and unifying aspect is magnetically induced phase transitions. Here we summarize transitions in the settling velocity of paramagnetic aggregates, suppression of spin fluctuations in UAl/sub 2/, the phase diagram of a ferroelectric chiral smectic liquid crystal near the Lifshitz point and the transition from 3D to 2D conduction in a GaAs FET. In no way does this represent a complete review of transitions, but rather a summary of phase transitions observedmore » at the magnet laboratory during the past year. 6 figures.« less
Calculating Free Energies Using Scaled-Force Molecular Dynamics Algorithm

NASA Technical Reports Server (NTRS)

Darve, Eric; Wilson, Micahel A.; Pohorille, Andrew

2000-01-01

One common objective of molecular simulations in chemistry and biology is to calculate the free energy difference between different states of the system of interest. Examples of problems that have such an objective are calculations of receptor-ligand or protein-drug interactions, associations of molecules in response to hydrophobic, and electrostatic interactions or partition of molecules between immiscible liquids. Another common objective is to describe evolution of the system towards a low energy (possibly the global minimum energy), 'native' state. Perhaps the best example of such a problem is folding of proteins or short RNA molecules. Both types of problems share the same difficulty. Often, different states of the system are separated by high energy barriers, which implies that transitions between these states are rare events. This, in turn, can greatly impede exploration of phase space. In some instances this can lead to 'quasi non-ergodicity', whereby a part of phase space is inaccessible on timescales of the simulation. A host of strategies has been developed to improve efficiency of sampling the phase space. For example, some Monte Carlo techniques involve large steps which move the system between low-energy regions in phase space without the need for sampling the configurations corresponding to energy barriers (J-walking). Most strategies, however, rely on modifying probabilities of sampling low and high-energy regions in phase space such that transitions between states of interest are encouraged. Perhaps the simplest implementation of this strategy is to increase the temperature of the system. This approach was successfully used to identify denaturation pathways in several proteins, but it is clearly not applicable to protein folding. It is also not a successful method for determining free energy differences. Finally, the approach is likely to fail for systems with co-existing phases, such as water-membrane systems, because it may lead to spontaneous mixing. A similar difficulty may be encountered in any method relying on global modifications of phase space.
Analysis of the gas phase reactivity of chlorosilanes.

PubMed

Ravasio, Stefano; Masi, Maurizio; Cavallotti, Carlo

2013-06-27

Trichlorosilane is the most used precursor to deposit silicon for photovoltaic applications. Despite of this, its gas phase and surface kinetics have not yet been completely understood. In the present work, it is reported a systematic investigation aimed at determining what is the dominant gas phase chemistry active during the chemical vapor deposition of Si from trichlorosilane. The gas phase mechanism was developed calculating the rate constant of each reaction using conventional transition state theory in the rigid rotor-harmonic oscillator approximation. Torsional vibrations were described using a hindered rotor model. Structures and vibrational frequencies of reactants and transition states were determined at the B3LYP/6-31+G(d,p) level, while potential energy surfaces and activation energies were computed at the CCSD(T) level using aug-cc-pVDZ and aug-cc-pVTZ basis sets extrapolating to the complete basis set limit. As gas phase and surface reactivities are mutually interlinked, simulations were performed using a microkinetic surface mechanism. It was found that the gas phase reactivity follows two different routes. The disilane mechanism, in which the formation of disilanes as reaction intermediates favors the conversion between the most stable monosilane species, and the radical pathway, initiated by the decomposition of Si2HCl5 and followed by a series of fast propagation reactions. Though both mechanisms are active during deposition, the simulations revealed that above a certain temperature and conversion threshold the radical mechanism provides a faster route for the conversion of SiHCl3 into SiCl4, a reaction that favors the overall Si deposition process as it is associated with the consumption of HCl, a fast etchant of Si. Also, this study shows that the formation of disilanes as reactant intermediates promotes significantly the gas phase reactivity, as they contribute both to the initiation of radical chain mechanisms and provide a catalytic route for the conversion between the most stable monosilanes.
Cell cycle progression is regulated by intertwined redox oscillators.

PubMed

da Veiga Moreira, Jorgelindo; Peres, Sabine; Steyaert, Jean-Marc; Bigan, Erwan; Paulevé, Loïc; Nogueira, Marcel Levy; Schwartz, Laurent

2015-05-29

The different phases of the eukaryotic cell cycle are exceptionally well-preserved phenomena. DNA decompaction, RNA and protein synthesis (in late G1 phase) followed by DNA replication (in S phase) and lipid synthesis (in G2 phase) occur after resting cells (in G0) are committed to proliferate. The G1 phase of the cell cycle is characterized by an increase in the glycolytic metabolism, sustained by high NAD+/NADH ratio. A transient cytosolic acidification occurs, probably due to lactic acid synthesis or ATP hydrolysis, followed by cytosolic alkalinization. A hyperpolarized transmembrane potential is also observed, as result of sodium/potassium pump (NaK-ATPase) activity. During progression of the cell cycle, the Pentose Phosphate Pathway (PPP) is activated by increased NADP+/NADPH ratio, converting glucose 6-phosphate to nucleotide precursors. Then, nucleic acid synthesis and DNA replication occur in S phase. Along with S phase, unpublished results show a cytosolic acidification, probably the result of glutaminolysis occurring during this phase. In G2 phase there is a decrease in NADPH concentration (used for membrane lipid synthesis) and a cytoplasmic alkalinization occurs. Mitochondria hyperfusion matches the cytosolic acidification at late G1/S transition and then triggers ATP synthesis by oxidative phosphorylation. We hypothesize here that the cytosolic pH may coordinate mitochondrial activity and thus the different redox cycles, which in turn control the cell metabolism.
Mobility restrictions and glass transition behaviour of an epoxy resin under confinement.

PubMed

Djemour, A; Sanctuary, R; Baller, J

2015-04-07

Confinement can have a big influence on the dynamics of glass formers in the vicinity of the glass transition. Already 40 to 50 K above the glass transition temperature, thermal equilibration of glass formers can be strongly influenced by the confining substrate. We investigate the linear thermal expansion and the specific heat capacity cp of an epoxy resin (diglycidyl ether of bisphenol A, DGEBA) in a temperature interval of 120 K around the glass transition temperature. The epoxy resin is filled into controlled pore glasses with pore diameters between 4 and 111 nm. Since DGEBA can form H-bonds with silica surfaces, we also investigate the influence of surface silanization of the porous substrates. In untreated substrates a core/shell structure of the epoxy resin can be identified. The glass transition behaviours of the bulk phase and that of the shell phase are different. In silanized substrates, the shell phase disappears. At a temperature well above the glass transition, a second transition is found for the bulk phase - both in the linear expansion data as well as in the specific heat capacity. The cp data do not allow excluding the glass transition of a third phase as being the cause for this transition, whereas the linear expansion data do so. The additional transition temperature is interpreted as a separation between two regimes: above this temperature, macroscopic flow of the bulk phase inside the porous structure is possible to balance the mismatch of thermal expansion coefficients between DGEBA and the substrate. Below the transition temperature, this degree of freedom is hindered by geometrical constraints of the porous substrates. Moreover, this second transition could also be found in the linear expansion data of the shell phase.
A time-dependent order parameter for ultrafast photoinduced phase transitions.

PubMed

Beaud, P; Caviezel, A; Mariager, S O; Rettig, L; Ingold, G; Dornes, C; Huang, S-W; Johnson, J A; Radovic, M; Huber, T; Kubacka, T; Ferrer, A; Lemke, H T; Chollet, M; Zhu, D; Glownia, J M; Sikorski, M; Robert, A; Wadati, H; Nakamura, M; Kawasaki, M; Tokura, Y; Johnson, S L; Staub, U

2014-10-01

Strongly correlated electron systems often exhibit very strong interactions between structural and electronic degrees of freedom that lead to complex and interesting phase diagrams. For technological applications of these materials it is important to learn how to drive transitions from one phase to another. A key question here is the ultimate speed of such phase transitions, and to understand how a phase transition evolves in the time domain. Here we apply time-resolved X-ray diffraction to directly measure the changes in long-range order during ultrafast melting of the charge and orbitally ordered phase in a perovskite manganite. We find that although the actual change in crystal symmetry associated with this transition occurs over different timescales characteristic of the many electronic and vibrational coordinates of the system, the dynamics of the phase transformation can be well described using a single time-dependent 'order parameter' that depends exclusively on the electronic excitation.
Thermodynamics around the first-order ferromagnetic phase transition of Fe2P single crystals

NASA Astrophysics Data System (ADS)

Hudl, M.; Campanini, D.; Caron, L.; Höglin, V.; Sahlberg, M.; Nordblad, P.; Rydh, A.

2014-10-01

The specific heat and thermodynamics of Fe2P single crystals around the first-order paramagnetic to ferromagnetic (FM) phase transition at TC≃217 K are empirically investigated. The magnitude and direction of the magnetic field relative to the crystal axes govern the derived H -T phase diagram. Strikingly different phase contours are obtained for fields applied parallel and perpendicular to the c axis of the crystal. In parallel fields, the FM state is stabilized, while in perpendicular fields the phase transition is split into two sections, with an intermediate FM phase where there is no spontaneous magnetization along the c axis. The zero-field transition displays a textbook example of a first-order transition with different phase stability limits on heating and cooling. The results have special significance since Fe2P is the parent material to a family of compounds with outstanding magnetocaloric properties.

Quantum phase transition from mixed atom-molecule phase to pure molecule phase: Characteristic scaling laws and Berry-curvature signature

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

Li Shengchang; Graduate School, China Academy of Engineering Physics, Beijing 100088; Fu Libin

2011-08-15

We investigate the quantum phase transition in an ultracold atom-molecule conversion system. It is found that the system undergoes a phase transition from a mixed atom-molecule phase to a pure molecule phase when the energy bias exceeds a critical value. By constructing a coherent state as variational state, we get a good approximation of the quantum ground state of the system. Using this variational state, we deduce the critical point analytically. We then discuss the scaling laws characterizing the transition and obtain the corresponding critical exponents. Furthermore, the Berry curvature signature of the transition is studied. In particular, we findmore » that the derivatives of the Berry curvature with respect to total particle number intersect at the critical point. The underlying mechanism of this finding is discussed as well.« less
Cisplatin Resistance: A Cellular Self-Defense Mechanism Resulting from Multiple Epigenetic and Genetic Changes

PubMed Central

Shen, Ding-Wu; Pouliot, Lynn M.; Hall, Matthew D.

2012-01-01

Cisplatin is one of the most effective broad-spectrum anticancer drugs. Its effectiveness seems to be due to the unique properties of cisplatin, which enters cells via multiple pathways and forms multiple different DNA-platinum adducts while initiating a cellular self-defense system by activating or silencing a variety of different genes, resulting in dramatic epigenetic and/or genetic alternations. As a result, the development of cisplatin resistance in human cancer cells in vivo and in vitro by necessity stems from bewilderingly complex genetic and epigenetic changes in gene expression and alterations in protein localization. Extensive published evidence has demonstrated that pleiotropic alterations are frequently detected during development of resistance to this toxic metal compound. Changes occur in almost every mechanism supporting cell survival, including cell growth-promoting pathways, apoptosis, developmental pathways, DNA damage repair, and endocytosis. In general, dozens of genes are affected in cisplatin-resistant cells, including pathways involved in copper metabolism as well as transcription pathways that alter the cytoskeleton, change cell surface presentation of proteins, and regulate epithelial-to-mesenchymal transition. Decreased accumulation is one of the most common features resulting in cisplatin resistance. This seems to be a consequence of numerous epigenetic and genetic changes leading to the loss of cell-surface binding sites and/or transporters for cisplatin, and decreased fluid phase endocytosis. PMID:22659329
Cisplatin resistance: a cellular self-defense mechanism resulting from multiple epigenetic and genetic changes.

PubMed

Shen, Ding-Wu; Pouliot, Lynn M; Hall, Matthew D; Gottesman, Michael M

2012-07-01

Cisplatin is one of the most effective broad-spectrum anticancer drugs. Its effectiveness seems to be due to the unique properties of cisplatin, which enters cells via multiple pathways and forms multiple different DNA-platinum adducts while initiating a cellular self-defense system by activating or silencing a variety of different genes, resulting in dramatic epigenetic and/or genetic alternations. As a result, the development of cisplatin resistance in human cancer cells in vivo and in vitro by necessity stems from bewilderingly complex genetic and epigenetic changes in gene expression and alterations in protein localization. Extensive published evidence has demonstrated that pleiotropic alterations are frequently detected during development of resistance to this toxic metal compound. Changes occur in almost every mechanism supporting cell survival, including cell growth-promoting pathways, apoptosis, developmental pathways, DNA damage repair, and endocytosis. In general, dozens of genes are affected in cisplatin-resistant cells, including pathways involved in copper metabolism as well as transcription pathways that alter the cytoskeleton, change cell surface presentation of proteins, and regulate epithelial-to-mesenchymal transition. Decreased accumulation is one of the most common features resulting in cisplatin resistance. This seems to be a consequence of numerous epigenetic and genetic changes leading to the loss of cell-surface binding sites and/or transporters for cisplatin, and decreased fluid phase endocytosis.
Developmental Pathways Are Blueprints for Designing Successful Crops

PubMed Central

Trevaskis, Ben

2018-01-01

Genes controlling plant development have been studied in multiple plant systems. This has provided deep insights into conserved genetic pathways controlling core developmental processes including meristem identity, phase transitions, determinacy, stem elongation, and branching. These pathways control plant growth patterns and are fundamentally important to crop biology and agriculture. This review describes the conserved pathways that control plant development, using Arabidopsis as a model. Historical examples of how plant development has been altered through selection to improve crop performance are then presented. These examples, drawn from diverse crops, show how the genetic pathways controlling development have been modified to increase yield or tailor growth patterns to suit local growing environments or specialized crop management practices. Strategies to apply current progress in genomics and developmental biology to future crop improvement are then discussed within the broader context of emerging trends in plant breeding. The ways that knowledge of developmental processes and understanding of gene function can contribute to crop improvement, beyond what can be achieved by selection alone, are emphasized. These include using genome re-sequencing, mutagenesis, and gene editing to identify or generate novel variation in developmental genes. The expanding scope for comparative genomics, the possibility to engineer new developmental traits and new approaches to resolve gene–gene or gene–environment interactions are also discussed. Finally, opportunities to integrate fundamental research and crop breeding are highlighted. PMID:29922318
Developmental Pathways Are Blueprints for Designing Successful Crops.

PubMed

Trevaskis, Ben

2018-01-01

Genes controlling plant development have been studied in multiple plant systems. This has provided deep insights into conserved genetic pathways controlling core developmental processes including meristem identity, phase transitions, determinacy, stem elongation, and branching. These pathways control plant growth patterns and are fundamentally important to crop biology and agriculture. This review describes the conserved pathways that control plant development, using Arabidopsis as a model. Historical examples of how plant development has been altered through selection to improve crop performance are then presented. These examples, drawn from diverse crops, show how the genetic pathways controlling development have been modified to increase yield or tailor growth patterns to suit local growing environments or specialized crop management practices. Strategies to apply current progress in genomics and developmental biology to future crop improvement are then discussed within the broader context of emerging trends in plant breeding. The ways that knowledge of developmental processes and understanding of gene function can contribute to crop improvement, beyond what can be achieved by selection alone, are emphasized. These include using genome re-sequencing, mutagenesis, and gene editing to identify or generate novel variation in developmental genes. The expanding scope for comparative genomics, the possibility to engineer new developmental traits and new approaches to resolve gene-gene or gene-environment interactions are also discussed. Finally, opportunities to integrate fundamental research and crop breeding are highlighted.
Possible existence of two amorphous phases of d-mannitol related by a first-order transition

NASA Astrophysics Data System (ADS)

Zhu, Men; Wang, Jun-Qiang; Perepezko, John H.; Yu, Lian

2015-06-01

We report that the common polyalcohol d-mannitol may have two amorphous phases related by a first-order transition. Slightly above its glass transition temperature Tg (284 K), the supercooled liquid (SCL) of d-mannitol transforms to a low-energy, apparently amorphous phase with stronger hydrogen bonds. The enthalpy of this so-called Phase X is approximately halfway between those of the known amorphous and crystalline phases, a position low for glass aging and high for crystal polymorphs. Similar to the SCL, Phase X is transparent with broad X-ray diffraction and Raman scattering; upon temperature cycling, it exhibits a glass-transition-like change of heat capacity. On fast heating, Phase X transforms back to the SCL near Tg + 50 K, enabling a determination of their equilibrium temperature. The presence of d-sorbitol as a plasticizer enables observation of a first-order transition from the SCL to Phase X entirely in the liquid state (liquid-liquid transition). The transition from d-mannitol's SCL to Phase X has intriguing similarities with the formation of the glacial phase of triphenyl phosphite (TPP) and the conversion from high-density to low-density amorphous ice, both studied intensely in the context of polyamorphism. All three processes occur near Tg with substantial enthalpy decrease toward the crystalline phases; the processes in water and d-mannitol both strengthen the hydrogen bonds. In contrast to TPP, d-mannitol's Phase X forms more rapidly and can transform back to the SCL. These features make d-mannitol a valuable new model for understanding polyamorphism.
Nature of the octahedral tilting phase transitions in perovskites: A case study of CaMnO3

NASA Astrophysics Data System (ADS)

Klarbring, Johan; Simak, Sergei I.

2018-01-01

The temperature-induced antiferrodistortive (AFD) structural phase transitions in CaMnO3, a typical perovskite oxide, are studied using first-principles density functional theory calculations. These transitions are caused by tilting of the MnO6 octahedra that are related to unstable phonon modes in the high-symmetry cubic perovskite phase. Transitions due to octahedral tilting in perovskites normally are believed to fit into the standard soft-mode picture of displacive phase transitions. We calculate phonon-dispersion relations and potential-energy landscapes as functions of the unstable phonon modes and argue based on the results that the phase transitions are better described as being of order-disorder type. This means that the cubic phase emerges as a dynamical average when the system hops between local minima on the potential-energy surface. We then perform ab initio molecular dynamics simulations and find explicit evidence of the order-disorder dynamics in the system. Our conclusions are expected to be valid for other perovskite oxides, and we finally suggest how to predict the nature (displacive or order-disorder) of the AFD phase transitions in any perovskite system.
Conformational Transition Pathways in Signaling and Enzyme Catalysis Explored by Computational Methods

NASA Astrophysics Data System (ADS)

Pachov, Dimitar V.

Biomolecules are dynamic in nature and visit a number of states while performing their biological function. However, understanding how they interconvert between functional substates is a challenging task. In this thesis, we employ enhanced computational strategies to reveal in atomistic resolution transition states and molecular mechanism along conformational pathways of the signaling protein Nitrogen Regulatory Protein C (NtrC) and the enzyme Adenylate Kinase (Adk). Targeted Molecular Dynamics (TMD) simulations and NMR experiments have previously found the active/inactive interconversion of NtrC is stabilized by non-native transient contacts. To find where along the conformational pathway they lie and probe the existence of multiple intermediates, a beyond 8mus-extensive mapping of the conformational landscape was performed by a multitude of straightforward MD simulations relaxed from the biased TMD pathway. A number of metastable states stabilized by local interactions was found to underline the conformational pathway of NtrC. Two spontaneous transitions of the last stage of the active-to-inactive conversion were identified and used in path sampling procedures to generate an ensemble of truly dynamic reactive pathways. The transition state ensemble (TSE) and mechanistic descriptors of this transition were revealed in atomic detail and verified by committor analysis. By analyzing how pressure affects the dynamics and function of two homologous Adk proteins - the P.Profundum Adk surviving at 700atm pressure in the deep sea, and the E. coli Adk that lives at ambient pressures - we indirectly obtained atomic information about the TSE of the large-amplitude rate-limiting conformational opening of the Adk lids. Guided by NMR experiments showing significantly decreased activation volumes of the piezophile compared to its mesophilic counterpart, TMD simulations revealed the formation of an extended hydrogen-bonded water network in the transition state of the piezophile that can explain the experimentally measured activation volume differences. The transition state of the conformational change was proposed to lie close to the closed state. Additionally, a number of descriptors were used to characterize the free energy landscape of the mesophile. It was found that the features of landscape are highly sensitive to the binding of different ligands, their protonation states and the presence of magnesium.
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.
New investigations of technical rhodium and iridium catalysts in homogeneous phase employing para-hydrogen induced polarization.

PubMed

Gutmann, Torsten; Ratajczyk, Tomasz; Dillenberger, Sonja; Xu, Yeping; Grünberg, Anna; Breitzke, Hergen; Bommerich, Ute; Trantzschel, Thomas; Bernarding, Johannes; Buntkowsky, Gerd

2011-09-01

It is shown that the para-hydrogen induced polarization (PHIP) phenomenon in homogenous solution containing the substrate styrene is also observable employing simple inorganic systems of the form MCl(3)·xH(2)O (M=Rh, Ir) as catalyst. Such observation confirms that already very simple metal complexes enable the creation of PHIP signal enhancement in solution. This opens up new pathways to increase the sensitivity of NMR and MRT by PHIP enhancement using cost-effective catalysts and will be essential for further mechanistic studies of simple transition metal systems. Copyright © 2011 Elsevier Inc. All rights reserved.
Phase separation and second-order phase transition in the phenomenological model for a Coulomb-frustrated two-dimensional system

NASA Astrophysics Data System (ADS)

Mamin, R. F.; Shaposhnikova, T. S.; Kabanov, V. V.

2018-03-01

We have considered the model of the phase transition of the second order for the Coulomb frustrated 2D charged system. The coupling of the order parameter with the charge was considered as the local temperature. We have found that in such a system, an appearance of the phase-separated state is possible. By numerical simulation, we have obtained different types ("stripes," "rings," "snakes") of phase-separated states and determined the parameter ranges for these states. Thus the system undergoes a series of phase transitions when the temperature decreases. First, the system moves from the homogeneous state with a zero order parameter to the phase-separated state with two phases in one of which the order parameter is zero and, in the other, it is nonzero (τ >0 ). Then a first-order transition occurs to another phase-separated state, in which both phases have different and nonzero values of the order parameter (for τ <0 ). Only a further decrease of temperature leads to a transition to a homogeneous ordered state.
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
Problem-Solving Phase Transitions During Team Collaboration.

PubMed

Wiltshire, Travis J; Butner, Jonathan E; Fiore, Stephen M

2018-01-01

Multiple theories of problem-solving hypothesize that there are distinct qualitative phases exhibited during effective problem-solving. However, limited research has attempted to identify when transitions between phases occur. We integrate theory on collaborative problem-solving (CPS) with dynamical systems theory suggesting that when a system is undergoing a phase transition it should exhibit a peak in entropy and that entropy levels should also relate to team performance. Communications from 40 teams that collaborated on a complex problem were coded for occurrence of problem-solving processes. We applied a sliding window entropy technique to each team's communications and specified criteria for (a) identifying data points that qualify as peaks and (b) determining which peaks were robust. We used multilevel modeling, and provide a qualitative example, to evaluate whether phases exhibit distinct distributions of communication processes. We also tested whether there was a relationship between entropy values at transition points and CPS performance. We found that a proportion of entropy peaks was robust and that the relative occurrence of communication codes varied significantly across phases. Peaks in entropy thus corresponded to qualitative shifts in teams' CPS communications, providing empirical evidence that teams exhibit phase transitions during CPS. Also, lower average levels of entropy at the phase transition points predicted better CPS performance. We specify future directions to improve understanding of phase transitions during CPS, and collaborative cognition, more broadly. Copyright © 2017 Cognitive Science Society, Inc.
Holographic Van der Waals phase transition of the higher-dimensional electrically charged hairy black hole

NASA Astrophysics Data System (ADS)

Li, Hui-Ling; Feng, Zhong-Wen; Zu, Xiao-Tao

2018-01-01

With motivation by holography, employing black hole entropy, two-point connection function and entanglement entropy, we show that, for the higher-dimensional Anti-de Sitter charged hairy black hole in the fixed charged ensemble, a Van der Waals-like phase transition can be observed. Furthermore, based on the Maxwell equal-area construction, we check numerically the equal-area law for a first order phase transition in order to further characterize the Van der Waals-like phase transition.
Phase transition of aragonite in abalone nacre

NASA Astrophysics Data System (ADS)

An, Yuanlin; Liu, Zhiming; Wu, Wenjian

2013-04-01

Nacre is composed of about 95 vol.% aragonite and 5 vol.% biopolymer and famous for its "brick and mortar" microstructure. The phase transition temperature of aragonite in nacre is lower than the pure aragonite. In situ XRD was used to identify the phase transition temperature from aragonite to calcite in nacre, based on the analysis of TG-DSC of fresh nacre and demineralized nacre. The results indicate that the microstructure and biopolymer are the two main factors that influence the phase transition temperature of aragonite in nacre.
Superfluid Black Holes.

PubMed

Hennigar, Robie A; Mann, Robert B; Tjoa, Erickson

2017-01-13

We present what we believe is the first example of a "λ-line" phase transition in black hole thermodynamics. This is a line of (continuous) second order phase transitions which in the case of liquid ^{4}He marks the onset of superfluidity. The phase transition occurs for a class of asymptotically anti-de Sitter hairy black holes in Lovelock gravity where a real scalar field is conformally coupled to gravity. We discuss the origin of this phase transition and outline the circumstances under which it (or generalizations of it) could occur.
Superfluid Black Holes

NASA Astrophysics Data System (ADS)

Hennigar, Robie A.; Mann, Robert B.; Tjoa, Erickson

2017-01-01

We present what we believe is the first example of a "λ -line" phase transition in black hole thermodynamics. This is a line of (continuous) second order phase transitions which in the case of liquid 4He marks the onset of superfluidity. The phase transition occurs for a class of asymptotically anti-de Sitter hairy black holes in Lovelock gravity where a real scalar field is conformally coupled to gravity. We discuss the origin of this phase transition and outline the circumstances under which it (or generalizations of it) could occur.
Colossal magnetic phase transition asymmetry in mesoscale FeRh stripes

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

Uhlir, V.; Arregi, J. A.; Fullerton, E. E.

Coupled order parameters in phase-transition materials can be controlled using various driving forces such as temperature, magnetic and electric field, strain, spin-polarized currents and optical pulses. Tuning the material properties to achieve efficient transitions would enable fast and low-power electronic devices. Here we show that the first-order metamagnetic phase transition in FeRh films becomes strongly asymmetric in mesoscale structures. In patterned FeRh stripes we observed pronounced supercooling and an avalanche-like abrupt transition from the ferromagnetic to the antiferromagnetic phase, while the reverse transition remains nearly continuous over a broad temperature range. Although modest asymmetry signatures have been found in FeRhmore » films, the effect is dramatically enhanced at the mesoscale. The activation volume of the antiferromagnetic phase is more than two orders of magnitude larger than typical magnetic heterogeneities observed in films. Finally, the collective behaviour upon cooling results from the role of long-range ferromagnetic exchange correlations that become important at the mesoscale and should be a general property of first-order metamagnetic phase transitions.« less
Colossal magnetic phase transition asymmetry in mesoscale FeRh stripes

DOE PAGES

Uhlir, V.; Arregi, J. A.; Fullerton, E. E.

2016-10-11

Coupled order parameters in phase-transition materials can be controlled using various driving forces such as temperature, magnetic and electric field, strain, spin-polarized currents and optical pulses. Tuning the material properties to achieve efficient transitions would enable fast and low-power electronic devices. Here we show that the first-order metamagnetic phase transition in FeRh films becomes strongly asymmetric in mesoscale structures. In patterned FeRh stripes we observed pronounced supercooling and an avalanche-like abrupt transition from the ferromagnetic to the antiferromagnetic phase, while the reverse transition remains nearly continuous over a broad temperature range. Although modest asymmetry signatures have been found in FeRhmore » films, the effect is dramatically enhanced at the mesoscale. The activation volume of the antiferromagnetic phase is more than two orders of magnitude larger than typical magnetic heterogeneities observed in films. Finally, the collective behaviour upon cooling results from the role of long-range ferromagnetic exchange correlations that become important at the mesoscale and should be a general property of first-order metamagnetic phase transitions.« less
Phase diagram of quantum critical system via local convertibility of ground state

PubMed Central

Liu, Si-Yuan; Quan, Quan; Chen, Jin-Jun; Zhang, Yu-Ran; Yang, Wen-Li; Fan, Heng

2016-01-01

We investigate the relationship between two kinds of ground-state local convertibility and quantum phase transitions in XY model. The local operations and classical communications (LOCC) convertibility is examined by the majorization relations and the entanglement-assisted local operations and classical communications (ELOCC) via Rényi entropy interception. In the phase diagram of XY model, LOCC convertibility and ELOCC convertibility of ground-states are presented and compared. It is shown that different phases in the phase diagram of XY model can have different LOCC or ELOCC convertibility, which can be used to detect the quantum phase transition. This study will enlighten extensive studies of quantum phase transitions from the perspective of local convertibility, e.g., finite-temperature phase transitions and other quantum many-body models. PMID:27381284

Heterogeneous nucleation and growth dynamics in the light-induced phase transition in vanadium dioxide

DOE PAGES

Brady, Nathaniel F.; Appavoo, Kannatassen; Seo, Minah; ...

2016-03-02

Here we report on ultrafast optical investigations of the light-induced insulator-to-metal phase transition in vanadium dioxide with controlled disorder generated by substrate mismatch. These results reveal common dynamics of this optically-induced phase transition that are independent of this disorder. Lastly, above the fluence threshold for completing the transition to the rutile crystalline phase, we find a common time scale, independent of sample morphology, of 40.5 ± 2 ps that is consistent with nucleation and growth dynamics of the R phase from the parent M1 ground state.
Fluctuation driven electroweak phase transition

NASA Technical Reports Server (NTRS)

Gleiser, Marcelo; Kolb, Edward W.

1991-01-01

We examine the dynamics of the electroweak phase transition in the early Universe. For Higgs masses in the range 46 less than or = M sub H less than or = 150 GeV and top quark masses less than 200 GeV, regions of symmetric and asymmetric vacuum coexist to below the critical temperature, with thermal equilibrium between the two phases maintained by fluctuations of both phases. We propose that the transition to the asymmetric vacuum is completed by percolation of these subcritical fluctuations. Our results are relevant to scenarios of baryogenesis that invoke a weakly first-order phase transition at the electroweak scale.
Fluctuation-driven electroweak phase transition. [in early universe

NASA Technical Reports Server (NTRS)

Gleiser, Marcelo; Kolb, Edward W.

1992-01-01

We examine the dynamics of the electroweak phase transition in the early Universe. For Higgs masses in the range 46 less than or = M sub H less than or = 150 GeV and top quark masses less than 200 GeV, regions of symmetric and asymmetric vacuum coexist to below the critical temperature, with thermal equilibrium between the two phases maintained by fluctuations of both phases. We propose that the transition to the asymmetric vacuum is completed by percolation of these subcritical fluctuations. Our results are relevant to scenarios of baryogenesis that invoke a weakly first-order phase transition at the electroweak scale.
Crystalline Structure and Vacancy Ordering across a Surface Phase Transition in Sn/Cu(001).

PubMed

Martínez-Blanco, J; Joco, V; Quirós, C; Segovia, P; Michel, E G

2018-01-18

We report a surface X-ray diffraction study of the crystalline structure changes and critical behavior across the (3√2 × √2)R45° → (√2 × √2)R45° surface phase transition at 360 K for 0.5 monolayers of Sn on Cu(100). The phase transition is of the order-disorder type and is due to the disordering of the Cu atomic vacancies present in the low temperature phase. Two different atomic sites for Sn atoms, characterized by two different heights, are maintained across the surface phase transition.
Direct evidence of an incommensurate phase in NaNbO{sub 3} and its implication in NaNbO{sub 3}-based lead-free antiferroelectrics

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

Guo, Hanzheng; Randall, Clive A., E-mail: car4@psu.edu; Shimizu, Hiroyuki

2015-09-14

Hot-stage in situ transmission electron microscopy was employed to investigate the temperature-induced complex sequence of phase transitions in NaNbO{sub 3} polycrystalline. In addition to the commonly recognized P (Pbma) → R (Pmnm) → S (Pnmm) phase transitions, incommensurate phases were observed to exist in P and R phase regions. The former (in the P → R transition region) is coincident with a diffused dielectric peak appearing at ∼170 °C, and the latter (in the R → S transition region) serves as an intermediate structure to bridge the two sub-phases in the R phase region. The incommensurate phase in the P phasemore » region can be inferred from the polarization current density and differential dielectric permittivity anomalies, and it provides the bridge structure during the electric field-induced polarization reversal and antiferroelectric-to-ferroelectric transition in NaNbO{sub 3} solid solutions.« less
Phase transitions in a system of hard rectangles on the square lattice

NASA Astrophysics Data System (ADS)

Kundu, Joyjit; Rajesh, R.

2014-05-01

The phase diagram of a system of monodispersed hard rectangles of size m ×mk on a square lattice is numerically determined for m =2,3 and aspect ratio k =1,2,...,7. We show the existence of a disordered phase, a nematic phase with orientational order, a columnar phase with orientational and partial translational order, and a solidlike phase with sublattice order, but no orientational order. The asymptotic behavior of the phase boundaries for large k is determined using a combination of entropic arguments and a Bethe approximation. This allows us to generalize the phase diagram to larger m and k, showing that for k ≥7, the system undergoes three entropy-driven phase transitions with increasing density. The nature of the different phase transitions is established and the critical exponents for the continuous transitions are determined using finite size scaling.
Pressure-Induced Phase Transitions of n-Tridecane

NASA Astrophysics Data System (ADS)

Yamashita, Motoi

Pressure-induced phase transition behavior of n-tridecane from the ordered phase through the rotator phase into the liquid phase has been investigated by using Fourier transform infrared spectroscopy at 25 °C. The transition between the ordered and rotator phases has been observed in the pressure range of 270-220 MPa and the transition between the rotator and liquid phases has been observed in the pressure range of 171-112 MPa, within the experimental error of ±50 MPa. The populations of the -gtg- + -gtg'-, -gg- and gt- defects determined from the methylene wagging mode are smaller in the rotator phase than in the liquid phase and are smaller under higher pressure in both of the rotator and liquid phases. A relationship has been found between the conformation and the intensity of the 890 cm-1 band, which has been assigned as the methyl rocking mode and has been considered as insensitive to conformation.
Observation of the Quantum Anomalous Hall Insulator to Anderson Insulator Quantum Phase Transition and its Scaling Behavior.

PubMed

Chang, Cui-Zu; Zhao, Weiwei; Li, Jian; Jain, J K; Liu, Chaoxing; Moodera, Jagadeesh S; Chan, Moses H W

2016-09-16

Fundamental insight into the nature of the quantum phase transition from a superconductor to an insulator in two dimensions, or from one plateau to the next or to an insulator in the quantum Hall effect, has been revealed through the study of its scaling behavior. Here, we report on the experimental observation of a quantum phase transition from a quantum-anomalous-Hall insulator to an Anderson insulator in a magnetic topological insulator by tuning the chemical potential. Our experiment demonstrates the existence of scaling behavior from which we extract the critical exponent for this quantum phase transition. We expect that our work will motivate much further investigation of many properties of quantum phase transition in this new context.
Topological phase transition in the quench dynamics of a one-dimensional Fermi gas with spin-orbit coupling

NASA Astrophysics Data System (ADS)

Wang, Pei; Yi, Wei; Xianlong, Gao

2015-01-01

We study the quench dynamics of a one-dimensional ultracold Fermi gas with synthetic spin-orbit coupling. At equilibrium, the ground state of the system can undergo a topological phase transition and become a topological superfluid with Majorana edge states. As the interaction is quenched near the topological phase boundary, we identify an interesting dynamical phase transition of the quenched state in the long-time limit, characterized by an abrupt change of the pairing gap at a critical quenched interaction strength. We further demonstrate the topological nature of this dynamical phase transition from edge-state analysis of the quenched states. Our findings provide interesting clues for the understanding of topological phase transitions in dynamical processes, and can be useful for the dynamical detection of Majorana edge states in corresponding systems.
Possible higher order phase transition in large-N gauge theory at finite temperature

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

Nishimura, Hiromichi

2017-08-07

We analyze the phase structure of SU(¥) gauge theory at finite temperature using matrix models. Our basic assumption is that the effective potential is dominated by double-trace terms for the Polyakov loops. As a function of the temperature, a background field for the Polyakov loop, and a quartic coupling, it exhibits a universal structure: in the large portion of the parameter space, there is a continuous phase transition analogous to the third-order phase transition of Gross,Witten and Wadia, but the order of phase transition can be higher than third. We show that different confining potentials give rise to drastically differentmore » behavior of the eigenvalue density and the free energy. Therefore lattice simulations at large N could probe the order of phase transition and test our results. Critical« less
On the thermodynamics of the black hole and hairy black hole transitions in the asymptotically flat spacetime with a box

NASA Astrophysics Data System (ADS)

Peng, Yan; Wang, Bin; Liu, Yunqi

2018-03-01

We study the asymptotically flat quasi-local black hole/hairy black hole model with nonzero mass of the scalar field. We disclose effects of the scalar mass on transitions in a grand canonical ensemble with condensation behaviors of the parameter ψ 2, which is similar to approaches in holographic theories. We find that a more negative scalar mass makes the phase transition easier. We also obtain the analytical relation ψ 2∝ (Tc-T)^{1/2} around the critical phase transition points, implying a second order phase transition. Besides the parameter ψ 2, we show that metric solutions can be used to disclose properties of the transitions. In this work, we observe that phase transitions in a box are strikingly similar to holographic transitions in AdS gravity and the similarity provides insights into holographic theories.
Density functional theory studies on the solvent effects in Al(H2O)63+ water-exchange reactions: the number and arrangement of outer-sphere water molecules.

PubMed

Liu, Li; Zhang, Jing; Dong, Shaonan; Zhang, Fuping; Wang, Ye; Bi, Shuping

2018-03-07

Density functional theory (DFT) calculations combined with cluster models are performed at the B3LYP/6-311+G(d,p) level for investigating the solvent effects in Al(H 2 O) 6 3+ water-exchange reactions. A "One-by-one" method is proposed to obtain the most representative number and arrangement of explicit H 2 Os in the second hydration sphere. First, all the possible ways to locate one explicit H 2 O in second sphere (N m ' = 1) based on the gas phase structure (N m ' = 0) are examined, and the optimal pathway (with the lowest energy barrier) for N m ' = 1 is determined. Next, more explicit H 2 Os are added one by one until the inner-sphere is fully hydrogen bonded. Finally, the optimal pathways with N m ' = 0-7 are obtained. The structural and energetic parameters as well as the lifetimes of the transition states are compared with the results obtained with the "Independent-minimum" method and the "Independent-average" method, and all three methods show that the pathway with N m ' = 6 may be representative. Our results give a new idea for finding the representative pathway for water-exchange reactions in other hydrated metal ion systems.
DOE Office of Scientific and Technical Information (OSTI.GOV)

Huang, Er-Wen; Department of Forensic Pathology, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou; Xue, Sheng-Jiang

Highlights: • Levels of EEN expression paralleled with the rate of cell proliferation. • EEN was involved in the proliferation and survival of multiple myeloma (MM) cells. • EEN regulated the activity of IGF-1-Akt/mTOR pathway. • EEN regulated proliferation and survival of MM cells by enhancing IGF-1 secretion. - Abstract: The molecular mechanisms of multiple myeloma are not well defined. EEN is an endocytosis-regulating molecule. Here we report that EEN regulates the proliferation and survival of multiple myeloma cells, by regulating IGF-1 secretion. In the present study, we observed that EEN expression paralleled with cell proliferation, EEN accelerated cell proliferation,more » facilitated cell cycle transition from G1 to S phase by regulating cyclin-dependent kinases (CDKs) pathway, and delayed cell apoptosis via Bcl2/Bax-mitochondrial pathway. Mechanistically, we found that EEN was indispensable for insulin-like growth factor-1 (IGF-1) secretion and the activation of protein kinase B-mammalian target of rapamycin (Akt-mTOR) pathway. Exogenous IGF-1 overcame the phenotype of EEN depletion, while IGF-1 neutralization overcame that of EEN over-expression. Collectively, these data suggest that EEN may play a pivotal role in excessive cell proliferation and insufficient cell apoptosis of bone marrow plasma cells in multiple myeloma. Therefore, EEN may represent a potential diagnostic marker or therapeutic target for multiple myeloma.« less
A Comparison of Transition Predictors between Students Following Different Diploma Pathways

ERIC Educational Resources Information Center

Vierno, Peter Joseph

2013-01-01

The purpose of this study was to determine the extent to which evidence of two secondary transition predictors, paid employment and independent living, exist in the Individualized Education Plans (IEPs) of students on two pathways to a high school diploma in a southeastern state. The IEPs of 538 students were examined from one urban district in…
Giant elastic tunability in strained BiFeO 3 near an electrically induced phase transition

DOE PAGES

Yu, Pu; Vasudevan, Rama K.; Tselev, Alexander; ...

2015-11-24

Elastic anomalies are signatures of phase transitions in condensed matters and have traditionally been studied using various techniques spanning from neutron scattering to static mechanical testing. Here, using band-excitation elastic/piezoresponse spectroscopy, we probed sub-MHz elastic dynamics of a tip bias-induced rhombohedral–tetragonal phase transition of strained (001)-BiFeO 3 (rhombohedral) ferroelectric thin films from ~10 3 nm 3 sample volumes. Near this transition, we observed that the Young's modulus intrinsically softens by over 30% coinciding with 2-3 folds enhancement of local piezoresponse. Coupled with phase-field modeling, we also addressed the influence of polarization switching and mesoscopic structural heterogeneities (e.g., domain walls) onmore » the kinetics of this phase transition, thereby providing fresh insights into the morphotropic phase boundary (MPB) in ferroelectrics. Moreover, the giant electrically tunable elastic stiffness and corresponding electromechanical properties observed here suggest potential applications of BiFeO 3 in next-generation frequency-agile electroacoustic devices, based on utilization of the soft modes underlying successive ferroelectric phase transitions.« less
The deconfining phase transition in and out of equilibrium

NASA Astrophysics Data System (ADS)

Bazavov, Oleksiy

Recent experiments carried out at the Relativistic Heavy Ion Collider at the Brookhaven National Laboratory provide strong evidence that a matter can be driven from a confined, low-temperature phase, observed in our every day world into a deconfined high-temperature phase of liberated quarks and gluons. The equilibrium and dynamical properties of the deconfining phase transition are thus of great theoretical interest, since they also provide an information about the first femtoseconds of the evolution of our Universe, when the hot primordial soup while cooling has undergone a chain of phase transitions. The aspects of the deconfining phase transition studied in this work include: the dynamics of the SU(3) gauge theory after the heating quench (which models rapid heating in the heavy-ion collisions), equilibrium properties of the phase transition in the SU(3) gauge theory with boundaries at low temperature (small volumes at RHIC suggest that boundary effects cannot be neglected and periodic boundary conditions normally used in lattice simulations do not correspond to the experimental situation), and a study of the order of the transition in U(1) gauge theory.
Quantum tricritical point in the temperature-pressure-magnetic field phase diagram of CeTiGe 3

DOE PAGES

Kaluarachchi, Udhara S.; Taufour, Valentin; Bud'ko, Sergey L.; ...

2018-01-22

We report the temperature-pressure-magnetic eld phase diagram of the ferromagnetic Kondolattice CeTiGe 3 determined by means of electrical resistivity measurements. Measurements up to ~5.8GPa reveal a rich phase diagram with multiple phase transitions. At ambient pressure, CeTiGe 3 orders ferromagnetically at T C =14 K. Application of pressure suppresses T C, but a pressure induced ferromagnetic quantum criticality is avoided by the appearance of two new successive transitions for p>4.1GPa that are probably antiferromagnetic in nature. These two transitions are suppressed under pressure, with the lower temperature phase being fully suppressed above 5.3GPa. The critical pressures for the presumed quantummore » phase transitions are p1≅4.1GPa and p2≅5.3GPa. Above 4.1GPa, application of magnetic eld shows a tricritical point evolving into a wing structure phase with a quantum tricritical point at 2.8T at 5.4GPa, where the rst order antiferromagneticferromagnetic transition changes into the second order antiferromagnetic-ferromagnetic transition.« less
Giant elastic tunability in strained BiFeO3 near an electrically induced phase transition

PubMed Central

Li, Q; Cao, Y.; Yu, P.; Vasudevan, R. K.; Laanait, N.; Tselev, A.; Xue, F.; Chen, L. Q.; Maksymovych, P.; Kalinin, S. V.; Balke, N.

2015-01-01

Elastic anomalies are signatures of phase transitions in condensed matters and have traditionally been studied using various techniques spanning from neutron scattering to static mechanical testing. Here, using band-excitation elastic/piezoresponse spectroscopy, we probed sub-MHz elastic dynamics of a tip bias-induced rhombohedral−tetragonal phase transition of strained (001)-BiFeO3 (rhombohedral) ferroelectric thin films from ∼103 nm3 sample volumes. Near this transition, we observed that the Young's modulus intrinsically softens by over 30% coinciding with two- to three-fold enhancement of local piezoresponse. Coupled with phase-field modelling, we also addressed the influence of polarization switching and mesoscopic structural heterogeneities (for example, domain walls) on the kinetics of this phase transition, thereby providing fresh insights into the morphotropic phase boundary in ferroelectrics. Furthermore, the giant electrically tunable elastic stiffness and corresponding electromechanical properties observed here suggest potential applications of BiFeO3 in next-generation frequency-agile electroacoustic devices, based on the utilization of the soft modes underlying successive ferroelectric phase transitions. PMID:26597483
Shock loading and release behavior of silicon nitride

NASA Astrophysics Data System (ADS)

Kawai, N.; Tsuru, T.; Hidaka, N.; Liu, X.; Mashimo, T.

2017-01-01

Shock-reshock and shock-release experiments were performed on silicon nitride ceramics above and below its phase transition pressure. Experimental results clearly show the occurrence of elastic-plastic transition and phase transition during initial shock loading. The HEL and phase transition stress are determined as 11.6 and 34.5 GPa, respectively. Below the phase transition stress, the reshock profile consists of the single shock with short rise time, while the release profile shows the gradual release followed by rapid one. Above phase transition stress, reshock and release behavior varies with the initial shock stress. In the case of reshock and release from about 40 GPa, the reshock structure is considerably dispersed, while the release structure shows rapid release. In the reshock profile from about 50 GPa, the formation of the shock wave with the small ramped precursor is observed. And, the release response from same shocked condition shows initial gradual release and subsequent quite rapid one. These results would provide the information about how phase transformation kinetics effects on the reshock and release behavior.
DOE Office of Scientific and Technical Information (OSTI.GOV)

Kaluarachchi, Udhara S.; Taufour, Valentin; Bud'ko, Sergey L.

We report the temperature-pressure-magnetic eld phase diagram of the ferromagnetic Kondolattice CeTiGe 3 determined by means of electrical resistivity measurements. Measurements up to ~5.8GPa reveal a rich phase diagram with multiple phase transitions. At ambient pressure, CeTiGe 3 orders ferromagnetically at T C =14 K. Application of pressure suppresses T C, but a pressure induced ferromagnetic quantum criticality is avoided by the appearance of two new successive transitions for p>4.1GPa that are probably antiferromagnetic in nature. These two transitions are suppressed under pressure, with the lower temperature phase being fully suppressed above 5.3GPa. The critical pressures for the presumed quantummore » phase transitions are p1≅4.1GPa and p2≅5.3GPa. Above 4.1GPa, application of magnetic eld shows a tricritical point evolving into a wing structure phase with a quantum tricritical point at 2.8T at 5.4GPa, where the rst order antiferromagneticferromagnetic transition changes into the second order antiferromagnetic-ferromagnetic transition.« less

The Stefan problem of solidification of ternary systems in the presence of moving phase transition regions

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

Alexandrov, D. V., E-mail: Dmitri.Alexandrov@usu.ru; Ivanov, A. A.

2009-05-15

The process of solidification of ternary systems in the presence of moving phase transition regions has been investigated theoretically in terms of the nonlinear equation of the liquidus surface. A mathematical model is developed and an approximate analytical solution to the Stefan problem is constructed for a linear temperature profile in two-phase zones. The temperature and impurity concentration distributions are determined, the solid-phase fractions in the phase transition regions are obtained, and the laws of motion of their boundaries are established. It is demonstrated that all boundaries move in accordance with the laws of direct proportionality to the square rootmore » of time, which is a general property of self-similar processes. It is substantiated that the concentration of an impurity of the substance undergoing a phase transition only in the cotectic zone increases in this zone and decreases in the main two-phase zone in which the other component of the substance undergoes a phase transition. In the process, the concentration reaches a maximum at the interface between the main two-phase zone and the cotectic two-phase zone. The revealed laws of motion of the outer boundaries of the entire phase transition region do not depend on the amount of the components under consideration and hold true for crystallization of a multicomponent system.« less
Exploring Polarization Rotation Phase Instabilities in Super-Tetragonal BiFeO3 Epitaxial Thin Films and Their Technological Implications

DOE PAGES

Cao, Ye; Yang, Mr. Shuzhen; Jesse, Stephen; ...

2016-01-01

Many functional properties of ferroelectrics are underlain by structural instabilities, which render these materials very susceptible to small alternating applied fields (electric, mechanical, etc.) through certain constitutive coupling relations, e.g., elastic compliance and piezoelectric response, and often such instabilities can be shifted by static applied fields thus meaning tunable dynamic properties. Structural instabilities are naturally accommodated on the brink of morphotropic phase boundaries (MPB s) where multiple phases of small energy difference coexist in different crystallographic forms. Canonical MPB is realized through compositional mixture, as is typically exemplified by Pb(Zr1-xTix)O3 solid solutions and relaxor ferroelectrics of (1-x)PbMg1/3Nb2/3O3-xPbTiO3. More recently, amore » strain-driven MPB has been discovered in BiFeO3 (BFO) thin films epitaxially grown on LaAlO3 (LAO) crystal substrates (which imposes about -4.5% in-plane strains). Such an MPB is in between a rhombohedral (R) phase that bulk BFO exhibits and a so-called super-tetragonal (T) phase, which name hints at its giant lattice axial ratio (c/a ~ 1.23) and accordingly high electric polarization (~1.5 C m-2). The discovery of an MPB in BFO has revealed another facet of this multiferroic system, further adding opportunities to its many exotic functionalities such as domain wall conduction, magnetoelectric and photovoltaic effects As with other MPB s, large electric-field induced strains as well as more underlying lattice softening effects are observed near this MPB promising piezoelectric-based applications. In addition, T-phase BFO itself shows distinct properties, e.g., electronic band gap and optical absorption, from the R-phase and the resultant switching effects between them may also be exploitable. However, unlike conventional ferroelectric oxides where the phases across an MPB usually have subtle difference caused by rotations of an ion off-centering polarization, the BFO system bears multiple structural degrees of freedom, in particular antiferrodistortive modes of oxygen octahedral tilt, and a multitude of structural transition paths are thereby facilitated. Moreover, since the MPB of BFO is driven by epitaxial strain, it is sensitive to the strain relaxation related to film thickness and growth conditions, and above some critical thickness the films appear in the form of a hierarchical mixed-phase microstructure involving several coexistent polymorphs with distinct lattice distortion (monoclinic phases) and tilts. Elastic and electrical heterogeneities are necessary consequences of such complex microstructure, which couple to the intrinsic order parameters and expectedly have profound influence on the structural dynamics and material properties. All these make it a demanding task to obtain a deep understanding of this MPB system on par with its application prospect. The thin-film material form also brings in experimental restrictions to the MPB phase transition studies of BFO since many pertinent techniques fail to operate at the nanoscale or suffer from formidably weak signals. Therefore, static structural characterizations using e.g. X-ray diffraction, electron microscopy and Raman scattering have prevailed thus far. Recently, we adapted band-excitation piezoresponse spectroscopy (BEPS) to probe the bias-induced R/T phase transition dynamics of BFO/SrTiO3 (STO) thin films, and revealed the soft-mode elastic behavior of the transition. The efficacy of our method, along with standard piezoresponse force microscopy (PFM), can be significantly leveraged by integrating a variety of local and/or global excitations, e.g., tip pressure (10 s GPa attainable), heating, photo-irradiation, available to modern scanning probe platforms. This can thus afford unique opportunities to survey the structural dynamics of ferroelectric materials coupled to those field variables, enabling rapid discovery or validation of their functional properties. In this study, we focus on the T-phase BFO/LAO system; we have examined its phase transition behavior not only due to local coaction of tip bias and loading force, but also under device-level global electric fields in a coplanar capacitor. The intrinsic elastic softening phenomena near the structural transitions are comprehensively revealed by BEPS and corroborated by phase-field modeling. Our findings may open a new pathway for technological utilization of the MPB phase instabilities of BFO.« less
Third Law of Thermodynamics and The Shape of the Phase Diagram for Systems With a First-Order Quantum Phase Transition.

PubMed

Kirkpatrick, T R; Belitz, D

2015-07-10

The third law of thermodynamics constrains the phase diagram of systems with a first-order quantum phase transition. For a zero conjugate field, the coexistence curve has an infinite slope at T=0. If a tricritical point exists at T>0, then the associated tricritical wings are perpendicular to the T=0 plane, but not to the zero-field plane. These results are based on the third law and basic thermodynamics only, and are completely general. As an explicit example we consider the ferromagnetic quantum phase transition in clean metals, where a first-order quantum phase transition is commonly observed.
Phase Transitions in Antibody Solutions: from Pharmaceuticals to Human Disease

NASA Astrophysics Data System (ADS)

Wang, Ying; Lomakin, Aleksey; Benedek, George; Dana Farber Cancer Institute Collaboration; Amgen Inc. Collaboration

2014-03-01

Antibodies are very important proteins. Natural antibodies play essential role in the immune system of human body. Pharmaceutical antibodies are used as drugs. Antibodies are also indispensable tools in biomedical research and diagnostics. Recently, a number of observations of phase transitions of pharmaceutical antibodies have been reported. These phase transitions are undesirable from the perspective of colloid stability of drug solutions in processing and storage, but can be used for protein purification, X-ray crystallography, and improving pharmokinetics of drugs. Phase transitions of antibodies can also take place in human body, particularly in multiple myeloma patients who overproduce monoclonal antibodies. These antibodies, in some cases, crystallize at body temperature and cause severe complications called cryoglobulinemia. I will present the results of our current studies on phase transitions of both pharmaceutical antibodies and cryoglobulinemia-associated antibodies. These studies have shown that different antibodies have different propensity to undergo phase transitions, but their phase behavior has universal features which are remarkably different from those of spherical proteins. I will discuss how studies of phase behavior can be useful in assessing colloid stability of pharmaceutical antibodies and in early diagnostics of cryoglobulinemia, as well as general implications of the fact that some antibodies can precipitate at physiological conditions.
Nonlinear two-dimensional terahertz photon echo and rotational spectroscopy in the gas phase.

PubMed

Lu, Jian; Zhang, Yaqing; Hwang, Harold Y; Ofori-Okai, Benjamin K; Fleischer, Sharly; Nelson, Keith A

2016-10-18

Ultrafast 2D spectroscopy uses correlated multiple light-matter interactions for retrieving dynamic features that may otherwise be hidden under the linear spectrum; its extension to the terahertz regime of the electromagnetic spectrum, where a rich variety of material degrees of freedom reside, remains an experimental challenge. We report a demonstration of ultrafast 2D terahertz spectroscopy of gas-phase molecular rotors at room temperature. Using time-delayed terahertz pulse pairs, we observe photon echoes and other nonlinear signals resulting from molecular dipole orientation induced by multiple terahertz field-dipole interactions. The nonlinear time domain orientation signals are mapped into the frequency domain in 2D rotational spectra that reveal J-state-resolved nonlinear rotational dynamics. The approach enables direct observation of correlated rotational transitions and may reveal rotational coupling and relaxation pathways in the ground electronic and vibrational state.
Nanoscale charge distribution and energy band modification in defect-patterned graphene.

PubMed

Wang, Shengnan; Wang, Rui; Wang, Xiaowei; Zhang, Dongdong; Qiu, Xiaohui

2012-04-21

Defects were introduced precisely to exfoliated graphene (G) sheets on a SiO(2)/n(+) Si substrate to modulate the local energy band structure and the electron pathway using solution-phase oxidation followed by thermal reduction. The resulting nanoscale charge distribution and band gap modification were investigated by electrostatic force microscopy and spectroscopy. A transition phase with coexisting submicron-sized metallic and insulating regions in the moderately oxidized monolayer graphene were visualized and measured directly. It was determined that the delocalization of electrons/holes in a graphene "island" is confined by the surrounding defective C-O matrix, which acts as an energy barrier for mobile charge carriers. In contrast to the irreversible structural variations caused by the oxidation process, the electrical properties of graphene can be restored by annealing. The defect-patterned graphene and graphene oxide heterojunctions were further characterized by electrical transport measurement.
Pressure-induced polymerization of P(CN) 3

DOE PAGES

Gou, Huiyang; Yonke, Brendan L.; Epshteyn, Albert; ...

2015-05-21

Motivated to explore the formation of novel extended carbon-nitrogen solids via well-defined molecular precursor pathways, we studied the chemical reactivity of highly pure phosphorous tricyanide, P(CN) 3, under conditions of high pressure at room temperature. Raman and infrared (IR) spectroscopic measurements reveal a series of phase transformations below 10 GPa, and several low-frequency vibrational modes are reported for the first time. Synchrotron powder Xray diffraction (PXRD) measurements taken during compression show that molecular P(CN) 3 is highly compressible with a bulk modulus of 10.0±0.3 GPa and polymerizes into an amorphous solid above ~10.0 GPa. Raman and infrared (IR) spectra, togethermore » with first-principles molecular-dynamics simulations, show that the amorphization transition is associated with polymerization of the cyanide groups into CN bonds with predominantly sp 2 character, similar to known carbon nitrides, resulting in a novel PCN polymeric phase, which is recoverable to ambient pressure.« less
Course 6: Physics of Composite Cell Membrane and Actin Based Cytoskeleton

NASA Astrophysics Data System (ADS)

Sackmann, E.; Bausch, A. R.; Vonna, L.

1 Architecture of composite cell membranes 1.1 The lipid/protein bilayer is a multicomponent smectic phase with mosaic like architecture 1.2 The spectrin/actin cytoskeleton as hyperelastic cell stabilizer 1.3 The actin cortex: Architecture and function 2 Physics of the actin based cytoskeleton 2.1 Actin is a living semiflexible polymer 2.2 Actin network as viscoelastic body 2.3 Correlation between macroscopic viscoelasticity and molecular 3 Heterogeneous actin gels in cells and biological function 3.1 Manipulation of actin gels 3.2 Control of organization and function of actin cortex by cell signalling 4 Micromechanics and microrheometry of cells 5 Activation of endothelial cells: On the possibility of formation of stress fibers as phase transition of actin-network triggered by cell signalling pathways 6 On cells as adaptive viscoplastic bodies 7 Controll of cellular protrusions controlled by actin/myosin cortex
Observation of polyamorphism in the phase change alloy Ge1Sb2Te4

NASA Astrophysics Data System (ADS)

Kalkan, B.; Sen, S.; Cho, J.-Y.; Joo, Y.-C.; Clark, S. M.

2012-10-01

A high-pressure synchrotron x-ray diffraction study of the phase change alloy Ge1Sb2Te4 demonstrates the existence of a polyamorphic phase transition between the "as deposited" low density amorphous (LDA) phase and a high density amorphous (HDA) phase at ˜10 GPa. The entropy of the HDA phase is expected to be higher than that of the LDA phase resulting in a negative Clapeyron slope for this transition. These phase relations may enable the polyamorphic transition to play a role in the memory and data storage applications.
First-order inflation

NASA Technical Reports Server (NTRS)

Kolb, Edward W.

1991-01-01

In the original proposal, inflation occurred in the process of a strongly first-order phase transition. This model was soon demonstrated to be fatally flawed. Subsequent models for inflation involved phase transitions that were second-order, or perhaps weakly first-order; some even involved no phase transition at all. Recently the possibility of inflation during a strongly first-order phase transition has been revived. In this talk I will discuss some models for first-order inflation, and emphasize unique signatures that result if inflation is realized in a first-order transition. Before discussing first-order inflation, I will briefly review some of the history of inflation to demonstrate how first-order inflation differs from other models.
First-order inflation. [in cosmology

NASA Technical Reports Server (NTRS)

Kolb, Edward W.

1991-01-01

In the original proposal, inflation occurred in the process of a strongly first-order phase transition. This model was soon demonstrated to be fatally flawed. Subsequent models for inflation involved phase transitions that were second-order, or perhaps weakly first-order; some even involved no phase transition at all. Recently the possibility of inflation during a strongly first-order phase transition has been revived. In this paper, some models for first-order inflation are discussed, and unique signatures that result if inflation is realized in a first-order transition are emphasized. Some of the history of inflation is reviewed to demonstrate how first-order inflation differs from other models.
NASA/SPAN and DOE/ESnet-DECnet transition strategy for DECnet OSI/phase 5

NASA Technical Reports Server (NTRS)

Porter, Linda; Demar, Phil

1991-01-01

The technical issues are examined involved with the transition of very large DECnet networks from DECnet phase IV protocols to DECnet OSI/Phase V protocols. The networks involved are the NASA's Science Internet (NSI-DECnet) and the DOE's Energy Science network (ESnet-DECnet). These networks, along with the many universities and research institutions connected to them, combine to form a single DECnet network containing more than 20,000 transitions and crossing numerous organizational boundaries. Discussion of transition planning, including decisions about Phase V naming, addressing, and routing are presented. Also discussed are transition issues related to the use of non-DEC routers in the network.
Ultrafast evolution and transient phases of a prototype out-of-equilibrium Mott–Hubbard material

DOE PAGES

Lantz, G.; Mansart, B.; Grieger, D.; ...

2017-01-09

Photoexcited strongly correlated materials is attracting growing interest since their rich phase diagram often translates into an equally rich out-of-equilibrium behavior, including non-thermal phases and photoinduced phase transitions. With femtosecond optical pulses, electronic and lattice degrees of freedom can be transiently decoupled, giving the opportunity of stabilizing new states of matter inaccessible by quasi-adiabatic pathways. We present a study of the ultrafast non-equilibrium evolution of the prototype Mott-Hubbard material V 2O 3, which presents a transient non-thermal phase developing immediately after photoexcitation and lasting few picoseconds. For both the insulating and the metallic phase, the formation of the transient configurationmore » is triggered by the excitation of electrons into the bonding a 1g orbital, and is then stabilized by a lattice distortion characterized by a marked hardening of the A 1g coherent phonon. Furthermore, this configuration is in stark contrast with the thermally accessible ones - the A 1g phonon frequency actually softens when heating the material. Our results show the importance of selective electron-lattice interplay for the ultrafast control of material parameters, and are of particular relevance for the optical manipulation of strongly correlated systems, whose electronic and structural properties are often strongly intertwinned.« less
Ultrafast evolution and transient phases of a prototype out-of-equilibrium Mott–Hubbard material

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

Lantz, G.; Mansart, B.; Grieger, D.

Photoexcited strongly correlated materials is attracting growing interest since their rich phase diagram often translates into an equally rich out-of-equilibrium behavior, including non-thermal phases and photoinduced phase transitions. With femtosecond optical pulses, electronic and lattice degrees of freedom can be transiently decoupled, giving the opportunity of stabilizing new states of matter inaccessible by quasi-adiabatic pathways. We present a study of the ultrafast non-equilibrium evolution of the prototype Mott-Hubbard material V 2O 3, which presents a transient non-thermal phase developing immediately after photoexcitation and lasting few picoseconds. For both the insulating and the metallic phase, the formation of the transient configurationmore » is triggered by the excitation of electrons into the bonding a 1g orbital, and is then stabilized by a lattice distortion characterized by a marked hardening of the A 1g coherent phonon. Furthermore, this configuration is in stark contrast with the thermally accessible ones - the A 1g phonon frequency actually softens when heating the material. Our results show the importance of selective electron-lattice interplay for the ultrafast control of material parameters, and are of particular relevance for the optical manipulation of strongly correlated systems, whose electronic and structural properties are often strongly intertwinned.« less
Finite-temperature phase transitions of third and higher order in gauge theories at large N

DOE PAGES

Nishimura, Hiromichi; Pisarski, Robert D.; Skokov, Vladimir V.

2018-02-15

We study phase transitions in SU(∞) gauge theories at nonzero temperature using matrix models. Our basic assumption is that the effective potential is dominated by double trace terms for the Polyakov loops. As a function of the various parameters, related to terms linear, quadratic, and quartic in the Polyakov loop, the phase diagram exhibits a universal structure. In a large region of this parameter space, there is a continuous phase transition whose order is larger than second. This is a generalization of the phase transition of Gross, Witten, and Wadia (GWW). Depending upon the detailed form of the matrix model,more » the eigenvalue density and the behavior of the specific heat near the transition differ drastically. Here, we speculate that in the pure gauge theory, that although the deconfining transition is thermodynamically of first order, it can be nevertheless conformally symmetric at infnite N.« less
Finite-temperature phase transitions of third and higher order in gauge theories at large N

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

Nishimura, Hiromichi; Pisarski, Robert D.; Skokov, Vladimir V.

We study phase transitions in SU(∞) gauge theories at nonzero temperature using matrix models. Our basic assumption is that the effective potential is dominated by double trace terms for the Polyakov loops. As a function of the various parameters, related to terms linear, quadratic, and quartic in the Polyakov loop, the phase diagram exhibits a universal structure. In a large region of this parameter space, there is a continuous phase transition whose order is larger than second. This is a generalization of the phase transition of Gross, Witten, and Wadia (GWW). Depending upon the detailed form of the matrix model,more » the eigenvalue density and the behavior of the specific heat near the transition differ drastically. Here, we speculate that in the pure gauge theory, that although the deconfining transition is thermodynamically of first order, it can be nevertheless conformally symmetric at infnite N.« less
Horava-Lifshitz cosmology, entropic interpretation and quark-hadron phase transition

NASA Astrophysics Data System (ADS)

Kheyri, F.; Khodadi, M.; Sepangi, Hamid Reza

2013-05-01

Based on the assumptions of the standard model of cosmology, a phase transition associated with chiral symmetry breaking after the electroweak transition has occurred at approximately 10 μs after the Big Bang to convert a plasma of free quarks and gluons into hadrons. We consider such a phase transition in the context of a deformed Horava-Lifshitz cosmology. The Friedmann equation for the deformed Horava-Lifshitz universe is obtained using the entropic interpretation of gravity, proposed by Verlinde. We investigate the effects of the parameter ω appearing in the theory on the evolution of the physical quantities relevant to a description of the early universe, namely, the energy density and temperature before, during and after the phase transition. Finally, we study the cross-over phase transition in both high and low temperature regions in view of the recent lattice QCD simulations data.
Reconstructive phase transition in (NH4)3TiF7 accompanied by the ordering of TiF6 octahedra.

PubMed

Molokeev, Maxim; Misjul, S V; Flerov, I N; Laptash, N M

2014-12-01

An unusual phase transition P4/mnc → Pa\\bar 3 has been detected after cooling the (NH4)3TiF7 compound. Some TiF6 octahedra, which are disordered in the room-temperature tetragonal structure, become ordered in the low-temperature cubic phase due to the disappearance of the fourfold axis. Other TiF6 octahedra undergo large rotations resulting in huge displacements of the F atoms by 1.5-1.8 Å that implies a reconstructive phase transition. It was supposed that phases P4/mbm and Pm\\bar 3m could be a high-temperature phase and a parent phase, respectively, in (NH4)3TiF7. Therefore, the sequence of phase transitions can be written as Pm\\bar 3m → P4/mbm → P4/mnc → Pa\\bar 3. The interrelation between (NH4)3TiF7, (NH4)3GeF7 and (NH4)3PbF7 is found, which allows us to suppose phase transitions in relative compounds.
The orthorhombic to high-P monoclinic phase transition in Mg-Fe Pyroxenes: Can it produce a seismic discontinuity?

NASA Astrophysics Data System (ADS)

Woodland, Alan B.

The orthorhombic to high-P monoclinic phase transition in (Mg,Fe)SiO3 pyroxene with a mantle-relevant composition (XFs = 0.1) is expected to occur at ˜300 km depth [Woodland and Angel, 1997]. However, the divariant nature of the phase transition in the Mg-Fe system leaves the question open as to whether this transition occurs over a narrow enough pressure interval to cause a seismic discontinuity. New experimental results with binary Mg-Fe pyroxenes constrain the divariant loop to be 0.2 GPa wide at the composition of XFs = 0.4 and on the order of 0.15 GPa for a mantle-relevant composition. This implies that the phase transition will be complete over a depth interval of about 5-6 km in the mantle and it is concluded that the divariant loop of the orthorhombic to high-P monoclinic phase transition in (Mg,Fe)SiO3 pyroxene is indeed narrow enough to produce a “jump” in seismic velocities. The experimentally observed metastable behavior of orthopyroxene could further reduce the effective depth interval of this phase transition. The expected location of this phase transition coincides with a small magnitude seismic discontinuity, the “X-discontinuity”, occasionally observed in seismic profiles at ˜300 km depth, and thus provides a viable petrologic explanation for the origin of this discontinuity, if it truly exists.
Arabidopsis JAGGED links floral organ patterning to tissue growth by repressing Kip-related cell cycle inhibitors.

PubMed

Schiessl, Katharina; Muiño, Jose M; Sablowski, Robert

2014-02-18

Plant morphogenesis requires coordinated cytoplasmic growth, oriented cell wall extension, and cell cycle progression, but it is debated which of these processes are primary drivers for tissue growth and directly targeted by developmental genes. Here, we used ChIP high-throughput sequencing combined with transcriptome analysis to identify global target genes of the Arabidopsis transcription factor JAGGED (JAG), which promotes growth of the distal region of floral organs. Consistent with the roles of JAG during organ initiation and subsequent distal organ growth, we found that JAG directly repressed genes involved in meristem development, such as CLAVATA1 and HANABA TARANU, and genes involved in the development of the basal region of shoot organs, such as BLADE ON PETIOLE 2 and the GROWTH REGULATORY FACTOR pathway. At the same time, JAG regulated genes involved in tissue polarity, cell wall modification, and cell cycle progression. In particular, JAG directly repressed KIP RELATED PROTEIN 4 (KRP4) and KRP2, which control the transition to the DNA synthesis phase (S-phase) of the cell cycle. The krp2 and krp4 mutations suppressed jag defects in organ growth and in the morphology of petal epidermal cells, showing that the interaction between JAG and KRP genes is functionally relevant. Our work reveals that JAG is a direct mediator between genetic pathways involved in organ patterning and cellular functions required for tissue growth, and it shows that a regulatory gene shapes plant organs by releasing a constraint on S-phase entry.

Akt-mediated phosphorylation of CDK2 regulates its dual role in cell cycle progression and apoptosis.

PubMed

Maddika, Subbareddy; Ande, Sudharsana Rao; Wiechec, Emilia; Hansen, Lise Lotte; Wesselborg, Sebastian; Los, Marek

2008-04-01

Here, we show that CDK2, an S-phase cyclin-dependent kinase, is a novel target for Akt during cell cycle progression and apoptosis. Akt phosphorylates CDK2 at threonine 39 residue both in vitro and in vivo. Although CDK2 threonine 39 phosphorylation mediated by Akt enhances cyclin-A binding, it is dispensable for its basal binding and the kinase activity. In addition, for the first time, we report a transient nucleo-cytoplasmic shuttling of Akt during specific stages of the cell cycle, in particular during the late S and G2 phases. The Akt that is re-localized to the nucleus phosphorylates CDK2 and causes the temporary cytoplasmic localization of the CDK2-cyclin-A complex. The CDK2 cytoplasmic redistribution is required for cell progression from S to G2-M phase, because the CDK2 T39A mutant, which lacks the phosphorylation site and is defective in cytoplasmic localization, severely affects cell cycle progression at the transition from S to G2-M. Interestingly, we also show that the Akt/CDK2 pathway is constitutively activated by some anticancer drugs, such as methotrexate and docetaxel, and under these conditions it promotes, rather than represses, cell death. Thus, the constitutive activation of the Akt/CDK2 pathway and changed subcellular localization promotes apoptosis. By contrast, the transient, physiological Akt/CDK2 activation is necessary for cell cycle progression.
Possible existence of two amorphous phases of D-mannitol related by a first-order transition

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

Zhu, Men; Yu, Lian, E-mail: lian.yu@wisc.edu; Wang, Jun-Qiang

2015-06-28

We report that the common polyalcohol D-mannitol may have two amorphous phases related by a first-order transition. Slightly above its glass transition temperature T{sub g} (284 K), the supercooled liquid (SCL) of D-mannitol transforms to a low-energy, apparently amorphous phase with stronger hydrogen bonds. The enthalpy of this so-called Phase X is approximately halfway between those of the known amorphous and crystalline phases, a position low for glass aging and high for crystal polymorphs. Similar to the SCL, Phase X is transparent with broad X-ray diffraction and Raman scattering; upon temperature cycling, it exhibits a glass-transition-like change of heat capacity.more » On fast heating, Phase X transforms back to the SCL near T{sub g} + 50 K, enabling a determination of their equilibrium temperature. The presence of D-sorbitol as a plasticizer enables observation of a first-order transition from the SCL to Phase X entirely in the liquid state (liquid-liquid transition). The transition from D-mannitol’s SCL to Phase X has intriguing similarities with the formation of the glacial phase of triphenyl phosphite (TPP) and the conversion from high-density to low-density amorphous ice, both studied intensely in the context of polyamorphism. All three processes occur near T{sub g} with substantial enthalpy decrease toward the crystalline phases; the processes in water and D-mannitol both strengthen the hydrogen bonds. In contrast to TPP, D-mannitol’s Phase X forms more rapidly and can transform back to the SCL. These features make D-mannitol a valuable new model for understanding polyamorphism.« less
Experimental and theoretical methods to study structural phase transition mechanisms in K{sub 3}WO{sub 3}F{sub 3} oxyfluoride

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

Krylov, A.S., E-mail: shusy@iph.krasn.ru; Sofronova, S.N.; Kolesnikova, E.M.

2014-10-15

The results of structural phase transitions mechanisms study in K{sub 3}WO{sub 3}F{sub 3}oxyfluoride are represented by different experimental and theoretical methods. The structural phase transition anomalies at T{sub 1}=452 K and T{sub 2}=414 K of Raman and IR spectra have been analyzed. Using vibrational spectroscopy methods, the NMR-experiment has been done to clarify the nature of found phase transitions: displacive types or order-disorder types. The model of “disordered” crystal was proposed, and the results of lattice dynamics calculation in frameworks of the generalized Gordon–Kim method of ordered (R3) and “disordered” crystals were compared. The high pressure phases were studied bymore » the Raman technique too. - Graphical abstract: (1) Two possible configuration of octahedra. (2). All phases Raman lines of octahedra. (3) All phases IR lines of octahedra. (4) NMR spectra of all phases. - Highlights: • The results of study oxyfluoride K{sub 3}WO{sub 3}F{sub 3} are represented by Raman, IR, NMR technique. • The high pressure phases were studied by the Raman technique. • The anionic octahedra [WO{sub 3}F{sub 3}]{sup 3−} are not ordered below the both phase transitions. • The ferroelectric phase is realized due to the shift of atoms without F/O ordering. • Both of found phase transitions are close to the second order.« less
In-field X-ray and neutron diffraction studies of re-entrant charge-ordering and field induced metastability in La0.175Pr0.45Ca0.375MnO3-δ

NASA Astrophysics Data System (ADS)

Sharma, Shivani; Shahee, Aga; Yadav, Poonam; da Silva, Ivan; Lalla, N. P.

2017-11-01

Low-temperature high-magnetic field (2 K, 8 T) (LTHM) powder X-ray diffraction (XRD) and time of flight powder neutron diffraction (NPD), low-temperature transmission electron microscopic (TEM), and resistivity and magnetization measurements have been carried out to investigate the re-entrant charge ordering (CO), field induced structural phase transitions, and metastability in phase-separated La0.175Pr0.45Ca0.375MnO3-δ (LPCMO). Low-temperature TEM and XRD studies reveal that on cooling under zero-field, paramagnetic Pnma phase transforms to P21/m CO antiferromagnetic (AFM) insulating phase below ˜233 K. Unlike reported literature, no structural signature of CO AFM P21/m to ferromagnetic (FM) Pnma phase-transition during cooling down to 2 K under zero-field was observed. However, the CO phase was found to undergo a re-entrant transition at ˜40 K. Neutron diffraction studies revealed a pseudo CE type spin arrangement of the observed CO phase. The low-temperature resistance, while cooled under zero-field, shows insulator to metal like transition below ˜105 K with minima at ˜25 K. On application of field, the CO P21/m phase was found to undergo field-induced transition to FM Pnma phase, which shows irreversibility on field removal below ˜40 K. Zero-field warming XRD and NPD studies reveal that field-induced FM Pnma phase is a metastable phase, which arise due to the arrest of kinetics of the first-order phase transition of FM Pnma to CO-AFM P21/m phase, below 40 K. Thus, a strong magneto-structural coupling is observed for this system. A field-temperature (H-T) phase-diagram has been constructed based on the LTHM-XRD, which matches very nicely with the reported H-T phase-diagram constructed based on magnetic measurements. Due to the occurrence of gradual growth of the re-entrant CO phase and the absence of a clear structural signature of phase-separation of CO-AFM P21/m and FM Pnma phases, the H-T minima in the phase-diagram of the present LPCMO sample has been attributed to the strengthening of AFM interaction during re-entrant CO transition and not to glass like "dynamic to frozen" transition.
Transition paths of Met-enkephalin from Markov state modeling of a molecular dynamics trajectory.

PubMed

Banerjee, Rahul; Cukier, Robert I

2014-03-20

Conformational states and their interconversion pathways of the zwitterionic form of the pentapeptide Met-enkephalin (MetEnk) are identified. An explicit solvent molecular dynamics (MD) trajectory is used to construct a Markov state model (MSM) based on dihedral space clustering of the trajectory, and transition path theory (TPT) is applied to identify pathways between open and closed conformers. In the MD trajectory, only four of the eight backbone dihedrals exhibit bistable behavior. Defining a conformer as the string XXXX with X = "+" or "-" denoting, respectively, positive or negative values of a given dihedral angle and obtaining the populations of these conformers shows that only four conformers are highly populated, implying a strong correlation among these dihedrals. Clustering in dihedral space to construct the MSM finds the same four bistable dihedral angles. These state populations are very similar to those found directly from the MD trajectory. TPT is used to obtain pathways, parametrized by committor values, in dihedral state space that are followed in transitioning from closed to open states. Pathway costs are estimated by introducing a kinetics-based procedure that orders pathways from least (shortest) to greater cost paths. The least costly pathways in dihedral space are found to only involve the same XXXX set of dihedral angles, and the conformers accessed in the closed to open transition pathways are identified. For these major pathways, a correlation between reaction path progress (committors) and the end-to-end distance is identified. A dihedral space principal component analysis of the MD trajectory shows that the first three modes capture most of the overall fluctuation, and pick out the same four dihedrals having essentially all the weight in those modes. A MSM based on root-mean-square backbone clustering was also carried out, with good agreement found with dihedral clustering for the static information, but with results that differ significantly for the pathway analysis.
Control of the orientation and photoinduced phase transitions of macrocyclic azobenzene.

PubMed

Uchida, Emi; Sakaki, Kouji; Nakamura, Yumiko; Azumi, Reiko; Hirai, Yuki; Akiyama, Haruhisa; Yoshida, Masaru; Norikane, Yasuo

2013-12-16

Photoinduced phase transitions caused by photochromic reactions bring about a change in the state of matter at constant temperature. Herein, we report the photoinduced phase transitions of crystals of a photoresponsive macrocyclic compound bearing two azobenzene groups (1) at room temperature on irradiation with UV (365 nm) and visible (436 nm) light. The trans/trans isomer undergoes photoinduced phase transitions (crystal-isotropic phase-crystal) on UV light irradiation. The photochemically generated crystal exhibited reversible phase transitions between the crystal and the mesophase on UV and visible light irradiation. The molecular order of the randomly oriented crystals could be increased by irradiating with linearly polarized visible light, and the value of the order parameter was determined to be -0.84. Heating enhances the thermal cis-to-trans isomerization and subsequent cooling returned crystals of the trans/trans isomer. Copyright © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.
Holographic insulator/superconductor transition with exponential nonlinear electrodynamics probed by entanglement entropy

NASA Astrophysics Data System (ADS)

Yao, Weiping; Yang, Chaohui; Jing, Jiliang

2018-05-01

From the viewpoint of holography, we study the behaviors of the entanglement entropy in insulator/superconductor transition with exponential nonlinear electrodynamics (ENE). We find that the entanglement entropy is a good probe to the properties of the holographic phase transition. Both in the half space and the belt space, the non-monotonic behavior of the entanglement entropy in superconducting phase versus the chemical potential is general in this model. Furthermore, the behavior of the entanglement entropy for the strip geometry shows that the confinement/deconfinement phase transition appears in both insulator and superconductor phases. And the critical width of the confinement/deconfinement phase transition depends on the chemical potential and the exponential coupling term. More interestingly, the behaviors of the entanglement entropy in their corresponding insulator phases are independent of the exponential coupling factor but depends on the width of the subsystem A.
Nonequilibrium Second-Order Phase Transition in a Cooper-Pair Insulator.

PubMed

Doron, A; Tamir, I; Mitra, S; Zeltzer, G; Ovadia, M; Shahar, D

2016-02-05

In certain disordered superconductors, upon increasing the magnetic field, superconductivity terminates with a direct transition into an insulating phase. This phase is comprised of localized Cooper pairs and is termed a Cooper-pair insulator. The current-voltage characteristics measured in this insulating phase are highly nonlinear and, at low temperatures, exhibit abrupt current jumps. Increasing the temperature diminishes the jumps until the current-voltage characteristics become continuous. We show that a direct correspondence exists between our system and systems that undergo an equilibrium, second-order, phase transition. We illustrate this correspondence by comparing our results to the van der Waals equation of state for the liquid-gas mixture. We use the similarities to identify a critical point where an out of equilibrium second-order-like phase transition occurs in our system. Approaching the critical point, we find a power-law behavior with critical exponents that characterizes the transition.
Instability of Insulators near Quantum Phase Transitions

NASA Astrophysics Data System (ADS)

Doron, A.; Tamir, I.; Levinson, T.; Ovadia, M.; Sacépé, B.; Shahar, D.

2017-12-01

Thin films of amorphous indium oxide undergo a magnetic field driven superconducting to insulator quantum phase transition. In the insulating phase, the current-voltage characteristics show large current discontinuities due to overheating of electrons. We show that the onset voltage for the discontinuities vanishes as we approach the quantum critical point. As a result, the insulating phase becomes unstable with respect to any applied voltage making it, at least experimentally, immeasurable. We emphasize that unlike previous reports of the absence of linear response near quantum phase transitions, in our system, the departure from equilibrium is discontinuous. Because the conditions for these discontinuities are satisfied in most insulators at low temperatures, and due to the decay of all characteristic energy scales near quantum phase transitions, we believe that this instability is general and should occur in various systems while approaching their quantum critical point. Accounting for this instability is crucial for determining the critical behavior of systems near the transition.
Holographic research on phase transitions for a five dimensional AdS black hole with conformally coupled scalar hair

NASA Astrophysics Data System (ADS)

Li, Hui-Ling; Yang, Shu-Zheng; Zu, Xiao-Tao

2017-01-01

In the framework of holography, we survey the phase structure for a higher dimensional hairy black hole including the effects of the scalar field hair. It is worth emphasizing that, not only black hole entropy, but also entanglement entropy and two point correlation function exhibit the Van der Waals-like phase transition in a fixed scalar charge ensemble. Furthermore, by making use of numerical computation, we show that the Maxwell's equal area law is valid for the first order phase transition. In addition, we also discuss how the hair parameter affects the black hole's phase transition.
On the Phase Transition of N-Isopropylcarbazole.

DTIC Science & Technology

1986-05-01

vacinity of the phase transition (ca. T 137 + 40 K). We propose a semiquantitative interpretation of the phase transition in NIPC based on this assumption...the order parameter fluctuations in the vacinity of TO . V. Conclusions. The elastic properties of NIPC in the temperature range 90 K - 295 K have
On entropy change measurements around first order phase transitions in caloric materials.

PubMed

Caron, Luana; Ba Doan, Nguyen; Ranno, Laurent

2017-02-22

In this work we discuss the measurement protocols for indirect determination of the isothermal entropy change associated with first order phase transitions in caloric materials. The magneto-structural phase transitions giving rise to giant magnetocaloric effects in Cu-doped MnAs and FeRh are used as case studies to exemplify how badly designed protocols may affect isothermal measurements and lead to incorrect entropy change estimations. Isothermal measurement protocols which allow correct assessment of the entropy change around first order phase transitions in both direct and inverse cases are presented.
Phase equilibrium in a water + n-hexane system with a high water content

NASA Astrophysics Data System (ADS)

Rasulov, S. M.; Orakova, S. M.; Isaev, Z. A.

2017-02-01

The P, ρ, and T-properties of a water + n-hexane system immiscible under normal conditions are measured piezometrically in the water mole fraction range of 0.918-0.977 at 309-685 K and pressures of up to 66 MPa. Two phase transitions are observed on each isochore corresponding to phase transitions of hydrocarbon liquid into gas or the dissolution of n-hexane in water and the transition of aqueous liquid into gas. The boundaries of phase transitions and their critical parameters are determined.
Superradiant phase transitions with three-level systems

NASA Astrophysics Data System (ADS)

Baksic, Alexandre; Nataf, Pierre; Ciuti, Cristiano

2013-02-01

We determine the phase diagram of N identical three-level systems interacting with a single photonic mode in the thermodynamical limit (N→∞) by accounting for the so-called diamagnetic term and the inequalities imposed by the Thomas-Reich-Kuhn (TRK) oscillator strength sum rule. The key role of transitions between excited levels and the occurrence of first-order phase transitions is discussed. We show that, in contrast to two-level systems, in the three-level case the TRK inequalities do not always prevent a superradiant phase transition in the presence of a diamagnetic term.
Conditions and Linear Stability Analysis at the Transition to Synchronization of Three Coupled Phase Oscillators in a Ring

NASA Astrophysics Data System (ADS)

El-Nashar, Hassan F.

2017-06-01

We consider a system of three nonidentical coupled phase oscillators in a ring topology. We explore the conditions that must be satisfied in order to obtain the phases at the transition to a synchrony state. These conditions lead to the correct mathematical expressions of phases that aid to find a simple analytic formula for critical coupling when the oscillators transit to a synchronization state having a common frequency value. The finding of a simple expression for the critical coupling allows us to perform a linear stability analysis at the transition to the synchronization stage. The obtained analytic forms of the eigenvalues show that the three coupled phase oscillators with periodic boundary conditions transit to a synchrony state when a saddle-node bifurcation occurs.
Phase transition in organic-inorganic perovskite (C9H19NH3)2 PbI2Br2 of long-chain alkylammonium

NASA Astrophysics Data System (ADS)

Abid, H.; Trigui, A.; Mlayah, A.; Hlil, E. K.; Abid, Y.

2012-01-01

Single perovskite slab alkylammonium lead iodides bromides (C9H19NH3)2PbI2Br2 is a new member of the family of hybrid organic-inorganic perovskite compounds. It exhibits a single structural phase transition with changes in the conformation of alkylammonium chains below room temperature. Differential scanning calorimetry (DSC), powder X-ray diffraction and FT-Raman spectroscopy were used to investigate this phase transition. These changes were characterized by a decreased conformational disorder of the methylene units of the alkyl chains. Phase transition was examined in light of the interesting optical properties of this material, as well as the relevance of this system as models for phase transitions in lipid bilayers.
An infrared spectroscopic study of the structural phase transition in the perovskite-type layer compound [ n-C 16H 33NH 3] 2CoCl 4

NASA Astrophysics Data System (ADS)

Ning, Guo; Guangfu, Zeng; Shiquan, Xi

1992-12-01

The solid-solid phase transitions in the perovskite-type layer compound [ n-C 16H 33NH 3] 2CoCl 4 have been studied by infrared spectroscopy. A new phase transition at 340 K was found by comparison with differential scanning calorimetry results. A temperature dependence study of the infrared spectra provides evidence of the occurrence of structural phase transitions related to the dynamics of the alkylammonium ions and hydrogen bonds. The main transition at 374 K corresponds to the conformational order-disorder change in the chain, which probably couples with reorientational motions of the NH 3 polar heads. GTG or GTG' defects appear in the high temperature disordered phase.
Signatures of a dissipative phase transition in photon correlation measurements

NASA Astrophysics Data System (ADS)

Fink, Thomas; Schade, Anne; Höfling, Sven; Schneider, Christian; Imamoglu, Ataç

2018-04-01

Understanding and characterizing phase transitions in driven-dissipative systems constitutes a new frontier for many-body physics1-8. A generic feature of dissipative phase transitions is a vanishing gap in the Liouvillian spectrum9, which leads to long-lived deviations from the steady state as the system is driven towards the transition. Here, we show that photon correlation measurements can be used to characterize the corresponding critical slowing down of non-equilibrium dynamics. We focus on the extensively studied phenomenon of optical bistability in GaAs cavity polaritons10,11, which can be described as a first-order dissipative phase transition12-14. Increasing the excitation strength towards the bistable range results in an increasing photon-bunching signal along with a decay time that is prolonged by more than nine orders of magnitude as compared with that of single polaritons. In the limit of strong polariton interactions leading to pronounced quantum fluctuations, the mean-field bistability threshold is washed out. Nevertheless, the functional form with which the Liouvillian gap closes as the thermodynamic limit is approached provides a signature of the emerging dissipative phase transition. Our results establish photon correlation measurements as an invaluable tool for studying dynamical properties of dissipative phase transitions without requiring phase-sensitive interferometric measurements.
A cost-effective process to prepare VO{sub 2} (M) powder and films with superior thermochromic properties

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

Xiao, Xiudi; Zhang, Hua; Chai, Guanqi

2014-03-01

Graphical abstract: Combining codeposition and short time post annealing, VO{sub 2} (M) with high quality and excellent phase transition performance is obtained. After mixing the VO{sub 2} powder with acrylic resin, the composite films deposited on glass show superior visible transmission and solar modulation, which can be used as an excellent candidate of low cost smart window in energy saving field. - Highlights: • The VO{sub 2} powder obtained by short time thermolysis method is high purity and crystallinity with superior phase transition performance. • The maximum decreasing efficiency of phase transition temperature is about −30 K/at% with w =more » 0.4 at%. • After mixing VO{sub 2} powder with acrylic resin, the maximal visible transmission of the composite films is 48% and the transmission modulation at 2000 nm is 37.3% with phase transition temperature of 66.2 °C. • Though the phase transition performance is weakened by tungsten doping, the film prepared by 1.3 at% tungsten doped VO{sub 2} still show superior transmission modulation about 26.4%, which means that it is a potential candidate as smart windows. - Abstract: VO{sub 2} powder with superior phase transition performance was prepared by convenient thermolysis method. The results illustrated that VO{sub 2} powder show high purity and crystallinity. VO{sub 2} particles are transformed from cluster to quasi-sphere with the increase of annealing temperature. The DSC analysis proves that VO{sub 2} show superior phase transition performance around 68 °C. The phase transition temperature can be reduced to 33.5 °C by 1.8 at% tungsten doping. The maximum decreasing efficiency of phase transition temperature is about −30 K/at% with w = 0.4 at%. After mixing VO{sub 2} powder with acrylic resin, the maximal visible transmission of the composite thin films on glass is 48% and the transmission modulation at 2000 nm is 37.3% with phase transition temperature of 66.2 °C. Though the phase transition performance is weakened by tungsten doping, the film prepared by 1.3 at% tungsten doped VO{sub 2} still show superior transmission modulation about 26.4% at 2000 nm, which means that it is a potential candidate as smart windows.« less
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

Nogo-B receptor promotes the chemoresistance of human hepatocellular carcinoma via the ubiquitination of p53 protein

PubMed Central

Long, Fei; Liu, Ying; Liu, Zhenzhen; Li, Song; Yang, Xuejun; Sun, Deguang; Wang, Haibo; Liu, Qinlong; Liang, Rui; Li, Yan; Gao, Zhenming; Shao, Shujuan; Miao, Qing Robert; Wang, Liming

2016-01-01

Nogo-B receptor (NgBR), a type I single transmembrane domain receptor is the specific receptor for Nogo-B. Our previous work demonstrated that NgBR is highly expressed in breast cancer cells, where it promotes epithelial mesenchymal transition (EMT), an important step in metastasis. Here, we show that both in vitro and in vivo increased expression of NgBR contributes to the increased chemoresistance of Bel7402/5FU cells, a stable 5-FU (5-Fluorouracil) resistant cell line related Bel7402 cells. NgBR knockdown abrogates S-phase arrest in Bel7402/5FU cells, which correlates with a reduction in G1/S phase checkpoint proteins p53 and p21. In addition, NgBR suppresses p53 protein levels through activation of the PI3K/Akt/MDM2 pathway, which promotes p53 degradation via the ubiquitin proteasome pathway and thus increases the resistance of human hepatocellular cancer cells to 5-FU. Furthermore, we found that NgBR expression is associated with a poor prognosis of human hepatocellular carcinoma (HCC) patients. These results suggest that targeting NgBR in combination with chemotherapeutic drugs, such as 5-FU, could improve the efficacy of current anticancer treatments. PMID:26840457
Pressure induced solid-solid reconstructive phase transition in LiGa O2 dominated by elastic strain

NASA Astrophysics Data System (ADS)

Hu, Qiwei; Yan, Xiaozhi; Lei, Li; Wang, Qiming; Feng, Leihao; Qi, Lei; Zhang, Leilei; Peng, Fang; Ohfuji, Hiroaki; He, Duanwei

2018-01-01

Pressure induced solid-solid reconstructive phase transitions for graphite-diamond, and wurtzite-rocksalt in GaN and AlN occur at significantly higher pressure than expected from equilibrium coexistence and their transition paths are always inconsistent with each other. These indicate that the underlying nucleation and growth mechanism in the solid-solid reconstructive phase transitions are poorly understood. Here, we propose an elastic-strain dominated mechanism in a reconstructive phase transition, β -LiGa O2 to γ -LiGa O2 , based on in situ high-pressure angle dispersive x-ray diffraction and single-crystal Raman scattering. This mechanism suggests that the pressure induced solid-solid reconstructive phase transition is neither purely diffusionless nor purely diffusive, as conventionally assumed, but a combination. The large elastic strains are accumulated, with the coherent nucleation, in the early stage of the transition. The elastic strains along the 〈100 〉 and 〈001 〉 directions are too large to be relaxed by the shear stress, so an intermediate structure emerges reducing the elastic strains and making the transition energetically favorable. At higher pressures, when the elastic strains become small enough to be relaxed, the phase transition to γ -LiGa O2 begins and the coherent nucleation is substituted with a semicoherent one with Li and Ga atoms disordered.
Temperature and magnetic field induced multiple magnetic transitions in DyAg(2).

PubMed

Arora, Parul; Chattopadhyay, M K; Sharath Chandra, L S; Sharma, V K; Roy, S B

2011-02-09

The magnetic properties of the rare-earth intermetallic compound DyAg(2) are studied in detail with the help of magnetization and heat capacity measurements. It is shown that the multiple magnetic phase transitions can be induced in DyAg(2) both by temperature and magnetic field. The detailed magnetic phase diagram of DyAg(2) is determined experimentally. It was already known that DyAg(2) undergoes an incommensurate to commensurate antiferromagnetic phase transition close to 10 K. The present experimental results highlight the first order nature of this phase transition, and show that this transition can be induced by magnetic field as well. It is further shown that another isothermal magnetic field induced transition or metamagnetic transition exhibited by DyAg(2) at still lower temperatures is also of first order nature. The multiple magnetic phase transitions in DyAg(2) give rise to large peaks in the temperature dependence of the heat capacity below 17 K, which indicates its potential as a magnetic regenerator material for cryocooler related applications. In addition it is found that because of the presence of the temperature and field induced magnetic phase transitions, and because of short range magnetic correlations deep inside the paramagnetic regime, DyAg(2) exhibits a fairly large magnetocaloric effect over a wide temperature window, e.g., between 10 and 60 K.
Modelling Phase Transition Phenomena in Fluids

DTIC Science & Technology

2015-07-01

Sublimation line r @@I Triple point ? Vapourisation liner @@I Critical point -Fusion line Solid Liquid Gas Figure 1: Schematic of a phase diagram means that the...velocity field can be set zero, and only the balance of energy constitutes the Stefan model. In contrast to this the liquid - gas phase transitions...defined by requiring that the phase-transition line is crossed in a direction from solid to liquid or from liquid to gas (vapour) phases. The term T∗ δs is
DOE Office of Scientific and Technical Information (OSTI.GOV)

Cao, Ye; Yang, Mr. Shuzhen; Jesse, Stephen

Many functional properties of ferroelectrics are underlain by structural instabilities, which render these materials very susceptible to small alternating applied fields (electric, mechanical, etc.) through certain constitutive coupling relations, e.g., elastic compliance and piezoelectric response, and often such instabilities can be shifted by static applied fields thus meaning tunable dynamic properties. Structural instabilities are naturally accommodated on the brink of morphotropic phase boundaries (MPB s) where multiple phases of small energy difference coexist in different crystallographic forms. Canonical MPB is realized through compositional mixture, as is typically exemplified by Pb(Zr1-xTix)O3 solid solutions and relaxor ferroelectrics of (1-x)PbMg1/3Nb2/3O3-xPbTiO3. More recently, amore » strain-driven MPB has been discovered in BiFeO3 (BFO) thin films epitaxially grown on LaAlO3 (LAO) crystal substrates (which imposes about -4.5% in-plane strains). Such an MPB is in between a rhombohedral (R) phase that bulk BFO exhibits and a so-called super-tetragonal (T) phase, which name hints at its giant lattice axial ratio (c/a ~ 1.23) and accordingly high electric polarization (~1.5 C m-2). The discovery of an MPB in BFO has revealed another facet of this multiferroic system, further adding opportunities to its many exotic functionalities such as domain wall conduction, magnetoelectric and photovoltaic effects As with other MPB s, large electric-field induced strains as well as more underlying lattice softening effects are observed near this MPB promising piezoelectric-based applications. In addition, T-phase BFO itself shows distinct properties, e.g., electronic band gap and optical absorption, from the R-phase and the resultant switching effects between them may also be exploitable. However, unlike conventional ferroelectric oxides where the phases across an MPB usually have subtle difference caused by rotations of an ion off-centering polarization, the BFO system bears multiple structural degrees of freedom, in particular antiferrodistortive modes of oxygen octahedral tilt, and a multitude of structural transition paths are thereby facilitated. Moreover, since the MPB of BFO is driven by epitaxial strain, it is sensitive to the strain relaxation related to film thickness and growth conditions, and above some critical thickness the films appear in the form of a hierarchical mixed-phase microstructure involving several coexistent polymorphs with distinct lattice distortion (monoclinic phases) and tilts. Elastic and electrical heterogeneities are necessary consequences of such complex microstructure, which couple to the intrinsic order parameters and expectedly have profound influence on the structural dynamics and material properties. All these make it a demanding task to obtain a deep understanding of this MPB system on par with its application prospect. The thin-film material form also brings in experimental restrictions to the MPB phase transition studies of BFO since many pertinent techniques fail to operate at the nanoscale or suffer from formidably weak signals. Therefore, static structural characterizations using e.g. X-ray diffraction, electron microscopy and Raman scattering have prevailed thus far. Recently, we adapted band-excitation piezoresponse spectroscopy (BEPS) to probe the bias-induced R/T phase transition dynamics of BFO/SrTiO3 (STO) thin films, and revealed the soft-mode elastic behavior of the transition. The efficacy of our method, along with standard piezoresponse force microscopy (PFM), can be significantly leveraged by integrating a variety of local and/or global excitations, e.g., tip pressure (10 s GPa attainable), heating, photo-irradiation, available to modern scanning probe platforms. This can thus afford unique opportunities to survey the structural dynamics of ferroelectric materials coupled to those field variables, enabling rapid discovery or validation of their functional properties. In this study, we focus on the T-phase BFO/LAO system; we have examined its phase transition behavior not only due to local coaction of tip bias and loading force, but also under device-level global electric fields in a coplanar capacitor. The intrinsic elastic softening phenomena near the structural transitions are comprehensively revealed by BEPS and corroborated by phase-field modeling. Our findings may open a new pathway for technological utilization of the MPB phase instabilities of BFO.« less
Self-Powered Temperature-Mapping Sensors Based on Thermo-Magneto-Electric Generator.

PubMed

Chun, Jinsung; Kishore, Ravi Anant; Kumar, Prashant; Kang, Min-Gyu; Kang, Han Byul; Sanghadasa, Mohan; Priya, Shashank

2018-04-04

We demonstrate a thermo-magneto-electric generator (TMEG) based on second-order phase transition of soft magnetic materials that provides a promising pathway for scavenging low-grade heat. It takes advantage of the cyclic magnetic forces of attraction and repulsion arising through ferromagnetic-to-paramagnetic phase transition to create mechanical vibrations that are converted into electricity through piezoelectric benders. To enhance the mechanical vibration frequency and thereby the output power of the TMEG, we utilize the nonlinear behavior of piezoelectric cantilevers and enhanced thermal transport through silver (Ag) nanoparticles (NPs) applied on the surface of a soft magnet. This results in large enhancement of the oscillation frequency reaching up to 9 Hz (300% higher compared with that of the prior literature). Optimization of the piezoelectric beam and Ag NP distribution resulted in the realization of nonlinear TMEGs that can generate a high output power of 80 μW across the load resistance of 0.91 MΩ, which is 2200% higher compared with that of the linear TMEG. Using a nonlinear TMEG, we fabricated and evaluated self-powered temperature-mapping sensors for monitoring the thermal variations across the surface. Combined, our results demonstrate that nonlinear TMEGs can provide additional functionality including temperature monitoring, thermal mapping, and powering sensor nodes.
Phase Transitions in Tetramethylammonium Hexachlorometalate Compounds (TMA) 2MCl 6 (M = U, Np, Pt, Sn, Hf, Zr)

DOE PAGES

Autillo, Matthieu; Wilson, Richard E.

2017-09-22

A study of the phase transitions occurring in tetramethylammonium hexachlorometalate compounds with M = U IV, Np IV, Zr IV, Sn IV, Hf IV and Pt IV were performed using single-crystal X-ray diffraction across the temperature range 120 - 400K. When the crystals were cooled, movement of the octahedral [MCl 6] 2- anions induces a phase transition from Fm3m to Fd3c with a doubling of the unit cell. For the actinide compounds, no correlation between the f-electron configuration and the transition temperature was observed, instead, a correlation between the transition temperatures and both the [MCl 6] 2- anion and themore » TMA cation size is highlighted. Two phase transitions were observed and characterized. The first phase transition occurs with the ordering of the TMA cation and the second from a rotation of the [MCl 6] 2- octahedra. A third phase transition was observed at lower temperatures and was ascribed to a tetragonal distortion of the [MCl 6] 2- anions. Synthesis and study of their deuterated compounds did not show a significant isotope effect. As a result, Raman spectra performed on the protonated and deuterated compounds indicate only weak hydrogen bonding interactions between the TMA cations and the [MCl 6] 2- octahedra.« less
0 - π Quantum transition in a carbon nanotube Josephson junction: Universal phase dependence and orbital degeneracy

NASA Astrophysics Data System (ADS)

Delagrange, R.; Weil, R.; Kasumov, A.; Ferrier, M.; Bouchiat, H.; Deblock, R.

2018-05-01

In a quantum dot hybrid superconducting junction, the behavior of the supercurrent is dominated by Coulomb blockade physics, which determines the magnetic state of the dot. In particular, in a single level quantum dot singly occupied, the sign of the supercurrent can be reversed, giving rise to a π-junction. This 0 - π transition, corresponding to a singlet-doublet transition, is then driven by the gate voltage or by the superconducting phase in the case of strong competition between the superconducting proximity effect and Kondo correlations. In a two-level quantum dot, such as a clean carbon nanotube, 0- π transitions exist as well but, because more cotunneling processes are allowed, are not necessarily associated to a magnetic state transition of the dot. In this proceeding, after a review of 0- π transitions in Josephson junctions, we present measurements of current-phase relation in a clean carbon nanotube quantum dot, in the single and two-level regimes. In the single level regime, close to orbital degeneracy and in a regime of strong competition between local electronic correlations and superconducting proximity effect, we find that the phase diagram of the phase-dependent transition is a universal characteristic of a discontinuous level-crossing quantum transition at zero temperature. In the case where the two levels are involved, the nanotube Josephson current exhibits a continuous 0 - π transition, independent of the superconducting phase, revealing a different physical mechanism of the transition.
Unconventional transformation of spin Dirac phase across a topological quantum phase transition

PubMed Central

Xu, Su-Yang; Neupane, Madhab; Belopolski, Ilya; Liu, Chang; Alidoust, Nasser; Bian, Guang; Jia, Shuang; Landolt, Gabriel; Slomski, Batosz; Dil, J. Hugo; Shibayev, Pavel P.; Basak, Susmita; Chang, Tay-Rong; Jeng, Horng-Tay; Cava, Robert J.; Lin, Hsin; Bansil, Arun; Hasan, M. Zahid

2015-01-01

The topology of a topological material can be encoded in its surface states. These surface states can only be removed by a bulk topological quantum phase transition into a trivial phase. Here we use photoemission spectroscopy to image the formation of protected surface states in a topological insulator as we chemically tune the system through a topological transition. Surprisingly, we discover an exotic spin-momentum locked, gapped surface state in the trivial phase that shares many important properties with the actual topological surface state in anticipation of the change of topology. Using a spin-resolved measurement, we show that apart from a surface bandgap these states develop spin textures similar to the topological surface states well before the transition. Our results offer a general paradigm for understanding how surface states in topological phases arise from a quantum phase transition and are suggestive for the future realization of Weyl arcs, condensed matter supersymmetry and other fascinating phenomena in the vicinity of a quantum criticality. PMID:25882717
Phase transitions in traffic flow on multilane roads.

PubMed

Kerner, Boris S; Klenov, Sergey L

2009-11-01

Based on empirical and numerical analyses of vehicular traffic, the physics of spatiotemporal phase transitions in traffic flow on multilane roads is revealed. The complex dynamics of moving jams observed in single vehicle data measured by video cameras on American highways is explained by the nucleation-interruption effect in synchronized flow, i.e., the spontaneous nucleation of a narrow moving jam with the subsequent jam dissolution. We find that (i) lane changing, vehicle merging from on-ramps, and vehicle leaving to off-ramps result in different traffic phases-free flow, synchronized flow, and wide moving jams-occurring and coexisting in different road lanes as well as in diverse phase transitions between the traffic phases; (ii) in synchronized flow, the phase transitions are responsible for a non-regular moving jam dynamics that explains measured single vehicle data: moving jams emerge and dissolve randomly at various road locations in different lanes; (iii) the phase transitions result also in diverse expanded general congested patterns occurring at closely located bottlenecks.
Unconventional transformation of spin Dirac phase across a topological quantum phase transition

DOE PAGES

Xu, Su -Yang; Neupane, Madhab; Belopolski, Ilya; ...

2015-04-17

The topology of a topological material can be encoded in its surface states. These surface states can only be removed by a bulk topological quantum phase transition into a trivial phase. Here we use photoemission spectroscopy to image the formation of protected surface states in a topological insulator as we chemically tune the system through a topological transition. Surprisingly, we discover an exotic spin-momentum locked, gapped surface state in the trivial phase that shares many important properties with the actual topological surface state in anticipation of the change of topology. Using a spin-resolved measurement, we show that apart from amore » surface bandgap these states develop spin textures similar to the topological surface states well before the transition. Our results provide a general paradigm for understanding how surface states in topological phases arise from a quantum phase transition and are suggestive for the future realization of Weyl arcs, condensed matter supersymmetry and other fascinating phenomena in the vicinity of a quantum criticality.« less
In situ imaging of the dynamics of photo-induced structural phase transition at high pressures by picosecond acoustic interferometry

NASA Astrophysics Data System (ADS)

Kuriakose, Maju; Chigarev, Nikolay; Raetz, Samuel; Bulou, Alain; Tournat, Vincent; Zerr, Andreas; Gusev, Vitalyi E.

2017-05-01

Picosecond acoustic interferometry is used to monitor in time the motion of the phase transition boundary between two water ice phases, VII and VI, coexisting at a pressure of 2.15 GPa when compressed in a diamond anvil cell at room temperature. By analyzing the time-domain Brillouin scattering signals accumulated for a single incidence direction of probe laser pulses, it is possible to access ratios of sound velocity values and of the refractive indices of the involved phases, and to distinguish between the structural phase transition and a recrystallization process. Two-dimensional spatial imaging of the phase transition dynamics indicates that it is initiated by the pump and probe laser pulses, preferentially at the diamond/ice interface. This method should find applications in three-dimensional monitoring with nanometer spatial resolution of the temporal dynamics of low-contrast material inhomogeneities caused by phase transitions or chemical reactions in optically transparent media.
Live cell plasma membranes do not exhibit a miscibility phase transition over a wide range of temperatures.

PubMed

Lee, Il-Hyung; Saha, Suvrajit; Polley, Anirban; Huang, Hector; Mayor, Satyajit; Rao, Madan; Groves, Jay T

2015-03-26

Lipid/cholesterol mixtures derived from cell membranes as well as their synthetic reconstitutions exhibit well-defined miscibility phase transitions and critical phenomena near physiological temperatures. This suggests that lipid/cholesterol-mediated phase separation plays a role in the organization of live cell membranes. However, macroscopic lipid-phase separation is not generally observed in cell membranes, and the degree to which properties of isolated lipid mixtures are preserved in the cell membrane remain unknown. A fundamental property of phase transitions is that the variation of tagged particle diffusion with temperature exhibits an abrupt change as the system passes through the transition, even when the two phases are distributed in a nanometer-scale emulsion. We support this using a variety of Monte Carlo and atomistic simulations on model lipid membrane systems. However, temperature-dependent fluorescence correlation spectroscopy of labeled lipids and membrane-anchored proteins in live cell membranes shows a consistently smooth increase in the diffusion coefficient as a function of temperature. We find no evidence of a discrete miscibility phase transition throughout a wide range of temperatures: 14-37 °C. This contrasts the behavior of giant plasma membrane vesicles (GPMVs) blebbed from the same cells, which do exhibit phase transitions and macroscopic phase separation. Fluorescence lifetime analysis of a DiI probe in both cases reveals a significant environmental difference between the live cell and the GPMV. Taken together, these data suggest the live cell membrane may avoid the miscibility phase transition inherent to its lipid constituents by actively regulating physical parameters, such as tension, in the membrane.
Pathways from School to Work: Can the Competences Acquired in Leisure Activities Improve the Construction of Pathways?

ERIC Educational Resources Information Center

Merino, Rafael

2007-01-01

The transition from school to work has been intensely examined by different disciplines. However, this transition has rarely been examined in relation to the experiences acquired by young people in their free time, from a longitudinal perspective. This article analyses the impact of one type of experience, membership in organisations, in the young…
High pressure spectroscopic studies of phase transition in VO2

NASA Astrophysics Data System (ADS)

Basu, Raktima; Mishra, K. K.; Ravindran, T. R.; Dhara, Sandip

2018-04-01

Vanadium dioxide (VO2) exhibits a reversible first-order metal to insulator transition (MIT) at a technologically important temperature of 340K. A structural phase transition (SPT) from monoclinic M1 to rutile tetragonal R is also reported via another two intermediate phases of monoclinic M2 and triclinic T. Metastable monoclinic M2 phase of VO2 was synthesized by Mg doping in the vapour transport process. Raman spectroscopic measurements were carried out at high pressure on V1-xMgxO2 microrods. Two reversible structural phase transitions from monoclinic M2 to triclinic T at 1.6 GPa and T to monoclinic M1 at 3.2 GPa are observed and are explained by structural relaxation of the strained phases.
Anomalous behaviour of thermodynamic properties at successive phase transitions in (NH4)3GeF7

NASA Astrophysics Data System (ADS)

Bogdanov, Evgeniy V.; Kartashev, Andrey V.; Pogoreltsev, Evgeniy I.; Gorev, Mikhail V.; Laptash, Natalia M.; Flerov, Igor N.

2017-12-01

Heat capacity, thermal dilatation, susceptibility to hydrostatic pressure and dielectric properties associated with succession of three phase transitions below room temperature in double fluoride salt (NH4)3GeF7 were studied. A possible transformation into the parent Pm-3m cubic phase was not observed up to the decomposition of compound. Nonferroelectric nature of structural distortions was confirmed. The DTA under pressure studies revealed a high temperature stability of two phases: P4/mbm and Pbam. The entropies of the phase transitions agree well with the model of structural distortions. Analysis of the thermal properties associated with the individual phase transitions in the framework of thermodynamic equations has shown a high reliability of the data obtained.
BKT phase transition in a 2D system with long-range dipole-dipole interaction

NASA Astrophysics Data System (ADS)

Fedichev, P. O.; Men'shikov, L. I.

2012-01-01

We consider phase transitions in 2D XY-like systems with long-range dipole-dipole interactions and demonstrate that BKT-type phase transition always occurs separating the ordered (ferroelectric) and the disordered (paraelectric) phases. The low-temperature phase corresponds to a thermal state with bound vortex-antivortex pairs characterized by linear attraction at large distances. Using the Maier-Schwabl topological charge model, we show that bound vortex pairs polarize and screen the vortex-antivortex interaction, leaving only the logarithmic attraction at sufficiently large separations between the vortices. At higher temperatures the pairs dissociate and the phase transition similar to BKT occurs, though at a larger temperature than in a system without the dipole-dipole interaction.
Conversion of neutron stars to 2 + 1 flavor Nambu-Jona-Lasinio quark stars as a mechanism for gamma-ray bursts

NASA Astrophysics Data System (ADS)

Shu, Xiao-Yu; Huang, Yong-Feng; Zong, Hong-Shi

2017-12-01

The phase transition from a neutron star to a quark star and its relation to gamma-ray bursts are investigated. A new model: the 2 + 1 flavor Nambu-Jona-Lasinio (NJL) model with the method of proper-time regularization (PTR) is utilized for the quark phase; while the Relativistic Mean Field (RMF) theory is used for the hadronic phase. The process of phase transition is studied by considering the chemical potential, paying special attention to the phase transition point and the emergence of strange quark matter. Characteristics of compact stars are illustrated, and the energy release during the phase transition is found to be ˜ 1052 erg.
Suppression of magnetostructural transition on GdSiGe thin film after thermal cyclings

DOE PAGES

Pires, A. L.; Belo, J. H.; Gomes, I. T.; ...

2016-09-08

The influence of thermal cycling on the microstructure, magnetic phase transition and magnetic entropy change of a Gd 5Si 1.3Ge 2.7 thin film up to 1000 cycles is investigated. The authors found that after 1000 cycles a strong reduction of the crystallographic phase responsible for the magnetostructural transition (Orthorhombic II phase) occurs. We attribute this to the chemical disorder, caused by the large number of expansion/compression cycles that the Orthorhombic II phase undergoes across the magnetostructural transition. The suppression of the magnetostructural transition corresponds to a drastic decrease of the thin film magnetic entropy change. Our results reveal the importancemore » of studying the thermal/magnetic cycles influence on magnetostructural transitions as they can damage a real-life device.« less
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.

Digestion of phospholipids after secretion of bile into the duodenum changes the phase behavior of bile components.

PubMed

Birru, Woldeamanuel A; Warren, Dallas B; Ibrahim, Ahmed; Williams, Hywel D; Benameur, Hassan; Porter, Christopher J H; Chalmers, David K; Pouton, Colin W

2014-08-04

Bile components play a significant role in the absorption of dietary fat, by solubilizing the products of fat digestion. The absorption of poorly water-soluble drugs from the gastrointestinal tract is often enhanced by interaction with the pathways of fat digestion and absorption. These processes can enhance drug absorption. Thus, the phase behavior of bile components and digested lipids is of great interest to pharmaceutical scientists who seek to optimize drug solubilization in the gut lumen. This can be achieved by dosing drugs after food or preferably by formulating the drug in a lipid-based delivery system. Phase diagrams of bile salts, lecithin, and water have been available for many years, but here we investigate the association structures that occur in dilute aqueous solution, in concentrations that are present in the gut lumen. More importantly, we have compared these structures with those that would be expected to be present in the intestine soon after secretion of bile. Phosphatidylcholines are rapidly hydrolyzed by pancreatic enzymes to yield equimolar mixtures of their monoacyl equivalents and fatty acids. We constructed phase diagrams that model the association structures formed by the products of digestion of biliary phospholipids. The micelle-vesicle phase boundary was clearly identifiable by dynamic light scattering and nephelometry. These data indicate that a significantly higher molar ratio of lipid to bile salt is required to cause a transition to lamellar phase (i.e., liposomes in dilute solution). Mixed micelles of digested bile have a higher capacity for solubilization of lipids and fat digestion products and can be expected to have a different capacity to solubilize lipophilic drugs. We suggest that mixtures of lysolecithin, fatty acid, and bile salts are a better model of molecular associations in the gut lumen, and such mixtures could be used to better understand the interaction of drugs with the fat digestion and absorption pathway.
Nutrient transitions are a source of persisters in Escherichia coli biofilms.

PubMed

Amato, Stephanie M; Brynildsen, Mark P

2014-01-01

Chronic and recurrent infections have been attributed to persisters in biofilms, and despite this importance, the mechanisms of persister formation in biofilms remain unclear. The plethora of biofilm characteristics that could give rise to persisters, including slower growth, quorum signaling, oxidative stress, and nutrient heterogeneity, have complicated efforts to delineate formation pathways that generate persisters during biofilm development. Here we sought to specifically determine whether nutrient transitions, which are a common metabolic stress encountered within surface-attached communities, stimulate persister formation in biofilms and if so, to then identify the pathway. To accomplish this, we established an experimental methodology where nutrient availability to biofilm cells could be controlled exogenously, and then used that method to discover that diauxic carbon source transitions stimulated persister formation in Escherichia coli biofilms. Previously, we found that carbon source transitions stimulate persister formation in planktonic E. coli cultures, through a pathway that involved ppGpp and nucleoid-associated proteins, and therefore, tested the functionality of that pathway in biofilms. Biofilm persister formation was also found to be dependent on ppGpp and nucleoid-associated proteins, but the importance of specific proteins and enzymes between biofilm and planktonic lifestyles was significantly different. Data presented here support the increasingly appreciated role of ppGpp as a central mediator of bacterial persistence and demonstrate that nutrient transitions can be a source of persisters in biofilms.
Phase Transition of H 2 in Subnanometer Pores Observed at 75 K

DOE PAGES

Olsen, Raina J.; Gillespie, Andrew K.; Contescu, Cristian I.; ...

2017-10-30

In this paper, we report a phase transition in H 2 adsorbed in a locally graphitic Saran carbon with subnanometer pores 0.5–0.65 nm in width, in which two layers of hydrogen can just barely squeeze, provided they pack tightly. The phase transition is observed at 75 K, temperatures far higher than other systems in which an adsorbent is known to increase phase transition temperatures: for instance, H 2 melts at 14 K in the bulk, but at 20 K on graphite because the solid H 2 is stabilized by the surface structure. Here we observe a transition at 75 Kmore » and 77–200 bar: from a low-temperature, low-density phase to a high-temperature, higher density phase. We model the low-density phase as a monolayer commensurate solid composed mostly of para-H 2 (the ground nuclear spin state, S = 0) and the high-density phase as an orientationally ordered bilayer commensurate solid composed mostly of ortho-H 2 (S = 1). We attribute the increase in density with temperature to the fact that the oblong ortho-H 2 can pack more densely. The transition is observed using two experiments. The high-density phase is associated with an increase in neutron backscatter by a factor of 7.0 ± 0.1. Normally, hydrogen produces no backscatter (scattering angle >90°). This backscatter appears along with a discontinuous increase in the excitation mass from 1.2 amu to 21.0 ± 2.3 amu, which we associate with collective nuclear spin excitations in the orientationally ordered phase. Film densities were measured using hydrogen adsorption. Finally, no phase transition was observed in H 2 adsorbed in control activated carbon materials.« less
Phase Transition of H 2 in Subnanometer Pores Observed at 75 K

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

Olsen, Raina J.; Gillespie, Andrew K.; Contescu, Cristian I.

In this paper, we report a phase transition in H 2 adsorbed in a locally graphitic Saran carbon with subnanometer pores 0.5–0.65 nm in width, in which two layers of hydrogen can just barely squeeze, provided they pack tightly. The phase transition is observed at 75 K, temperatures far higher than other systems in which an adsorbent is known to increase phase transition temperatures: for instance, H 2 melts at 14 K in the bulk, but at 20 K on graphite because the solid H 2 is stabilized by the surface structure. Here we observe a transition at 75 Kmore » and 77–200 bar: from a low-temperature, low-density phase to a high-temperature, higher density phase. We model the low-density phase as a monolayer commensurate solid composed mostly of para-H 2 (the ground nuclear spin state, S = 0) and the high-density phase as an orientationally ordered bilayer commensurate solid composed mostly of ortho-H 2 (S = 1). We attribute the increase in density with temperature to the fact that the oblong ortho-H 2 can pack more densely. The transition is observed using two experiments. The high-density phase is associated with an increase in neutron backscatter by a factor of 7.0 ± 0.1. Normally, hydrogen produces no backscatter (scattering angle >90°). This backscatter appears along with a discontinuous increase in the excitation mass from 1.2 amu to 21.0 ± 2.3 amu, which we associate with collective nuclear spin excitations in the orientationally ordered phase. Film densities were measured using hydrogen adsorption. Finally, no phase transition was observed in H 2 adsorbed in control activated carbon materials.« less
Design principles for enhancing phase sensitivity and suppressing phase fluctuations simultaneously in biochemical oscillatory systems.

PubMed

Fei, Chenyi; Cao, Yuansheng; Ouyang, Qi; Tu, Yuhai

2018-04-12

Biological systems need to function accurately in the presence of strong noise and at the same time respond sensitively to subtle external cues. Here we study design principles in biochemical oscillatory circuits to achieve these two seemingly incompatible goals. We show that energy dissipation can enhance phase sensitivity linearly by driving the phase-amplitude coupling and increase timing accuracy by suppressing phase diffusion. Two general design principles in the key underlying reaction loop formed by two antiparallel pathways are found to optimize oscillation performance with a given energy budget: balancing the forward-to-backward flux ratio between the two pathways to reduce phase diffusion and maximizing the net flux of the phase-advancing pathway relative to that of the phase-retreating pathway to enhance phase sensitivity. Experimental evidences consistent with these design principles are found in the circadian clock of cyanobacteria. Future experiments to test the predicted dependence of phase sensitivity on energy dissipation are proposed.
Direct Observations of a Dynamically Driven Phase Transition with in situ X-Ray Diffraction in a Simple Ionic Crystal

NASA Astrophysics Data System (ADS)

Kalita, Patricia; Specht, Paul; Root, Seth; Sinclair, Nicholas; Schuman, Adam; White, Melanie; Cornelius, Andrew L.; Smith, Jesse; Sinogeikin, Stanislav

2017-12-01

We report real-time observations of a phase transition in the ionic solid CaF2 , a model A B2 structure in high-pressure physics. Synchrotron x-ray diffraction coupled with dynamic loading to 27.7 GPa, and separately with static compression, follows, in situ, the fluorite to cotunnite structural phase transition, both on nanosecond and on minute time scales. Using Rietveld refinement techniques, we examine the kinetics and hysteresis of the transition. Our results give insight into the kinetic time scale of the fluorite-cotunnite phase transition under shock compression, which is relevant to a number of isomorphic compounds.
Domain wall formation in late-time phase transitions

NASA Technical Reports Server (NTRS)

Kolb, Edward W.; Wang, Yun

1992-01-01

We examine domain wall formulation in late time phase transitions. We find that in the invisible axion domain wall phenomenon, thermal effects alone are insufficient to drive different parts of the disconnected vacuum manifold. This suggests that domain walls do not form unless either there is some supplemental (but perhaps not unreasonable) dynamics to localize the scalar field responsible for the phase transition to the low temperature maximum (to an extraordinary precision) before the onset of the phase transition, or there is some non-thermal mechanism to produce large fluctuations in the scalar field. The fact that domain wall production is not a robust prediction of late time transitions may suggest future directions in model building.
Direct Observations of a Dynamically Driven Phase Transition with in situ X-Ray Diffraction in a Simple Ionic Crystal

DOE PAGES

Kalita, Patricia E.; Specht, Paul Elliot; Root, Seth; ...

2017-12-21

Here, we report real-time observations of a phase transition in the ionic solid CaF 2, a model AB 2 structure in high-pressure physics. Synchrotron x-ray diffraction coupled with dynamic loading to 27.7 GPa, and separately with static compression, follows, in situ, the fluorite to cotunnite structural phase transition, both on nanosecond and on minute time scales. Using Rietveld refinement techniques, we examine the kinetics and hysteresis of the transition. Our results give insight into the kinetic time scale of the fluorite-cotunnite phase transition under shock compression, which is relevant to a number of isomorphic compounds.
A resonant ultrasound spectroscopy study of the phase transitions in Na0.75CoO2

NASA Astrophysics Data System (ADS)

Keppens, Veerle; Sergienko, Ivan; Jin, Rongying

2005-03-01

The layered transition metal oxides NaxCoO2 have attracted much interest in the past few years. Crystals with the x˜0.75 composition undergo an order-disorder transition near 340 K, a spin-density-wave transition near 22 K and other subtle transitions at intermediate temperatures. These phase transitions, likely related to a rearrangement of the Na atoms among the available sites, have been mapped out using resonant ultrasound spectroscopy. The results are modeled within the Landau theory for second order phase transitions. [Oak Ridge National Laboratory is managed by UT-Battelle, LLC, for the U.S. Dept. of Energy under contract DE-AC05-00OR22725
Calorimetric Study of Phase Transitions Involving Twist-Grain-Boundary TGB{A} and TGB{C} Phases

NASA Astrophysics Data System (ADS)

Navailles, L.; Garland, C. W.; Nguyen, H. T.

1996-09-01

High-resolution calorimetry has been used to determine the heat capacity and latent heat associated with phase transitions in the homologous series of chiral liquid crystals nF_2BTFO_1M_7 [ 3-fluoro-4(1-methylheptyloxy)4'-(4''-alkoxy-2'', 3''-difluorobenzoyloxy)tolane] . These compounds exhibit smectic-C^* (SmC^*), twist-grain-boundary (TGBA for n=10, TGBC for n=11, 12) and cholesteric (N^*) phases. All the phase transitions are first order with small to moderate latent heats. There is a large rounded excess heat capacity peak in the N^* phase that is consistent with the predicted appearance of short-range TGB order (chiral line liquid character). This is analogous to the development of an Abrikosov flux vortex liquid in type-II superconductors. Both the n=11 and 12 homologs exhibit two closely spaced transitions in the region where a single TGBC - N^* transition was expected. This suggests the existence of two thermodynamically distinct TGBC phases. Des exprériences de calorimétrie haute résolution ont été réalisées pour déterminer les chaleurs spécifiques et les chaleurs latentes associées aux transitions de phase des homologues de la série crystal liquide nF_2BTFO_1M_7: 3-fluoro-4[1-methyl-heptyloxy]4'-(4''-alcoxy-2'', 3''-difluorobenzoyloxy)tolanes. Ces produits présentent la phase smectique C^* (SmC^*), les phases à torsion par joint de grain (TGBA pour n=10 et TGBC pour n=11, 12) et la phase cholestérique (N^*). Toutes les transitions de phase sont du premier ordre. La chaleur latente associée à ces transitions est faibles ou modérée. Nous observons, dans la phase N^*, un grand pic arrondi qui est en accord avec les prédictions de l'apparition d'un ordre TGB à courte distance (liquide de ligne de dislocation). Ce phénomène est l'analogue du liquide de vortex dans les supraconducteurs de type II. Les composés n=11 et 12 présentent, dans la région où nous attendions une transition TGBC - N^* unique, deux transitions sur un très faible domaine de température. Ce résultat suggère l'existence de deux phases TGBC thermodynamiquement distinctes.
Effect of water phase transition on dynamic ruptures with thermal pressurization: Numerical simulations with changes in physical properties of water

NASA Astrophysics Data System (ADS)

Urata, Yumi; Kuge, Keiko; Kase, Yuko

2015-02-01

Phase transitions of pore water have never been considered in dynamic rupture simulations with thermal pressurization (TP), although they may control TP. From numerical simulations of dynamic rupture propagation including TP, in the absence of any water phase transition process, we predict that frictional heating and TP are likely to change liquid pore water into supercritical water for a strike-slip fault under depth-dependent stress. This phase transition causes changes of a few orders of magnitude in viscosity, compressibility, and thermal expansion among physical properties of water, thus affecting the diffusion of pore pressure. Accordingly, we perform numerical simulations of dynamic ruptures with TP, considering physical properties that vary with the pressure and temperature of pore water on a fault. To observe the effects of the phase transition, we assume uniform initial stress and no fault-normal variations in fluid density and viscosity. The results suggest that the varying physical properties decrease the total slip in cases with high stress at depth and small shear zone thickness. When fault-normal variations in fluid density and viscosity are included in the diffusion equation, they activate TP much earlier than the phase transition. As a consequence, the total slip becomes greater than that in the case with constant physical properties, eradicating the phase transition effect. Varying physical properties do not affect the rupture velocity, irrespective of the fault-normal variations. Thus, the phase transition of pore water has little effect on dynamic ruptures. Fault-normal variations in fluid density and viscosity may play a more significant role.
Revisiting non-Gaussianity from non-attractor inflation models

NASA Astrophysics Data System (ADS)

Cai, Yi-Fu; Chen, Xingang; Namjoo, Mohammad Hossein; Sasaki, Misao; Wang, Dong-Gang; Wang, Ziwei

2018-05-01

Non-attractor inflation is known as the only single field inflationary scenario that can violate non-Gaussianity consistency relation with the Bunch-Davies vacuum state and generate large local non-Gaussianity. However, it is also known that the non-attractor inflation by itself is incomplete and should be followed by a phase of slow-roll attractor. Moreover, there is a transition process between these two phases. In the past literature, this transition was approximated as instant and the evolution of non-Gaussianity in this phase was not fully studied. In this paper, we follow the detailed evolution of the non-Gaussianity through the transition phase into the slow-roll attractor phase, considering different types of transition. We find that the transition process has important effect on the size of the local non-Gaussianity. We first compute the net contribution of the non-Gaussianities at the end of inflation in canonical non-attractor models. If the curvature perturbations keep evolving during the transition—such as in the case of smooth transition or some sharp transition scenarios—the Script O(1) local non-Gaussianity generated in the non-attractor phase can be completely erased by the subsequent evolution, although the consistency relation remains violated. In extremal cases of sharp transition where the super-horizon modes freeze immediately right after the end of the non-attractor phase, the original non-attractor result can be recovered. We also study models with non-canonical kinetic terms, and find that the transition can typically contribute a suppression factor in the squeezed bispectrum, but the final local non-Gaussianity can still be made parametrically large.
Final Technical Report: Application of in situ Neutron Diffraction to Understand the Mechanism of Phase Transitions

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

Chandran, Ravi

In this research, phase transitions in the bulk electrodes for Li-ion batteries were investigated using neutron diffraction (ND) as well as neutron imaging techniques. The objectives of this research is to design of a novel in situ electrochemical cell to obtain Rietveld refinable neutron diffraction experiments using small volume electrodes of various laboratory/research-scale electrodes intended for Li-ion batteries. This cell is also to be used to investigate the complexity of phase transitions in Li(Mg) alloy electrodes, either by diffraction or by neutron imaging, which occur under electrochemical lithiation and delithiation, and to determine aspects of phase transition that enable/limit energymore » storage capacity. Additional objective is to investigate the phase transitions in electrodes made of etched micro-columns of silicon and investigate the effect of particle/column size on phase transitions and nonequilibrium structures. An in situ electrochemical cell was designed successfully and was used to study the phase transitions under in-situ neutron diffraction in both the electrodes (anode/cathode) simultaneously in graphite/LiCoO 2 and in graphite/LiMn 2O 4 cells each with two cells. The diffraction patterns fully validated the working of the in situ cell. Additional experimental were performed using the Si micro-columnar electrodes. The results revealed new lithiation phenomena, as evidenced by mosaicity formation in silicon electrode. These experiments were performed in Vulcan diffractometer at SNS, Oak Ridge National Laboratory. In parallel, the spatial distribution of Li during lithiation and delithiation processes in Li-battery electrodes were investigated. For this purpose, neutron tomographic imaging technique has been used for 3D mapping of Li distribution in bulk Li(Mg) alloy electrodes. It was possible to observe the phase boundary of Li(Mg) alloy indicating phase transition from Li-rich BCC β-phase to Li-lean α-phase. These experiments have been performed at CG-1D Neutron Imaging Prototype Station at SNS.« less
Study of temperature-dependent Raman spectroscopy and electrical properties in [001]-oriented 0.35Pb(In1/2Nb1/2)O3-0.35Pb(Mg1/3Nb2/3)O3-0.30PbTiO3-Mn single crystals

NASA Astrophysics Data System (ADS)

Liu, Xing; Fang, Bijun; Deng, Ji; Yan, Hong; Deng, Hao; Yue, Qingwen; Ding, Jianning; Zhao, Xiangyong; Luo, Haosu

2016-01-01

In this work, the temperature-dependent Raman spectra and electrical properties of the [001]-oriented 0.5 mol. % Mn-doped 0.35Pb(In1/2Nb1/2)O3-0.35Pb(Mg1/3Nb2/3)O3-0.30PbTiO3-Mn (PIMNT-Mn) single crystals were investigated. All the unpoled and poled PIMNT-Mn single crystals experience a ferroelectric tetragonal phase to paraelectric cubic phase transition (FET-PC) around 183 °C (TC), which exhibits a second-order transition behavior. Whereas, the poled PIMNT-Mn single crystals exhibit another two dielectric anomalies around 130 °C (TRM) and 148 °C (TMT), in which the ferroelectric rhombohedral phase to ferroelectric monoclinic phase (FER-FEM) and the ferroelectric monoclinic phase to ferroelectric tetragonal phase (FEM-FET) transitions take place, respectively. Both the two ferroelectric phase transitions exhibit a first-order transition behavior. The discontinuous change of the phase degree (θ) and frequencies (fr and fa) around TRM suggest the occurrence of the FER-FEM phase transition in the poled PIMNT-Mn single crystals. The narrowing of the 510 cm-1 and 582 cm-1 Raman modes around the TRM, TMT, and TC temperatures shown in the temperature-dependent Raman spectra suggests their increased ordering of the local structure. The intensity ratio of I272 cm-1/I801 cm-1 increases obviously around the phase transition temperatures (TRM, TMT, and TC), indicating the reduction of the long-range order. The anomalous broadening of the 272 cm-1 Raman mode around the TRM, TMT, and TC temperatures indicates the occurrence of the successive ferroelectric phase transitions (FER-FEM, FEM-FET, and FET-PC) with increasing temperature in the poled PIMNT-Mn single crystals.
Phase transitions in core-collapse supernova matter at sub-saturation densities

NASA Astrophysics Data System (ADS)

Pais, Helena; Newton, William G.; Stone, Jirina R.

2014-12-01

Phase transitions in hot, dense matter in the collapsing cores of massive stars have an important impact on the core-collapse supernova mechanism as they absorb heat, disrupt homology, and so weaken the developing shock. We perform a three-dimensional, finite temperature Skyrme-Hartree-Fock (SHF) study of inhomogeneous nuclear matter to determine the critical density and temperature for the phase transition between the pasta phase and homogeneous matter and its properties. We employ four different parametrizations of the Skyrme nuclear energy-density functional, SkM*, SLy4, NRAPR, and SQMC700, which span a range of saturation-density symmetry energy behaviors constrained by a variety of nuclear experimental probes. For each of these interactions we calculate free energy, pressure, entropy, and chemical potentials in the range of particle number densities where the nuclear pasta phases are expected to exist, 0.02-0.12 fm-3, temperatures 2-8 MeV, and a proton fraction of 0.3. We find unambiguous evidence for a first-order phase transition to uniform matter, unsoftened by the presence of the pasta phases. No conclusive signs of a first-order phase transition between the pasta phases is observed, and it is argued that the thermodynamic quantities vary continuously right up to the first-order phase transition to uniform matter. We compare our results with thermodynamic spinodals calculated using the same Skyrme parametrizations, finding that the effect of short-range Coulomb correlations and quantum shell effects included in our model leads to the pasta phases existing at densities up to 0.01 fm-3 above the spinodal boundaries, thus increasing the transition density to uniform matter by the same amount. The transition density is otherwise shown to be insensitive to the symmetry energy at saturation density within the range constrained by the concordance of a variety of experimental constraints, and can be taken to be a well determined quantity.
Interface mobility and the liquid-glass transition in a one-component system described by an embedded atom method potential

NASA Astrophysics Data System (ADS)

Mendelev, M. I.; Schmalian, J.; Wang, C. Z.; Morris, J. R.; Ho, K. M.

2006-09-01

We present molecular dynamics (MD) studies of the liquid structure, thermodynamics, and dynamics in a one-component system described by the Ercolessi-Adams embedded atom method potential for Al. We find two distinct noncrystalline phases in this system. One of them is a liquid phase and the second phase has similar structure but different equation of state. Moreover, this phase has qualitatively different dynamics than that in the liquid phase. The transitions between these two noncrystalline phases can be seen during MD simulation. The hysteresis in this transition suggests that this is a first-order transition. This conclusion is strongly supported by simulations of the two phases that demonstrate that these phases may coexist with a well-defined interface. We find the coexistent temperature and the interface mobility. Finally, we discuss how these results can be explained using modern models of vitrification.
Flipping the Switch from G1 to S Phase with E3 Ubiquitin Ligases

PubMed Central

Rizzardi, Lindsay F.

2012-01-01

The cell cycle ensures genome maintenance by coordinating the processes of DNA replication and chromosome segregation. Of particular importance is the irreversible transition from the G1 phase of the cell cycle to S phase. This transition marks the switch from preparing chromosomes for replication (“origin licensing”) to active DNA synthesis (“origin firing”). Ubiquitin-mediated proteolysis is essential for restricting DNA replication to only once per cell cycle and is the major mechanism regulating the G1 to S phase transition. Although some changes in protein levels are attributable to regulated mRNA abundance, protein degradation elicits very rapid changes in protein abundance and is critical for the sharp and irreversible transition from one cell cycle stage to the next. Not surprisingly, regulation of the G1-to-S phase transition is perturbed in most cancer cells, and deregulation of key molecular events in G1 and S phase drives not only cell proliferation but also genome instability. In this review we focus on the mechanisms by which E3 ubiquitin ligases control the irreversible transition from G1 to S phase in mammalian cells. PMID:23634252
The influence of the relative thermal expansion and electric permittivity on phase transitions in the perovskite-type bidimensional layered NH3(CH2)3NH3CdBr4 compound

NASA Astrophysics Data System (ADS)

Staśkiewicz, Beata; Staśkiewicz, Anna

2017-07-01

Hydrothermal method has been used to synthesized the layered hybrid compound NH3(CH2)3NH3CdBr4 of perovskite architecture. Structural, dielectric and dilatometric properties of the compound have been analyzed. Negative thermal expansion (NTE) effect in the direction perpendicular to the perovskite plane as well as an unusual phase sequence have been reported based on X-ray diffraction analysis. Electric permittivity measurements evidenced the phase transitions at Tc1=326/328 K and Tc2=368/369 K. Relative linear expansion measurements almost confirmed these temperatures of phase transitions. Anomalies of electric permittivity and expansion behavior connected with the phase transitions are detected at practically the same temperatures as those observed earlier in differential scanning calorimetry (DSC), infrared (IR), far infrared (FIR) and Raman spectroscopy studies. Mechanism of the phase transitions is explained. Relative linear expansion study was prototype to estimate critical exponent value β for continuous phase transition at Tc1. It has been inferred that there is a strong interplay between the distortion of the inorganic network, those hydrogen bonds and the intermolecular interactions of the organic component.
Dielectric Study of the Phase Transitions in [P(CH3)4]2CuY4 (Y = Cl, Br)

NASA Astrophysics Data System (ADS)

Gesi, Kazuo

2002-05-01

Phase transitions in [P(CH3)4]2CuY4 (Y = Cl, Br) have been studied by dielectric measurements. In [P(CH3)4]2CuCl4, a slight break and a discontinuous jump on the dielectric constant vs. temperature curve are seen at the normal-incommensurate and the incommensurate-commensurate phase transitions, respectively. A small peak of dielectric constant along the b-direction exists just above the incommensurate-to-commensurate transition temperature. The anisotropic dielectric anomalies of [P(CH3)4]2CuBr4 at phase transitions were measured along the three crystallographic axes. The pressure-temperature phase diagram of [P(CH3)4]2CuCl4 was determined. The initial pressure coefficients of the normal-to-incommensurate and the incommensurate-to-commensurate transition temperatures are 0.19 K/MPa and 0.27 K/MPa, respectively. The incommensurate phase in [P(CH3)4]2CuCl4 disappears at a triple point which exists at 335 MPa and 443 K. The stability and the pressure effects of the incommensurate phases are much different among the four [Z(CH3)4]2CuY4 crystals (Z = N, P; Y = Cl, Br).
High-pressure phase transitions - Examples of classical predictability

NASA Astrophysics Data System (ADS)

Celebonovic, Vladan

1992-09-01

The applicability of the Savic and Kasanin (1962-1967) classical theory of dense matter to laboratory experiments requiring estimates of high-pressure phase transitions was examined by determining phase transition pressures for a set of 19 chemical substances (including elements, hydrocarbons, metal oxides, and salts) for which experimental data were available. A comparison between experimental and transition points and those predicted by the Savic-Kasanin theory showed that the theory can be used for estimating values of transition pressures. The results also support conclusions obtained in previous astronomical applications of the Savic-Kasanin theory.

Molecular candidates for early-stage flower-to-fruit transition in stenospermocarpic table grape (Vitis vinifera L.) inflorescences ascribed by differential transcriptome and metabolome profiles.

PubMed

Domingos, Sara; Fino, Joana; Paulo, Octávio S; Oliveira, Cristina M; Goulao, Luis F

2016-03-01

Flower-to-fruit transition depends of nutrient availability and regulation at the molecular level by sugar and hormone signalling crosstalk. However, in most species, the identities of fruit initiation regulators and their targets are largely unknown. To ascertain the main pathways involved in stenospermocarpic table grape fruit set, comprehensive transcriptional and metabolomic analyses were conducted specifically targeting the early phase of this developmental stage in 'Thompson Seedless'. The high-throughput analyses performed disclosed the involvement of 496 differentially expressed genes and 28 differently accumulated metabolites in the sampled inflorescences. Our data show broad transcriptome reprogramming of molecule transporters, globally down-regulating gene expression, and suggest that regulation of sugar- and hormone-mediated pathways determines the downstream activation of berry development. The most affected gene was the SWEET14 sugar transporter. Hormone-related transcription changes were observed associated with increased indole-3-acetic acid, stimulation of ethylene and gibberellin metabolisms and cytokinin degradation, and regulation of MADS-box and AP2-like ethylene-responsive transcription factor expression. Secondary metabolism, the most representative biological process at transcriptome level, was predominantly repressed. The results add to the knowledge of molecular events occurring in grapevine inflorescence fruit set and provide a list of candidates, paving the way for genetic manipulation aimed at model research and plant breeding. Copyright © 2015 Elsevier Ireland Ltd. All rights reserved.
Mixed-order phase transition in a two-step contagion model with a single infectious seed.

PubMed

Choi, Wonjun; Lee, Deokjae; Kahng, B

2017-02-01

Percolation is known as one of the most robust continuous transitions, because its occupation rule is intrinsically local. As one of the ways to break the robustness, occupation is allowed to more than one species of particles and they occupy cooperatively. This generalized percolation model undergoes a discontinuous transition. Here we investigate an epidemic model with two contagion steps and characterize its phase transition analytically and numerically. We find that even though the order parameter jumps at a transition point r_{c}, then increases continuously, it does not exhibit any critical behavior: the fluctuations of the order parameter do not diverge at r_{c}. However, critical behavior appears in mean outbreak size, which diverges at the transition point in a manner that the ordinary percolation shows. Such a type of phase transition is regarded as a mixed-order phase transition. We also obtain scaling relations of cascade outbreak statistics when the order parameter jumps at r_{c}.
Plasmonic Structures for CMOS Photonics and Control of Spontaneous Emission

DTIC Science & Technology

2013-04-01

structures; v) developed CMOS Si photonic switching device based on the vanadium dioxide ( VO2 ) phase transition. vi) also engaged in a partnership with...CMOS Si photonic switching device based on the vanadium dioxide ( VO2 ) phase transition. vii. exploring approaches to enhance spontaneous emission in...size and bandwidth, we are exploring phase-change materials and, in particular, vanadium dioxide. VO2 undergoes an insulator-to-metal phase transition
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
Quantum multicriticality in disordered Weyl semimetals

NASA Astrophysics Data System (ADS)

Luo, Xunlong; Xu, Baolong; Ohtsuki, Tomi; Shindou, Ryuichi

2018-01-01

In electronic band structure of solid-state material, two band-touching points with linear dispersion appear in pairs in the momentum space. When they annihilate each other, the system undergoes a quantum phase transition from a three-dimensional (3D) Weyl semimetal (WSM) phase to a band insulator phase such as a Chern band insulator (CI) phase. The phase transition is described by a new critical theory with a "magnetic dipole"-like object in the momentum space. In this paper, we reveal that the critical theory hosts a novel disorder-driven quantum multicritical point, which is encompassed by three quantum phases: a renormalized WSM phase, a CI phase, and a diffusive metal (DM) phase. Based on the renormalization group argument, we first clarify scaling properties around the band-touching points at the quantum multicritical point as well as all phase boundaries among these three phases. Based on numerical calculations of localization length, density of states, and critical conductance distribution, we next prove that a localization-delocalization transition between the CI phase with a finite zero-energy density of states (zDOS) and DM phase belongs to an ordinary 3D unitary class. Meanwhile, a localization-delocalization transition between the Chern insulator phase with zero zDOS and a renormalized WSM phase turns out to be a direct phase transition whose critical exponent ν =0.80 ±0.01 . We interpret these numerical results by a renormalization group analysis on the critical theory.
Second order phase transition in thermodynamic geometry and holographic superconductivity in low-energy stringy black holes

NASA Astrophysics Data System (ADS)

Rizwan, C. L. Ahmed; Vaid, Deepak

2018-05-01

We study holographic superconductivity in low-energy stringy Garfinkle-Horowitz-Strominger (GHS) dilaton black hole background. We finds that superconducting properties are much similar to s-wave superconductors. We show that the second-order phase transition indicated from thermodynamic geometry is not different from superconducting phase transition.
Multipartite entanglement characterization of a quantum phase transition

NASA Astrophysics Data System (ADS)

Costantini, G.; Facchi, P.; Florio, G.; Pascazio, S.

2007-07-01

A probability density characterization of multipartite entanglement is tested on the one-dimensional quantum Ising model in a transverse field. The average and second moment of the probability distribution are numerically shown to be good indicators of the quantum phase transition. We comment on multipartite entanglement generation at a quantum phase transition.
40 CFR Appendix II to Part 1042 - Steady-State Duty Cycles

Code of Federal Regulations, 2011 CFR

2011-07-01

... the maximum test power. 3 Advance from one mode to the next within a 20-second transition phase. During the transition phase, command a linear progression from the torque setting of the current mode to... transition phase, command a linear progression from the torque setting of the current mode to the torque...
Shock loading and release behavior of silicon nitride

NASA Astrophysics Data System (ADS)

Kawai, Nobuaki; Tsuru, Taiki; Hidaka, Naoto; Liu, Xun; Mashimo, Tsutomu

2015-06-01

Shock-reshock and shock-release experiments were performed on silicon nitride ceramics above and below its phase transition pressure. Experimental results clearly show the occurrence of elastic-plastic transition and phase transition during initial shock loading. The HEL and phase transition stress are determined as 11.6 GPa and 34.5 GPa, respectively. Below the phase transition point, the reshock profile consists of the single shock with short rise time, while the release profile shows the gradual release followed by more rapid one. Above the phase transition point, reshock and release behavior varies with the initial shock stress. In the case of reshock and release from about 40 GPa, the reshock structure is considerably dispersed, while the release structure shows rapid release. In the reshock profile from about 50 GPa, the formation of the shock wave with the small ramped precursor is observed. And, the release response from same condition shows initial gradual release and subsequent quite rapid one. These results would provide the information about how phase transformation kinetics effects on the reshock and release behavior.
Non-resonant collider signatures of a singlet-driven electroweak phase transition

NASA Astrophysics Data System (ADS)

Chen, Chien-Yi; Kozaczuk, Jonathan; Lewis, Ian M.

2017-08-01

We analyze the collider signatures of the real singlet extension of the Standard Model in regions consistent with a strong first-order electroweak phase transition and a singlet-like scalar heavier than the Standard Model-like Higgs. A definitive correlation exists between the strength of the phase transition and the trilinear coupling of the Higgs to two singlet-like scalars, and hence between the phase transition and non-resonant scalar pair production involving the singlet at colliders. We study the prospects for observing these processes at the LHC and a future 100 TeV pp collider, focusing particularly on double singlet production. We also discuss correlations between the strength of the electroweak phase transition and other observables at hadron and future lepton colliders. Searches for non-resonant singlet-like scalar pair production at 100 TeV would provide a sensitive probe of the electroweak phase transition in this model, complementing resonant di-Higgs searches and precision measurements. Our study illustrates a strategy for systematically exploring the phenomenologically viable parameter space of this model, which we hope will be useful for future work.
Non-resonant collider signatures of a singlet-driven electroweak phase transition

DOE PAGES

Chen, Chien-Yi; Kozaczuk, Jonathan; Lewis, Ian M.

2017-08-22

We analyze the collider signatures of the real singlet extension of the Standard Model in regions consistent with a strong first-order electroweak phase transition and a singlet-like scalar heavier than the Standard Model-like Higgs. A definitive correlation exists between the strength of the phase transition and the trilinear coupling of the Higgs to two singlet-like scalars, and hence between the phase transition and non-resonant scalar pair production involving the singlet at colliders. We study the prospects for observing these processes at the LHC and a future 100 TeV pp collider, focusing particularly on double singlet production. We also discuss correlationsmore » between the strength of the electroweak phase transition and other observables at hadron and future lepton colliders. Searches for non-resonant singlet-like scalar pair production at 100 TeV would provide a sensitive probe of the electroweak phase transition in this model, complementing resonant di-Higgs searches and precision measurements. Our study illustrates a strategy for systematically exploring the phenomenologically viable parameter space of this model, which we hope will be useful for future work.« less
Histological characterization of peppermint shrimp ( Lysmata wurdemanni) androgenic gland

NASA Astrophysics Data System (ADS)

Liu, Xin; Zhang, Dong; Lin, Tingting

2017-12-01

The androgenic gland (AG) is an important endocrine gland for male reproductive function in crustaceans. In the present study, we investigated the histological characteristics of the androgenic gland of peppermint shrimp, Lysmata wurdemanni. The peppermint shrimp matures as male first, then some individuals may become euhermaphrodite after several moltings (transitional phase). Euhermaphrodite-phase shrimp acts as male at intermolts. However, it can be fertilized as a female immediately after molting. Considering the male reproductive function acts in its lifespan except for at larval stages, and female reproductive system starts to develop at transitional phase, we hypothesized that AG activity might be reduced to allow and promote vitellogenesis onset in early transitional phase and the following euhermaphrodite phase. So AG cell structure might be different in three phases in L. wurdemanni. The results showed that AG exists in the male in transitional and euhermaphrodite phases. The gland cell clusters surrounding the ejaculatory ducts locate at the roots of the fifth pereopods. The nucleus diameters are similar in the three phases while the nucleus- to-cell ratio is the lowest in euhermaphrodite phase. Our results indicated that for the individuals that will become euhermaphrodite, the cellular structure of AG changes since transitional phase. Male reproductive function which is still available in euhermaphrodite-phase shrimp should be due to the existence of the gland.
Calcineurin plays key roles in the dimorphic transition and virulence of the human pathogenic zygomycete Mucor circinelloides.

PubMed

Lee, Soo Chan; Li, Alicia; Calo, Silvia; Heitman, Joseph

2013-01-01

Many pathogenic fungi are dimorphic and switch between yeast and filamentous states. This switch alters host-microbe interactions and is critical for pathogenicity. However, in zygomycetes, whether dimorphism contributes to virulence is a central unanswered question. The pathogenic zygomycete Mucor circinelloides exhibits hyphal growth in aerobic conditions but switches to multi-budded yeast growth under anaerobic/high CO₂ conditions. We found that in the presence of the calcineurin inhibitor FK506, Mucor exhibits exclusively multi-budded yeast growth. We also found that M. circinelloides encodes three calcineurin catalytic A subunits (CnaA, CnaB, and CnaC) and one calcineurin regulatory B subunit (CnbR). Mutations in the latch region of CnbR and in the FKBP12-FK506 binding domain of CnaA result in hyphal growth of Mucor in the presence of FK506. Disruption of the cnbR gene encoding the sole calcineurin B subunit necessary for calcineurin activity yielded mutants locked in permanent yeast phase growth. These findings reveal that the calcineurin pathway plays key roles in the dimorphic transition from yeast to hyphae. The cnbR yeast-locked mutants are less virulent than the wild-type strain in a heterologous host system, providing evidence that hyphae or the yeast-hyphal transition are linked to virulence. Protein kinase A activity (PKA) is elevated during yeast growth under anaerobic conditions, in the presence of FK506, or in the yeast-locked cnbR mutants, suggesting a novel connection between PKA and calcineurin. cnaA mutants lacking the CnaA catalytic subunit are hypersensitive to calcineurin inhibitors, display a hyphal polarity defect, and produce a mixture of yeast and hyphae in aerobic culture. The cnaA mutants also produce spores that are larger than wild-type, and spore size is correlated with virulence potential. Our results demonstrate that the calcineurin pathway orchestrates the yeast-hyphal and spore size dimorphic transitions that contribute to virulence of this common zygomycete fungal pathogen.
Measurement of a solid-state triple point at the metal-insulator transition in VO2.

PubMed

Park, Jae Hyung; Coy, Jim M; Kasirga, T Serkan; Huang, Chunming; Fei, Zaiyao; Hunter, Scott; Cobden, David H

2013-08-22

First-order phase transitions in solids are notoriously challenging to study. The combination of change in unit cell shape, long range of elastic distortion and flow of latent heat leads to large energy barriers resulting in domain structure, hysteresis and cracking. The situation is worse near a triple point, where more than two phases are involved. The well-known metal-insulator transition in vanadium dioxide, a popular candidate for ultrafast optical and electrical switching applications, is a case in point. Even though VO2 is one of the simplest strongly correlated materials, experimental difficulties posed by the first-order nature of the metal-insulator transition as well as the involvement of at least two competing insulating phases have led to persistent controversy about its nature. Here we show that studying single-crystal VO2 nanobeams in a purpose-built nanomechanical strain apparatus allows investigation of this prototypical phase transition with unprecedented control and precision. Our results include the striking finding that the triple point of the metallic phase and two insulating phases is at the transition temperature, Ttr = Tc, which we determine to be 65.0 ± 0.1 °C. The findings have profound implications for the mechanism of the metal-insulator transition in VO2, but they also demonstrate the importance of this approach for mastering phase transitions in many other strongly correlated materials, such as manganites and iron-based superconductors.
Quantum phase transition with dissipative frustration

NASA Astrophysics Data System (ADS)

Maile, D.; Andergassen, S.; Belzig, W.; Rastelli, G.

2018-04-01

We study the quantum phase transition of the one-dimensional phase model in the presence of dissipative frustration, provided by an interaction of the system with the environment through two noncommuting operators. Such a model can be realized in Josephson junction chains with shunt resistances and resistances between the chain and the ground. Using a self-consistent harmonic approximation, we determine the phase diagram at zero temperature which exhibits a quantum phase transition between an ordered phase, corresponding to the superconducting state, and a disordered phase, corresponding to the insulating state with localized superconducting charge. Interestingly, we find that the critical line separating the two phases has a nonmonotonic behavior as a function of the dissipative coupling strength. This result is a consequence of the frustration between (i) one dissipative coupling that quenches the quantum phase fluctuations favoring the ordered phase and (ii) one that quenches the quantum momentum (charge) fluctuations leading to a vanishing phase coherence. Moreover, within the self-consistent harmonic approximation, we analyze the dissipation induced crossover between a first and second order phase transition, showing that quantum frustration increases the range in which the phase transition is second order. The nonmonotonic behavior is reflected also in the purity of the system that quantifies the degree of correlation between the system and the environment, and in the logarithmic negativity as an entanglement measure that encodes the internal quantum correlations in the chain.
Higher order cumulants in colorless partonic plasma

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

Cherif, S.; Laboratoire de Physique et de Mathématiques Appliquées; Ahmed, M. A. A.

2016-06-10

Any physical system considered to study the QCD deconfinement phase transition certainly has a finite volume, so the finite size effects are inevitably present. This renders the location of the phase transition and the determination of its order as an extremely difficult task, even in the simplest known cases. In order to identify and locate the colorless QCD deconfinement transition point in finite volume T{sub 0}(V), a new approach based on the finite-size cumulant expansion of the order parameter and the ℒ{sub m,n}-Method is used. We have shown that both cumulants of higher order and their ratios, associated to themore » thermodynamical fluctuations of the order parameter, in QCD deconfinement phase transition behave in a particular enough way revealing pronounced oscillations in the transition region. The sign structure and the oscillatory behavior of these in the vicinity of the deconfinement phase transition point might be a sensitive probe and may allow one to elucidate their relation to the QCD phase transition point. In the context of our model, we have shown that the finite volume transition point is always associated to the appearance of a particular point in whole higher order cumulants under consideration.« less
Liquid-liquid phase transformations and the shape of the melting curve.

PubMed

Makov, G; Yahel, E

2011-05-28

The phase diagram of elemental liquids has been found to be surprisingly rich, including variations in the melting curve and transitions in the liquid phase. The effect of these transitions in the liquid state on the shape of the melting curve is analyzed. First-order phase transitions intersecting the melting curve imply piecewise continuous melting curves, with solid-solid transitions generating upward kinks or minima and liquid-liquid transitions generating downward kinks or maxima. For liquid-liquid phase transitions proposed for carbon, phosphorous selenium, and possibly nitrogen, we find that the melting curve exhibits a kink. Continuous transitions imply smooth extrema in the melting curve, the curvature of which is described by an exact thermodynamic relation. This expression indicates that a minimum in the melting curve requires the solid compressibility to be greater than that of the liquid, a very unusual situation. This relation is employed to predict the loci of smooth maxima at negative pressures for liquids with anomalous melting curves. The relation between the location of the melting curve maximum and the two-state model of continuous liquid-liquid transitions is discussed and illustrated by the case of tellurium. © 2011 American Institute of Physics
Compact stars in Eddington-inspired Born-Infeld gravity: Anomalies associated with phase transitions

NASA Astrophysics Data System (ADS)

Sham, Y.-H.; Leung, P. T.; Lin, L.-M.

2013-03-01

We study how generic phase transitions taking place in compact stars constructed in the framework of the Eddington-inspired Born-Infeld (EiBI) gravity can lead to anomalous behavior of these stars. For the case with first-order phase transitions, compact stars in EiBI gravity with a positive coupling parameter κ exhibit a finite region with constant pressure, which is absent in general relativity. However, for the case with a negative κ, an equilibrium stellar configuration cannot be constructed. Hence EiBI gravity seems to impose stricter constraints on the microphysics of stellar matter. Besides, in the presence of spatial discontinuities in the sound speed cs due to phase transitions, the Ricci scalar is spatially discontinuous and contains δ-function singularities proportional to the jump in cs2 acquired in the associated phase transition.
Cubic to tetragonal phase transition of Tm{sup 3+} doped nanocrystals in oxyfluoride glass ceramics

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

Li, Yiming; Fu, Yuting; Shi, Yahui

2016-02-15

Tm{sup 3+} ions doped β-PbF{sub 2} nanocrystals in oxyfluoride glass ceramics with different doping concentrations and thermal temperatures are prepared by a traditional melt-quenching and thermal treatment method to investigate the structure and the phase transition of Tm{sup 3+} doped nanocrystals. The structures are characterized by X-ray diffraction Rietveld analysis and confirmed with numerical simulation. The phase transitions are proved further by the emission spectra. Both of the doping concentration and thermal temperature can induce an O{sub h} to D{sub 4h} site symmetry distortion and a cubic to tetragonal phase transition. The luminescence of Tm{sup 3+} doped nanocrystals at 800more » nm was modulated by the phase transition of the surrounding crystal field.« less
The Higgs vacuum uplifted: revisiting the electroweak phase transition with a second Higgs doublet

NASA Astrophysics Data System (ADS)

Dorsch, G. C.; Huber, S. J.; Mimasu, K.; No, J. M.

2017-12-01

The existence of a second Higgs doublet in Nature could lead to a cosmological first order electroweak phase transition and explain the origin of the matter-antimatter asymmetry in the Universe. We explore the parameter space of such a two-Higgs-doublet-model and show that a first order electroweak phase transition strongly correlates with a significant uplifting of the Higgs vacuum w.r.t. its Standard Model value. We then obtain the spectrum and properties of the new scalars H 0, A 0 and H ± that signal such a phase transition, showing that the decay A 0 → H 0 Z at the LHC and a sizable deviation in the Higgs self-coupling λ hhh from its SM value are sensitive indicators of a strongly first order electroweak phase transition in the 2HDM.

Some links on this page may take you to non-federal websites. Their policies may differ from this site.