Dynamics and intramolecular ligand binding of DtxR studied by MD simulations and NMR spectroscopy

NASA Astrophysics Data System (ADS)

Yi, Myunggi; Bhattacharya, Nilakshee; Zhou, Huan-Xiang

2005-11-01

Diphtheria toxin repressor (DtxR) regulates the expression of the diphtheria toxin gene through intramolecular ligand binding (Wylie et al., Biochemistry 2005, 44:40-51). Protein dynamics is essential to the binding process of the Pro-rich (Pr) ligand to the C-terminal SH3 domain. We present MD and NMR results on the dynamics and ligand interactions of a Pr-SH3 construct of DtxR. NMR relaxation data (T1, T2, and NOE) showed that the Pr ligand is very flexible, suggesting that it undergoes binding/unbinding transitions. A 50-ns MD trajectory of the protein was used to calculate T1, T2, and NOE, reproducing the NMR results for the SH3 domain but not for the Pr segment. During the MD simulation, the ligand stayed bound to the SH3 domain; thus the simulation represented the bound state. The NMR data for the Pr-segment could be explained by assuming that they represented the average behavior of a fast binding/unbinding exchange. Though unbinding was not observed in the MD simulation, the simulation did show large fluctuations of a loop which forms part of the wall of the binding pocket. The fluctuations led to opening up of the binding pocket, thus weakening the interaction with the Pr segment and perhaps ultimately leading to ligand unbinding.

Orbital-differentiated coherence-incoherence crossover identified by photoemission spectroscopy in LiFeAs

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

Miao, H.; Yin, Z. P.; Wu, S. F.

In the iron-based superconductors (FeSCs), orbital differentiation is an important phenomenon, whereby correlations stronger on the d xy orbital than on the d xz/d yz orbital yield quasi-particles with d xy orbital character having larger mass renormalization and abnormal temperature evolution. However, the physical origin of this orbital di erentiation is debated between the Hund's coupling induced unbinding of spin and orbital degrees of freedom and the Hubbard interaction instigated orbital selective Mott transition. Here we use angle-resolved photoemission spectroscopy to identify an orbital-dependent correlation-induced quasi-particle (QP) anomaly in LiFeAs. Lastly, the excellent agreement between our photoemission measurements and first-principlesmore » many-body theory calculations shows that the orbital-differentiated QP lifetime anomalies in LiFeAs are controlled by the Hund's coupling.« less

Orbital-differentiated coherence-incoherence crossover identified by photoemission spectroscopy in LiFeAs

DOE PAGES

Miao, H.; Yin, Z. P.; Wu, S. F.; ...

2016-11-14

In the iron-based superconductors (FeSCs), orbital differentiation is an important phenomenon, whereby correlations stronger on the d xy orbital than on the d xz/d yz orbital yield quasi-particles with d xy orbital character having larger mass renormalization and abnormal temperature evolution. However, the physical origin of this orbital di erentiation is debated between the Hund's coupling induced unbinding of spin and orbital degrees of freedom and the Hubbard interaction instigated orbital selective Mott transition. Here we use angle-resolved photoemission spectroscopy to identify an orbital-dependent correlation-induced quasi-particle (QP) anomaly in LiFeAs. Lastly, the excellent agreement between our photoemission measurements and first-principlesmore » many-body theory calculations shows that the orbital-differentiated QP lifetime anomalies in LiFeAs are controlled by the Hund's coupling.« less

Curvature-induced defect unbinding and dynamics in active nematic toroids

NASA Astrophysics Data System (ADS)

Ellis, Perry W.; Pearce, Daniel J. G.; Chang, Ya-Wen; Goldsztein, Guillermo; Giomi, Luca; Fernandez-Nieves, Alberto

2018-01-01

Nematic order on curved surfaces is often disrupted by the presence of topological defects, which are singular regions in which the orientational order is undefined. In the presence of force-generating active materials, these defects are able to migrate through space like swimming microorganisms. We use toroidal surfaces to show that despite their highly chaotic and non-equilibrium dynamics, pairs of defects unbind and segregate in regions of opposite Gaussian curvature. Using numerical simulations, we find that the degree of defect unbinding can be controlled by tuning the system activity, and even suppressed in strongly active systems. Furthermore, by using the defects as active microrheological tracers and quantitatively comparing our experimental and theoretical results, we are able to determine material properties of the active nematic. Our results illustrate how topology and geometry can be used to control the behaviour of active materials, and introduce a new avenue for the quantitative mechanical characterization of active fluids.

Direct measurements of multiple adhesive alignments and unbinding trajectories between cadherin extracellular domains.

PubMed Central

Sivasankar, S; Gumbiner, B; Leckband, D

2001-01-01

Direct measurements of the interactions between antiparallel, oriented monolayers of the complete extracellular region of C-cadherin demonstrate that, rather than binding in a single unique orientation, the cadherins adhere in three distinct alignments. The strongest adhesion is observed when the opposing extracellular fragments are completely interdigitated. A second adhesive alignment forms when the interdigitated proteins separate by 70 +/- 10 A. A third complex forms at a bilayer separation commensurate with the approximate overlap of cadherin extracellular domains 1 and 2 (CEC1-2). The locations of the energy minima are independent of both the surface density of bound cadherin and the stiffness of the force transducer. Using surface element integration, we show that two flat surfaces that interact through an oscillatory potential will exhibit discrete minima at the same locations in the force profile measured between hemicylinders covered with identical materials. The measured interaction profiles, therefore, reflect the relative separations at which the antiparallel proteins adhere, and are unaffected by the curvature of the underlying substrate. The successive formation and rupture of multiple protein contacts during detachment can explain the observed sluggish unbinding of cadherin monolayers. Velocity-distance profiles, obtained by quantitative video analysis of the unbinding trajectory, exhibit three velocity regimes, the transitions between which coincide with the positions of the adhesive minima. These findings suggest that cadherins undergo multiple stage unbinding, which may function to impede adhesive failure under force. PMID:11259289

Revealing the favorable dissociation pathway of type II kinase inhibitors via enhanced sampling simulations and two-end-state calculations.

PubMed

Sun, Huiyong; Tian, Sheng; Zhou, Shunye; Li, Youyong; Li, Dan; Xu, Lei; Shen, Mingyun; Pan, Peichen; Hou, Tingjun

2015-02-13

How does a type II inhibitor bind to/unbind from a kinase target is still a confusing question because the small molecule occupies both the ATP pocket and the allosteric pocket of the kinase binding site. Here, by using enhanced sampling simulations (umbrella sampling, US) and two-end-state free energy calculations (MM/GSBA), we systemically studied the dissociation processes of two distinct small molecules escaping from the binding pocket of p38 MAP kinase through the allosteric channel and the ATP channel. The results show that the unbinding pathways along the allosteric channel have much lower PMF depths than those along the ATP channel, suggesting that the allosteric channel is more favorable for the dissociations of the two inhibitors and thereby supporting the general understanding that the largest channel of a target is usually the entry/exit pathway for the binding/dissociation of small molecules. Interestingly, the MM/GBSA approach yielded similar PMF profiles compared with those based on US, a much time consuming approach, indicating that for a general study, such as detecting the important transition state of a ligand binding/unbinding process, MM/GBSA may be a feasible choice.

Structural Rheology of the Smectic Phase

PubMed Central

Fujii, Shuji; Komura, Shigeyuki; Lu, Chun-Yi David

2014-01-01

In this review article, we discuss the rheological properties of the thermotropic smectic liquid crystal 8CB with focal conic domains (FCDs) from the viewpoint of structural rheology. It is known that the unbinding of the dislocation loops in the smectic phase drives the smectic-nematic transition. Here we discuss how the unbinding of the dislocation loops affects the evolution of the FCD size, linear and nonlinear rheological behaviors of the smectic phase. By studying the FCD formation from the perpendicularly oriented smectic layers, we also argue that dislocations play a key role in the structural development in layered systems. Furthermore, similarities in the rheological behavior between the FCDs in the smectic phase and the onion structures in the lyotropic lamellar phase suggest that these systems share a common physical origin for the elasticity. PMID:28788123

Molecular determinants of cadherin ideal bond formation: Conformation-dependent unbinding on a multidimensional landscape

PubMed Central

Manibog, Kristine; Sankar, Kannan; Kim, Sun-Ae; Zhang, Yunxiang; Jernigan, Robert L.; Sivasankar, Sanjeevi

2016-01-01

Classical cadherin cell–cell adhesion proteins are essential for the formation and maintenance of tissue structures; their primary function is to physically couple neighboring cells and withstand mechanical force. Cadherins from opposing cells bind in two distinct trans conformations: strand-swap dimers and X-dimers. As cadherins convert between these conformations, they form ideal bonds (i.e., adhesive interactions that are insensitive to force). However, the biophysical mechanism for ideal bond formation is unknown. Here, we integrate single-molecule force measurements with coarse-grained and atomistic simulations to resolve the mechanistic basis for cadherin ideal bond formation. Using simulations, we predict the energy landscape for cadherin adhesion, the transition pathways for interconversion between X-dimers and strand-swap dimers, and the cadherin structures that form ideal bonds. Based on these predictions, we engineer cadherin mutants that promote or inhibit ideal bond formation and measure their force-dependent kinetics using single-molecule force-clamp measurements with an atomic force microscope. Our data establish that cadherins adopt an intermediate conformation as they shuttle between X-dimers and strand-swap dimers; pulling on this conformation induces a torsional motion perpendicular to the pulling direction that unbinds the proteins and forms force-independent ideal bonds. Torsional motion is blocked when cadherins associate laterally in a cis orientation, suggesting that ideal bonds may play a role in mechanically regulating cadherin clustering on cell surfaces. PMID:27621473

Tension-induced binding of semiflexible biopolymers

NASA Astrophysics Data System (ADS)

Benetatos, Panayotis; von der Heydt, Alice; Zippelius, Annette

2015-03-01

We investigate theoretically the effect of polymer tension on the collective behaviour of reversible cross-links. We use a model of two parallel-aligned, weakly-bending wormlike chains with a regularly spaced sequence of binding sites subjected to a tensile force. Reversible cross-links attach and detach at the binding sites with an affinity controlled by a chemical potential. In a mean-field approach, we calculate the free energy of the system and we show the emergence of a free energy barrier which controls the reversible (un)binding. The tension affects the conformational entropy of the chains which competes with the binding energy of the cross-links. This competition gives rise to a sudden increase in the fraction of bound sites as the polymer tension increases. The force-induced first-order transition in the number of cross-links implies a sudden force-induced stiffening of the effective stretching modulus of the polymers. This mechanism may be relevant to the formation and stress-induced strengthening of stress fibers in the cytoskeleton. We acknowledge support by the Deutsche Forschungsgemeinschaft (DFG) via grant SFB-937/A1.

Non-Markovian effects in the first-passage dynamics of obstructed tracer particle diffusion in one-dimensional systems

NASA Astrophysics Data System (ADS)

Forsling, Robin; Sanders, Lloyd P.; Ambjörnsson, Tobias; Lizana, Ludvig

2014-09-01

The standard setup for single-file diffusion is diffusing particles in one dimension which cannot overtake each other, where the dynamics of a tracer (tagged) particle is of main interest. In this article, we generalize this system and investigate first-passage properties of a tracer particle when flanked by identical crowder particles which may, besides diffuse, unbind (rebind) from (to) the one-dimensional lattice with rates koff (kon). The tracer particle is restricted to diffuse with rate kD on the lattice and the density of crowders is constant (on average). The unbinding rate koff is our key parameter and it allows us to systematically study the non-trivial transition between the completely Markovian case (koff ≫ kD) to the non-Markovian case (koff ≪ kD) governed by strong memory effects. This has relevance for several quasi one-dimensional systems. One example is gene regulation where regulatory proteins are searching for specific binding sites on a crowded DNA. We quantify the first-passage time distribution, f (t) (t is time), numerically using the Gillespie algorithm, and estimate f (t) analytically. In terms of koff (keeping kD fixed), we study the transition between the two known regimes: (i) when koff ≫ kD the particles may effectively pass each other and we recover the single particle result f (t) ˜ t-3/2, with a reduced diffusion constant; (ii) when koff ≪ kD unbinding is rare and we obtain the single-file result f (t) ˜ t-7/4. The intermediate region displays rich dynamics where both the characteristic f (t) - peak and the long-time power-law slope are sensitive to koff.

Probing the ATP-induced conformational flexibility of the PcrA helicase protein using molecular dynamics simulation.

PubMed

Mhashal, Anil R; Choudhury, Chandan Kumar; Roy, Sudip

2016-03-01

Helicases are enzymes that unwind double-stranded DNA (dsDNA) into its single-stranded components. It is important to understand the binding and unbinding of ATP from the active sites of helicases, as this knowledge can be used to elucidate the functionality of helicases during the unwinding of dsDNA. In this work, we investigated the unbinding of ATP and its effect on the active-site residues of the helicase PcrA using molecular dynamic simulations. To mimic the unbinding process of ATP from the active site of the helicase, we simulated the application of an external force that pulls ATP from the active site and computed the free-energy change during this process. We estimated an energy cost of ~85 kJ/mol for the transformation of the helicase from the ATP-bound state (1QHH) to the ATP-free state (1PJR). Unbinding led to conformational changes in the residues of the protein at the active site. Some of the residues at the ATP-binding site were significantly reoriented when the ATP was pulled. We observed a clear competition between reorientation of the residues and energy stabilization by hydrogen bonds between the ATP and active-site residues. We also checked the flexibility of the PcrA protein using a principal component analysis of domain motion. We found that the ATP-free state of the helicase is more flexible than the ATP-bound state.

Global Conformational Selection and Local Induced Fit for the Recognition between Intrinsic Disordered p53 and CBP

PubMed Central

Yu, Qingfen; Ye, Wei; Wang, Wei; Chen, Hai-Feng

2013-01-01

The transactivation domain (TAD) of tumor suppressor p53 can bind with the nuclear coactivator binding domain (NCBD) of cyclic-AMP response element binding protein (CBP) and activate transcription. NMR experiments demonstrate that both apo-NCBD and TAD are intrinsic disordered and bound NCBD/TAD undergoes a transition to well folded. The recognition mechanism between intrinsic disordered proteins is still hotly debated. Molecular dynamics (MD) simulations in explicit solvent are used to study the recognition mechanism between intrinsic disordered TAD and NCBD. The average RMSD values between bound and corresponding apo states and Kolmogorov-Smirnov P test analysis indicate that TAD and NCBD may follow an induced fit mechanism. Quantitative analysis indicates there is also a global conformational selection. In summary, the recognition of TAD and NCBD might obey a local induced fit and global conformational selection. These conclusions are further supported by high-temperature unbinding kinetics and room temperature landscape analysis. These methods can be used to study the recognition mechanism of other intrinsic disordered proteins. PMID:23555731

Cross-Linker Unbinding and Self-Similarity in Bundled Cytoskeletal Networks

NASA Astrophysics Data System (ADS)

Lieleg, O.; Bausch, A. R.

2007-10-01

The macromechanical properties of purely bundled in vitro actin networks are not only determined by the micromechanical properties of individual bundles but also by molecular unbinding events of the actin-binding protein (ABP) fascin. Under high mechanical load the network elasticity depends on the forced unbinding of individual ABPs in a rate dependent manner. Cross-linker unbinding in combination with the structural self-similarity of the network enables the introduction of a concentration-time superposition principle—broadening the mechanically accessible frequency range over 8 orders of magnitude.

Energy landscape of the reactions governing the Na+ deeply occluded state of the Na+/K+-ATPase in the giant axon of the Humboldt squid

PubMed Central

Castillo, Juan P.; De Giorgis, Daniela; Basilio, Daniel; Gadsby, David C.; Rosenthal, Joshua J. C.; Latorre, Ramon; Holmgren, Miguel; Bezanilla, Francisco

2011-01-01

The Na+/K+ pump is a nearly ubiquitous membrane protein in animal cells that uses the free energy of ATP hydrolysis to alternatively export 3Na+ from the cell and import 2K+ per cycle. This exchange of ions produces a steady-state outwardly directed current, which is proportional in magnitude to the turnover rate. Under certain ionic conditions, a sudden voltage jump generates temporally distinct transient currents mediated by the Na+/K+ pump that represent the kinetics of extracellular Na+ binding/release and Na+ occlusion/deocclusion transitions. For many years, these events have escaped a proper thermodynamic treatment due to the relatively small electrical signal. Here, taking the advantages offered by the large diameter of the axons from the squid Dosidicus gigas, we have been able to separate the kinetic components of the transient currents in an extended temperature range and thus characterize the energetic landscape of the pump cycle and those transitions associated with the extracellular release of the first Na+ from the deeply occluded state. Occlusion/deocclusion transition involves large changes in enthalpy and entropy as the ion is exposed to the external milieu for release. Binding/unbinding is substantially less costly, yet larger than predicted for the energetic cost of an ion diffusing through a permeation pathway, which suggests that ion binding/unbinding must involve amino acid side-chain rearrangements at the site. PMID:22143771

Energy landscape of the reactions governing the Na+ deeply occluded state of the Na+/K+-ATPase in the giant axon of the Humboldt squid.

PubMed

Castillo, Juan P; De Giorgis, Daniela; Basilio, Daniel; Gadsby, David C; Rosenthal, Joshua J C; Latorre, Ramon; Holmgren, Miguel; Bezanilla, Francisco

2011-12-20

The Na(+)/K(+) pump is a nearly ubiquitous membrane protein in animal cells that uses the free energy of ATP hydrolysis to alternatively export 3Na(+) from the cell and import 2K(+) per cycle. This exchange of ions produces a steady-state outwardly directed current, which is proportional in magnitude to the turnover rate. Under certain ionic conditions, a sudden voltage jump generates temporally distinct transient currents mediated by the Na(+)/K(+) pump that represent the kinetics of extracellular Na(+) binding/release and Na(+) occlusion/deocclusion transitions. For many years, these events have escaped a proper thermodynamic treatment due to the relatively small electrical signal. Here, taking the advantages offered by the large diameter of the axons from the squid Dosidicus gigas, we have been able to separate the kinetic components of the transient currents in an extended temperature range and thus characterize the energetic landscape of the pump cycle and those transitions associated with the extracellular release of the first Na(+) from the deeply occluded state. Occlusion/deocclusion transition involves large changes in enthalpy and entropy as the ion is exposed to the external milieu for release. Binding/unbinding is substantially less costly, yet larger than predicted for the energetic cost of an ion diffusing through a permeation pathway, which suggests that ion binding/unbinding must involve amino acid side-chain rearrangements at the site.

Impact of human galectin-1 binding to saccharide ligands on dimer dissociation kinetics and structure.

PubMed

Romero, Juan M; Trujillo, Madia; Estrin, Darío A; Rabinovich, Gabriel A; Di Lella, Santiago

2016-12-01

Endogenous lectins can control critical biological responses, including cell communication, signaling, angiogenesis and immunity by decoding glycan-containing information on a variety of cellular receptors and the extracellular matrix. Galectin-1 (Gal-1), a prototype member of the galectin family, displays only one carbohydrate recognition domain and occurs in a subtle homodimerization equilibrium at physiologic concentrations. Such equilibrium critically governs the function of this lectin signaling by allowing tunable interactions with a preferential set of glycosylated receptors. Here, we used a combination of experimental and computational approaches to analyze the kinetics and mechanisms connecting Gal-1 ligand unbinding and dimer dissociation processes. Kinetic constants of both processes were found to differ by an order of magnitude. By means of steered molecular dynamics simulations, the ligand unbinding process was followed monitoring water occupancy changes. By determining the water sites in a carbohydrate binding place during the unbinding process, we found that rupture of ligand-protein interactions induces an increase in energy barrier while ligand unbinding process takes place, whereas the entry of water molecules to the binding groove and further occupation of their corresponding water sites contributes to lowering of the energy barrier. Moreover, our findings suggested local asymmetries between the two subunits in the dimer structure detected at a nanosecond timescale. Thus, integration of experimental and computational data allowed a more complete understanding of lectin ligand binding and dimerization processes, suggesting new insights into the relationship between Gal-1 structure and function and renewing the discussion on the biophysics and biochemistry of lectin-ligand lattices. © The Author 2016. Published by Oxford University Press. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Kinetics of protein–ligand unbinding: Predicting pathways, rates, and rate-limiting steps

PubMed Central

Tiwary, Pratyush; Limongelli, Vittorio; Salvalaglio, Matteo; Parrinello, Michele

2015-01-01

The ability to predict the mechanisms and the associated rate constants of protein–ligand unbinding is of great practical importance in drug design. In this work we demonstrate how a recently introduced metadynamics-based approach allows exploration of the unbinding pathways, estimation of the rates, and determination of the rate-limiting steps in the paradigmatic case of the trypsin–benzamidine system. Protein, ligand, and solvent are described with full atomic resolution. Using metadynamics, multiple unbinding trajectories that start with the ligand in the crystallographic binding pose and end with the ligand in the fully solvated state are generated. The unbinding rate koff is computed from the mean residence time of the ligand. Using our previously computed binding affinity we also obtain the binding rate kon. Both rates are in agreement with reported experimental values. We uncover the complex pathways of unbinding trajectories and describe the critical rate-limiting steps with unprecedented detail. Our findings illuminate the role played by the coupling between subtle protein backbone fluctuations and the solvation by water molecules that enter the binding pocket and assist in the breaking of the shielded hydrogen bonds. We expect our approach to be useful in calculating rates for general protein–ligand systems and a valid support for drug design. PMID:25605901

One night of sleep is insufficient to achieve sleep-to-forget emotional decontextualisation processes.

PubMed

Deliens, Gaétane; Peigneux, Philippe

2014-01-01

Neutral memories unbind from their emotional acquisition context when sleep is allowed the night after learning and testing takes place after two additional nights of sleep. However, mood-dependent memory (MDM) effects are not abolished after a restricted sleep episode mostly featuring non rapid-eye-movement (NREM) or rapid-eye-movement (REM) sleep. Here, we tested whether (1) one night of sleep featuring several NREM-REM sleep cycles is sufficient to suppress MDM effects and (2) a neutral mood is a sufficiently contrasting state to induce MDM effects, i.e. interfere with the recall of information learned in happy or sad states. Results disclosed MDM effects both in the post-learning sleep and wake conditions, with better recall in congruent than incongruent emotional contexts. Our findings suggest that the emotional unbinding needs several consecutive nights of sleep to be complete, and that even subtle mood changes are sufficient to produce MDM effects.

Theory of interacting dislocations on cylinders.

PubMed

Amir, Ariel; Paulose, Jayson; Nelson, David R

2013-04-01

We study the mechanics and statistical physics of dislocations interacting on cylinders, motivated by the elongation of rod-shaped bacterial cell walls and cylindrical assemblies of colloidal particles subject to external stresses. The interaction energy and forces between dislocations are solved analytically, and analyzed asymptotically. The results of continuum elastic theory agree well with numerical simulations on finite lattices even for relatively small systems. Isolated dislocations on a cylinder act like grain boundaries. With colloidal crystals in mind, we show that saddle points are created by a Peach-Koehler force on the dislocations in the circumferential direction, causing dislocation pairs to unbind. The thermal nucleation rate of dislocation unbinding is calculated, for an arbitrary mobility tensor and external stress, including the case of a twist-induced Peach-Koehler force along the cylinder axis. Surprisingly rich phenomena arise for dislocations on cylinders, despite their vanishing Gaussian curvature.

Crucial role of dynamic linker histone binding and divalent ions for DNA accessibility and gene regulation revealed by mesoscale modeling of oligonucleosomes

PubMed Central

Collepardo-Guevara, Rosana; Schlick, Tamar

2012-01-01

Monte Carlo simulations of a mesoscale model of oligonucleosomes are analyzed to examine the role of dynamic-linker histone (LH) binding/unbinding in high monovalent salt with divalent ions, and to further interpret noted chromatin fiber softening by dynamic LH in monovalent salt conditions. We find that divalent ions produce a fiber stiffening effect that competes with, but does not overshadow, the dramatic softening triggered by dynamic-LH behavior. Indeed, we find that in typical in vivo conditions, dynamic-LH binding/unbinding reduces fiber stiffening dramatically (by a factor of almost 5, as measured by the elasticity modulus) compared with rigidly fixed LH, and also the force needed to initiate chromatin unfolding, making it consistent with those of molecular motors. Our data also show that, during unfolding, divalent ions together with LHs induce linker-DNA bending and DNA–DNA repulsion screening, which guarantee formation of heteromorphic superbeads-on-a-string structures that combine regions of loose and compact fiber independently of the characteristics of the LH–core bond. These structures might be important for gene regulation as they expose regions of the DNA selectively. Dynamic control of LH binding/unbinding, either globally or locally, in the presence of divalent ions, might constitute a mechanism for regulation of gene expression. PMID:22790986

Rates and equilibrium constants of the ligand-induced conformational transition of an HCN ion channel protein domain determined by DEER spectroscopy.

PubMed

Collauto, Alberto; DeBerg, Hannah A; Kaufmann, Royi; Zagotta, William N; Stoll, Stefan; Goldfarb, Daniella

2017-06-14

Ligand binding can induce significant conformational changes in proteins. The mechanism of this process couples equilibria associated with the ligand binding event and the conformational change. Here we show that by combining the application of W-band double electron-electron resonance (DEER) spectroscopy with microfluidic rapid freeze quench (μRFQ) it is possible to resolve these processes and obtain both equilibrium constants and reaction rates. We studied the conformational transition of the nitroxide labeled, isolated carboxy-terminal cyclic-nucleotide binding domain (CNBD) of the HCN2 ion channel upon binding of the ligand 3',5'-cyclic adenosine monophosphate (cAMP). Using model-based global analysis, the time-resolved data of the μRFQ DEER experiments directly provide fractional populations of the open and closed conformations as a function of time. We modeled the ligand-induced conformational change in the protein using a four-state model: apo/open (AO), apo/closed (AC), bound/open (BO), bound/closed (BC). These species interconvert according to AC + L ⇌ AO + L ⇌ BO ⇌ BC. By analyzing the concentration dependence of the relative contributions of the closed and open conformations at equilibrium, we estimated the equilibrium constants for the two conformational equilibria and the open-state ligand dissociation constant. Analysis of the time-resolved μRFQ DEER data gave estimates for the intrinsic rates of ligand binding and unbinding as well as the rates of the conformational change. This demonstrates that DEER can quantitatively resolve both the thermodynamics and the kinetics of ligand binding and the associated conformational change.

Determining the elastic properties of aptamer-ricin single molecule multiple pathway interactions

NASA Astrophysics Data System (ADS)

Wang, Bin; Park, Bosoon; Kwon, Yongkuk; Xu, Bingqian

2014-05-01

We report on the elastic properties of ricin and anti-ricin aptamer interactions, which showed three stable binding conformations, each of which has its special elastic properties. These different unbinding pathways were investigated by the dynamic force spectroscopy. A series-spring model combining the worm-like-chain model and Hook's law was used to estimate the apparent spring constants of the aptamer and linker molecule polyethylene glycol. The aptamer in its three different unbinding pathways showed different apparent spring constants. The two reaction barriers in the unbinding pathways also influence the apparent spring constant of the aptamer. This special elastic behavior of aptamer was used to distinguish its three unbinding pathways under different loading rates. This method also offered a way to distinguish and discard the non-specific interactions in single molecule experiments.

The ties to unbind: age-related differences in feature (un)binding in working memory for emotional faces

PubMed Central

Pehlivanoglu, Didem; Jain, Shivangi; Ariel, Robert; Verhaeghen, Paul

2014-01-01

In the present study, we investigated age-related differences in the processing of emotional stimuli. Specifically, we were interested in whether older adults would show deficits in unbinding emotional expression (i.e., either no emotion, happiness, anger, or disgust) from bound stimuli (i.e., photographs of faces expressing these emotions), as a hyper-binding account of age-related differences in working memory would predict. Younger and older adults completed different N-Back tasks (side-by-side 0-Back, 1-Back, 2-Back) under three conditions: match/mismatch judgments based on either the identity of the face (identity condition), the face’s emotional expression (expression condition), or both identity and expression of the face (both condition). The two age groups performed more slowly and with lower accuracy in the expression condition than in the both condition, indicating the presence of an unbinding process. This unbinding effect was more pronounced in older adults than in younger adults, but only in the 2-Back task. Thus, older adults seemed to have a specific deficit in unbinding in working memory. Additionally, no age-related differences were found in accuracy in the 0-Back task, but such differences emerged in the 1-Back task, and were further magnified in the 2-Back task, indicating independent age-related differences in attention/STM and working memory. Pupil dilation data confirmed that the attention/STM version of the task (1-Back) is more effortful for older adults than younger adults. PMID:24795660

The ties to unbind: age-related differences in feature (un)binding in working memory for emotional faces.

PubMed

Pehlivanoglu, Didem; Jain, Shivangi; Ariel, Robert; Verhaeghen, Paul

2014-01-01

In the present study, we investigated age-related differences in the processing of emotional stimuli. Specifically, we were interested in whether older adults would show deficits in unbinding emotional expression (i.e., either no emotion, happiness, anger, or disgust) from bound stimuli (i.e., photographs of faces expressing these emotions), as a hyper-binding account of age-related differences in working memory would predict. Younger and older adults completed different N-Back tasks (side-by-side 0-Back, 1-Back, 2-Back) under three conditions: match/mismatch judgments based on either the identity of the face (identity condition), the face's emotional expression (expression condition), or both identity and expression of the face (both condition). The two age groups performed more slowly and with lower accuracy in the expression condition than in the both condition, indicating the presence of an unbinding process. This unbinding effect was more pronounced in older adults than in younger adults, but only in the 2-Back task. Thus, older adults seemed to have a specific deficit in unbinding in working memory. Additionally, no age-related differences were found in accuracy in the 0-Back task, but such differences emerged in the 1-Back task, and were further magnified in the 2-Back task, indicating independent age-related differences in attention/STM and working memory. Pupil dilation data confirmed that the attention/STM version of the task (1-Back) is more effortful for older adults than younger adults.

Unbinding of fluorinated oxime drug from the AChE gorge in polarizable water: a well-tempered metadynamics study.

PubMed

Pathak, Arup Kumar; Bandyopadhyay, Tusar

2017-02-15

Despite the fact that fluorination makes a drug more lipophilic, the molecular level understanding of protein-fluorinated drug interactions is very poor. Due to their enhanced ability to penetrate the blood brain barrier, they are suitable for reactivation of organophosphorus inactivated acetylcholinesterase (AChE) in the central nervous system. We systematically studied the unbinding of fluorinated obidoxime (FOBI) and non-fluorinated obidoxime (OBI) from the active site gorge of the serine hydrolase AChE in mean field polarizable water by employing all atom molecular dynamics simulations. It is observed that the unbinding process is strongly influenced by cation-π, hydrogen bond (HB) and water bridge interactions. The FOBI drug interacts more strongly with the protein residues than OBI and this is also verified from quantum mechanical calculations. Distinct unbinding pathways for FOBI and OBI are observed as evident from the 1D and 2D potential of mean force of the unbinding profiles. The present study suggests that the FOBI drug is held more firmly in the gorge of AChE in comparison to OBI and may lead to higher reactivation efficiency of the inactivated enzyme.

How wet should be the reaction coordinate for ligand unbinding?

PubMed

Tiwary, Pratyush; Berne, B J

2016-08-07

We use a recently proposed method called Spectral Gap Optimization of Order Parameters (SGOOP) [P. Tiwary and B. J. Berne, Proc. Natl. Acad. Sci. U. S. A. 113, 2839 (2016)], to determine an optimal 1-dimensional reaction coordinate (RC) for the unbinding of a bucky-ball from a pocket in explicit water. This RC is estimated as a linear combination of the multiple available order parameters that collectively can be used to distinguish the various stable states relevant for unbinding. We pay special attention to determining and quantifying the degree to which water molecules should be included in the RC. Using SGOOP with under-sampled biased simulations, we predict that water plays a distinct role in the reaction coordinate for unbinding in the case when the ligand is sterically constrained to move along an axis of symmetry. This prediction is validated through extensive calculations of the unbinding times through metadynamics and by comparison through detailed balance with unbiased molecular dynamics estimate of the binding time. However when the steric constraint is removed, we find that the role of water in the reaction coordinate diminishes. Here instead SGOOP identifies a good one-dimensional RC involving various motional degrees of freedom.

How wet should be the reaction coordinate for ligand unbinding?

NASA Astrophysics Data System (ADS)

Tiwary, Pratyush; Berne, B. J.

2016-08-01

We use a recently proposed method called Spectral Gap Optimization of Order Parameters (SGOOP) [P. Tiwary and B. J. Berne, Proc. Natl. Acad. Sci. U. S. A. 113, 2839 (2016)], to determine an optimal 1-dimensional reaction coordinate (RC) for the unbinding of a bucky-ball from a pocket in explicit water. This RC is estimated as a linear combination of the multiple available order parameters that collectively can be used to distinguish the various stable states relevant for unbinding. We pay special attention to determining and quantifying the degree to which water molecules should be included in the RC. Using SGOOP with under-sampled biased simulations, we predict that water plays a distinct role in the reaction coordinate for unbinding in the case when the ligand is sterically constrained to move along an axis of symmetry. This prediction is validated through extensive calculations of the unbinding times through metadynamics and by comparison through detailed balance with unbiased molecular dynamics estimate of the binding time. However when the steric constraint is removed, we find that the role of water in the reaction coordinate diminishes. Here instead SGOOP identifies a good one-dimensional RC involving various motional degrees of freedom.

How wet should be the reaction coordinate for ligand unbinding?

PubMed Central

Tiwary, Pratyush; Berne, B. J.

2016-01-01

We use a recently proposed method called Spectral Gap Optimization of Order Parameters (SGOOP) [P. Tiwary and B. J. Berne, Proc. Natl. Acad. Sci. U. S. A. 113, 2839 (2016)], to determine an optimal 1-dimensional reaction coordinate (RC) for the unbinding of a bucky-ball from a pocket in explicit water. This RC is estimated as a linear combination of the multiple available order parameters that collectively can be used to distinguish the various stable states relevant for unbinding. We pay special attention to determining and quantifying the degree to which water molecules should be included in the RC. Using SGOOP with under-sampled biased simulations, we predict that water plays a distinct role in the reaction coordinate for unbinding in the case when the ligand is sterically constrained to move along an axis of symmetry. This prediction is validated through extensive calculations of the unbinding times through metadynamics and by comparison through detailed balance with unbiased molecular dynamics estimate of the binding time. However when the steric constraint is removed, we find that the role of water in the reaction coordinate diminishes. Here instead SGOOP identifies a good one-dimensional RC involving various motional degrees of freedom. PMID:27497545

Conformational Transitions and Convergence of Absolute Binding Free Energy Calculations

PubMed Central

Lapelosa, Mauro; Gallicchio, Emilio; Levy, Ronald M.

2011-01-01

The Binding Energy Distribution Analysis Method (BEDAM) is employed to compute the standard binding free energies of a series of ligands to a FK506 binding protein (FKBP12) with implicit solvation. Binding free energy estimates are in reasonably good agreement with experimental affinities. The conformations of the complexes identified by the simulations are in good agreement with crystallographic data, which was not used to restrain ligand orientations. The BEDAM method is based on λ -hopping Hamiltonian parallel Replica Exchange (HREM) molecular dynamics conformational sampling, the OPLS-AA/AGBNP2 effective potential, and multi-state free energy estimators (MBAR). Achieving converged and accurate results depends on all of these elements of the calculation. Convergence of the binding free energy is tied to the level of convergence of binding energy distributions at critical intermediate states where bound and unbound states are at equilibrium, and where the rate of binding/unbinding conformational transitions is maximal. This finding mirrors similar observations in the context of order/disorder transitions as for example in protein folding. Insights concerning the physical mechanism of ligand binding and unbinding are obtained. Convergence for the largest FK506 ligand is achieved only after imposing strict conformational restraints, which however require accurate prior structural knowledge of the structure of the complex. The analytical AGBNP2 model is found to underestimate the magnitude of the hydrophobic driving force towards binding in these systems characterized by loosely packed protein-ligand binding interfaces. Rescoring of the binding energies using a numerical surface area model corrects this deficiency. This study illustrates the complex interplay between energy models, exploration of conformational space, and free energy estimators needed to obtain robust estimates from binding free energy calculations. PMID:22368530

Correlation between superfluid density and T(C) of underdoped YBa2Cu3O6+x near the superconductor-insulator transition.

PubMed

Zuev, Yuri; Kim, Mun Seog; Lemberger, Thomas R

2005-09-23

We report measurements of the ab-plane superfluid density n(s) (magnetic penetration depth lambda) of heavily underdoped films of YBa2Cu3O6+x, with T(C)'s from 6 to 50 K. We find the characteristic length for vortex unbinding transition equal to the film thickness, suggesting strongly coupled CuO2 layers. At the lowest dopings, T(C) is as much as 5 times larger than the upper limit set by the 2D Kosterlitz-Thouless-Berezinskii transition temperature calculated for individual CuO2 bilayers. Our main finding is that T(C) is not proportional to n(s)(0); instead, we find T(C) proportional to ns(1/2.3+/-0.4). This conflicts with a popular point of view that quasi-2D thermal phase fluctuations determine the transition temperature.

Force and Stress along Simulated Dissociation Pathways of Cucurbituril-Guest Systems.

PubMed

Velez-Vega, Camilo; Gilson, Michael K

2012-03-13

The field of host-guest chemistry provides computationally tractable yet informative model systems for biomolecular recognition. We applied molecular dynamics simulations to study the forces and mechanical stresses associated with forced dissociation of aqueous cucurbituril-guest complexes with high binding affinities. First, the unbinding transitions were modeled with constant velocity pulling (steered dynamics) and a soft spring constant, to model atomic force microscopy (AFM) experiments. The computed length-force profiles yield rupture forces in good agreement with available measurements. We also used steered dynamics with high spring constants to generate paths characterized by a tight control over the specified pulling distance; these paths were then equilibrated via umbrella sampling simulations and used to compute time-averaged mechanical stresses along the dissociation pathways. The stress calculations proved to be informative regarding the key interactions determining the length-force profiles and rupture forces. In particular, the unbinding transition of one complex is found to be a stepwise process, which is initially dominated by electrostatic interactions between the guest's ammoniums and the host's carbonyl groups, and subsequently limited by the extraction of the guest's bulky bicyclooctane moiety; the latter step requires some bond stretching at the cucurbituril's extraction portal. Conversely, the dissociation of a second complex with a more slender guest is mainly driven by successive electrostatic interactions between the different guest's ammoniums and the host's carbonyl groups. The calculations also provide information on the origins of thermodynamic irreversibilities in these forced dissociation processes.

Impact of disease-causing mutations on inter-domain interactions in cMyBP-C: a steered molecular dynamics study.

PubMed

Krishnamoorthy, Navaneethakrishnan; Gajendrarao, Poornima; Olivotto, Iacopo; Yacoub, Magdi

2017-07-01

The molecular interactions of the sarcomeric proteins are essential in the regulation of various cardiac functions. Mutations in the gene MYBPC3 coding for cardiac myosin-binding protein-C (cMyBP-C), a multi-domain protein, are the most common cause of hypertrophic cardiomyopathy (HCM). The N-terminal complex, C1-motif-C2 is a central region in cMyBP-C for the regulation of cardiac muscle contraction. However, the mechanism of binding/unbinding of this complex during health and disease is unknown. Here, we study possible mechanisms of unbinding using steered molecular dynamics simulations for the complex in the wild type, in single mutations (E258K in C1, E441K in C2), as well as in a double mutation (E258K in C1 + E441K in C2), which are associated with severe HCM. The observed molecular events and the calculation of force utilized for the unbinding suggest the following: (i) double mutation can encourage the formation of rigid complex that required large amount of force and long-time to unbind, (ii) C1 appears to start to unbind ahead of C2 regardless of the mutation, and (iii) unbinding of C2 requires larger amount of force than C1. This molecular insight suggests that key HCM-causing mutations might significantly modify the native affinity required for the assembly of the domains in cMyBP-C, which is essential for normal cardiac function.

Decoding the Role of Water Dynamics in Ligand-Protein Unbinding: CRF1R as a Test Case.

PubMed

Bortolato, Andrea; Deflorian, Francesca; Weiss, Dahlia R; Mason, Jonathan S

2015-09-28

The residence time of a ligand-protein complex is a crucial aspect in determining biological effect in vivo. Despite its importance, the prediction of ligand koff still remains challenging for modern computational chemistry. We have developed aMetaD, a fast and generally applicable computational protocol to predict ligand-protein unbinding events using a molecular dynamics (MD) method based on adiabatic-bias MD and metadynamics. This physics-based, fully flexible, and pose-dependent ligand scoring function evaluates the maximum energy (RTscore) required to move the ligand from the bound-state energy basin to the next. Unbinding trajectories are automatically analyzed and translated into atomic solvation factor (SF) values representing the water dynamics during the unbinding event. This novel computational protocol was initially tested on two M3 muscarinic receptor and two adenosine A2A receptor antagonists and then evaluated on a test set of 12 CRF1R ligands. The resulting RTscores were used successfully to classify ligands with different residence times. Additionally, the SF analysis was used to detect key differences in the degree of accessibility to water molecules during the predicted ligand unbinding events. The protocol provides actionable working hypotheses that are applicable in a drug discovery program for the rational optimization of ligand binding kinetics.

Direction-dependent force-induced dissociation dynamics of an entropic-driven lock-and-key assembly.

PubMed

Chen, Yen-Fu; Chen, Hsuan-Yi; Sheng, Yu-Jane; Tsao, Heng-Kwong

2017-09-01

The unbinding dynamics of a nanosized sphere-and-cavity assembly under the pulling of constant force and constant loading rate is explored by dissipative particle dynamics simulations. The formation of this matched lock-and-key pair in a polymer solution is driven by the depletion attraction. The two-dimensional free energy landscape U(x,z) associated with this assembly is constructed. Our results indicate that the unbinding pathway along the orientation of the assembly is unfavorable due to the relatively high energy barrier compared to that along the tortuous minimum path whose energy barrier is not high. It is also found that the dissociation rate depends on the direction of the external force (θ) with respect to the assembly orientation. The presence of the force component perpendicular to the assembly orientation can reduce the bond lifetime significantly by driving the key particle to approach the minimum path. Moreover, the dissociation dynamics can be facilitated even by a pushing force compared to the spontaneous dissociation (without forces). To elucidate the effective pathway under pulling, the escaping position is analyzed and its mean direction with respect to the assembly orientation rises generally with increasing θ, revealing that the presence of the force component along the minimum pathway is helpful. The importance of the direction of the external pulling has been demonstrated in our simple system. Therefore, this effect should be considered in more complicated unbinding experiments.

Direction-dependent force-induced dissociation dynamics of an entropic-driven lock-and-key assembly

NASA Astrophysics Data System (ADS)

Chen, Yen-Fu; Chen, Hsuan-Yi; Sheng, Yu-Jane; Tsao, Heng-Kwong

2017-09-01

The unbinding dynamics of a nanosized sphere-and-cavity assembly under the pulling of constant force and constant loading rate is explored by dissipative particle dynamics simulations. The formation of this matched lock-and-key pair in a polymer solution is driven by the depletion attraction. The two-dimensional free energy landscape U (x ,z ) associated with this assembly is constructed. Our results indicate that the unbinding pathway along the orientation of the assembly is unfavorable due to the relatively high energy barrier compared to that along the tortuous minimum path whose energy barrier is not high. It is also found that the dissociation rate depends on the direction of the external force (θ ) with respect to the assembly orientation. The presence of the force component perpendicular to the assembly orientation can reduce the bond lifetime significantly by driving the key particle to approach the minimum path. Moreover, the dissociation dynamics can be facilitated even by a pushing force compared to the spontaneous dissociation (without forces). To elucidate the effective pathway under pulling, the escaping position is analyzed and its mean direction with respect to the assembly orientation rises generally with increasing θ , revealing that the presence of the force component along the minimum pathway is helpful. The importance of the direction of the external pulling has been demonstrated in our simple system. Therefore, this effect should be considered in more complicated unbinding experiments.

Why are para-hydrogen clusters superfluid? A quantum theorem of corresponding states study.

PubMed

Sevryuk, Mikhail B; Toennies, J Peter; Ceperley, David M

2010-08-14

The quantum theorem of corresponding states is applied to N=13 and N=26 cold quantum fluid clusters to establish where para-hydrogen clusters lie in relation to more and less quantum delocalized systems. Path integral Monte Carlo calculations of the energies, densities, radial and pair distributions, and superfluid fractions are reported at T=0.5 K for a Lennard-Jones (LJ) (12,6) potential using six different de Boer parameters including the accepted value for hydrogen. The results indicate that the hydrogen clusters are on the borderline to being a nonsuperfluid solid but that the molecules are sufficiently delocalized to be superfluid. A general phase diagram for the total and kinetic energies of LJ (12,6) clusters encompassing all sizes from N=2 to N=infinity and for the entire range of de Boer parameters is presented. Finally the limiting de Boer parameters for quantum delocalization induced unbinding ("quantum unbinding") are estimated and the new results are found to agree with previous calculations for the bulk and smaller clusters.

Exploration of gated ligand binding recognizes an allosteric site for blocking FABP4-protein interaction.

PubMed

Li, Yan; Li, Xiang; Dong, Zigang

2015-12-28

Fatty acid binding protein 4 (FABP4), reversibly binding to fatty acids and other lipids with high affinities, is a potential target for treatment of cancers. The binding site of FABP4 is buried in an interior cavity and thereby ligand binding/unbinding is coupled with opening/closing of FABP4. It is a difficult task both experimentally and computationally to illuminate the entry or exit pathway, especially with the conformational gating. In this report we combine extensive computer simulations, clustering analysis, and the Markov state model to investigate the binding mechanism of FABP4 and troglitazone. Our simulations capture spontaneous binding and unbinding events as well as the conformational transition of FABP4 between the open and closed states. An allosteric binding site on the protein surface is recognized for the development of novel FABP4 inhibitors. The binding affinity is calculated and compared with the experimental value. The kinetic analysis suggests that ligand residence on the protein surface may delay the binding process. Overall, our results provide a comprehensive picture of ligand diffusion on the protein surface, ligand migration into the buried cavity, and the conformational change of FABP4 at an atomic level.

Probing Protein-Protein Interactions by Dynamic Force Correlation Spectroscopy

NASA Astrophysics Data System (ADS)

Barsegov, V.; Thirumalai, D.

2005-10-01

We develop a formalism for single molecule dynamic force spectroscopy to map the energy landscape of protein-protein complex (P1P2). The joint distribution P(τ1,τ2) of unbinding lifetimes τ1 and τ2, measurable in a compression-tension cycle, which accounts for the internal relaxation dynamics of the proteins under tension, shows that the histogram of τ1 is not Poissonian. The theory is applied to the forced unbinding of protein P1, modeled as a wormlike chain, from P1P2. We propose a new class of experiments which can resolve the effect of internal protein dynamics on the unbinding lifetimes.

Effects of electrostatic interactions on ligand dissociation kinetics

NASA Astrophysics Data System (ADS)

Erbaş, Aykut; de la Cruz, Monica Olvera; Marko, John F.

2018-02-01

We study unbinding of multivalent cationic ligands from oppositely charged polymeric binding sites sparsely grafted on a flat neutral substrate. Our molecular dynamics simulations are suggested by single-molecule studies of protein-DNA interactions. We consider univalent salt concentrations spanning roughly a 1000-fold range, together with various concentrations of excess ligands in solution. To reveal the ionic effects on unbinding kinetics of spontaneous and facilitated dissociation mechanisms, we treat electrostatic interactions both at a Debye-Hückel (DH) (or implicit ions, i.e., use of an electrostatic potential with a prescribed decay length) level and by the more precise approach of considering all ionic species explicitly in the simulations. We find that the DH approach systematically overestimates unbinding rates, relative to the calculations where all ion pairs are present explicitly in solution, although many aspects of the two types of calculation are qualitatively similar. For facilitated dissociation (FD) (acceleration of unbinding by free ligands in solution) explicit-ion simulations lead to unbinding at lower free-ligand concentrations. Our simulations predict a variety of FD regimes as a function of free-ligand and ion concentrations; a particularly interesting regime is at intermediate concentrations of ligands where nonelectrostatic binding strength controls FD. We conclude that explicit-ion electrostatic modeling is an essential component to quantitatively tackle problems in molecular ligand dissociation, including nucleic-acid-binding proteins.

Children's Assertive Behavior: The Reliability and Validity of Three Self-Report Measures.

ERIC Educational Resources Information Center

Scanlon, Elizabeth M.; Ollendick, Thomas H.

1985-01-01

The internal consistency and validity of three new scales for measuring assertiveness in children were tested. Two of the scales were able to "unbind" aggressive from assertive behavior, while the third was able to "unbind" submissive from assertive behavior. At present, a combination of the three scales is recommended. (KH)

Entropic-elasticity-controlled dissociation and energetic-elasticity-controlled rupture induce catch-to-slip bonds in cell-adhesion molecules.

PubMed

Wei, YuJie

2008-03-01

We develop a physical model to describe the kinetic behavior in cell-adhesion molecules. Unbinding of noncovalent biological bonds is assumed to occur by both bond dissociation and bond rupture. Such a decomposition of debonding processes is a space decomposition of the debonding events. Dissociation under thermal fluctuation is nondirectional in a three-dimensional space, and its energy barrier to escape is not influenced by a tensile force, but the microstates that could lead to dissociation are changed by the tensile force; rupture happens along the tensile force direction. An applied force effectively lowers the energy barrier to escape along the loading direction. The lifetime of the biological bond, due to the two concurrent off rates, may grow with increasing tensile force to a moderate amount and then decrease with further increasing load. We hypothesize that a catch-to-slip bond transition is a generic feature in biological bonds. The model also predicts that catch bonds in a more flexible molecular structure have longer lifetimes and need less force to be fully activated.

On the Application of the Onsager DFT Theory to Two-Dimensional System of Hard Needles

NASA Astrophysics Data System (ADS)

Chrzanowska, A.

2005-10-01

We present a simple Onsager type density functional theory (DFT) of a two-dimensional system of hard needles and assume that it can be applied to describe intensive and short range properties of a real system which, on the other hand, on larger scales exhibits topological order. It is shown that the transition point of the isotropic-nematic transformation and the state equation obtained are almost the same as those predicted from the computer simulations [ Phys. Rev. A31, 1776 (1985)] for small and undistorted system, which is never the case in liquid crystals, where these results are shifted in the density and require rescalings like, for instance, the Parson--Lee approach Phys. Rev. A19, 1225 (1979); J. Chem. Phys. 87, 4972 (1987); J. Chem. Phys. 89, 7036 (1988). Similar effect occurs for the chemical potential. Such behavior is attributed to the presence of negative values of higher virial coefficients, which may cancel the influence of the other positive coefficients in such a way that the second virial approximation gives accurate predictions. The above conclusion coincides with the Onsager idea that the second virial DFT theory for infinitely 3D hard particles is accurate. We notice that this coincidence comes from the fact that the 3D and 2D interaction models are governed by the same theoretical formulation. We also claim that the observed in the Monte Carlo simulation the disclinations unbinding process does not mean the change from the isotropic to the nematic phase (IN), as believed before, since the spontaneously drifting disclinations cannot be responsible for the changes of the system symmetry. The IN transition, as usual, is driven by the molecular interactions and the disclination unbinding must undergo then in the uniaxial phase. We also confirm that the chemical potential has a smooth character as a function of pressure, whereas it has an abrupt change in the slope at the point of transition while plotted versus density.

CaMKII in the Cardiovascular System: Sensing Redox States

PubMed Central

Erickson, Jeffrey R.; He, B. Julie; Grumbach, Isabella M.; Anderson, Mark E

2013-01-01

The multifunctional Ca2+ and calmodulin-dependent protein kinase II (CaMKII) is now recognized to play a central role in pathological events in the cardiovascular system. CaMKII has diverse downstream targets that promote vascular disease, heart failure and arrhythmias, so improved understanding of CaMKII signaling has the potential to lead to new therapies for cardiovascular disease. CaMKII is a multimeric serine-threonine kinase that is initially activated by binding calcified calmodulin (Ca2+/CaM). Under conditions of sustained exposure to elevated Ca2+/CaM CaMKII transitions into a Ca2+/CaM-autonomous enzyme by two distinct but parallel processes. Autophosphorylation of threonine 287 in the CaMKII regulatory domain ‘traps’ CaMKII into an open configuration even after Ca2+/CaM unbinding. More recently, our group identified a pair of methionines (281/282) in the CaMKII regulatory domain that undergo a partially reversible oxidation which, like autophosphorylation, prevents CaMKII from inactivating after Ca2+/CaM unbinding. Here we review roles of CaMKII in cardiovascular disease with an eye to understanding how CaMKII may act as a transduction signal to connect pro-oxidant conditions into specific downstream pathological effects that are relevant to rare and common forms of cardiovascular disease. PMID:21742790

Force-extension behavior of DNA in the presence of DNA-bending nucleoid associated proteins

NASA Astrophysics Data System (ADS)

Dahlke, K.; Sing, C. E.

2018-02-01

Interactions between nucleoid associated proteins (NAPs) and DNA affect DNA polymer conformation, leading to phenomena such as concentration dependent force-extension behavior. These effects, in turn, also impact the local binding behavior of the protein, such as high forces causing proteins to unbind, or proteins binding favorably to locally bent DNA. We develop a coarse-grained NAP-DNA simulation model that incorporates both force- and concentration-dependent behaviors, in order to study the interplay between NAP binding and DNA conformation. This model system includes multi-state protein binding and unbinding, motivated by prior work, but is now dependent on the local structure of the DNA, which is related to external forces acting on the DNA strand. We observe the expected qualitative binding behavior, where more proteins are bound at lower forces than at higher forces. Our model also includes NAP-induced DNA bending, which affects DNA elasticity. We see semi-quantitative matching of our simulated force-extension behavior to the reported experimental data. By using a coarse-grained simulation, we are also able to look at non-equilibrium behaviors, such as dynamic extension of a DNA strand. We stretch a DNA strand at different rates and at different NAP concentrations to observe how the time scales of the system (such as pulling time and unbinding time) work in concert. When these time scales are similar, we observe measurable rate-dependent changes in the system, which include the number of proteins bound and the force required to extend the DNA molecule. This suggests that the relative time scales of different dynamic processes play an important role in the behavior of NAP-DNA systems.

An elastic dimpling instability with Kosterlitz-Thouless character and a precursor role in creasing

NASA Astrophysics Data System (ADS)

Engstrom, Tyler; Paulsen, Joseph; Schwarz, Jennifer

Creasing instability, also known as sulcification, occurs in a variety of quasi-2d elastic systems subject to compressive plane strain, and has been proposed as a mechanism of brain folding. While the dynamics of pre-existing creases can be understood in terms of crack propagation, a detailed critical phenomena picture of the instability is lacking. We show that surface dimpling is an equilibrium phase transition, and can be described in a language of quasi-particle excitations conceptualized as ``ghost fibers'' within the shear lag model. Tension-compression pairs (dipoles) of ghost fibers are energetically favorable at low strains, and the pairs unbind at a critical compressive plane strain, analogously to vortices in the Kosterlitz-Thouless transition. This dimpling transition bears strong resemblance to the creasing instability. We argue that zero-length creases are ghost fibers, which are a special case of ``ghost slabs''. Critical strain of a ghost slab increases linearly with its length, and is independent of both shear modulus and system thickness.

Mechanism and Energetics of Charybdotoxin Unbinding from a Potassium Channel from Molecular Dynamics Simulations

PubMed Central

Chen, Po-chia; Kuyucak, Serdar

2009-01-01

Ion channel-toxin complexes are ideal systems for computational studies of protein-ligand interactions, because, in most cases, the channel axis provides a natural reaction coordinate for unbinding of a ligand and a wealth of physiological data is available to check the computational results. We use a recently determined structure of a potassium channel-charybdotoxin complex in molecular dynamics simulations to investigate the mechanism and energetics of unbinding. Pairs of residues on the channel protein and charybdotoxin that are involved in the binding are identified, and their behavior is traced during umbrella-sampling simulations as charybdotoxin is moved away from the binding site. The potential of mean force for the unbinding of charybdotoxin is constructed from the umbrella sampling simulations using the weighted histogram analysis method, and barriers observed are correlated with specific breaking of interactions and influx of water molecules into the binding site. Charybdotoxin is found to undergo conformational changes as a result of the reaction coordinate choice—a nontrivial decision for larger ligands—which we explore in detail, and for which we propose solutions. Agreement between the calculated and the experimental binding energies is obtained once the energetic consequences of these conformational changes are included in the calculations. PMID:19348743

Unbinding Pathways of an Agonist and an Antagonist from the 5-HT3 Receptor

PubMed Central

Thompson, A. J.; Chau, P.-L.; Chan, S. L.; Lummis, S. C. R.

2006-01-01

The binding sites of 5-HT3 and other Cys-loop receptors have been extensively studied, but there are no data on the entry and exit routes of ligands for these sites. Here we have used molecular dynamics simulations to predict the pathway for agonists and antagonists exiting from the 5-HT3 receptor binding site. The data suggest that the unbinding pathway follows a tunnel at the interface of two subunits, which is ∼8 Å long and terminates ∼20 Å above the membrane. The exit routes for an agonist (5-HT) and an antagonist (granisetron) were similar, with trajectories toward the membrane and outward from the ligand binding site. 5-HT appears to form many hydrogen bonds with residues in the unbinding pathway, and experiments show that mutating these residues significantly affects function. The location of the pathway is also supported by docking studies of granisetron, which show a potential binding site for granisetron on the unbinding route. We propose that leaving the binding pocket along this tunnel places the ligands close to the membrane and prevents their immediate reentry into the binding pocket. We anticipate similar exit pathways for other members of the Cys-loop receptor family. PMID:16387779

Vortices and antivortices in two-dimensional ultracold Fermi gases

PubMed Central

Bighin, G.; Salasnich, L.

2017-01-01

Vortices are commonly observed in the context of classical hydrodynamics: from whirlpools after stirring the coffee in a cup to a violent atmospheric phenomenon such as a tornado, all classical vortices are characterized by an arbitrary circulation value of the local velocity field. On the other hand the appearance of vortices with quantized circulation represents one of the fundamental signatures of macroscopic quantum phenomena. In two-dimensional superfluids quantized vortices play a key role in determining finite-temperature properties, as the superfluid phase and the normal state are separated by a vortex unbinding transition, the Berezinskii-Kosterlitz-Thouless transition. Very recent experiments with two-dimensional superfluid fermions motivate the present work: we present theoretical results based on the renormalization group showing that the universal jump of the superfluid density and the critical temperature crucially depend on the interaction strength, providing a strong benchmark for forthcoming investigations. PMID:28374762

Vortices and antivortices in two-dimensional ultracold Fermi gases

NASA Astrophysics Data System (ADS)

Bighin, G.; Salasnich, L.

2017-04-01

Vortices are commonly observed in the context of classical hydrodynamics: from whirlpools after stirring the coffee in a cup to a violent atmospheric phenomenon such as a tornado, all classical vortices are characterized by an arbitrary circulation value of the local velocity field. On the other hand the appearance of vortices with quantized circulation represents one of the fundamental signatures of macroscopic quantum phenomena. In two-dimensional superfluids quantized vortices play a key role in determining finite-temperature properties, as the superfluid phase and the normal state are separated by a vortex unbinding transition, the Berezinskii-Kosterlitz-Thouless transition. Very recent experiments with two-dimensional superfluid fermions motivate the present work: we present theoretical results based on the renormalization group showing that the universal jump of the superfluid density and the critical temperature crucially depend on the interaction strength, providing a strong benchmark for forthcoming investigations.

Direct measurement of torque and twist generated by a dye binding to DNA

NASA Astrophysics Data System (ADS)

Gore, Jeff; Bryant, Zev; Bustamante, Carlos

2004-03-01

Many biologically important chemicals and proteins change the twist of DNA upon binding. We have used magnetic tweezers to directly measure the torque and twist generated when ethidium bromide binds and unbinds to DNA. One end of the DNA is bound specifically to a glass coverslip and the opposite end is held away from the surface by a paramagnetic bead. Attached to the middle of the DNA is a second fluorescent bead whose position can be tracked with high angular and temporal resolution. On one side of the fluorescent bead binding site we have engineered a single strand nick that acts like a free swivel. Addition of ethidium bromide then powered rotation of the central fluorescent bead. After the ethidium bromide was bound we used magnesium to compete out the intercalated ethidium bromide, thus inducing a rotation in the opposite direction. We studied the torque generation, energetics, and kinetics associated with ethidium bromide binding and unbinding by tracking the rotation of the fluorescent bead. This system is a demonstration of a reversible chemically powered DNA-based rotary motor. We also expect that this technique will be useful in studying proteins that bind to or rotate DNA, including recA, polymerases, and topoisomerases.

Influence of surface interactions on folding and forced unbinding of semiflexible chains.

PubMed

Barsegov, V; Thirumalai, D

2005-11-24

We have investigated the folding and forced unbinding transitions of adsorbed semiflexible polymer chains using theory and simulations. These processes describe, at an elementary level, a number of biologically relevant phenomena that include adhesive interactions between proteins and tethering of receptors to cell walls. The binding interface is modeled as a solid surface, and the wormlike chain (WLC) is used for the semiflexible chain (SC). Using Langevin simulations, in the overdamped limit we examine the ordering kinetics of racquet-like and toroidal structures in the presence of an attractive interaction between the surface and the polymer chain. For a range of interactions, temperature, and the persistence length, l(p), we obtained the monomer density distribution, n(x), (x is the perpendicular distance of a tagged chain end from the surface) for all of the relevant morphologies. There is a single peak in n(x) inside the range of attractive forces, b, for chains in the extended conformations, whereas in racquet and toroidal structures there is an additional peak at x approximately b. The simulated results for n(x) are in good agreement with theory. The formation of toroids on the surface appears to be a first-order transition as evidenced by the bimodal distribution in n(x). The theoretical result underestimates the simulated n(x) for x < b and follows n(x) closely for x >/= b; the calculated density agrees exactly with n(x) in the range x < b. The chain-surface interaction is probed by subjecting the surface structures to a pulling force, f. The average extension, x( f), as a function of f exhibits a sigmoidal profile with sharp all-or-none transition at the unfolding force threshold f = f(c) which increases for more structured states. Simulated x(f) compare well with the theoretical predictions. The critical force, f(c), is a function of l(s)/l(c) for a fixed temperature, where l(c) and l(s) are the length scales that express the strength of the intramolecular and SC-surface attraction, respectively. For a fixed l(s), f(c) increases as l(p) decreases.

Phase diagram for a two-dimensional, two-temperature, diffusive XY model.

PubMed

Reichl, Matthew D; Del Genio, Charo I; Bassler, Kevin E

2010-10-01

Using Monte Carlo simulations, we determine the phase diagram of a diffusive two-temperature conserved order parameter XY model. When the two temperatures are equal the system becomes the equilibrium XY model with the continuous Kosterlitz-Thouless (KT) vortex-antivortex unbinding phase transition. When the two temperatures are unequal the system is driven by an energy flow from the higher temperature heat-bath to the lower temperature one and reaches a far-from-equilibrium steady state. We show that the nonequilibrium phase diagram contains three phases: A homogenous disordered phase and two phases with long range, spin texture order. Two critical lines, representing continuous phase transitions from a homogenous disordered phase to two phases of long range order, meet at the equilibrium KT point. The shape of the nonequilibrium critical lines as they approach the KT point is described by a crossover exponent φ=2.52±0.05. Finally, we suggest that the transition between the two phases with long-range order is first-order, making the KT-point where all three phases meet a bicritical point.

Frequency modulation atomic force microscopy: a dynamic measurement technique for biological systems

NASA Astrophysics Data System (ADS)

Higgins, Michael J.; Riener, Christian K.; Uchihashi, Takayuki; Sader, John E.; McKendry, Rachel; Jarvis, Suzanne P.

2005-03-01

Frequency modulation atomic force microscopy (FM-AFM) has been modified to operate in a liquid environment within an atomic force microscope specifically designed for investigating biological samples. We demonstrate the applicability of FM-AFM to biological samples using the spectroscopy mode to measure the unbinding forces of a single receptor-ligand (biotin-avidin) interaction. We show that quantitative adhesion force measurements can only be obtained provided certain modifications are made to the existing theory, which is used to convert the detected frequency shifts to an interaction force. Quantitative force measurements revealed that the unbinding forces for the biotin-avidin interaction were greater than those reported in previous studies. This finding was due to the use of high average tip velocities, which were calculated to be two orders of magnitude greater than those typically used in unbinding receptor-ligand experiments. This study therefore highlights the potential use of FM-AFM to study a range of biological systems, including living cells and/or single biomolecule interactions.

AFM force measurements of the gp120-sCD4 and gp120 or CD4 antigen-antibody interactions

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

Chen, Yong, E-mail: dr_yongchen@hotmail.com; Department of Microbiology and Immunology, University of Illinois at Chicago, Chicago, IL 60612; Zeng, Gucheng

2011-04-08

Highlights: {yields} The unbinding force of sCD4-gp120 interaction was 25.45 {+-} 20.46 pN. {yields} The unbinding force of CD4 antigen-antibody interaction was 51.22 {+-} 34.64 pN. {yields} The unbinding force of gp120 antigen-antibody interaction was 89.87 {+-} 44.63 pN. {yields} The interaction forces between various HIV inhibitors and the target molecules are significantly different. {yields} Functionalizing on AFM tip or substrate of an interaction pair caused different results. -- Abstract: Soluble CD4 (sCD4), anti-CD4 antibody, and anti-gp120 antibody have long been regarded as entry inhibitors in human immunodeficiency virus (HIV) therapy. However, the interactions between these HIV entry inhibitors andmore » corresponding target molecules are still poorly understood. In this study, atomic force microscopy (AFM) was utilized to investigate the interaction forces among them. We found that the unbinding forces of sCD4-gp120 interaction, CD4 antigen-antibody interaction, and gp120 antigen-antibody interaction were 25.45 {+-} 20.46, 51.22 {+-} 34.64, and 89.87 {+-} 44.63 pN, respectively, which may provide important mechanical information for understanding the effects of viral entry inhibitors on HIV infection. Moreover, we found that the functionalization of an interaction pair on AFM tip or substrate significantly influenced the results, implying that we must perform AFM force measurement and analyze the data with more caution.« less

Calcium waves in a grid of clustered channels with synchronous IP3 binding and unbinding.

PubMed

Rückl, M; Rüdiger, S

2016-11-01

Calcium signals in cells occur at multiple spatial scales and variable temporal duration. However, a physical explanation for transitions between long-lasting global oscillations and localized short-term elevations (puffs) of cytoplasmic Ca 2+ is still lacking. Here we introduce a phenomenological, coarse-grained model for the calcium variable, which is represented by ordinary differential equations. Due to its small number of parameters, and its simplicity, this model allows us to numerically study the interplay of multi-scale calcium concentrations with stochastic ion channel gating dynamics even in larger systems. We apply this model to a single cluster of inositol trisphosphate (IP 3 ) receptor channels and find further evidence for the results presented in earlier work: a single cluster may be capable of producing different calcium release types, where long-lasting events are accompanied by unbinding of IP 3 from the receptor (Rückl et al., PLoS Comput. Biol. 11, e1003965 (2015)). Finally, we show the practicability of the model in a grid of 64 clusters which is computationally intractable with previous high-resolution models. Here long-lasting events can lead to synchronized oscillations and waves, while short events stay localized. The frequency of calcium releases as well as their coherence can thereby be regulated by the amplitude of IP 3 stimulation. Finally the model allows for a new explanation of oscillating [IP 3 ], which is not based on metabolic production and degradation of IP 3 .

Chemomechanical coupling in hexameric protein-protein interfaces harness energy within V–type ATPases

PubMed Central

Singharoy, Abhishek; Chipot, Christophe; Moradi, Mahmoud

2017-01-01

ATP synthase is the most prominent bioenergetic macromolecular motor in all life-forms, utilizing the proton gradient across the cell membrane to fuel the synthesis of ATP. Notwithstanding the wealth of available biochemical and structural information inferred from years of experiments, the precise molecular mechanism whereby vacuolar (V–type) ATP synthase fulfills its biological function remains largely fragmentary. Recently, crystallographers provided the first high-resolution view of ATP activity in Enterococcus hirae V1–ATPase. Employing a combination of transition-path sampling and high-performance free-energy methods, the sequence of conformational transitions involved in a functional cycle accompanying ATP hydrolysis has been investigated in unprecedented detail over an aggregate simulation time of 65 μs. Our simulated pathways reveal that the chemical energy produced by ATP hydrolysis is harnessed via the concerted motion of the protein–protein interfaces in the V1-ring, and is nearly entirely consumed in the rotation of the central stalk. Surprisingly, in an ATPase devoid of a central stalk, the interfaces of this ring are perfectly designed for inducing ATP hydrolysis. Yet, in a complete V1-ATPase, the mechanical property of the central stalk is a key determinant of the rate of ATP turnover. The simulations further unveil a sequence of events, whereby unbinding of the hydrolysis product (ADP+Pi) is followed by ATP uptake, which, in turn, leads to the torque generation step and rotation of the center stalk. Molecular trajectories also bring to light multiple intermediates, two of which have been isolated in independent crystallography experiments. PMID:27936329

Chemomechanical Coupling in Hexameric Protein-Protein Interfaces Harnesses Energy within V-Type ATPases.

PubMed

Singharoy, Abhishek; Chipot, Christophe; Moradi, Mahmoud; Schulten, Klaus

2017-01-11

ATP synthase is the most prominent bioenergetic macromolecular motor in all life forms, utilizing the proton gradient across the cell membrane to fuel the synthesis of ATP. Notwithstanding the wealth of available biochemical and structural information inferred from years of experiments, the precise molecular mechanism whereby vacuolar (V-type) ATP synthase fulfills its biological function remains largely fragmentary. Recently, crystallographers provided the first high-resolution view of ATP activity in Enterococcus hirae V 1 -ATPase. Employing a combination of transition-path sampling and high-performance free-energy methods, the sequence of conformational transitions involved in a functional cycle accompanying ATP hydrolysis has been investigated in unprecedented detail over an aggregate simulation time of 65 μs. Our simulated pathways reveal that the chemical energy produced by ATP hydrolysis is harnessed via the concerted motion of the protein-protein interfaces in the V 1 -ring, and is nearly entirely consumed in the rotation of the central stalk. Surprisingly, in an ATPase devoid of a central stalk, the interfaces of this ring are perfectly designed for inducing ATP hydrolysis. However, in a complete V 1 -ATPase, the mechanical property of the central stalk is a key determinant of the rate of ATP turnover. The simulations further unveil a sequence of events, whereby unbinding of the hydrolysis product (ADP + P i ) is followed by ATP uptake, which, in turn, leads to the torque generation step and rotation of the center stalk. Molecular trajectories also bring to light multiple intermediates, two of which have been isolated in independent crystallography experiments.

Method for measuring the unbinding energy of strongly-bound membrane-associated proteins

DOE PAGES

La Bauve, Elisa; Vernon, Briana C.; Ye, Dongmei; ...

2016-07-15

Here, we describe a new method to measure the activation energy for unbinding (enthalpy ΔH* u and free energy ΔG* u) of a strongly-bound membrane-associated protein from a lipid membrane. It is based on measuring the rate of release of a liposome-bound protein during centrifugation on a sucrose gradient as a function of time and temperature. The method is used to determine ΔH*u and ΔG*u for the soluble dengue virus envelope protein (sE) strongly bound to 80:20 POPC:POPG liposomes at pH 5.5. ΔH*u is determined from the Arrhenius equation whereas ΔG*u is determined by fitting the data to a modelmore » based on mean first passage time for escape from a potential well. The binding free energy ΔG b of sE was also measured at the same pH for the initial, predominantly reversible, phase of binding to a 70:30 PC:PG lipid bilayer. The unbinding free energy (20 ± 3 kcal/mol, 20% PG) was found to be roughly three times the binding energy per monomer, (7.8 ± 0.3 kcal/mol for 30% PG, or est. 7.0 kcal/mol for 20% PG). This is consistent with data showing that free sE is a monomer at pH 5.5, but assembles into trimers after associating with membranes. Furthermore, this new method to determine unbinding energies should be useful to understand better the complex interactions of integral monotopic proteins and strongly-bound peripheral membrane proteins with lipid membranes.« less

Method for measuring the unbinding energy of strongly-bound membrane-associated proteins

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

La Bauve, Elisa; Vernon, Briana C.; Ye, Dongmei

Here, we describe a new method to measure the activation energy for unbinding (enthalpy ΔH* u and free energy ΔG* u) of a strongly-bound membrane-associated protein from a lipid membrane. It is based on measuring the rate of release of a liposome-bound protein during centrifugation on a sucrose gradient as a function of time and temperature. The method is used to determine ΔH*u and ΔG*u for the soluble dengue virus envelope protein (sE) strongly bound to 80:20 POPC:POPG liposomes at pH 5.5. ΔH*u is determined from the Arrhenius equation whereas ΔG*u is determined by fitting the data to a modelmore » based on mean first passage time for escape from a potential well. The binding free energy ΔG b of sE was also measured at the same pH for the initial, predominantly reversible, phase of binding to a 70:30 PC:PG lipid bilayer. The unbinding free energy (20 ± 3 kcal/mol, 20% PG) was found to be roughly three times the binding energy per monomer, (7.8 ± 0.3 kcal/mol for 30% PG, or est. 7.0 kcal/mol for 20% PG). This is consistent with data showing that free sE is a monomer at pH 5.5, but assembles into trimers after associating with membranes. Furthermore, this new method to determine unbinding energies should be useful to understand better the complex interactions of integral monotopic proteins and strongly-bound peripheral membrane proteins with lipid membranes.« less

Membrane-based actuation for high-speed single molecule force spectroscopy studies using AFM.

PubMed

Sarangapani, Krishna; Torun, Hamdi; Finkler, Ofer; Zhu, Cheng; Degertekin, Levent

2010-07-01

Atomic force microscopy (AFM)-based dynamic force spectroscopy of single molecular interactions involves characterizing unbinding/unfolding force distributions over a range of pulling speeds. Owing to their size and stiffness, AFM cantilevers are adversely affected by hydrodynamic forces, especially at pulling speeds >10 microm/s, when the viscous drag becomes comparable to the unbinding/unfolding forces. To circumvent these adverse effects, we have fabricated polymer-based membranes capable of actuating commercial AFM cantilevers at speeds >or=100 microm/s with minimal viscous drag effects. We have used FLUENT, a computational fluid dynamics (CFD) software, to simulate high-speed pulling and fast actuation of AFM cantilevers and membranes in different experimental configurations. The simulation results support the experimental findings on a variety of commercial AFM cantilevers and predict significant reduction in drag forces when membrane actuators are used. Unbinding force experiments involving human antibodies using these membranes demonstrate that it is possible to achieve bond loading rates >or=10(6) pN/s, an order of magnitude greater than that reported with commercial AFM cantilevers and systems.

Characterizing the Free-Energy Landscape of MDM2 Protein-Ligand Interactions by Steered Molecular Dynamics Simulations.

PubMed

Hu, Guodong; Xu, Shicai; Wang, Jihua

2015-12-01

Inhibition of p53-MDM2 interaction by small molecules is considered to be a promising approach to re-activate wild-type p53 for tumor suppression. Several inhibitors of the MDM2-p53 interaction were designed and studied by the experimental methods and the molecular dynamics simulation. However, the unbinding mechanism was still unclear. The steered molecular dynamics simulations combined with Brownian dynamics fluctuation-dissipation theorem were employed to obtain the free-energy landscape of unbinding between MDM2 and their four ligands. It was shown that compounds 4 and 8 dissociate faster than compounds 5 and 7. The absolute binding free energies for these four ligands are in close agreement with experimental results. The open movement of helix II and helix IV in the MDM2 protein-binding pocket upon unbinding is also consistent with experimental MDM2-unbound conformation. We further found that different binding mechanisms among different ligands are associated with H-bond with Lys51 and Glu25. These mechanistic results may be useful for improving ligand design. © 2015 John Wiley & Sons A/S.

Single-molecule force measurement via optical tweezers reveals different kinetic features of two BRaf mutants responsible for cardio-facial-cutaneous (CFC) syndrome

PubMed Central

Wen, Cheng; Ye, Anpei

2013-01-01

BRaf (B- Rapid Accelerated Fibrosarcoma) protein is an important serine/threonine-protein kinase. Two domains on BRaf can independently bind its upstream kinase, Ras (Rat Sarcoma) protein. These are the Ras binding domain (RBD) and cysteine-rich-domain (CRD). Herein we use customized optical tweezers to compare the Ras binding process in two pathological mutants of BRaf responsible for CFC syndrome, abbreviated BRaf (A246P) and BRaf (Q257R). The two mutants differ in their kinetics of Ras-binding, though both bind Ras with similar increased overall affinity. BRaf (A246P) exhibits a slightly higher Ras/CRD unbinding force and a significantly higher Ras/RBD unbinding force versus the wild type. The contrary phenomenon is observed in the Q257R mutation. Simulations of the unstressed-off rate, koff(0), yield results in accordance with the changes revealed by the mean unbinding force. Our approach can be applied to rapidly assess other mutated proteins to deduce the effects of mutation on their kinetics compared to wild type proteins and to each other. PMID:24409384

Peeling off an elastica from a smooth attractive substrate

NASA Astrophysics Data System (ADS)

Oyharcabal, Xabier; Frisch, Thomas

2005-03-01

Using continuum mechanics, we study theoretically the unbinding of an inextensible rod with free ends attracted by a smooth substrate and submitted to a vertical force. We use the elastica model in a medium-range van der Waals potential. We numerically solve a nonlinear boundary value problem and obtain the force-stretching relation at zero temperature. We obtain the critical force for which the rod unbinds from the substrate as a function of three dimensionless parameters, and we find two different regimes of adhesion. We study analytically the contact potential case as the van der Waals radius goes to zero.

Interactions among DIV voltage-sensor movement, fast inactivation, and resurgent Na current induced by the NaVβ4 open-channel blocking peptide

PubMed Central

Lewis, Amanda H.

2013-01-01

Resurgent Na current flows as voltage-gated Na channels recover through open states from block by an endogenous open-channel blocking protein, such as the NaVβ4 subunit. The open-channel blocker and fast-inactivation gate apparently compete directly, as slowing the onset of fast inactivation increases resurgent currents by favoring binding of the blocker. Here, we tested whether open-channel block is also sensitive to deployment of the DIV voltage sensor, which facilitates fast inactivation. We expressed NaV1.4 channels in HEK293t cells and assessed block by a free peptide replicating the cytoplasmic tail of NaVβ4 (the “β4 peptide”). Macroscopic fast inactivation was disrupted by mutations of DIS6 (L443C/A444W; “CW” channels), which reduce fast-inactivation gate binding, and/or by the site-3 toxin ATX-II, which interferes with DIV movement. In wild-type channels, the β4 peptide competed poorly with fast inactivation, but block was enhanced by ATX. With the CW mutation, large peptide-induced resurgent currents were present even without ATX, consistent with increased open-channel block upon depolarization and slower deactivation after blocker unbinding upon repolarization. The addition of ATX greatly increased transient current amplitudes and further enlarged resurgent currents, suggesting that pore access by the blocker is actually decreased by full deployment of the DIV voltage sensor. ATX accelerated recovery from block at hyperpolarized potentials, however, suggesting that the peptide unbinds more readily when DIV voltage-sensor deployment is disrupted. These results are consistent with two open states in Na channels, dependent on the DIV voltage-sensor position, which differ in affinity for the blocking protein. PMID:23940261

Molecular mechanisms of the effect of ultrasound on the fibrinolysis of clots

PubMed Central

Chernysh, Irina N.; Everbach, E. Carr; Purohit, Prashant K.; Weisel, John W.

2016-01-01

Summary Background Ultrasound accelerates tissue-type plasminogen activator (t-PA)-induced fibrinolysis of clots in vitro and in vivo. Objective To identify mechanisms for the enhancement of t-PA-induced fibrinolysis of clots. Methods Turbidity is an accurate and convenient method, not previously used, to follow the effects of ultrasound. Deconvolution microscopy was used to determine changes in structure, while fluorescence recovery after photobleaching was used to characterize the kinetics of binding/unbinding and transport. Results The ultrasound pulse repetition frequency affected clot lysis times, but there were no thermal effects. Ultrasound in the absence of t-PA produced a slight but consistent decrease in turbidity, suggesting a decrease in fibrin diameter due solely to the action of the ultrasound, likely caused by an increase in protofibril tension because of vibration from ultrasound. Changes in fibrin network structure during lysis with ultrasound were visualized in real time by deconvolution microscopy, revealing that the network becomes unstable when 30–40% of the protein in the network was digested, whereas without ultrasound, the fibrin network was digested gradually and retained structural integrity. Fluorescence recovery after photobleaching during lysis revealed that the off-rate of oligomers from digesting fibers was not much affected but the number of binding/unbinding sites was increased. Conclusions Ultrasound causes a decrease in the diameter of the fibers due to tension as a result of vibration, leading to increased binding sites for plasmin(ogen)/t-PA. The positive feedback of this structural change together with increased mixing/transport of t-PA/plasmin(ogen) is likely to account for the observed enhancement of fibrinolysis by ultrasound. PMID:25619618

The Mechanochemical Cycle of Mammalian Kinesin-2 KIF3A/B under Load.

PubMed

Andreasson, Johan O L; Shastry, Shankar; Hancock, William O; Block, Steven M

2015-05-04

The response of motor proteins to external loads underlies their ability to work in teams and determines the net speed and directionality of cargo transport. The mammalian kinesin-2, KIF3A/B, is a heterotrimeric motor involved in intraflagellar transport and vesicle motility in neurons. Bidirectional cargo transport is known to result from the opposing activities of KIF3A/B and dynein bound to the same cargo, but the load-dependent properties of kinesin-2 are poorly understood. We used a feedback-controlled optical trap to probe the velocity, run length, and unbinding kinetics of mouse KIF3A/B under various loads and nucleotide conditions. The kinesin-2 motor velocity is less sensitive than kinesin-1 to external forces, but its processivity diminishes steeply with load, and the motor was observed occasionally to slip and reattach. Each motor domain was characterized by studying homodimeric constructs, and a global fit to the data resulted in a comprehensive pathway that quantifies the principal force-dependent kinetic transitions. The properties of the KIF3A/B heterodimer are intermediate between the two homodimers, and the distinct load-dependent behavior is attributable to the properties of the motor domains and not to the neck linkers or the coiled-coil stalk. We conclude that the force-dependent movement of KIF3A/B differs significantly from conventional kinesin-1. Against opposing dynein forces, KIF3A/B motors are predicted to rapidly unbind and rebind, resulting in qualitatively different transport behavior from kinesin-1. Copyright © 2015 Elsevier Ltd. All rights reserved.

The mechanochemical cycle of mammalian kinesin-2 KIF3A/B under load

PubMed Central

Andreasson, Johan O.L.; Shastry, Shankar; Hancock, William O.; Block, Steven M.

2015-01-01

Summary The response of motor proteins to external loads underlies their ability to work in teams and determines the net speed and directionality of cargo transport. The mammalian kinesin-2, KIF3A/B, is a heterotrimeric motor involved in intraflagellar transport and vesicle motility in neurons. Bidirectional cargo transport is known to result from the opposing activities of KIF3A/B and dynein bound to the same cargo, but the load-dependent properties of kinesin-2 are poorly understood. We used a feedback-controlled optical trap to probe the velocity, run length and unbinding kinetics of mouse KIF3A/B under various loads and nucleotide conditions. The kinesin-2 motor velocity is less sensitive than kinesin-1 to external forces, but its processivity diminishes steeply with load, and the motor was observed occasionally to slip and reattach. Each motor domain was characterized by studying homodimeric constructs, and a global fit to the data resulted in a comprehensive pathway that quantifies the principal force-dependent kinetic transitions. The properties of the KIF3A/B heterodimer are intermediate between the two homodimers, and the distinct load-dependent behavior is attributable to the properties of the motor domains, and not to the neck-linkers or the coiled-coil stalk. We conclude that the force-dependent movement of KIF3A/B differs significantly from conventional kinesin-1. Against opposing dynein forces, KIF3A/B motors are predicted to rapidly unbind and rebind, resulting in qualitatively different transport behavior from kinesin-1. PMID:25866395

Method for measuring the unbinding energy of strongly-bound membrane-associated proteins.

PubMed

Bauve, Elisa La; Vernon, Briana C; Ye, Dongmei; Rogers, David M; Siegrist, Cathryn M; Carson, Bryan D; Rempe, Susan B; Zheng, Aihua; Kielian, Margaret; Shreve, Andrew P; Kent, Michael S

2016-11-01

We describe a new method to measure the activation energy for unbinding (enthalpy ΔH* u and free energy ΔG* u ) of a strongly-bound membrane-associated protein from a lipid membrane. It is based on measuring the rate of release of a liposome-bound protein during centrifugation on a sucrose gradient as a function of time and temperature. The method is used to determine ΔH* u and ΔG* u for the soluble dengue virus envelope protein (sE) strongly bound to 80:20 POPC:POPG liposomes at pH5.5. ΔH* u is determined from the Arrhenius equation whereas ΔG* u is determined by fitting the data to a model based on mean first passage time for escape from a potential well. The binding free energy ΔG b of sE was also measured at the same pH for the initial, predominantly reversible, phase of binding to a 70:30 PC:PG lipid bilayer. The unbinding free energy (20±3kcal/mol, 20% PG) was found to be roughly three times the binding energy per monomer, (7.8±0.3kcal/mol for 30% PG, or est. 7.0kcal/mol for 20% PG). This is consistent with data showing that free sE is a monomer at pH5.5, but assembles into trimers after associating with membranes. This new method to determine unbinding energies should be useful to understand better the complex interactions of integral monotopic proteins and strongly-bound peripheral membrane proteins with lipid membranes. Copyright © 2016 Elsevier B.V. All rights reserved.

Efficient analysis of stochastic gene dynamics in the non-adiabatic regime using piecewise deterministic Markov processes

PubMed Central

2018-01-01

Single-cell experiments show that gene expression is stochastic and bursty, a feature that can emerge from slow switching between promoter states with different activities. In addition to slow chromatin and/or DNA looping dynamics, one source of long-lived promoter states is the slow binding and unbinding kinetics of transcription factors to promoters, i.e. the non-adiabatic binding regime. Here, we introduce a simple analytical framework, known as a piecewise deterministic Markov process (PDMP), that accurately describes the stochastic dynamics of gene expression in the non-adiabatic regime. We illustrate the utility of the PDMP on a non-trivial dynamical system by analysing the properties of a titration-based oscillator in the non-adiabatic limit. We first show how to transform the underlying chemical master equation into a PDMP where the slow transitions between promoter states are stochastic, but whose rates depend upon the faster deterministic dynamics of the transcription factors regulated by these promoters. We show that the PDMP accurately describes the observed periods of stochastic cycles in activator and repressor-based titration oscillators. We then generalize our PDMP analysis to more complicated versions of titration-based oscillators to explain how multiple binding sites lengthen the period and improve coherence. Last, we show how noise-induced oscillation previously observed in a titration-based oscillator arises from non-adiabatic and discrete binding events at the promoter site. PMID:29386401

Antibody-Unfolding and Metastable-State Binding in Force Spectroscopy and Recognition Imaging

PubMed Central

Kaur, Parminder; Qiang-Fu; Fuhrmann, Alexander; Ros, Robert; Kutner, Linda Obenauer; Schneeweis, Lumelle A.; Navoa, Ryman; Steger, Kirby; Xie, Lei; Yonan, Christopher; Abraham, Ralph; Grace, Michael J.; Lindsay, Stuart

2011-01-01

Force spectroscopy and recognition imaging are important techniques for characterizing and mapping molecular interactions. In both cases, an antibody is pulled away from its target in times that are much less than the normal residence time of the antibody on its target. The distribution of pulling lengths in force spectroscopy shows the development of additional peaks at high loading rates, indicating that part of the antibody frequently unfolds. This propensity to unfold is reversible, indicating that exposure to high loading rates induces a structural transition to a metastable state. Weakened interactions of the antibody in this metastable state could account for reduced specificity in recognition imaging where the loading rates are always high. The much weaker interaction between the partially unfolded antibody and target, while still specific (as shown by control experiments), results in unbinding on millisecond timescales, giving rise to rapid switching noise in the recognition images. At the lower loading rates used in force spectroscopy, we still find discrepancies between the binding kinetics determined by force spectroscopy and those determined by surface plasmon resonance—possibly a consequence of the short tethers used in recognition imaging. Recognition imaging is nonetheless a powerful tool for interpreting complex atomic force microscopy images, so long as specificity is calibrated in situ, and not inferred from equilibrium binding kinetics. PMID:21190677

Stochastic dynamics of small ensembles of non-processive molecular motors: The parallel cluster model

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

Erdmann, Thorsten; Albert, Philipp J.; Schwarz, Ulrich S.

2013-11-07

Non-processive molecular motors have to work together in ensembles in order to generate appreciable levels of force or movement. In skeletal muscle, for example, hundreds of myosin II molecules cooperate in thick filaments. In non-muscle cells, by contrast, small groups with few tens of non-muscle myosin II motors contribute to essential cellular processes such as transport, shape changes, or mechanosensing. Here we introduce a detailed and analytically tractable model for this important situation. Using a three-state crossbridge model for the myosin II motor cycle and exploiting the assumptions of fast power stroke kinetics and equal load sharing between motors inmore » equivalent states, we reduce the stochastic reaction network to a one-step master equation for the binding and unbinding dynamics (parallel cluster model) and derive the rules for ensemble movement. We find that for constant external load, ensemble dynamics is strongly shaped by the catch bond character of myosin II, which leads to an increase of the fraction of bound motors under load and thus to firm attachment even for small ensembles. This adaptation to load results in a concave force-velocity relation described by a Hill relation. For external load provided by a linear spring, myosin II ensembles dynamically adjust themselves towards an isometric state with constant average position and load. The dynamics of the ensembles is now determined mainly by the distribution of motors over the different kinds of bound states. For increasing stiffness of the external spring, there is a sharp transition beyond which myosin II can no longer perform the power stroke. Slow unbinding from the pre-power-stroke state protects the ensembles against detachment.« less

Energy Balance for a Sonoluminescence Bubble Yields a Measure of Ionization Potential Lowering

NASA Astrophysics Data System (ADS)

Kappus, B.; Bataller, A.; Putterman, S. J.

2013-12-01

Application of energy conservation between input sound and the microplasma which forms at the moment of sonoluminescence places bounds on the process, whereby the gas is ionized. Detailed pulsed Mie scattering measurements of the radius versus time for a xenon bubble in sulfuric acid provide a complete characterization of the hydrodynamics and minimum radius. For a range of emission intensities, the blackbody spectrum emitted during collapse matches the minimum bubble radius, implying opaque conditions are attained. This requires a degree of ionization >36%. Analysis reveals only 2.1±0.6eV/atom of energy available during light emission. In order to unbind enough charge, collective processes must therefore reduce the ionization potential by at least 75%. We interpret this as evidence that a phase transition to a highly ionized plasma is occurring during sonoluminescence.

Energy balance for a sonoluminescence bubble yields a measure of ionization potential lowering.

PubMed

Kappus, B; Bataller, A; Putterman, S J

2013-12-06

Application of energy conservation between input sound and the microplasma which forms at the moment of sonoluminescence places bounds on the process, whereby the gas is ionized. Detailed pulsed Mie scattering measurements of the radius versus time for a xenon bubble in sulfuric acid provide a complete characterization of the hydrodynamics and minimum radius. For a range of emission intensities, the blackbody spectrum emitted during collapse matches the minimum bubble radius, implying opaque conditions are attained. This requires a degree of ionization >36%. Analysis reveals only 2.1±0.6  eV/atom of energy available during light emission. In order to unbind enough charge, collective processes must therefore reduce the ionization potential by at least 75%. We interpret this as evidence that a phase transition to a highly ionized plasma is occurring during sonoluminescence.

Cooperative Allosteric Ligand Binding in Calmodulin

NASA Astrophysics Data System (ADS)

Nandigrami, Prithviraj

Conformational dynamics is often essential for a protein's function. For example, proteins are able to communicate the effect of binding at one site to a distal region of the molecule through changes in its conformational dynamics. This so called allosteric coupling fine tunes the sensitivity of ligand binding to changes in concentration. A conformational change between a "closed" (apo) and an "open" (holo) conformation upon ligation often produces this coupling between binding sites. Enhanced sensitivity between the unbound and bound ensembles leads to a sharper binding curve. There are two basic conceptual frameworks that guide our visualization about ligand binding mechanisms. First, a ligand can stabilize the unstable "open" state from a dynamic ensemble of conformations within the unbound basin. This binding mechanism is called conformational selection. Second, a ligand can weakly bind to the low-affinity "closed" state followed by a conformational transition to the "open" state. In this dissertation, I focus on molecular dynamics simulations to understand microscopic origins of ligand binding cooperativity. A minimal model of allosteric binding transitions must include ligand binding/unbinding events, while capturing the transition mechanism between two distinct meta-stable free energy basins. Due in part to computational timescales limitations, work in this dissertation describes large-scale conformational transitions through a simplified, coarse-grained model based on the energy basins defined by the open and closed conformations of the protein Calmodulin (CaM). CaM is a ubiquitous calcium-binding protein consisting of two structurally similar globular domains connected by a flexible linker. The two domains of CaM, N-terminal domain (nCaM) and C-terminal domain (cCaM) consists of two helix-loop-helix motifs (the EF-hands) connected by a flexible linker. Each domain of CaM consists of two binding loops and binds 2 calcium ions each. The intact domain binds up to 4 calcium ions. The simulations use a coupled molecular dynamics/monte carlo scheme where the protein dynamics is simulated explicitly, while ligand binding/unbinding are treated implicitly. In the model, ligand binding/unbinding events coupled with a conformational change of the protein within the grand canonical ensemble. Here, ligand concentration is controlled through the chemical potential (micro). This allows us to use a simple thermodynamic model to analyze the simulated data and quantify binding cooperativity. Simulated binding titration curves are calculated through equilibrium simulations at different values of micro. First, I study domain opening transitions of isolated nCaM and cCaM in the absence of calcium. This work is motivated by results from a recent analytic variational model that predicts distinct domain opening transition mechanism for the domains of CaM. This is a surprising result because the domains have the same folded state topology. In the simulations, I find the two domains of CaM have distinct transition mechanism over a broad range of temperature, in harmony with the analytic predictions. In particular, the simulated transition mechanism of nCaM follows a two-state behavior, while domain opening in cCaM involves global unfolding and refolding of the tertiary structure. The unfolded intermediate also appears in the landscape of nCaM, but at a higher temperature than it appears in cCaM's energy landscape. This is consistent with nCaM's higher thermal stability. Under approximate physiological conditions, majority of the sampled transitions in cCaM involves unfolding and refolding during conformational change. Kinetically, the transient unfolding and refolding in cCaM significantly slows the domain opening and closing rates in cCaM. Second, I investigate the structural origins of binding affinity and allosteric cooperativity of binding 2 calcium-ions to each domain of CaM. In my work, I predict the order of binding strength of CaM's loops. I analyze simulated binding curves within the framework of the classic Monod-Wyman-Changeux (MWC) model of allostery to extract the binding free energies to the closed and open ensembles. The simulations predict that cCaM binds calcium with higher affinity and greater cooperativity than nCaM. Where it is possible to compare, these predictions are in good agreement with experimental results. The analysis of the simulations offers a rationale for why the two domains differ in cooperativity: the higher cooperativity of cCaM is due to larger difference in affinity of its binding loops. Third, I extend the work to investigate structural origins of binding cooperativity of 4 calcium-ions to intact CaM. I characterize the microscopic cooperativities of each ligation state and provide a kinetic description of the binding mechanism. Due to the heterogeneous nature of CaM's loops, as predicted in our simulations of isolated domains, I focus on investigating the influence of this heterogeneity on the kinetic flux of binding pathways as a function of concentration. The formalism developed for Network Models of protein folding kinetics, is used to evaluate the directed flux of all possible pathways between unligated and fully loaded CaM. (Abstract shortened by ProQuest.).

The Biotin/Avidin complex adhesion force

NASA Astrophysics Data System (ADS)

Balsera, Manel A.; Izrailev, Sergei; Stepaniants, Sergey; Oono, Yoshitsugu; Schulten, Klaus

1997-03-01

The vitamin Biotin and the protein avidin form one of the strongest non-covalent bonds between biological molecules. We have performed molecular and stochastic dynamic modeling of the unbinding of this complex(Izrailev et al., Biophysical Journal, In press). These simulations provide insight into the effect of particular residues and water on the tight binding of the system. With the aid of simple phenomenological models we have related qualitatively our results to Atomic Force Microscopy adhesion force measurements (E.-L. Florin, V. T. Moy and H. E. Gaub Science) 264:415-417 and kinetic dissociation experiments( A. Chilcotti and P. S. Stayton, J. Am. Chem. Soc.) 117:10622-10628. We will discuss the difficulties preventing a more quantitative understanding of the unbinding force and kinetics.

Producing the deuteron in stars: anthropic limits on fundamental constants

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

Barnes, Luke A.; Lewis, Geraint F., E-mail: luke.barnes@sydney.edu.au, E-mail: gfl@physics.usyd.edu.au

2017-07-01

Stellar nucleosynthesis proceeds via the deuteron (D), but only a small change in the fundamental constants of nature is required to unbind it. Here, we investigate the effect of altering the binding energy of the deuteron on proton burning in stars. We find that the most definitive boundary in parameter space that divides probably life-permitting universes from probably life-prohibiting ones is between a bound and unbound deuteron. Due to neutrino losses, a ball of gas will undergo rapid cooling or stabilization by electron degeneracy pressure before it can form a stable, nuclear reaction-sustaining star. We also consider a less-bound deuteron,more » which changes the energetics of the pp and pep reactions. The transition to endothermic pp and pep reactions, and the resulting beta-decay instability of the deuteron, do not seem to present catastrophic problems for life.« less

Dynein's Network of Chemomechanical Motor Cycles

NASA Astrophysics Data System (ADS)

Shen, Weibo; Wang, Ziqing; Wang, Guodong

2012-07-01

An eight-state network model of dynein's chemomechanical motor cycles is developed, in which the states of an effective single dynein head are represented by the number of ATP binding at the primary site and the number of ATP binding at other three secondary sites. The binding and unbinding of ATP, as well as the hydrolysis of ATP and the reverse process, are characterized by transition rates between certain states. Our results show that the stall force of dynein increases fast with ATP up to 1 mM ATP, beyond which it increases slowly to a saturated value, and that load and ATP concentration can adjust the step size of dynein, i.e., dynein can shift gears according to conditions. These results are in agreement with experiments [R. Mallik, B. C. Carter, S. A. Lex, S. J. King and S. P. Gross, Nature 427, 649 (2004)].

Multiple crossovers and coherent states in a Mott-Peierls insulator

NASA Astrophysics Data System (ADS)

Nájera, O.; Civelli, M.; Dobrosavljević, V.; Rozenberg, M. J.

2018-01-01

We consider the dimer Hubbard model within dynamical mean-field theory to study the interplay and competition between Mott and Peierls physics. We describe the various metal-insulator transition lines of the phase diagram and the breakdown of the different solutions that occur along them. We focus on the specific issue of the debated Mott-Peierls insulator crossover and describe the systematic evolution of the electronic structure across the phase diagram. We found that at low intradimer hopping, the emerging local magnetic moments can unbind above a characteristic singlet temperature T*. Upon increasing the interdimer hopping, subtle changes occur in the electronic structure. Notably, we find Hubbard bands of a mix character with coherent and incoherent excitations. We argue that this state might be relevant for materials such as VO2 and its signatures may be observed in spectroscopic studies, and possibly through pump-probe experiments.

Visualizing Chemical Interaction Dynamics of Confined DNA Molecules

NASA Astrophysics Data System (ADS)

Henkin, Gilead; Berard, Daniel; Stabile, Frank; Leslie, Sabrina

We present a novel nanofluidic approach to controllably introducing reagent molecules to interact with confined biopolymers and visualizing the reaction dynamics in real time. By dynamically deforming a flow cell using CLiC (Convex Lens-induced Confinement) microscopy, we are able to tune reaction chamber dimensions from micrometer to nanometer scales. We apply this gentle deformation to load and extend DNA polymers within embedded nanotopographies and visualize their interactions with other molecules in solution. Quantifying the change in configuration of polymers within embedded nanotopographies in response to binding/unbinding of reagent molecules provides new insights into their consequent change in physical properties. CLiC technology enables an ultra sensitive, massively parallel biochemical analysis platform which can acces a broader range of interaction parameters than existing devices.

Efficient analysis of stochastic gene dynamics in the non-adiabatic regime using piecewise deterministic Markov processes

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

Lin, Yen Ting; Buchler, Nicolas E.

Single-cell experiments show that gene expression is stochastic and bursty, a feature that can emerge from slow switching between promoter states with different activities. In addition to slow chromatin and/or DNA looping dynamics, one source of long-lived promoter states is the slow binding and unbinding kinetics of transcription factors to promoters, i.e. the non-adiabatic binding regime. Here, we introduce a simple analytical framework, known as a piecewise deterministic Markov process (PDMP), that accurately describes the stochastic dynamics of gene expression in the non-adiabatic regime. We illustrate the utility of the PDMP on a non-trivial dynamical system by analysing the propertiesmore » of a titration-based oscillator in the non-adiabatic limit. We first show how to transform the underlying chemical master equation into a PDMP where the slow transitions between promoter states are stochastic, but whose rates depend upon the faster deterministic dynamics of the transcription factors regulated by these promoters. We show that the PDMP accurately describes the observed periods of stochastic cycles in activator and repressor-based titration oscillators. We then generalize our PDMP analysis to more complicated versions of titration-based oscillators to explain how multiple binding sites lengthen the period and improve coherence. Finally, we show how noise-induced oscillation previously observed in a titration-based oscillator arises from non-adiabatic and discrete binding events at the promoter site.« less

Efficient analysis of stochastic gene dynamics in the non-adiabatic regime using piecewise deterministic Markov processes

DOE PAGES

Lin, Yen Ting; Buchler, Nicolas E.

2018-01-31

Single-cell experiments show that gene expression is stochastic and bursty, a feature that can emerge from slow switching between promoter states with different activities. In addition to slow chromatin and/or DNA looping dynamics, one source of long-lived promoter states is the slow binding and unbinding kinetics of transcription factors to promoters, i.e. the non-adiabatic binding regime. Here, we introduce a simple analytical framework, known as a piecewise deterministic Markov process (PDMP), that accurately describes the stochastic dynamics of gene expression in the non-adiabatic regime. We illustrate the utility of the PDMP on a non-trivial dynamical system by analysing the propertiesmore » of a titration-based oscillator in the non-adiabatic limit. We first show how to transform the underlying chemical master equation into a PDMP where the slow transitions between promoter states are stochastic, but whose rates depend upon the faster deterministic dynamics of the transcription factors regulated by these promoters. We show that the PDMP accurately describes the observed periods of stochastic cycles in activator and repressor-based titration oscillators. We then generalize our PDMP analysis to more complicated versions of titration-based oscillators to explain how multiple binding sites lengthen the period and improve coherence. Finally, we show how noise-induced oscillation previously observed in a titration-based oscillator arises from non-adiabatic and discrete binding events at the promoter site.« less

Rapid eye movement sleep does not seem to unbind memories from their emotional context.

PubMed

Deliens, Gaétane; Neu, Daniel; Peigneux, Philippe

2013-12-01

Sleep unbinds memories from their emotional learning context, protecting them from emotional interference due to a change of mood between learning and recall. According to the 'sleep to forget and sleep to remember' model, emotional unbinding takes place during rapid eye movement sleep. To test this hypothesis, we investigated emotional contextual interference effects after early versus late post-learning sleep periods, in which slow wave and rapid eye movement sleep, respectively, predominate. Participants learned a list of neutral word pairs after induction of a happy or a sad mood, then slept immediately afterwards for 3 h of early or late sleep under polysomnographic recording, in a within-subject counterbalanced design. They slept for 3 h before learning in the late sleep condition. Polysomnographic data confirmed more rapid eye movement sleep in the late than in the early sleep condition. After awakening, half the list was recalled after induction of a similar mood than during the encoding session (non-interference condition), and the other half of the list was recalled after induction of a different mood (interference condition). The results disclosed an emotional interference effect on recall both in the early and late sleep conditions, which does not corroborate the hypothesis of a rapid eye movement sleep-related protection of recent memories from emotional contextual interference. Alternatively, the contextual demodulation process initiated during the first post-learning night might need several consecutive nights of sleep to be achieved. © 2013 European Sleep Research Society.

Exploring the unbinding of Leishmania (L.) amazonensis CPB derived-epitopes from H2 MHC class I proteins.

PubMed

Brandt, Artur M L; Batista, Paulo Ricardo; Souza-Silva, Franklin; Alves, Carlos Roberto; Caffarena, Ernesto Raul

2016-04-01

New strategies to control Leishmania disease demand an extensive knowledge about several aspects of infection including the understanding of its molecular events. In murine models, cysteine proteinase B from Leishmania amazonensis promotes regulation of immune response, and fragments from its C-terminus extension (cyspep) can play a decisive role in the host-parasite interaction. The interaction between cyspep-derived peptides and major histocompatibility complex (MHC) proteins is a crucial factor in Leishmania infections. Seven cyspep-derived peptides, previously identified as capable of interacting with H-2 (murine) MHC class I proteins, were studied in this work. We established a protocol to simulate the unbinding of these peptides from the cleft of H-2 receptors. From the simulations, we estimated the corresponding free energy of dissociation (ΔGd ) and described the molecular events that occur during the exit of peptides from the cleft. To test the reliability of this method, we first applied it to a calibration set of four crystallographic MHC/peptide complexes. Next, we explored the unbinding of the seven complexes mentioned above. Results were consistent with ΔGd values obtained from surface plasmon resonance (SPR) experiments. We also identified some of the primary interactions between peptides and H-2 receptors, and we detected three regions of influence for the interaction. This pattern was systematically observed for the peptides and helped determine a minimum distance for the real interaction between peptides and H-2 proteins occurring at ∼ 25 Å. © 2016 Wiley Periodicals, Inc.

A Peptide Filtering Relation Quantifies MHC Class I Peptide Optimization

PubMed Central

Goldstein, Leonard D.; Howarth, Mark; Cardelli, Luca; Emmott, Stephen; Elliott, Tim; Werner, Joern M.

2011-01-01

Major Histocompatibility Complex (MHC) class I molecules enable cytotoxic T lymphocytes to destroy virus-infected or cancerous cells, thereby preventing disease progression. MHC class I molecules provide a snapshot of the contents of a cell by binding to protein fragments arising from intracellular protein turnover and presenting these fragments at the cell surface. Competing fragments (peptides) are selected for cell-surface presentation on the basis of their ability to form a stable complex with MHC class I, by a process known as peptide optimization. A better understanding of the optimization process is important for our understanding of immunodominance, the predominance of some T lymphocyte specificities over others, which can determine the efficacy of an immune response, the danger of immune evasion, and the success of vaccination strategies. In this paper we present a dynamical systems model of peptide optimization by MHC class I. We incorporate the chaperone molecule tapasin, which has been shown to enhance peptide optimization to different extents for different MHC class I alleles. Using a combination of published and novel experimental data to parameterize the model, we arrive at a relation of peptide filtering, which quantifies peptide optimization as a function of peptide supply and peptide unbinding rates. From this relation, we find that tapasin enhances peptide unbinding to improve peptide optimization without significantly delaying the transit of MHC to the cell surface, and differences in peptide optimization across MHC class I alleles can be explained by allele-specific differences in peptide binding. Importantly, our filtering relation may be used to dynamically predict the cell surface abundance of any number of competing peptides by MHC class I alleles, providing a quantitative basis to investigate viral infection or disease at the cellular level. We exemplify this by simulating optimization of the distribution of peptides derived from Human Immunodeficiency Virus Gag-Pol polyprotein. PMID:22022238

Spontaneous-curvature theory of clathrin-coated membranes.

PubMed Central

Mashl, R J; Bruinsma, R F

1998-01-01

Clathrin-coated membranes are precursors to coated vesicles in the receptor-mediated endocytic pathway. In this paper we present a physical model for the first steps of the transformation of a clathrin-coated membrane into a coated vesicle. The theory is based on in vitro cytoplasmic acidification experiments of Heuser (J. Cell Biol. 108:401-411) that suggest the transformation proceeds by changes in the chemical environment of the clathrin lattice, wherein the chemical environment determines the amount of intrinsic, or spontaneous, curvature of the network. We show that a necessary step of the transformation, formation of free pentagons in the clathrin network, can proceed via dislocation unbinding, driven by changes in the spontaneous curvature. Dislocation unbinding is shown to favor formation of coated vesicles that are quite small compared to those predicted by the current continuum theories, which do not include the topology of the clathrin lattice. PMID:9635740

Weighted Ensemble Simulation: Review of Methodology, Applications, and Software

PubMed Central

Zuckerman, Daniel M.; Chong, Lillian T.

2018-01-01

The weighted ensemble (WE) methodology orchestrates quasi-independent parallel simulations run with intermittent communication that can enhance sampling of rare events such as protein conformational changes, folding, and binding. The WE strategy can achieve superlinear scaling—the unbiased estimation of key observables such as rate constants and equilibrium state populations to greater precision than would be possible with ordinary parallel simulation. WE software can be used to control any dynamics engine, such as standard molecular dynamics and cell-modeling packages. This article reviews the theoretical basis of WE and goes on to describe successful applications to a number of complex biological processes—protein conformational transitions, (un)binding, and assembly processes, as well as cell-scale processes in systems biology. We furthermore discuss the challenges that need to be overcome in the next phase of WE methodological development. Overall, the combined advances in WE methodology and software have enabled the simulation of long-timescale processes that would otherwise not be practical on typical computing resources using standard simulation. PMID:28301772

Weighted Ensemble Simulation: Review of Methodology, Applications, and Software.

PubMed

Zuckerman, Daniel M; Chong, Lillian T

2017-05-22

The weighted ensemble (WE) methodology orchestrates quasi-independent parallel simulations run with intermittent communication that can enhance sampling of rare events such as protein conformational changes, folding, and binding. The WE strategy can achieve superlinear scaling-the unbiased estimation of key observables such as rate constants and equilibrium state populations to greater precision than would be possible with ordinary parallel simulation. WE software can be used to control any dynamics engine, such as standard molecular dynamics and cell-modeling packages. This article reviews the theoretical basis of WE and goes on to describe successful applications to a number of complex biological processes-protein conformational transitions, (un)binding, and assembly processes, as well as cell-scale processes in systems biology. We furthermore discuss the challenges that need to be overcome in the next phase of WE methodological development. Overall, the combined advances in WE methodology and software have enabled the simulation of long-timescale processes that would otherwise not be practical on typical computing resources using standard simulation.

Efficient sampling of reversible cross-linking polymers: Self-assembly of single-chain polymeric nanoparticles

NASA Astrophysics Data System (ADS)

Oyarzún, Bernardo; Mognetti, Bortolo Matteo

2018-03-01

We present a new simulation technique to study systems of polymers functionalized by reactive sites that bind/unbind forming reversible linkages. Functionalized polymers feature self-assembly and responsive properties that are unmatched by the systems lacking selective interactions. The scales at which the functional properties of these materials emerge are difficult to model, especially in the reversible regime where such properties result from many binding/unbinding events. This difficulty is related to large entropic barriers associated with the formation of intra-molecular loops. In this work, we present a simulation scheme that sidesteps configurational costs by dedicated Monte Carlo moves capable of binding/unbinding reactive sites in a single step. Cross-linking reactions are implemented by trial moves that reconstruct chain sections attempting, at the same time, a dimerization reaction between pairs of reactive sites. The model is parametrized by the reaction equilibrium constant of the reactive species free in solution. This quantity can be obtained by means of experiments or atomistic/quantum simulations. We use the proposed methodology to study the self-assembly of single-chain polymeric nanoparticles, starting from flexible precursors carrying regularly or randomly distributed reactive sites. We focus on understanding differences in the morphology of chain nanoparticles when linkages are reversible as compared to the well-studied case of irreversible reactions. Intriguingly, we find that the size of regularly functionalized chains, in good solvent conditions, is non-monotonous as a function of the degree of functionalization. We clarify how this result follows from excluded volume interactions and is peculiar of reversible linkages and regular functionalizations.

A structural insight into the inhibitory mechanism of an orally active PI3K/mTOR dual inhibitor, PKI-179 using computational approaches.

PubMed

Mohd Rehan

2015-11-01

The PI3K/AKT/mTOR signaling pathway has been identified as an important target for cancer therapy. Attempts are increasingly made to design the inhibitors against the key proteins of this pathway for anti-cancer therapy. The PI3K/mTOR dual inhibitors have proved more effective than the inhibitors against only single protein targets. Recently discovered PKI-179, an orally effective compound, is one such dual inhibitor targeting both PI3K and mTOR. This anti-cancer compound is efficacious both in vitro and in vivo. However, the binding mechanisms and the molecular interactions of PKI-179 with PI3K and mTOR are not yet available. The current study investigated the exact binding mode and the molecular interactions of PKI-179 with PI3Kγ and mTOR using molecular docking and (un)binding simulation analyses. The study identified PKI-179 interacting residues of both the proteins and their importance in binding was ranked by the loss in accessible surface area, number of molecular interactions of the residue, and consistent appearance of the residue in (un)binding simulation analysis. The key residues involved in binding of PKI-179 were Ala-805 in PI3Kγ and Ile-2163 in mTOR as they have lost maximum accessible surface area due to binding. In addition, the residues which played a role in binding of the drug but were away from the catalytic site were also identified using (un)binding simulation analyses. Finally, comparison of the interacting residues in the respective catalytic sites was done for the difference in the binding of the drug to the two proteins. Thus, the pairs of the residues falling at the similar location with respect to the docked drug were identified. The striking similarity in the interacting residues of the catalytic site explains the concomitant inhibition of both proteins by a number of inhibitors. In conclusion, the docking and (un)binding simulation analyses of dual inhibitor PKI-179 with PI3K and mTOR will provide a suitable multi-target model for studying drug-protein interactions and thus help in designing the novel drugs with higher potency. Copyright © 2015 Elsevier Inc. All rights reserved.

From first galaxies to QSOs - feeding the baby monsters

NASA Astrophysics Data System (ADS)

Danese, L.; Shankar, F.; Granato, G. L.; Silva, L.; Bressan, A.; de Zotti, G.; Salucci, P.; Cirasuolo, M.

We present a physical model for the coevolution of massive spheroidal galaxies and active nuclei at their centers. Supernova heating is increasingly effective in slowing down the star formation and in driving gas outflows in smaller and smaller dark matter halos. Thus the more massive protogalaxies virializing at early times are the sites of faster star formation. The correspondingly higher radiation drag causes a faster angular momentum loss by the gas and induces a larger accretion rate onto the central black hole. In turn, the kinetic energy of the outflows powered by the active nuclei can unbind the residual gas in a time shorter for larger halos. The model accounts for a broad variety of dynamical, photometric and metallicity properties of early-type galaxies, for the MBH-σ relation and for the local supermassive black-hole mass function.

Neuroscience: toward unbinding the binding problem.

PubMed

Whitney, David

2009-03-24

How the brain 'binds' information to create a coherent perceptual experience is an enduring question. Recent research in the psychophysics of perceptual binding and developments in fMRI analysis techniques are bringing us closer to an understanding of how the brain solves the binding problem.

Neutron stars and millisecond pulsars from accretion-induced collapse in globular clusters

NASA Technical Reports Server (NTRS)

Bailyn, Charles D.; Grindlay, Jonathan E.

1990-01-01

This paper examines the limits on the number of millisecond pulsars which could be formed in globular clusters by the generally accepted scenario (in which a neutron star is created by the supernova of an initially massive star and subsequently captures a companion to form a low-mass X-ray binary which eventually becomes a millisecond pulsar). It is found that, while the number of observed low-mass X-ray binaries can be adequately explained in this way, the reasonable assumption that the pulsar luminosity function in clusters extends below the current observational limits down to the luminosity of the faintest millisecond pulsars in the field suggests a cluster population of millisecond pulsars which is substantially larger than the standard model can produce. Alleviating this problem by postulating much shorter lifetimes for the X-ray binaries requires massive star populations sufficiently large that the mass loss resulting from their evolution would be likely to unbind the cluster. It is argued that neutron star formation in globular clusters by accretion-induced collapse of white dwarfs may resolve the discrepancy in birthrates.

Single molecular dynamic interactions between glycophorin A and lectin as probed by atomic force microscopy.

PubMed

Yan, Chao; Yersin, Alexandre; Afrin, Rehana; Sekiguchi, Hiroshi; Ikai, Atsushi

2009-09-01

Glycophorin A (GpA) is one of the most abundant transmembrane proteins in human erythrocytes and its interaction with lectins has been studied as model systems for erythrocyte related biological processes. We performed a force measurement study using the force mode of atomic force microscopy (AFM) to investigate the single molecular level biophysical mechanisms involved in GpA-lectin interactions. GpA was mounted on a mica surface or natively presented on the erythrocyte membrane and probed with an AFM tip coated with the monomeric but multivalent Psathyrella velutina lectin (PVL) through covalent crosslinkers. A dynamic force spectroscopy study revealed similar interaction properties in both cases, with the unbinding force centering around 60 pN with a weak loading rate dependence. Hence we identified the presence of one energy barrier in the unbinding process. Force profile analysis showed that more than 70% of GpAs are free of cytoskeletal associations in agreement with previous reports.

Spectrin-ankyrin interaction mechanics: A key force balance factor in the red blood cell membrane skeleton.

PubMed

Saito, Masakazu; Watanabe-Nakayama, Takahiro; Machida, Shinichi; Osada, Toshiya; Afrin, Rehana; Ikai, Atsushi

2015-01-01

As major components of red blood cell (RBC) cytoskeleton, spectrin and F-actin form a network that covers the entire cytoplasmic surface of the plasma membrane. The cross-linked two layered structure, called the membrane skeleton, keeps the structural integrity of RBC under drastically changing mechanical environment during circulation. We performed force spectroscopy experiments on the atomic force microscope (AFM) as a means to clarify the mechanical characteristics of spectrin-ankyrin interaction, a key factor in the force balance of the RBC cytoskeletal structure. An AFM tip was functionalized with ANK1-62k and used to probe spectrin crosslinked to mica surface. A force spectroscopy study gave a mean unbinding force of ~30 pN under our experimental conditions. Two energy barriers were identified in the unbinding process. The result was related to the well-known flexibility of spectrin tetramer and participation of ankyrin 1-spectrin interaction in the overall balance of membrane skeleton dynamics. Copyright © 2015 Elsevier B.V. All rights reserved.

Electrical detection of single viruses

NASA Astrophysics Data System (ADS)

Patolsky, Fernando; Zheng, Gengfeng; Hayden, Oliver; Lakadamyali, Melike; Zhuang, Xiaowei; Lieber, Charles M.

2004-09-01

We report direct, real-time electrical detection of single virus particles with high selectivity by using nanowire field effect transistors. Measurements made with nanowire arrays modified with antibodies for influenza A showed discrete conductance changes characteristic of binding and unbinding in the presence of influenza A but not paramyxovirus or adenovirus. Simultaneous electrical and optical measurements using fluorescently labeled influenza A were used to demonstrate conclusively that the conductance changes correspond to binding/unbinding of single viruses at the surface of nanowire devices. pH-dependent studies further show that the detection mechanism is caused by a field effect, and that the nanowire devices can be used to determine rapidly isoelectric points and variations in receptor-virus binding kinetics for different conditions. Lastly, studies of nanowire devices modified with antibodies specific for either influenza or adenovirus show that multiple viruses can be selectively detected in parallel. The possibility of large-scale integration of these nanowire devices suggests potential for simultaneous detection of a large number of distinct viral threats at the single virus level.

Putting Humpty together and pulling him apart: accessing and unbinding the hippocampal item-context engram.

PubMed

Sadeh, Talya; Maril, Anat; Bitan, Tali; Goshen-Gottstein, Yonatan

2012-03-01

A remarkable act of memory entails binding different forms of information. We focus on the timeless question of how the bound engram is accessed such that its component features-item and context-are extracted. To shed light on this question, we investigate the dynamics between brain structures that together mediate the binding and extraction of item and context. Converging evidence has implicated the Parahippocampal cortex (PHc) in contextual processing, the Perirhinal cortex (PRc) in item processing, and the hippocampus in item-context binding. Effective connectivity analysis was conducted on fMRI data gathered during retrieval on tests that differ with regard to the to-be-extracted information. Results revealed that recall is initiated by context-related PHc activity, followed by hippocampal item-context engram activation, and completed with retrieval of the study-item by the PRc. The reverse path was found for recognition. We thus provide novel evidence for dissociative patterns of item-context unbinding during retrieval. Copyright © 2011 Elsevier Inc. All rights reserved.

Rock-degrading endophytic bacteria in cacti

Treesearch

M. Esther Puente; Ching Y. Li; Yoav Bashan

2009-01-01

A plant-bacterium association of the cardon cactus (Pachycereus pringlei) and endophytic bacteria promotes establishment of seedlings and growth on igneous rocks without soil. These bacteria weather several rock types and minerals, unbind significant amounts of useful minerals for plants from the rocks, fix in vitro N2. produce...

‘Life is motion’: multiscale motility of molecular motors

NASA Astrophysics Data System (ADS)

Lipowsky, Reinhard; Klumpp, Stefan

2005-07-01

Life is intimately related to complex patterns of directed movement. It is quite remarkable that all of this movement is based on filaments and motor molecules which perform mechanical work on the nanometer scale. This article reviews recent theoretical work on the motility of molecular motors and motor particles that bind to cytoskeletal filaments and walk along these filaments in a directed fashion. It is emphasized that these systems exhibit several motility regimes which are well seperated in time. In their bound state, the motor particles move with a typical velocity of about 1 μm/s. The motor cycles underlying this bound motor movement can be understood in terms of driven Brownian ratchets and networks. On larger length and time scales, the motor particles unbind from the filaments and undergo peculiar motor walks consisting of many diffusional encounters with the filaments. If the mutual exclusion (or hardcore repulsion) of these motor particles is taken into account, one finds a variety of cooperative phenomena and self-organized processes: build-up of traffic jams; active structure formation leading to steady states with spatially nonuniform density and current patterns; and active phase transitions between different steady states far from equilibrium. A particularly simple active phase transition with spontaneous symmetry breaking is predicted to occur in systems with two species of motor particles which walk on the filaments in opposite directions.

Theory of activated transport in bilayer quantum Hall systems.

PubMed

Roostaei, B; Mullen, K J; Fertig, H A; Simon, S H

2008-07-25

We analyze the transport properties of bilayer quantum Hall systems at total filling factor nu=1 in drag geometries as a function of interlayer bias, in the limit where the disorder is sufficiently strong to unbind meron-antimeron pairs, the charged topological defects of the system. We compute the typical energy barrier for these objects to cross incompressible regions within the disordered system using a Hartree-Fock approach, and show how this leads to multiple activation energies when the system is biased. We then demonstrate using a bosonic Chern-Simons theory that in drag geometries current in a single layer directly leads to forces on only two of the four types of merons, inducing dissipation only in the drive layer. Dissipation in the drag layer results from interactions among the merons, resulting in very different temperature dependences for the drag and drive layers, in qualitative agreement with experiment.

A Reversible Light-Operated Nanovalve on Mesoporous Silica Nanoparticles

PubMed Central

Tarn, Derrick; Ferris, Daniel P.; Barnes, Jonathan C.; Ambrogio, Michael W.; Stoddart, J. Fraser

2014-01-01

Two azobenzene α-cyclodextrin based nanovalves are designed, synthesized and assembled on mesoporous silica nanoparticles. When in aqueous conditions, the cyclodextrin cap is tightly bound to the azobenzene moiety and capable of holding back loaded cargo molecules. Upon irradiation with a near-UV light laser, trans to cis- photoisomerization of azobenzene initiates a dethreading process, which causes the cyclodextrin cap to unbind followed by the release of cargo. The addition of a bulky stopper group to the end of the stalk allows this design to be reversible; complete dethreading of cyclodextrin as a result of unbinding with azobenzene is prevented as a consequence of steric interference. As a result, thermal relaxation of cis- to trans-azobenzene allows for the rebinding of cyclodextrin and resealing of the nanopores, a process which entraps the remaining cargo. Two stalks were designed with different lengths and tested with alizarin red S and propidium iodide. No cargo release was observed prior to light irradiation, and the system was capable of multiuse. On / off control was also demonstrated by monitoring the release of cargo when the light stimulus was applied and removed, respectively. PMID:24519642

New perspectives on the computational characterization of the kinetics of binding-unbinding in drug design: implications for novel therapies.

PubMed

Moreno-Vargas, Liliana M; Prada-Gracia, Diego

The efficiency and the propensity of a drug to be bound to its target protein have been inseparable concepts for decades now. The correlation between the pharmacological activity and the binding affinity has been the first rule to design and optimize a new drug rationally. However, this argument does not prove to be infallible when the results of in vivo assays have to be confronted. Only recently, we understand that other magnitudes as the kinetic rates of binding and unbinding, or the mean residence time of the complex drug-protein, are equally relevant to draw a more accurate model of the mechanism of action of a drug. It is in this scenario where new computational techniques to simulate the all-atom dynamics of the biomolecular system find its valuable place on the challenge of designing new molecules for more effective and less toxic therapies. Copyright © 2016 Hospital Infantil de México Federico Gómez. Publicado por Masson Doyma México S.A. All rights reserved.

The role of transmembrane segment 5 (TM5) in Na2 release and the conformational transition of neurotransmitter:sodium symporters toward the inward-open state

PubMed Central

Stolzenberg, Sebastian; Li, Zheng; Quick, Matthias; Malinauskaite, Lina; Nissen, Poul; Weinstein, Harel; Javitch, Jonathan A.; Shi, Lei

2017-01-01

Neurotransmitter:sodium symporters (NSSs) terminate neurotransmission by the reuptake of released neurotransmitters. This active accumulation of substrate against its concentration gradient is driven by the transmembrane Na+ gradient and requires that the transporter traverses several conformational states. LeuT, a prokaryotic NSS homolog, has been crystallized in outward-open, outward-occluded, and inward-open states. Two crystal structures of another prokaryotic NSS homolog, the multihydrophobic amino acid transporter (MhsT) from Bacillus halodurans, have been resolved in novel inward-occluded states, with the extracellular vestibule closed and the intracellular portion of transmembrane segment 5 (TM5i) in either an unwound or a helical conformation. We have investigated the potential involvement of TM5i in binding and unbinding of Na2, i.e. the Na+ bound in the Na2 site, by carrying out comparative molecular dynamics simulations of the models derived from the two MhsT structures. We find that the helical TM5i conformation is associated with a higher propensity for Na2 release, which leads to the repositioning of the N terminus and transition to an inward-open state. By using comparative interaction network analysis, we also identify allosteric pathways connecting TM5i and the Na2 binding site to the extracellular and intracellular regions. Based on our combined computational and mutagenesis studies of MhsT and LeuT, we propose that TM5i plays a key role in Na2 binding and release associated with the conformational transition toward the inward-open state, a role that is likely to be shared across the NSS family. PMID:28320858

Mechanism of the Pseudoirreversible Binding of Amantadine to the M2 Proton Channel.

PubMed

Llabrés, Salomé; Juárez-Jiménez, Jordi; Masetti, Matteo; Leiva, Rosana; Vázquez, Santiago; Gazzarrini, Sabrina; Moroni, Anna; Cavalli, Andrea; Luque, F Javier

2016-11-30

The M2 proton channel of influenza A virus is an integral membrane protein involved in the acidification of the viral interior, a step necessary for the release of the viral genetic material and replication of new virions. The aim of this study is to explore the mechanism of drug (un)binding to the M2 channel in order to gain insight into the structural and energetic features relevant for the development of novel inhibitors. To this end, we have investigated the binding of amantadine (Amt) to the wild type (wt) M2 channel and its V27A variant using multiple independent molecular dynamics simulations, exploratory conventional metadynamics, and multiple-walkers well-tempered metadynamics calculations. The results allow us to propose a sequential mechanism for the (un)binding of Amt to the wt M2 channel, which involves the adoption of a transiently populated intermediate (up state) leading to the thermodynamically favored down binding mode in the channel pore. Furthermore, they suggest that chloride anions play a relevant role in stabilizing the down binding mode of Amt to the wt channel, giving rise to a kinetic trapping that explains the experimentally observed pseudoirreversible inhibition of the wt channel by Amt. We propose that this trapping mechanism underlies the inhibitory activity of potent M2 channel blockers, as supported by the experimental confirmation of the irreversible binding of a pyrrolidine analogue from electrophysiological current assays. Finally, the results reveal that the thermodynamics and kinetics of Amt (un)binding is very sensitive to the V27A mutation, providing a quantitative rationale to the drastic decrease in inhibitory potency against the V27A variant. Overall, these findings pave the way to explore the inhibitory activity of Amt-related analogues in mutated M2 channel variants, providing guidelines for the design of novel inhibitors against resistant virus strains.

Interface bonding in silicon oxide nanocontacts: interaction potentials and force measurements.

PubMed

Wierez-Kien, M; Craciun, A D; Pinon, A V; Roux, S Le; Gallani, J L; Rastei, M V

2018-04-01

The interface bonding between two silicon-oxide nanoscale surfaces has been studied as a function of atomic nature and size of contacting asperities. The binding forces obtained using various interaction potentials are compared with experimental force curves measured in vacuum with an atomic force microscope. In the limit of small nanocontacts (typically <10 3 nm 2 ) measured with sensitive probes the bonding is found to be influenced by thermal-induced fluctuations. Using interface interactions described by Morse, embedded atom model, or Lennard-Jones potential within reaction rate theory, we investigate three bonding types of covalent and van der Waals nature. The comparison of numerical and experimental results reveals that a Lennard-Jones-like potential originating from van der Waals interactions captures the binding characteristics of dry silicon oxide nanocontacts, and likely of other nanoscale materials adsorbed on silicon oxide surfaces. The analyses reveal the importance of the dispersive surface energy and of the effective contact area which is altered by stretching speeds. The mean unbinding force is found to decrease as the contact spends time in the attractive regime. This contact weakening is featured by a negative aging coefficient which broadens and shifts the thermal-induced force distribution at low stretching speeds.

Regulation of 1, 4, 5-triphosphate receptor channel gating dynamics by mutant presenilin in Alzheimer's disease cells

NASA Astrophysics Data System (ADS)

Wei, Fang; Li, Xiang; Cai, Meichun; Liu, Yanping; Jung, Peter; Shuai, Jianwei

2017-06-01

In neurons of patients with Alzheimer's disease, the intracellular Ca2+ concentration is increased by its release from the endoplasmic reticulum via the inositol 1, 4, 5-triphosphate receptor (IP3R). In this paper, we discuss the IP3R gating dynamics in familial Alzheimer's disease (FAD) cells induced with presenilin mutation PS1. By fitting the parameters of an IP3R channel model to experimental data of the open probability, the mean open time and the mean closed time of IP3R channels, in control cells and FAD mutant cells, we suggest that the interaction of presenilin mutation PS1 with IP3R channels leads the decrease in the unbinding rates of IP3 and the activating Ca2+ from IP3Rs. As a result, the increased affinities of IP3 and activating Ca2+ for IP3R channels induce the increase in the Ca2+ signal in FAD mutant cells. Specifically, the PS1 mutation decreases the IP3 dissociation rate of IP3R channels significantly in FAD mutant cells. Our results suggest possible novel targets for FAD therapeutic intervention.

Role of Nucleoid Associated Proteins in Stabilizing Supercoils

NASA Astrophysics Data System (ADS)

Dahlke, Katelyn; Sing, Charles

Nucleoid associated proteins (NAPs) play an important role in prokaryotic cells by manipulating the shape and structure of the DNA. These NAPs act by bending or twisting DNA, and there are indications that NAPs bind preferentially to DNA that is already bent or twisted. We hypothesize that these binding behaviors strongly impact the stability and structure of DNA. We use coarse-grained simulation of NAPs and DNA that allow us to achieve the time and length scales where DNA supercoiling occurs. Supercoils are twist-induced structures that are the result of relaxing highly-twisted DNA by inducing higher degrees of bending and writhe. We are able to reproduce experimental observations, such as the extension of a DNA molecule as a function of force, linking number, and NAP concentration. Building upon these test cases, we allow the binding and unbinding energy of the simulated NAPs to be a function of the bending angle of the DNA at the site of binding (ΔEB (θ)). Consequently, NAPs localize along the contour of the supercoil, and this binding preference is capable of stabilizing supercoils that form within the nucleoid. National Institute Of General Medical Sciences of the National Institutes of Health under Award Number T32GM070421.

Interface bonding in silicon oxide nanocontacts: interaction potentials and force measurements

NASA Astrophysics Data System (ADS)

Wierez-Kien, M.; Craciun, A. D.; Pinon, A. V.; Le Roux, S.; Gallani, J. L.; Rastei, M. V.

2018-04-01

The interface bonding between two silicon-oxide nanoscale surfaces has been studied as a function of atomic nature and size of contacting asperities. The binding forces obtained using various interaction potentials are compared with experimental force curves measured in vacuum with an atomic force microscope. In the limit of small nanocontacts (typically <103 nm2) measured with sensitive probes the bonding is found to be influenced by thermal-induced fluctuations. Using interface interactions described by Morse, embedded atom model, or Lennard-Jones potential within reaction rate theory, we investigate three bonding types of covalent and van der Waals nature. The comparison of numerical and experimental results reveals that a Lennard-Jones-like potential originating from van der Waals interactions captures the binding characteristics of dry silicon oxide nanocontacts, and likely of other nanoscale materials adsorbed on silicon oxide surfaces. The analyses reveal the importance of the dispersive surface energy and of the effective contact area which is altered by stretching speeds. The mean unbinding force is found to decrease as the contact spends time in the attractive regime. This contact weakening is featured by a negative aging coefficient which broadens and shifts the thermal-induced force distribution at low stretching speeds.

Role of the protein in the DNA sequence specificity of the cleavage site stabilized by the camptothecin topoisomerase IB inhibitor: a metadynamics study

PubMed Central

Coletta, Andrea; Desideri, Alessandro

2013-01-01

Camptothecin (CPT) is a topoisomerase IB (TopIB) selective inhibitor whose derivatives are currently used in cancer therapy. TopIB cleaves DNA at any sequence, but in the presence of CPT the only stabilized protein–DNA covalent complex is the one having a thymine in position −1 with respect to the cleavage site. A metadynamics simulation of two TopIB–DNA–CPT ternary complexes differing for the presence of a thymine or a cytosine in position −1 indicates the occurrence of two different drug’s unbinding pathways. The free-energy difference between the bound state and the transition state is large when a thymine is present in position −1 and is strongly reduced in presence of a cytosine, in line with the different drug stabilization properties of the two systems. Such a difference is strictly related to the changes in the hydrogen bond network between the protein, the DNA and the drug in the two systems, indicating a direct role of the protein in determining the specificity of the cleavage site sequence stabilized by the CPT. Calculations carried out in presence of one compound of the indenoisoquinoline family (NSC314622) indicate a comparable energy difference between the bound and the transition state independently of the presence of a thymine or a cytosine in position −1, in line with the experimental results. PMID:24003027

Emergent phases of fractonic matter

NASA Astrophysics Data System (ADS)

Prem, Abhinav; Pretko, Michael; Nandkishore, Rahul M.

2018-02-01

Fractons are emergent particles which are immobile in isolation, but which can move together in dipolar pairs or other small clusters. These exotic excitations naturally occur in certain quantum phases of matter described by tensor gauge theories. Previous research has focused on the properties of small numbers of fractons and their interactions, effectively mapping out the "standard model" of fractons. In the present work, however, we consider systems with a finite density of either fractons or their dipolar bound states, with a focus on the U (1 ) fracton models. We study some of the phases in which emergent fractonic matter can exist, thereby initiating the study of the "condensed matter" of fractons. We begin by considering a system with a finite density of fractons, which we show can exhibit microemulsion physics, in which fractons form small-scale clusters emulsed in a phase dominated by long-range repulsion. We then move on to study systems with a finite density of mobile dipoles, which have phases analogous to many conventional condensed matter phases. We focus on two major examples: Fermi liquids and quantum Hall phases. A finite density of fermionic dipoles will form a Fermi surface and enter a Fermi liquid phase. Interestingly, this dipolar Fermi liquid exhibits a finite-temperature phase transition, corresponding to an unbinding transition of fractons. Finally, we study chiral two-dimensional phases corresponding to dipoles in "quantum Hall" states of their emergent magnetic field. We study numerous aspects of these generalized quantum Hall systems, such as their edge theories and ground state degeneracies.

Dewey's Liberalisms: Depression-Era Insights for the Great Recession

ERIC Educational Resources Information Center

Rogers, John

2013-01-01

This article explores John Dewey's Depression-era analysis of "liberalism" in an effort to clarify our own neoliberal moment. As Dewey argues, liberalism is a term used in the 1930s to signify diverse and often contradictory meanings. It variously refers to a minimalist state aimed at unbinding markets (laissez-faire liberalism) or…

Molecular Basis of Ligand Dissociation in β-Adrenergic Receptors

PubMed Central

González, Angel; Perez-Acle, Tomas; Pardo, Leonardo; Deupi, Xavier

2011-01-01

The important and diverse biological functions of β-adrenergic receptors (βARs) have promoted the search for compounds to stimulate or inhibit their activity. In this regard, unraveling the molecular basis of ligand binding/unbinding events is essential to understand the pharmacological properties of these G protein-coupled receptors. In this study, we use the steered molecular dynamics simulation method to describe, in atomic detail, the unbinding process of two inverse agonists, which have been recently co-crystallized with β1 and β2ARs subtypes, along four different channels. Our results indicate that this type of compounds likely accesses the orthosteric binding site of βARs from the extracellular water environment. Importantly, reconstruction of forces and energies from the simulations of the dissociation process suggests, for the first time, the presence of secondary binding sites located in the extracellular loops 2 and 3 and transmembrane helix 7, where ligands are transiently retained by electrostatic and Van der Waals interactions. Comparison of the residues that form these new transient allosteric binding sites in both βARs subtypes reveals the importance of non-conserved electrostatic interactions as well as conserved aromatic contacts in the early steps of the binding process. PMID:21915263

Solid-state nanopore detection of protein complexes: applications in healthcare and protein kinetics.

PubMed

Freedman, Kevin J; Bastian, Arangassery R; Chaiken, Irwin; Kim, Min Jun

2013-03-11

Protein conjugation provides a unique look into many biological phenomena and has been used for decades for molecular recognition purposes. In this study, the use of solid-state nanopores for the detection of gp120-associated complexes are investigated. They exhibit monovalent and multivalent binding to anti-gp120 antibody monomer and dimers. In order to investigate the feasibility of many practical applications related to nanopores, detection of specific protein complexes is attempted within a heterogeneous protein sample, and the role of voltage on complexed proteins is researched. It is found that the electric field within the pore can result in unbinding of a freely translocating protein complex within the transient event durations measured experimentally. The strong dependence of the unbinding time with voltage can be used to improve the detection capability of the nanopore system by adding an additional level of specificity that can be probed. These data provide a strong framework for future protein-specific detection schemes, which are shown to be feasible in the realm of a 'real-world' sample and an automated multidimensional method of detecting events. Copyright © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Binding and unbinding the auditory and visual streams in the McGurk effect.

PubMed

Nahorna, Olha; Berthommier, Frédéric; Schwartz, Jean-Luc

2012-08-01

Subjects presented with coherent auditory and visual streams generally fuse them into a single percept. This results in enhanced intelligibility in noise, or in visual modification of the auditory percept in the McGurk effect. It is classically considered that processing is done independently in the auditory and visual systems before interaction occurs at a certain representational stage, resulting in an integrated percept. However, some behavioral and neurophysiological data suggest the existence of a two-stage process. A first stage would involve binding together the appropriate pieces of audio and video information before fusion per se in a second stage. Then it should be possible to design experiments leading to unbinding. It is shown here that if a given McGurk stimulus is preceded by an incoherent audiovisual context, the amount of McGurk effect is largely reduced. Various kinds of incoherent contexts (acoustic syllables dubbed on video sentences or phonetic or temporal modifications of the acoustic content of a regular sequence of audiovisual syllables) can significantly reduce the McGurk effect even when they are short (less than 4 s). The data are interpreted in the framework of a two-stage "binding and fusion" model for audiovisual speech perception.

Fluorescence correlation spectroscopy experiments to quantify free diffusion coefficients in reaction-diffusion systems: The case of Ca2 + and its dyes

NASA Astrophysics Data System (ADS)

Sigaut, Lorena; Villarruel, Cecilia; Ponce, María Laura; Ponce Dawson, Silvina

2017-06-01

Many cell signaling pathways involve the diffusion of messengers that bind and unbind to and from intracellular components. Quantifying their net transport rate under different conditions then requires having separate estimates of their free diffusion coefficient and binding or unbinding rates. In this paper, we show how performing sets of fluorescence correlation spectroscopy (FCS) experiments under different conditions, it is possible to quantify free diffusion coefficients and on and off rates of reaction-diffusion systems. We develop the theory and present a practical implementation for the case of the universal second messenger, calcium (Ca2 +) and single-wavelength dyes that increase their fluorescence upon Ca2 + binding. We validate the approach with experiments performed in aqueous solutions containing Ca2 + and Fluo4 dextran (both in its high and low affinity versions). Performing FCS experiments with tetramethylrhodamine-dextran in Xenopus laevis oocytes, we infer the corresponding free diffusion coefficients in the cytosol of these cells. Our approach can be extended to other physiologically relevant reaction-diffusion systems to quantify biophysical parameters that determine the dynamics of various variables of interest.

Molecular Dynamics Simulations and Dynamic Network Analysis Reveal the Allosteric Unbinding of Monobody to H-Ras Triggered by R135K Mutation.

PubMed

Ni, Duan; Song, Kun; Zhang, Jian; Lu, Shaoyong

2017-10-26

Ras proteins, as small GTPases, mediate cell proliferation, survival and differentiation. Ras mutations have been associated with a broad spectrum of human cancers and thus targeting Ras represents a potential way forward for cancer therapy. A recently reported monobody NS1 allosterically disrupts the Ras-mediated signaling pathway, but its efficacy is reduced by R135K mutation in H-Ras. However, the detailed mechanism is unresolved. Here, using molecular dynamics (MD) simulations and dynamic network analysis, we explored the molecular mechanism for the unbinding of NS1 to H-Ras and shed light on the underlying allosteric network in H-Ras. MD simulations revealed that the overall structures of the two complexes did not change significantly, but the H-Ras-NS1 interface underwent significant conformational alteration in the mutant Binding free energy analysis showed that NS1 binding was unfavored after R135K mutation, which resulted in the unfavorable binding of NS1. Furthermore, the critical residues on H-Ras responsible for the loss of binding of NS1 were identified. Importantly, the allosteric networks for these important residues were revealed, which yielded a novel insight into the allosteric regulatory mechanism of H-Ras.

Effects of TiO2 crystal structure on the luminescence quenching of [Ru(bpy)2(dppz)]2 +-intercalated into DNA

NASA Astrophysics Data System (ADS)

Chen, Linlin; Wang, Yi; Huang, Minggao; Li, Xiaodan; Zhu, Licai; Li, Hong

2017-06-01

The intercalation of [Ru(bpy)2(dppz)]2 + labeled as Ru(II) (bpy = 2,2‧-bipyridine and dppz = dipyrido[3,2,-a:2‧,3‧-c]phenazine) into herring sperm DNA leads to the formation of emissive Ru(II)-DNA dyads, which can be quenched by TiO2 nanoparticles (NPs) and sol-gel silica matrices at heterogeneous interfaces. The calcinations temperature exhibits a remarkable influence on the luminescence quenching of the Ru(II)-DNA dyads by TiO2 NPs. With increasing calcinations temperature in the range from 200 to 850 °C, the anatase-to-rutile TiO2 crystal structure transformation increases the average particle size and hydrodynamic diameter of TiO2 and DNA@TiO2. The anatase TiO2 has the stronger ability to unbind the Ru(II)-DNA dyads than the rutile TiO2 at room temperature. The TiO2 NPs and sol-gel silica matrices can quench the luminescence of the Ru(II) complex intercalated into DNA by selectively capturing the negatively DNA and positively charged Ru(II) complex to unbind the dyads, respectively. This present results provide new insights into the luminescence quenching and competitive binding of dye-labeled DNA dyads by inorganic NPs.

Molecular Dynamics Simulations and Dynamic Network Analysis Reveal the Allosteric Unbinding of Monobody to H-Ras Triggered by R135K Mutation

PubMed Central

Song, Kun; Zhang, Jian; Lu, Shaoyong

2017-01-01

Ras proteins, as small GTPases, mediate cell proliferation, survival and differentiation. Ras mutations have been associated with a broad spectrum of human cancers and thus targeting Ras represents a potential way forward for cancer therapy. A recently reported monobody NS1 allosterically disrupts the Ras-mediated signaling pathway, but its efficacy is reduced by R135K mutation in H-Ras. However, the detailed mechanism is unresolved. Here, using molecular dynamics (MD) simulations and dynamic network analysis, we explored the molecular mechanism for the unbinding of NS1 to H-Ras and shed light on the underlying allosteric network in H-Ras. MD simulations revealed that the overall structures of the two complexes did not change significantly, but the H-Ras–NS1 interface underwent significant conformational alteration in the mutant Binding free energy analysis showed that NS1 binding was unfavored after R135K mutation, which resulted in the unfavorable binding of NS1. Furthermore, the critical residues on H-Ras responsible for the loss of binding of NS1 were identified. Importantly, the allosteric networks for these important residues were revealed, which yielded a novel insight into the allosteric regulatory mechanism of H-Ras. PMID:29072601

A minimal rupture cascade model for living cell plasticity

NASA Astrophysics Data System (ADS)

Polizzi, Stefano; Laperrousaz, Bastien; Perez-Reche, Francisco J.; Nicolini, Franck E.; Maguer Satta, Véronique; Arneodo, Alain; Argoul, Françoise

2018-05-01

Under physiological and pathological conditions, cells experience large forces and deformations that often exceed the linear viscoelastic regime. Here we drive CD34+ cells isolated from healthy and leukemic bone marrows in the highly nonlinear elasto-plastic regime, by poking their perinuclear region with a sharp AFM cantilever tip. We use the wavelet transform mathematical microscope to identify singular events in the force-indentation curves induced by local rupture events in the cytoskeleton (CSK). We distinguish two types of rupture events, brittle failures likely corresponding to irreversible ruptures in a stiff and highly cross-linked CSK and ductile failures resulting from dynamic cross-linker unbindings during plastic deformation without loss of CSK integrity. We propose a stochastic multiplicative cascade model of mechanical ruptures that reproduces quantitatively the experimental distributions of the energy released during these events, and provides some mathematical and mechanistic understanding of the robustness of the log-normal statistics observed in both brittle and ductile situations. We also show that brittle failures are relatively more prominent in leukemia than in healthy cells suggesting their greater fragility.

Cooperative effect of random and time-periodic coupling strength on synchronization transitions in one-way coupled neural system: mean field approach.

PubMed

Jiancheng, Shi; Min, Luo; Chusheng, Huang

2017-08-01

The cooperative effect of random coupling strength and time-periodic coupling strengh on synchronization transitions in one-way coupled neural system has been investigated by mean field approach. Results show that cooperative coupling strength (CCS) plays an active role for the enhancement of synchronization transitions. There exist an optimal frequency of CCS which makes the system display the best CCS-induced synchronization transitions, a critical frequency of CCS which can not further affect the CCS-induced synchronization transitions, and a critical amplitude of CCS which can not occur the CCS-induced synchronization transitions. Meanwhile, noise intensity plays a negative role for the CCS-induced synchronization transitions. Furthermore, it is found that the novel CCS amplitude-induced synchronization transitions and CCS frequency-induced synchronization transitions are found.

The delayed-detonation model of Type Ia supernovae. 2: The detonation phase

NASA Technical Reports Server (NTRS)

Arnett, David; Livne, Eli

1994-01-01

The investigation, by use of two-dimensional numerical hydrodynamics simulations, of the 'delayed detonation' mechanism of Khokhlov for the explosion of Type Ia supernovae is continued. Previously we found that the deflagration is insufficient to unbind the star. Expansion shuts off the flame; much of this small production of iron group nuclei occurs at lower densities, which reduces the electron-capture problem. Because the degenerate star has an adiabatic exponent only slightly above 4/3, the energy released by deflagration drives a pulsation of large amplitude. During the first expansion phase, adiabatic cooling shuts off the burning, and a Rayleigh-Taylor instability then gives mixing of high-entropy ashes with low-entropy fuel. During the first contraction phase, compressional heating reignites the material. The burning was allowed to develop into a detonation in these nonspherical models. The detonation grows toward spherical symmetry at late times. At these densities (rho approx. 10(exp 7) to 10(exp 8) g cm(exp -3)), either Ni-56 or nuclei of the Si-Ca group are the dominant products of the burning. The bulk yields are sensitive to the density of the star when the transition to detonation occurs. The relevance of the abundances, velocities, mixing, and total energy release to the theory and interpretation of Type Ia supernovae is discussed.

Dancing the night away: Improving the persistence of locomotion on the micron scale

NASA Astrophysics Data System (ADS)

Gehrels, Emily W.; Rogers, W. Benjamin; Zeravcic, Zorana; Manoharan, Vinothan N.

In recent years a range of nano and microscale walkers (motors that are able to move along a preformed track) have been developed. Many of these walkers bind to their tracks using a single binding site at each station along the track. A disadvantage of these systems is that any failure involving a single site becoming unbound leads to the walker falling off of the track and locomotion being prematurely terminated. For this reason, it has been difficult to develop a motor that can reliably take more than a few sequential steps. We present an experimental system of DNA-functionalized colloidal particles which exhibit directed motion along patterned substrates in response to temperature cycling. Many DNA bridges form between each pair of interacting particles, adding redundancy to the binding at each station to realize a system that should be able to consistently take many steps. We take advantage of toehold exchange in the design of the DNA sequences that mediate the colloidal interactions to produce broadened, flat, or even re-entrant binding and unbinding transitions between the particles and substrate. Using this new freedom of design, we devise systems where, by thermal ratcheting, we can externally control the direction of motion and sequence of steps of the colloidal motor.

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.

Dynamical organization of the cytoskeletal cortex probed by micropipette aspiration

PubMed Central

Brugués, Jan; Maugis, Benoit; Casademunt, Jaume; Nassoy, Pierre; Amblard, François; Sens, Pierre

2010-01-01

Bleb-based cell motility proceeds by the successive inflation and retraction of large spherical membrane protrusions (“blebs”) coupled with substrate adhesion. In addition to their role in motility, cellular blebs constitute a remarkable illustration of the dynamical interactions between the cytoskeletal cortex and the plasma membrane. Here we study the bleb-based motions of Entamoeba histolytica in the constrained geometry of a micropipette. We construct a generic theoretical model that combines the polymerization of an actin cortex underneath the plasma membrane with the myosin-generated contractile stress in the cortex and the stress-induced failure of membrane-cortex adhesion. One major parameter dictating the cell response to micropipette suction is the stationary cortex thickness, controlled by actin polymerization and depolymerization. The other relevant physical parameters can be combined into two characteristic cortex thicknesses for which the myosin stress (i) balances the suction pressure and (ii) provokes membrane-cortex unbinding. We propose a general phase diagram for cell motions inside a micropipette by comparing these three thicknesses. In particular, we theoretically predict and experimentally verify the existence of saltatory and oscillatory motions for a well-defined range of micropipette suction pressures. PMID:20713731

UNIFYING THE ZOO OF JET-DRIVEN STELLAR EXPLOSIONS

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

Lazzati, Davide; Blackwell, Christopher H.; Morsony, Brian J.

We present a set of numerical simulations of stellar explosions induced by relativistic jets emanating from a central engine sitting at the center of compact, dying stars. We explore a wide range of durations of the central engine activity, two candidate stellar progenitors, and two possible values of the total energy release. We find that even if the jets are narrowly collimated, their interaction with the star unbinds the stellar material, producing a stellar explosion. We also find that the outcome of the explosion can be very different depending on the duration of the engine activity. Only the longest-lasting enginesmore » result in successful gamma-ray bursts. Engines that power jets only for a short time result in relativistic supernova (SN) explosions, akin to observed engine-driven SNe such as SN2009bb. Engines with intermediate durations produce weak gamma-ray bursts, with properties similar to nearby bursts such as GRB 980425. Finally, we find that the engines with the shortest durations, if they exist in nature, produce stellar explosions that lack sizable amounts of relativistic ejecta and are therefore dynamically indistinguishable from ordinary core-collapse SNe.« less

A Chimeric Kinesin-1 Head/Kinesin-5 Tail Motor Switches between Diffusive and Processive Motility

PubMed Central

Thiede, Christina; Lakämper, Stefan; Wessel, Alok D.; Kramer, Stefanie; Schmidt, Christoph F.

2013-01-01

Homotetrameric kinesin-5 motors are essential for chromosome separation and assembly of the mitotic spindle. These kinesins bind between two microtubules (MTs) and slide them apart, toward the spindle poles. This process must be tightly regulated in mitosis. In in vitro assays, Eg5 moves diffusively on single MTs and switches to a directed mode between MTs. How allosteric communication between opposing motor domains works remains unclear, but kinesin-5 tail domains may be involved. Here we present a single-molecule fluorescence study of a tetrameric kinesin-1 head/kinesin-5 tail chimera, DK4mer. This motor exhibited fast processive motility on single MTs interrupted by pauses. Like Eg5, DK4mer diffused along MTs with ADP, and slid antiparallel MTs apart with ATP. In contrast to Eg5, diffusive and processive periods were clearly distinguishable. This allowed us to measure transition rates among states and for unbinding as a function of buffer ionic strength. These data, together with results from controls using tail-less dimers, indicate that there are two modes of interaction with MTs, separated by an energy barrier. This result suggests a scheme of motor regulation that involves switching between two bound states, possibly allosterically controlled by the opposing tetramer end. Such a scheme is likely to be relevant for the regulation of native kinesin-5 motors. PMID:23442865

Pre-supernova outbursts via wave heating in massive stars - II. Hydrogen-poor stars

NASA Astrophysics Data System (ADS)

Fuller, Jim; Ro, Stephen

2018-05-01

Pre-supernova (SN) outbursts from massive stars may be driven by hydrodynamical wave energy emerging from the core of the progenitor star during late nuclear-burning phases. Here, we examine the effects of wave heating in stars containing little or no hydrogen, i.e. progenitors of Type IIb/Ib SNe. Because there is no massive hydrogen envelope, wave energy is thermalized near the stellar surface where the overlying atmospheric mass is small but the optical depth is large. Wave energy can thus unbind this material, driving an optically thick, super-Eddington wind. Using 1D hydrodynamic MESA simulations of ˜5 M⊙ He stars, we find that wave heating can drive pre-SN outbursts composed of a dense wind whose mass-loss rate can exceed ˜0.1 M⊙ yr-1. The wind terminal velocities are a few 100 km s-1, and outburst luminosities can reach ˜106 L⊙. Wave-driven outbursts may be linked with observed or inferred pre-SN outbursts of Type Ibn/transitional/transformational SNe, and pre-SN wave-driven mass loss is a good candidate to produce these types of SNe. However, we also show that non-linear wave breaking in the core of the star may prevent such outbursts in stars with thick convective helium-burning shells. Hence, only a limited subset of SN progenitors is likely to experience wave-driven pre-SN outbursts.

Fast and reliable symplectic integration for planetary system N-body problems

NASA Astrophysics Data System (ADS)

Hernandez, David M.

2016-06-01

We apply one of the exactly symplectic integrators, which we call HB15, of Hernandez & Bertschinger, along with the Kepler problem solver of Wisdom & Hernandez, to solve planetary system N-body problems. We compare the method to Wisdom-Holman (WH) methods in the MERCURY software package, the MERCURY switching integrator, and others and find HB15 to be the most efficient method or tied for the most efficient method in many cases. Unlike WH, HB15 solved N-body problems exhibiting close encounters with small, acceptable error, although frequent encounters slowed the code. Switching maps like MERCURY change between two methods and are not exactly symplectic. We carry out careful tests on their properties and suggest that they must be used with caution. We then use different integrators to solve a three-body problem consisting of a binary planet orbiting a star. For all tested tolerances and time steps, MERCURY unbinds the binary after 0 to 25 years. However, in the solutions of HB15, a time-symmetric HERMITE code, and a symplectic Yoshida method, the binary remains bound for >1000 years. The methods' solutions are qualitatively different, despite small errors in the first integrals in most cases. Several checks suggest that the qualitative binary behaviour of HB15's solution is correct. The Bulirsch-Stoer and Radau methods in the MERCURY package also unbind the binary before a time of 50 years, suggesting that this dynamical error is due to a MERCURY bug.

Quantitative Detection of Small Molecule/DNA Complexes Employing a Force-Based and Label-Free DNA-Microarray

PubMed Central

Ho, Dominik; Dose, Christian; Albrecht, Christian H.; Severin, Philip; Falter, Katja; Dervan, Peter B.; Gaub, Hermann E.

2009-01-01

Force-based ligand detection is a promising method to characterize molecular complexes label-free at physiological conditions. Because conventional implementations of this technique, e.g., based on atomic force microscopy or optical traps, are low-throughput and require extremely sensitive and sophisticated equipment, this approach has to date found only limited application. We present a low-cost, chip-based assay, which combines high-throughput force-based detection of dsDNA·ligand interactions with the ease of fluorescence detection. Within the comparative unbinding force assay, many duplicates of a target DNA duplex are probed against a defined reference DNA duplex each. The fractions of broken target and reference DNA duplexes are determined via fluorescence. With this assay, we investigated the DNA binding behavior of artificial pyrrole-imidazole polyamides. These small compounds can be programmed to target specific dsDNA sequences and distinguish between D- and L-DNA. We found that titration with polyamides specific for a binding motif, which is present in the target DNA duplex and not in the reference DNA duplex, reliably resulted in a shift toward larger fractions of broken reference bonds. From the concentration dependence nanomolar to picomolar dissociation constants of dsDNA·ligand complexes were determined, agreeing well with prior quantitative DNAase footprinting experiments. This finding corroborates that the forced unbinding of dsDNA in presence of a ligand is a nonequilibrium process that produces a snapshot of the equilibrium distribution between dsDNA and dsDNA·ligand complexes. PMID:19486688

Single-Molecule Unbinding Forces between the Polysaccharide Hyaluronan and Its Binding Proteins.

PubMed

Bano, Fouzia; Tammi, Markku I; Kang, David W; Harris, Edward N; Richter, Ralf P

2018-06-19

The extracellular polysaccharide hyaluronan (HA) is ubiquitous in all vertebrate tissues, where its various functions are encoded in the supramolecular complexes and matrices that it forms with HA-binding proteins (hyaladherins). In tissues, these supramolecular architectures are frequently subjected to mechanical stress, yet how this affects the intermolecular bonding is largely unknown. Here, we used a recently developed single-molecule force spectroscopy platform to analyze and compare the mechanical strength of bonds between HA and a panel of hyaladherins from the Link module superfamily, namely the complex of the proteoglycan aggrecan and cartilage link protein, the proteoglycan versican, the inflammation-associated protein TSG-6, the HA receptor for endocytosis (stabilin-2/HARE), and the HA receptor CD44. We find that the resistance to tensile stress for these hyaladherins correlates with the size of the HA-binding domain. The lowest mean rupture forces are observed for members of the type A subgroup (i.e., with the shortest HA-binding domains; TSG-6 and HARE). In contrast, the mechanical stability of the bond formed by aggrecan in complex with cartilage link protein (two members of the type C subgroup, i.e., with the longest HA-binding domains) and HA is equal or even superior to the high affinity streptavidin⋅biotin bond. Implications for the molecular mechanism of unbinding of HA⋅hyaladherin bonds under force are discussed, which underpin the mechanical properties of HA⋅hyaladherin complexes and HA-rich extracellular matrices. Copyright © 2018 Biophysical Society. Published by Elsevier Inc. All rights reserved.

Cooperative DNA Recognition Modulated by an Interplay between Protein-Protein Interactions and DNA-Mediated Allostery

PubMed Central

Merino, Felipe; Bouvier, Benjamin; Cojocaru, Vlad

2015-01-01

Highly specific transcriptional regulation depends on the cooperative association of transcription factors into enhanceosomes. Usually, their DNA-binding cooperativity originates from either direct interactions or DNA-mediated allostery. Here, we performed unbiased molecular simulations followed by simulations of protein-DNA unbinding and free energy profiling to study the cooperative DNA recognition by OCT4 and SOX2, key components of enhanceosomes in pluripotent cells. We found that SOX2 influences the orientation and dynamics of the DNA-bound configuration of OCT4. In addition SOX2 modifies the unbinding free energy profiles of both DNA-binding domains of OCT4, the POU specific and POU homeodomain, despite interacting directly only with the first. Thus, we demonstrate that the OCT4-SOX2 cooperativity is modulated by an interplay between protein-protein interactions and DNA-mediated allostery. Further, we estimated the change in OCT4-DNA binding free energy due to the cooperativity with SOX2, observed a good agreement with experimental measurements, and found that SOX2 affects the relative DNA-binding strength of the two OCT4 domains. Based on these findings, we propose that available interaction partners in different biological contexts modulate the DNA exploration routes of multi-domain transcription factors such as OCT4. We consider the OCT4-SOX2 cooperativity as a paradigm of how specificity of transcriptional regulation is achieved through concerted modulation of protein-DNA recognition by different types of interactions. PMID:26067358

Cooperative DNA Recognition Modulated by an Interplay between Protein-Protein Interactions and DNA-Mediated Allostery.

PubMed

Merino, Felipe; Bouvier, Benjamin; Cojocaru, Vlad

2015-06-01

Highly specific transcriptional regulation depends on the cooperative association of transcription factors into enhanceosomes. Usually, their DNA-binding cooperativity originates from either direct interactions or DNA-mediated allostery. Here, we performed unbiased molecular simulations followed by simulations of protein-DNA unbinding and free energy profiling to study the cooperative DNA recognition by OCT4 and SOX2, key components of enhanceosomes in pluripotent cells. We found that SOX2 influences the orientation and dynamics of the DNA-bound configuration of OCT4. In addition SOX2 modifies the unbinding free energy profiles of both DNA-binding domains of OCT4, the POU specific and POU homeodomain, despite interacting directly only with the first. Thus, we demonstrate that the OCT4-SOX2 cooperativity is modulated by an interplay between protein-protein interactions and DNA-mediated allostery. Further, we estimated the change in OCT4-DNA binding free energy due to the cooperativity with SOX2, observed a good agreement with experimental measurements, and found that SOX2 affects the relative DNA-binding strength of the two OCT4 domains. Based on these findings, we propose that available interaction partners in different biological contexts modulate the DNA exploration routes of multi-domain transcription factors such as OCT4. We consider the OCT4-SOX2 cooperativity as a paradigm of how specificity of transcriptional regulation is achieved through concerted modulation of protein-DNA recognition by different types of interactions.

The mechanism of water/ion exchange at a protein surface: a weakly bound chloride in Helicobacter pylori apoflavodoxin.

PubMed

Galano-Frutos, Juan J; Morón, M Carmen; Sancho, Javier

2015-11-21

Binding/unbinding of small ligands, such as ions, to/from proteins influences biochemical processes such as protein folding, enzyme catalysis or protein/ligand recognition. We have investigated the mechanism of chloride/water exchange at a protein surface (that of the apoflavodoxin from Helicobacter pylori) using classical all-atom molecular dynamics simulations. They reveal a variety of chloride exit routes and residence times; the latter is related to specific coordination modes of the anion. The role of solvent molecules in the mechanism of chloride unbinding has been studied in detail. We see no temporary increase in chloride coordination along the release process. Instead, the coordination of new water molecules takes place in most cases after the chloride/protein atom release event has begun. Moreover, the distribution function of water entrance events into the first chloride solvation shell peaks after chloride protein atom dissociation events. All these observations together seem to indicate that water molecules simply fill the vacancies left by the previously coordinating protein residues. We thus propose a step-by-step dissociation pathway in which protein/chloride interactions gradually break down before new water molecules progressively fill the vacant positions left by protein atoms. As observed for other systems, water molecules associated with bound chloride or with protein atoms have longer residence times than those bound to the free anion. The implications of the exchange mechanism proposed for the binding of the FMN (Flavin Mononucleotide) protein cofactor are discussed.

Single-Molecule Patch-Clamp FRET Anisotropy Microscopy Studies of NMDA Receptor Ion Channel Activation and Deactivation under Agonist Ligand Binding in Living Cells.

PubMed

Sasmal, Dibyendu Kumar; Yadav, Rajeev; Lu, H Peter

2016-07-20

N-methyl-d-aspartate (NMDA) receptor ion channel is activated by the binding of two pairs of glycine and glutamate along with the application of action potential. Binding and unbinding of ligands changes its conformation that plays a critical role in the open-close activities of NMDA receptor. Conformation states and their dynamics due to ligand binding are extremely difficult to characterize either by conventional ensemble experiments or single-channel electrophysiology method. Here we report the development of a new correlated technical approach, single-molecule patch-clamp FRET anisotropy imaging and demonstrate by probing the dynamics of NMDA receptor ion channel and kinetics of glycine binding with its ligand binding domain. Experimentally determined kinetics of ligand binding with receptor is further verified by computational modeling. Single-channel patch-clamp and four-channel fluorescence measurement are recorded simultaneously to get correlation among electrical on and off states, optically determined conformational open and closed states by FRET, and binding-unbinding states of the glycine ligand by anisotropy measurement at the ligand binding domain of GluN1 subunit. This method has the ability to detect the intermediate states in addition to electrical on and off states. Based on our experimental results, we have proposed that NMDA receptor gating goes through at least one electrically intermediate off state, a desensitized state, when ligands remain bound at the ligand binding domain with the conformation similar to the fully open state.

Discrete elastic model for two-dimensional melting.

PubMed

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

2006-04-01

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

Disorder induced semiconductor to metal transition and modifications of grain boundaries in nanocrystalline zinc oxide thin film

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

Singh, Fouran; Kumar, Vinod; Chaudhary, Babloo

2012-10-01

This paper report on the disorder induced semiconductor to metal transition (SMT) and modifications of grain boundaries in nanocrystalline zinc oxide thin film. Disorder is induced using energetic ion irradiation. It eliminates the possibility of impurities induced transition. However, it is revealed that some critical concentration of defects is needed for inducing such kind of SMT at certain critical temperature. Above room temperature, the current-voltage characteristics in reverse bias attributes some interesting phenomenon, such as electric field induced charge transfer, charge trapping, and diffusion of defects. The transition is explained by the defects induced disorder and strain in ZnO crystallitesmore » created by high density of electronic excitations.« less

A look at the effect of sequence complexity on pressure destabilisation of DNA polymers.

PubMed

Rayan, Gamal; Macgregor, Robert B

2015-04-01

Our previous studies on the helix-coil transition of double-stranded DNA polymers have demonstrated that molar volume change (ΔV) accompanying the thermally-induced transition can be positive or negative depending on the experimental conditions, that the pressure-induced transition is more cooperative than the heat-induced transition [Rayan and Macgregor, J Phys Chem B2005, 109, 15558-15565], and that the pressure-induced transition does not occur in the absence of water [Rayan and Macgregor, Biophys Chem, 2009, 144, 62-66]. Additionally, we have shown that ΔV values obtained by pressure-dependent techniques differ from those obtained by ambient pressure techniques such as PPC [Rayan et al. J Phys Chem B2009, 113, 1738-1742] thus shedding light on the effects of pressure on DNA polymers. Herein, we examine the effect of sequence complexity, and hence cooperativity on pressure destabilisation of DNA polymers. Working with Clostridium perfringes DNA under conditions such that the estimated ΔV of the helix-coil transition corresponds to -1.78 mL/mol (base pair) at atmospheric pressure, we do not observe the pressure-induced helix-coil transition of this DNA polymer, whereas synthetic copolymers poly[d(A-T)] and poly[d(I-C)] undergo cooperative pressure-induced transitions at similar ΔV values. We hypothesise that the reason for the lack of pressure-induced helix-coil transition of C. perfringens DNA under these experimental conditions lies in its sequence complexity. Copyright © 2015 Elsevier B.V. All rights reserved.

Single ricin detection by atomic force microscopy chemomechanical mapping

NASA Astrophysics Data System (ADS)

Chen, Guojun; Zhou, Jianfeng; Park, Bosoon; Xu, Bingqian

2009-07-01

The authors report on a study of detecting ricin molecules immobilized on chemically modified Au (111) surface by chemomechanically mapping the molecular interactions with a chemically modified atomic force microscopy (AFM) tip. AFM images resolved the different fold-up conformations of single ricin molecule as well as their intramolecule structure of A- and B-chains. AFM force spectroscopy study of the interaction indicates that the unbinding force has a linear relation with the logarithmic force loading rate, which agrees well with calculations using one-barrier bond dissociation model.

Recent heavy particle decay in a matter dominated universe

NASA Astrophysics Data System (ADS)

Olive, K. A.; Seckel, D.; Vishniac, E.

1984-09-01

The cold matter scenario for galaxy formation solves the dark matter problem very nicely on small scales corresponding to galaxies and clusters of galaxies. It is, however, difficult to reconcile with a Universe with an Einstein-deSitter value of (UC OMEGA) = 1. Cold matter and (UC OMEGA) = 1 can be made compatible while retaining the feature that the Universe is matter dominated today. This is done by means of heavy (cold) particles whose decay subsequently leads to the unbinding of a large fraction of lighter clustered matter.

Recent heavy-particle decay in a matter-dominated universe

NASA Astrophysics Data System (ADS)

Olive, K. A.; Seckel, D.; Vishniac, E.

1985-05-01

The cold-matter scenario for galaxy formation solves the dark-matter problem very nicely on small scales corresponding to galaxies and clusters of galaxies. It is, however, difficult to reconcile with a universe with an Einstein-deSitter value of Ω = 1. It is shown here that cold matter and Ω = 1 can be made compatible while retaining the feature that the universe is matter-dominated today. This is done by means of heavy (cold) particles whose decay subsequently leads to the unbinding of a large fraction of lighter clustered matter.

Dimebon Inhibits Calcium-Induced Swelling of Rat Brain Mitochondria But Does Not Alter Calcium Retention or Cytochrome C Release

PubMed Central

Naga, Kranthi Kumari

2012-01-01

Dimebon was originally introduced as an antihistamine and subsequently investigated as a possible therapeutic for a variety of disorders, including Alzheimer's disease. One putative mechanism underlying the neuroprotective properties of Dimebon is inhibition of mitochondrial permeability transition, based on the observation that Dimebon inhibited the swelling of rat liver mitochondria induced by calcium and other agents that induce permeability transition. Because liver and brain mitochondria differ substantially in their properties and response to conditions associated with opening of the permeability transition pore, we sought to determine whether Dimebon inhibited permeability transition in brain mitochondria. Dimebon reduced calcium-induced mitochondrial swelling but did not enhance the calcium retention capacity or impair calcium-induced cytochrome C release from non-synaptic mitochondria isolated from rat brain cerebral cortex. These findings indicate that Dimebon does not inhibit mitochondrial permeability transition, induced by excessive calcium uptake, in brain mitochondria. PMID:20625939

Dimebon inhibits calcium-induced swelling of rat brain mitochondria but does not alter calcium retention or cytochrome C release.

PubMed

Naga, Kranthi Kumari; Geddes, James W

2011-03-01

Dimebon was originally introduced as an antihistamine and subsequently investigated as a possible therapeutic for a variety of disorders, including Alzheimer's disease. One putative mechanism underlying the neuroprotective properties of Dimebon is inhibition of mitochondrial permeability transition, based on the observation that Dimebon inhibited the swelling of rat liver mitochondria induced by calcium and other agents that induce permeability transition. Because liver and brain mitochondria differ substantially in their properties and response to conditions associated with opening of the permeability transition pore, we sought to determine whether Dimebon inhibited permeability transition in brain mitochondria. Dimebon reduced calcium-induced mitochondrial swelling but did not enhance the calcium retention capacity or impair calcium-induced cytochrome C release from non-synaptic mitochondria isolated from rat brain cerebral cortex. These findings indicate that Dimebon does not inhibit mitochondrial permeability transition, induced by excessive calcium uptake, in brain mitochondria.

Role of thermal heating on the voltage induced insulator-metal transition in VO2.

PubMed

Zimmers, A; Aigouy, L; Mortier, M; Sharoni, A; Wang, Siming; West, K G; Ramirez, J G; Schuller, Ivan K

2013-02-01

We show that the main mechanism for the dc voltage or dc current induced insulator-metal transition in vanadium dioxide VO(2) is due to local Joule heating and not a purely electronic effect. This "tour de force" experiment was accomplished by using the fluorescence spectra of rare-earth doped micron sized particles as local temperature sensors. As the insulator-metal transition is induced by a dc voltage or dc current, the local temperature reaches the transition temperature indicating that Joule heating plays a predominant role. This has critical implications for the understanding of the dc voltage or dc current induced insulator-metal transition and has a direct impact on applications which use dc voltage or dc current to externally drive the transition.

Multistable orientation in a nematic liquid crystal cell induced by external field and interfacial interaction

NASA Astrophysics Data System (ADS)

Ong, Hiap Liew; Meyer, Robert B.; Hurd, Alan J.

1984-04-01

The effects of a short-range, arbitrary strength interfacial potential on the magnetic field, electric field, and optical field induced Freedericksz transition in a nematic liquid crystal cell are examined and the exact solution is obtained. By generalizing the criterion for the existence of a first-order optical field induced Freedericksz transition that was obtained previously [H. L. Ong, Phys. Rev. A 28, 2393 (1983)], the general criterion for the transition to be first order is obtained. Based on the existing experimental results, the possibility of surface induced first-order transitions is discussed and three simple empirical approaches are suggested for observing multistable orientation. The early results on the magnetic and electric fields induced Freedericksz transition and the inadequacy of the usual experimental observation methods (phase shift and capacitance measurements) are also discussed.

Force spectroscopy of quadruple H-bonded dimers by AFM: dynamic bond rupture and molecular time-temperature superposition.

PubMed

Zou, Shan; Schönherr, Holger; Vancso, G Julius

2005-08-17

We report on the application of the time-temperature superposition principle to supramolecular bond-rupture forces on the single-molecule level. The construction of force-loading rate master curves using atomic force microscopy (AFM)-based single-molecule force spectroscopy (SMFS) experiments carried out in situ at different temperatures allows one to extend the limited range of the experimentally accessible loading rates and hence to cross from thermodynamic nonequilibrium to quasi-equilibrium states. The approach is demonstrated for quadruple H-bonded ureido-4[1H]-pyrimidinone (UPy) moieties studied by variable-temperature SMFS in organic media. The unbinding forces of single quadruple H-bonding (UPy)2 complexes, which were identified based on a polymeric spacer strategy, were found to depend on the loading rate in the range of 5 nN/s to 500 nN/s at 301 K in hexadecane. By contrast, these rupture forces were independent of the loading rate from 5 to 200 nN/s at 330 K. These results indicate that the unbinding behavior of individual supramolecular complexes can be directly probed under both thermodynamic nonequilibrium and quasi-equilibrium conditions. On the basis of the time-temperature superposition principle, a master curve was constructed for a reference temperature of 301 K, and the crossover force (from loading-rate independent to -dependent regimes) was determined as approximately 145 pN (at a loading rate of approximately 5.6 nN/s). This approach significantly broadens the accessible loading-rate range and hence provides access to fine details of potential energy landscape of supramolecular complexes based on SMFS experiments.

Binding Characteristics of Sphingosine-1-Phosphate to ApoM hints to Assisted Release Mechanism via the ApoM Calyx-Opening

NASA Astrophysics Data System (ADS)

Zhang, Hansi; Pluhackova, Kristyna; Jiang, Zhenyan; Böckmann, Rainer A.

2016-08-01

Sphingosine-1-phosphate (S1P) is a lysophospholipid mediator carried by the HDL-associated apoM protein in blood, regulating many physiological processes by activating the G protein-coupled S1P receptor in mammals. Despite the solved crystal structure of the apoM-S1P complex, the mechanism of S1P release from apoM as a part of the S1P pathway is unknown. Here, the dynamics of the wild type apoM-S1P complex as well as of mutants were investigated by means of atomistic molecular dynamics simulations. The potential of mean force for S1P unbinding from apoM reflected a large binding strength of more than 60 kJ/mol. This high unbinding free energy for S1P underlines the observed specificity of the physiological effects of S1P as it suggests that the spontaneous release of S1P from apoM is unlikely. Instead, S1P release and thus the control of this bioactive lipid probably requires the tight interaction with other molecules, e.g. with the S1P receptor. Mutations of specific S1P anchoring residues of apoM decreased the energetic barrier by up to 20 kJ/mol. Moreover, the ligand-free apoM protein is shown to adopt a more open upper hydrophilic binding pocket and to result in complete closure of the lower hydrophobic cavity, suggesting a mechanism for adjusting the gate for ligand access.

Localization and force analysis at the single virus particle level using atomic force microscopy

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

Liu, Chih-Hao; Horng, Jim-Tong; Chang, Jeng-Shian

2012-01-06

Highlights: Black-Right-Pointing-Pointer Localization of single virus particle. Black-Right-Pointing-Pointer Force measurements. Black-Right-Pointing-Pointer Force mapping. -- Abstract: Atomic force microscopy (AFM) is a vital instrument in nanobiotechnology. In this study, we developed a method that enables AFM to simultaneously measure specific unbinding force and map the viral glycoprotein at the single virus particle level. The average diameter of virus particles from AFM images and the specificity between the viral surface antigen and antibody probe were integrated to design a three-stage method that sets the measuring area to a single virus particle before obtaining the force measurements, where the influenza virus was usedmore » as the object of measurements. Based on the purposed method and performed analysis, several findings can be derived from the results. The mean unbinding force of a single virus particle can be quantified, and no significant difference exists in this value among virus particles. Furthermore, the repeatability of the proposed method is demonstrated. The force mapping images reveal that the distributions of surface viral antigens recognized by antibody probe were dispersed on the whole surface of individual virus particles under the proposed method and experimental criteria; meanwhile, the binding probabilities are similar among particles. This approach can be easily applied to most AFM systems without specific components or configurations. These results help understand the force-based analysis at the single virus particle level, and therefore, can reinforce the capability of AFM to investigate a specific type of viral surface protein and its distributions.« less

Gigantic magnetoelectric effect caused by magnetic-field-induced canted antiferromagnetic-paramagnetic transition in quasi-two-dimensional Ca2CoSi2O7 crystal

NASA Astrophysics Data System (ADS)

Akaki, M.; Tozawa, J.; Akahoshi, D.; Kuwahara, H.

2009-05-01

We have investigated the magnetic and dielectric properties of Ca2CoSi2O7 crystal. The dielectricity and magnetism of Ca2CoSi2O7 are strongly coupled below a canted antiferromagnetic transition temperature (TN). Magnetic fields induce electric polarization below TN. Interestingly, the magnetic-field-induced electric polarization is detected even without poling electric fields. Below TN, a canted antiferromagnetic-paramagnetic transition is induced by magnetic fields. The large magnetocapacitance is observed around TN. The origin of the large magnetocapacitance is due to the magnetic-field-induced the canted antiferromagnetic-paramagnetic transition.

Spike-timing-dependent plasticity enhanced synchronization transitions induced by autapses in adaptive Newman-Watts neuronal networks.

PubMed

Gong, Yubing; Wang, Baoying; Xie, Huijuan

2016-12-01

In this paper, we numerically study the effect of spike-timing-dependent plasticity (STDP) on synchronization transitions induced by autaptic activity in adaptive Newman-Watts Hodgkin-Huxley neuron networks. It is found that synchronization transitions induced by autaptic delay vary with the adjusting rate A p of STDP and become strongest at a certain A p value, and the A p value increases when network randomness or network size increases. It is also found that the synchronization transitions induced by autaptic delay become strongest at a certain network randomness and network size, and the values increase and related synchronization transitions are enhanced when A p increases. These results show that there is optimal STDP that can enhance the synchronization transitions induced by autaptic delay in the adaptive neuronal networks. These findings provide a new insight into the roles of STDP and autapses for the information transmission in neural systems. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

A framework for modelling gene regulation which accommodates non-equilibrium mechanisms.

PubMed

Ahsendorf, Tobias; Wong, Felix; Eils, Roland; Gunawardena, Jeremy

2014-12-05

Gene regulation has, for the most part, been quantitatively analysed by assuming that regulatory mechanisms operate at thermodynamic equilibrium. This formalism was originally developed to analyse the binding and unbinding of transcription factors from naked DNA in eubacteria. Although widely used, it has made it difficult to understand the role of energy-dissipating, epigenetic mechanisms, such as DNA methylation, nucleosome remodelling and post-translational modification of histones and co-regulators, which act together with transcription factors to regulate gene expression in eukaryotes. Here, we introduce a graph-based framework that can accommodate non-equilibrium mechanisms. A gene-regulatory system is described as a graph, which specifies the DNA microstates (vertices), the transitions between microstates (edges) and the transition rates (edge labels). The graph yields a stochastic master equation for how microstate probabilities change over time. We show that this framework has broad scope by providing new insights into three very different ad hoc models, of steroid-hormone responsive genes, of inherently bounded chromatin domains and of the yeast PHO5 gene. We find, moreover, surprising complexity in the regulation of PHO5, which has not yet been experimentally explored, and we show that this complexity is an inherent feature of being away from equilibrium. At equilibrium, microstate probabilities do not depend on how a microstate is reached but, away from equilibrium, each path to a microstate can contribute to its steady-state probability. Systems that are far from equilibrium thereby become dependent on history and the resulting complexity is a fundamental challenge. To begin addressing this, we introduce a graph-based concept of independence, which can be applied to sub-systems that are far from equilibrium, and prove that history-dependent complexity can be circumvented when sub-systems operate independently. As epigenomic data become increasingly available, we anticipate that gene function will come to be represented by graphs, as gene structure has been represented by sequences, and that the methods introduced here will provide a broader foundation for understanding how genes work.

Numerical investigation of hypersonic flat-plate boundary layer transition mechanism induced by different roughness shapes

NASA Astrophysics Data System (ADS)

Zhou, Yunlong; Zhao, Yunfei; Xu, Dan; Chai, Zhenxia; Liu, Wei

2016-10-01

The roughness-induced laminar-turbulent boundary layer transition is significant for high-speed aerospace applications. The transition mechanism is closely related to the roughness shape. In this paper, high-order numerical method is used to investigate the effect of roughness shape on the flat-plate laminar-to-turbulent boundary layer transition. Computations are performed in both the supersonic and hypersonic regimes (free-stream Mach number from 3.37 up to 6.63) for the square, cylinder, diamond and hemisphere roughness elements. It is observed that the square and diamond roughness elements are more effective in inducing transition compared with the cylinder and hemisphere ones. The square roughness element has the longest separated region in which strong unsteadiness exists and the absolute instability is formed, thus resulting in the earliest transition. The diamond roughness element has a maximum width of the separated region leading to the widest turbulent wake region far downstream. Furthermore, transition location moves backward as the Mach number increases, which indicates that the compressibility significantly suppresses the roughness-induced boundary layer transition.

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.

Convergence and Sampling in Determining Free Energy Landscapes for Membrane Protein Association

PubMed Central

2016-01-01

Potential of mean force (PMF) calculations are used to characterize the free energy landscape of protein–lipid and protein–protein association within membranes. Coarse-grained simulations allow binding free energies to be determined with reasonable statistical error. This accuracy relies on defining a good collective variable to describe the binding and unbinding transitions, and upon criteria for assessing the convergence of the simulation toward representative equilibrium sampling. As examples, we calculate protein–lipid binding PMFs for ANT/cardiolipin and Kir2.2/PIP2, using umbrella sampling on a distance coordinate. These highlight the importance of replica exchange between windows for convergence. The use of two independent sets of simulations, initiated from bound and unbound states, provide strong evidence for simulation convergence. For a model protein–protein interaction within a membrane, center-of-mass distance is shown to be a poor collective variable for describing transmembrane helix–helix dimerization. Instead, we employ an alternative intermolecular distance matrix RMS (DRMS) coordinate to obtain converged PMFs for the association of the glycophorin transmembrane domain. While the coarse-grained force field gives a reasonable Kd for dimerization, the majority of the bound population is revealed to be in a near-native conformation. Thus, the combination of a refined reaction coordinate with improved sampling reveals previously unnoticed complexities of the dimerization free energy landscape. We propose the use of replica-exchange umbrella sampling starting from different initial conditions as a robust approach for calculation of the binding energies in membrane simulations. PMID:27807980

k-space image correlation to probe the intracellular dynamics of gold nanoparticles

NASA Astrophysics Data System (ADS)

Bouzin, M.; Sironi, L.; Chirico, G.; D'Alfonso, L.; Inverso, D.; Pallavicini, P.; Collini, M.

2016-04-01

The collective action of dynein, kinesin and myosin molecular motors is responsible for the intracellular active transport of cargoes, vesicles and organelles along the semi-flexible oriented filaments of the cytoskeleton. The overall mobility of the cargoes upon binding and unbinding to motor proteins can be modeled as an intermittency between Brownian diffusion in the cell cytoplasm and active ballistic excursions along actin filaments or microtubules. Such an intermittent intracellular active transport, exhibited by star-shaped gold nanoparticles (GNSs, Gold Nanostars) upon internalization in HeLa cancer cells, is investigated here by combining live-cell time-lapse confocal reflectance microscopy and the spatio-temporal correlation, in the reciprocal Fourier space, of the acquired image sequences. At first, the analytical theoretical framework for the investigation of a two-state intermittent dynamics is presented for Fourier-space Image Correlation Spectroscopy (kICS). Then simulated kICS correlation functions are employed to evaluate the influence of, and sensitivity to, all the kinetic and dynamic parameters the model involves (the transition rates between the diffusive and the active transport states, the diffusion coefficient and drift velocity of the imaged particles). The optimal procedure for the analysis of the experimental data is outlined and finally exploited to derive whole-cell maps for the parameters underlying the GNSs super-diffusive dynamics. Applied here to the GNSs subcellular trafficking, the proposed kICS analysis can be adopted for the characterization of the intracellular (super-) diffusive dynamics of any fluorescent or scattering biological macromolecule.

Convergence and Sampling in Determining Free Energy Landscapes for Membrane Protein Association.

PubMed

Domański, Jan; Hedger, George; Best, Robert B; Stansfeld, Phillip J; Sansom, Mark S P

2017-04-20

Potential of mean force (PMF) calculations are used to characterize the free energy landscape of protein-lipid and protein-protein association within membranes. Coarse-grained simulations allow binding free energies to be determined with reasonable statistical error. This accuracy relies on defining a good collective variable to describe the binding and unbinding transitions, and upon criteria for assessing the convergence of the simulation toward representative equilibrium sampling. As examples, we calculate protein-lipid binding PMFs for ANT/cardiolipin and Kir2.2/PIP 2 , using umbrella sampling on a distance coordinate. These highlight the importance of replica exchange between windows for convergence. The use of two independent sets of simulations, initiated from bound and unbound states, provide strong evidence for simulation convergence. For a model protein-protein interaction within a membrane, center-of-mass distance is shown to be a poor collective variable for describing transmembrane helix-helix dimerization. Instead, we employ an alternative intermolecular distance matrix RMS (D RMS ) coordinate to obtain converged PMFs for the association of the glycophorin transmembrane domain. While the coarse-grained force field gives a reasonable K d for dimerization, the majority of the bound population is revealed to be in a near-native conformation. Thus, the combination of a refined reaction coordinate with improved sampling reveals previously unnoticed complexities of the dimerization free energy landscape. We propose the use of replica-exchange umbrella sampling starting from different initial conditions as a robust approach for calculation of the binding energies in membrane simulations.

Kinetics of veratridine action on Na channels of skeletal muscle

PubMed Central

Sutro, JB

1986-01-01

Veratridine bath-applied to frog muscle makes inactivation of INa incomplete during a depolarizing voltage-clamp pulse and leads to a persistent veratridine-induced Na tail current. During repetitive depolarizations, the size of successive tail currents grows to a plateau and then gradually decreases. When pulsing is stopped, the tail current declines to zero with a time constant of approximately 3 s. Higher rates of stimulation result in a faster build-up of the tail current and a larger maximum value. I propose that veratridine binds only to open channels and, when bound, prevents normal fast inactivation and rapid shutting of the channel on return to rest. Veratridine-modified channels are also subject to a "slow" inactivation during long depolarizations or extended pulse trains. At rest, veratridine unbinds with a time constant of approximately 3 s. Three tests confirm these hypotheses: (a) the time course of the development of veratridine-induced tail currents parallels a running time integral of gNa during the pulse; (b) inactivating prepulses reduce the ability to evoke tails, and the voltage dependence of this reduction parallels the voltage dependence of h infinity; (c) chloramine-T, N-bromoacetamide, and scorpion toxin, agents that decrease inactivation in Na channels, each greatly enhance the tail currents and alter the time course of the appearance of the tails as predicted by the hypothesis. Veratridine-modified channels shut during hyperpolarizations from -90 mV and reopen on repolarization to -90 mV, a process that resembles normal activation gating. Veratridine appears to bind more rapidly during larger depolarizations. PMID:2419478

Cytoplasmic dynein binding, run length, and velocity are guided by long-range electrostatic interactions

PubMed Central

Li, Lin; Alper, Joshua; Alexov, Emil

2016-01-01

Dyneins are important molecular motors involved in many essential biological processes, including cargo transport along microtubules, mitosis, and in cilia. Dynein motility involves the coupling of microtubule binding and unbinding to a change in the configuration of the linker domain induced by ATP hydrolysis, which occur some 25 nm apart. This leaves the accuracy of dynein stepping relatively inaccurate and susceptible to thermal noise. Using multi-scale modeling with a computational focusing technique, we demonstrate that the microtubule forms an electrostatic funnel that guides the dynein’s microtubule binding domain (MTBD) as it finally docks to the precise, keyed binding location on the microtubule. Furthermore, we demonstrate that electrostatic component of the MTBD’s binding free energy is linearly correlated with the velocity and run length of dynein, and we use this linearity to predict the effect of mutating each glutamic and aspartic acid located in MTBD domain to alanine. Lastly, we show that the binding of dynein to the microtubule is associated with conformational changes involving several helices, and we localize flexible hinge points within the stalk helices. Taken all together, we demonstrate that long range electrostatic interactions bring a level of precision to an otherwise noisy dynein stepping process. PMID:27531742

Unbinding slave spins in the Anderson impurity model

NASA Astrophysics Data System (ADS)

Guerci, Daniele; Fabrizio, Michele

2017-11-01

We show that a generic single-orbital Anderson impurity model, lacking, for instance, any kind of particle-hole symmetry, can be exactly mapped without any constraint onto a resonant level model coupled to two Ising variables, which reduce to one if the hybridization is particle-hole symmetric. The mean-field solution of this model is found to be stable to unphysical spontaneous magnetization of the impurity, unlike the saddle-point solution in the standard slave-boson representation. Remarkably, the mean-field estimate of the Wilson ratio approaches the exact value RW=2 in the Kondo regime.

Time, Not Sleep, Unbinds Contexts from Item Memory

PubMed Central

Cox, Roy; Tijdens, Ron R.; Meeter, Martijn M.; Sweegers, Carly C. G.; Talamini, Lucia M.

2014-01-01

Contextual cues are known to benefit memory retrieval, but whether and how sleep affects this context effect remains unresolved. We manipulated contextual congruence during memory retrieval in human volunteers across 12 h and 24 h intervals beginning with either sleep or wakefulness. Our data suggest that whereas contextual cues lose their potency with time, sleep does not modulate this process. Furthermore, our results are consistent with the idea that sleep's beneficial effect on memory retention depends on the amount of waking time that has passed between encoding and sleep onset. The findings are discussed in the framework of competitive consolidation theory. PMID:24498441

Computational modeling approaches to quantitative structure-binding kinetics relationships in drug discovery.

PubMed

De Benedetti, Pier G; Fanelli, Francesca

2018-03-21

Simple comparative correlation analyses and quantitative structure-kinetics relationship (QSKR) models highlight the interplay of kinetic rates and binding affinity as an essential feature in drug design and discovery. The choice of the molecular series, and their structural variations, used in QSKR modeling is fundamental to understanding the mechanistic implications of ligand and/or drug-target binding and/or unbinding processes. Here, we discuss the implications of linear correlations between kinetic rates and binding affinity constants and the relevance of the computational approaches to QSKR modeling. Copyright © 2018 Elsevier Ltd. All rights reserved.

Tetramers of Two Heavy and Two Light Bosons

NASA Astrophysics Data System (ADS)

Naidon, Pascal

2018-07-01

This article considers the bound states of two heavy and two light bosons, when a short-range force attracts the bosons of different mass, and a short-range force repels the light bosons. The existence of such four-body bound states results from the competition between these two forces. For a given strength of the attraction, the critical strength of the repulsion necessary to unbind the four particles is calculated. This study is motivated by the experimental realisation of impurity atoms immersed in an atomic Bose-Einstein condensate, and aims at determining in which regime only one boson contributes to binding two impurities.

Control of the Speed of a Light-Induced Spin Transition through Mesoscale Core-Shell Architecture.

PubMed

Felts, Ashley C; Slimani, Ahmed; Cain, John M; Andrus, Matthew J; Ahir, Akhil R; Abboud, Khalil A; Meisel, Mark W; Boukheddaden, Kamel; Talham, Daniel R

2018-05-02

The rate of the light-induced spin transition in a coordination polymer network solid dramatically increases when included as the core in mesoscale core-shell particles. A series of photomagnetic coordination polymer core-shell heterostructures, based on the light-switchable Rb a Co b [Fe(CN) 6 ] c · mH 2 O (RbCoFe-PBA) as core with the isostructural K j Ni k [Cr(CN) 6 ] l · nH 2 O (KNiCr-PBA) as shell, are studied using temperature-dependent powder X-ray diffraction and SQUID magnetometry. The core RbCoFe-PBA exhibits a charge transfer-induced spin transition (CTIST), which can be thermally and optically induced. When coupled to the shell, the rate of the optically induced transition from low spin to high spin increases. Isothermal relaxation from the optically induced high spin state of the core back to the low spin state and activation energies associated with the transition between these states were measured. The presence of a shell decreases the activation energy, which is associated with the elastic properties of the core. Numerical simulations using an electro-elastic model for the spin transition in core-shell particles supports the findings, demonstrating how coupling of the core to the shell changes the elastic properties of the system. The ability to tune the rate of optically induced magnetic and structural phase transitions through control of mesoscale architecture presents a new approach to the development of photoswitchable materials with tailored properties.

Variability-induced transition in a net of neural elements: From oscillatory to excitable behavior.

PubMed

Glatt, Erik; Gassel, Martin; Kaiser, Friedemann

2006-06-01

Starting with an oscillatory net of neural elements, increasing variability induces a phase transition to excitability. This transition is explained by a systematic effect of the variability, which stabilizes the formerly unstable, spatially uniform, temporally constant solution of the net. Multiplicative noise may also influence the net in a systematic way and may thus induce a similar transition. Adding noise into the model, the interplay of noise and variability with respect to the reported transition is investigated. Finally, pattern formation in a diffusively coupled net is studied, because excitability implies the ability of pattern formation and information transmission.

Pressure induced structural, electronic topological, and semiconductor to metal transition in AgBiSe2

NASA Astrophysics Data System (ADS)

Rajaji, V.; Malavi, Pallavi S.; Yamijala, Sharma S. R. K. C.; Sorb, Y. A.; Dutta, Utpal; Guin, Satya N.; Joseph, B.; Pati, Swapan K.; Karmakar, S.; Biswas, Kanishka; Narayana, Chandrabhas

2016-10-01

We report the effect of strong spin orbit coupling inducing electronic topological and semiconductor to metal transitions on the thermoelectric material AgBiSe2 at high pressures. The synchrotron X-ray diffraction and the Raman scattering measurement provide evidence for a pressure induced structural transition from hexagonal (α-AgBiSe2) to rhombohedral (β-AgBiSe2) at a relatively very low pressure of around 0.7 GPa. The sudden drop in the electrical resistivity and clear anomalous changes in the Raman line width of the A1g and Eg(1) modes around 2.8 GPa was observed suggesting a pressure induced electronic topological transition. On further increasing the pressure, anomalous pressure dependence of phonon (A1g and Eg(1)) frequencies and line widths along with the observed temperature dependent electrical resistivity show a pressure induced semiconductor to metal transition above 7.0 GPa in β-AgBiSe2. First principles theoretical calculations reveal that the metallic character of β-AgBiSe2 is induced mainly due to redistributions of the density of states (p orbitals of Bi and Se) near to the Fermi level. Based on its pressure induced multiple electronic transitions, we propose that AgBiSe2 is a potential candidate for the good thermoelectric performance and pressure switches at high pressure.

Tensile-strain effect of inducing the indirect-to-direct band-gap transition and reducing the band-gap energy of Ge

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

Inaoka, Takeshi, E-mail: inaoka@phys.u-ryukyu.ac.jp; Furukawa, Takuro; Toma, Ryo

By means of a hybrid density-functional method, we investigate the tensile-strain effect of inducing the indirect-to-direct band-gap transition and reducing the band-gap energy of Ge. We consider [001], [111], and [110] uniaxial tensility and (001), (111), and (110) biaxial tensility. Under the condition of no normal stress, we determine both normal compression and internal strain, namely, relative displacement of two atoms in the primitive unit cell, by minimizing the total energy. We identify those strain types which can induce the band-gap transition, and evaluate the critical strain coefficient where the gap transition occurs. Either normal compression or internal strain operatesmore » unfavorably to induce the gap transition, which raises the critical strain coefficient or even blocks the transition. We also examine how each type of tensile strain decreases the band-gap energy, depending on its orientation. Our analysis clearly shows that synergistic operation of strain orientation and band anisotropy has a great influence on the gap transition and the gap energy.« less

Identification of salivary components that induce transition of hyphae to yeast in Candida albicans.

PubMed

Leito, Jelani T D; Ligtenberg, Antoon J M; Nazmi, Kamran; Veerman, Enno C I

2009-10-01

Candida albicans, the major human fungal pathogen, undergoes a reversible morphological transition from single yeast cells to pseudohyphae and hyphae filaments. The hyphae form is considered the most invasive form of the fungus. The purpose of this study is to investigate the effect of saliva on hyphae growth of C. albicans. Candida albicans hyphae were inoculated in Roswell Park Memorial Institute medium with whole saliva, parotid saliva or buffer mimicking the saliva ion composition, and cultured for 18 h at 37 degrees C under aerobic conditions with 5% CO(2). Whole saliva and parotid saliva induced transition to yeast growth, whereas the culture with buffer remained in the hyphae form. Parotid saliva was fractionated on a reverse-phase C8 column and each fraction was tested for inducing transition to yeast growth. By immunoblotting, the salivary component in the active fraction was identified as statherin, a phosphoprotein of 43 amino acids that has been implicated in remineralization of the teeth. Synthetically made statherin induced transition of hyphae to yeast. By deletion of five amino acids at the negatively charged N-terminal site (DpSpSEE), yeast-inducing activity and binding to C. albicans were increased. In conclusion, statherin induces transition to yeast of C. albicans hyphae and may thus contribute to the oral defense against candidiasis.

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

Comparison of gating dynamics of different IP3R channels with immune algorithm searching for channel parameter distributions

NASA Astrophysics Data System (ADS)

Cai, Xiuhong; Li, Xiang; Qi, Hong; Wei, Fang; Chen, Jianyong; Shuai, Jianwei

2016-10-01

The gating properties of the inositol 1, 4, 5-trisphosphate (IP3) receptor (IP3R) are determined by the binding and unbinding capability of Ca2+ ions and IP3 messengers. With the patch clamp experiments, the stationary properties have been discussed for Xenopus oocyte type-1 IP3R (Oo-IP3R1), type-3 IP3R (Oo-IP3R3) and Spodoptera frugiperda IP3R (Sf-IP3R). In this paper, in order to provide insights about the relation between the observed gating characteristics and the gating parameters in different IP3Rs, we apply the immune algorithm to fit the parameters of a modified DeYoung-Keizer model. By comparing the fitting parameter distributions of three IP3Rs, we suggest that the three types of IP3Rs have the similar open sensitivity in responding to IP3. The Oo-IP3R3 channel is easy to open in responding to low Ca2+ concentration, while Sf-IP3R channel is easily inhibited in responding to high Ca2+ concentration. We also show that the IP3 binding rate is not a sensitive parameter for stationary gating dynamics for three IP3Rs, but the inhibitory Ca2+ binding/unbinding rates are sensitive parameters for gating dynamics for both Oo-IP3R1 and Oo-IP3R3 channels. Such differences may be important in generating the spatially and temporally complex Ca2+ oscillations in cells. Our study also demonstrates that the immune algorithm can be applied for model parameter searching in biological systems.

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.

Chimaphilin inhibits human osteosarcoma cell invasion and metastasis through suppressing the TGF-β1-induced epithelial-to-mesenchymal transition markers via PI-3K/Akt, ERK1/2, and Smad signaling pathways.

PubMed

Dong, Feng; Liu, Tingting; Jin, Hao; Wang, Wenbo

2018-01-01

Epithelial-to-mesenchymal transition is a cellular process associated with cancer invasion and metastasis. However, the antimetastatic effects of chimaphilin remain elusive. In this study, we attempted to investigate the potential use of chimaphilin as an inhibitor of TGF-β1-induced epithelial-to-mesenchymal transition in U2OS cells. We found that TGF-β1 induced epithelial-to-mesenchymal transition to promote U2OS cell invasion and metastasis. Western blotting demonstrated that chimaphilin inhibited U2OS cell invasion and migration, increased the expression of the epithelial phenotype marker E-cadherin, repressed the expression of the mesenchymal phenotype marker vimentin, as well as decreased the level of epithelial-to-mesenchymal-inducing transcription factors Snail1 and Slug during the initiation of TGF-β1-induced epithelial-to-mesenchymal transition. In this study, we revealed that chimaphilin up-regulated the E-cadherin expression level and inhibited the production of vimentin, Snail1, and Slug in TGF-β1-induced U2OS cells by blocking PI-3K/Akt and ERK 1/2 signaling pathway. Additionally, the TGF-β1-mediated phosphorylated levels of Smad2/3 were inhibited by chimaphilin pretreatment. Above all, we conclude that chimaphilin represents an effective inhibitor of the metastatic potential of U2OS cells through suppression of TGF-β1-induced epithelial-to-mesenchymal transition.

Noise Levels Associated With New York City's Mass Transit Systems

PubMed Central

Gershon, Robyn R. M.; Zeltser, Marina; Canton, Allison; Akram, Muhammad

2009-01-01

Objectives. We measured noise levels associated with various forms of mass transit and compared them to exposure guidelines designed to protect against noise-induced hearing loss. Methods. We used noise dosimetry to measure time-integrated noise levels in a representative sample of New York City mass transit systems (subways, buses, ferries, tramway, and commuter railways) aboard transit vehicles and at vehicle boarding platforms or terminals during June and July 2007. Results. Of the transit types evaluated, subway cars and platforms had the highest associated equivalent continuous average (Leq) and maximum noise levels. All transit types had Leq levels appreciably above 70 A-weighted decibels, the threshold at which noise-induced hearing loss is considered possible. Conclusions. Mass transit noise exposure has the potential to exceed limits recommended by the World Health Organization and the US Environmental Protection Agency and thus cause noise-induced hearing loss among riders of all forms of mass transit given sufficient exposure durations. Environmental noise–control efforts in mass transit and, in cases in which controls are infeasible, the use of personal hearing protection would benefit the ridership's hearing health. PMID:19542046

Fermion-induced quantum critical points.

PubMed

Li, Zi-Xiang; Jiang, Yi-Fan; Jian, Shao-Kai; Yao, Hong

2017-08-22

A unified theory of quantum critical points beyond the conventional Landau-Ginzburg-Wilson paradigm remains unknown. According to Landau cubic criterion, phase transitions should be first-order when cubic terms of order parameters are allowed by symmetry in the Landau-Ginzburg free energy. Here, from renormalization group analysis, we show that second-order quantum phase transitions can occur at such putatively first-order transitions in interacting two-dimensional Dirac semimetals. As such type of Landau-forbidden quantum critical points are induced by gapless fermions, we call them fermion-induced quantum critical points. We further introduce a microscopic model of SU(N) fermions on the honeycomb lattice featuring a transition between Dirac semimetals and Kekule valence bond solids. Remarkably, our large-scale sign-problem-free Majorana quantum Monte Carlo simulations show convincing evidences of a fermion-induced quantum critical points for N = 2, 3, 4, 5 and 6, consistent with the renormalization group analysis. We finally discuss possible experimental realizations of the fermion-induced quantum critical points in graphene and graphene-like materials.Quantum phase transitions are governed by Landau-Ginzburg theory and the exceptions are rare. Here, Li et al. propose a type of Landau-forbidden quantum critical points induced by gapless fermions in two-dimensional Dirac semimetals.

Determination of hyperfine-induced transition rates from observations of a planetary nebula.

PubMed

Brage, Tomas; Judge, Philip G; Proffitt, Charles R

2002-12-31

Observations of the planetary nebula NGC3918 made with the STIS instrument on the Hubble Space Telescope reveal the first unambiguous detection of a hyperfine-induced transition 2s2p 3P(o)(0)-->2s2 1S0 in the berylliumlike emission line spectrum of N IV at 1487.89 A. A nebular model allows us to confirm a transition rate of 4x10(-4) sec(-1)+/-33% for this line. The measurement represents the first independent confirmation of the transition rate of hyperfine-induced lines in low ionization stages, and it provides support for the techniques used to compute these transitions for the determination of very low densities and isotope ratios.

FRAME (Force Review Automation Environment): MATLAB-based AFM data processor.

PubMed

Partola, Kostyantyn R; Lykotrafitis, George

2016-05-03

Data processing of force-displacement curves generated by atomic force microscopes (AFMs) for elastic moduli and unbinding event measurements is very time consuming and susceptible to user error or bias. There is an evident need for consistent, dependable, and easy-to-use AFM data processing software. We have developed an open-source software application, the force review automation environment (or FRAME), that provides users with an intuitive graphical user interface, automating data processing, and tools for expediting manual processing. We did not observe a significant difference between manually processed and automatically processed results from the same data sets. Copyright © 2016 Elsevier Ltd. All rights reserved.

Ligand Binding: Molecular Mechanics Calculation of the Streptavidin-Biotin Rupture Force

NASA Astrophysics Data System (ADS)

Grubmuller, Helmut; Heymann, Berthold; Tavan, Paul

1996-02-01

The force required to rupture the streptavidin-biotin complex was calculated here by computer simulations. The computed force agrees well with that obtained by recent single molecule atomic force microscope experiments. These simulations suggest a detailed multiple-pathway rupture mechanism involving five major unbinding steps. Binding forces and specificity are attributed to a hydrogen bond network between the biotin ligand and residues within the binding pocket of streptavidin. During rupture, additional water bridges substantially enhance the stability of the complex and even dominate the binding inter-actions. In contrast, steric restraints do not appear to contribute to the binding forces, although conformational motions were observed.

Biomolecule recognition using piezoresistive nanomechanical force probes

NASA Astrophysics Data System (ADS)

Tosolini, Giordano; Scarponi, Filippo; Cannistraro, Salvatore; Bausells, Joan

2013-06-01

Highly sensitive sensors are one of the enabling technologies for the biomarker detection in early stage diagnosis of pathologies. We have developed a self-sensing nanomechanical force probe able for detecting the unbinding of single couples of biomolecular partners in nearly physiological conditions. The embedding of a piezoresistive transducer into a nanomechanical cantilever enabled high force measurement capability with sub 10-pN resolution. Here, we present the design, microfabrication, optimization, and complete characterization of the sensor. The exceptional electromechanical performance obtained allowed us to detect biorecognition specific events underlying the biotin-avidin complex formation, by integrating the sensor in a commercial atomic force microscope.

Discover binding pathways using the sliding binding-box docking approach: application to binding pathways of oseltamivir to avian influenza H5N1 neuraminidase

NASA Astrophysics Data System (ADS)

Tran, Diem-Trang T.; Le, Ly T.; Truong, Thanh N.

2013-08-01

Drug binding and unbinding are transient processes which are hardly observed by experiment and difficult to analyze by computational techniques. In this paper, we employed a cost-effective method called "pathway docking" in which molecular docking was used to screen ligand-receptor binding free energy surface to reveal possible paths of ligand approaching protein binding pocket. A case study was applied on oseltamivir, the key drug against influenza a virus. The equilibrium pathways identified by this method are found to be similar to those identified in prior studies using highly expensive computational approaches.

Delay correlation analysis and representation for vital complaint VHDL models

DOEpatents

Rich, Marvin J.; Misra, Ashutosh

2004-11-09

A method and system unbind a rise/fall tuple of a VHDL generic variable and create rise time and fall time generics of each generic variable that are independent of each other. Then, according to a predetermined correlation policy, the method and system collect delay values in a VHDL standard delay file, sort the delay values, remove duplicate delay values, group the delay values into correlation sets, and output an analysis file. The correlation policy may include collecting all generic variables in a VHDL standard delay file, selecting each generic variable, and performing reductions on the set of delay values associated with each selected generic variable.

A Simple Bioconjugate Attachment Protocol for Use in Single Molecule Force Spectroscopy Experiments Based on Mixed Self-Assembled Monolayers

PubMed Central

Attwood, Simon J.; Simpson, Anna M. C.; Stone, Rachael; Hamaia, SamirW.; Roy, Debdulal; Farndale, RichardW.; Ouberai, Myriam; Welland, Mark E.

2012-01-01

Single molecule force spectroscopy is a technique that can be used to probe the interaction force between individual biomolecular species. We focus our attention on the tip and sample coupling chemistry, which is crucial to these experiments. We utilised a novel approach of mixed self-assembled monolayers of alkanethiols in conjunction with a heterobifunctional crosslinker. The effectiveness of the protocol is demonstrated by probing the biotin-avidin interaction. We measured unbinding forces comparable to previously reported values measured at similar loading rates. Specificity tests also demonstrated a significant decrease in recognition after blocking with free avidin. PMID:23202965

Pressure-Induced Valence Crossover and Novel Metamagnetic Behavior near the Antiferromagnetic Quantum Phase Transition of YbNi3Ga9

NASA Astrophysics Data System (ADS)

Matsubayashi, K.; Hirayama, T.; Yamashita, T.; Ohara, S.; Kawamura, N.; Mizumaki, M.; Ishimatsu, N.; Watanabe, S.; Kitagawa, K.; Uwatoko, Y.

2015-02-01

We report electrical resistivity, ac magnetic susceptibility, and x-ray absorption spectroscopy measurements of intermediate valence YbNi3Ga9 under pressure and magnetic field. We have revealed a characteristic pressure-induced Yb valence crossover within the temperature-pressure phase diagram, and a first-order metamagnetic transition is found below Pc˜9 GPa where the system undergoes a pressure-induced antiferromagnetic transition. As a possible origin of the metamagnetic behavior, a critical valence fluctuation emerging near the critical point of the first-order valence transition is discussed on the basis of the temperature-field-pressure phase diagram.

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

β2 adrenergic agonist suppresses eosinophil-induced epithelial-to-mesenchymal transition of bronchial epithelial cells.

PubMed

Kainuma, Keigo; Kobayashi, Tetsu; D'Alessandro-Gabazza, Corina N; Toda, Masaaki; Yasuma, Taro; Nishihama, Kota; Fujimoto, Hajime; Kuwabara, Yu; Hosoki, Koa; Nagao, Mizuho; Fujisawa, Takao; Gabazza, Esteban C

2017-05-02

Epithelial-mesenchymal transition is currently recognized as an important mechanism for the increased number of myofibroblasts in cancer and fibrotic diseases. We have already reported that epithelial-mesenchymal transition is involved in airway remodeling induced by eosinophils. Procaterol is a selective and full β 2 adrenergic agonist that is used as a rescue of asthmatic attack inhaler form and orally as a controller. In this study, we evaluated whether procaterol can suppress epithelial-mesenchymal transition of airway epithelial cells induced by eosinophils. Epithelial-mesenchymal transition was assessed using a co-culture system of human bronchial epithelial cells and primary human eosinophils or an eosinophilic leukemia cell line. Procaterol significantly inhibited co-culture associated morphological changes of bronchial epithelial cells, decreased the expression of vimentin, and increased the expression of E-cadherin compared to control. Butoxamine, a specific β 2 -adrenergic antagonist, significantly blocked changes induced by procaterol. In addition, procaterol inhibited the expression of adhesion molecules induced during the interaction between eosinophils and bronchial epithelial cells, suggesting the involvement of adhesion molecules in the process of epithelial-mesenchymal transition. Forskolin, a cyclic adenosine monophosphate-promoting agent, exhibits similar inhibitory activity of procaterol. Overall, these observations support the beneficial effect of procaterol on airway remodeling frequently associated with chronic obstructive pulmonary diseases.

Behavioral transitions induced by speed and noise in animal aggregates

NASA Astrophysics Data System (ADS)

Cambui, Dorílson S.; Iliass, Tarras

2017-04-01

In this paper, we used a self-propelled particle model to study the transition between phases of collective behavior observed in animal aggregates. In these systems, transitions occur when individuals shift from one collective state to another. We investigated transitions induced by both the speed and the noise. Statistical quantities that characterize the phase transition driven by noise, such as order parameter, the Binder cumulant and the susceptibility were analyzed, and we used the finite-size scaling theory to estimate the critical exponent ratios β/ν and γ/ν.

Multiscaled exploration of coupled folding and binding of an intrinsically disordered molecular recognition element in measles virus nucleoprotein

PubMed Central

Wang, Yong; Chu, Xiakun; Longhi, Sonia; Roche, Philippe; Han, Wei; Wang, Erkang; Wang, Jin

2013-01-01

Numerous relatively short regions within intrinsically disordered proteins (IDPs) serve as molecular recognition elements (MoREs). They fold into ordered structures upon binding to their partner molecules. Currently, there is still a lack of in-depth understanding of how coupled binding and folding occurs in MoREs. Here, we quantified the unbound ensembles of the α-MoRE within the intrinsically disordered C-terminal domain of the measles virus nucleoprotein. We developed a multiscaled approach by combining a physics-based and an atomic hybrid model to decipher the mechanism by which the α-MoRE interacts with the X domain of the measles virus phosphoprotein. Our multiscaled approach led to remarkable qualitative and quantitative agreements between the theoretical predictions and experimental results (e.g., chemical shifts). We found that the free α-MoRE rapidly interconverts between multiple discrete partially helical conformations and the unfolded state, in accordance with the experimental observations. We quantified the underlying global folding–binding landscape. This leads to a synergistic mechanism in which the recognition event proceeds via (minor) conformational selection, followed by (major) induced folding. We also provided evidence that the α-MoRE is a compact molten globule-like IDP and behaves as a downhill folder in the induced folding process. We further provided a theoretical explanation for the inherent connections between “downhill folding,” “molten globule,” and “intrinsic disorder” in IDP-related systems. Particularly, we proposed that binding and unbinding of IDPs proceed in a stepwise way through a “kinetic divide-and-conquer” strategy that confers them high specificity without high affinity. PMID:24043820

Disorder-induced transitions in resonantly driven Floquet topological insulators

NASA Astrophysics Data System (ADS)

Titum, Paraj; Lindner, Netanel H.; Refael, Gil

2017-08-01

We investigate the effects of disorder in Floquet topological insulators (FTIs) occurring in semiconductor quantum wells. Such FTIs are induced by resonantly driving a transition between the valence and conduction bands. We show that when disorder is added, the topological nature of such FTIs persists as long as there is a mobility gap at the resonant quasienergy. For strong enough disorder, this gap closes and all the states become localized as the system undergoes a transition to a trivial insulator. Interestingly, the effects of disorder are not necessarily adverse: we show that in the same quantum well, disorder can also induce a transition from a trivial to a topological system, thereby establishing a Floquet topological Anderson insulator (FTAI). We identify the conditions on the driving field necessary for observing such a transition.

Backbone dynamics in an intramolecular prolylpeptide-SH3 complex from the diphtheria toxin repressor, DtxR

PubMed Central

Bhattacharya, Nilakshee; Yi, Myunggi; Zhou, Huan-Xiang; Logan, Timothy M.

2008-01-01

Summary The diphtheria toxin repressor contains an SH3-like domain that forms an intramolecular complex with a proline-rich (Pr) peptide segment and stabilizes the inactive state of the repressor. Upon activation of DtxR by transition metals, this intramolecular complex must dissociate as the SH3 domain and Pr segment form different interactions in the active repressor. In this study we investigate the dynamics of this intramolecular complex using backbone amide nuclear spin relaxation rates determined using NMR spectroscopy and molecular dynamics trajectories. The SH3 domain in the unbound and bound states showed typical dynamics in that the secondary structures were fairly ordered with high generalized order parameters and low effective correlation times while residues in the loops connecting β-strands exhibited reduced generalized order parameters and required additional motional terms to adequately model the relaxation rates. Residues forming the Pr segment exhibited low order parameters with internal rotational correlation times on the order of 0.6 – 1 ns. Further analysis showed that the SH3 domain was rich in millisecond timescale motions while the Pr segment was rich in motions on the 100s μs timescale. Molecular dynamics simultations indicated structural rearrangements that may contribute to the observed relaxation rates and, together with the observed relaxation rate data, suggested that the Pr segment exhibits a binding ↔ unbinding equilibrium. The results of this study provide new insights into the nature of the intramolecular complex and provide a better understanding of the biological role of the SH3 domain in regulating DtxR activity. PMID:17976643

Induced interaction in a Fermi gas with a BEC-BCS crossover

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

Yu Zengqiang; Huang Kun; Yin Lan

2009-05-15

We study the effect of the induced interaction on the superfluid transition temperature of a Fermi gas with a Bose-Einstein condensation-Bardeen-Cooper-Schrieffer (BEC-BCS) crossover. The Gorkov-Melik-Barkhudarov theory about the induced interaction is extended from the BCS side to the entire crossover and the pairing fluctuation is treated in the approach by Nozieres and Schmitt-Rink. At unitarity, the induced interaction reduces the transition temperature by about 20%. In the BCS limit, the transition temperature is reduced by a factor of about 2.22, as found by Gorkov and Melik-Barkhudarov. Our result shows that the effect of the induced interaction is important both onmore » the BCS side and in the unitary region.« less

Force-driven unbinding of proteins HU and Fis from DNA quantified using a thermodynamic Maxwell relation

PubMed Central

Xiao, Botao; Zhang, Houyin; Johnson, Reid C.; Marko, John F.

2011-01-01

Determining numbers of proteins bound to large DNAs is important for understanding their chromosomal functions. Protein numbers may be affected by physical factors such as mechanical forces generated in DNA, e.g. by transcription or replication. We performed single-DNA stretching experiments with bacterial nucleoid proteins HU and Fis, verifying that the force–extension measurements were in thermodynamic equilibrium. We, therefore, could use a thermodynamic Maxwell relation to deduce the change of protein number on a single DNA due to varied force. For the binding of both HU and Fis under conditions studied, numbers of bound proteins decreased as force was increased. Our experiments showed that most of the bound HU proteins were driven off the DNA at 6.3 pN for HU concentrations lower than 150 nM; our HU data were fit well by a statistical-mechanical model of protein-induced bending of DNA. In contrast, a significant amount of Fis proteins could not be forced off the DNA at forces up to 12 pN and Fis concentrations up to 20 nM. This thermodynamic approach may be applied to measure changes in numbers of a wide variety of molecules bound to DNA or other polymers. Force-dependent DNA binding by proteins suggests mechano-chemical mechanisms for gene regulation. PMID:21427084

Effect of rotation on the elastic moduli of solid 4He

NASA Astrophysics Data System (ADS)

Tsuiki, T.; Takahashi, D.; Murakawa, S.; Okuda, Y.; Kono, K.; Shirahama, K.

2018-02-01

We report measurements of elastic moduli of hcp solid 4He down to 15 mK when the samples are rotated unidirectionally. Recent investigations have revealed that the elastic behavior of solid 4He is dominated by gliding of dislocations and pinning of them by 3He impurities, which move in the solidlike Bloch waves (impuritons). Motivated by the recent controversy of torsional oscillator studies, we have performed direct measurements of shear and Young's moduli of annular solid 4He using pairs of quarter-circle-shape piezoelectric transducers (PZTs) while the whole apparatus is rotated with angular velocity Ω up to 4 rad/s. We have found that shear modulus μ is suppressed by rotation below 80 mK, when shear strain applied by PZT exceeds a critical value, above which μ decreases because the shear strain unbinds dislocations from 3He impurities. The rotation-induced decrement of μ at Ω =4 rad/s is about 14.7(12.3)% of the total change of temperature dependent μ for solid samples of pressure 3.6(5.4) MPa. The decrements indicate that the probability of pinning of 3He on dislocation segment G decreases by several orders of magnitude. We propose that the motion of 3He impuritons under rotation becomes strongly anisotropic by the Coriolis force, resulting a decrease in G for dislocation lines aligning parallel to the rotation axis.

Laser Induced Optical Pumping Measurements of Cross Sections for Fine and Hyperfine Structure Transitions in Sodium Induced by Collisions with Helium Argon Atoms

NASA Technical Reports Server (NTRS)

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

1998-01-01

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

Laser-Induced Optical Pumping Measurements of Cross Section for Fine- and Hyperfine-Structure Transitions in Sodium Induced by Collisions with Helium and Argon Atoms

NASA Technical Reports Server (NTRS)

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

1999-01-01

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

Ebselen induces mitochondrial permeability transition because of its interaction with adenine nucleotide translocase.

PubMed

Pavón, Natalia; Correa, Francisco; Buelna-Chontal, Mabel; Hernández-Esquivel, Luz; Chávez, Edmundo

2015-10-15

Mitochondrial permeability transition is a process established through massive Ca(2+) load in addition to an inducer reagent. Ebselen (Ebs), an antioxidant seleno compound, has been introduced as a reagent which inhibits mitochondrial dysfunction induced by permeability transition. Paradoxically enough, it has been shown that Ebs may also be able to induce the opening of the mitochondrial non-selective pores. This study was performed with the purpose of establishing the membrane system involved in Ebs-induced pore opening. Permeability transition was appraised by analyzing the following: i) matrix Ca(2+) release, and mitochondrial swelling, ii) efflux of cytochrome c, and iii) the inhibition of superoxide dismutase. All of these adverse reactions were inhibited by N-ethylmaleimide and cyclosporin A. At concentrations from 5 to 20 μM, we found that Ebs induces non-specific membrane permeability. Remarkably, Ebs blocks the binding of the fluorescent reagent eosin-5-maleimide to the thiol groups of the adenine nucleotide translocase. Based on the above, it is tempting to hypothesize that Ebs induces pore opening through its binding to the ADP/ATP carrier. Copyright © 2015 Elsevier Inc. All rights reserved.

α-melanocyte stimulating hormone modulates the central acyl ghrelin-induced stimulation of feeding, gastrointestinal motility, and colonic secretion.

PubMed

Huang, Hsien-Hao; Chen, Liang-Yu; Doong, Ming-Luen; Chang, Shi-Chuan; Chen, Chih-Yen

2017-01-01

Acyl ghrelin-induced intake depends on hypothalamic neuropeptide Y and agouti-related protein (AgRP) neurotransmitters. Intracerebroventricular (ICV) injection of AgRP increases feeding through competitive antagonism at melanocortin receptors. ICV administration of α-melanocyte stimulating hormone (α-MSH), a natural antagonist of AgRP, may modulate the acyl ghrelin-induced orexigenic effect. This study aimed to investigate the modulating effect of α-MSH on the central acyl ghrelin-induced food intake, gastrointestinal motility, and colonic secretion in rats. We examined the effects of α-MSH and acyl ghrelin on food intake, gastric emptying, small intestinal transit, colonic motility, and secretion in conscious rats with a chronic implant of ICV catheters. ICV injection of O - n -octanoylated ghrelin (0.1 nmol/rat) significantly increased the cumulative food intake up to 8 h ( P <0.01), enhanced non-nutrient semi-liquid gastric emptying ( P <0.001), increased the geometric center and running percentage of small intestinal transit ( P <0.001), accelerated colonic transit time ( P <0.05), and increased fecal pellet output ( P <0.01) and total fecal weight ( P <0.01). Pretreatment with ICV injection of α-MSH (1.0 and 2.0 nmol/rat) attenuated the acyl ghrelin-induced hyperphagic effect, fecal pellet output, and total fecal weight, while higher dose of α-MSH (2.0 nmol/rat) attenuated the increase in the geometric center of small intestinal transit ( P <0.01). However, neither dose of α-MSH altered acyl ghrelin-stimulated gastroprokinetic effect, increase in the running percentage of small intestinal transit, nor accelerated colonic transit time. α-MSH is involved in central acyl ghrelin-elicited feeding, small intestinal transit, fecal pellet output, and fecal weight. α-MSH does not affect central acyl ghrelin-induced acceleration of gastric emptying and colonic transit time in rats.

Mechanical twinning and omega transition by ⟨111⟩ {112} shear in a metastable β titanium alloy

NASA Astrophysics Data System (ADS)

Xing, H.; Sun, J.

2008-07-01

{112} ⟨111⟩ mechanical twinning and stress-induced omega transition were observed by high-resolution transmission electron microscope in a metastable β titanium alloy with chemical composition of Ti-23Nb-0.7Ta-2Zr-1.2O at. % after deformation. The orientation relationships between the ω phase and β parent matrix are (accent="true">1¯010)ω‖(211)β, [1accent="true">2¯10]ω‖[0accent="true">1¯1]β and [0001]ω‖[accent="true">1¯11]β, and the habit plane of (accent="true">1¯010)ω‖(211)β for the stress-induced ω transition is different from that of (0001)ω‖(111)β often observed for the thermal ω transition. Both mechanical twinning and ω transition arise from the shear along ⟨111⟩ {112}. A dislocation mechanism for mechanical twinning and stress-induced ω transition was discussed additionally.

Coherent structures in bypass transition induced by a cylinder wake

NASA Astrophysics Data System (ADS)

Pan, Chong; Wang, Jin Jun; Zhang, Pan Feng; Feng, Li Hao

Flat-plate boundary layer transition induced by the wake vortex of a two-dimensional circular cylinder is experimentally investigated. Combined visualization and velocity measurements show a different transition route from the Klebanoff mode in free-stream turbulence-induced transition. This transition scenario is mainly characterized as: (i) generation of secondary transverse vortical structures near the flat plate surface in response to the von Kn vortex street of the cylinder; (ii) formation of hairpin vortices due to the secondary instability of secondary vortical structures; (iii) growth of hairpins which is accelerated by wake-vortex induction; (iv) formation of hairpin packets and the associated streaky structures. Detailed investigation shows that during transition the evolution dynamics and self-sustaining mechanisms of hairpins, hairpin packets and streaks are consistent with those in a turbulent boundary layer. The wake vortex mainly plays the role of generating and destabilizing secondary transverse vortices. After that, the internal mechanisms become dominant and lead to the setting up of a self-sustained turbulent boundary layer.

Successive Magnetic-Field-Induced Transitions and Colossal Magnetoelectric Effect in Ni 3 TeO 6

DOE PAGES

Kim, Jae Wook; Artyukhin, Sergei; Mun, Eun Deok; ...

2015-09-24

In this paper, we report the discovery of a metamagnetic phase transition in a polar antiferromagnet Ni 3TeO 6 that occurs at 52 T. The new phase transition accompanies a colossal magnetoelectric effect, with a magnetic-field-induced polarization change of 0.3 μC/cm 2, a value that is 4 times larger than for the spin-flop transition at 9 T in the same material, and also comparable to the largest magnetically induced polarization changes observed to date. Via density-functional calculations we construct a full microscopic model that describes the data. We model the spin structures in all fields and clarify the physics behindmore » the 52 T transition. The high-field transition involves a competition between multiple different exchange interactions which drives the polarization change through the exchange-striction mechanism. Finally, the resultant spin structure is rather counterintuitive and complex, thus providing new insights on design principles for materials with strong magnetoelectric coupling.« less

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

Field-induced antiferroelectric to ferroelectric transitions in (Pb 1–xLa x)(Zr 0.90Ti 0.10) 1–x/ 4O 3 investigated by in situ X-ray diffraction

DOE PAGES

Ciuchi, Ioana V.; Chung, Ching -Chang; Fancher, Christopher M.; ...

2017-06-17

Phase transitions and field-induced preferred orientation in (Pb 1-xLa x)(Zr 0.90Ti 0.10) 1–x/ 4O 3 (PLZT x/90/10) ceramics upon electric field cycling using in situ X-ray diffraction were studied. The evolution of the {200} pc and {111} pc diffraction line profiles indicate that PLZT 4/90/10 and PLZT 3/90/10 compositions undergo an antiferroelectric (AFE)–ferroelectric (FE) phase switching. Both PLZT 4/90/10 and PLZT 3/90/10 exhibit irreversible preferred orientation after experiencing the field-induced AFE-to-FE phase switching. An electric field-induced structure develops in both compositions which has a reversible character during the field decreasing in PLZT 4/90/10 and an irreversible character in PLZT 3/90/10.more » In addition, structural analysis of pre-poled PLZT 3/90/10 ceramics show that it is possible to induce consecutive FE-to-AFE and AFE-to-FE transitions when fields of reversed polarity are applied in sequence. The field range required to induce the AFE phase is broad, and the phase transition is kinetically slow. In conclusion, this kind of transition has rarely been reported before.« less

Field-induced antiferroelectric to ferroelectric transitions in (Pb 1–xLa x)(Zr 0.90Ti 0.10) 1–x/ 4O 3 investigated by in situ X-ray diffraction

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

Ciuchi, Ioana V.; Chung, Ching -Chang; Fancher, Christopher M.

Phase transitions and field-induced preferred orientation in (Pb 1-xLa x)(Zr 0.90Ti 0.10) 1–x/ 4O 3 (PLZT x/90/10) ceramics upon electric field cycling using in situ X-ray diffraction were studied. The evolution of the {200} pc and {111} pc diffraction line profiles indicate that PLZT 4/90/10 and PLZT 3/90/10 compositions undergo an antiferroelectric (AFE)–ferroelectric (FE) phase switching. Both PLZT 4/90/10 and PLZT 3/90/10 exhibit irreversible preferred orientation after experiencing the field-induced AFE-to-FE phase switching. An electric field-induced structure develops in both compositions which has a reversible character during the field decreasing in PLZT 4/90/10 and an irreversible character in PLZT 3/90/10.more » In addition, structural analysis of pre-poled PLZT 3/90/10 ceramics show that it is possible to induce consecutive FE-to-AFE and AFE-to-FE transitions when fields of reversed polarity are applied in sequence. The field range required to induce the AFE phase is broad, and the phase transition is kinetically slow. In conclusion, this kind of transition has rarely been reported before.« less

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.

Pressure-induced cooperative spin transition in ironII 2D coordination polymers: room-temperature visible spectroscopic study.

PubMed

Levchenko, G; Bukin, G V; Terekhov, S A; Gaspar, A B; Martínez, V; Muñoz, M C; Real, J A

2011-06-30

For the 2D coordination polymers [Fe(3-Fpy)(2)M(II)(CN)(4)] (M(II) = Ni, Pd, Pt), the pressure-induced spin crossover behavior has been investigated at 298 K by monitoring the distinct optical properties associated with each spin state. Cooperative first-order spin transition characterized by a piezohysteresis loop ca. 0.1 GPa wide was observed for the three derivatives. Application of the mean field regular solution theory has enabled estimation of the cooperative parameter, Γ(p), and the enthalpy, ΔH(HL)(p), associated with the spin transition for each derivative. These values, found in the intervals 6.8-7.9 and 18.6-20.8 kJ mol(-1), respectively, are consistent with those previously reported for thermally induced spin transition at constant pressure for the title compounds (Chem.-Eur. J.2009, 15, 10960). Relevance of the elastic energy, Δ(elast), as a corrective parameter accounting for the pressure dependence of the critical temperature of thermally induced spin transitions (Clausius-Clapeiron equation) is also demonstrated and discussed.

Structural studies of degradation process of zirconium dioxide tetragonal phase induced by grinding with dental bur

NASA Astrophysics Data System (ADS)

Piosik, A.; Żurowski, K.; Pietralik, Z.; Hędzelek, W.; Kozak, M.

2017-11-01

Zirconium dioxide has been widely used in dental prosthetics. However, the improper mechanical treatment can induce changes in the microstructure of zirconium dioxide. From the viewpoint of mechanical properties and performance, the phase transitions of ZrO2 from the tetragonal to the monoclinic phase induced by mechanical processing, are particularly undesirable. In this study, the phase transitions of yttrium stabilized zirconium dioxide (Y-TZP) induced by mechanical treatment are investigated by the scanning electron microscopy (SEM), atomic force microscopy (AFM) and powder diffraction (XRD). Mechanical stress was induced by different types of drills used presently in dentistry. At the same time the surface temperature was monitored during milling using a thermal imaging camera. Diffraction analysis allowed determination of the effect of temperature and mechanical processing on the scale of induced changes. The observed phase transition to the monoclinic phase was correlated with the methods of mechanical processing.

Efficient computation of co-transcriptional RNA-ligand interaction dynamics.

PubMed

Wolfinger, Michael T; Flamm, Christoph; Hofacker, Ivo L

2018-05-04

Riboswitches form an abundant class of cis-regulatory RNA elements that mediate gene expression by binding a small metabolite. For synthetic biology applications, they are becoming cheap and accessible systems for selectively triggering transcription or translation of downstream genes. Many riboswitches are kinetically controlled, hence knowledge of their co-transcriptional mechanisms is essential. We present here an efficient implementation for analyzing co-transcriptional RNA-ligand interaction dynamics. This approach allows for the first time to model concentration-dependent metabolite binding/unbinding kinetics. We exemplify this novel approach by means of the recently studied I-A 2 ' -deoxyguanosine (2 ' dG)-sensing riboswitch from Mesoplasma florum. Copyright © 2018 Elsevier Inc. All rights reserved.

The Dynamic Process of Drug-GPCR Binding at Either Orthosteric or Allosteric Sites Evaluated by Metadynamics

PubMed Central

Schneider, Sebastian; Provasi, Davide; Filizola, Marta

2015-01-01

Major advances in G Protein-Coupled Receptor (GPCR) structural biology over the past few years have yielded a significant number of high-resolution crystal structures for several different receptor subtypes. This dramatic increase in GPCR structural information has underscored the use of automated docking algorithms for the discovery of novel ligands that can eventually be developed into improved therapeutics. However, these algorithms are often unable to discriminate between different, yet energetically similar, poses because of their relatively simple scoring functions. Here, we describe a metadynamics-based approach to study the dynamic process of ligand binding to/unbinding from GPCRs with a higher level of accuracy and yet satisfying efficiency. PMID:26260607

Investigating Small-Molecule Ligand Binding to G Protein-Coupled Receptors with Biased or Unbiased Molecular Dynamics Simulations

PubMed Central

Marino, Kristen A.; Filizola, Marta

2017-01-01

An increasing number of G protein-coupled receptor (GPCR) crystal structures provide important—albeit static—pictures of how small molecules or peptides interact with their receptors. These high-resolution structures represent a tremendous opportunity to apply molecular dynamics (MD) simulations to capture atomic-level dynamical information that is not easy to obtain experimentally. Understanding ligand binding and unbinding processes, as well as the related responses of the receptor, is crucial to the design of better drugs targeting GPCRs. Here, we discuss possible ways to study the dynamics involved in the binding of small molecules to GPCRs, using long timescale MD simulations or metadynamics-based approaches. PMID:29188572

Investigating Small-Molecule Ligand Binding to G Protein-Coupled Receptors with Biased or Unbiased Molecular Dynamics Simulations.

PubMed

Marino, Kristen A; Filizola, Marta

2018-01-01

An increasing number of G protein-coupled receptor (GPCR) crystal structures provide important-albeit static-pictures of how small molecules or peptides interact with their receptors. These high-resolution structures represent a tremendous opportunity to apply molecular dynamics (MD) simulations to capture atomic-level dynamical information that is not easy to obtain experimentally. Understanding ligand binding and unbinding processes, as well as the related responses of the receptor, is crucial to the design of better drugs targeting GPCRs. Here, we discuss possible ways to study the dynamics involved in the binding of small molecules to GPCRs, using long timescale MD simulations or metadynamics-based approaches.

Formation mechanisms and characteristics of transition patterns in oblique detonations

NASA Astrophysics Data System (ADS)

Miao, Shikun; Zhou, Jin; Liu, Shijie; Cai, Xiaodong

2018-01-01

The transition structures of wedge-induced oblique detonation waves (ODWs) in high-enthalpy supersonic combustible mixtures are studied with two-dimensional reactive Euler simulations based on the open-source program AMROC (Adaptive Mesh Refinement in Object-oriented C++). The formation mechanisms of different transition patterns are investigated through theoretical analysis and numerical simulations. Results show that transition patterns of ODWs depend on the pressure ratio Pd/Ps, (Pd, Ps are the pressure behind the ODW and the pressure behind the induced shock, respectively). When Pd/Ps > 1.3, an abrupt transition occurs, while when Pd/Ps < 1.3, a smooth transition appears. A parameter ε is introduced to describe the transition patterns quantitatively. Besides, a criterion based on the velocity ratio Φ=U0/UCJ is proposed to predict the transition patterns based on the inflow conditions. It is concluded that an abrupt transition appears when Φ < 0.98Φ*, while a smooth transition occurs when Φ > 1.02Φ∗ (Φ∗ is the critical velocity ratio calculated with an empirical formula).

Hydroquinone, a benzene metabolite, induces Hog1-dependent stress response signaling and causes aneuploidy in Saccharomyces cerevisiae.

PubMed

Shiga, Takeki; Suzuki, Hiroyuki; Yamamoto, Ayumi; Yamamoto, Hiroaki; Yamamoto, Kazuo

2010-01-01

Previously, we have shown that phenyl hydroquinone, a hepatic metabolite of the Ames test-negative carcinogen o-phenylphenol, efficiently induced aneuploidy in Saccharomyces cerevisiae by arresting the cell cycle at the G2/M transition as a result of the activation of the Hog1 (p38 MAPK homolog)-Swe1 (Wee1 homolog) pathway. In this experiment, we examined the aneuploidy forming effects of hydroquinone, a benzene metabolite, since both phenyl hydroquinone and hydroquinone are Ames-test negative carcinogens and share similar molecular structures. As was seen in phenyl hydroquinone, hydroquinone induced aneuploidy in yeast by delaying the cell cycle at the G2/M transition. Deficiencies in SWE1 and HOG1 abolished the hydroquinone-induced delay at the G2/M transition and aneuploidy formation. Furthermore, Hog1 was phosphorylated by hydroquinone, which may stabilize Swe1. These data indicate that the hydroquinone-induced G2/M transition checkpoint, which is activated by the Hog1-Swe1 pathway, plays a role in the formation of aneuploidy.

Giant electric-field-induced strain in lead-free piezoelectric materials

PubMed Central

Chen, Lan; Yang, Yurong; Meng, X. K.

2016-01-01

First-principles calculations are performed to investigate the structures, electrical, and magnetic properties of compressive BiFeO3 films under electric-field and pressure perpendicular to the films. A reversible electric-field-induced strain up 10% is achieved in the compressive BiFeO3 films. The giant strain originates from rhombohedral-tetragonal (R-T) phase transition under electric-filed, and is recoverable from tetragonal-rhombohedral (T-R) phase transition by compressive stress. Additionally, the weak ferromagnetism in BiFeO3 films is largely changed in R-T phase transition under electric-filed and T-R phase transition under pressure – reminiscent of magnetoelectric effect and magnetoelastic effect. These results suggest exciting device opportunities arising from the giant filed-induced strain, large magnetoelectric effect and magnetoelastic effect. PMID:27139526

Diabetes attenuates the inhibitory effects of endomorphin-2, but not endomorphin-1 on gastrointestinal transit in mice.

PubMed

Wang, Chang-lin; Diao, Yu-xiang; Xiang, Qiong; Ren, Yu-kun; Gu, Ning

2014-09-05

Diabetes affects the entire gastrointestinal tract from the esophagus to the anus. In the present study, the charcoal meal test was undertaken to evaluate and compare the effects of intracerebroventricular (i.c.v.) administration of endomorphins (EMs) on gastrointestinal transit in non-diabetic and diabetic mice. Significantly delayed gastrointestinal transit was found in both 4 and 8 weeks alloxan-induced diabetes compared to non-diabetes. Moreover, i.c.v. EM-1 and EM-2 dose-dependently delayed gastrointestinal transit in non-diabetes and diabetes. The EM-1-induced inhibitory effects of gastrointestinal transit in 4 weeks diabetes were qualitatively similar to those of non-diabetes. However, at higher doses, the EM-1-induced effects in 8 weeks diabetes were largely enhanced. Different to EM-1, the EM-2-induced inhibition of gastrointestinal transit in diabetic mice was significantly attenuated compared to non-diabetic mice. Moreover, these effects were further decreased in 8 weeks diabetes. The delayed gastrointestinal transit effects caused by EM-1 may be primarily mediated by μ2-opioid receptor in both non-diabetes and 4 weeks diabetes. Interestingly, in 8 weeks diabetes, these effects were mediated by μ2- and δ-receptors. However, the inhibitory effects of EM-2 were mediated by μ1-opioid receptor, which exerted a reduced function in diabetes. Also, poor blood glucose control might result in the attenuated effects of EM-2. Our present results demonstrated that diabetes attenuates the inhibitory effects of EM-2, but not EM-1 on gastrointestinal transit in mice. The different effects of EM-1 and EM-2 on gastrointestinal transit in diabetes may be due to changes of opioid receptor subtypes and their functional responses. Copyright © 2014 Elsevier B.V. All rights reserved.

Laser spectroscopic study of the Rydberg state structure of atomic lithium

NASA Astrophysics Data System (ADS)

Ballard, M. Kent

1998-07-01

Pulsed laser induced fluorescence spectroscopy was performed on both isotopic species of atomic lithium. Nonresonant multiphoton excitation spectra were recorded. The laser induced fluorescence of the lithium vapor was measured following excitation with a tunable, pulsed, nanosecond laser. Both two- and three-photon allowed transitions were observed resulting in four different transition series originating from the 22S and 22P levels, the latter likely originating from photodissociation products of the lithium dimer, Li2. Forty-seven identifiable transitions were assigned for 6Li. Evidence for a parity forbidden multiphoton transition is also present. For 7Li, fifty-three identifiable transitions were assigned including an additional series of parity forbidden multiphoton transitions. Laser polarization and power dependencies were measured and found to be consistent with the multiphoton transition probabilities. Due to the intense laser fields needed to produce the nonresonant multiphoton excitations, the lithium vapor was subjected to the laser induced ac Stark effect. The Autler-Townes doublets observed for the nF gets 2P transition series were found to exhibit normal asymmetry. The observed asymmetrical Autler-Townes profiles are explained in terms of the two-level and the three-level atomic systems which are based on different excitation schemes. A new computerized data acquisition system was developed as well as associated computer programs needed to analyze spectra.

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.

Cyclosporin A is unable to inhibit carboxyatractyloside-induced permeability transition in aged mitochondria.

PubMed

García, Noemí; Zazueta, Cecilia; Martínez-Abundis, Eduardo; Pavón, Natalia; Chávez, Edmundo

2009-04-01

We studied the effect of mitochondrial ageing on membrane permeability transition. The results obtained indicate that aged mitochondria are neither able to retain Ca2+ nor to maintain a high transmembrane electric gradient. In addition, aged mitochondria undergo a large amplitude swelling. These dysfunctions were circumvented by the addition of cyclosporin A. Furthermore, it is shown that ageing-induced permeability transition causes oxidative damage on the matrix enzyme aconitase. The observed damage in aged mitochondria requires Ca2+ addition; therefore, it was not seen when Sr2+ replaced Ca2+. Two important findings in this work were the fact that despite of the presence of cyclosporin A, carboxyatractyloside was still able to induce permeability transition, and that ageing induced mitochondrial DNA disruption and release of cytochrome c. It is likely that the membrane's increased permeability is due to the effect of fatty acids, since bovine serum albumin makes mitochondria able to retain Ca2+. However, the possibility that the damage might be the result of oxidative stress cannot be discarded.

Fermion-induced quantum criticality with two length scales in Dirac systems

NASA Astrophysics Data System (ADS)

Torres, Emilio; Classen, Laura; Herbut, Igor F.; Scherer, Michael M.

2018-03-01

The quantum phase transition to a Z3-ordered Kekulé valence bond solid in two-dimensional Dirac semimetals is governed by a fermion-induced quantum critical point, which renders the putatively discontinuous transition continuous. We study the resulting universal critical behavior in terms of a functional RG approach, which gives access to the scaling behavior on the symmetry-broken side of the phase transition, for general dimensions and number of Dirac fermions. In particular, we investigate the emergence of the fermion-induced quantum critical point for spacetime dimensions 2

Sensing (un)binding events via surface plasmons: effects of resonator geometry

NASA Astrophysics Data System (ADS)

Antosiewicz, Tomasz J.; Claudio, Virginia; Käll, Mikael

2016-04-01

The resonance conditions of localized surface plasmon resonances (LSPRs) can be perturbed in any number ways making plasmon nanoresonators viable tools in detection of e.g. phase changes, pH, gasses, and single molecules. Precise measurement via LSPR of molecular concentrations hinge on the ability to confidently count the number of molecules attached to a metal resonator and ideally to track binding and unbinding events in real-time. These two requirements make it necessary to rigorously quantify relations between the number of bound molecules and response of plasmonic sensors. This endeavor is hindered on the one hand by a spatially varying response of a given plasmonic nanosensor. On the other hand movement of molecules is determined by stochastic effects (Brownian motion) as well as deterministic flow, if present, in microfluidic channels. The combination of molecular dynamics and the electromagnetic response of the LSPR yield an uncertainty which is little understood and whose effect is often disregarded in quantitative sensing experiments. Using a combination of electromagnetic finite-difference time-domain (FDTD) calculations of the plasmon resonance peak shift of various metal nanosensors (disk, cone, rod, dimer) and stochastic diffusion-reaction simulations of biomolecular interactions on a sensor surface we clarify the interplay between position dependent binding probability and inhomogeneous sensitivity distribution. We show, how the statistical characteristics of the total signal upon molecular binding are determined. The proposed methodology is, in general, applicable to any sensor and any transduction mechanism, although the specifics of implementation will vary depending on circumstances. In this work we focus on elucidating how the interplay between electromagnetic and stochastic effects impacts the feasibility of employing particular shapes of plasmonic sensors for real-time monitoring of individual binding reactions or sensing low concentrations - which characteristics make a given sensor optimal for a given task. We also address the issue of how particular illumination conditions affect the level of uncertainty of the measured signal upon molecular binding.

Improving estimation of kinetic parameters in dynamic force spectroscopy using cluster analysis

NASA Astrophysics Data System (ADS)

Yen, Chi-Fu; Sivasankar, Sanjeevi

2018-03-01

Dynamic Force Spectroscopy (DFS) is a widely used technique to characterize the dissociation kinetics and interaction energy landscape of receptor-ligand complexes with single-molecule resolution. In an Atomic Force Microscope (AFM)-based DFS experiment, receptor-ligand complexes, sandwiched between an AFM tip and substrate, are ruptured at different stress rates by varying the speed at which the AFM-tip and substrate are pulled away from each other. The rupture events are grouped according to their pulling speeds, and the mean force and loading rate of each group are calculated. These data are subsequently fit to established models, and energy landscape parameters such as the intrinsic off-rate (koff) and the width of the potential energy barrier (xβ) are extracted. However, due to large uncertainties in determining mean forces and loading rates of the groups, errors in the estimated koff and xβ can be substantial. Here, we demonstrate that the accuracy of fitted parameters in a DFS experiment can be dramatically improved by sorting rupture events into groups using cluster analysis instead of sorting them according to their pulling speeds. We test different clustering algorithms including Gaussian mixture, logistic regression, and K-means clustering, under conditions that closely mimic DFS experiments. Using Monte Carlo simulations, we benchmark the performance of these clustering algorithms over a wide range of koff and xβ, under different levels of thermal noise, and as a function of both the number of unbinding events and the number of pulling speeds. Our results demonstrate that cluster analysis, particularly K-means clustering, is very effective in improving the accuracy of parameter estimation, particularly when the number of unbinding events are limited and not well separated into distinct groups. Cluster analysis is easy to implement, and our performance benchmarks serve as a guide in choosing an appropriate method for DFS data analysis.

Electric-field-driven phase transition in vanadium dioxide

NASA Astrophysics Data System (ADS)

Wu, B.; Zimmers, A.; Aubin, H.; Ghosh, R.; Liu, Y.; Lopez, R.

2011-12-01

We report on local probe measurements of current-voltage and electrostatic force-voltage characteristics of electric-field-induced insulator to metal transition in VO2 thin film. In conducting AFM mode, switching from the insulating to metallic state occurs for electric-field threshold E˜6.5×107Vm-1 at 300K. Upon lifting the tip above the sample surface, we find that the transition can also be observed through a change in electrostatic force and in tunneling current. In this noncontact regime, the transition is characterized by random telegraphic noise. These results show that electric field alone is sufficient to induce the transition; however, the electronic current provides a positive feedback effect that amplifies the phenomena.

Transition Induced by Fence Geometrics on Shuttle Orbiter at Mach 10

NASA Technical Reports Server (NTRS)

Everhart, Joel L.

2010-01-01

Fence-induced transition data simulating a raised gap filler have been acquired on the wing lower surface of a Shuttle Orbiter model in the Langley 31-Inch Mach 10 Tunnel to compare with the Shuttle Boundary Layer Transition Flight and HYTHIRM Experiments, and to provide additional correlation data for the Boundary Layer Transition Tool. In a qualitative assessment, the data exhibit the expected response to all parameter variations; however, it is unclear whether fully effective tripping at the fence was ever realized at any test condition with the present model hardware. A preliminary, qualitative comparison of the ground-based transition measurements with those obtained from the STS-128 HYTHIRM imagery at Mach 15 reveal similar transition-wake response characteristics in terms of the spreading and the path along the vehicle surface.

Probing the electronic and local structural changes across the pressure-induced insulator-to-metal transition in VO2

NASA Astrophysics Data System (ADS)

Marini, C.; Bendele, M.; Joseph, B.; Kantor, I.; Mitrano, M.; Mathon, O.; Baldini, M.; Malavasi, L.; Pascarelli, S.; Postorino, P.

2014-11-01

Local and electronic structures of vanadium in \\text{VO}2 are studied across the high-pressure insulator-to-metal (IMT) transition using V K-edge x-ray absorption spectroscopy. Unlike the temperature-induced IMT, pressure-induced metallization leads to only subtle changes in the V K-edge prepeak structure, indicating a different mechanism involving smaller electronic spectral weight transfer close to the chemical potential. Intriguingly, upon application of the hydrostatic pressure, the electronic structure begins to show substantial changes well before the occurrence of the IMT and the associated structural transition to an anisotropic compression of the monoclinic metallic phase.

Pressure-induced phase transition of 1-butyl-3-methylimidazolium hexafluorophosphate [bmim][PF6

NASA Astrophysics Data System (ADS)

Takekiyo, Takahiro; Hatano, Naohiro; Imai, Yusuke; Abe, Hiroshi; Yoshimura, Yukihiro

2011-03-01

We have investigated the pressure-induced Raman spectral change of 1-butyl-3-methylimidazolium hexafluorophosphate ([bmim][PF6]) using Raman spectroscopy. The relative Raman intensity at 590 cm-1 of the CH2 rocking band assigned to the gauche conformer of the NCCC dihedral angle of the butyl group in the [bmim]+ cation increases when the pressure-induced liquid-crystalline phase transition occurs, while that at 610 cm-1 assigned to the trans conformer decreases. Our results show that the high-pressure phase transition of [bmim][PF6] causes the increase of the gauche conformer of the [bmim]+ cation.

Coloration of tyrosine by organic-semiconductor interfacial charge-transfer transitions

NASA Astrophysics Data System (ADS)

Fujisawa, Jun-ichi; Kikuchi, Natsumi; Hanaya, Minoru

2016-11-01

L-tyrosine (Tyr) plays a crucial role as a proteinogenic amino acid and also as a precursor to several neurotransmitters and hormones. Here we demonstrate coloration of Tyr based on organic-semiconductor interfacial charge-transfer (ICT) transitions. The ICT transitions from Tyr to TiO2 are induced by the chemisorption of Tyr on TiO2 surfaces via the hydroxy group of the phenol moiety. Because other amino acids possess no chemical group to induce ICT transitions, this coloration method enables to detect Tyr selectively without drastic structural change in contrast to the conventional coloration methods.

Gap Filler Induced Transition on the Mars Science Laboratory Heatshield

NASA Technical Reports Server (NTRS)

Yoon, Seokkwan; Barnhardt, Michael D.; Tang, Chun Y.; Sozer, Emre; Candler, Graham

2012-01-01

Detached Eddy Simulations have been performed to investigate the effects of high-fidelity turbulence modeling on roughness-induced transition to turbulence during Mars entry. Chemically reacting flow solutions will be obtained for a gap filler of Mars Science Laboratory at the peak heating condition.

Controlling the delocalization-localization transition of light via electromagnetically induced transparency

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

Cheng Jing; Huang Guoxiang; State Key Laboratory of Precision Spectroscopy, East China Normal University, Shanghai 200062

2011-05-15

We propose a scheme to realize a transition from delocalization to localization of light waves via electromagnetically induced transparency. The system we suggested is a resonant cold atomic ensemble having N configuration, with a control field consisting of two pairs of laser beams with different cross angles, which produce an electromagnetically induced quasiperiodic waveguide (EIQPW) for the propagation of a signal field. By appropriately tuning the incommensurate rate or relative modulation strength between the two pairs of control-field components, the signal field can exhibit the delocalization-localization transition as it transports inside the atomic ensemble. The delocalization-localization transition point is determinedmore » and the propagation property of the signal field is studied in detail. Our work provides a way of realizing wave localization via atomic coherence, which is quite different from the conventional, off-resonant mechanism-based Aubry-Andre model, and the great controllability of the EIQPW also allows an easy manipulation of the delocalization-localization transition.« less

Phase transition induced strain in ZnO under high pressure

DOE PAGES

Yan, Xiaozhi; Dong, Haini; Li, Yanchun; ...

2016-05-13

Under high pressure, the phase transition mechanism and mechanical property of material are supposed to be largely associated with the transformation induced elastic strain. However, the experimental evidences for such strain are scanty. The elastic and plastic properties of ZnO, a leading material for applications in chemical sensor, catalyst, and optical thin coatings, were determined using in situ high pressure synchrotron axial and radial x-ray diffraction. The abnormal elastic behaviors of selected lattice planes of ZnO during phase transition revealed the existence of internal elastic strain, which arise from the lattice misfit between wurtzite and rocksalt phase. Furthermore, the strengthmore » decrease of ZnO during phase transition under non-hydrostatic pressure was observed and could be attributed to such internal elastic strain, unveiling the relationship between pressure induced internal strain and mechanical property of material. Ultimately, these findings are of fundamental importance to understanding the mechanism of phase transition and the properties of materials under pressure.« less

Stress induces pain transition by potentiation of AMPA receptor phosphorylation.

PubMed

Li, Changsheng; Yang, Ya; Liu, Sufang; Fang, Huaqiang; Zhang, Yong; Furmanski, Orion; Skinner, John; Xing, Ying; Johns, Roger A; Huganir, Richard L; Tao, Feng

2014-10-08

Chronic postsurgical pain is a serious issue in clinical practice. After surgery, patients experience ongoing pain or become sensitive to incident, normally nonpainful stimulation. The intensity and duration of postsurgical pain vary. However, it is unclear how the transition from acute to chronic pain occurs. Here we showed that social defeat stress enhanced plantar incision-induced AMPA receptor GluA1 phosphorylation at the Ser831 site in the spinal cord and greatly prolonged plantar incision-induced pain. Interestingly, targeted mutation of the GluA1 phosphorylation site Ser831 significantly inhibited stress-induced prolongation of incisional pain. In addition, stress hormones enhanced GluA1 phosphorylation and AMPA receptor-mediated electrical activity in the spinal cord. Subthreshold stimulation induced spinal long-term potentiation in GluA1 phosphomimetic mutant mice, but not in wild-type mice. Therefore, spinal AMPA receptor phosphorylation contributes to the mechanisms underlying stress-induced pain transition. Copyright © 2014 the authors 0270-6474/14/3413737-10$15.00/0.

Shear induced phase transitions induced in edible fats

NASA Astrophysics Data System (ADS)

Mazzanti, Gianfranco; Welch, Sarah E.; Marangoni, Alejandro G.; Sirota, Eric B.; Idziak, Stefan H. J.

2003-03-01

The food industry crystallizes fats under different conditions of temperature and shear to obtain products with desired crystalline phases. Milk fat, palm oil, cocoa butter and chocolate were crystallized from the melt in a temperature controlled Couette cell. Synchrotron x-ray diffraction studies were conducted to examine the role of shear on the phase transitions seen in edible fats. The shear forces on the crystals induced acceleration of the alpha to beta-prime phase transition with increasing shear rate in milk fat and palm oil. The increase was slow at low shear rates and became very strong above 360 s-1. In cocoa butter the acceleration between beta-prime-III and beta-V phase transition increased until a maximum of at 360 s-1, and then decreased, showing competition between enhanced heat transfer and viscous heat generation.

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.

Supernova 2007bi as a pair-instability explosion.

PubMed

Gal-Yam, A; Mazzali, P; Ofek, E O; Nugent, P E; Kulkarni, S R; Kasliwal, M M; Quimby, R M; Filippenko, A V; Cenko, S B; Chornock, R; Waldman, R; Kasen, D; Sullivan, M; Beshore, E C; Drake, A J; Thomas, R C; Bloom, J S; Poznanski, D; Miller, A A; Foley, R J; Silverman, J M; Arcavi, I; Ellis, R S; Deng, J

2009-12-03

Stars with initial masses such that 10M[symbol: see text] or= 140M[symbol: see text] (if such exist) develop oxygen cores with masses, M(core), that exceed 50M[symbol: see text], where high temperatures are reached at relatively low densities. Conversion of energetic, pressure-supporting photons into electron-positron pairs occurs before oxygen ignition and leads to a violent contraction which triggers a nuclear explosion that unbinds the star in a pair-instability supernova. Transitional objects with 100M[symbol: see text] < M(initial) < 140M[symbol: see text] may end up as iron-core-collapse supernovae following violent mass ejections, perhaps as a result of brief episodes of pair instability, and may already have been identified. Here we report observations of supernova SN 2007bi, a luminous, slowly evolving object located within a dwarf galaxy. We estimate the exploding core mass to be M(core) approximately 100M[symbol: see text], in which case theory unambiguously predicts a pair-instability supernova. We show that >3M[symbol: see text] of radioactive (56)Ni was synthesized during the explosion and that our observations are well fitted by models of pair-instability supernovae. This indicates that nearby dwarf galaxies probably host extremely massive stars, above the apparent Galactic stellar mass limit, which perhaps result from processes similar to those that created the first stars in the Universe.

Single-Molecule Interactions of a Monoclonal Anti-DNA Antibody with DNA

PubMed Central

Nevzorova, Tatiana A.; Zhao, Qingze; Lomakin, Yakov A.; Ponomareva, Anastasia A.; Mukhitov, Alexander R.; Purohit, Prashant K.; Weisel, John W.; Litvinov, Rustem I.

2017-01-01

Interactions of DNA with proteins are essential for key biological processes and have both a fundamental and practical significance. In particular, DNA binding to anti-DNA antibodies is a pathogenic mechanism in autoimmune pathology, such as systemic lupus erythematosus. Here we measured at the single-molecule level binding and forced unbinding of surface-attached DNA and a monoclonal anti-DNA antibody MRL4 from a lupus erythematosus mouse. In optical trap-based force spectroscopy, a microscopic antibodycoated latex bead is trapped by a focused laser beam and repeatedly brought into contact with a DNA-coated surface. After careful discrimination of non-specific interactions, we showed that the DNA-antibody rupture force spectra had two regimes, reflecting formation of weaker (20–40 pN) and stronger (>40 pN) immune complexes that implies the existence of at least two bound states with different mechanical stability. The two-dimensional force-free off-rate for the DNA-antibody complexes was ~2.2 × 10−3 s−1, the transition state distance was ~0.94 nm, the apparent on-rate was ~5.26 s−1, and the stiffness of the DNA-antibody complex was characterized by a spring constant of 0.0021 pN/nm, suggesting that the DNA-antibody complex is a relatively stable, but soft and deformable macromolecular structure. The stretching elasticity of the DNA molecules was characteristic of single-stranded DNA, suggesting preferential binding of the MRL4 antibody to one strand of DNA. Collectively, the results provide fundamental characteristics of formation and forced dissociation of DNA-antibody complexes that help to understand principles of DNA-protein interactions and shed light on the molecular basis of autoimmune diseases accompanied by formation of anti-DNA antibodies. PMID:29104846

Photo-induced reactions from efficient molecular dynamics with electronic transitions using the FIREBALL local-orbital density functional theory formalism.

PubMed

Zobač, Vladimír; Lewis, James P; Abad, Enrique; Mendieta-Moreno, Jesús I; Hapala, Prokop; Jelínek, Pavel; Ortega, José

2015-05-08

The computational simulation of photo-induced processes in large molecular systems is a very challenging problem. Firstly, to properly simulate photo-induced reactions the potential energy surfaces corresponding to excited states must be appropriately accessed; secondly, understanding the mechanisms of these processes requires the exploration of complex configurational spaces and the localization of conical intersections; finally, photo-induced reactions are probability events, that require the simulation of hundreds of trajectories to obtain the statistical information for the analysis of the reaction profiles. Here, we present a detailed description of our implementation of a molecular dynamics with electronic transitions algorithm within the local-orbital density functional theory code FIREBALL, suitable for the computational study of these problems. As an example of the application of this approach, we also report results on the [2 + 2] cycloaddition of ethylene with maleic anhydride and on the [2 + 2] photo-induced polymerization reaction of two C60 molecules. We identify different deactivation channels of the initial electron excitation, depending on the time of the electronic transition from LUMO to HOMO, and the character of the HOMO after the transition.

Pressure induced structural phase transition in IB transition metal nitrides compounds

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

Soni, Shubhangi; Kaurav, Netram, E-mail: netramkaurav@yahoo.co.uk; Jain, A.

2015-06-24

Transition metal mononitrides are known as refractory compounds, and they have, relatively, high hardness, brittleness, melting point, and superconducting transition temperature, and they also have interesting optical, electronic, catalytic, and magnetic properties. Evolution of structural properties would be an important step towards realizing the potential technological scenario of this material of class. In the present study, an effective interionic interaction potential (EIOP) is developed to investigate the pressure induced phase transitions in IB transition metal nitrides TMN [TM = Cu, Ag, and Au] compounds. The long range Coulomb, van der Waals (vdW) interaction and the short-range repulsive interaction upto second-neighbormore » ions within the Hafemeister and Flygare approach with modified ionic charge are properly incorporated in the EIOP. The vdW coefficients are computed following the Slater-Kirkwood variational method, as both the ions are polarizable. The estimated value of the phase transition pressure (Pt) and the magnitude of the discontinuity in volume at the transition pressure are consistent as compared to the reported data.« less

“Ultra-high resolution optical trap with single fluorophore sensitivity”

PubMed Central

Comstock, Matthew J; Ha, Taekjip; Chemla, Yann R

2013-01-01

We present a single-molecule instrument that combines a timeshared ultra-high resolution dual optical trap interlaced with a confocal fluorescence microscope. In a demonstration experiment, individual single-fluorophore labeled DNA oligonucleotides were observed to bind and unbind to complementary DNA suspended between two trapped beads. Simultaneous with the single-fluorophore detection, coincident angstrom-scale changes in tether extension could be clearly observed. Fluorescence readout allowed us to determine the duplex melting rate as a function of force. The new instrument will enable the simultaneous measurement of angstrom-scale mechanical motion of individual DNA-binding proteins (e.g., single base pair stepping of DNA translocases) along with the detection of fluorescently labeled protein properties (e.g., internal configuration). PMID:21336286

Disorder-Induced Topological State Transition in Photonic Metamaterials

NASA Astrophysics Data System (ADS)

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

2017-11-01

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

Large magnetoresistance dips and perfect spin-valley filter induced by topological phase transitions in silicene

NASA Astrophysics Data System (ADS)

Prarokijjak, Worasak; Soodchomshom, Bumned

2018-04-01

Spin-valley transport and magnetoresistance are investigated in silicene-based N/TB/N/TB/N junction where N and TB are normal silicene and topological barriers. The topological phase transitions in TB's are controlled by electric, exchange fields and circularly polarized light. As a result, we find that by applying electric and exchange fields, four groups of spin-valley currents are perfectly filtered, directly induced by topological phase transitions. Control of currents, carried by single, double and triple channels of spin-valley electrons in silicene junction, may be achievable by adjusting magnitudes of electric, exchange fields and circularly polarized light. We may identify that the key factor behind the spin-valley current filtered at the transition points may be due to zero and non-zero Chern numbers. Electrons that are allowed to transport at the transition points must obey zero-Chern number which is equivalent to zero mass and zero-Berry's curvature, while electrons with non-zero Chern number are perfectly suppressed. Very large magnetoresistance dips are found directly induced by topological phase transition points. Our study also discusses the effect of spin-valley dependent Hall conductivity at the transition points on ballistic transport and reveals the potential of silicene as a topological material for spin-valleytronics.

Spin transition in a four-coordinate iron oxide

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

Kawakami, T.; Sutou, S.; Hirama, H.

2009-01-01

The spin transition, or spin crossover, is a manifestation of electronic instability induced by external constraints such as pressure1. Among known examples that exhibit spin transition, 3d ions with d6 electron configurations represent the vast majority, but the spin transition observed thus far has been almost exclusively limited to that between high-spin (S = 2) and low-spin (S = 0) states2-9. Here we report a novel high-spin to intermediate-spin (S = 1) state transition at 33 GPa induced by pressurization of an antiferromagnetic insulator SrFeO2 with a square planar coordination10. The change in spin multiplicity brings to ferromagnetism as wellmore » as metallicity, yet keeping the ordering temperature far above ambient. First-principles calculations attribute the origin of the transition to the strong inlayer hybridization between Fe dx 2 -y 2 O p , leading to a pressure-induced electronic instability toward the depopulation of Fe dx 2 -y 2 O p antibonding states. Furthermore, the ferromagnetic S = 1 state is half-metallic due to the inception of half-occupied spin-down (dxz, dyz) degenerate states upon spin transition. These results highlight the square-planar coordinated iron oxides as a new class of magnetic and electric materials and provide new avenues toward realizing multi-functional sensors and data-storage devices.« less

Tunable, high-sensitive measurement of inter-dot transition via tunneling induced absorption

NASA Astrophysics Data System (ADS)

Peng, Yandong; Yang, Aihong; Chen, Bing; Li, Lei; Liu, Shande; Guo, Hongju

2016-10-01

A tunable, narrow absorption spectrum induced by resonant tunneling is demonstrated and proposed for measuring interdot tunneling. Tunneling-induced absorption (TIA) arises from constructive interference between different transition paths, and the large nonlinear TIA significantly enhances the total absorption. The narrow nonlinear TIA spectrum is sensitive to inter-dot tunneling, and its sensor characteristics, including sensitivity and bandwidth, are investigated in weak-coupling and strong-coupling regimes, respectively.

FAILURE OF A NEUTRINO-DRIVEN EXPLOSION AFTER CORE-COLLAPSE MAY LEAD TO A THERMONUCLEAR SUPERNOVA

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

Kushnir, Doron; Katz, Boaz, E-mail: kushnir@ias.edu

We demonstrate that ∼10 s after the core-collapse of a massive star, a thermonuclear explosion of the outer shells is possible for some (tuned) initial density and composition profiles, assuming that the neutrinos failed to explode the star. The explosion may lead to a successful supernova, as first suggested by Burbidge et al. We perform a series of one-dimensional (1D) calculations of collapsing massive stars with simplified initial density profiles (similar to the results of stellar evolution calculations) and various compositions (not similar to 1D stellar evolution calculations). We assume that the neutrinos escaped with a negligible effect on themore » outer layers, which inevitably collapse. As the shells collapse, they compress and heat up adiabatically, enhancing the rate of thermonuclear burning. In some cases, where significant shells of mixed helium and oxygen are present with pre-collapsed burning times of ≲100 s (≈10 times the free-fall time), a thermonuclear detonation wave is ignited, which unbinds the outer layers of the star, leading to a supernova. The energy released is small, ≲10{sup 50} erg, and negligible amounts of synthesized material (including {sup 56}Ni) are ejected, implying that these 1D simulations are unlikely to represent typical core-collapse supernovae. However, they do serve as a proof of concept that the core-collapse-induced thermonuclear explosions are possible, and more realistic two-dimensional and three-dimensional simulations are within current computational capabilities.« less

Shock wave induced phase transition in α -FePO 4

NASA Astrophysics Data System (ADS)

Joshi, K. D.; Suresh, N.; Jyoti, G.; Kulshreshtha, S. K.; Gupta, S. C.; Sikka, S. K.

Shock wave induced response of the berlinite form of FePO 4 has been investigated up to 8.5 GPa. The X-ray diffraction measurements on the shock recovered samples reveal transition to the mixture of an amorphous phase and an orthorhombic phase around 5 GPa. The proportion of the amorphous material in the recovered sample is found to decrease at higher pressure. The results are interpreted in terms of a three-level free energy diagram for the crystal to amorphous transitions.

Spin-glass polyamorphism induced by a magnetic field in LaMnO3 single crystal

NASA Astrophysics Data System (ADS)

Eremenko, V. V.; Sirenko, V. A.; Baran, A.; Čižmár, E.; Feher, A.

2018-05-01

We present experimental evidence of field-driven transition in spin-glass state, similar to pressure-induced transition between amorphous phases in structural and metallic glasses, attributed to the polyamorphism phenomena. Cusp in temperature dependences of ac magnetic susceptibility of weakly disordered LaMnO3 single crystal is registered below the temperature of magnetic ordering. Frequency dependence of the cusp temperature proves its spin-glass origin. The transition induced by a magnetic field in spin-glass state, is manifested by peculiarity in dependence of cusp temperature on applied magnetic field. Field dependent maximum of heat capacity is observed in the same magnetic field and temperature range.

Pressure and magnetic field effects on the valence transition of EuRh2Si2

NASA Astrophysics Data System (ADS)

Mitsuda, Akihiro; Kishaba, Eigo; Fujimoto, Takumi; Oyama, Kohei; Wada, Hirofumi; Mizumaki, Masaichiro; Kawamura, Naomi; Ishimatsu, Naoki

2018-05-01

We have measured the X-ray absorption spectra (XAS), electrical resistivity and magnetic susceptibility of EuRh2Si2, which undergoes a valence transition under high pressures. A sharp decrease in the Eu valence determined from the XAS was observed at around 70 K in the temperature dependence at P = 1.2-1.9 GPa. In the temperature dependence of electrical resistivity and magnetic susceptibility, we observed jumps associated with the temperature-induced valence transition under high pressures. The magnetoresistance detected a field-induced valence transition. The results are discussed from the thermodynamic point of view.

A stable frequency comb directly referenced to rubidium electromagnetically induced transparency and two-photon transitions

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

Hou, Dong; Wu, Jiutao; Zhang, Shuangyou

2014-03-17

We demonstrate an approach to create a stable erbium-fiber-based frequency comb at communication band by directly locking the combs to two rubidium atomic transitions resonances (electromagnetically induced transparency absorption and two-photon absorption), respectively. This approach directly transfers the precision and stability of the atomic transitions to the comb. With its distinguishing feature of compactness by removing the conventional octave-spanning spectrum and f-to-2f beating facilities and the ability to directly control the comb's frequency at the atomic transition frequency, this stable optical comb can be widely used in optical communication, frequency standard, and optical spectroscopy and microscopy.

Theoretical study of the partial molar volume change associated with the pressure-induced structural transition of ubiquitin

PubMed Central

Imai, Takashi; Ohyama, Shusaku; Kovalenko, Andriy; Hirata, Fumio

2007-01-01

The partial molar volume (PMV) change associated with the pressure-induced structural transition of ubiquitin is analyzed by the three-dimensional reference interaction site model (3D-RISM) theory of molecular solvation. The theory predicts that the PMV decreases upon the structural transition, which is consistent with the experimental observation. The volume decomposition analysis demonstrates that the PMV reduction is primarily caused by the decrease in the volume of structural voids in the protein, which is partially canceled by the volume expansion due to the hydration effects. It is found from further analysis that the PMV reduction is ascribed substantially to the penetration of water molecules into a specific part of the protein. Based on the thermodynamic relation, this result implies that the water penetration causes the pressure-induced structural transition. It supports the water penetration model of pressure denaturation of proteins proposed earlier. PMID:17660257

Theoretical study of the partial molar volume change associated with the pressure-induced structural transition of ubiquitin.

PubMed

Imai, Takashi; Ohyama, Shusaku; Kovalenko, Andriy; Hirata, Fumio

2007-09-01

The partial molar volume (PMV) change associated with the pressure-induced structural transition of ubiquitin is analyzed by the three-dimensional reference interaction site model (3D-RISM) theory of molecular solvation. The theory predicts that the PMV decreases upon the structural transition, which is consistent with the experimental observation. The volume decomposition analysis demonstrates that the PMV reduction is primarily caused by the decrease in the volume of structural voids in the protein, which is partially canceled by the volume expansion due to the hydration effects. It is found from further analysis that the PMV reduction is ascribed substantially to the penetration of water molecules into a specific part of the protein. Based on the thermodynamic relation, this result implies that the water penetration causes the pressure-induced structural transition. It supports the water penetration model of pressure denaturation of proteins proposed earlier.

Magnetocaloric effect in Heusler alloys Ni50Mn34In16 and Ni50Mn34Sn16

NASA Astrophysics Data System (ADS)

Sharma, V. K.; Chattopadhyay, M. K.; Kumar, Ravi; Ganguli, Tapas; Tiwari, Pragya; Roy, S. B.

2007-12-01

We present results of detailed ac susceptibility, magnetization and specific heat measurements in Heusler alloys Ni50Mn34In16 and Ni50Mn34Sn16. These alloys undergo a paramagnetic to ferromagnetic transition around 305 K, which is followed by a martensitic transition in the temperature regime around 220 K. Inside the martensite phase both the alloys show signatures of field-induced transition from martensite to austenite phase. Both field- and temperature-induced martensite-austenite transitions are relatively sharp in Ni50Mn34In16. We estimate the isothermal magnetic entropy change and adiabatic temperature change across the various phase transitions in these alloys and investigate the possible influence of these transitions on the estimated magnetocaloric effect. The sharp martensitic transition in Ni50Mn34In16 gives rise to a comparatively large inverse magnetocaloric effect across this transition. On the other hand the magnitudes of the conventional magnetocaloric effect associated with the paramagnetic to ferromagnetic transition are quite comparable in these alloys.

Explore Stochastic Instabilities of Periodic Points by Transition Path Theory

NASA Astrophysics Data System (ADS)

Cao, Yu; Lin, Ling; Zhou, Xiang

2016-06-01

We consider the noise-induced transitions from a linearly stable periodic orbit consisting of T periodic points in randomly perturbed discrete logistic map. Traditional large deviation theory and asymptotic analysis at small noise limit cannot distinguish the quantitative difference in noise-induced stochastic instabilities among the T periodic points. To attack this problem, we generalize the transition path theory to the discrete-time continuous-space stochastic process. In our first criterion to quantify the relative instability among T periodic points, we use the distribution of the last passage location related to the transitions from the whole periodic orbit to a prescribed disjoint set. This distribution is related to individual contributions to the transition rate from each periodic points. The second criterion is based on the competency of the transition paths associated with each periodic point. Both criteria utilize the reactive probability current in the transition path theory. Our numerical results for the logistic map reveal the transition mechanism of escaping from the stable periodic orbit and identify which periodic point is more prone to lose stability so as to make successful transitions under random perturbations.

Spectroscopic Studies on Unfolding Processes of Apo-Neuroglobin Induced by Guanidine Hydrochloride and Urea

PubMed Central

Zhang, Cui; Gao, Chaohui; Qiu, Zhanglei

2013-01-01

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

Hyperfine Induced Transitions as Diagnostics of Isotopic Composition and Densities of Low-Density Plasmas

NASA Astrophysics Data System (ADS)

Brage, Tomas; Judge, Philip G.; Aboussaïd, Abdellatif; Godefroid, Michel R.; Jönsson, Per; Ynnerman, Anders; Froese Fischer, Charlotte; Leckrone, David S.

1998-06-01

The J = 0 --> J' = 0 radiative transitions, usually viewed as allowed through two-photon decay, may also be induced by the hyperfine (HPF) interaction in atoms or ions having a nonzero nuclear spin. We compute new and review existing decay rates for the nsnp 3PoJ --> ns2 1SJ'=0 transitions in ions of the Be (n = 2) and Mg (n = 3) isoelectronic sequences. The HPF induced decay rates for the J = 0 --> J' = 0 transitions are many orders of magnitude larger than those for the competing two-photon processes, and when present are typically 1 or 2 orders of magnitude smaller than the decay rates of the magnetic quadrupole (J = 2 --> J' = 0) transitions for these ions. Several HPF induced transitions are potentially of astrophysical interest in ions of C, N, Na, Mg, Al, Si, K, Cr, Fe, and Ni. We highlight those cases that may be of particular diagnostic value for determining isotopic abundance ratios and/or electron densities from UV or EUV emission-line data. We present our atomic data in the form of scaling laws so that, given the isotopic nuclear spin and magnetic moment, a simple expression yields estimates for HPF induced decay rates. We examine some UV and EUV solar and nebular data in light of these new results and suggest possible applications for future study. We could not find evidence for the existence of HPF induced lines in the spectra we examined, but we demonstrate that existing data have come close to providing interesting upper limits. For the planetary nebula SMC N2, we derive an upper limit of 0.1 for 13C/12C from Goddard High-Resolution Spectrograph data obtained by Clegg. It is likely that more stringent limits could be obtained using newer data with higher sensitivities in a variety of objects.

Metabolic reprogramming during TGFβ1-induced epithelial-to-mesenchymal transition

PubMed Central

Jiang, Lei; Xiao, Ling; Sugiura, Hidekazu; Huang, Xiumei; Ali, Aktar; Kuro-o, Makoto; Deberardinis, Ralph J.; Boothman, David A.

2014-01-01

Metastatic progression, including extravasation and micro-metastatic outgrowth, is the main cause of cancer patient death. Recent studies suggest that cancer cells reprogram their metabolism to support increased proliferation through increased glycolysis and biosynthetic activities, including lipogenesis pathways. However, metabolic changes during metastatic progression, including alterations in regulatory gene expression, remain undefined. We show that transforming growth factor beta 1 (TGFβ1) induced Epithelial-to-Mesenchymal Transition (EMT) is accompanied by coordinately reduced enzyme expression required to convert glucose into fatty acids, and concomitant enhanced respiration. Over-expressed Snail1, a transcription factor mediating TGFβ1-induced EMT, was sufficient to suppress carbohydrate-responsive-element-binding protein (ChREBP, a master lipogenic regulator), and fatty acid synthase (FASN), its effector lipogenic gene. Stable FASN knock-down was sufficient to induce EMT, stimulate migration and extravasation in vitro. FASN silencing enhanced lung metastasis and death in vivo. These data suggest that a metabolic transition that suppresses lipogenesis and favors energy production is an essential component of TGFβ1-induced EMT and metastasis. PMID:25284588

Water-induced ethanol dewetting transition.

PubMed

Ren, Xiuping; Zhou, Bo; Wang, Chunlei

2012-07-14

The dewetting transitions of two hydrophobic plates immersed in pure water, aqueous ethanol solutions with concentrations from 25% to 90%, and pure ethanol were investigated by molecular dynamics simulations, where the dewetting transition was analogous to a first-order phase transition from liquid to vapor. It was found that the dewetting transitions occurred except that in the pure ethanol system. Although the ethanol molecules prefer to locate in the vicinity of the two plates, the inter-plate region is unfavorable for water molecules, due to losing more than one hydrogen bond. Moreover, each inter-plate water molecule forms hydrogen bonds on average with about two ethanol molecules. These intermolecular hydrogen bonds cause water and ethanol to cooperatively fill or exit the inter-plate region. Thus, water molecules play a more important role in the inter-plate filling/empty process, and induce the ethanol dewetting transition. Our results provide insight into the effect of water on the ethanol dewetting phenomena.

Ultrafast photo-induced dynamics across the metal-insulator transition of VO2

NASA Astrophysics Data System (ADS)

Wang, Siming; Ramírez, Juan Gabriel; Jeffet, Jonathan; Bar-Ad, Shimshon; Huppert, Dan; Schuller, Ivan K.

2017-04-01

The transient reflectivity of VO2 films across the metal-insulator transition clearly shows that with low-fluence excitation, when insulating domains are dominant, energy transfer from the optically excited electrons to the lattice is not instantaneous, but precedes the superheating-driven expansion of the metallic domains. This implies that the phase transition in the coexistence regime is lattice-, not electronically-driven, at weak laser excitation. The superheated phonons provide the latent heat required for the propagation of the optically-induced phase transition. For VO2 this transition path is significantly different from what has been reported in the strong-excitation regime. We also observe a slow-down of the superheating-driven expansion of the metallic domains around the metal-insulator transition, which is possibly due to the competition among several co-existing phases, or an emergent critical-like behavior.

Strain-induced metal-insulator transitions in d1 perovskites within DFT+DMFT

NASA Astrophysics Data System (ADS)

Dymkowski, Krzysztof; Ederer, Claude

2014-03-01

We present results of combined density functional theory plus dynamical mean-field theory (DFT+DMFT) calculations, assessing the effect of epitaxial strain on the electronic properties of the Mott insulator LaTiO3 and the correlated metal SrVO3. In particular, we take into account the effect of strain on the collective tilts and rotations of the oxygen octahedra in the orthorhombically distorted Pbnm perovskite structure of LaTiO3. We find that LaTiO3 undergoes an insulator-to-metal transition under a compressive strain of about - 2 %, consistent with recent experimental observations. We show that this transition is driven mainly by strain-induced changes in the crystal-field splitting between the Ti t2 g orbitals, which in turn are related to changes in the octahedral tilt distortion. We compare this with the case of SrVO3, without octahedral tilts, where we find a metal-to-insulator transition under tensile epitaxial strain. Similar to LaTiO3, this metal-insulator transition is linked to the strain-induced change in the crystal-field splitting within the t2 g orbitals.

Circular dichroism of magnetically induced transitions for D2 lines of alkali atoms

NASA Astrophysics Data System (ADS)

Tonoyan, A.; Sargsyan, A.; Klinger, E.; Hakhumyan, G.; Leroy, C.; Auzinsh, M.; Papoyan, A.; Sarkisyan, D.

2018-03-01

In this letter we study magnetic circular dichroism in alkali atoms exhibiting asymmetric behaviour of magnetically induced transitions. The magnetic field \\textbf{B}\\parallel\\textbf{k} induces transitions between Δ F = +/-2 hyperfine levels of alkali atoms and in the range of ∼0.1{\\text{--}}3 \\text{kG} magnetic field, the intensities of these transitions experience significant enhancement. We have inferred a general rule applicable for the D 2 lines of all alkali atoms, that is the transition intensity enhancement is around four times larger for the case of σ+ than for σ- excitation for Δ F = +2 , whereas it is several hundreds of thousand times larger in the case of σ- than that for σ+ polarization for Δ F = -2 . This asymmetric behaviour results in circular dichroism. For experimental verification we employed half-wavelength-thick atomic vapor nanocells using a derivative of the selective reflection technique, which provides a sub-Doppler spectroscopic linewidth (∼50 \\text{MHz} ). The presented theoretical curves well describe the experimental results. This effect can find applications particularly in parity violation experiments.

Destruction of the Kondo effect in the cubic heavy-fermion compound Ce3Pd20Si6

NASA Astrophysics Data System (ADS)

Custers, J.; Lorenzer, K.-A.; Müller, M.; Prokofiev, A.; Sidorenko, A.; Winkler, H.; Strydom, A. M.; Shimura, Y.; Sakakibara, T.; Yu, R.; Si, Q.; Paschen, S.

2012-03-01

How ground states of quantum matter transform between one another reveals deep insights into the mechanisms stabilizing them. Correspondingly, quantum phase transitions are explored in numerous materials classes, with heavy-fermion compounds being among the most prominent ones. Recent studies in an anisotropic heavy-fermion compound have shown that different types of transitions are induced by variations of chemical or external pressure, raising the question of the extent to which heavy-fermion quantum criticality is universal. To make progress, it is essential to broaden both the materials basis and the microscopic parameter variety. Here, we identify a cubic heavy-fermion material as exhibiting a field-induced quantum phase transition, and show how the material can be used to explore one extreme of the dimensionality axis. The transition between two different ordered phases is accompanied by an abrupt change of Fermi surface, reminiscent of what happens across the field-induced antiferromagnetic to paramagnetic transition in the anisotropic YbRh2Si2. This finding leads to a materials-based global phase diagram—a precondition for a unified theoretical description.

Shock, release and Taylor impact of the semicrystalline thermoplastic polytetrafluoroethylene

NASA Astrophysics Data System (ADS)

Bourne, N. K.; Brown, E. N.; Millett, J. C. F.; Gray, G. T.

2008-04-01

The high strain-rate response of polymers is a subject that has gathered interest over recent years due to their increasing engineering importance, particularly in load bearing applications subject to extremes of pressure and strain rate. The current work presents two specific sets of experiments interrogating the effect of dynamic, high-pressure loading in the regime of the phase II to phase III pressure-induced crystalline phase transition in polytetrafluoroethylene (PTFE). These are gas-gun driven plate- and Taylor impact. Together these experiments highlight several effects associated with the dynamic, pressure-induced phase transitions in PTFE. An elevated release wave speed shows evidence of a pressure-induced phase change at a stress commensurate with that observed statically. It is shown that convergence between analytic derivations of release wave speed and the data requires the phase II to III transition to occur. Taylor impact is an integrated test that highlights continuum behavior that has origin in mesoscale response. There is a rapid transition from ductile to brittle behavior observed that occurs at a pressure consistent with this phase transition.

High-Speed Boundary-Layer Transition Induced by an Isolated Roughness Element

NASA Technical Reports Server (NTRS)

Kegerise, Michael A.; Owens, Lewis R.; King, Rudolph A.

2010-01-01

Progress on an experimental effort to quantify the instability mechanisms associated with roughness-induced transition in a high-speed boundary layer is reported in this paper. To simulate the low-disturbance environment encountered during high-altitude flight, the experimental study was performed in the NASA-Langley Mach 3.5 Supersonic Low-Disturbance Tunnel. A flat plate trip sizing study was performed first to identify the roughness height required to force transition. That study, which included transition onset measurements under both quiet and noisy freestream conditions, confirmed the sensitivity of roughness-induced transition to freestream disturbance levels. Surveys of the laminar boundary layer on a 7deg half-angle sharp-tipped cone were performed via hot-wire anemometry and pitot-pressure measurements. The measured mean mass-flux and Mach-number profiles agreed very well with computed mean-flow profiles. Finally, surveys of the boundary layer developing downstream of an isolated roughness element on the cone were performed. The measurements revealed an instability in the far wake of the roughness element that grows exponentially and has peak frequencies in the 150 to 250 kHz range.

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.

Radio frequency-assisted fast superconducting switch

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

Solovyov, Vyacheslav; Li, Qiang

A radio frequency-assisted fast superconducting switch is described. A superconductor is closely coupled to a radio frequency (RF) coil. To turn the switch "off," i.e., to induce a transition to the normal, resistive state in the superconductor, a voltage burst is applied to the RF coil. This voltage burst is sufficient to induce a current in the coupled superconductor. The combination of the induced current with any other direct current flowing through the superconductor is sufficient to exceed the critical current of the superconductor at the operating temperature, inducing a transition to the normal, resistive state. A by-pass MOSFET maymore » be configured in parallel with the superconductor to act as a current shunt, allowing the voltage across the superconductor to drop below a certain value, at which time the superconductor undergoes a transition to the superconducting state and the switch is reset.« less

Photo-induced Low Temperature Structural Transition in the "114" YbaFe 4O 7 oxide

DOE PAGES

Duffort, V.; Caignaert, Vincent; Pralong, V.; ...

2013-11-11

Synchrotron irradiation of the oxide YBaFe 4O 7.0 below 190 K converts the low temperature monoclinic structure to a higher symmetry tetragonal form analogous to the room temperature structure. This photo-induced metastable tetragonal form is stable even in the absence of irradiation over the range 4-60 K, however, above 60 K the photo-transition is reversible. These structural phenomena are correlated to the magnetic behaviour of this system, suggesting possible spin-lattice coupling. Lastly, a scenario explaining the low temperature photo-induced transition is proposed, based on the different distributions of the valence electrons in the iron sub-lattice of the monoclinic and tetragonalmore » phases.« less

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.

Xanthine crystals induced by topiroxostat, a xanthine oxidoreductase inhibitor, in rats, cause transitional cell tumors.

PubMed

Shimo, Takeo; Moto, Mitsuyoshi; Ashizawa, Naoki; Matsumoto, Koji; Iwanaga, Takashi; Saito, Kazuhiro

2014-04-01

The present study was performed to elucidate the underlying mechanism of transitional cell tumors found in the carcinogenicity testing of topiroxostat, a xanthine oxidoreductase inhibitor, in which topiroxostat was orally given to F344 rats at 0.3, 1, and 3 mg/kg for 2 years. In the urinary bladder, transitional cell papillomas and/or carcinomas were seen in males receiving 0.3, 1, and 3 mg/kg (1/49, 3/49, and 10/50, respectively). In the kidney, transitional cell papillomas and/or carcinomas in the pelvis were seen in 2/50 males and 1/50 females receiving 3 mg/kg. In the mechanistic study by 52-week oral treatment with topiroxostat at 3 mg/kg to F344 male rats, with and without citrate, simple and papillary transitional cell hyperplasias of the urinary bladder epithelium were observed in 5/17 in the topiroxostat-alone treatment group, along with xanthine-induced nephropathy, in contrast to neither xanthine crystals nor lesions in urinary organs by co-treatment group with citrate. As for sex differences of urinary bladder tumors, the BrdU labeling index for epithelial cells of the urinary bladder by 5-week oral treatment with topiroxostat at 10 mg/kg to F344 rats was increased in males only, showing consistency with histopathological findings. Therefore, the present study indicates that transitional cell tumors induced by topiroxostat in rats were due to physical stimulation to transitional cells of xanthine crystals/calculi and provides that other factors were not implicated in this tumorigenesis. Furthermore, the present study suggests that such tumors do not predict for humans since topiroxostat-induced xanthine deposition is a rodent-specific event.

Mode transition induced by the magnetic field gradient in Hall thrusters

NASA Astrophysics Data System (ADS)

Han, Liang; Wei, Liqiu; Yu, Daren

2016-09-01

A mode transition phenomenon was found in Hall thrusters, which was induced by the increase of the magnetic field gradient. In the transition process, we observed experimentally that there have been obvious changes in the oscillation, the mean value of the discharge current, the thrust, the anode efficiency, and the plume pattern. The shifting and compression of the high magnetic field causes the electron density in the discharge channel to decrease and the ionization zone to move towards the exit plane. This also corresponds to a low atom density in the discharge channel, resulting in a loss of stability of the ionization at a high magnetic field gradient, which presents the transition of the discharge mode.

External noise-induced transitions in a current-biased Josephson junction

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

Huang, Qiongwei; Xue, Changfeng, E-mail: cfxue@163.com; Tang, Jiashi

We investigate noise-induced transitions in a current-biased and weakly damped Josephson junction in the presence of multiplicative noise. By using the stochastic averaging procedure, the averaged amplitude equation describing dynamic evolution near a constant phase difference is derived. Numerical results show that a stochastic Hopf bifurcation between an absorbing and an oscillatory state occurs. This means the external controllable noise triggers a transition into the non-zero junction voltage state. With the increase of noise intensity, the stationary probability distribution peak shifts and is characterised by increased width and reduced height. And the different transition rates are shown for large andmore » small bias currents.« less

Coherently coupled ZnO and VO2 interface studied by photoluminescence and electrical transport across a phase transition

NASA Astrophysics Data System (ADS)

Srivastava, Amar; Herng, T. S.; Saha, Surajit; Nina, Bao; Annadi, A.; Naomi, N.; Liu, Z. Q.; Dhar, S.; Ariando; Ding, J.; Venkatesan, T.

2012-06-01

We have investigated the photoluminescence and electrical properties of a coherently coupled interface consisting of a ZnO layer grown on top of an oriented VO2 layer on sapphire across the phase transition of VO2. The band edge and defect luminescence of the ZnO overlayer exhibit hysteresis in opposite directions induced by the phase transition of VO2. Concomitantly the phase transition of VO2 was seen to induce defects in the ZnO layer. Such coherently coupled interfaces could be of use in characterizing the stability of a variety of interfaces in situ and also for novel device application.

Experiments on Hypersonic Roughness Induced Transition by Means of Infrared Thermography

NASA Astrophysics Data System (ADS)

Schrijer, F. F. J.; Scarano, F.; van Oudheusden, B. W.; Bannink, W. J.

2005-02-01

Roughness induced boundary layer transition is experimentally investigated in the hypersonic flow regime at M = 9. The primary interest is the possible effect of stepwise geometry imperfections (2D isolated roughness) on (boundary layer) transition which may be caused on the EXPERT vehicle by the difference in thermal expansion due to the different materials used in the vehicle-nose construction. Also 3D isolated and 3D distributed roughness configurations were studied. Quantitative Infra-Red Thermography (QIRT) is used as primary diagnostic technique to measure the surface convective heat transfer and to detect boundary layer laminar-to-turbulent transition. The investigation shows that for a given height of the roughness element, the boundary layer is least sensitive to a step-like disturbance, whereas distributed 3D roughness was found to be effective in triggering transition. The experimental results have been compared to existing hypersonic transition correlations (PANT and Shuttle). Finally a transition criterion is evaluated which is based on the critical roughness height Reynolds number. Usage of this criterion enables a straightforward extrapolation to flight. Key words: hypersonic flow, boundary layer transition.

Fatigue crack closure: a review of the physical phenomena

PubMed Central

Pippan, R.

2017-01-01

Abstract Plasticity‐induced, roughness‐induced and oxide‐induced crack closures are reviewed. Special attention is devoted to the physical origin, the consequences for the experimental determination and the prediction of the effective crack driving force for fatigue crack propagation. Plasticity‐induced crack closure under plane stress and plane strain conditions require, in principle, a different explanation; however, both types are predictable. This is even the case in the transition region from the plane strain to the plane stress state and all types of loading conditions including constant and variable amplitude loading, the short crack case or the transition from small‐scale to large‐scale yielding. In contrast, the prediction of roughness‐induced and oxide‐induced closures is not as straightforward. PMID:28616624

Dynamic Conformational Changes in MUNC18 Prevent Syntaxin Binding

PubMed Central

Bar-On, Dana; Nachliel, Esther; Gutman, Menachem; Ashery, Uri

2011-01-01

The Sec1/munc18 protein family is essential for vesicle fusion in eukaryotic cells via binding to SNARE proteins. Protein kinase C modulates these interactions by phosphorylating munc18a thereby reducing its affinity to one of the central SNARE members, syntaxin-1a. The established hypothesis is that the reduced affinity of the phosphorylated munc18a to syntaxin-1a is a result of local electrostatic repulsion between the two proteins, which interferes with their compatibility. The current study challenges this paradigm and offers a novel mechanistic explanation by revealing a syntaxin-non-binding conformation of munc18a that is induced by the phosphomimetic mutations. In the present study, using molecular dynamics simulations, we explored the dynamics of the wild-type munc18a versus phosphomimetic mutant munc18a. We focused on the structural changes that occur in the cavity between domains 3a and 1, which serves as the main syntaxin-binding site. The results of the simulations suggest that the free wild-type munc18a exhibits a dynamic equilibrium between several conformations differing in the size of its cavity (the main syntaxin-binding site). The flexibility of the cavity's size might facilitate the binding or unbinding of syntaxin. In silico insertion of phosphomimetic mutations into the munc18a structure induces the formation of a conformation where the syntaxin-binding area is rigid and blocked as a result of interactions between residues located on both sides of the cavity. Therefore, we suggest that the reduced affinity of the phosphomimetic mutant/phosphorylated munc18a is a result of the closed-cavity conformation, which makes syntaxin binding energetically and sterically unfavorable. The current study demonstrates the potential of phosphoryalation, an essential biological process, to serve as a driving force for dramatic conformational changes of proteins modulating their affinity to target proteins. PMID:21390273

Mesoscopic Metal-Insulator Transition at Ferroelastic Domain Walls in VO2

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

Jones, Keith M; Kalinin, Sergei V; Kolmakov, Andrei

2010-01-01

The novel phenomena induced by symmetry breaking at homointerfaces between ferroic variants in ferroelectric and ferroelastic materials have attracted recently much attention. Using variable temperature scanning microwave microscopy, we demonstrate the mesoscopic strain-induced metal-insulator phase transitions in the vicinity of ferroelastic domain walls in the semiconductive VO2 that nucleated at temperatures as much as 10-12 C below bulk transition, resulting in the formation of conductive channels in the material. Density functional theory is used to rationalize the process low activation energy. This behavior, linked to the strain inhomogeneity inherent in ferroelastic materials, can strongly affect interpretation of phase-transition studies inmore » VO2 and similar materials with symmetry-lowering transitions, and can also be used to enable new generations of electronic devices though strain engineering of conductive and semiconductive regions.« less

Evidence for a pressure-induced spin transition in olivine-type LiFePO4 triphylite

NASA Astrophysics Data System (ADS)

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

2018-05-01

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

A permeability transition in liver mitochondria and liposomes induced by α,ω-dioic acids and Ca(2+).

PubMed

Dubinin, Mikhail V; Samartsev, Victor N; Astashev, Maxim E; Kazakov, Alexey S; Belosludtsev, Konstantin N

2014-11-01

The article examines the molecular mechanism of the Ca(2+)-dependent cyclosporin A (CsA)-insensitive permeability transition in rat liver mitochondria induced by α,ω-dioic acids. The addition of α,ω-hexadecanedioic acid (HDA) to Ca(2+)-loaded liver mitochondria was shown to induce a high-amplitude swelling of the organelles, a drop of membrane potential and the release of Ca(2+) from the matrix, the effects being insensitive to CsA. The experiments with liposomes loaded with sulforhodamine B (SRB) revealed that, like palmitic acid (PA), HDA was able to cause permeabilization of liposomal membranes. However, the kinetics of HDA- and PA-induced release of SRB from liposomes was different, and HDA was less effective than PA in the induction of SRB release. Using the method of ultrasound interferometry, we also showed that the addition of Ca(2+) to HDA-containing liposomes did not change the phase state of liposomal membranes-in contrast to what was observed when Ca(2+) was added to PA-containing vesicles. It was suggested that HDA/Ca(2+)- and PA/Ca(2+)-induced permeability transition occurs by different mechanisms. Using the method of dynamic light scattering, we further revealed that the addition of Ca(2+) to HDA-containing liposomes induced their aggregation/fusion. Apparently, these processes result in a partial release of SRB due to the formation of fusion pores. The possibility that this mechanism underlies the HDA/Ca(2+)-induced permeability transition of the mitochondrial membrane is discussed.

Asbestos-Induced Mesothelial to Fibroblastic Transition Is Modulated by the Inflammasome.

PubMed

Thompson, Joyce K; MacPherson, Maximilian B; Beuschel, Stacie L; Shukla, Arti

2017-03-01

Despite the causal relationship established between malignant mesothelioma (MM) and asbestos exposure, the exact mechanism by which asbestos induces this neoplasm and other asbestos-related diseases is still not well understood. MM is characterized by chronic inflammation, which is believed to play an intrinsic role in the origin of this disease. We recently found that asbestos activates the nod-like receptor family member containing a pyrin domain 3 (NLRP3) inflammasome in a protracted manner, leading to an up-regulation of IL-1β and IL-18 production in human mesothelial cells. Combined with biopersistence of asbestos fibers, we hypothesize that this creates an environment of chronic IL-1β signaling in human mesothelial cells, which may promote mesothelial to fibroblastic transition (MFT) in an NLRP3-dependent manner. Using a series of experiments, we found that asbestos induces a fibroblastic transition of mesothelial cells with a gain of mesenchymal markers (vimentin and N-cadherin), whereas epithelial markers, such as E-cadherin, are down-regulated. Use of siRNA against NLRP3, recombinant IL-1β, and IL-1 receptor antagonist confirmed the role of NLRP3 inflammasome-dependent IL-1β in the process. In vivo studies using wild-type and various inflammasome component knockout mice also revealed the process of asbestos-induced mesothelial to fibroblastic transition and its amelioration in caspase-1 knockout mice. Taken together, our data are the first to suggest that asbestos induces mesothelial to fibroblastic transition in an inflammasome-dependent manner. Copyright © 2017 American Society for Investigative Pathology. Published by Elsevier Inc. All rights reserved.

Cannabis-induced attenuated psychotic symptoms: implications for prognosis in young people at ultra-high risk for psychosis.

PubMed

McHugh, M J; McGorry, P D; Yung, A R; Lin, A; Wood, S J; Hartmann, J A; Nelson, B

2017-03-01

Cannabis use shows a robust dose-dependent relationship with psychosis risk among the general population. Despite this, it has been difficult to link cannabis use with risk for transitioning to a psychotic disorder among individuals at ultra-high risk (UHR) for psychosis. The present study examined UHR transition risk as a function of cannabis use characteristics which vary substantially between individuals including age of first use, cannabis abuse severity and a history of cannabis-induced attenuated psychotic symptoms (APS). Participants were 190 UHR individuals (76 males) recruited at entry to treatment between 2000 and 2006. They completed a comprehensive baseline assessment including a survey of cannabis use characteristics during the period of heaviest use. Outcome was transition to a psychotic disorder, with mean time to follow-up of 5.0 years (range 2.4-8.7 years). A history of cannabis abuse was reported in 58% of the sample. Of these, 26% reported a history of cannabis-induced APS. These individuals were 4.90 (95% confidence interval 1.93-12.44) times more likely to transition to a psychotic disorder (p = 0.001). Greater severity of cannabis abuse also predicted transition to psychosis (p = 0.036). However, this effect was mediated by higher abuse severity among individuals with a history of cannabis-induced APS. Findings suggest that cannabis use poses risk in a subpopulation of UHR individuals who manifest cannabis-induced APS. Whether this reflects underlying genetic vulnerability requires further study. Nevertheless, findings reveal an important early marker of risk with potentially significant prognostic utility for UHR individuals.

Experimental investigations on characteristics of boundary layer and control of transition on an airfoil by AC-DBD

NASA Astrophysics Data System (ADS)

Geng, Xi; Shi, Zhiwei; Cheng, Keming; Dong, Hao; Zhao, Qun; Chen, Sinuo

2018-03-01

Plasma-based flow control is one of the most promising techniques for aerodynamic problems, such as delaying the boundary layer transition. The boundary layer’s characteristics induced by AC-DBD plasma actuators and applied by the actuators to delay the boundary layer transition on airfoil at Ma = 0.3 were experimentally investigated. The PIV measurement was used to study the boundary layer’s characteristics induced by the plasma actuators. The measurement plane, which was parallel to the surface of the actuators and 1 mm above the surface, was involved in the test, including the perpendicular plane. The instantaneous results showed that the induced flow field consisted of many small size unsteady vortices which were eliminated by the time average. The subsequent oil-film interferometry skin friction measurement was conducted on a NASA SC(2)-0712 airfoil at Ma = 0.3. The coefficient of skin friction demonstrates that the plasma actuators successfully delay the boundary layer transition and the efficiency is better at higher driven voltage.

Direct Observation on Spin-Coating Process of PS- b -P2VP Thin Films

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

Ogawa, Hiroki; Takenaka, Mikihito; Miyazaki, Tsukasa

We studied the structural development of symmetric poly(styrene-b-2-vinylpyridine) (PS-b-P2VP) block copolymers during spin-coating using in situ grazing incidence small angle X-ray scattering (GISAXS) measurements. During the spin-coating process, after the formation of the micelles in dilute solution, the selective solvent induced two kinds of the morphological transition. Firstly, the disordered spherical micelles were transformed into a BCC lattice of spheres of which the (110) plane was oriented perpendicularly to the substrate surface. Secondly, further evaporation induced a transition from spheres on the BCC lattice into cylindrical structures. The orientation of the cylinders perpendicular to the substrate surface was induced bymore » solvent convection perpendicular to the substrate, which occurs during rapid solvent evaporation. After this transition, vitrification of PS and P2VP prevented any further transition from cylinders to the more thermodynamically stable lamellar structures, as are generally observed as the bulk equilibrium state.« less

TRPM1: the endpoint of the mGluR6 signal transduction cascade in retinal ON-bipolar cells.

PubMed

Morgans, Catherine W; Brown, Ronald Lane; Duvoisin, Robert M

2010-07-01

For almost 30 years the ion channel that initiates the ON visual pathway in vertebrate vision has remained elusive. Recent findings now indicate that the pathway, which begins with unbinding of glutamate from the metabotropic glutamate receptor 6 (mGluR6), ends with the opening of the transient receptor potential (TRP)M1 cation channel. As a component of the mGluR6 signal transduction pathway, mutations in TRPM1 would be expected to cause congenital stationary night blindness (CSNB), and several such mutations have already been identified in CSNB families. Furthermore, expression of TRPM1 in both the retina and skin raises the possibility that a genetic link exists between certain types of visual and skin disorders.

Modelling and enhanced molecular dynamics to steer structure-based drug discovery.

PubMed

Kalyaanamoorthy, Subha; Chen, Yi-Ping Phoebe

2014-05-01

The ever-increasing gap between the availabilities of the genome sequences and the crystal structures of proteins remains one of the significant challenges to the modern drug discovery efforts. The knowledge of structure-dynamics-functionalities of proteins is important in order to understand several key aspects of structure-based drug discovery, such as drug-protein interactions, drug binding and unbinding mechanisms and protein-protein interactions. This review presents a brief overview on the different state of the art computational approaches that are applied for protein structure modelling and molecular dynamics simulations of biological systems. We give an essence of how different enhanced sampling molecular dynamics approaches, together with regular molecular dynamics methods, assist in steering the structure based drug discovery processes. Copyright © 2013 Elsevier Ltd. All rights reserved.

Transition scenario and transition control of the flow over a semi-infinite square leading-edge plate

NASA Astrophysics Data System (ADS)

Huang, Yadong; Zhou, Benmou; Tang, Zhaolie; Zhang, Fei

2017-07-01

In recent investigations of the flow over a square leading-edge flat plate, elliptic instability and transient growth of perturbations are proposed to explain the turbulent transition mechanism of the separating and reattaching flow reported in early experimental visualizations. An original transition scenario as well as a transition control method is presented by a detailed numerical study in this paper. The transient growth of perturbations in the separation bubble induces the primary instability that causes the 2D unsteady flow consisting of Kelvin-Helmholtz (KH) vortices. The pairing instability of the KH vortices induces the subharmonic secondary instability, and then resonance transition occurs. The streamwise Lorentz force as the control input is applied in the recirculation region where the separation bubble generates. The maximum energy amplification magnitude of perturbations takes a linear attenuation with the interaction number; thus, the primary instability is reduced under control. The interaction number represents the strength of the streamwise Lorentz force relative to the inertial force of the fluid. The reduced primary instability is not strong enough to induce the secondary instability, so the flow is globally stable under control. Three-dimensional direct numerical simulation confirms the results of the linear stability analysis. Although the growth rate of the convectively unstable secondary instability is limited by the flow field scale, the feedback loop of the energy transfer promotes the resonance transition. However, as the separation bubble scale is reduced and the feedback loop is broken by the streamwise Lorentz force, the three-dimensional transition is suppressed and a skin-friction drag reduction is achieved.

Boundary-layer development and transition due to free-stream exothermic reactions in shock-induced flows

NASA Technical Reports Server (NTRS)

Hall, J. L.

1974-01-01

A study of the effect of free-stream thermal-energy release from shock-induced exothermic reactions on boundary-layer development and transition is presented. The flow model is that of a boundary layer developing behind a moving shock wave in two-dimensional unsteady flow over a shock-tube wall. Matched sets of combustible hydrogen-oxygen-nitrogen mixtures and inert hydrogen-nitrogen mixtures were used to obtain transition data over a range of transition Reynolds numbers from 1,100,000 to 21,300,000. The heat-energy is shown to significantly stabilize the boundary layer without changing its development character. A method for application of this data to flat-plate steady flows is included.

Error catastrophe and phase transition in the empirical fitness landscape of HIV

NASA Astrophysics Data System (ADS)

Hart, Gregory R.; Ferguson, Andrew L.

2015-03-01

We have translated clinical sequence databases of the p6 HIV protein into an empirical fitness landscape quantifying viral replicative capacity as a function of the amino acid sequence. We show that the viral population resides close to a phase transition in sequence space corresponding to an "error catastrophe" beyond which there is lethal accumulation of mutations. Our model predicts that the phase transition may be induced by drug therapies that elevate the mutation rate, or by forcing mutations at particular amino acids. Applying immune pressure to any combination of killer T-cell targets cannot induce the transition, providing a rationale for why the viral protein can exist close to the error catastrophe without sustaining fatal fitness penalties due to adaptive immunity.

Quantum mechanical/molecular mechanical/continuum style solvation model: time-dependent density functional theory.

PubMed

Thellamurege, Nandun M; Cui, Fengchao; Li, Hui

2013-08-28

A combined quantum mechanical/molecular mechanical/continuum (QM/MMpol/C) style method is developed for time-dependent density functional theory (TDDFT, including long-range corrected TDDFT) method, induced dipole polarizable force field, and induced surface charge continuum model. Induced dipoles and induced charges are included in the TDDFT equations to solve for the transition energies, relaxed density, and transition density. Analytic gradient is derived and implemented for geometry optimization and molecular dynamics simulation. QM/MMpol/C style DFT and TDDFT methods are used to study the hydrogen bonding of the photoactive yellow protein chromopore in ground state and excited state.

Field induced metastable ferroelectric phase in Pb 0.97La 0.03(Zr 0.90Ti 0.10) 0.9925O 3 ceramics

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

Ciuchi, I. V.; Chung, C. C.; Fancher, C. M.

2017-11-06

Pb 0.97La 0.03(Zr 0.9T i0.1)0.9925O3 (PLZT 3/90/10) ceramics prepared by solid-state reaction with the compositions near the antiferroelectric/ferroelectric (FE/AFE) phase boundary were studied. From the polarization–electric field P(E) dependence and ex situ X-ray study, an irreversible electric field induced AFE-to-FE phase transition is verified at room temperature. Dielectric and in situ temperature dependent X-ray analysis evidence that the phase transition sequence in PLZT 3/90/10-based ceramics can be readily altered by poling. A first order antiferroelectric-paraelectric (AFE-to-PE) transition occurred at ~190 °C in virgin sample and at ~180 °C in poled sample. In addition, a FE-to-AFE transition occurs in the poledmore » ceramic at much lower temperatures (~120 °C) with respect to the Curie range (~190 °C). The temperature-induced FE-to-AFE transition is diffuse and takes place in a broad temperature range of 72–135 °C. Lastly, the recovery of AFE is accompanied by an enhancement in the piezoelectric properties.« less

P-chlorophenoxyisobutyric acid impairs auxin response for gravity-regulated peg formation in cucumber (Cucumis sativus) seedlings.

PubMed

Shimizu, Minobu; Miyazawa, Yutaka; Fujii, Nobuharu; Takahashi, Hideyuki

2008-01-01

Cucumber (Cucumis sativus L.) seedlings form a specialized protuberance, the peg, on the transition zone between the hypocotyl and the root. When cucumber seeds germinate in a horizontal position, the seedlings develop a peg on the lower side of the transition zone. To verify the role of auxin action in peg formation, we examined the effect of the anti-auxin, p-chlorophenoxyisobutyric acid (PCIB), on peg formation and mRNA accumulation of auxin-regulated genes. Application of PCIB to cucumber seedlings inhibited peg formation. The application of indole-3-acetic acid (IAA) competed with PCIB and induced peg formation. Furthermore, application of PCIB decreased auxin-inducible CsIAA1 mRNA and increased auxin-repressible CsGRP1 mRNA in the lower side of the transition zone. The differential accumulation of CsIAA1 and CsGRP1 mRNAs in the transition zone of cucumber seedlings grown in a horizontal position was smaller in the PCIB-treated seedlings. These results demonstrate that endogenous auxin redistributes and induces the differential expression of auxin-regulated genes, and ultimately results in the suppression or induction of peg formation in the gravistimulated transition zone of cucumber seedlings.

Polarization-induced interference within electromagnetically induced transparency for atoms of double-V linkage

NASA Astrophysics Data System (ADS)

Sun, Yuan; Liu, Chang; Chen, Ping-Xing; Liu, Liang

2018-02-01

People have been paying attention to the role of atoms' complex internal level structures in the research of electromagnetically induced transparency (EIT) for a long time, where the various degenerate Zeeman levels usually generate complex linkage patterns for the atomic transitions. It turns out, with special choices of the atomic states and the atomic transitions' linkage structure, clear signatures of quantum interference induced by the probe and coupling light's polarizations can emerge from a typical EIT phenomena. We propose to study a four-state system with double-V linkage pattern for the transitions and analyze the polarization-induced interference under the EIT condition. We show that such interference arises naturally under mild conditions on the optical field and atom manipulation techniques. Moreover, we construct a variation form of double-M linkage pattern where the polarization-induced interference enables polarization-dependent cross modulation between incident weak lights that can be effective even at the few-photon level. The theme is to gain more insight into the essential question: how can we build a nontrivial optical medium where incident lights experience polarization-dependent nonlinear optical interactions, valid for a wide range of incidence intensities down to the few-photon level?

Importance of correlation effects in hcp iron revealed by a pressure-induced electronic topological transition.

PubMed

Glazyrin, K; Pourovskii, L V; Dubrovinsky, L; Narygina, O; McCammon, C; Hewener, B; Schünemann, V; Wolny, J; Muffler, K; Chumakov, A I; Crichton, W; Hanfland, M; Prakapenka, V B; Tasnádi, F; Ekholm, M; Aichhorn, M; Vildosola, V; Ruban, A V; Katsnelson, M I; Abrikosov, I A

2013-03-15

We discover that hcp phases of Fe and Fe(0.9)Ni(0.1) undergo an electronic topological transition at pressures of about 40 GPa. This topological change of the Fermi surface manifests itself through anomalous behavior of the Debye sound velocity, c/a lattice parameter ratio, and Mössbauer center shift observed in our experiments. First-principles simulations within the dynamic mean field approach demonstrate that the transition is induced by many-electron effects. It is absent in one-electron calculations and represents a clear signature of correlation effects in hcp Fe.

Reversible Hydrophobic to Hydrophilic Transition in Graphene via Water Splitting Induced by UV Irradiation

PubMed Central

Xu, Zhemi; Ao, Zhimin; Chu, Dewei; Younis, Adnan; Li, Chang Ming; Li, Sean

2014-01-01

Although the reversible wettability transition between hydrophobic and hydrophilic graphene under ultraviolet (UV) irradiation has been observed, the mechanism for this phenomenon remains unclear. In this work, experimental and theoretical investigations demonstrate that the H2O molecules are split into hydrogen and hydroxyl radicals, which are then captured by the graphene surface through chemical binding in an ambient environment under UV irradiation. The dissociative adsorption of H2O molecules induces the wettability transition in graphene from hydrophobic to hydrophilic. Our discovery may hold promise for the potential application of graphene in water splitting. PMID:25245110

Role of Reynolds Stress-Induced Poloidal Flow in Triggering the Transition to Improved Ohmic Confinement on the HT-6M Tokamak

NASA Astrophysics Data System (ADS)

Xu, Y. H.; Yu, C. X.; Luo, J. R.; Mao, J. S.; Liu, B. H.; Li, J. G.; Wan, B. N.; Wan, Y. X.

2000-04-01

Time and space resolved measurements of electrostatic Reynolds stress, radial electric field Er, and plasma rotations have been performed across the transition to improved Ohmic confinement in the Hefei Tokamak-6M (HT-6M). The first experimental evidence of the correlation between the enhanced Reynolds stress gradient and the poloidal flow acceleration in the edge plasma is presented. The results indicate that the turbulence-induced Reynolds stress might be the dominant mechanism to create the sheared poloidal flow and Er, which may further trigger the transition.

Role of reynolds stress-induced poloidal flow in triggering the transition to improved ohmic confinement on the HT-6M tokamak

PubMed

Xu; Yu; Luo; Mao; Liu; Li; Wan; Wan

2000-04-24

Time and space resolved measurements of electrostatic Reynolds stress, radial electric field E(r), and plasma rotations have been performed across the transition to improved Ohmic confinement in the Hefei Tokamak-6M (HT-6M). The first experimental evidence of the correlation between the enhanced Reynolds stress gradient and the poloidal flow acceleration in the edge plasma is presented. The results indicate that the turbulence-induced Reynolds stress might be the dominant mechanism to create the sheared poloidal flow and E(r), which may further trigger the transition.

Forward-facing steps induced transition in a subsonic boundary layer

NASA Astrophysics Data System (ADS)

Zh, Hui; Fu, Song

2017-10-01

A forward-facing step (FFS) immersed in a subsonic boundary layer is studied through a high-order flux reconstruction (FR) method to highlight the flow transition induced by the step. The step height is a third of the local boundary-layer thickness. The Reynolds number based on the step height is 720. Inlet disturbances are introduced giving rise to streamwise vortices upstream of the step. It is observed that these small-scale streamwise structures interact with the step and hairpin vortices are quickly developed after the step leading to flow transition in the boundary layer.

Heparin Induced Thrombocytopenia and Re-Thrombosis Associated with Warfarin and Fondaparinux in a Child

PubMed Central

Maurer, Scott H.; Wilimas, Judith A.; Wang, Winfred C.; Reiss, Ulrike M.

2016-01-01

An 11 year-old female developed heparin induced thrombocytopenia (HIT) with thrombosis during therapy for lower extremity deep vein thrombosis and pulmonary embolism. Transition from bivalirudin, a direct thrombin inhibitor (DTI), to warfarin resulted in extensive re-thrombosis, and fondaparinux therapy similarly failed. She was then treated with argatroban, and transitioned successfully to warfarin after nine weeks. The risk of re-thrombosis was ultimately reduced by allowing time for the thrombogenic potential to abate. The argatroban/warfarin transition was monitored with chromogenic factor X levels. This case highlights several difficult problems in pediatric thrombosis. PMID:19415734

The Influence of the Aspheric Profiles for Transition Zone on Optical Performance of Human Eye After Conventional Ablation

NASA Astrophysics Data System (ADS)

Fang, L.

2014-12-01

The analysis in the impact of transition zone on the optical performance of human eye after laser refractive surgery is important for improving visual correction technology. By designing the ablation profiles of aspheric transition zone and creating the ablation profile for conventional refractive surgery in optical zone, the influence of aspheric transition zone on residual aberrations was studied. The results indicated that the ablation profiles of transition zone had a significant influence on the residual wavefront aberrations. For a hyperopia correction, the profile #9 shows a larger induced coma and spherical aberration when the translation of the centre of pupil remains constant. However, for a myopia astigmatism correction, the induced coma and spherical aberration in profile #1 shows relatively larger RMS values than those in other profiles. Therefore, the residual higher order aberrations may be decreased by optimizing ablation profiles of transition zone, but they cannot be eliminated. In order to achieve the best visual performance, the design of ablation pattern of transition zone played a crucial role.

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

Kim, Jae Wook; Artyukhin, Sergei; Mun, Eun Deok

In this paper, we report the discovery of a metamagnetic phase transition in a polar antiferromagnet Ni 3TeO 6 that occurs at 52 T. The new phase transition accompanies a colossal magnetoelectric effect, with a magnetic-field-induced polarization change of 0.3 μC/cm 2, a value that is 4 times larger than for the spin-flop transition at 9 T in the same material, and also comparable to the largest magnetically induced polarization changes observed to date. Via density-functional calculations we construct a full microscopic model that describes the data. We model the spin structures in all fields and clarify the physics behindmore » the 52 T transition. The high-field transition involves a competition between multiple different exchange interactions which drives the polarization change through the exchange-striction mechanism. Finally, the resultant spin structure is rather counterintuitive and complex, thus providing new insights on design principles for materials with strong magnetoelectric coupling.« less

An intermittency model for predicting roughness induced transition

NASA Astrophysics Data System (ADS)

Ge, Xuan; Durbin, Paul

2014-11-01

An extended model for roughness-induced transition is proposed based on an intermittency transport equation for RANS modeling formulated in local variables. To predict roughness effects in the fully turbulent boundary layer, published boundary conditions for k and ω are used, which depend on the equivalent sand grain roughness height, and account for the effective displacement of wall distance origin. Similarly in our approach, wall distance in the transition model for smooth surfaces is modified by an effective origin, which depends on roughness. Flat plate test cases are computed to show that the proposed model is able to predict the transition onset in agreement with a data correlation of transition location versus roughness height, Reynolds number, and inlet turbulence intensity. Experimental data for a turbine cascade are compared with the predicted results to validate the applicability of the proposed model. Supported by NSF Award Number 1228195.

Waves on radial film flows

NASA Astrophysics Data System (ADS)

Cholemari, Murali R.; Arakeri, Jaywant H.

2005-08-01

We study the stability of surface waves on the radial film flow created by a vertical cylindrical water jet striking a horizontal plate. In such flows, surface waves have been found to be unstable and can cause transition to turbulence. This surface-wave-induced transition is different from the well-known Tollmien-Schlichting wave-induced transition. The present study aims at understanding the instability and the transition process. We do a temporal stability analysis by assuming the flow to be locally two-dimensional but including spatial variations to first order in the basic flow. The waves are found to be dispersive, mostly unstable, and faster than the mean flow. Spatial variation is the major destabilizing factor. Experiments are done to test the results of the linear stability analysis and to document the wave breakup and transition. Comparison between theory and experiments is fairly good and indicates the adequacy of the model.

Possible observation of the Berezinskii-Kosterlitz-Thouless transition in boron-doped diamond films

NASA Astrophysics Data System (ADS)

Coleman, Christopher; Bhattacharyya, Somnath

2017-11-01

The occurrence of the Berezinskii-Kosterlitz-Thouless (BKT) transition is investigated in heavily boron-doped nanocrystalline diamond films through a combination of current-voltage and resistance measurements. We observe transport features suggesting a robust BKT transition along with transport features related to vortex pinning in nanocrystalline diamond films with smaller grain size. The vortex core energy determined through analysis of the resistance temperature curves was found to be anti-correlated to the BKT transition temperatures. It is also observed that the higher BKT temperature is related to an increased vortex-antivortex binding energy derived from the activated transport regions. Further, the magnetic field induced superconductor insulator transition shows the possibility of the charge glass state. The consequences of granularity such as localization and vortex pinning can lead to tuneable BKT temperatures and strongly affects the field induced insulating state.

An investigation of nonsimultaneous laser-induced fluorescence

NASA Technical Reports Server (NTRS)

Fletcher, D. G.

1993-01-01

An alternative to simultaneous, two-line laser-induced fluorescence for thermodynamic property measurement is presented. This spectroscopic approach is similar to multiple-overheat hot-wire anemometry and is based on laser excitation of different fluorescence transitions for separate, sequential wind tunnel runs. Both fluctuating and mean thermodynamic property measurements seem to be achievable with this method without exciting the transitions during the same laser pulse.

Vibronic bands in the HOMO-LUMO excitation of linear polyyne molecules

NASA Astrophysics Data System (ADS)

Wakabayashi, Tomonari; Wada, Yoriko; Iwahara, Naoya; Sato, Tohru

2013-04-01

Hydrogen-capped linear carbon chain molecules, namely polyynes H(C≡C)nH (n>=2), give rise to three excited states in the HOMO-LUMO excitation. Electric dipole transition from the ground state is fully allowed to one of the three excited states, while forbidden for the other two low-lying excited states. In addition to the strong absorption bands in the UV for the allowed transition, the molecules exhibit weak absorption and emission bands in the near UV and visible wavelength regions. The weak features are the vibronic bands in the forbidden transition. In this article, symmetry considerations are presented for the optical transitions in the centrosymmetric linear polyyne molecule. The argument includes Herzberg-Teller expansion for the state mixing induced by nuclear displacements along the normal coordinate of the molecule, intensity borrowing from fully allowed transitions, and inducing vibrational modes excited in the vibronic transition. The vibronic coupling considered here includes off-diagonal matrix elements for second derivatives along the normal coordinate. The vibronic selection rule for the forbidden transition is derived and associated with the transition moment with respect to the molecular axis. Experimental approaches are proposed for the assignment of the observed vibronic bands.

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.

Distribution, transition and thermodynamic stability of protein conformations in the denaturant-induced unfolding of proteins.

PubMed

Bian, Liujiao; Ji, Xu

2014-01-01

Extensive and intensive studies on the unfolding of proteins require appropriate theoretical model and parameter to clearly illustrate the feature and characteristic of the unfolding system. Over the past several decades, four approaches have been proposed to describe the interaction between proteins and denaturants, but some ambiguity and deviations usually occur in the explanation of the experimental data. In this work, a theoretical model was presented to show the dependency of the residual activity ratio of the proteins on the molar denaturant concentration. Through the characteristic unfolding parameters ki and Δmi in this model, the distribution, transition and thermodynamic stability of protein conformations during the unfolding process can be quantitatively described. This model was tested with the two-state unfolding of bovine heart cytochrome c and the three-state unfolding of hen egg white lysozyme induced by both guanidine hydrochloride and urea, the four-state unfolding of bovine carbonic anhydrase b induced by guanidine hydrochloride and the unfolding of some other proteins induced by denaturants. The results illustrated that this model could be used accurately to reveal the distribution and transition of protein conformations in the presence of different concentrations of denaturants and to evaluate the unfolding tendency and thermodynamic stability of different conformations. In most denaturant-induced unfolding of proteins, the unfolding became increasingly hard in next transition step and the proteins became more unstable as they attained next successive stable conformation. This work presents a useful method for people to study the unfolding of proteins and may be used to describe the unfolding and refolding of other biopolymers induced by denaturants, inducers, etc.

Successive disorder to disorder phase transitions in ionic liquid [HMIM][BF4] under high pressure

NASA Astrophysics Data System (ADS)

Zhu, Xiang; Yuan, Chaosheng; Li, Haining; Zhu, Pinwen; Su, Lei; Yang, Kun; Wu, Jie; Yang, Guoqiang; Liu, Jing

2016-02-01

In situ high-pressure Raman spectroscopy and synchrotron X-ray diffraction have been employed to investigate the phase behavior of ionic liquid, 1-hexyl-3-methylimidazolium tetrafluoroborate ([HMIM][BF4]) under high pressure up to 20 GPa at room temperature. With increasing pressure, some characteristic bands of [HMIM][BF4] disappear, and some characteristic bands of [HMIM][BF4] display non-monotonic pressure-induced frequency shift and non-monotonic variation of full width at half-maximum. Two successive phase transitions at ˜1.7 GPa and 7.3 GPa have been corroborated by the results above. The glass transition pressure (Pg) of [HMIM][BF4] at ˜7.3 GPa has been obtained by ruby R1 line broadening measurements and analysis of synchrotron X-ray diffraction patterns, and its glass transition mechanism is also analyzed in detail. These facts are suggestive of two successive disorder to disorder phase transitions induced by compression, that is, [HMIM][BF4] serves as a superpressurized glass under the pressure above 7.3 GPa, which is similar to the glassy state at low temperature, and a compression-induced liquid to liquid phase transition in [HMIM][BF4] occurs at ˜1.7 GPa. Besides, the conformational equilibrium of the GAAA conformer and AAAA conformer was converted easily in liquid [HMIM][BF4], while it was difficult to be influenced in glassy state.

The investigation of order–disorder transition process of ZSM-5 induced by spark plasma sintering

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

Wang, Liang; Wang, Lianjun, E-mail: wanglj@dhu.edu.cn; Jiang, Wan

2014-04-01

Based on the amorphization of zeolites, an order–disorder transition method was used to prepare silica glass via Spark Plasma Sintering (SPS). In order to get a better understanding about the mechanism of amorphization induced by SPS, the intermediate products in this process were prepared and characterized by different characterization techniques. X-ray diffraction and High-energy synchrotron X-ray scattering show a gradual transformation from ordered crystal to glass. Local structural changes in glass network including Si–O bond length, O–Si–O bond angle, size of rings, coordination were detected by Infrared spectroscopy and {sup 29}Si magic-angle spinning nuclear magnetic resonance (NMR) spectroscopy. Topologically ordered,more » amorphous material with a different intermediate-range structure can be obtained by precise control of intermediate process which can be expected to optimize and design material. - Graphical abstract: Low-density, ordered zeolites collapse to the rigid amorphous glass through spark plasma sintering. The intermediate-range structure formed in the process of order–disorder transition may give rise to specific property. - Highlights: • Order–disorder transition process of ZSM-5 induced by spark plasma sintering was investigated using several methods including XRD, High-energy synchrotron X-ray scattering, SAXS, IR, NMR, ect. • Order–disorder transition induced by SPS was compared with TIA and PIA. • Three stages has been divided during the whole process. • The collapse temperature range which may give rise to intermediate-range structure has been located.« less

Field-induced magnetic phase transitions and memory effect in bilayer ruthenate Ca 3Ru 2O 7 with Fe substitution

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

Zhu, M.; Hong, Tao; Peng, J.

Bilayer ruthenate Ca 3(Ru 1-xFe x) 2O 7 (x = 0.05) exhibits an incommensurate magnetic soliton lattice driven by the Dzyaloshinskii–Moriya interaction. Here, in this work, we report complex field-induced magnetic phase transitions and memory effect in this system via single-crystal neutron diffraction and magnetotransport measurements. We observe first-order incommensurate-to-commensurate magnetic transitions upon applying the magnetic field both along and perpendicular to the propagation axis of the incommensurate spin structure. Furthermore, we find that the metastable states formed upon decreasing the magnetic field depend on the temperature and the applied field orientation. Lastly, we suggest that the observed field-induced metastabilitymore » may be ascribable to the quenched kinetics at low temperature.« less

Field-induced magnetic phase transitions and memory effect in bilayer ruthenate Ca 3Ru 2O 7 with Fe substitution

DOE PAGES

Zhu, M.; Hong, Tao; Peng, J.; ...

2018-01-09

Bilayer ruthenate Ca 3(Ru 1-xFe x) 2O 7 (x = 0.05) exhibits an incommensurate magnetic soliton lattice driven by the Dzyaloshinskii–Moriya interaction. Here, in this work, we report complex field-induced magnetic phase transitions and memory effect in this system via single-crystal neutron diffraction and magnetotransport measurements. We observe first-order incommensurate-to-commensurate magnetic transitions upon applying the magnetic field both along and perpendicular to the propagation axis of the incommensurate spin structure. Furthermore, we find that the metastable states formed upon decreasing the magnetic field depend on the temperature and the applied field orientation. Lastly, we suggest that the observed field-induced metastabilitymore » may be ascribable to the quenched kinetics at low temperature.« less

Hypoxia, Epithelial-Mesenchymal Transition, and TET-Mediated Epigenetic Changes

PubMed Central

Kao, Shih-Han; Wu, Kou-Juey; Lee, Wen-Hwa

2016-01-01

Tumor hypoxia is a pathophysiologic outcome of disrupted microcirculation with inadequate supply of oxygen, leading to enhanced proliferation, epithelial-mesenchymal transition (EMT), metastasis, and chemo-resistance. Epigenetic changes induced by hypoxia are well documented, and they lead to tumor progression. Recent advances show that DNA demethylation mediated by the Ten-eleven translocation (TET) proteins induces major epigenetic changes and controls key steps of cancer development. TET enzymes serve as 5mC (5-methylcytosine)-specific dioxygenases and cause DNA demethylation. Hypoxia activates the expression of TET1, which also serves as a co-activator of HIF-1α transcriptional regulation to modulate HIF-1α downstream target genes and promote epithelial-mesenchymal transition. As HIF is a negative prognostic factor for tumor progression, hypoxia-activated prodrugs (HAPs) may provide a favorable therapeutic approach to lessen hypoxia-induced malignancy. PMID:26861406

Magnetic-field-induced irreversible antiferromagnetic-ferromagnetic phase transition around room temperature in as-cast Sm-Co based SmCo7-xSix alloys

NASA Astrophysics Data System (ADS)

Feng, D. Y.; Zhao, L. Z.; Liu, Z. W.

2016-04-01

A magnetic-field-induced irreversible metamagnetic phase transition from antiferro- to ferromagnetism, which leads to an anomalous initial-magnetization curve lying outside the magnetic hysteresis loop, is reported in arc-melted SmCo7-xSix alloys. The transition temperatures are near room temperature, much higher than other compounds with similar initial curves. Detailed investigation shows that this phenomenon is dependent on temperature, magnetic field and Si content and shows some interesting characteristics. It is suggested that varying interactions between the Sm and Co layers in the crystal are responsible for the formation of a metastable AFM structure, which induces the anomalous phenomenon in as-cast alloys. The random occupation of 3g sites by Si and Co atoms also has an effect on this phenomenon.

Single molecule force spectroscopy for in-situ probing oridonin inhibited ROS-mediated EGF-EGFR interactions in living KYSE-150 cells.

PubMed

Pi, Jiang; Jin, Hua; Jiang, Jinhuan; Yang, Fen; Cai, Huaihong; Yang, Peihui; Cai, Jiye; Chen, Zheng W

2017-05-01

As the active anticancer component of Rabdosia Rubescens, oridonin has been proved to show strong anticancer activity in cancer cells, which is also found to be closely related to its specific inhibition effects on the EGFR tyrosine kinase activity. In this study, atomic force microscopy based single molecule force spectroscopy (AFM-SMFS) was used for real-time and in-situ detection of EGF-EGFR interactions in living esophageal cancer KYSE-150 cells to evaluate the anticancer activity of oridonin for the first time. Oridonin was found to induce apoptosis and also reduce EGFR expression in KYSE-150 cells. AFM-SMFS results demonstrated that oridonin could inhibit the binding between EGF and EGFR in KYSE-150 cells by decreasing the unbinding force and binding probability for EGF-EGFR complexes, which was further proved to be closely associated with the intracellular ROS level. More precise mechanism studies based on AFM-SMFS demonstrated that oridonin treatment could decrease the energy barrier width, increase the dissociation off rate constant and decrease the activation energy of EGF-EGFR complexes in ROS dependent way, suggesting oridonin as a strong anticancer agent targeting EGF-EGFR interactions in cancer cells through ROS dependent mechanism. Our results not only suggested oridonin as a strong anticancer agent targeting EGF-EGFR interactions in ROS dependent mechanism, but also highlighted AFM-SMFS as a powerful technique for pharmacodynamic studies by detecting ligand-receptor interactions, which was also expected to be developed into a promising tool for the screening and mechanism studies of drugs. Copyright © 2016 Elsevier Ltd. All rights reserved.

Exploring resistance mechanisms of HCV NS3/4A protease mutations to MK5172: insight from molecular dynamics simulations and free energy calculations.

PubMed

Guan, Yan; Sun, Huiyong; Pan, Peichen; Li, Youyong; Li, Dan; Hou, Tingjun

2015-09-01

Mutations at a number of key positions (Ala156, Asp168 and Arg155) of the HCV NS3/4A protease can induce medium to high resistance to MK5172. The emergence of the resistant mutations seriously compromises the antiviral therapy efficacy to hepatitis C. In this study, molecular dynamics (MD) simulations, free energy calculations and free energy decomposition were used to explore the interaction profiles of MK5172 with the wild-type (WT) and four mutated (R155K, D168A, D168V and A156T) HCV NS3/4A proteases. The binding free energies predicted by Molecular Mechanics/Generalized Born Solvent Area (MM/GBSA) are consistent with the trend of the experimental drug resistance data. The free energy decomposition analysis shows that the resistant mutants may change the protein-MK5172 interaction profiles, resulting in the unbalanced energetic distribution amongst the catalytic triad, the strand 135-139 and the strand 154-160. Moreover, umbrella sampling (US) simulations were employed to elucidate the unbinding processes of MK5172 from the active pockets of the WT HCV NS3/4A protease and the four mutants. The US simulations demonstrate that the dissociation pathways of MK5172 escaping from the binding pockets of the WT and mutants are quite different, and it is quite possible that MK5172 will be harder to get access to the correct binding sites of the mutated proteases, thereafter leading to drug resistance.

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

PubMed

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

2017-07-26

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

Towards predictive models for transitionally rough surfaces

NASA Astrophysics Data System (ADS)

Abderrahaman-Elena, Nabil; Garcia-Mayoral, Ricardo

2017-11-01

We analyze and model the previously presented decomposition for flow variables in DNS of turbulence over transitionally rough surfaces. The flow is decomposed into two contributions: one produced by the overlying turbulence, which has no footprint of the surface texture, and one induced by the roughness, which is essentially the time-averaged flow around the surface obstacles, but modulated in amplitude by the first component. The roughness-induced component closely resembles the laminar steady flow around the roughness elements at the same non-dimensional roughness size. For small - yet transitionally rough - textures, the roughness-free component is essentially the same as over a smooth wall. Based on these findings, we propose predictive models for the onset of the transitionally rough regime. Project supported by the Engineering and Physical Sciences Research Council (EPSRC).

Pressure induced structural phase transition from NaCl-type (B1) to CsCl-type (B2) structure in sodium chloride

NASA Astrophysics Data System (ADS)

Jain, Aayushi; Dixit, R. C.

2018-05-01

Pressure induced structural phase transition of NaCl-type (B1) to CsCl-type (B2) structure in Sodium Chloride NaCl are presented. An effective interionic interaction potential (EIOP) with long range Coulomb, van der Waals (vdW) interaction and the short-range repulsive interaction upto second-neighbor ions within the Hafemeister and Flygare approach with modified ionic charge is reported here. The reckon value of the phase transition pressure (Pt) and the magnitude of the discontinuity in volume at the transition pressure are compatible as compared with reported data. The variations of elastic constants and their combinations with pressure follow ordered behavior. The present approach has also succeeded in predicting the Born and relative stability criteria.

Effect of Internal Pressure and Temperature on Phase Transitions in Perovskite Oxides: The Case of the Solid Oxide Fuel Cell Cathode Materials of the La2-xSrxCoTiO6 Series.

PubMed

Gómez-Pérez, Alejandro; Hoelzel, Markus; Muñoz-Noval, Álvaro; García-Alvarado, Flaviano; Amador, Ulises

2016-12-19

The symmetry of the room-temperature (RT) structure of title compounds La 2-x Sr x CoTiO 6-δ changes with x, from P2 1 /n (0 ≤ x ≤ 0.2) to Pnma (0.3 ≤ x ≤ 0.5) and to R3̅c (0.6 ≤ x ≤ 1). For x = 1 the three pseudocubic cell parameters become very close suggesting a transition to a cubic structure for higher Sr contents. Similar phase transitions were expected to occur on heating, paralleling the effect of internal pressure induced by substitution of La 3+ by Sr 2+ . However, only some of these aforementioned transitions have been thermally induced. The symmetry-adapted modes formalism is used in the structural refinements and fitting of neutron diffraction data recorded from RT to 1273 K. Thus, for x = 1, the out-of-phase tilting of the BO 6 octahedra vanishes progressively on heating, and a cubic structure with Pm3̅m symmetry is found at 1073 K. For lower Sr contents this transition is predicted to occur far above the temperature limit of common experimental setups. The analysis of the evolution of the perovskite tolerance factor, t-factor, with both Sr content and temperature indicates that temperature has a limited ability to release structural stress and thus to enable transitions to more symmetric phases. This is particularly true when compared to the effect of internal pressure induced by substitution of La by Sr. The existence of phase transitions in materials for solid oxide fuel cells that are usually exposed to heating-cooling cycles may have a detrimental effect. This work suggests strategies to stabilize the high-symmetry high-temperature phase of perovskite oxides through internal-pressure chemically induced.

Phenomenological Considerations of the Electric Field Induced Transitions in Improper Ferroelectrics and Ferroelastics. III. Application to Gd2(MoO4)3

NASA Astrophysics Data System (ADS)

Suzuki, Ikuo; Ishibashi, Yoshihiro

1987-02-01

The electric field induced phase transitions are discussed in the improper ferroelectrics and ferroelastics, where the high symmetry phase is assumed to be piezoelectric as in the gadolinium molybdate (GMO). The dependence on the electric field of the polarization is discussed, and the D-E hysteresis loops are compared with the one experimentally observed in GMO.

Evidence for a Peierls phase-transition in a three-dimensional multiple charge-density waves solid

PubMed Central

Mansart, Barbara; Cottet, Mathieu J. G.; Penfold, Thomas J.; Dugdale, Stephen B.; Tediosi, Riccardo; Chergui, Majed; Carbone, Fabrizio

2012-01-01

The effect of dimensionality on materials properties has become strikingly evident with the recent discovery of graphene. Charge ordering phenomena can be induced in one dimension by periodic distortions of a material’s crystal structure, termed Peierls ordering transition. Charge-density waves can also be induced in solids by strong coulomb repulsion between carriers, and at the extreme limit, Wigner predicted that crystallization itself can be induced in an electrons gas in free space close to the absolute zero of temperature. Similar phenomena are observed also in higher dimensions, but the microscopic description of the corresponding phase transition is often controversial, and remains an open field of research for fundamental physics. Here, we photoinduce the melting of the charge ordering in a complex three-dimensional solid and monitor the consequent charge redistribution by probing the optical response over a broad spectral range with ultrashort laser pulses. Although the photoinduced electronic temperature far exceeds the critical value, the charge-density wave is preserved until the lattice is sufficiently distorted to induce the phase transition. Combining this result with ab initio electronic structure calculations, we identified the Peierls origin of multiple charge-density waves in a three-dimensional system for the first time. PMID:22451898

Calculating electronic correlation effects from densities of transitions

NASA Astrophysics Data System (ADS)

Haydock, Roger

Adding a localized electron to a system of interacting electrons induces a density of transitions described by the time-independent Heisenberg equation. Sequences of these transitions generate interacting states whose total energy is the sum of energies of the constituent transitions. A calculation of magnetic moments for itinerant electrons with Ising interactions illustrates this method. supported by the H. V. Snyder Gift to the University of Oregon.

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

Yu, Cun; Ren, Yang; Cui, Lishan

Under high pressure, materials usually shrink during compression as described by an equation of state. Here, we present the anomalous volume expansion behavior of a one-dimensional Nb nanowire embedded in a NiTi transforming matrix, while the matrix undergoes a pressure-induced martensitic transformation. The Nb volume expansion depends on the NiTi transition pressure range from the matrix, which is controlled by the shear strain induced by different pressure transmitting media. The transformation-induced interfacial stresses between Nb and NiTi may play a major role in this anomaly. In conclusion, our discovery sheds new light on the nano-interfacial effect on mechanical anomalies inmore » heterogeneous systems during a pressure-induced phase transition.« less

Strain controlled ferromagnetic-ferrimagnetic transition and vacancy formation energy of defective graphene.

PubMed

Zhang, Yajun; Sahoo, Mpk; Wang, Jie

2016-09-23

Single vacancy (SV)-induced magnetism in graphene has attracted much attention motivated by its potential in achieving new functionalities. However, a much higher vacancy formation energy limits its direct application in electronic devices and the dependency of spin interaction on the strain is unclear. Here, through first-principles density-functional theory calculations, we investigate the possibility of strain engineering towards lowering vacancy formation energy and inducing new magnetic states in defective graphene. It is found that the SV-graphene undergoes a phase transition from an initial ferromagnetic state to a ferrimagnetic state under a biaxial tensile strain. At the same time, the biaxial tensile strain significantly lowers the vacancy formation energy. The charge density, density of states and band theory successfully identify the origin and underlying physics of the transition. The predicted magnetic phase transition is attributed to the strain driven spin flipping at the C-atoms nearest to the SV-site. The magnetic semiconducting graphene induced by defect and strain engineering suggests an effective way to modulate both spin and electronic degrees of freedom in future spintronic devices.

Control of boundary layer transition location and plate vibration in the presence of an external acoustic field

NASA Technical Reports Server (NTRS)

Maestrello, L.; Grosveld, F. W.

1991-01-01

The experiment is aimed at controlling the boundary layer transition location and the plate vibration when excited by a flow and an upstream sound source. Sound has been found to affect the flow at the leading edge and the response of a flexible plate in a boundary layer. Because the sound induces early transition, the panel vibration is acoustically coupled to the turbulent boundary layer by the upstream radiation. Localized surface heating at the leading edge delays the transition location downstream of the flexible plate. The response of the plate excited by a turbulent boundary layer (without sound) shows that the plate is forced to vibrate at different frequencies and with different amplitudes as the flow velocity changes indicating that the plate is driven by the convective waves of the boundary layer. The acoustic disturbances induced by the upstream sound dominate the response of the plate when the boundary layer is either turbulent or laminar. Active vibration control was used to reduce the sound induced displacement amplitude of the plate.

Jet-cooled laser-induced fluorescence spectroscopy of ScH: Observation of an Ω‧=2-Ω″=1 transition

NASA Astrophysics Data System (ADS)

Mukund, Sheo; Bhattacharyya, Soumen; Nakhate, S. G.

2014-11-01

New bands of scandium monohydride at origins 17,914.5 and 17,942.3 cm-1 have been observed in a jet-cooled beam with laser-induced fluorescence spectroscopy. Mass-selected resonant photoionization spectroscopy also confirmed the carrier of the band as ScH. The rotational analysis indicated that both transitions at 17,914.5 and 17,942.3 cm-1 are of Ω‧=2-Ω″=1 type with vibrational assignments (0,0) and (1,1) respectively. The assigned g3Φ2-a3Δ1 excitation is the first observed triplet-triplet transition in ScH.

Cascade of Magnetic Field Induced Spin Transitions in LaCoO3

NASA Astrophysics Data System (ADS)

Altarawneh, M. M.; Chern, G.-W.; Harrison, N.; Batista, C. D.; Uchida, A.; Jaime, M.; Rickel, D. G.; Crooker, S. A.; Mielke, C. H.; Betts, J. B.; Mitchell, J. F.; Hoch, M. J. R.

2012-07-01

We present magnetization and magnetostriction studies of LaCoO3 in magnetic fields approaching 100 T. In contrast with expectations from single-ion models, the data reveal two distinct first-order transitions and well-defined magnetization plateaus. The magnetization at the higher plateau is only about half the saturation value expected for spin-1 Co3+ ions. These findings strongly suggest collective behavior induced by interactions between different electronic configurations of Co3+ ions. We propose a model that predicts crystalline spin textures and a cascade of four magnetic phase transitions at high fields, of which the first two account for the experimental data.

Field-induced phase transitions in chiral smectic liquid crystals studied by the constant current method

NASA Astrophysics Data System (ADS)

H, Dhaouadi; R, Zgueb; O, Riahi; F, Trabelsi; T, Othman

2016-05-01

In ferroelectric liquid crystals, phase transitions can be induced by an electric field. The current constant method allows these transition to be quickly localized and thus the (E,T) phase diagram of the studied product can be obtained. In this work, we make a slight modification to the measurement principles based on this method. This modification allows the characteristic parameters of ferroelectric liquid crystal to be quantitatively measured. The use of a current square signal highlights a phenomenon of ferroelectric hysteresis with remnant polarization at null field, which points out an effect of memory in this compound.

Curvature perturbation and waterfall dynamics in hybrid inflation

NASA Astrophysics Data System (ADS)

Akbar Abolhasani, Ali; Firouzjahi, Hassan; Sasaki, Misao

2011-10-01

We investigate the parameter spaces of hybrid inflation model with special attention paid to the dynamics of waterfall field and curvature perturbations induced from its quantum fluctuations. Depending on the inflaton field value at the time of phase transition and the sharpness of the phase transition inflation can have multiple extended stages. We find that for models with mild phase transition the induced curvature perturbation from the waterfall field is too large to satisfy the COBE normalization. We investigate the model parameter space where the curvature perturbations from the waterfall quantum fluctuations vary between the results of standard hybrid inflation and the results obtained here.

Laser-stimulated electric quadrupole transitions in the molecular hydrogen ion H2+

NASA Astrophysics Data System (ADS)

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

2018-03-01

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

Bistability and State Transition of a Delay Differential Equation Model of Neutrophil Dynamics

NASA Astrophysics Data System (ADS)

Ma, Suqi; Zhu, Kaiyi; Lei, Jinzhi

This paper studies the existence of bistable states and control strategies to induce state transitions of a delay differential equation model of neutrophil dynamics. We seek the conditions that a stable steady state and an oscillatory state coexist in the neutrophil dynamical system. Physiologically, stable steady state represents the healthy state, while oscillatory state is usually associated with diseases such as cyclical neutropenia. We study the control strategies to induce the transitions from the disease state to the healthy state by introducing temporal perturbations to system parameters. This study is valuable in designing clinical protocols for the treatment of cyclical neutropenia.

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

Mechanistic insight into the functional transition of the enzyme guanylate kinase induced by a single mutation

PubMed Central

Zhang, Yuebin; Niu, Huiyan; Li, Yan; Chu, Huiying; Shen, Hujun; Zhang, Dinglin; Li, Guohui

2015-01-01

Dramatic functional changes of enzyme usually require scores of alterations in amino acid sequence. However, in the case of guanylate kinase (GK), the functional novelty is induced by a single (S→P) mutation, leading to the functional transition of the enzyme from a phosphoryl transfer kinase into a phosphorprotein interaction domain. Here, by using molecular dynamic (MD) and metadynamics simulations, we provide a comprehensive description of the conformational transitions of the enzyme after mutating serine to proline. Our results suggest that the serine plays a crucial role in maintaining the closed conformation of wild-type GK and the GMP recognition. On the contrary, the S→P mutant exhibits a stable open conformation and loses the ability of ligand binding, which explains its functional transition from the GK enzyme to the GK domain. Furthermore, the free energy profiles (FEPs) obtained by metadymanics clearly demonstrate that the open-closed conformational transition in WT GK is positive correlated with the process of GMP binding, indicating the GMP-induced closing motion of GK enzyme, which is not observed in the mutant. In addition, the FEPs show that the S→P mutation can also leads to the mis-recognition of GMP, explaining the vanishing of catalytic activity of the mutant. PMID:25672880

Identifying intrinsically disordered protein regions likely to undergo binding-induced helical transitions.

PubMed

Glover, Karen; Mei, Yang; Sinha, Sangita C

2016-10-01

Many proteins contain intrinsically disordered regions (IDRs) lacking stable secondary and ordered tertiary structure. IDRs are often implicated in macromolecular interactions, and may undergo structural transitions upon binding to interaction partners. However, as binding partners of many protein IDRs are unknown, these structural transitions are difficult to verify and often are poorly understood. In this study we describe a method to identify IDRs that are likely to undergo helical transitions upon binding. This method combines bioinformatics analyses followed by circular dichroism spectroscopy to monitor 2,2,2-trifluoroethanol (TFE)-induced changes in secondary structure content of these IDRs. Our results demonstrate that there is no significant change in the helicity of IDRs that are not predicted to fold upon binding. IDRs that are predicted to fold fall into two groups: one group does not become helical in the presence of TFE and includes examples of IDRs that form β-strands upon binding, while the other group becomes more helical and includes examples that are known to fold into helices upon binding. Therefore, we propose that bioinformatics analyses combined with experimental evaluation using TFE may provide a general method to identify IDRs that undergo binding-induced disorder-to-helix transitions. Copyright © 2016 Elsevier B.V. All rights reserved.

Continuous Isotropic-Nematic Transition in Amyloid Fibril Suspensions Driven by Thermophoresis.

PubMed

Vigolo, Daniele; Zhao, Jianguo; Handschin, Stephan; Cao, Xiaobao; deMello, Andrew J; Mezzenga, Raffaele

2017-04-27

The isotropic and nematic (I + N) coexistence for rod-like colloids is a signature of the first-order thermodynamics nature of this phase transition. However, in the case of amyloid fibrils, the biphasic region is too small to be experimentally detected, due to their extremely high aspect ratio. Herein, we study the thermophoretic behaviour of fluorescently labelled β-lactoglobulin amyloid fibrils by inducing a temperature gradient across a microfluidic channel. We discover that fibrils accumulate towards the hot side of the channel at the temperature range studied, thus presenting a negative Soret coefficient. By exploiting this thermophoretic behaviour, we show that it becomes possible to induce a continuous I-N transition with the I and N phases at the extremities of the channel, starting from an initially single N phase, by generating an appropriate concentration gradient along the width of the microchannel. Accordingly, we introduce a new methodology to control liquid crystal phase transitions in anisotropic colloidal suspensions. Because the induced order-order transitions are achieved under stationary conditions, this may have important implications in both applied colloidal science, such as in separation and fractionation of colloids, as well as in fundamental soft condensed matter, by widening the accessibility of target regions in the phase diagrams.

Hyperfine induced transition probabilities from 4{f}^{14}5s5p{}^{3}{{\\rm{P}}}_{0,2}^{o} states in Sm-like ions

NASA Astrophysics Data System (ADS)

Zhou, Fuyang; Li, Jiguang; Qu, Yizhi; Wang, Jianguo

2017-11-01

The hyperfine induced 4{f}145s5p{}3{{{P}}}0,2o-4{f}145{s}2{}1{{{S}}}0 transition probabilities for highly charged Sm-like ions are calculated within the framework of the multiconfiguration Dirac-Hartree-Fock method. Electron correlation, the Breit interaction and quantum electrodynamical effects are taken into account. For ions ranging from Z = 79 to Z=94,4{f}145s5p{}3{{{P}}}0o is the first excited state, and the hyperfine induced transition (HIT) is a dominant decay channel. For the 4{f}145s5p{}3{{{P}}}2o state, the HIT rates of Sm-like ions with Z=82-94 are reported as well as the magnetic dipole (M1) {}3{{{P}}}2o-{}3{{{P}}}1o, the electric quadrupole (E2) {}3{{{P}}}2o-{}3{{{P}}}0,1o, and the magnetic quadrupole (M2) {}3{{{P}}}2o-{}1{{{S}}}0 transition probabilities. It is found that M1 transition from the 4{f}145s5p{}3{{{P}}}2o state is the most important decay channel in this range on Z≥slant 82.

Quantum Hooke's Law to classify pulse laser induced ultrafast melting

DOE PAGES

Hu, Hao; Ding, Hepeng; Liu, Feng

2015-02-03

Ultrafast crystal-to-liquid phase transition induced by femtosecond pulse laser excitation is an interesting material's behavior manifesting the complexity of light-matter interaction. There exist two types of such phase transitions: one occurs at a time scale shorter than a picosecond via a nonthermal process mediated by electron-hole plasma formation; the other at a longer time scale via a thermal melting process mediated by electron-phonon interaction. However, it remains unclear what material would undergo which process and why? Here, by exploiting the property of quantum electronic stress (QES) governed by quantum Hooke's law, we classify the transitions by two distinct classes ofmore » materials: the faster nonthermal process can only occur in materials like ice having an anomalous phase diagram characterized with dT m/dP < 0, where T m is the melting temperature and P is pressure, above a high threshold laser fluence; while the slower thermal process may occur in all materials. Especially, the nonthermal transition is shown to be induced by the QES, acting like a negative internal pressure, which drives the crystal into a “super pressing” state to spontaneously transform into a higher-density liquid phase. Our findings significantly advance fundamental understanding of ultrafast crystal-to-liquid phase transitions, enabling quantitative a priori predictions.« less

Mechanistic insight into the functional transition of the enzyme guanylate kinase induced by a single mutation.

PubMed

Zhang, Yuebin; Niu, Huiyan; Li, Yan; Chu, Huiying; Shen, Hujun; Zhang, Dinglin; Li, Guohui

2015-02-12

Dramatic functional changes of enzyme usually require scores of alterations in amino acid sequence. However, in the case of guanylate kinase (GK), the functional novelty is induced by a single (S→P) mutation, leading to the functional transition of the enzyme from a phosphoryl transfer kinase into a phosphorprotein interaction domain. Here, by using molecular dynamic (MD) and metadynamics simulations, we provide a comprehensive description of the conformational transitions of the enzyme after mutating serine to proline. Our results suggest that the serine plays a crucial role in maintaining the closed conformation of wild-type GK and the GMP recognition. On the contrary, the S→P mutant exhibits a stable open conformation and loses the ability of ligand binding, which explains its functional transition from the GK enzyme to the GK domain. Furthermore, the free energy profiles (FEPs) obtained by metadymanics clearly demonstrate that the open-closed conformational transition in WT GK is positive correlated with the process of GMP binding, indicating the GMP-induced closing motion of GK enzyme, which is not observed in the mutant. In addition, the FEPs show that the S→P mutation can also leads to the mis-recognition of GMP, explaining the vanishing of catalytic activity of the mutant.

Quantum Hooke's Law to Classify Pulse Laser Induced Ultrafast Melting

NASA Astrophysics Data System (ADS)

Hu, Hao; Ding, Hepeng; Liu, Feng

2015-02-01

Ultrafast crystal-to-liquid phase transition induced by femtosecond pulse laser excitation is an interesting material's behavior manifesting the complexity of light-matter interaction. There exist two types of such phase transitions: one occurs at a time scale shorter than a picosecond via a nonthermal process mediated by electron-hole plasma formation; the other at a longer time scale via a thermal melting process mediated by electron-phonon interaction. However, it remains unclear what material would undergo which process and why? Here, by exploiting the property of quantum electronic stress (QES) governed by quantum Hooke's law, we classify the transitions by two distinct classes of materials: the faster nonthermal process can only occur in materials like ice having an anomalous phase diagram characterized with dTm/dP < 0, where Tm is the melting temperature and P is pressure, above a high threshold laser fluence; while the slower thermal process may occur in all materials. Especially, the nonthermal transition is shown to be induced by the QES, acting like a negative internal pressure, which drives the crystal into a ``super pressing'' state to spontaneously transform into a higher-density liquid phase. Our findings significantly advance fundamental understanding of ultrafast crystal-to-liquid phase transitions, enabling quantitative a priori predictions.

Quantum Hooke's Law to Classify Pulse Laser Induced Ultrafast Melting

PubMed Central

Hu, Hao; Ding, Hepeng; Liu, Feng

2015-01-01

Ultrafast crystal-to-liquid phase transition induced by femtosecond pulse laser excitation is an interesting material's behavior manifesting the complexity of light-matter interaction. There exist two types of such phase transitions: one occurs at a time scale shorter than a picosecond via a nonthermal process mediated by electron-hole plasma formation; the other at a longer time scale via a thermal melting process mediated by electron-phonon interaction. However, it remains unclear what material would undergo which process and why? Here, by exploiting the property of quantum electronic stress (QES) governed by quantum Hooke's law, we classify the transitions by two distinct classes of materials: the faster nonthermal process can only occur in materials like ice having an anomalous phase diagram characterized with dTm/dP < 0, where Tm is the melting temperature and P is pressure, above a high threshold laser fluence; while the slower thermal process may occur in all materials. Especially, the nonthermal transition is shown to be induced by the QES, acting like a negative internal pressure, which drives the crystal into a “super pressing” state to spontaneously transform into a higher-density liquid phase. Our findings significantly advance fundamental understanding of ultrafast crystal-to-liquid phase transitions, enabling quantitative a priori predictions. PMID:25645258

Quantum Hooke's law to classify pulse laser induced ultrafast melting.

PubMed

Hu, Hao; Ding, Hepeng; Liu, Feng

2015-02-03

Ultrafast crystal-to-liquid phase transition induced by femtosecond pulse laser excitation is an interesting material's behavior manifesting the complexity of light-matter interaction. There exist two types of such phase transitions: one occurs at a time scale shorter than a picosecond via a nonthermal process mediated by electron-hole plasma formation; the other at a longer time scale via a thermal melting process mediated by electron-phonon interaction. However, it remains unclear what material would undergo which process and why? Here, by exploiting the property of quantum electronic stress (QES) governed by quantum Hooke's law, we classify the transitions by two distinct classes of materials: the faster nonthermal process can only occur in materials like ice having an anomalous phase diagram characterized with dTm/dP < 0, where Tm is the melting temperature and P is pressure, above a high threshold laser fluence; while the slower thermal process may occur in all materials. Especially, the nonthermal transition is shown to be induced by the QES, acting like a negative internal pressure, which drives the crystal into a "super pressing" state to spontaneously transform into a higher-density liquid phase. Our findings significantly advance fundamental understanding of ultrafast crystal-to-liquid phase transitions, enabling quantitative a priori predictions.

A Molecular Dynamics Simulation of the Human Lysozyme – Camelid VHH HL6 Antibody System

PubMed Central

Su, Zhi-Yuan; Wang, Yeng-Tseng

2009-01-01

Amyloid diseases such as Alzheimer’s and thrombosis are characterized by an aberrant assembly of specific proteins or protein fragments into fibrils and plaques that are deposited in various tissues and organs. The single-domain fragment of a camelid antibody was reported to be able to combat against wild-type human lysozyme for inhibiting in-vitro aggregations of the amyloidogenic variant (D67H). The present study is aimed at elucidating the unbinding mechanics between the D67H lysozyme and VHH HL6 antibody fragment by using steered molecular dynamics (SMD) simulations on a nanosecond scale with different pulling velocities. The results of the simulation indicated that stretching forces of more than two nano Newton (nN) were required to dissociate the proteinantibody system, and the hydrogen bond dissociation pathways were computed. PMID:19468335

Molecular dynamics simulation reveals how phosphorylation of tyrosine 26 of phosphoglycerate mutase 1 upregulates glycolysis and promotes tumor growth.

PubMed

Wang, Yan; Cai, Wen-Sheng; Chen, Luonan; Wang, Guanyu

2017-02-14

Phosphoglycerate mutase 1 (PGAM1) catalyzes the eighth step of glycolysis and is often found upregulated in cancer cells. To test the hypothesis that the phosphorylation of tyrosine 26 residue of PGAM1 greatly enhances its activity, we performed both conventional and steered molecular dynamics simulations on the binding and unbinding of PGAM1 to its substrates, with tyrosine 26 either phosphorylated or not. We analyzed the simulated data in terms of structural stability, hydrogen bond formation, binding free energy, etc. We found that tyrosine 26 phosphorylation enhances the binding of PGAM1 to its substrates through generating electrostatic environment and structural features that are advantageous to the binding. Our results may provide valuable insights into computer-aided design of drugs that specifically target cancer cells with PGAM1 tyrosine 26 phosphorylated.

Immersed Boundary Simulations of Active Fluid Droplets

PubMed Central

Hawkins, Rhoda J.

2016-01-01

We present numerical simulations of active fluid droplets immersed in an external fluid in 2-dimensions using an Immersed Boundary method to simulate the fluid droplet interface as a Lagrangian mesh. We present results from two example systems, firstly an active isotropic fluid boundary consisting of particles that can bind and unbind from the interface and generate surface tension gradients through active contractility. Secondly, a droplet filled with an active polar fluid with homeotropic anchoring at the droplet interface. These two systems demonstrate spontaneous symmetry breaking and steady state dynamics resembling cell motility and division and show complex feedback mechanisms with minimal degrees of freedom. The simulations outlined here will be useful for quantifying the wide range of dynamics observable in these active systems and modelling the effects of confinement in a consistent and adaptable way. PMID:27606609

Probing fibronectin–antibody interactions using AFM force spectroscopy and lateral force microscopy

PubMed Central

Kulik, Andrzej J; Lee, Kyumin; Pyka-Fościak, Grazyna; Nowak, Wieslaw

2015-01-01

Summary The first experiment showing the effects of specific interaction forces using lateral force microscopy (LFM) was demonstrated for lectin–carbohydrate interactions some years ago. Such measurements are possible under the assumption that specific forces strongly dominate over the non-specific ones. However, obtaining quantitative results requires the complex and tedious calibration of a torsional force. Here, a new and relatively simple method for the calibration of the torsional force is presented. The proposed calibration method is validated through the measurement of the interaction forces between human fibronectin and its monoclonal antibody. The results obtained using LFM and AFM-based classical force spectroscopies showed similar unbinding forces recorded at similar loading rates. Our studies verify that the proposed lateral force calibration method can be applied to study single molecule interactions. PMID:26114080

A force-based protein biochip

NASA Astrophysics Data System (ADS)

Blank, K.; Mai, T.; Gilbert, I.; Schiffmann, S.; Rankl, J.; Zivin, R.; Tackney, C.; Nicolaus, T.; Spinnler, K.; Oesterhelt, F.; Benoit, M.; Clausen-Schaumann, H.; Gaub, H. E.

2003-09-01

A parallel assay for the quantification of single-molecule binding forces was developed based on differential unbinding force measurements where ligand-receptor interactions are compared with the unzipping forces of DNA hybrids. Using the DNA zippers as molecular force sensors, the efficient discrimination between specific and nonspecific interactions was demonstrated for small molecules binding to specific receptors, as well as for protein-protein interactions on protein arrays. Finally, an antibody sandwich assay with different capture antibodies on one chip surface and with the detection antibodies linked to a congruent surface via the DNA zippers was used to capture and quantify a recombinant hepatitis C antigen from solution. In this case, the DNA zippers enable not only discrimination between specific and nonspecific binding, but also allow for the local application of detection antibodies, thereby eliminating false-positive results caused by cross-reactive antibodies and nonspecific binding.

Col1A1 Production and Apoptotic Resistance in TGF-β1-Induced Epithelial-to-Mesenchymal Transition-Like Phenotype of 603B Cells

PubMed Central

Liu, Jun; Eischeid, Alex N.; Chen, Xian-Ming

2012-01-01

Recent studies have suggested that proliferating cholangiocytes have an important role in the induction of fibrosis, either directly via epithelial-to-mesenchymal transition (EMT), or indirectly via activation of other liver cell types. Transforming growth factor beta 1 (TGF-β1), a critical fibrotic cytokine for hepatic fibrosis, is a potent EMT inducer. This study aimed to clarify the potential contributions of TGF-β1-induced EMT-like cholangiocyte phenotype to collagen production and cell survival of cholangiocytes in vitro. Mouse cholangiocytes (603B cells) were treated with TGF-β1 and EMT-like phenotype alterations were monitored by morphological changes and expression of EMT-associated genes. Alterations in Col1A1 gene, Col1A1-associated miR-29s, and pro-apoptotic genes were measured in TGF-β1-treated 603B cells. Snail1 knockdown was achieved using shRNA to evaluate the contribution of EMT-associated changes to Col1A1 production and cell survival. We found TGF-β1 treatment induced partial EMT-like phenotype transition in 603B cells in a Snail1-dependent manner. TGF-β1 also stimulated collagen α1(I) expression in 603B cells. However, this induction was not parallel to the EMT-like alterations and independent of Snail1 or miR-29 expression. Cells undergoing EMT-like changes showed a modest down-regulation of multiple pro-apoptotic genes and displayed resistance to TNF-α-induced apoptosis. TGF-β1-induced apoptosis resistance was attenuated in Snail1 knockdown 603B cells. TGF-β1-induced Col1A1 production seems to be independent of EMT-like transition and miR-29 expression. Nevertheless, TGF-β1-induced EMT may contribute to the increased survival capacity of cholangiocytes via modulating the expression of pro-apoptotic genes. PMID:23236489

Deceleration-driven wetting transition of "gently" deposited drops on textured hydrophobic surfaces

NASA Astrophysics Data System (ADS)

Varanasi, Kripa; Kwon, Hyukmin; Paxson, Adam; Patankar, Neelesh

2010-11-01

Many applications of rough superhydrophobic surfaces rely on the presence of droplets in a Cassie state on the substrates. A well established understanding is that if sessile droplets are smaller than a critical size, then the large Laplace pressure induces wetting transition from a Cassie to a Wenzel state, i.e., the liquid impales the roughness grooves. Thus, larger droplets are expected to remain in the Cassie state. In this work we report a surprising wetting transition where even a "gentle" deposition of droplets on rough substrates lead to the transition of larger droplets to the Wenzel state. A hitherto unknown mechanism based on rapid deceleration is identified. It is found that modest amount of energy, during the deposition process, is channeled through rapid deceleration into high water hammer pressure which induces wetting transition. A new "phase" diagram is reported which shows that both large and small droplets can transition to Wenzel states due to the deceleration and Laplace mechanisms, respectively. This novel insight reveals for the first time that the attainment of a Cassie state is more restrictive than previous criteria based on the Laplace pressure transition mechanism.

Hearing Loss Severity: Impaired Processing of Formant Transition Duration

ERIC Educational Resources Information Center

Coez, A.; Belin, P.; Bizaguet, E.; Ferrary, E.; Zilbovicius, M.; Samson, Y.

2010-01-01

Normal hearing listeners exploit the formant transition (FT) detection to identify place of articulation for stop consonants. Neuro-imaging studies revealed that short FT induced less cortical activation than long FT. To determine the ability of hearing impaired listeners to distinguish short and long formant transitions (FT) from vowels of the…

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

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

Developing a Novel Therapeutic Strategy Targeting Kallikrein-4 to Inhibit Prostate Cancer Growth and Metastasis

DTIC Science & Technology

2015-08-01

mesenchymal transition (EMT), animal models, cancer imaging, cancer stem cells , circulating tumor cells (CTCs), metabolomics, targeted therapeutics and...metastatic tissue, and has been reported to increase PCa cell proliferation, induce epithelial-to- mesenchymal (EMT)-like changes, and could have a role...KLK4 has been reported to increase PCa cell proliferation, induce an epithelial to mesenchymal transition (EMT)-like response in PC3 PCa cells [4

Direct observation of the flux-line vortex glass phase in a type II superconductor.

PubMed

Divakar, U; Drew, A J; Lee, S L; Gilardi, R; Mesot, J; Ogrin, F Y; Charalambous, D; Forgan, E M; Menon, G I; Momono, N; Oda, M; Dewhurst, C D; Baines, C

2004-06-11

The order of the vortex state in La1.9Sr0.1CuO4 is probed using muon-spin rotation and small-angle neutron scattering. A transition from a Bragg glass to a vortex glass is observed, where the latter is composed of disordered vortex lines. In the vicinity of the transition the microscopic behavior reflects a delicate interplay of thermally induced and pinning-induced disorder.

Magnetic phase diagram and electronic structure of UPt 2 Si 2 at high magnetic fields: A possible field-induced Lifshitz transition

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

Grachtrup, D. Schulze; Steinki, N.; Süllow, S.

2017-04-14

We have measured Hall effect, magnetotransport and magnetostriction on the field induced phases of single crystalline UPt2Si2 in magnetic fields up to 60T at temperatures down to 50mK, this way firmly establishing the phase diagram for magnetic fields Bka and c axes. Moreover, for Bkc axis we observe strong changes in the Hall effect at the phase boundaries. From a comparison to band structure calculations utilizing the concept of a dual nature of the uranium 5f electrons, we propose that these represent field induced topological changes of the Fermi surface due to at least one Lifshitz transition. Furthermore, we findmore » a unique history dependence of the magnetotransport and magnetostriction data, indicating that the proposed Lifshitz type transition is of a discontinuous nature, as predicted for interacting electron systems.« less

Dynamic Test Method Based on Strong Electromagnetic Pulse for Electromagnetic Shielding Materials with Field-Induced Insulator-Conductor Phase Transition

NASA Astrophysics Data System (ADS)

Wang, Yun; Zhao, Min; Wang, Qingguo

2018-01-01

In order to measure the pulse shielding performance of materials with the characteristic of field-induced insulator-conductor phase transition when materials are used for electromagnetic shielding, a dynamic test method was proposed based on a coaxial fixture. Experiment system was built by square pulse source, coaxial cable, coaxial fixture, attenuator, and oscilloscope and insulating components. S11 parameter of the test system was obtained, which suggested that the working frequency ranges from 300 KHz to 7.36 GHz. Insulating performance is good enough to avoid discharge between conductors when material samples is exposed in the strong electromagnetic pulse field up to 831 kV/m. This method is suitable for materials with annular shape, certain thickness and the characteristic of field-induced insulator-conductor phase transition to get their shielding performances of strong electromagnetic pulse.

Theoretical and Experimental Investigation of the Translational Diffusion of Proteins in the Vicinity of Temperature-Induced Unfolding Transition.

PubMed

Molchanov, Stanislav; Faizullin, Dzhigangir A; Nesmelova, Irina V

2016-10-06

Translational diffusion is the most fundamental form of transport in chemical and biological systems. The diffusion coefficient is highly sensitive to changes in the size of the diffusing species; hence, it provides important information on the variety of macromolecular processes, such as self-assembly or folding-unfolding. Here, we investigate the behavior of the diffusion coefficient of a macromolecule in the vicinity of heat-induced transition from folded to unfolded state. We derive the equation that describes the diffusion coefficient of the macromolecule in the vicinity of the transition and use it to fit the experimental data from pulsed-field-gradient nuclear magnetic resonance (PFG NMR) experiments acquired for two globular proteins, lysozyme and RNase A, undergoing temperature-induced unfolding. A very good qualitative agreement between the theoretically derived diffusion coefficient and experimental data is observed.

Quasiperiodic Quantum Ising Transitions in 1D

NASA Astrophysics Data System (ADS)

Crowley, P. J. D.; Chandran, A.; Laumann, C. R.

2018-04-01

Unlike random potentials, quasiperiodic modulation can induce localization-delocalization transitions in one dimension. In this Letter, we analyze the implications of this for symmetry breaking in the quasiperiodically modulated quantum Ising chain. Although weak modulation is irrelevant, strong modulation induces new ferromagnetic and paramagnetic phases which are fully localized and gapless. The quasiperiodic potential and localized excitations lead to quantum criticality that is intermediate to that of the clean and randomly disordered models with exponents of ν =1+ (exact) and z ≈1.9 , Δσ≈0.16 , and Δγ≈0.63 (up to logarithmic corrections). Technically, the clean Ising transition is destabilized by logarithmic wandering of the local reduced couplings. We conjecture that the wandering coefficient w controls the universality class of the quasiperiodic transition and show its stability to smooth perturbations that preserve the quasiperiodic structure of the model.

Strain-induced insulator-to-metal transition in LaTiO3 within DFT + DMFT

NASA Astrophysics Data System (ADS)

Dymkowski, Krzysztof; Ederer, Claude

2014-04-01

We present results of combined density functional theory plus dynamical mean-field theory (DFT + DMFT) calculations, which show that the Mott insulator LaTiO3 undergoes an insulator-to-metal transition under compressive epitaxial strain of about -2%. This transition is driven by strain-induced changes in the crystal-field splitting between the Ti t2g orbitals, which in turn are intimately related to the collective tilts and rotations of the oxygen octahedra in the orthorhombically distorted Pbnm perovskite structure. An accurate treatment of the underlying crystal structure is therefore crucial for a correct description of the observed metal-insulator transition. Our theoretical results are consistent with recent experimental observations and demonstrate that metallic behavior in heterostructures of otherwise insulating materials can emerge also from mechanisms other than genuine interface effects.

Positron annihilation induced Auger electron spectroscopy

NASA Technical Reports Server (NTRS)

Weiss, Alex; Koymen, A. R.; Mehl, David; Jensen, K. O.; Lei, Chun; Lee, K. H.

1990-01-01

Recently, Weiss et al. have demonstrated that it is possible to excite Auger transitions by annihilating core electrons using a low energy (less than 30eV) beam of positrons. This mechanism makes possible a new electron spectroscopy, Positron annihilation induced Auger Electron Spectroscopy (PAES). The probability of exciting an Auger transition is proportional to the overlap of the positron wavefunction with atomic core levels. Since the Auger electron energy provides a signature of the atomic species making the transition, PAES makes it possible to determine the overlap of the positron wavefunction with a particular element. PAES may therefore provide a means of detecting positron-atom complexes. Measurements of PAES intensities from clean and adsorbate covered Cu surfaces are presented which indicate that approx. 5 percent of positrons injected into CU at 25eV produce core annihilations that result in Auger transitions.

Pressure-induced structural phase transition in transition metal carbides TMC (TM = Ru, Rh, Pd, Os, Ir, Pt): a DFT study

NASA Astrophysics Data System (ADS)

Manikandan, M.; Rajeswarapalanichamy, R.; Iyakutti, K.

2018-03-01

First-principles calculations based on density functional theory was performed to analyse the structural stability of transition metal carbides TMC (TM = Ru, Rh, Pd, Os, Ir, Pt). It is observed that zinc-blende phase is the most stable one for these carbides. Pressure-induced structural phase transition from zinc blende to NiAs phase is predicted at the pressures of 248.5 GPa, 127 GPa and 142 GPa for OsC, IrC and PtC, respectively. The electronic structure reveals that RuC exhibits a semiconducting behaviour with an energy gap of 0.7056 eV. The high bulk modulus values of these carbides indicate that these metal carbides are super hard materials. The high B/G value predicts that the carbides are ductile in their most stable phase.

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

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

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

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

Effects of homogeneous condensation in compressible flows: Ludwieg-tube experiments and simulations

NASA Astrophysics Data System (ADS)

Luo, Xisheng; Lamanna, Grazia; Holten, A. P. C.; van Dongen, M. E. H.

Effects of homogeneous nucleation and subsequent droplet growth in compressible flows in humid nitrogen are investigated numerically and experimentally. A Ludwieg tube is employed to produce expansion flows. Corresponding to different configurations, three types of experiment are carried out in such a tube. First, the phase transition in a strong unsteady expansion wave is investigated to demonstrate the mutual interaction between the unsteady flow and the condensation process and also the formation of condensation-induced shock waves. The role of condensation-induced shocks in the gradual transition from a frozen initial structure to an equilibrium structure is explained. Second, the condensing flow in a slender supersonic nozzle G2 is considered. Particular attention is given to condensation-induced oscillations and to the transition from symmetrical mode-1 oscillations to asymmetrical mode-2 oscillations in a starting nozzle flow, as first observed by Adam & Schnerr. The transition is also found numerically, but the amplitude, frequency and transition time are not yet well predicted. Third, a sharp-edged obstacle is placed in the tube to generate a starting vortex. Condensation in the vortex is found. Owing to the release of latent heat of condensation, an increase in the pressure and temperature in the vortex core is observed. Condensation-induced shock waves are found, for a sufficiently high initial saturation ratio, which interact with the starting vortex, resulting in a very complex flow. As time proceeds, a subsonic or transonic free jet is formed downstream of the sharp-edged obstacle, which becomes oscillatory for a relatively high main-flow velocity and for a sufficiently high humidity.

Pressure induced band inversion, electronic and structural phase transitions in InTe: A combined experimental and theoretical study

NASA Astrophysics Data System (ADS)

Rajaji, V.; Pal, Koushik; Sarma, Saurav Ch.; Joseph, B.; Peter, Sebastian C.; Waghmare, Umesh V.; Narayana, Chandrabhas

2018-04-01

We report high-pressure Raman scattering measurements on the tetragonal phase of InTe corroborated with the first-principles density functional theory and synchrotron x-ray diffraction measurements. Anomalous pressure-dependent linewidths of the A1 g and Eg phonon modes provide evidence of an isostructural electronic transition at ˜3.6 GPa . The first-principles theoretical analysis reveals that it is associated with a semiconductor-to-metal transition due to increased density of states near the Fermi level. Further, this pressure induced metallization acts as a precursor for structural phase transition to a face centered cubic phase (F m 3 ¯m ) at ˜6.0 GPa . Interestingly, theoretical results reveal a pressure induced band inversion at the Z and M points of the Brillouin zone corresponding to pressures ˜1.0 and ˜1.4 GPa , respectively. As the parity of bands undergoing inversions is the same, the topology of the electronic state remains unchanged, and hence InTe retains its trivial band topology (Z2=0 ) . The pressure dependent behavior of the A1 g and Eg modes can be understood based on the results from the synchrotron x-ray diffraction, which shows anisotropic compressibility of the lattice in the a and c directions. Our Raman measurements up to ˜19 GPa further confirms the pressure induced structural phase transition from a face-centered to primitive cubic (F m 3 ¯m to P m 3 ¯m ) at P ˜15 GPa .

Quasi-dynamic pressure and temperature initiated β<-->δ solid phase transitions in HMX

NASA Astrophysics Data System (ADS)

Zaug, Joseph M.; Farber, Daniel L.; Craig, Ian M.; Blosch, Laura L.; Shuh, David K.; Hansen, Donald W.; Aracne-Ruddle, Chantel M.

2000-04-01

The phase transformation of β-HMX (>0.5% RDX) to δ phase has been studied for over twenty years and more recently with an high-contrast optical second harmonic generation technique. Shock studies of the plastic binder composites of HMX have indicated that the transition is perhaps irreversible, a result that concurs with the static pressure results published by F. Goetz et al. [1] in 1978. However, the stability field favors the β polymorph over δ as pressure is increased (up to 5.4 GPa) along any thermodynamically reasonable isotherm. In this experiment, strict control of pressure and temperature is maintained while x-ray and optical diagnostics are applied to monitor the conformational dynamics of HMX. Unlike the temperature induced β→δ transition, the pressure induced is heterogeneous in nature. The 1 bar 25 °C δ→β transition is not immediate, occuring over tens of hours. Transition points and kinetics are path dependent and consequently this paper describes our work in progress.

Pressure-induced fcc to hcp phase transition in Ni-based high entropy solid solution alloys

DOE PAGES

Zhang, Fuxiang; Zhao, Shijun; Jin, Ke; ...

2017-01-04

In this research, pressure-induced phase transition from the fcc to a hexagonal close-packed (hcp) structure wasfound in NiCoCrFe solid solution alloy starting at 13.5 GPa. The phase transition is very sluggish and the transition did not complete at ~ 40 GPa. The hcp structure is quenchable to ambient pressure. Only a very small amount (<5%) of hcp phase was found in the isostructural NiCoCr ternary alloy up to the pressure of 45 GPa and no obvious hcp phase was found in NiCoCrFePd system till to 74 GPa. Ab initio Gibbs free energy calculations indicated the energy differences between the fccmore » and the hcp phases for the three alloys are very small, but they are sensitive to temperature. Finally, the critical transition pressure in NiCoCrFe varies from 1 GPa at room temperature to 6 GPa at 500 K.« less

Hysteresis, nucleation and growth phenomena in spin-crossover solids

NASA Astrophysics Data System (ADS)

Ridier, Karl; Molnár, Gábor; Salmon, Lionel; Nicolazzi, William; Bousseksou, Azzedine

2017-12-01

The observation and the study of first-order phase transitions in cooperative spin-crossover (SCO) solids exhibiting hysteresis behaviours are of particular interest and currently constitute a burgeoning area in the field of bistable molecular materials. The understanding and the control of the transition mechanisms (nucleation and growth processes) and their dynamics within the hysteresis region appear to be a general and appealing problem from a fundamental point of view and for technological applications as well. This review reports on the recent progresses and most important findings made on the spatiotemporal dynamics of the spin transition in SCO solids, particularly through the universal nucleation and growth process. Both thermally induced and light-induced spin transitions are discussed. We open up this review to the central question of the evolution of the transition mechanisms and dynamics in SCO nano-objects, which constitute promising systems to reach ultra-fast switching, and the experimental issues inherent to such studies at the micro- and nanometric scale.

Dendrimersomes Exhibit Lamellar-to-Sponge Phase Transitions.

PubMed

Wilner, Samantha E; Xiao, Qi; Graber, Zachary T; Sherman, Samuel E; Percec, Virgil; Baumgart, Tobias

2018-05-15

Lamellar to nonlamellar membrane shape transitions play essential roles in key cellular processes, such as membrane fusion and fission, and occur in response to external stimuli, including drug treatment and heat. A subset of these transitions can be modeled by means of thermally inducible amphiphile assemblies. We previously reported on mixtures of hydrogenated, fluorinated, and hybrid Janus dendrimers (JDs) that self-assemble into complex dendrimersomes (DMSs), including dumbbells, and serve as promising models for understanding the complexity of biological membranes. Here we show, by means of a variety of complementary techniques, that DMSs formed by single JDs or by mixtures of JDs undergo a thermally induced lamellar-to-sponge transition. Consistent with the formation of a three-dimensional bilayer network, we show that DMSs become more permeable to water-soluble fluorophores after transitioning to the sponge phase. These DMSs may be useful not only in modeling isotropic membrane rearrangements of biological systems but also in drug delivery since nonlamellar delivery vehicles can promote endosomal disruption and cargo release.

Pressure-induced fcc to hcp phase transition in Ni-based high entropy solid solution alloys

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

Zhang, F. X.; Zhao, Shijun; Jin, Ke

2017-01-04

A pressure-induced phase transition from the fcc to a hexagonal close-packed (hcp) structure was found in NiCoCrFe solid solution alloy starting at 13.5 GPa. The phase transition is very sluggish and the transition did not complete at ~40 GPa. The hcp structure is quenchable to ambient pressure. Only a very small amount (<5%) of hcp phase was found in the isostructural NiCoCr ternary alloy up to the pressure of 45 GPa and no obvious hcp phase was found in NiCoCrFePd system till to 74 GPa. Ab initio Gibbs free energy calculations indicated the energy differences between the fcc and themore » hcp phases for the three alloys are very small, but they are sensitive to temperature. The critical transition pressure in NiCoCrFe varies from ~1 GPa at room temperature to ~6 GPa at 500 K.« less

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

All-optical materials design of chiral edge modes in transition-metal dichalcogenides

PubMed Central

Claassen, Martin; Jia, Chunjing; Moritz, Brian; Devereaux, Thomas P.

2016-01-01

Monolayer transition-metal dichalcogenides are novel materials which at low energies constitute a condensed-matter realization of massive relativistic fermions in two dimensions. Here, we show that this picture breaks for optical pumping—instead, the added complexity of a realistic materials description leads to a new mechanism to optically induce topologically protected chiral edge modes, facilitating optically switchable conduction channels that are insensitive to disorder. In contrast to graphene and previously discussed toy models, the underlying mechanism relies on the intrinsic three-band nature of transition-metal dichalcogenide monolayers near the band edges. Photo-induced band inversions scale linearly in applied pump field and exhibit transitions from one to two chiral edge modes on sweeping from red to blue detuning. We develop an ab initio strategy to understand non-equilibrium Floquet–Bloch bands and topological transitions, and illustrate for WS2 that control of chiral edge modes can be dictated solely from symmetry principles and is not qualitatively sensitive to microscopic materials details. PMID:27721504

Field-Induced Transitions in Anisotropic Kondo Lattice — Application to CeT2Al10 —

NASA Astrophysics Data System (ADS)

Kikuchi, Taku; Hoshino, Shintaro; Shibata, Naokazu; Kuramoto, Yoshio

2017-09-01

The magnetic properties of an anisotropic Kondo lattice are investigated under a magnetic field using dynamical mean field theory and the continuous-time quantum Monte Carlo method. The magnetic phase diagram is determined from the temperature dependence of both uniform and staggered magnetizations in magnetic fields. We find a spin-flop transition inside the antiferromagnetic (AF) phase, whose transition field increases with increasing Kondo coupling while the AF transition temperature decreases. These results cannot be described by a simple spin Hamiltonian and are consistent with the experimental results of the field-induced transition observed in CeT2Al10 (T = Ru, Os). The anisotropic susceptibilities of CeT2Al10 are reproduced in the whole temperature range by incorporating the effects of the crystalline electric field (CEF) in the anisotropic Kondo lattice. We also propose a possible explanation for the difference in anisotropies between the magnetic susceptibility and AF moments observed in experiments.

Reversible superconductor-insulator transition in LiTi2O4 induced by Li-ion electrochemical reaction

PubMed Central

Yoshimatsu, K.; Niwa, M.; Mashiko, H.; Oshima, T.; Ohtomo, A.

2015-01-01

Transition metal oxides display various electronic and magnetic phases such as high-temperature superconductivity. Controlling such exotic properties by applying an external field is one of the biggest continuous challenges in condensed matter physics. Here, we demonstrate clear superconductor-insulator transition of LiTi2O4 films induced by Li-ion electrochemical reaction. A compact electrochemical cell of pseudo-Li-ion battery structure is formed with a superconducting LiTi2O4 film as an anode. Li content in the film is controlled by applying a constant redox voltage. An insulating state is achieved by Li-ion intercalation to the superconducting film by applying reduction potential. In contrast, the superconducting state is reproduced by applying oxidation potential to the Li-ion intercalated film. Moreover, superconducting transition temperature is also recovered after a number of cycles of Li-ion electrochemical reactions. This complete reversible transition originates in difference in potentials required for deintercalation of initially contained and electrochemically intercalated Li+ ions. PMID:26541508

Reversible superconductor-insulator transition in LiTi2O4 induced by Li-ion electrochemical reaction.

PubMed

Yoshimatsu, K; Niwa, M; Mashiko, H; Oshima, T; Ohtomo, A

2015-11-06

Transition metal oxides display various electronic and magnetic phases such as high-temperature superconductivity. Controlling such exotic properties by applying an external field is one of the biggest continuous challenges in condensed matter physics. Here, we demonstrate clear superconductor-insulator transition of LiTi2O4 films induced by Li-ion electrochemical reaction. A compact electrochemical cell of pseudo-Li-ion battery structure is formed with a superconducting LiTi2O4 film as an anode. Li content in the film is controlled by applying a constant redox voltage. An insulating state is achieved by Li-ion intercalation to the superconducting film by applying reduction potential. In contrast, the superconducting state is reproduced by applying oxidation potential to the Li-ion intercalated film. Moreover, superconducting transition temperature is also recovered after a number of cycles of Li-ion electrochemical reactions. This complete reversible transition originates in difference in potentials required for deintercalation of initially contained and electrochemically intercalated Li(+) ions.

Tension-dependent structural deformation alters single-molecule transition kinetics.

PubMed

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

2011-02-01

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

Tension-dependent structural deformation alters single-molecule transition kinetics

PubMed Central

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

2011-01-01

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

Photoswitching of glass transition temperatures of azobenzene-containing polymers induces reversible solid-to-liquid transitions.

PubMed

Zhou, Hongwei; Xue, Changguo; Weis, Philipp; Suzuki, Yasuhito; Huang, Shilin; Koynov, Kaloian; Auernhammer, Günter K; Berger, Rüdiger; Butt, Hans-Jürgen; Wu, Si

2017-02-01

The development of polymers with switchable glass transition temperatures (T g ) can address scientific challenges such as the healing of cracks in high-T g polymers and the processing of hard polymers at room temperature without using plasticizing solvents. Here, we demonstrate that light can switch the T g of azobenzene-containing polymers (azopolymers) and induce reversible solid-to-liquid transitions of the polymers. The azobenzene groups in the polymers exhibit reversible cis-trans photoisomerization abilities. Trans azopolymers are solids with T g above room temperature, whereas cis azopolymers are liquids with T g below room temperature. Because of the photoinduced solid-to-liquid transitions of these polymers, light can reduce the surface roughness of azopolymer films by almost 600%, repeatedly heal cracks in azopolymers, and control the adhesion of azopolymers for transfer printing. The photoswitching of T g provides a new strategy for designing healable polymers with high T g and allows for control over the mechanical properties of polymers with high spatiotemporal resolution.

Optical studies of the charge localization and delocalization in conducting polymers

NASA Astrophysics Data System (ADS)

Kim, Youngmin

A systematic charge transport study on the thermochromism of polyaniline (PAN) doped with a plasticizing dopant, and on a field effect device using conducting poly (3,4-ethylenedioxythiophene) (PEDOT) as its active material, was made at optical (20--45,000 cm-1) frequencies to probe the charge localization and delocalization phenomena and the insulator to metal transition (IMT) in the inhomogeneous conducting polymer system. Temperature dependent reflectance [20--8000 cm -1 (2.5 meV--1eV)] of the PAN sample, together with absorbance and do transport study done by Dr. Pron at the Laboratoire de Physique des Metaux Synthetiques in Grenoble, France, shows spectral weight loss in the infrared region but the reflectance in the very low frequency (below 100 cm-1) remains unaffected. There are two localization transitions. The origin of the 200 K localization transition that affect >˜15% of the electrons is the glass transition emanating from the dopants. The transition principally affects the IR response in the range of 200--8000 cm -1. The low temperature (<75K) localization transition affects the few electrons that provide the high conductivity. It is suggested that these electrons are localized by disorder at the lowest temperature and become delocalized through phonon induced delocalization as the temperature increases to 75K. It is noted that this temperature is typical of a Debye temperature in many organic materials. The thermocromism is attributed to the weak localization to strong localization transition through the glass transition temperature. Below the glass transition temperature (Tg), the lattice is "frozen" in configuration that reduces the charge delocalization and lead to cause increase of strongly localized polarons. Time variation of source-drain current, real-time IR reflectance [20--8000 cm-1 (2.5 meV--1eV)] modulation, and real-time UV/VIS/NIR absorbance [380--2400 nm (0.5--3.3 eV)] modulation were measured to investigate the field induced charge localization of PEDOT field effect device. Layer by layer thin film analysis showed strong localization of free carriers. The temperature dependence of the do conductivity changes with application of the gate voltage demonstrating that the electric field effect has changed bulk charge transport in the active channel despite the expected screening due to mobile charge carriers. Mid IR (500--8000 cm-1) reflectance showed little change in the vibrational modes, which distinguish this phenomenon from the doping-dedoping induced electrochemical MIT. UV/Vis/NIR absorbance modulation clearly showed that the increase of the strong localization of charges with the pi-pi* bandgap transition unchanged. It is proposed that conducting polymer is near the metal to insulator transition and that the applied gate voltage leads to this transition through field induced ion motion.

Anomalous expansion of Nb nanowires in a NiTi matrix under high pressure

DOE PAGES

Yu, Cun; Ren, Yang; Cui, Lishan; ...

2016-10-17

Under high pressure, materials usually shrink during compression as described by an equation of state. Here, we present the anomalous volume expansion behavior of a one-dimensional Nb nanowire embedded in a NiTi transforming matrix, while the matrix undergoes a pressure-induced martensitic transformation. The Nb volume expansion depends on the NiTi transition pressure range from the matrix, which is controlled by the shear strain induced by different pressure transmitting media. The transformation-induced interfacial stresses between Nb and NiTi may play a major role in this anomaly. In conclusion, our discovery sheds new light on the nano-interfacial effect on mechanical anomalies inmore » heterogeneous systems during a pressure-induced phase transition.« less

Current-induced strong diamagnetism in the Mott insulator Ca2RuO4

NASA Astrophysics Data System (ADS)

Sow, Chanchal; Yonezawa, Shingo; Kitamura, Sota; Oka, Takashi; Kuroki, Kazuhiko; Nakamura, Fumihiko; Maeno, Yoshiteru

2017-11-01

Mott insulators can host a surprisingly diverse set of quantum phenomena when their frozen electrons are perturbed by various stimuli. Superconductivity, metal-insulator transition, and colossal magnetoresistance induced by element substitution, pressure, and magnetic field are prominent examples. Here we report strong diamagnetism in the Mott insulator calcium ruthenate (Ca2RuO4) induced by dc electric current. The application of a current density of merely 1 ampere per centimeter squared induces diamagnetism stronger than that in other nonsuperconducting materials. This change is coincident with changes in the transport properties as the system becomes semimetallic. These findings suggest that dc current may be a means to control the properties of materials in the vicinity of a Mott insulating transition.

Spin crossover in liquid (Mg,Fe)O at extreme conditions

NASA Astrophysics Data System (ADS)

Holmström, E.; Stixrude, L.

2016-05-01

We use first-principles free-energy calculations to predict a pressure-induced spin crossover in the liquid planetary material (Mg,Fe)O, whereby the magnetic moments of Fe ions vanish gradually over a range of hundreds of GPa. Because electronic entropy strongly favors the nonmagnetic low-spin state of Fe, the crossover has a negative effective Clapeyron slope, in stark contrast to the crystalline counterpart of this transition-metal oxide. Diffusivity of liquid (Mg,Fe)O is similar to that of MgO, displaying a weak dependence on element and spin state. Fe-O and Mg-O coordination increases from approximately 4 to 7 as pressure goes from 0 to 200 GPa. We find partitioning of Fe to induce a density inversion between the crystal and melt, implying separation of a basal magma ocean from a surficial one in the early Earth. The spin crossover induces an anomaly into the density contrast, and the oppositely signed Clapeyron slopes for the crossover in the liquid and crystalline phases imply that the solid-liquid transition induces a spin transition in (Mg,Fe)O.

[NF-kappaB-induced gp96 up-regulation promotes hepatocyte growth, cell cycle progression and transition].

PubMed

Feng, Cong; Wu, Bo; Fan, Hongxia; Li, Changfei; Meng, Songdong

2014-10-04

To investigate the mechanism of gp96 raised during hepatitis B virus (HBV) infection and the pathological mechanism. The mechanism of NF-KB activating gp96 expression was determined by bioinformatics analysis, luciferase reporter assay, real-time PCR and Western blot. The effect of over-expression and knockdown gp96 expression by transfection or RNA interference on hepatocyte proliferation, apoptosis and cell cycle was examined by CCK-8 and flow cytometry. The role of gp96 for HCC development was determined by epithelial-mesenchymal transition (EMT) and colony formation assay. NF-kB significantly increased the gp96 expression by binding to the NF-kappaB binding site. Over-expression and knockdown studies both show that gp96 promoted hepatocyte proliferation, inhibited apoptosis, and induced G0/G1 to S phase cell cycle progression. Moreover, gp96 induced epithelial-mesenchymal transition and increased colony formation ability of hepatocytes. Our results therefore provide insights in chronic HBV infection-induced gp96 expression, and indicate that elevated gp96 may contribute to HCC development during chronic inflammation.

Reversible shear-induced crystallization above equilibrium freezing temperature in a lyotropic surfactant system

PubMed Central

Rathee, Vikram; Krishnaswamy, Rema; Pal, Antara; Raghunathan, V. A.; Impéror-Clerc, Marianne; Pansu, Brigitte; Sood, A. K.

2013-01-01

We demonstrate a unique shear-induced crystallization phenomenon above the equilibrium freezing temperature in weakly swollen isotropic and lamellar mesophases with bilayers formed in a cationic-anionic mixed surfactant system. Synchrotron rheological X-ray diffraction study reveals the crystallization transition to be reversible under shear (i.e., on stopping the shear, the nonequilibrium crystalline phase melts back to the equilibrium mesophase). This is different from the shear-driven crystallization below , which is irreversible. Rheological optical observations show that the growth of the crystalline phase occurs through a preordering of the phase to an phase induced by shear flow, before the nucleation of the phase. Shear diagram of the phase constructed in the parameter space of shear rate vs. temperature exhibits and transitions above the equilibrium crystallization temperature , in addition to the irreversible shear-driven nucleation of in the phase below . In addition to revealing a unique class of nonequilibrium phase transition, the present study urges a unique approach toward understanding shear-induced phenomena in concentrated mesophases of mixed amphiphilic systems. PMID:23986497

Melting along the Hugoniot and solid phase transition for Sn via sound velocity measurements

NASA Astrophysics Data System (ADS)

Song, Ping; Cai, Ling-cang; Tao, Tian-jiong; Yuan, Shuai; Chen, Hong; Huang, Jin; Zhao, Xin-wen; Wang, Xue-jun

2016-11-01

It is very important to determine the phase boundaries for materials with complex crystalline phase structures to construct their corresponding multi-phase equation of state. By measuring the sound velocity of Sn with different porosities, different shock-induced melting pressures along the solid-liquid phase boundary could be obtained. The incipient shock-induced melting of porous Sn samples with two different porosities occurred at a pressure of about 49.1 GPa for a porosity of 1.01 and 45.6 GPa for a porosity of 1.02, based on measurements of the sound velocity. The incipient shock-induced melting pressure of solid Sn was revised to 58.1 GPa using supplemental measurements of the sound velocity. Trivially, pores in Sn decreased the shock-induced melting pressure. Based on the measured longitudinal sound velocity data, a refined solid phase transition and the Hugoniot temperature-pressure curve's trend are discussed. No bcc phase transition occurs along the Hugoniot for porous Sn; further investigation is required to understand the implications of this finding.

Tailoring transition-metal hydroxides and oxides by photon-induced reactions

DOE PAGES

Niu, Kai -Yang; Fang, Liang; Ye, Rong; ...

2016-10-18

Controlled synthesis of transition-metal hydroxides and oxides with earth-abundant elements have attracted significant interest because of their wide applications, for example as battery electrode materials or electrocatalysts for fuel generation. Here, we report the tuning of the structure of transition-metal hydroxides and oxides by controlling chemical reactions using an unfocused laser to irradiate the precursor solution. A Nd:YAG laser with wavelengths of 532 nm or 1064 nm was used. The Ni 2+, Mn 2+, and Co 2+ ion-containing aqueous solution undergoes photo-induced reactions and produces hollow metal-oxide nanospheres (Ni 0.18Mn 0.45Co 0.37O x) or core–shell metal hydroxide nanoflowers ([Ni 0.15Mnmore » 0.15Co 0.7(OH) 2](NO 3) 0.2•H 2O), depending on the laser wavelengths. We propose two reaction pathways, either by photo-induced redox reaction or hydrolysis reaction, which are responsible for the formation of distinct nanostructures. As a result, the study of photon-induced materials growth shines light on the rational design of complex nanostructures with advanced functionalities.« less

Dynamics of Propofol-Induced Loss of Consciousness Across Primate Neocortex.

PubMed

Ishizawa, Yumiko; Ahmed, Omar J; Patel, Shaun R; Gale, John T; Sierra-Mercado, Demetrio; Brown, Emery N; Eskandar, Emad N

2016-07-20

The precise neural mechanisms underlying transitions between consciousness and anesthetic-induced unconsciousness remain unclear. Here, we studied intracortical neuronal dynamics leading to propofol-induced unconsciousness by recording single-neuron activity and local field potentials directly in the functionally interconnecting somatosensory (S1) and frontal ventral premotor (PMv) network during a gradual behavioral transition from full alertness to loss of consciousness (LOC) and on through a deeper anesthetic level. Macaque monkeys were trained for a behavioral task designed to determine the trial-by-trial alertness and neuronal response to tactile and auditory stimulation. We show that disruption of coherent beta oscillations between S1 and PMv preceded, but did not coincide with, the LOC. LOC appeared to correspond to pronounced but brief gamma-/high-beta-band oscillations (lasting ∼3 min) in PMv, followed by a gamma peak in S1. We also demonstrate that the slow oscillations appeared after LOC in S1 and then in PMv after a delay, together suggesting that neuronal dynamics are very different across S1 versus PMv during LOC. Finally, neurons in both S1 and PMv transition from responding to bimodal (tactile and auditory) stimulation before LOC to only tactile modality during unconsciousness, consistent with an inhibition of multisensory integration in this network. Our results show that propofol-induced LOC is accompanied by spatiotemporally distinct oscillatory neuronal dynamics across the somatosensory and premotor network and suggest that a transitional state from wakefulness to unconsciousness is not a continuous process, but rather a series of discrete neural changes. How information is processed by the brain during awake and anesthetized states and, crucially, during the transition is not clearly understood. We demonstrate that neuronal dynamics are very different within an interconnecting cortical network (primary somatosensory and frontal premotor area) during the loss of consciousness (LOC) induced by propofol in nonhuman primates. Coherent beta oscillations between these regions are disrupted before LOC. Pronounced but brief gamma-band oscillations appear to correspond to LOC. In addition, neurons in both of these cortices transition from responding to both tactile and auditory stimulation before LOC to only tactile modality during unconsciousness. We demonstrate that propofol-induced LOC is accompanied by spatiotemporally distinctive neuronal dynamics in this network with concurrent changes in multisensory processing. Copyright © 2016 the authors 0270-6474/16/367718-09$15.00/0.

Enhancement of yield strength in zirconium metal through high-pressure induced structural phase transition

NASA Astrophysics Data System (ADS)

Zhao, Yusheng; Zhang, Jianzhong

2007-11-01

We report here a high-pressure phase-transition induced strengthening in ultrapure zirconium metal. The determined yield strength shows more than sixfold abrupt increase at the transition pressure of Pc=6GPa, from σyα≈180MPa in the low-pressure phase of α-Zr to σyω≈1180MPa in the high-pressure phase of ω-Zr. The observed enhancement provides an alternate route for material strengthening and is the most significant among the known strengthening techniques for metals. Our findings support the theoretical simulations of the substantial covalent bonding and "rougher" corrugation of slip planes for dislocations in the ω-phase of zirconium.

Phonon-induced ultrafast band gap control in LaTiO3

NASA Astrophysics Data System (ADS)

Gu, Mingqiang; Rondinelli, James M.

We propose a route for ultrafast band gap engineering in correlated transition metal oxides by using optically driven phonons. We show that the ∖Gamma-point electron band energies can be deterministically tuned in the nonequilibrium state. Taking the Mott insulator LaTiO3 as an example, we show that such phonon-assisted processes dynamically induce an indirect-to-direct band gap transition or even a metal-to-insulator transition, depending on the electron correlation strength. We explain the origin of the dynamical band structure control and also establish its generality by examining related oxides. Lastly, we describe experimental routes to realize the band structure control with impulsive stimulated Raman scattering.

High pressure and temperature induced structural and elastic properties of lutetium chalcogenides

NASA Astrophysics Data System (ADS)

Shriya, S.; Kinge, R.; Khenata, R.; Varshney, Dinesh

2018-04-01

The high-pressure structural phase transition and pressure as well temperature induced elastic properties of rock salt to CsCl structures in semiconducting LuX (X = S, Se, and Te) chalcogenides compound have been performed using effective interionic interaction potential with emphasis on charge transfer interactions and covalent contribution. Estimated values of phase transition pressure and the volume discontinuity in pressure-volume phase diagram indicate the structural phase transition from ZnS to NaCl structure. From the investigations of elastic constants the pressure (temperature) dependent volume collapse/expansion, melting temperature TM, Hardness (HV), and young modulus (E) the LuX lattice infers mechanical stiffening, and thermal softening.

Application of MCR-ALS to reveal intermediate conformations in the thermally induced α-β transition of poly-L-lysine monitored by FT-IR spectroscopy

NASA Astrophysics Data System (ADS)

Alcaráz, Mirta R.; Schwaighofer, Andreas; Goicoechea, Héctor; Lendl, Bernhard

2017-10-01

Temperature-induced conformational transitions of poly-L-lysine were monitored with Fourier-transform infrared (FT-IR) spectroscopy between 10 °C and 70 °C. Chemometric analysis of dynamic IR spectra was performed by multivariate curve analysis-alternating least squares (MCR-ALS) of the amide I‧ and amide II‧ spectral region. With this approach, the pure spectral and concentration profiles of the conformational transition were obtained. Beside the initial α-helical, the intermediate random coil/extended helices and the final β-sheet structure, an additional intermediate PLL conformation was identified and attributed to a transient β-sheet structure.

Force Induced Globule-to-Coil Transition of Single Polymer Chains.

NASA Astrophysics Data System (ADS)

Gunari, Nikhil; Walker, Gilbert

2008-03-01

Force induced structural transitions of individual homopolymer chains have been studied in different solvent conditions using single molecule force spectroscopy. Single molecule mechanics in the ``fly-fishing'' mode showed a first-order like transition for polystyrene (PS) in water exhibiting a characteristic three regime force extension curve. In contrast, poly methylmethacrylate (PMMA) showed a characteristic saw-tooth pattern reminiscent of multidomain disassembly behavior similar to that seen in modular protein mechanics. The plateau force for PS and the saw-tooth pattern for PMMA disappear when measured in aqueous guanidine hydrochloride solution and in other non-solvents showing that the characteristic deformational behavior observed for the two polymers in water may be due to hydrophobic interactions .

Water deficit severity during berry development alters timing of dormancy transitions in wine grape cultivar Malbec

USDA-ARS?s Scientific Manuscript database

The objective of this study was to test the hypothesis that vine water stress during the growing season can lengthen the dormancy cycle by inducing earlier transition into endodormancy. A bud forcing assay was used to compare the dormancy transitions of field-grown ‘Malbec’ grapevines that had been ...

Bounded noise induced first-order phase transitions in a baseline non-spatial model of gene transcription

NASA Astrophysics Data System (ADS)

d'Onofrio, Alberto; Caravagna, Giulio; de Franciscis, Sebastiano

2018-02-01

In this work we consider, from a statistical mechanics point of view, the effects of bounded stochastic perturbations of the protein decay rate for a bistable biomolecular network module. Namely, we consider the perturbations of the protein decay/binding rate constant (DBRC) in a circuit modeling the positive feedback of a transcription factor (TF) on its own synthesis. The DBRC models both the spontaneous degradation of the TF and its linking to other unknown biomolecular factors or drugs. We show that bounded perturbations of the DBRC preserve the positivity of the parameter value (and also its limited variation), and induce effects of interest. First, the noise amplitude induces a first-order phase transition. This is of interest since the system in study has neither spatial components nor it is composed by multiple interacting networks. In particular, we observe that the system passes from two to a unique stochastic attractor, and vice-versa. This behavior is different from noise-induced transitions (also termed phenomenological bifurcations), where a unique stochastic attractor changes its shape depending on the values of a parameter. Moreover, we observe irreversible jumps as a consequence of the above-mentioned phase transition. We show that the illustrated mechanism holds for general models with the same deterministic hysteresis bifurcation structure. Finally, we illustrate the possible implications of our findings to the intracellular pharmacodynamics of drugs delivered in continuous infusion.

Solid-solid collapse transition in a two dimensional model molecular system.

PubMed

Singh, Rakesh S; Bagchi, Biman

2013-11-21

Solid-solid collapse transition in open framework structures is ubiquitous in nature. The real difficulty in understanding detailed microscopic aspects of such transitions in molecular systems arises from the interplay between different energy and length scales involved in molecular systems, often mediated through a solvent. In this work we employ Monte-Carlo simulation to study the collapse transition in a model molecular system interacting via both isotropic as well as anisotropic interactions having different length and energy scales. The model we use is known as Mercedes-Benz (MB), which, for a specific set of parameters, sustains two solid phases: honeycomb and oblique. In order to study the temperature induced collapse transition, we start with a metastable honeycomb solid and induce transition by increasing temperature. High density oblique solid so formed has two characteristic length scales corresponding to isotropic and anisotropic parts of interaction potential. Contrary to the common belief and classical nucleation theory, interestingly, we find linear strip-like nucleating clusters having significantly different order and average coordination number than the bulk stable phase. In the early stage of growth, the cluster grows as a linear strip, followed by branched and ring-like strips. The geometry of growing cluster is a consequence of the delicate balance between two types of interactions, which enables the dominance of stabilizing energy over destabilizing surface energy. The nucleus of stable oblique phase is wetted by intermediate order particles, which minimizes the surface free energy. In the case of pressure induced transition at low temperature the collapsed state is a disordered solid. The disordered solid phase has diverse local quasi-stable structures along with oblique-solid like domains.

Solid-solid collapse transition in a two dimensional model molecular system

NASA Astrophysics Data System (ADS)

Singh, Rakesh S.; Bagchi, Biman

2013-11-01

Solid-solid collapse transition in open framework structures is ubiquitous in nature. The real difficulty in understanding detailed microscopic aspects of such transitions in molecular systems arises from the interplay between different energy and length scales involved in molecular systems, often mediated through a solvent. In this work we employ Monte-Carlo simulation to study the collapse transition in a model molecular system interacting via both isotropic as well as anisotropic interactions having different length and energy scales. The model we use is known as Mercedes-Benz (MB), which, for a specific set of parameters, sustains two solid phases: honeycomb and oblique. In order to study the temperature induced collapse transition, we start with a metastable honeycomb solid and induce transition by increasing temperature. High density oblique solid so formed has two characteristic length scales corresponding to isotropic and anisotropic parts of interaction potential. Contrary to the common belief and classical nucleation theory, interestingly, we find linear strip-like nucleating clusters having significantly different order and average coordination number than the bulk stable phase. In the early stage of growth, the cluster grows as a linear strip, followed by branched and ring-like strips. The geometry of growing cluster is a consequence of the delicate balance between two types of interactions, which enables the dominance of stabilizing energy over destabilizing surface energy. The nucleus of stable oblique phase is wetted by intermediate order particles, which minimizes the surface free energy. In the case of pressure induced transition at low temperature the collapsed state is a disordered solid. The disordered solid phase has diverse local quasi-stable structures along with oblique-solid like domains.

Rogue-wave pattern transition induced by relative frequency.

PubMed

Zhao, Li-Chen; Xin, Guo-Guo; Yang, Zhan-Ying

2014-08-01

We revisit a rogue wave in a two-mode nonlinear fiber whose dynamics is described by two-component coupled nonlinear Schrödinger equations. The relative frequency between two modes can induce different rogue wave patterns transition. In particular, we find a four-petaled flower structure rogue wave can exist in the two-mode coupled system, which possesses an asymmetric spectrum distribution. Furthermore, spectrum analysis is performed on these different type rogue waves, and the spectrum relations between them are discussed. We demonstrate qualitatively that different modulation instability gain distribution can induce different rogue wave excitation patterns. These results would deepen our understanding of rogue wave dynamics in complex systems.

Optically induced Lifshitz transition in bilayer graphene

NASA Astrophysics Data System (ADS)

Iorsh, I. V.; Dini, K.; Kibis, O. V.; Shelykh, I. A.

2017-10-01

It is shown theoretically that the renormalization of the electron energy spectrum of bilayer graphene with a strong high-frequency electromagnetic field (dressing field) results in the Lifshitz transition—the abrupt change in the topology of the Fermi surface near the band edge. This effect substantially depends on the polarization of the field: The linearly polarized dressing field induces the Lifshitz transition from the quadruply connected Fermi surface to the doubly connected one, whereas the circularly polarized field induces the multicritical point where the four different Fermi topologies may coexist. As a consequence, the discussed phenomenon creates a physical basis to control the electronic properties of bilayer graphene with light.

Shear-induced conformational ordering, relaxation, and crystallization of isotactic polypropylene.

PubMed

An, Haining; Li, Xiangyang; Geng, Yong; Wang, Yunlong; Wang, Xiao; Li, Liangbin; Li, Zhongming; Yang, Chuanlu

2008-10-02

The shear-induced coil-helix transition of isotactic polypropylene (iPP) has been studied with time-resolved Fourier transform infrared spectroscopy at various temperatures. The effects of temperature, shear rate, and strain on the coil-helix transition were studied systematically. The induced conformational order increases with the shear rate and strain. A threshold of shear strain is required to induce conformational ordering. High temperature reduces the effect of shear on the conformational order, though a simple correlation was not found. Following the shear-induced conformational ordering, relaxation of helices occurs, which follows the first-order exponential decay at temperatures well above the normal melting point of iPP. The relaxation time versus temperature is fitted with an Arrhenius law, which generates an activation energy of 135 kJ/mol for the helix-coil transition of iPP. At temperatures around the normal melting point, two exponential decays are needed to fit well on the relaxation kinetic of helices. This suggests that two different states of helices are induced by shear: (i) isolated single helices far away from each other without interactions, which have a fast relaxation kinetic; (ii) aggregations of helices or helical bundles with strong interactions among each other, which have a much slower relaxation process. The helical bundles are assumed to be the precursors of nuclei for crystallization. The different helix concentrations and distributions are the origin of the three different processes of crystallization after shear. The correlation between the shear-induced conformational order and crystallization is discussed.

Induced adult stem (iAS) cells and induced transit amplifying progenitor (iTAP) cells-a possible alternative to induced pluripotent stem (iPS) cells?

PubMed

Heng, Boon Chin; Richards, Mark; Ge, Zigang; Shu, Yimin

2010-02-01

The successful derivation of iPSC lines effectively demonstrates that it is possible to reset the 'developmental clock' of somatic cells all the way back to the initial embryonic state. Hence, it is plausible that this clock may instead be turned back half-way to a less immature developmental stage that is more directly applicable to clinical therapeutic applications or for in vitro pharmacology/toxicology screening assays. Such a suitable developmental state is postulated to be either the putative transit amplifying progenitor stage or adult stem cell stage. It is hypothetically possible to reprogram mature and terminally differentiated somatic cells back to the adult stem cell or transit amplifying progenitor stage, in a manner similar to the derivation of iPSC. It is proposed that the terminology 'Induced Adult Stem Cells' (iASC) or 'Induced Transit Amplifying Progenitor Cells' (iTAPC) be used to described such reprogrammed somatic cells. Of particular interest, is the possibility of resetting the developmental clock of mature differentiated somatic cells of the mesenchymal lineage, explanted from adipose tissue, bone marrow and cartilage. The putative adult stem cell sub-population from which these cells are derived, commonly referred to as 'mesenchymal stem cells', are highly versatile and hold much therapeutic promise in regenerative medicine, as attested to by numerous human clinical trials and animal studies. Perhaps it may be appropriate to term such reprogrammed cells as 'Induced Mesenchymal Stem Cells' (iMSC) or as 'Induced Mesenchumal Progenitor Cells' (iMPC). Given that cells from the same organ/tissue will share some commonalities in gene expression, we hypothesize that the generation of iASC or iTAPC would be more efficient as compared to iPSC generation, since a common epigenetic program must exist between the reprogrammed cells, adult stem cell or progenitor cell types and terminally differentiated cell types from the same organ/tissue.

Prevention of Diet-Induced Obesity Effects on Body Weight and Gut Microbiota in Mice Treated Chronically with Δ9-Tetrahydrocannabinol

PubMed Central

Cluny, Nina L.; Keenan, Catherine M.; Reimer, Raylene A.; Le Foll, Bernard; Sharkey, Keith A.

2015-01-01

Objective Acute administration of cannabinoid CB1 receptor agonists, or the ingestion of cannabis, induces short-term hyperphagia. However, the incidence of obesity is lower in frequent cannabis users compared to non-users. Gut microbiota affects host metabolism and altered microbial profiles are observed in obese states. Gut microbiota modifies adipogenesis through actions on the endocannabinoid system. This study investigated the effect of chronic THC administration on body weight and gut microbiota in diet-induced obese (DIO) and lean mice. Methods Adult male DIO and lean mice were treated daily with vehicle or THC (2mg/kg for 3 weeks and 4 mg/kg for 1 additional week). Body weight, fat mass, energy intake, locomotor activity, whole gut transit and gut microbiota were measured longitudinally. Results THC reduced weight gain, fat mass gain and energy intake in DIO but not lean mice. DIO-induced changes in select gut microbiota were prevented in mice chronically administered THC. THC had no effect on locomotor activity or whole gut transit in either lean or DIO mice. Conclusions Chronic THC treatment reduced energy intake and prevented high fat diet-induced increases in body weight and adiposity; effects that were unlikely to be a result of sedation or altered gastrointestinal transit. Changes in gut microbiota potentially contribute to chronic THC-induced actions on body weight in obesity. PMID:26633823

Helium induced fine structure in the electronic spectra of anthracene derivatives doped into superfluid helium nanodroplets

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

Pentlehner, D.; Slenczka, A., E-mail: alkwin.slenczka@chemie.uni-regensburg.de

2015-01-07

Electronic spectra of organic molecules doped into superfluid helium nanodroplets show characteristic features induced by the helium environment. Besides a solvent induced shift of the electronic transition frequency, in many cases, a spectral fine structure can be resolved for electronic and vibronic transitions which goes beyond the expected feature of a zero phonon line accompanied by a phonon wing as known from matrix isolation spectroscopy. The spectral shape of the zero phonon line and the helium induced phonon wing depends strongly on the dopant species. Phonon wings, for example, are reported ranging from single or multiple sharp transitions to broadmore » (Δν > 100 cm{sup −1}) diffuse signals. Despite the large number of example spectra in the literature, a quantitative understanding of the helium induced fine structure of the zero phonon line and the phonon wing is missing. Our approach is a systematic investigation of related molecular compounds, which may help to shed light on this key feature of microsolvation in superfluid helium droplets. This paper is part of a comparative study of the helium induced fine structure observed in electronic spectra of anthracene derivatives with particular emphasis on a spectrally sharp multiplet splitting at the electronic origin. In addition to previously discussed species, 9-cyanoanthracene and 9-chloroanthracene will be presented in this study for the first time.« less

Prevention of Diet-Induced Obesity Effects on Body Weight and Gut Microbiota in Mice Treated Chronically with Δ9-Tetrahydrocannabinol.

PubMed

Cluny, Nina L; Keenan, Catherine M; Reimer, Raylene A; Le Foll, Bernard; Sharkey, Keith A

2015-01-01

Acute administration of cannabinoid CB1 receptor agonists, or the ingestion of cannabis, induces short-term hyperphagia. However, the incidence of obesity is lower in frequent cannabis users compared to non-users. Gut microbiota affects host metabolism and altered microbial profiles are observed in obese states. Gut microbiota modifies adipogenesis through actions on the endocannabinoid system. This study investigated the effect of chronic THC administration on body weight and gut microbiota in diet-induced obese (DIO) and lean mice. Adult male DIO and lean mice were treated daily with vehicle or THC (2mg/kg for 3 weeks and 4 mg/kg for 1 additional week). Body weight, fat mass, energy intake, locomotor activity, whole gut transit and gut microbiota were measured longitudinally. THC reduced weight gain, fat mass gain and energy intake in DIO but not lean mice. DIO-induced changes in select gut microbiota were prevented in mice chronically administered THC. THC had no effect on locomotor activity or whole gut transit in either lean or DIO mice. Chronic THC treatment reduced energy intake and prevented high fat diet-induced increases in body weight and adiposity; effects that were unlikely to be a result of sedation or altered gastrointestinal transit. Changes in gut microbiota potentially contribute to chronic THC-induced actions on body weight in obesity.

EML4-ALK induces epithelial–mesenchymal transition consistent with cancer stem cell properties in H1299 non-small cell lung cancer cells

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

Guo, Fuchun; Liu, Xiaoke, E-mail: liuxk57@163.com; Qing, Qin, E-mail: qinqingscu@126.com

2015-04-10

The echinoderm microtubule-associated protein-like 4(EML4) – anaplastic lymphoma kinase (ALK) fusion gene has been identified as a driver mutation in non-small-cell lung cancer (NSCLC). However, the role of EML4-ALK in malignant transformation is not entirely clear. Here, for the first time, we showed that H1299 NSCLC cells stably expressing EML4-ALK acquire EMT phenotype, associated with enhanced invasive migration and increased expression of EMT-inducing transcription factors. H1299-EML4-ALK cells also displayed cancer stem cell-like properties with a concomitant up-regulation of CD133 and enhanced ability of mammospheres formation. Moreover, we found that inhibition of ERK1/2 reversed EMT induced by EML4-ALK in H1299 cells.more » Taken together, these results suggested that EML4-ALK induced ERK activation is mechanistically associated with EMT phenotype. Thus, inhibition of ERK signaling pathway could be a potential strategy in treatment of NSCLC patients with EML4-ALK translocation. - Highlights: • EML4-ALK induced epithelial–mesenchymal transition in H1299 cells. • Expression of EML4-ALK promotes invasion and migration in vitro. • EML4-ALK enhanced sphere formation and stem cell-like properties in H1299 cells. • Blockage of ERK1/2 reverse Epithelial–Mesenchymal transition induced by EML4-ALK.« less

The herbal medicine, Dai-Kenchu-to, accelerates delayed gastrointestinal transit after the operation in rats.

PubMed

Fukuda, Hiroyuki; Chen, Cindy; Mantyh, Christopher; Ludwig, Kirk; Pappas, Theodore N; Takahashi, Toku

2006-04-01

Post-operative ileus (POI) is a transient bowel dysmotility after operation. We have previously shown that laparotomy alone significantly delayed gastrointestinal (GI) transit, compared to anesthesia alone. The GI transit was further delayed after laparotomy plus intestinal manipulation. Dai-Kenchu-to (DKT), an herbal medicine, has been used for treating adhesive bowel obstruction in Japan. We studied whether DKT improves delayed GI transit after the operation, with or without morphine administration in rats. Under isoflurane anesthesia, POI was induced by laparotomy with intestinal manipulation. Immediately after the operation, the rats received 51Cr by gavage. Three hours after the operation, the rats were sacrificed and GI transit was estimated by calculating the geometric center (GC). DKT (120, 360, and 1,200 mg/kg) were administered by gavage after the operation, with or without morphine administration (1 mg/kg s.c.). A muscarinic receptor antagonist (atropine; 50 mug/kg), a 5HT3 receptor antagonist (ondansetron; 1 mg/kg) and a 5HT4 receptor antagonist (GR113,808; 3 mg/kg) were administered before the operation. Truncal vagotomy was performed preceding the operation. Laparotomy with intestinal manipulation produced a significant delay in GI transit (GC = 2.93 +/- 0.16), compared to that of anesthesia alone (9.51 +/- 0.45). DKT at the dose of 360 mg/kg (GC = 3.77 +/- 0.10, P < 0.01) and 1,200 mg/kg (GC = 3.77 +/- 0.20, P < 0.01) significantly accelerated delayed GI transit induced by operation. Ondansetron, GR113,808, atropine, and truncal vagotomy abolished the stimulatory effect of DKT (360 mg/kg). When morphine was administered, GI transit was further reduced (GC = 1.97 +/- 0.10). DKT at the dose of 360 mg/kg (GC = 2.81 +/- 0.22, P < 0.05) and 1,200 mg/kg (GC = 2.87 +/- 0.23, P < 0.05) significantly improved delayed GI transit in morphine treated rats. DKT accelerates delayed GI transit induced by intestinal manipulation with and without concomitant morphine administration. DKT treatment may be useful for the patients with POI.

Cholesteric-nematic transitions induced by a shear flow and a magnetic field

NASA Astrophysics Data System (ADS)

Zakhlevnykh, A. N.; Makarov, D. V.; Novikov, A. A.

2017-10-01

The untwisting of the helical structure of a cholesteric liquid crystal under the action of a magnetic field and a shear flow has been studied theoretically. Both factors can induce the cholesteric-nematic transition independently; however, the difference in the orienting actions of the magnetic field and the shear flow leads to competition between magnetic and hydrodynamic mechanisms of influence on the cholesteric liquid crystal. We have analyzed different orientations of the magnetic field relative to the direction of the flow in the shear plane. In a number of limiting cases, the analytic dependences are obtained for the pitch of the cholesteric helix deformed by the shear flow. The phase diagrams of the cholesteric-nematic transitions and the pitch of the cholesteric helix are calculated for different values of the magnetic field strength and the angle of orientation, the flow velocity gradient, and the reactive parameter. It is shown that the magnetic field stabilizes the orientation of the director in the shear flow and expands the boundaries of orientability of cholesterics. It has been established that the shear flow shifts the critical magnetic field strength of the transition. It is shown that a sequence of reentrant orientational cholesteric-nematic-cholesteric transitions can be induced by rotating the magnetic field in certain intervals of its strength and shear flow velocity gradients.

A Conserved Behavioral State Barrier Impedes Transitions between Anesthetic-Induced Unconsciousness and Wakefulness: Evidence for Neural Inertia

PubMed Central

Friedman, Eliot B.; Sun, Yi; Moore, Jason T.; Hung, Hsiao-Tung; Meng, Qing Cheng; Perera, Priyan; Joiner, William J.; Thomas, Steven A.; Eckenhoff, Roderic G.; Sehgal, Amita; Kelz, Max B.

2010-01-01

One major unanswered question in neuroscience is how the brain transitions between conscious and unconscious states. General anesthetics offer a controllable means to study these transitions. Induction of anesthesia is commonly attributed to drug-induced global modulation of neuronal function, while emergence from anesthesia has been thought to occur passively, paralleling elimination of the anesthetic from its sites in the central nervous system (CNS). If this were true, then CNS anesthetic concentrations on induction and emergence would be indistinguishable. By generating anesthetic dose-response data in both insects and mammals, we demonstrate that the forward and reverse paths through which anesthetic-induced unconsciousness arises and dissipates are not identical. Instead they exhibit hysteresis that is not fully explained by pharmacokinetics as previously thought. Single gene mutations that affect sleep-wake states are shown to collapse or widen anesthetic hysteresis without obvious confounding effects on volatile anesthetic uptake, distribution, or metabolism. We propose a fundamental and biologically conserved concept of neural inertia, a tendency of the CNS to resist behavioral state transitions between conscious and unconscious states. We demonstrate that such a barrier separates wakeful and anesthetized states for multiple anesthetics in both flies and mice, and argue that it contributes to the hysteresis observed when the brain transitions between conscious and unconscious states. PMID:20689589

Ferroelasticity and domain physics in two-dimensional transition metal dichalcogenide monolayers.

PubMed

Li, Wenbin; Li, Ju

2016-02-24

Monolayers of transition metal dichalcogenides can exist in several structural polymorphs, including 2H, 1T and 1T'. The low-symmetry 1T' phase has three orientation variants, resulting from the three equivalent directions of Peierls distortion in the parental 1T phase. Using first-principles calculations, we predict that mechanical strain can switch the relative thermodynamic stability between the orientation variants of the 1T' phase. We find that such strain-induced variant switching only requires a few percent elastic strain, which is eminently achievable experimentally with transition metal dichalcogenide monolayers. Calculations indicate that the transformation barrier associated with such variant switching is small (<0.2 eV per chemical formula unit), suggesting that strain-induced variant switching can happen under laboratory conditions. Monolayers of transition metal dichalcogenides with 1T' structure therefore have the potential to be ferroelastic and shape memory materials with interesting domain physics.

Light-induced catalytic and cytotoxic properties of phosphorescent transition metal compounds with a d8 electronic configuration.

PubMed

To, Wai-Pong; Zou, Taotao; Sun, Raymond Wai-Yin; Che, Chi-Ming

2013-07-28

Transition metal compounds are well documented to have diverse applications such as in catalysis, light-emitting materials and therapeutics. In the areas of photocatalysis and photodynamic therapy, metal compounds of heavy transition metals are highly sought after because they can give rise to triplet excited states upon photoexcitation. The long lifetimes (more than 1 μs) of the triplet states of transition metal compounds allow for bimolecular reactions/processes such as energy transfer and/or electron transfer to occur. Reactions of triplet excited states of luminescent metal compounds with oxygen in cells may generate reactive oxygen species and/or induce damage to DNA, leading to cell death. This article recaps the recent findings on photochemical and phototoxic properties of luminescent platinum(II) and gold(III) compounds both from the literature and experimental results from our group.

Evidence for photo-induced monoclinic metallic VO{sub 2} under high pressure

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

Hsieh, Wen-Pin, E-mail: wphsieh@stanford.edu; Mao, Wendy L.; Department of Geological and Environmental Sciences, Stanford University, Stanford, California 94305

2014-01-13

We combine ultrafast pump-probe spectroscopy with a diamond-anvil cell to decouple the insulator-metal electronic transition from the lattice symmetry changing structural transition in the archetypal strongly correlated material vanadium dioxide. Coherent phonon spectroscopy enables tracking of the photo-excited phonon vibrational frequencies of the low temperature, monoclinic (M{sub 1})-insulating phase that transforms into the metallic, tetragonal rutile structured phase at high temperature or via non-thermal photo-excitations. We find that in contrast with ambient pressure experiments where strong photo-excitation promptly induces the electronic transition along with changes in the lattice symmetry, at high pressure, the coherent phonons of the monoclinic (M{sub 1})more » phase are still clearly observed upon the photo-driven phase transition to a metallic state. These results demonstrate the possibility of synthesizing and studying transient phases under extreme conditions.« less

Ferroelasticity and domain physics in two-dimensional transition metal dichalcogenide monolayers

DOE PAGES

Li, Wenbin; Li, Ju

2016-02-24

Monolayers of transition metal dichalcogenides can exist in several structural polymorphs, including 2H, 1T and 1T'. The low-symmetry 1T' phase has three orientation variants, resulting from the three equivalent directions of Peierls distortion in the parental 1T phase. Using first-principles calculations, we predict that mechanical strain can switch the relative thermodynamic stability between the orientation variants of the 1T' phase. We find that such strain-induced variant switching only requires a few percent elastic strain, which is eminently achievable experimentally with transition metal dichalcogenide monolayers. Calculations indicate that the transformation barrier associated with such variant switching is small (<0.2 eV permore » chemical formula unit), suggesting that strain-induced variant switching can happen under laboratory conditions. Furthermore, monolayers of transition metal dichalcogenides with 1T' structure therefore have the potential to be ferroelastic and shape memory materials with interesting domain physics.« less

Raman signatures of inversion symmetry breaking and structural phase transition in type-II Weyl semimetal MoTe2.

PubMed

Zhang, Kenan; Bao, Changhua; Gu, Qiangqiang; Ren, Xiao; Zhang, Haoxiong; Deng, Ke; Wu, Yang; Li, Yuan; Feng, Ji; Zhou, Shuyun

2016-12-09

Transition metal dichalcogenide MoTe 2 is an important candidate for realizing the newly predicted type-II Weyl fermions, for which the breaking of the inversion symmetry is a prerequisite. Here we present direct spectroscopic evidence for the inversion symmetry breaking in the low-temperature phase of MoTe 2 by systematic Raman experiments and first-principles calculations. We identify five lattice vibrational modes that are Raman-active only in the low-temperature noncentrosymmetric structure. A hysteresis is also observed in the peak intensity of inversion symmetry-activated Raman modes, confirming a temperature-induced structural phase transition with a concomitant change in the inversion symmetry. Our results provide definitive evidence for the low-temperature noncentrosymmetric T d phase from vibrational spectroscopy, and suggest MoTe 2 as an ideal candidate for investigating the temperature-induced topological phase transition.

Raman signatures of inversion symmetry breaking and structural phase transition in type-II Weyl semimetal MoTe2

PubMed Central

Zhang, Kenan; Bao, Changhua; Gu, Qiangqiang; Ren, Xiao; Zhang, Haoxiong; Deng, Ke; Wu, Yang; Li, Yuan; Feng, Ji; Zhou, Shuyun

2016-01-01

Transition metal dichalcogenide MoTe2 is an important candidate for realizing the newly predicted type-II Weyl fermions, for which the breaking of the inversion symmetry is a prerequisite. Here we present direct spectroscopic evidence for the inversion symmetry breaking in the low-temperature phase of MoTe2 by systematic Raman experiments and first-principles calculations. We identify five lattice vibrational modes that are Raman-active only in the low-temperature noncentrosymmetric structure. A hysteresis is also observed in the peak intensity of inversion symmetry-activated Raman modes, confirming a temperature-induced structural phase transition with a concomitant change in the inversion symmetry. Our results provide definitive evidence for the low-temperature noncentrosymmetric Td phase from vibrational spectroscopy, and suggest MoTe2 as an ideal candidate for investigating the temperature-induced topological phase transition. PMID:27934874

Substrate effects on photoluminescence and low temperature phase transition of methylammonium lead iodide hybrid perovskite thin films

NASA Astrophysics Data System (ADS)

Shojaee, S. A.; Harriman, T. A.; Han, G. S.; Lee, J.-K.; Lucca, D. A.

2017-07-01

We examine the effects of substrates on the low temperature photoluminescence (PL) spectra and phase transition in methylammonium lead iodide hybrid perovskite (CH3NH3PbI3) thin films. Structural characterization at room temperature with X-ray diffraction (XRD), scanning electron microscopy (SEM), and Raman spectroscopy indicated that while the chemical structure of films deposited on glass and quartz was similar, the glass substrate induced strain in the perovskite films and suppressed the grain growth. The luminescence response and phase transition of the perovskite thin films were studied by PL spectroscopy. The induced strain was found to affect both the room temperature and low temperature PL spectra of the hybrid perovskite films. In addition, it was found that the effects of the glass substrate inhibited a tetragonal to orthorhombic phase transition such that it occurred at lower temperatures.

Channel Noise-Enhanced Synchronization Transitions Induced by Time Delay in Adaptive Neuronal Networks with Spike-Timing-Dependent Plasticity

NASA Astrophysics Data System (ADS)

Xie, Huijuan; Gong, Yubing; Wang, Baoying

In this paper, we numerically study the effect of channel noise on synchronization transitions induced by time delay in adaptive scale-free Hodgkin-Huxley neuronal networks with spike-timing-dependent plasticity (STDP). It is found that synchronization transitions by time delay vary as channel noise intensity is changed and become most pronounced when channel noise intensity is optimal. This phenomenon depends on STDP and network average degree, and it can be either enhanced or suppressed as network average degree increases depending on channel noise intensity. These results show that there are optimal channel noise and network average degree that can enhance the synchronization transitions by time delay in the adaptive neuronal networks. These findings could be helpful for better understanding of the regulation effect of channel noise on synchronization of neuronal networks. They could find potential implications for information transmission in neural systems.

Acoustic Emission from Organic Martensites.

PubMed

Panda, Manas K; Etter, Martin; Dinnebier, Robert E; Naumov, Panče

2017-07-03

In salient effects, still crystals of solids that switch between phases acquire a momentum and are autonomously propelled because of rapid release of elastic energy accrued during a latent structural transition induced by heat, light, or mechanical stimulation. When mechanical reconfiguration is induced by change of temperature in thermosalient crystals, bursts of detectable acoustic waves are generated prior to self-actuation. These observations provide compelling evidence that the thermosalient transitions in organic and organic-containing crystals are molecular analogues of the martensitic transitions in some metals, and metal alloys such as steel and shape-memory alloys. Within a broader context, these results reveal that, akin to metallic bonding, the intermolecular interactions in molecular solids are capable of gradual accrual and sudden release of a substantial amount of strain during anisotropic thermal expansion, followed by a rapid transformation of the crystal packing in a diffusionless, non-displacive transition. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Firing patterns transition and desynchronization induced by time delay in neural networks

NASA Astrophysics Data System (ADS)

Huang, Shoufang; Zhang, Jiqian; Wang, Maosheng; Hu, Chin-Kun

2018-06-01

We used the Hindmarsh-Rose (HR) model (Hindmarsh and Rose, 1984) to study the effect of time delay on the transition of firing behaviors and desynchronization in neural networks. As time delay is increased, neural networks exhibit diversity of firing behaviors, including regular spiking or bursting and firing patterns transitions (FPTs). Meanwhile, the desynchronization of firing and unstable bursting with decreasing amplitude in neural system, are also increasingly enhanced with the increase of time delay. Furthermore, we also studied the effect of coupling strength and network randomness on these phenomena. Our results imply that time delays can induce transition and desynchronization of firing behaviors in neural networks. These findings provide new insight into the role of time delay in the firing activities of neural networks, and can help to better understand the firing phenomena in complex systems of neural networks. A possible mechanism in brain that can cause the increase of time delay is discussed.

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.

Raman signatures of inversion symmetry breaking and structural phase transition in type-II Weyl semimetal MoTe2

NASA Astrophysics Data System (ADS)

Zhang, Kenan; Bao, Changhua; Gu, Qiangqiang; Ren, Xiao; Zhang, Haoxiong; Deng, Ke; Wu, Yang; Li, Yuan; Feng, Ji; Zhou, Shuyun

2016-12-01

Transition metal dichalcogenide MoTe2 is an important candidate for realizing the newly predicted type-II Weyl fermions, for which the breaking of the inversion symmetry is a prerequisite. Here we present direct spectroscopic evidence for the inversion symmetry breaking in the low-temperature phase of MoTe2 by systematic Raman experiments and first-principles calculations. We identify five lattice vibrational modes that are Raman-active only in the low-temperature noncentrosymmetric structure. A hysteresis is also observed in the peak intensity of inversion symmetry-activated Raman modes, confirming a temperature-induced structural phase transition with a concomitant change in the inversion symmetry. Our results provide definitive evidence for the low-temperature noncentrosymmetric Td phase from vibrational spectroscopy, and suggest MoTe2 as an ideal candidate for investigating the temperature-induced topological phase transition.

First principles study of pressure induced polymorphic phase transition in trimethylamine

NASA Astrophysics Data System (ADS)

Abraham, B. Moses; Vaitheeswaran, G.

2018-04-01

The pressure induced variations on the crystal structure of various polymorphs of Trimethyamine (TMA-I, TMA-II, TMAIII) has been studied theoretically using first principles calculations up to 5 GPa. The obtained equilibrium lattice parameters using standard PBE-GGA functional for the ambient and high pressure phases are found to be in good agreement with the experimental values. We calculated the enthalpies of each phase to assess their relative stability. Our results also supports the existence of additional phase transitions of TMA into two new polymorphs under external pressure. The TMA-I to TMA-II transition is found to occur at 1.41 GPa and the TMA-II to TMA-III transition at 3.33 GPa. The electronic band structure calculations using Tran Blaha-modified Becke Johnson (TB-mBJ) potential show that these polymorphs of TMA are indirect band gap insulators.

Resistance to antitumor chemotherapy due to bounded-noise-induced transitions

NASA Astrophysics Data System (ADS)

D'Onofrio, Alberto; Gandolfi, Alberto

2010-12-01

Tumor angiogenesis is a landmark of solid tumor development, but it is also directly relevant to chemotherapy. Indeed, the density and quality of neovessels may influence the effectiveness of therapies based on blood-born agents. In this paper, first we define a deterministic model of antiproliferative chemotherapy in which the drug efficacy is a unimodal function of vessel density, and then we show that under constant continuous infusion therapy the tumor-vessel system may be multistable. However, the actual drug concentration profiles are affected by bounded even if possibly large fluctuations. Through numerical simulations, we show that the tumor volume may undergo transitions to the higher equilibrium value induced by the bounded noise. In case of periodically delivered boli-based chemotherapy, we model the fluctuations due to time variability of both the drug clearance rate and the distribution volume, as well as those due to irregularities in drug delivery. We observed noise-induced transitions also in case of periodic delivering. By applying a time dense scheduling with constant average delivered drug (metronomic scheduling), we observed an easier suppression of the transitions. Finally, we propose to interpret the above phenomena as an unexpected non-genetic kind of resistance to chemotherapy.

Optical transitions in GaNAs quantum wells with variable nitrogen content embedded in AlGaAs

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

Elborg, M., E-mail: ELBORG.Martin@nims.go.jp; Noda, T.; Mano, T.

2016-06-15

We investigate the optical transitions of GaN{sub x}As{sub 1−x} quantum wells (QWs) embedded in wider band gap AlGaAs. A combination of absorption and emission spectroscopic techniques is employed to systematically investigate the properties of GaNAs QWs with N concentrations ranging from 0 – 3%. From measurement of the photocurrent spectra, we find that besides QW ground state and first excited transition, distinct increases in photocurrent generation are observed. Their origin can be explained by N-induced modifications in the density of states at higher energies above the QW ground state. Photoluminescence experiments reveal that peak position dependence with temperature changes withmore » N concentration. The characteristic S-shaped dependence for low N concentrations of 0.5% changes with increasing N concentration where the low temperature red-shift of the S-shape gradually disappears. This change indicates a gradual transition from impurity picture, where localized N induced energy states are present, to alloying picture, where an impurity-band is formed. In the highest-N sample, photoluminescence emission shows remarkable temperature stability. This phenomenon is explained by the interplay of N-induced energy states and QW confined states.« less

Calorimetric Measurements of Magnetic-Field-Induced Inhomogeneous Superconductivity Above the Paramagnetic Limit

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

Agosta, Charles C.; Fortune, Nathanael A.; Hannahs, Scott T.

We report the first magnetocaloric and calorimetric observations of a magnetic-field-induced phase transition within a superconducting state to the long-sought exotic Fulde-Ferrell-Larkin-Ovchinnikov (FFLO) superconducting state, first predicted over 50 years ago. Through the combination of bulk thermodynamic calorimetric and magnetocaloric measurements in the organic superconductor. kappa-(BEDT-TTF)(2) Cu(NCS)(2) as a function of temperature, magnetic field strength, and magnetic field orientation, we establish for the first time that this field-induced first-order phase transition at the paramagnetic limit Hp is a transition to a higher-entropy superconducting phase, uniquely characteristic of the FFLO state. We also establish that this high-field superconducting state displays themore » bulk paramagnetic ordering of spin domains required of the FFLO state. These results rule out the alternate possibility of spin-density wave ordering in the high-field superconducting phase. The phase diagram determined from our measurements-including the observation of a phase transition into the FFLO phase at Hp-is in good agreement with recent NMR results and our own earlier tunnel-diode magnetic penetration depth experiments but is in disagreement with the only previous calorimetric report.« less

Calorimetric Measurements of Magnetic-Field-Induced Inhomogeneous Superconductivity Above the Paramagnetic Limit

NASA Astrophysics Data System (ADS)

Agosta, Charles C.; Fortune, Nathanael A.; Hannahs, Scott T.; Gu, Shuyao; Liang, Lucy; Park, Ju-Hyun; Schleuter, John A.

2017-06-01

We report the first magnetocaloric and calorimetric observations of a magnetic-field-induced phase transition within a superconducting state to the long-sought exotic Fulde-Ferrell-Larkin-Ovchinnikov (FFLO) superconducting state, first predicted over 50 years ago. Through the combination of bulk thermodynamic calorimetric and magnetocaloric measurements in the organic superconductor κ -(BEDT -TTF )2Cu (NCS )2 as a function of temperature, magnetic field strength, and magnetic field orientation, we establish for the first time that this field-induced first-order phase transition at the paramagnetic limit Hp is a transition to a higher-entropy superconducting phase, uniquely characteristic of the FFLO state. We also establish that this high-field superconducting state displays the bulk paramagnetic ordering of spin domains required of the FFLO state. These results rule out the alternate possibility of spin-density wave ordering in the high-field superconducting phase. The phase diagram determined from our measurements—including the observation of a phase transition into the FFLO phase at Hp—is in good agreement with recent NMR results and our own earlier tunnel-diode magnetic penetration depth experiments but is in disagreement with the only previous calorimetric report.

Transition of Care from Childhood to Adulthood: Turner Syndrome.

PubMed

Conway, Gerard

2018-01-01

Girls with Turner syndrome (TS) require special consideration during transition from childhood to adult care. During the transition years, treatment for short stature will be completed and sexual development induced in parallel with the peer group. The timing of sexual development may have later repercussions with respect to psychosocial development and partnership status. Late presentation of TS, which is so common, can result in additional difficulties with the transition process. © 2018 S. Karger AG, Basel.

Electronic Two-Transition-Induced Enhancement of Emission Efficiency in Polymer Light-Emitting Diodes

PubMed Central

Chen, Ren-Ai; Wang, Cong; Li, Sheng; George, Thomas F.

2013-01-01

With the development of experimental techniques, effective injection and transportation of electrons is proven as a way to obtain polymer light-emitting diodes (PLEDs) with high quantum efficiency. This paper reveals a valid mechanism for the enhancement of quantum efficiency in PLEDs. When an external electric field is applied, the interaction between a negative polaron and triplet exciton leads to an electronic two-transition process, which induces the exciton to emit light and thus improve the emission efficiency of PLEDs. PMID:28809346

Radiative lifetimes in B I using ultraviolet and vacuum-ultraviolet laser-induced fluorescence

NASA Technical Reports Server (NTRS)

O'Brian, T. R.; Lawler, J. E.

1992-01-01

Radiative lifetimes of the eight lowest even parity levels in the doublet system of B I are measured using time-resolved laser-induced fluorescence in the UV and VUV on an atomic beam of boron. The accurate lifetimes provide a base for improved determination of absolute transition probabilities in B I. The techniques described are broadly applicable to measurement of lifetimes of levels with transitions in the visible, UV, and VUV in almost any element.

Pressure induced phase transitions studies using advanced synchrotron techniques

NASA Astrophysics Data System (ADS)

Liu, Haozhe; Liu, Lisa; Zhao, Jinggeng; HIT Overseas Collaborative Base at Argonne Collaboration

2013-06-01

In this presentation, the joint effort on high pressure research through program of Harbin Institute of Technology (HIT) Overseas Collaborative Base at Argonne will be introduced. Selected research projects on pressure induced phase transitions at room temperature and high/low temperature conditions, such as A2B3 type topological insulators, iron arsenide superconductors, piezoelectric/ferroelectric materials, ABO3 type single crystals and metallic glasses, will be presented. Recent development on imaging and diffraction tomography techniques in diamond anvil cell will be reviewed as well.

Origin of nonlinear transport across the magnetically induced superconductor-metal-insulator transition in two dimensions.

PubMed

Seo, Y; Qin, Y; Vicente, C L; Choi, K S; Yoon, Jongsoo

2006-08-04

We have studied the effect of perpendicular magnetic fields and temperatures on nonlinear electronic transport in amorphous Ta superconducting thin films. The films exhibit a magnetic field-induced metallic behavior intervening the superconductor-insulator transition in the zero temperature limit. We show that the phase-identifying nonlinear transport in the superconducting and metallic phases arises from an intrinsic origin, not from an electron heating effect. The nonlinear transport is found to accompany an extraordinarily long voltage response time.

Pressure-induced phase transition in GaN nanocrystals

NASA Astrophysics Data System (ADS)

Cui, Q.; Pan, Y.; Zhang, W.; Wang, X.; Zhang, J.; Cui, T.; Xie, Y.; Liu, J.; Zou, G.

2002-11-01

High-pressure in situ energy-dispersive x-ray diffraction experiments on GaN nanocrystals with 50 nm diameter have been carried out using a synchrotron x-ray source and a diamond-anvil cell up to about 79 GPa at room temperature. A pressure-induced first-order structural phase transition from the wurtzite-type structure to the rock-salt-type structure starts at about 48.8 GPa. The rock-salt-type phase persists to the highest pressure in our experimental range.

Laser-induced spin protection and switching in a specially designed magnetic dot: A theoretical investigation

NASA Astrophysics Data System (ADS)

Zhang, G. P.; Si, M. S.; George, T. F.

2011-04-01

Most laser-induced femtosecond magnetism investigations are done in magnetic thin films. Nanostructured magnetic dots, with their reduced dimensionality, present new opportunities for spin manipulation. Here we predict that if a magnetic dot has a dipole-forbidden transition between the lowest occupied molecular orbital (LUMO) and the highest unoccupied molecular orbital (HOMO), but a dipole-allowed transition between LUMO+1 and HOMO, electromagnetically induced transparency can be used to prevent ultrafast laser-induced spin momentum reduction, or spin protection. This is realized through a strong dump pulse to funnel the population into LUMO+1. If the time delay between the pump and dump pulses is longer than 60 fs, a population inversion starts and spin switching is achieved. These predictions are detectable experimentally.

Electric-field-induced modification of the magnon energy, exchange interaction, and curie temperature of transition-metal thin films.

PubMed

Oba, M; Nakamura, K; Akiyama, T; Ito, T; Weinert, M; Freeman, A J

2015-03-13

The electric-field-induced modification in the Curie temperature of prototypical transition-metal thin films with the perpendicular magnetic easy axis, a freestanding Fe(001) monolayer and a Co monolayer on Pt(111), is investigated by first-principles calculations of spin-spiral structures in an external electric field (E field). An applied E field is found to modify the magnon (spin-spiral formation) energy; the change arises from the E-field-induced screening charge density in the spin-spiral states due to p-d hybridizations. The Heisenberg exchange parameters obtained from the magnon energy suggest an E-field-induced modification of the Curie temperature, which is demonstrated via Monte Carlo simulations that take the magnetocrystalline anisotropy into account.

Current-induced strong diamagnetism in the Mott insulator Ca2RuO4.

PubMed

Sow, Chanchal; Yonezawa, Shingo; Kitamura, Sota; Oka, Takashi; Kuroki, Kazuhiko; Nakamura, Fumihiko; Maeno, Yoshiteru

2017-11-24

Mott insulators can host a surprisingly diverse set of quantum phenomena when their frozen electrons are perturbed by various stimuli. Superconductivity, metal-insulator transition, and colossal magnetoresistance induced by element substitution, pressure, and magnetic field are prominent examples. Here we report strong diamagnetism in the Mott insulator calcium ruthenate (Ca 2 RuO 4 ) induced by dc electric current. The application of a current density of merely 1 ampere per centimeter squared induces diamagnetism stronger than that in other nonsuperconducting materials. This change is coincident with changes in the transport properties as the system becomes semimetallic. These findings suggest that dc current may be a means to control the properties of materials in the vicinity of a Mott insulating transition. Copyright © 2017, American Association for the Advancement of Science.

High-pressure studies on electronic transport properties of Te-substituted Bi2Se3–xTex topological insulators

NASA Astrophysics Data System (ADS)

Devidas, T. R.; Abhirami, S.; Sharma, Shilpam; Amaladas, E. P.; Mani, Awadhesh

2018-03-01

Studies on the electrical transport properties of the 3D topological insulators Bi2Se3 under iso-electronic substitution of Te at Se sites and the application of external pressure have been performed to understand the evolution of its ground-state properties and to explore possible electronic phase transitions in Bi2Se3‑x Te x (x=0\\text{--}3 ) systems. While the external pressure suppresses the metallic behaviour of Bi2Se3 arising from defect charge carriers leading ultimately to non-metal behaviour, the effect of pressure on Te-doped samples x=1\\text{--}2 seems to be more striking, and causes multiple electronic phase transitions such as an insulator-to-metal transition (MIT) followed by pressure-induced superconducting transition at higher pressures. All the critical parameters such as critical pressure for the occurrence of MIT (PMIT}) , superconductivity (PSC}) and maximum pressure induced superconducting transition temperature (Tc,max}) for given compositions are seen to exhibit maxima at x=1.6 which is the composition that exhibits the most insulating behaviour with least concentration of defect charge carriers among the samples of Bi2Se3‑x Te x (x=0\\text{--}3 ) series. The superconducting transition temperature (Tc}) decreases with increasing pressure in x=1\\text{--}2 samples, while it remains nearly constant for Bi2Te3. Based on the analysis of the experimental data it is surmised that the pressure-induced superconductivity seen in these systems is of conventional (BCS) type.

Kinetics and mechanism of the pressure-induced lamellar order/disorder transition in phosphatidylethanolamine: a time-resolved X-ray diffraction study.

PubMed

Mencke, A P; Caffrey, M

1991-03-05

By using synchrotron radiation, a movie was made of the X-ray scattering pattern from a biological liquid crystal undergoing a phase transition induced by a pressure jump. The system studied includes the fully hydrated phospholipid dihexadecylphosphatidylethanolamine in the lamellar gel (L beta') phase at a temperature of 68 degrees C and a pressure of 9.7 MPa (1400 psig). Following the rapid release of pressure to atmospheric the L beta' phase transforms slowly into the lamellar liquid crystal (L alpha) phase. The pressure perturbation is applied with the intention of producing a sudden phase disequilibrium followed by monitoring the system as it relaxes to its new equilibrium condition. Remarkably, the proportion of sample in the L alpha phase grows linearly with time, taking 37 s to totally consume the L beta' phase. The time dependencies of radius, peak intensity, and width of the powder diffraction ring of the low-angle (001) lamellar reflections were obtained from the movie by image processing. The concept of an "effective pressure" is introduced to account for the temperature variations that accompany the phase transition and to establish that the observed large transit time is indeed intrinsic to the sample and not due to heat exchange with the environment. The reverse transformation, L alpha to L beta', induced by a sudden jump from atmospheric pressure to 9.7 MPa, is complete in less than 13 s. These measurements represent a new approach for studying the kinetics of lipid phase transitions and for gaining insights into the mechanism of the lamellar order/disorder transition.

Theoretical potential for low energy consumption phase change memory utilizing electrostatically-induced structural phase transitions in 2D materials

NASA Astrophysics Data System (ADS)

Rehn, Daniel A.; Li, Yao; Pop, Eric; Reed, Evan J.

2018-01-01

Structural phase-change materials are of great importance for applications in information storage devices. Thermally driven structural phase transitions are employed in phase-change memory to achieve lower programming voltages and potentially lower energy consumption than mainstream nonvolatile memory technologies. However, the waste heat generated by such thermal mechanisms is often not optimized, and could present a limiting factor to widespread use. The potential for electrostatically driven structural phase transitions has recently been predicted and subsequently reported in some two-dimensional materials, providing an athermal mechanism to dynamically control properties of these materials in a nonvolatile fashion while achieving potentially lower energy consumption. In this work, we employ DFT-based calculations to make theoretical comparisons of the energy required to drive electrostatically-induced and thermally-induced phase transitions. Determining theoretical limits in monolayer MoTe2 and thin films of Ge2Sb2Te5, we find that the energy consumption per unit volume of the electrostatically driven phase transition in monolayer MoTe2 at room temperature is 9% of the adiabatic lower limit of the thermally driven phase transition in Ge2Sb2Te5. Furthermore, experimentally reported phase change energy consumption of Ge2Sb2Te5 is 100-10,000 times larger than the adiabatic lower limit due to waste heat flow out of the material, leaving the possibility for energy consumption in monolayer MoTe2-based devices to be orders of magnitude smaller than Ge2Sb2Te5-based devices.

Ultrafast studies of shock-induced melting and phase transitions at LCLS

NASA Astrophysics Data System (ADS)

McMahon, Malcolm

The study of shock-induced phase transitions, which is vital to the understanding of material response to rapid pressure changes, dates back to the 1950s, when Bankcroft et al reported a transition in iron. Since then, many transitions have been reported in a wide range of materials, but, due to the lack of sufficiently bright x-ray sources, the structural details of these new phases has been notably lacking. While the development of nanosecond in situ x-ray diffraction has meant that lattice-level studies of such phenomena have become possible, including studies of the phase transition reported 60 years ago in iron, the quality of the diffraction data from such studies is noticeably poorer than that obtained from statically-compressed samples on synchrotrons. The advent of x-ray free electron lasers (XFELs), such as the LCLS, has resulted in an unprecedented improvement in the quality of diffraction data that can be obtained from shock-compressed matter. Here I describe the results from three recent experiment at the LCLS that looked at the solid-solid and solid-liquid phase transitions in Sb, Bi and Sc using single 50 fs x-ray exposures. The results provide new insight into the structural changes and melting induced by shock compression. This work is supported by EPSRC under Grant No. EP/J017051/1. Use of the LCLS, SLAC National Accelerator Laboratory, is supported by the U.S. Department of Energy, Office of Science, Office of Basic Energy Sciences under Contract No. DE-AC02-76SF00515.

Isolation of cucumber CsARF cDNAs and expression of the corresponding mRNAs during gravity-regulated morphogenesis of cucumber seedlings

NASA Astrophysics Data System (ADS)

Saito, Y.; Yamasaki, S.; Fujii, N.; Hagen, G.; Guilfoyle, T.; Takahashi, H.

Cucumber seedlings grown in a horizontal position develop a protuberance called peg on the lower side of the transition zone between the hypocotyl and the root. We have suggested that peg formation on the upper side of the gravistimulated transition zone is suppressed because cucumber seedlings grown in a vertical position or microgravity symmetrically develop two pegs on the transition zone. Plant hormone, auxin, is considered to play a crucial role in the gravity-regulated formation of peg. We have shown that the mRNAs of auxin-inducible genes (CsIAAs) isolated from cucumber accumulate more abundantly in the lower side of the transition zone than in the upper side when peg formation initiates. To reveal the mechanism of transcriptional regulation by auxin for peg formation, we isolated five cDNAs of Auxin Response Factors (ARFs) from cucumber and compared their mRNA accumulation with those of CsIAA1 and CsIAA2. The tissue specificity of mRNA accumulation of CsARF2 was similar to those of CsIAA1 and CsIAA2. The structural character of CsARF2 predicts it is transcriptional activator. These results suggest that CsARF2 may be involved in activation of the transcription of auxin-inducible genes including CsIAA1 for peg formation. Because mRNA accumulation of five CsARFs, including CsARF2, were affected by neither gravity nor auxin, transcriptional activity of CsARF2 may be regulated at post-transcriptional level to induce asymmetric mRNA accumulation of auxin-inducible genes in the transition zone.

Wettability transition induced transformation and entrapment of polymer nanostructures in cylindrical nanopores.

PubMed

Feng, Xunda; Mei, Shilin; Jin, Zhaoxia

2011-12-06

We apply the concept of wettability transition to manipulate the morphology and entrapment of polymer nanostructures inside cylindrical nanopores of anodic aluminum oxide (AAO) membranes. When AAO/polystyrene (PS) hybrids, i.e., AAO/PS nanorods or AAO/PS nanotubes, are immersed into a polyethylene glycol (PEG) reservoir above the glass transition temperature of PS, a wettability transition from wetting to nonwetting of PS can be triggered due to the invasion of the more wettable PEG melt. The wettability transition enables us to develop a nondestructive method to entrap hemispherically capped nanorods inside nanopores. Moreover, we can obtain single nanorods with the desired aspect ratio by further dissolving the AAO template, in contrast to the drawbacks of nonuniformity or destructiveness from the conventional ultrasonication method. In the case of AAO/PS nanotubes, the wettability transition induced dewetting of PS nanotube walls results in the disconnection and entrapment of nonwetting PS domains (i.e., nanospheres, nanocapsules, or capped nanorods). Moreover, PEG is then washed to recover the pristine wettability of PS on the alumina surface; further annealing of the PS nanospheres inside AAO nanopores under vacuum can generate some unique nanostructures, particularly semicylindrical nanorods. © 2011 American Chemical Society

[Study on different responses of rats' small intestine mucous membrane and bladder transitional epithelium in the same carcinogenic urine environment].

PubMed

Wu, B; Pan, C; Song, G

2001-10-25

To preliminarily verify the tentative idea of replacement of bladder transitional epithelium with small intestine mucous membrane to prevent recurrence of carcinoma of bladder. A certain segment of small intestine was transplanted to the urinary bladder of the same body in 17 rats. Then N-butyl-N-(4-hydroxy-butyl) nitrosamine (BBN) was used to induce carcinoma of bladder. BBN was used to 11 control rats that did not undergo operation. Bladder carcinoma failed to be found in the transplanted small intestine mucous membrane in all experimental rats except one. After stimulation of BBN, carcinoma of urinary bladder occurred in all rats' bladder transitional epithelium. 1) The carcinogenic substances in the urine of rats suffering from BBN-induced bladder carcinoma are carcinogenic only to bladder transitional epithelium and have no effect on small intestine epithelium. 2) Bladder transitional epithelium may be more sensitive to the urine carcinogenic substances and easier to be cancerized than small intestine epithelium. 3) The tentative idea of substitution of small intestine mucous membrane for bladder transitional epithelium to prevent the recurrence of bladder carcinoma is worth further studying.

Epigenetic silencing of miR-218 by the lncRNA CCAT1, acting via BMI1, promotes an altered cell cycle transition in the malignant transformation of HBE cells induced by cigarette smoke extract

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

Lu, Lu; Xu, Hui; Luo, Fei

Cigarette smoking is the strongest risk factor for the development of lung cancer, the leading cause of cancer-related deaths. However, the molecular mechanisms leading to lung cancer are largely unknown. A long-noncoding RNA (lncRNA), CCAT1, regarded as cancer-associated, has been investigated extensively. Moreover, the molecular mechanisms of lncRNAs in regulation of microRNAs (miRNAs) induced by cigarette smoke remain unclear. In the present investigation, cigarette smoke extract (CSE) caused an altered cell cycle and increased CCAT1 levels and decreased miR-218 levels in human bronchial epithelial (HBE) cells. Depletion of CCAT1 attenuated the CSE-induced decreases of miR-218 levels, suggesting that miR-218 ismore » negatively regulated by CCAT1 in HBE cells exposed to CSE. The CSE-induced increases of BMI1 levels and blocked by CCAT1 siRNA were attenuated by an miR-218 inhibitor. Moreover, in CSE-transformed HBE cells, the CSE-induced cell cycle changes and elevated neoplastic capacity were reversed by CCAT1 siRNA or BMI1 siRNA. This epigenetic silencing of miR-218 by CCAT1 induces an altered cell cycle transition through BMI1 and provides a new mechanism for CSE-induced lung carcinogenesis. - Highlights: • CSE exposure induces increases of CCAT1 levels and decreases of miR-218 levels. • CCAT1 negatively regulates miR-218 expression. • CCAT1, regulated by miR-218, via BMI1, is involved in the CSE-induced altered cell cycle transition.« 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.

Exchange pathways of plastoquinone and plastoquinol in the photosystem II complex

PubMed Central

Van Eerden, Floris J.; Melo, Manuel N.; Frederix, Pim W. J. M.; Periole, Xavier; Marrink, Siewert J.

2017-01-01

Plastoquinone (PLQ) acts as an electron carrier between photosystem II (PSII) and the cytochrome b6f complex. To understand how PLQ enters and leaves PSII, here we show results of coarse grained molecular dynamics simulations of PSII embedded in the thylakoid membrane, covering a total simulation time of more than 0.5 ms. The long time scale allows the observation of many spontaneous entries of PLQ into PSII, and the unbinding of plastoquinol (PLQol) from the complex. In addition to the two known channels, we observe a third channel for PLQ/PLQol diffusion between the thylakoid membrane and the PLQ binding sites. Our simulations point to a promiscuous diffusion mechanism in which all three channels function as entry and exit channels. The exchange cavity serves as a PLQ reservoir. Our simulations provide a direct view on the exchange of electron carriers, a key step of the photosynthesis machinery. PMID:28489071

Debye screening in single-molecule carbon nanotube field-effect sensors.

PubMed

Sorgenfrei, Sebastian; Chiu, Chien-Yang; Johnston, Matthew; Nuckolls, Colin; Shepard, Kenneth L

2011-09-14

Point-functionalized carbon nanotube field-effect transistors can serve as highly sensitive detectors for biomolecules. With a probe molecule covalently bound to a defect in the nanotube sidewall, two-level random telegraph noise (RTN) in the conductance of the device is observed as a result of a charged target biomolecule binding and unbinding at the defect site. Charge in proximity to the defect modulates the potential (and transmission) of the conductance-limiting barrier created by the defect. In this Letter, we study how these single-molecule electronic sensors are affected by ionic screening. Both charge in proximity to the defect site and buffer concentration are found to affect RTN amplitude in a manner that follows from simple Debye length considerations. RTN amplitude is also dependent on the potential of the electrolyte gate as applied to the reference electrode; at high enough gate potentials, the target DNA is completely repelled and RTN is suppressed.

Binding site stoichiometry and the effects of phosphorylation on human α1 homomeric glycine receptors

PubMed Central

Gentet, Luc J; Clements, John D

2002-01-01

The kinetic properties of the human α1 homomeric glycine receptor were investigated. Receptors were expressed in HEK 293 cells, and glycine was applied to outside-out membrane patches with sub-millisecond solution exchange. The activation time course of the glycine response was used to investigate receptor stoichiometry. The unbinding of three strychnine molecules and the cooperative binding of two glycine molecules were required to activate the channel. The effects of phosphorylation on glycine receptor kinetics were investigated by pretreating cells with phosphorylators or with phosphatases. Phosphorylation accelerated desensitisation, but slowed deactivation and recovery from desensitisation. A chemical-kinetic model was developed that reproduced the experimental observations. The model suggests that only three binding sites on the glycine channel are functional, while the remaining two binding sites are ‘silent’, possibly due to strong negative cooperativity. PMID:12356883

Quantum simulation of ultrafast dynamics using trapped ultracold atoms.

PubMed

Senaratne, Ruwan; Rajagopal, Shankari V; Shimasaki, Toshihiko; Dotti, Peter E; Fujiwara, Kurt M; Singh, Kevin; Geiger, Zachary A; Weld, David M

2018-05-25

Ultrafast electronic dynamics are typically studied using pulsed lasers. Here we demonstrate a complementary experimental approach: quantum simulation of ultrafast dynamics using trapped ultracold atoms. Counter-intuitively, this technique emulates some of the fastest processes in atomic physics with some of the slowest, leading to a temporal magnification factor of up to 12 orders of magnitude. In these experiments, time-varying forces on neutral atoms in the ground state of a tunable optical trap emulate the electric fields of a pulsed laser acting on bound charged particles. We demonstrate the correspondence with ultrafast science by a sequence of experiments: nonlinear spectroscopy of a many-body bound state, control of the excitation spectrum by potential shaping, observation of sub-cycle unbinding dynamics during strong few-cycle pulses, and direct measurement of carrier-envelope phase dependence of the response to an ultrafast-equivalent pulse. These results establish cold-atom quantum simulation as a complementary tool for studying ultrafast dynamics.

Fundamental High-Speed Limits in Single-Molecule, Single-Cell, and Nanoscale Force Spectroscopies

PubMed Central

2016-01-01

Force spectroscopy is enhancing our understanding of single-biomolecule, single-cell, and nanoscale mechanics. Force spectroscopy postulates the proportionality between the interaction force and the instantaneous probe deflection. By studying the probe dynamics, we demonstrate that the total force acting on the probe has three different components: the interaction, the hydrodynamic, and the inertial. The amplitudes of those components depend on the ratio between the resonant frequency and the frequency at which the data are measured. A force–distance curve provides a faithful measurement of the interaction force between two molecules when the inertial and hydrodynamic components are negligible. Otherwise, force spectroscopy measurements will underestimate the value of unbinding forces. Neglecting the above force components requires the use of frequency ratios in the 50–500 range. These ratios will limit the use of high-speed methods in force spectroscopy. The theory is supported by numerical simulations. PMID:27359243

α-Actinin/titin interaction: A dynamic and mechanically stable cluster of bonds in the muscle Z-disk

PubMed Central

Grison, Marco; Merkel, Ulrich; Kostan, Julius; Djinović-Carugo, Kristina; Rief, Matthias

2017-01-01

Stable anchoring of titin within the muscle Z-disk is essential for preserving muscle integrity during passive stretching. One of the main candidates for anchoring titin in the Z-disk is the actin cross-linker α-actinin. The calmodulin-like domain of α-actinin binds to the Z-repeats of titin. However, the mechanical and kinetic properties of this important interaction are still unknown. Here, we use a dual-beam optical tweezers assay to study the mechanics of this interaction at the single-molecule level. A single interaction of α-actinin and titin turns out to be surprisingly weak if force is applied. Depending on the direction of force application, the unbinding forces can more than triple. Our results suggest a model where multiple α-actinin/Z-repeat interactions cooperate to ensure long-term stable titin anchoring while allowing the individual components to exchange dynamically. PMID:28096424

α-Actinin/titin interaction: A dynamic and mechanically stable cluster of bonds in the muscle Z-disk.

PubMed

Grison, Marco; Merkel, Ulrich; Kostan, Julius; Djinović-Carugo, Kristina; Rief, Matthias

2017-01-31

Stable anchoring of titin within the muscle Z-disk is essential for preserving muscle integrity during passive stretching. One of the main candidates for anchoring titin in the Z-disk is the actin cross-linker α-actinin. The calmodulin-like domain of α-actinin binds to the Z-repeats of titin. However, the mechanical and kinetic properties of this important interaction are still unknown. Here, we use a dual-beam optical tweezers assay to study the mechanics of this interaction at the single-molecule level. A single interaction of α-actinin and titin turns out to be surprisingly weak if force is applied. Depending on the direction of force application, the unbinding forces can more than triple. Our results suggest a model where multiple α-actinin/Z-repeat interactions cooperate to ensure long-term stable titin anchoring while allowing the individual components to exchange dynamically.

Can correlations among receptors affect the information about the stimulus?

NASA Astrophysics Data System (ADS)

Singh, Vijay; Tchernookov, Martin; Nemenman, Ilya

2014-03-01

In the context of neural information processing, it has been observed that, compared to the case of independent receptors, correlated receptors can often carry more information about the stimulus. We explore similar ideas in the context of molecular information processing, analyzing a cell with receptors whose activity is intrinsically negatively correlated because they compete for the same ligand molecules. We show analytically that, in case the involved biochemical interactions are linear, the information between the number of molecules captured by the receptors and the ligand concentration does not depend on correlations among the receptors. For a nonlinear kinetic network, correlations similarly do not change the amount of information for observation times much shorter or much longer than the characteristic time scale of ligand molecule binding and unbinding. However, at intermediate times, correlations can increase the amount of available information. This work has been supported by the James S McDonnell foundation.

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

None

A system for removing components of a gaseous mixture is provided comprising: a reactor fluid containing vessel having conduits extending therefrom, aqueous fluid within the reactor, the fluid containing a ligand and a metal, and at least one reactive surface within the vessel coupled to a power source. A method for removing a component from a gaseous mixture is provided comprising exposing the gaseous mixture to a fluid containing a ligand and a reactive metal, the exposing chemically binding the component of the gaseous mixture to the ligand. A method of capturing a component of a gaseous mixture is providedmore » comprising: exposing the gaseous mixture to a fluid containing a ligand and a reactive metal, the exposing chemically binding the component of the gaseous mixture to the ligand, altering the oxidation state of the metal, the altering unbinding the component from the ligand, and capturing the component.« less

GPCRs: What Can We Learn from Molecular Dynamics Simulations?

PubMed

Velgy, Naushad; Hedger, George; Biggin, Philip C

2018-01-01

Advances in the structural biology of G-protein Coupled Receptors have resulted in a significant step forward in our understanding of how this important class of drug targets function at the molecular level. However, it has also become apparent that they are very dynamic molecules, and moreover, that the underlying dynamics is crucial in shaping the response to different ligands. Molecular dynamics simulations can provide unique insight into the dynamic properties of GPCRs in a way that is complementary to many experimental approaches. In this chapter, we describe progress in three distinct areas that are particularly difficult to study with other techniques: atomic level investigation of the conformational changes that occur when moving between the various states that GPCRs can exist in, the pathways that ligands adopt during binding/unbinding events and finally, the influence of lipids on the conformational dynamics of GPCRs.

Micrometer-Scale Ballistic Transport of Electron Pairs in LaAlO_{3}/SrTiO_{3} Nanowires.

PubMed

Tomczyk, Michelle; Cheng, Guanglei; Lee, Hyungwoo; Lu, Shicheng; Annadi, Anil; Veazey, Joshua P; Huang, Mengchen; Irvin, Patrick; Ryu, Sangwoo; Eom, Chang-Beom; Levy, Jeremy

2016-08-26

High-mobility complex-oxide heterostructures and nanostructures offer new opportunities for extending the paradigm of quantum transport beyond the realm of traditional III-V or carbon-based materials. Recent quantum transport investigations with LaAlO_{3}/SrTiO_{3}-based quantum dots reveal the existence of a strongly correlated phase in which electrons form spin-singlet pairs without becoming superconducting. Here, we report evidence for the micrometer-scale ballistic transport of electron pairs in quasi-1D LaAlO_{3}/SrTiO_{3} nanowire cavities. In the paired phase, Fabry-Perot-like quantum interference is observed, in sync with conductance oscillations observed in the superconducting regime (at a zero magnetic field). Above a critical magnetic field B_{p}, the electron pairs unbind and the conductance oscillations shift with the magnetic field. These experimental observations extend the regime of ballistic electronic transport to strongly correlated phases.

Debye screening in single-molecule carbon nanotube field-effect transistors

PubMed Central

Sorgenfrei, Sebastian; Chiu, Chien-yang; Johnston, Matthew; Nuckolls, Colin; Shepard, Kenneth L.

2013-01-01

Point-functionalized carbon nanotube field-effect transistors can serve as highly sensitive detectors for biomolecules. With a probe molecule covalently bound to a defect in the nanotube sidewall, two-level random telegraph noise (RTN) in the conductance of the device is observed as a result of a charged target biomolecule binding and unbinding at the defect site. Charge in proximity to the defect modulates the potential (and transmission) of the conductance-limiting barrier created by the defect. In this Letter, we study how these single-molecule electronic sensors are affected by ionic screening. Both charge in proximity to the defect site and buffer concentration are found to affect RTN amplitude in a manner that follows from simple Debye length considerations. RTN amplitude is also dependent on the potential of the electrolyte gate as applied to the reference electrode; at high enough repulsive potentials, the target DNA is completely repelled and RTN is suppressed. PMID:21806018

Probing microbubble targeting with atomic force microscopy.

PubMed

Sboros, V; Glynos, E; Ross, J A; Moran, C M; Pye, S D; Butler, M; McDicken, W N; Brown, S B; Koutsos, V

2010-10-01

Microbubble science is expanding beyond ultrasound imaging applications to biological targeting and drug/gene delivery. The characteristics of molecular targeting should be tested by a measurement system that can assess targeting efficacy and strength. Atomic force microscopy (AFM) is capable of piconewton force resolution, and is reported to measure the strength of single hydrogen bonds. An in-house targeted microbubble modified using the biotin-avidin chemistry and the CD31 antibody was used to probe cultures of Sk-Hep1 hepatic endothelial cells. We report that the targeted microbubbles provide a single distribution of adhesion forces with a median of 93pN. This interaction is assigned to the CD31 antibody-antigen unbinding event. Information on the distances between the interaction forces was obtained and could be important for future microbubble fabrication. In conclusion, the capability of single microbubbles to target cell lines was shown to be feasible with AFM.

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.

Semiclassical theory of electronically nonadiabatic transitions in molecular collision processes

NASA Technical Reports Server (NTRS)

Lam, K. S.; George, T. F.

1979-01-01

An introductory account of the semiclassical theory of the S-matrix for molecular collision processes is presented, with special emphasis on electronically nonadiabatic transitions. This theory is based on the incorporation of classical mechanics with quantum superposition, and in practice makes use of the analytic continuation of classical mechanics into the complex space of time domain. The relevant concepts of molecular scattering theory and related dynamical models are described and the formalism is developed and illustrated with simple examples - collinear collision of the A+BC type. The theory is then extended to include the effects of laser-induced nonadiabatic transitions. Two bound continuum processes collisional ionization and collision-induced emission also amenable to the same general semiclassical treatment are discussed.

Nonequilibrium transition induced by mass media in a model for social influence

NASA Astrophysics Data System (ADS)

González-Avella, J. C.; Cosenza, M. G.; Tucci, K.

2005-12-01

We study the effect of mass media, modeled as an applied external field, on a social system based on Axelrod’s model for the dissemination of culture. The numerical simulations show that the system undergoes a nonequilibrium phase transition between an ordered phase (homogeneous culture) specified by the mass media and a disordered (culturally fragmented) one. The critical boundary separating these phases is calculated on the parameter space of the system, given by the intensity of the mass media influence and the number of options per cultural attribute. Counterintuitively, mass media can induce cultural diversity when its intensity is above some threshold value. The nature of the phase transition changes from continuous to discontinuous at some critical value of the number of options.

Endotoxin-Induced Structural Transformations in Liquid Crystalline Droplets

NASA Astrophysics Data System (ADS)

Lin, I.-Hsin; Miller, Daniel S.; Bertics, Paul J.; Murphy, Christopher J.; de Pablo, Juan J.; Abbott, Nicholas L.

2011-06-01

The ordering of liquid crystals (LCs) is known to be influenced by surfaces and contaminants. Here, we report that picogram per milliliter concentrations of endotoxin in water trigger ordering transitions in micrometer-size LC droplets. The ordering transitions, which occur at surface concentrations of endotoxin that are less than 10-5 Langmuir, are not due to adsorbate-induced changes in the interfacial energy of the LC. The sensitivity of the LC to endotoxin was measured to change by six orders of magnitude with the geometry of the LC (droplet versus slab), supporting the hypothesis that interactions of endotoxin with topological defects in the LC mediate the response of the droplets. The LC ordering transitions depend strongly on glycophospholipid structure and provide new designs for responsive soft matter.

Chain-reaction crash in traffic flow controlled by taillights

NASA Astrophysics Data System (ADS)

Nagatani, Takashi

2015-02-01

We study the chain-reaction crash (multiple-vehicle collision) in low-visibility condition on a road. In the traffic situation, drivers brake according to taillights of the forward vehicle. The first crash may induce more collisions. We investigate whether or not the first collision induces the chain-reaction crash, numerically and analytically. The dynamic transitions occur from no collisions through a single collision, double collisions and triple collisions, to multiple collisions with decreasing the headway. Also, we find that the dynamic transition occurs from the finite chain reaction to the infinite chain reaction when the headway is less than the critical value. We derive, analytically, the transition points and the region maps for the chain-reaction crash in traffic flow controlled by taillights.

Plasma induced sp 2 to sp 3 transition in boron nitride

NASA Astrophysics Data System (ADS)

Zhang, J.; Cui, Q.; Li, X.; He, Z.; Li, W.; Ma, Y.; Guan, Q.; Gao, W.; Zou, G.

2004-12-01

The transition from sp 2 to sp 3 hybridization in boron nitride has been induced in plasma. Nano-crystals of cubic boron nitride (cBN) have been synthesized by direct current arc discharge method using hexagonal boron nitride (hBN) as the starting material. The characterization of the as-grown powders is carried out by X-ray diffraction, Fourier transform infrared spectroscopy and transmission electron microscopy. It has been shown that cBN and hBN grains with 20-60 nm in size co-exist in the powders. A reaction route of sublimation - re-hybridization - crystallization had been put forward to explain the mechanism of the hybridization transition and the growth of cBN by this method.

Molybdenum Carbamate Nanosheets as a New Class of Potential Phase Change Materials.

PubMed

Zhukovskyi, Maksym; Plashnitsa, Vladimir; Petchsang, Nattasamon; Ruth, Anthony; Bajpai, Anshumaan; Vietmeyer, Felix; Wang, Yuanxing; Brennan, Michael; Pang, Yunsong; Werellapatha, Kalpani; Bunker, Bruce; Chattopadhyay, Soma; Luo, Tengfei; Janko, Boldizsar; Fay, Patrick; Kuno, Masaru

2017-06-14

We report for the first time the synthesis of large, free-standing, Mo 2 O 2 (μ-S) 2 (Et 2 dtc) 2 (MoDTC) nanosheets (NSs), which exhibit an electron-beam induced crystalline-to-amorphous phase transition. Both electron beam ionization and femtosecond (fs) optical excitation induce the phase transition, which is size-, morphology-, and composition-preserving. Resulting NSs are the largest, free-standing regularly shaped two-dimensional amorphous nanostructures made to date. More importantly, amorphization is accompanied by dramatic changes to the NS electrical and optical response wherein resulting amorphous species exhibit room-temperature conductivities 5 orders of magnitude larger than those of their crystalline counterparts. This enhancement likely stems from the amorphization-induced formation of sulfur vacancy-related defects and is supported by temperature-dependent transport measurements, which reveal efficient variable range hopping. MoDTC NSs represent one instance of a broader class of transition metal carbamates likely having applications because of their intriguing electrical properties as well as demonstrated ability to toggle metal oxidation states.

Temperature and electric field induced metal-insulator transition in atomic layer deposited VO2 thin films

NASA Astrophysics Data System (ADS)

Tadjer, Marko J.; Wheeler, Virginia D.; Downey, Brian P.; Robinson, Zachary R.; Meyer, David J.; Eddy, Charles R.; Kub, Fritz J.

2017-10-01

Amorphous vanadium oxide (VO2) films deposited by atomic layer deposition (ALD) were crystallized with an ex situ anneal at 660-670 °C for 1-2 h under a low oxygen pressure (10-4 to 10-5 Torr). Under these conditions the crystalline VO2 phase was maintained, while formation of the V2O5 phase was suppressed. Electrical transition from the insulator to the metallic phase was observed in the 37-60 °C range, with an ROFF/RON ratio of up to about 750 and ΔTC ≅ 7-10 °C. Lateral electric field applied across two-terminal device structures induced a reversible phase change, with a room temperature transition field of about 25 kV/cm in the VO2 sample processed with the 2 h long O2 anneal. Both the width and slope of the field induced MIT I-V hysteresis were dependent upon the VO2 crystalline quality.

Pressure-induced structural change in liquid GaIn eutectic alloy.

PubMed

Yu, Q; Ahmad, A S; Ståhl, K; Wang, X D; Su, Y; Glazyrin, K; Liermann, H P; Franz, H; Cao, Q P; Zhang, D X; Jiang, J Z

2017-04-25

Synchrotron x-ray diffraction reveals a pressure induced crystallization at about 3.4 GPa and a polymorphic transition near 10.3 GPa when compressed a liquid GaIn eutectic alloy up to ~13 GPa at room temperature in a diamond anvil cell. Upon decompression, the high pressure crystalline phase remains almost unchanged until it transforms to the liquid state at around 2.3 GPa. The ab initio molecular dynamics calculations can reproduce the low pressure crystallization and give some hints on the understanding of the transition between the liquid and the crystalline phase on the atomic level. The calculated pair correlation function g(r) shows a non-uniform contraction reflected by the different compressibility between the short (1st shell) and the intermediate (2nd to 4th shells). It is concluded that the pressure-induced liquid-crystalline phase transformation likely arises from the changes in local atomic packing of the nearest neighbors as well as electronic structures at the transition pressure.

MHz-rate nitric oxide planar laser-induced fluorescence imaging in a Mach 10 hypersonic wind tunnel.

PubMed

Jiang, Naibo; Webster, Matthew; Lempert, Walter R; Miller, Joseph D; Meyer, Terrence R; Ivey, Christopher B; Danehy, Paul M

2011-02-01

Nitric oxide planar laser-induced fluorescence (NO PLIF) imaging at repetition rates as high as 1 MHz is demonstrated in the NASA Langley 31 in. Mach 10 hypersonic wind tunnel. Approximately 200 time-correlated image sequences of between 10 and 20 individual frames were obtained over eight days of wind tunnel testing spanning two entries in March and September of 2009. The image sequences presented were obtained from the boundary layer of a 20° flat plate model, in which transition was induced using a variety of different shaped protuberances, including a cylinder and a triangle. The high-speed image sequences captured a variety of laminar and transitional flow phenomena, ranging from mostly laminar flow, typically at a lower Reynolds number and/or in the near wall region of the model, to highly transitional flow in which the temporal evolution and progression of characteristic streak instabilities and/or corkscrew-shaped vortices could be clearly identified.

Voltage-induced switching of an antiferromagnetically ordered topological Dirac semimetal

NASA Astrophysics Data System (ADS)

Kim, Youngseok; Kang, Kisung; Schleife, André; Gilbert, Matthew J.

2018-04-01

An antiferromagnetic semimetal has been recently identified as a new member of topological semimetals that may host three-dimensional symmetry-protected Dirac fermions. A reorientation of the Néel vector may break the underlying symmetry and open a gap in the quasiparticle spectrum, inducing the (semi)metal-insulator transition. Here, we predict that such a transition may be controlled by manipulating the chemical potential location of the material. We perform both analytical and numerical analysis on the thermodynamic potential of the model Hamiltonian and find that the gapped spectrum is preferred when the chemical potential is located at the Dirac point. As the chemical potential deviates from the Dirac point, the system shows a possible transition from the gapped to the gapless phase and switches the corresponding Néel vector configuration. We perform density functional theory calculations to verify our analysis using a realistic material and discuss a two terminal transport measurement as a possible route to identify the voltage-induced switching of the Néel vector.

The increase of microRNA-21 during lung fibrosis and its contribution to epithelial-mesenchymal transition in pulmonary epithelial cells.

PubMed

Yamada, Mitsuhiro; Kubo, Hiroshi; Ota, Chiharu; Takahashi, Toru; Tando, Yukiko; Suzuki, Takaya; Fujino, Naoya; Makiguchi, Tomonori; Takagi, Kiyoshi; Suzuki, Takashi; Ichinose, Masakazu

2013-09-24

The excess and persistent accumulation of fibroblasts due to aberrant tissue repair results in fibrotic diseases such as idiopathic pulmonary fibrosis. Recent reports have revealed significant changes in microRNAs during idiopathic pulmonary fibrosis and evidence in support of a role for microRNAs in myofibroblast differentiation and the epithelial-mesenchymal transition in the context of fibrosis. It has been reported that microRNA-21 is up-regulated in myofibroblasts during fibrosis and promotes transforming growth factor-beta signaling by inhibiting Smad7. However, expression changes in microRNA-21 and the role of microRNA-21 in epithelial-mesenchymal transition during lung fibrosis have not yet been defined. Lungs from saline- or bleomycin-treated C57BL/6 J mice and lung specimens from patients with idiopathic pulmonary fibrosis were analyzed. Enzymatic digestions were performed to isolate single lung cells. Lung epithelial cells were isolated by flow cytometric cell sorting. The expression of microRNA-21 was analyzed using both quantitative PCR and in situ hybridization. To induce epithelial-mesenchymal transition in culture, isolated mouse lung alveolar type II cells were cultured on fibronectin-coated chamber slides in the presence of transforming growth factor-β, thus generating conditions that enhance epithelial-mesenchymal transition. To investigate the role of microRNA-21 in epithelial-mesenchymal transition, we transfected cells with a microRNA-21 inhibitor. Total RNA was isolated from the freshly isolated and cultured cells. MicroRNA-21, as well as mRNAs of genes that are markers of alveolar epithelial or mesenchymal cell differentiation, were quantified using quantitative PCR. The lung epithelial cells isolated from the bleomycin-induced lung fibrosis model system had decreased expression of epithelial marker genes, whereas the expression of mesenchymal marker genes was increased. MicroRNA-21 was significantly upregulated in isolated lung epithelial cells during bleomycin-induced lung fibrosis and human idiopathic pulmonary fibrosis. MicroRNA-21 was also upregulated in the cultured alveolar epithelial cells under the conditions that enhance epithelial-mesenchymal transition. Exogenous administration of a microRNA-21 inhibitor prevented the increased expression of vimentin and alpha-smooth muscle actin in cultured primary mouse alveolar type II cells under culture conditions that induce epithelial-mesenchymal transition. Our experiments demonstrate that microRNA-21 is increased in lung epithelial cells during lung fibrosis and that it promotes epithelial-mesenchymal transition.

Phase Transitions on Surfaces. An International Conference. Abstracts and Program, 3-7 August 1981, Orono, Maine.

DTIC Science & Technology

1982-04-16

P. J. Estrup Chemisorption-Induced Phase Transitions and Adatom Interactions on GaAs(110) P. Skeath, C. Y. Su, P. W. Chye , I. Lindau and W. E. Spicer...Transitions and Adatom Interactions on GaAs(ll0)* Perry Skeath, C. Y. Su, P. W. Chye , I Lindau, and W. E. Spicer Stanford Electronics Labs Stanford...ORDER PHASE TRANSITIONS* P. KLEBAN and CHIN -KUN HU, Department of Physics and Astronomy and Laboratory for Surface Science and Technology University of

Demonstration of the role of turbulence-driven poloidal flow generation in the L-H transition

NASA Astrophysics Data System (ADS)

Yu, C. X.; Xu, Y. H.; Luo, J. R.; Mao, J. S.; Liu, B. H.; Li, J. G.; Wan, B. N.; Wan, Y. X.

2000-05-01

This paper presents the evidence for the role of turbulence-driven poloidal flow generation in the L-H transition induced by a turbulent heating pulse on the HT-6M tokamak. It is found that the poloidal flow υθ plays a key role in developing the electric field Er and triggering the transition. The acceleration of υθ across the transition is clearly correlated with the enhancement of the Reynolds stress gradient.

Cholesteric pitch transitions induced by mechanical strain.

PubMed

Lelidis, I; Barbero, G; Alexe-Ionescu, A L

2013-02-01

We investigate thickness and surface anchoring strength influence on pitch transitions in a planar cholesteric liquid crystal layer. The cholesteric-nematic transition is also investigated. We assume planar boundary conditions, with strong anchoring strength at one interface and weak anchoring strength at the other. The surface anchoring energy we consider to describe the deviation of the surface twist angle from the easy axis induced by a bulk deformation is a parabolic potential or Rapini and Papoular periodic potential, respectively. We show that under strain, all pitch transitions take place at a critical thickness that is equal to the quarter of the natural cholesteric pitch. The latter result does not depend on the anchoring strength, the particular surface potential, or material properties. The twist angle on the limiting surface characterized by weak anchoring varies with strain either by slipping and or in a discontinuous manner according to the thickness of the sample. The position of the bifurcation point depends only on the ratio of the extrapolation length over the layer thickness, but its value is model dependent. Multistability and multiplicity of the transition are discussed.

Kinetic effects on the transition to relativistic self-induced transparency in laser-driven ion acceleration

NASA Astrophysics Data System (ADS)

Siminos, Evangelos; Svedung Wettervik, Benjamin; Grech, Mickael; Fülöp, Tünde

2016-10-01

We study kinetic effects responsible for the transition to relativistic self-induced transparency in the interaction of a circularly-polarized laser-pulse with an overdense plasma and their relation to hole-boring and ion acceleration. It is shown, using particle-in-cell simulations and an analysis of separatrices in single-particle phase-space, that this transition is mediated by the complex interplay of fast electron dynamics and ion motion at the initial stage of the interaction. It thus depends on the ion charge-to-mass ratio and can be controlled by varying the laser temporal profile. Moreover, we find a new regime in which a transition from relativistic transparency to hole-boring occurs dynamically during the course of the interaction. It is shown that, for a fixed laser intensity, this dynamic transition regime allows optimal ion acceleration in terms of both energy and energy spread. This work was supported by the Knut and Alice Wallenberg Foundation (pliona project) and the European Research Council (ERC-2014-CoG Grant 647121).

Pressure-induced valence change and moderate heavy fermion state in Eu-compounds

NASA Astrophysics Data System (ADS)

Honda, Fuminori; Okauchi, Keigo; Sato, Yoshiki; Nakamura, Ai; Akamine, Hiromu; Ashitomi, Yosuke; Hedo, Masato; Nakama, Takao; Takeuchi, Tetsuya; Valenta, Jaroslav; Prchal, Jiri; Sechovský, Vladimir; Aoki, Dai; Ōnuki, Yoshichika

2018-05-01

A pressure-induced valence transition has attracted much attention in Eu-compounds. Among them, EuRh2Si2, EuNi2Ge2, and EuCo2Ge2 reveal the valence transition around 1, 2, and 3 GPa, respectively. We have succeeded in growing single crystals of EuT2X2 (T: transition metal, X: Si, Ge) and studied electronic properties under pressure. EuRh2Si2 indicates a first-order valence transition between 1 and 2 GPa, with a large and prominent hysteresis in the electrical resistivity. At higher pressures, the first-order valence transition changes to a cross-over regime with an intermediate valence state. Tuning of the valence state with pressure is reflected in a drastic change of the temperature dependence of the electrical resistivity in EuRh2Si2 single crystals. Effect of pressure on the valence states on EuRh2Si2, EuIr2Si2, EuNi2Ge2, and EuCo2Ge2, as well as an isostructural related compound EuGa4, are reviewed.

Hook1 inhibits malignancy and epithelial-mesenchymal transition in hepatocellular carcinoma.

PubMed

Sun, Xu; Zhang, Qi; Chen, Wei; Hu, Qida; Lou, Yu; Fu, Qi-Han; Zhang, Jing-Ying; Chen, Yi-Wen; Ye, Long-Yun; Wang, Yi; Xie, Shang-Zhi; Hu, Li-Qiang; Liang, Ting-Bo; Bai, Xue-Li

2017-07-01

Hook1 is a member of the hook family of coiled-coil proteins, which is recently found to be associated with malignant tumors. However, its biological function in hepatocellular carcinoma is yet unknown. Here, we evaluated the Hook1 levels in human hepatocellular carcinoma samples and matched peritumoral tissues by real-time polymerase chain reaction. Small interfering RNA knockdown and a transforming growth factor-β-induced epithelial-mesenchymal transition model were employed to investigate the biological effects of Hook1 in hepatocellular carcinoma. Our results indicated that Hook1 levels were significantly lower in hepatocellular carcinoma tissues than in the peritumoral tissues. In addition, Hook1 expression was significantly associated with hepatocellular carcinoma malignancy. Hook1 was downregulated after transforming growth factor-β-induced epithelial-mesenchymal transition. Moreover, Hook1 knockdown promoted epithelial-mesenchymal transition and attenuated the sensitivity of hepatocellular carcinoma cells to doxorubicin. In summary, our results indicate that downregulation of Hook1 plays a pivotal role in hepatocellular carcinoma progression via epithelial-mesenchymal transition. Hook1 may be used as a novel marker and therapeutic molecular target in hepatocellular carcinoma.

Evaluation of uranium transitions for isotopically-selective laser induced fluorescence with diode lasers (technical report for ST064)

NASA Astrophysics Data System (ADS)

Cannon, B. D.

1993-10-01

Isotopically-selective excitation of uranium atoms by diode lasers can be the basis for a portable instrument to perform uranium isotopic assays in the field. Such an instrument would improve the ability of on-site inspections to detect and deter nuclear proliferation. Published and unpublished spectroscopic data on atomic uranium were examined to identify candidate transitions for isotopically-selective laser excitation with diode lasers. Eleven candidate transitions were identified and evaluated for their potential usefulness for a portable uranium assay instrument. Eight of these transitions are suitable for laser induced fluorescence using different excitation and detection wavelengths, which will improve sensitivity and elemental selectivity. Data sheets on the 25 uranium transitions in the wavelength range 629 nm to 1,000 nm that originate in the ground or first excited states of neutral atomic uranium are included. Each data sheet provides the wavelength, upper and lower energy levels, angular momentum quantum numbers, U-235 isotope shift (relative to U-238, and high-resolution spectra of weapons-grade uranium (93% U-235 and 7% U-238).

Pressure-induced structural and semiconductor-semiconductor transitions in C o0.5M g0.5C r2O4

NASA Astrophysics Data System (ADS)

Rahman, S.; Saqib, Hajra; Zhang, Jinbo; Errandonea, D.; Menéndez, C.; Cazorla, C.; Samanta, Sudeshna; Li, Xiaodong; Lu, Junling; Wang, Lin

2018-05-01

The effect of pressure on the structural, vibrational, and electronic properties of Mg-doped Cr bearing spinel C o0.5M g0.5C r2O4 was studied up to 55 GPa at room-temperature using x-ray diffraction, Raman spectroscopy, electrical transport measurements, and ab initio calculations. We found that the ambient-pressure phase is cubic (spinel-type, F d 3 ¯m ) and underwent a pressure-induced structural transition to a tetragonal phase (space group I 4 ¯m 2 ) above 28 GPa. The ab initio calculation confirmed this first-order phase transition. The resistivity of the sample decreased at low pressures with the existence of a low-pressure (LP) phase and started to increase with the emergence of a high-pressure (HP) phase. The temperature dependent resistivity experiments at different pressures illustrated the wide band gap semiconducting nature of both the LP and HP phases with different activation energies, suggesting a semiconductor-semiconductor transition at HP. No evidence of chemical decomposition or a semiconductor-metal transition was observed in our studies.

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

PubMed

Machon, Denis; Mélinon, Patrice

2015-01-14

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

Nonlinear Parametric Excitation Effect Induces Stability Transitions in Swimming Direction of Flexible Superparamagnetic Microswimmers.

PubMed

Harduf, Yuval; Jin, Dongdong; Or, Yizhar; Zhang, Li

2018-04-05

Microscopic artificial swimmers have recently become highly attractive due to their promising potential for biomedical microrobotic applications. Previous pioneering work has demonstrated the motion of a robotic microswimmer with a flexible chain of superparamagnetic beads, which is actuated by applying an oscillating external magnetic field. Interestingly, they have shown that the microswimmer's orientation undergoes a 90°-transition when the magnetic field's oscillation amplitude is increased above a critical value. This unexpected transition can cause severe problems in steering and manipulation of flexible magnetic microrobotic swimmers. Thus, theoretical understanding and analysis of the physical origins of this effect are of crucial importance. In this work, we investigate this transition both theoretically and experimentally by using numerical simulations and presenting a novel flexible microswimmer with an anisotropic superparamagnetic head. We prove that this effect depends on both frequency and amplitude of the oscillating magnetic field, and demonstrate existence of an optimal amplitude achieving maximal swimming speed. Asymptotic analysis of a minimal two-link model reveals that the changes in the swimmer's direction represent stability transitions, which are induced by a nonlinear parametric excitation.

Electric control of magnetization reorientation in FeRh /BaTiO3 mediated by a magnetic phase transition

NASA Astrophysics Data System (ADS)

Odkhuu, Dorj

2017-10-01

Employing first-principles calculations we predict magnetization reorientation in FeRh films epitaxially grown on BaTiO3 by reversing the electric polarization or applying the strain effect, which is associated with the recently discovered voltage-induced interfacial magnetic-phase transition by R. O. Cherifi et al. [Nat. Mater. 13, 345 (2014), 10.1038/nmat3870]. We propose that this transition from antiferromagnetic to ferromagnetic phase is the results of the mutual mechanisms of the polarization-reversal-induced volume/strain expansion in the interfacial FeRh layers and the competition between direct and indirect exchange interactions. These mechanisms are mainly driven by the ferroelectrically driven hybridization between Fe and Ti 3 d orbital states at the interface. Such a strong hybridization can further involve Rh 4 d states with large spin-orbit coupling, which, rather than the Fe 3 d orbitals, is responsible for magnetization reorientation at the magnetic-phase transition. These findings point toward the feasibility of electric field control of magnetization switching associated with the magnetic-phase transition in an antiferromagnet structure.

Neutron-star–black-hole binaries produced by binary-driven hypernovae

DOE PAGES

Fryer, Chris L.; Oliveira, F. G.; Rueda, Jorge A.; ...

2015-12-04

Here, binary-driven hypernovae (BdHNe) within the induced gravitational collapse paradigm have been introduced to explain energetic (E iso ≳10 52 erg), long gamma-ray bursts (GRBs) associated with type Ic supernovae (SNe). The progenitor is a tight binary composed of a carbon-oxygen (CO) core and a neutron-star (NS) companion, a subclass of the newly proposed “ultrastripped” binaries. The CO-NS short-period orbit causes the NS to accrete appreciable matter from the SN ejecta when the CO core collapses, ultimately causing it to collapse to a black hole (BH) and producing a GRB. These tight binaries evolve through the SN explosion very differentlymore » than compact binaries studied in population synthesis calculations. First, the hypercritical accretion onto the NS companion alters both the mass and the momentum of the binary. Second, because the explosion time scale is on par with the orbital period, the mass ejection cannot be assumed to be instantaneous. This dramatically affects the post-SN fate of the binary. Finally, the bow shock created as the accreting NS plows through the SN ejecta transfers angular momentum, braking the orbit. These systems remain bound even if a large fraction of the binary mass is lost in the explosion (well above the canonical 50% limit), and even large kicks are unlikely to unbind the system. Indeed, BdHNe produce a new family of NS-BH binaries unaccounted for in current population synthesis analyses and, although they may be rare, the fact that nearly 100% remain bound implies that they may play an important role in the compact merger rate, important for gravitational waves that, in turn, can produce a new class of ultrashort GRBs.« less

Neutron-Star-Black-Hole Binaries Produced by Binary-Driven Hypernovae.

PubMed

Fryer, Chris L; Oliveira, F G; Rueda, J A; Ruffini, R

2015-12-04

Binary-driven hypernovae (BdHNe) within the induced gravitational collapse paradigm have been introduced to explain energetic (E_{iso}≳10^{52}  erg), long gamma-ray bursts (GRBs) associated with type Ic supernovae (SNe). The progenitor is a tight binary composed of a carbon-oxygen (CO) core and a neutron-star (NS) companion, a subclass of the newly proposed "ultrastripped" binaries. The CO-NS short-period orbit causes the NS to accrete appreciable matter from the SN ejecta when the CO core collapses, ultimately causing it to collapse to a black hole (BH) and producing a GRB. These tight binaries evolve through the SN explosion very differently than compact binaries studied in population synthesis calculations. First, the hypercritical accretion onto the NS companion alters both the mass and the momentum of the binary. Second, because the explosion time scale is on par with the orbital period, the mass ejection cannot be assumed to be instantaneous. This dramatically affects the post-SN fate of the binary. Finally, the bow shock created as the accreting NS plows through the SN ejecta transfers angular momentum, braking the orbit. These systems remain bound even if a large fraction of the binary mass is lost in the explosion (well above the canonical 50% limit), and even large kicks are unlikely to unbind the system. Indeed, BdHNe produce a new family of NS-BH binaries unaccounted for in current population synthesis analyses and, although they may be rare, the fact that nearly 100% remain bound implies that they may play an important role in the compact merger rate, important for gravitational waves that, in turn, can produce a new class of ultrashort GRBs.

Lacosamide Inhibition of Nav1.7 Voltage-Gated Sodium Channels: Slow Binding to Fast-Inactivated States

PubMed Central

Jo, Sooyeon

2017-01-01

Lacosamide is an antiseizure agent that targets voltage-dependent sodium channels. Previous experiments have suggested that lacosamide is unusual in binding selectively to the slow-inactivated state of sodium channels, in contrast to drugs like carbamazepine and phenytoin, which bind tightly to fast-inactivated states. Using heterologously expressed human Nav1.7 sodium channels, we examined the state-dependent effects of lacosamide. Lacosamide induced a reversible shift in the voltage dependence of fast inactivation studied with 100-millisecond prepulses, suggesting binding to fast-inactivated states. Using steady holding potentials, lacosamide block was very weak at −120 mV (3% inhibition by 100 µM lacosamide) but greatly enhanced at −80 mV (43% inhibition by 100 µM lacosamide), where there is partial fast inactivation but little or no slow inactivation. During long depolarizations, lacosamide slowly (over seconds) put channels into states that recovered availability slowly (hundreds of milliseconds) at −120 mV. This resembles enhancement of slow inactivation, but the effect was much more pronounced at −40 mV, where fast inactivation is complete, but slow inactivation is not, than at 0 mV, where slow inactivation is maximal, more consistent with slow binding to fast-inactivated states than selective binding to slow-inactivated states. Furthermore, inhibition by lacosamide was greatly reduced by pretreatment with 300 µM lidocaine or 300 µM carbamazepine, suggesting that lacosamide, lidocaine, and carbamazepine all bind to the same site. The results suggest that lacosamide binds to fast-inactivated states in a manner similar to other antiseizure agents but with slower kinetics of binding and unbinding. PMID:28119481

Lacosamide Inhibition of Nav1.7 Voltage-Gated Sodium Channels: Slow Binding to Fast-Inactivated States.

PubMed

Jo, Sooyeon; Bean, Bruce P

2017-04-01

Lacosamide is an antiseizure agent that targets voltage-dependent sodium channels. Previous experiments have suggested that lacosamide is unusual in binding selectively to the slow-inactivated state of sodium channels, in contrast to drugs like carbamazepine and phenytoin, which bind tightly to fast-inactivated states. Using heterologously expressed human Nav1.7 sodium channels, we examined the state-dependent effects of lacosamide. Lacosamide induced a reversible shift in the voltage dependence of fast inactivation studied with 100-millisecond prepulses, suggesting binding to fast-inactivated states. Using steady holding potentials, lacosamide block was very weak at -120 mV (3% inhibition by 100 µ M lacosamide) but greatly enhanced at -80 mV (43% inhibition by 100 µ M lacosamide), where there is partial fast inactivation but little or no slow inactivation. During long depolarizations, lacosamide slowly (over seconds) put channels into states that recovered availability slowly (hundreds of milliseconds) at -120 mV. This resembles enhancement of slow inactivation, but the effect was much more pronounced at -40 mV, where fast inactivation is complete, but slow inactivation is not, than at 0 mV, where slow inactivation is maximal, more consistent with slow binding to fast-inactivated states than selective binding to slow-inactivated states. Furthermore, inhibition by lacosamide was greatly reduced by pretreatment with 300 µ M lidocaine or 300 µ M carbamazepine, suggesting that lacosamide, lidocaine, and carbamazepine all bind to the same site. The results suggest that lacosamide binds to fast-inactivated states in a manner similar to other antiseizure agents but with slower kinetics of binding and unbinding. Copyright © 2017 by The American Society for Pharmacology and Experimental Therapeutics.

Neutron-Star-Black-Hole Binaries Produced by Binary-Driven Hypernovae

NASA Astrophysics Data System (ADS)

Fryer, Chris L.; Oliveira, F. G.; Rueda, J. A.; Ruffini, R.

2015-12-01

Binary-driven hypernovae (BdHNe) within the induced gravitational collapse paradigm have been introduced to explain energetic (Eiso≳1052 erg ), long gamma-ray bursts (GRBs) associated with type Ic supernovae (SNe). The progenitor is a tight binary composed of a carbon-oxygen (CO) core and a neutron-star (NS) companion, a subclass of the newly proposed "ultrastripped" binaries. The CO-NS short-period orbit causes the NS to accrete appreciable matter from the SN ejecta when the CO core collapses, ultimately causing it to collapse to a black hole (BH) and producing a GRB. These tight binaries evolve through the SN explosion very differently than compact binaries studied in population synthesis calculations. First, the hypercritical accretion onto the NS companion alters both the mass and the momentum of the binary. Second, because the explosion time scale is on par with the orbital period, the mass ejection cannot be assumed to be instantaneous. This dramatically affects the post-SN fate of the binary. Finally, the bow shock created as the accreting NS plows through the SN ejecta transfers angular momentum, braking the orbit. These systems remain bound even if a large fraction of the binary mass is lost in the explosion (well above the canonical 50% limit), and even large kicks are unlikely to unbind the system. Indeed, BdHNe produce a new family of NS-BH binaries unaccounted for in current population synthesis analyses and, although they may be rare, the fact that nearly 100% remain bound implies that they may play an important role in the compact merger rate, important for gravitational waves that, in turn, can produce a new class of ultrashort GRBs.

Chemical doping in pnictides superconductors: The case of Ca(Fe1-xXx) 2As2 , X = Co, Ni, Pt

NASA Astrophysics Data System (ADS)

Continenza, Alessandra; Profeta, Gianni

2018-04-01

We present a comparative and detailed study of transition metal doping in CaFe2As2. Comparing with several experimental results and carefully analyzing how the states at the Fermi level are affected by doping we show that: i) simulation of real doping and considering induces structural relaxations are crucial to correctly address the physical mechanisms induced by transition metal substitutions; ii) different dopant concentration induces changes on the band structure that can not be described within a simple rigid-band picture; iii) careful comparison with the available ARPES results shows that the main effects on band filling and symmetry can be caught within DFT.

Targeted medication delivery using magnetic nanostructures

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

Yoon, Mina

We use quaternion molecular dynamics simulations to describe field-induced structural transitions in systems of few magnetic dipoles and their use for targeted medication delivery. Compact ring isomers of magnetic particles are contained, together with molecules of an active medication, inside inert microcapsules. The filled microcapsules may be transported within the body using a weak,inhomogeneous magnetic field. Medication release is triggered by puncturing the container during a structural transition within the magnetic subsystem, induced by an externally applied strong magnetic field. Our simulations describe not only the time evolution of the magnetic subsystem during a successful medication release, but also addressmore » ways to suppress an accidental release induced by thermal and magnetic fluctuations.« less

Time delay induced different synchronization patterns in repulsively coupled chaotic oscillators

NASA Astrophysics Data System (ADS)

Yao, Chenggui; Yi, Ming; Shuai, Jianwei

2013-09-01

Time delayed coupling plays a crucial role in determining the system's dynamics. We here report that the time delay induces transition from the asynchronous state to the complete synchronization (CS) state in the repulsively coupled chaotic oscillators. In particular, by changing the coupling strength or time delay, various types of synchronous patterns, including CS, antiphase CS, antiphase synchronization (ANS), and phase synchronization, can be generated. In the transition regions between different synchronous patterns, bistable synchronous oscillators can be observed. Furthermore, we show that the time-delay-induced phase flip bifurcation is of key importance for the emergence of CS. All these findings may light on our understanding of neuronal synchronization and information processing in the brain.

Stress-induced nematicity in EuFe 2 As 2 studied by Raman spectroscopy

DOE PAGES

Zhang, W. -L.; Sefat, Athena S.; Ding, H.; ...

2016-07-18

Here, we use polarized Raman scattering to study the structural phase transition in EuFe 2 As 2 , the parent compound of the 122-ferropnictide superconductors. The in-plane lattice anisotropy is characterized by measurements of the side surface with different strains induced by different preparation methods. We also show that while a fine surface polishing leaves the samples free of residual internal strain, in which case the onset of the C 4 symmetry breaking is observed at the nominal structural phase transition temperature T S , cutting the side surface induces a permanent fourfold rotational symmetry breaking spanning tens ofmore » degrees above T S .« less

Pilot Study for Definition of Track Component Load Environments

DOT National Transportation Integrated Search

1981-02-01

This report describes the results of an experimental and analytical effort to define the vehicle induced load environment in an at-grade, concrete tie/ballast transit track structure. The experiment was performed on the UMTA transit track oval at the...

Structural and electronic phase transitions of ThS 2 from first-principles calculations

DOE PAGES

Guo, Yongliang; Wang, Changying; Qiu, Wujie; ...

2016-10-07

Performed a systematic study using first-principles methods of the pressure-induced structural and electronic phase transitions in ThS 2, which may play an important role in the next generation nuclear energy fuel technology.

Pressure-induced amorphization of La{sub 1/3}TaO{sub 3}

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

Noked, O., E-mail: noked@bgu.ac.il; Physics Department, Ben-Gurion University, Beer Sheva 84105; Melchior, A.

2013-06-15

La{sub 1/3}TaO{sub 3}, an A-site cation deficient perovskite, has been studied under pressure by synchrotron X-ray powder diffraction and Raman spectroscopy. It undergoes irreversible pressure induced amorphization at P=18.5 GPa. An almost linear unit cell volume decrease vs. pressure is observed from ambient pressure up to the phase transition. The Raman spectroscopy also shows amorphization at the same pressure, with positive shifts of all modes as a function of pressure. The pressure dependence of the E{sub g} and A{sub 1g} Raman modes arising from the octahedral oxygen network is discussed. - Graphical abstract: La{sub 1/3}Tao{sub 3} exhibits linear pressure–volume relationmore » until irreversible pressure induced amorphization at 18.5 Gpa. - Highlights: • La{sub 1/3}TaO{sub 3} has been studied under pressure by synchrotron XRD and Raman spectroscopy. • La{sub 1/3}TaO{sub 3} undergoes irreversible pressure induced amorphization around 18.5 GPa. • The transition is manifested in both XRD and Raman measurements. • A linear P–V relation is observed from ambient pressure up to the phase transition.« less

Temperature-induced changes in lecithin model membranes detected by novel covalent spin-labelled phospholipids.

PubMed

Stuhne-Sekalec, L; Stanacev, N Z

1977-02-01

Several spin-labelled phospholipids carrying covalently bound 5-doxylstearic acid (2-(3-carboxydecyl)-2-hexyl-4,4-dimethyl-3-oxazolidinoxyl) were intercalated in liposomes of saturated and unsaturated lecithins. Temperature-induced changes of these liposomes, detected by the spin-labelled phospholipids, were found to be in agreement with the previously described transitions of hydrocarbon chains of host lecithins detected by different probes and different techniques, establishing that spin-labelled phosopholipids are sensitive probes for the detection of temperature-induced changes in lecithin model membranes. In addition to the detection of already-known transitions in lecithin liposomes, the coexistence of two distinctly different enviroments was observed above the characteristic transition temperature. This phenomenon was tentatively attributed to the influence of the lecithin polar group on the fluidity of fatty acyl chains near the polar group. Combined with other results from the literature, the coexistence of two environments could be associated with the coexistence of two conformational isomers of lecithin, differing in the orientation of the polar head group with respect to the plane of bilayer. These findings have been discussed in view of the present state of knowledge regarding temperature-induced changes in model membranes.

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.