An ab initio investigation of possible intermediates in the reaction of the hydroxyl and hydroperoxyl radicals

NASA Technical Reports Server (NTRS)

Jackels, C. F.

1985-01-01

Ab initio quantum chemical techniques are used to investigate covalently-bonded and hydrogen-bonded species that may be important intermediates in the reaction of hydroxyl and hydroperoxyl radicals. Stable structures of both types are identified. Basis sets of polarized double zeta quality and large scale configuration interaction wave functions are utilized. Based on electronic energies, the covalently bonded HOOOH species is 26.4 kcal/mol more stable than the OH and HO2 radicals. Similarly, the hydrogen bonded HO---HO2 species has an electronic energy 4.7 kcal/mol below that of the component radicals, after correction is made for the basis set superposition error. The hydrogen bonded form is planar, possesses one relatively normal hydrogen bond, and has the lowest energy 3A' and 1A' states that are essentially degenerate. The 1A" and 3A" excited states produced by rotation of the unpaired OH electron into the molecular plane are very slightly bound.

Characterization of folding intermediates during urea-induced denaturation of human carbonic anhydrase II.

PubMed

Wahiduzzaman; Dar, Mohammad Aasif; Haque, Md Anzarul; Idrees, Danish; Hassan, Md Imtaiyaz; Islam, Asimul; Ahmad, Faizan

2017-02-01

Knowledge of folding/unfolding pathway is fundamental basis to study protein structure and stability. Human carbonic anhydrase II (HCAII) is a ∼29kDa, β-sheet dominated monomeric protein of 259 amino acid residues. In the present study, the urea-induced denaturation of HCAII was carried out which was a tri-phasic process, i.e., N (native) ↔ X I ↔ X II ↔ D (denatured) with stable intermediates X I and X II populated around 2 and 4M urea, respectively. The far-UV CD was used to characterize the intermediate states (X I and X II ) for secondary structural content, near-UV CD for tertiary structure, dynamic light scattering for hydrodynamic radius and ANS fluorescence spectroscopy for the presence of exposed hydrophobic patches. Based on these experiments, we concluded that urea-induced X I state has characteristics of molten globule state while X II state bears characteristics features of pre-molten globule state. Characterization of the intermediates on the folding pathway will contribute to a deeper understanding of the structure-function relationship of HCAII. Furthermore, this system may provide an excellent model to study urea stress and the strategies adopted by the organisms to combat such a stress. Copyright © 2016 Elsevier B.V. All rights reserved.

Prediction and validation of protein intermediate states from structurally rich ensembles and coarse-grained simulations

NASA Astrophysics Data System (ADS)

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

2016-08-01

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

Chimera states for coupled oscillators.

PubMed

Abrams, Daniel M; Strogatz, Steven H

2004-10-22

Arrays of identical oscillators can display a remarkable spatiotemporal pattern in which phase-locked oscillators coexist with drifting ones. Discovered two years ago, such "chimera states" are believed to be impossible for locally or globally coupled systems; they are peculiar to the intermediate case of nonlocal coupling. Here we present an exact solution for this state, for a ring of phase oscillators coupled by a cosine kernel. We show that the stable chimera state bifurcates from a spatially modulated drift state, and dies in a saddle-node bifurcation with an unstable chimera state.

Towards a drift-free multi-level Phase Change Memory

NASA Astrophysics Data System (ADS)

Cinar, Ibrahim; Ozdemir, Servet; Cogulu, Egecan; Gokce, Aisha; Stipe, Barry; Katine, Jordan; Aktas, Gulen; Ozatay, Ozhan

For ultra-high density data storage applications, Phase Change Memory (PCM) is considered a potentially disruptive technology. Yet, the long-term reliability of the logic levels corresponding to the resistance states of a PCM device is an important issue for a stable device operation since the resistance levels drift uncontrollably in time. The underlying mechanism for the resistance drift is considered as the structural relaxation and spontaneous crystallization at elevated temperatures. We fabricated a nanoscale single active layer-phase change memory cell with three resistance levels corresponding to crystalline, amorphous and intermediate states by controlling the current injection site geometry. For the intermediate state and the reset state, the activation energies and the trap distances have been found to be 0.021 eV and 0.235 eV, 1.31 nm and 7.56 nm, respectively. We attribute the ultra-low and weakly temperature dependent drift coefficient of the intermediate state (ν = 0.0016) as opposed to that of the reset state (ν = 0.077) as being due to the dominant contribution of the interfacial defects in electrical transport in the case of the mixed phase. Our results indicate that the engineering of interfacial defects will enable a drift-free multi-level PCM device design.

Highly durable organic electrode for sodium-ion batteries via a stabilized α-C radical intermediate

NASA Astrophysics Data System (ADS)

Wu, Shaofei; Wang, Wenxi; Li, Minchan; Cao, Lujie; Lyu, Fucong; Yang, Mingyang; Wang, Zhenyu; Shi, Yang; Nan, Bo; Yu, Sicen; Sun, Zhifang; Liu, Yao; Lu, Zhouguang

2016-11-01

It is a challenge to prepare organic electrodes for sodium-ion batteries with long cycle life and high capacity. The highly reactive radical intermediates generated during the sodiation/desodiation process could be a critical issue because of undesired side reactions. Here we present durable electrodes with a stabilized α-C radical intermediate. Through the resonance effect as well as steric effects, the excessive reactivity of the unpaired electron is successfully suppressed, thus developing an electrode with stable cycling for over 2,000 cycles with 96.8% capacity retention. In addition, the α-radical demonstrates reversible transformation between three states: C=C α-C.radical and α-C- anion. Such transformation provides additional Na+ storage equal to more than 0.83 Na+ insertion per α-C radical for the electrodes. The strategy of intermediate radical stabilization could be enlightening in the design of organic electrodes with enhanced cycling life and energy storage capability.

GdnHCl-induced unfolding intermediate in the mitochondrial carbonic anhydrase VA.

PubMed

Idrees, Danish; Prakash, Amresh; Haque, Md Anzarul; Islam, Asimul; Hassan, Md Imtaiyaz; Ahmad, Faizan

2016-10-01

Carbonic anhydrase VA (CAVA) is a mitochondrial enzyme belonging to the α-family of CAs, which is involved in several physiological processes including ureagenesis, lipogenesis, gluconeogenesis and neuronal transmission. Here, we have tried to understand the folding mechanism of CAVA using guanidine hydrochloride (GdnHCl)-induced denaturation at pH 8.0 and 25°C. The conformational stability was measured from the GdnHCl-induced denaturation study of CAVA monitored by circular dichroism (CD) and fluorescence measurements. On increasing the concentration of GdnHCl up to 5.0, a stable intermediate was observed between the concentrations 3.25M to 3.40M of the denaturant. However, CAVA gets completely denatured at 4.0M GdnHCl. The existence of a stable intermediate state was validated by 1-anilinonaphthalene-8-sulfonic acid (ANS binding) fluorescence and near-UV CD measurements. In silico studies were also performed to analyse the effect of GdnHCl on the structure and stability of CAVA under explicit conditions. Molecular dynamics simulations for 40ns were carried out and a well-defined correlation was established for both in vitro and in silico studies. Copyright © 2016 Elsevier B.V. All rights reserved.

Multistabilities and symmetry-broken one-color and two-color states in closely coupled single-mode lasers.

PubMed

Clerkin, Eoin; O'Brien, Stephen; Amann, Andreas

2014-03-01

We theoretically investigate the dynamics of two mutually coupled, identical single-mode semi-conductor lasers. For small separation and large coupling between the lasers, symmetry-broken one-color states are shown to be stable. In this case the light outputs of the lasers have significantly different intensities while at the same time the lasers are locked to a single common frequency. For intermediate coupling we observe stable symmetry-broken two-color states, where both lasers lase simultaneously at two optical frequencies which are separated by up to 150 GHz. Using a five-dimensional model, we identify the bifurcation structure which is responsible for the appearance of symmetric and symmetry-broken one-color and two-color states. Several of these states give rise to multistabilities and therefore allow for the design of all-optical memory elements on the basis of two coupled single-mode lasers. The switching performance of selected designs of optical memory elements is studied numerically.

Multistabilities and symmetry-broken one-color and two-color states in closely coupled single-mode lasers

NASA Astrophysics Data System (ADS)

Clerkin, Eoin; O'Brien, Stephen; Amann, Andreas

2014-03-01

We theoretically investigate the dynamics of two mutually coupled, identical single-mode semi-conductor lasers. For small separation and large coupling between the lasers, symmetry-broken one-color states are shown to be stable. In this case the light outputs of the lasers have significantly different intensities while at the same time the lasers are locked to a single common frequency. For intermediate coupling we observe stable symmetry-broken two-color states, where both lasers lase simultaneously at two optical frequencies which are separated by up to 150 GHz. Using a five-dimensional model, we identify the bifurcation structure which is responsible for the appearance of symmetric and symmetry-broken one-color and two-color states. Several of these states give rise to multistabilities and therefore allow for the design of all-optical memory elements on the basis of two coupled single-mode lasers. The switching performance of selected designs of optical memory elements is studied numerically.

Intermediate states and structure evolution in the free-falling process of the dislocation in graphene

NASA Astrophysics Data System (ADS)

Wang, Shaofeng; Yao, Yin; Bai, Jianhui; Wang, Rui

2017-04-01

This paper investigated the intermediate states and the structure evolution of the dislocation in graphene when it falls freely from the saddle point of the energy landscape. The O-type dislocation, an unstable equilibrium structure located at the saddle point, is obtained from the lattice theory of the dislocation structure and improved by the ab initio calculation to take the buckling into account. Intermediate states along the kinetics path in the falling process are obtained from the ab initio simulation. Once the dislocation falls from the saddle point to the energy valley, this O-type dislocation transforms into the stable structure that is referred to as the B-type dislocation, and in the meantime, it moves a distance that equals half a Burgers vector. The structure evolution and the energy variation in the free-falling process are revealed explicitly. It is observed that rather than smooth change, a platform manifests itself in the energy curve. The unusual behaviour in the energy curve is mainly originated from symmetry breaking and bond formation in the dislocation core. The results can provide deep insight in the mechanism of the brittle feature of covalent materials.

Two-dimensional symmetry breaking of fluid density distribution in closed nanoslits.

PubMed

Berim, Gersh O; Ruckenstein, Eli

2008-01-14

Stable and metastable fluid density distributions (FDDs) in a closed nanoslit between two identical parallel solid walls have been identified on the basis of a nonlocal canonical ensemble density functional theory. Similar to Monte Carlo simulations, periodicity of the FDD in one of the lateral (parallel to the walls surfaces) directions, denoted as the x direction, was assumed. In the other lateral direction, y direction, the FDD was considered uniform. It was found that depending on the average fluid density in the slit, both uniform as well as nonuniform FDDs in the x direction can occur. The uniform FDDs are either symmetric or asymmetric about the middle plane between walls; the latter FDD being the consequence of a symmetry breaking across the slit. The nonuniform FDDs in the x direction occur either in the form of a bump on a thin liquid film covering the walls or as a liquid bridge between those walls and provide symmetry breaking in the x direction. For small and large average densities, the stable state is uniform in the x direction and is symmetric about the middle plane between walls. In the intermediate range of the average density and depending on the length L(x) of the FDD period, the stable state can be represented either by a FDD, which is uniform in the x direction and asymmetric about the middle of the slit (small values of L(x)), or by a bump- and bridgelike FDD for intermediate and large values of L(x), respectively. These results are in agreement with the Monte Carlo simulations performed earlier by other authors. Because the free energy of the stable state decreases monotonically with increasing L(x), one can conclude that the real period is very large (infinite) and that for the values of the parameters employed, a single bridge of finite length over the entire slit is generated.

Quantum chemical study of the mechanism of reaction between NH (X 3sigma-) and H2, H2O, and CO2 under combustion conditions.

PubMed

Mackie, John C; Bacskay, George B

2005-12-29

Reactions of ground-state NH (3sigma-) radicals with H2, H2O, and CO2 have been investigated quantum chemically, whereby the stationary points of the appropriate reaction potential energy surfaces, that is, reactants, products, intermediates, and transition states, have been identified at the G3//B3LYP level of theory. Reaction between NH and H2 takes place via a simple abstraction transition state, and the rate coefficient for this reaction as derived from the quantum chemical calculations, k(NH + H2) = (1.1 x 10(14)) exp(-20.9 kcal mol(-1)/RT) cm3 mol(-1) s(-1) between 1000 and 2000 K, is found to be in good agreement with experiment. For reaction between triplet NH and H2O, no stable intermediates were located on the triplet reaction surface although several stable species were found on the singlet surface. No intersystem crossing seam between triplet NH + H2O and singlet HNO + H2 (the products of lowest energy) was found; hence there is no evidence to support the existence of a low-energy pathway to these products. A rate coefficient of k(NH + H2O) = (6.1 x 10(13)) exp(-32.8 kcal mol(-1)/RT) cm3 mol(-1) s(-1) between 1000 and 2000 K for the reaction NH (3sigma-) + H2O --> NH2 (2B) + OH (2pi) was derived from the quantum chemical results. The reverse rate coefficient, calculated via the equilibrium constant, is in agreement with values used in modeling the thermal de-NO(x) process. For the reaction between triplet NH and CO2, several stable intermediates on both triplet and singlet reaction surfaces were located. Although a pathway from triplet NH + CO2 to singlet HNO + CO involving intersystem crossing in an HN-CO2 adduct was discovered, no pathway of sufficiently low activation energy was discovered to compare with that found in an earlier experiment [Rohrig, M.; Wagner, H. G. Proc. Combust. Inst. 1994, 25, 993.].

The optimal imaging strategy for patients with stable chest pain: a cost-effectiveness analysis.

PubMed

Genders, Tessa S S; Petersen, Steffen E; Pugliese, Francesca; Dastidar, Amardeep G; Fleischmann, Kirsten E; Nieman, Koen; Hunink, M G Myriam

2015-04-07

The optimal imaging strategy for patients with stable chest pain is uncertain. To determine the cost-effectiveness of different imaging strategies for patients with stable chest pain. Microsimulation state-transition model. Published literature. 60-year-old patients with a low to intermediate probability of coronary artery disease (CAD). Lifetime. The United States, the United Kingdom, and the Netherlands. Coronary computed tomography (CT) angiography, cardiac stress magnetic resonance imaging, stress single-photon emission CT, and stress echocardiography. Lifetime costs, quality-adjusted life-years (QALYs), and incremental cost-effectiveness ratios. The strategy that maximized QALYs and was cost-effective in the United States and the Netherlands began with coronary CT angiography, continued with cardiac stress imaging if angiography found at least 50% stenosis in at least 1 coronary artery, and ended with catheter-based coronary angiography if stress imaging induced ischemia of any severity. For U.K. men, the preferred strategy was optimal medical therapy without catheter-based coronary angiography if coronary CT angiography found only moderate CAD or stress imaging induced only mild ischemia. In these strategies, stress echocardiography was consistently more effective and less expensive than other stress imaging tests. For U.K. women, the optimal strategy was stress echocardiography followed by catheter-based coronary angiography if echocardiography induced mild or moderate ischemia. Results were sensitive to changes in the probability of CAD and assumptions about false-positive results. All cardiac stress imaging tests were assumed to be available. Exercise electrocardiography was included only in a sensitivity analysis. Differences in QALYs among strategies were small. Coronary CT angiography is a cost-effective triage test for 60-year-old patients who have nonacute chest pain and a low to intermediate probability of CAD. Erasmus University Medical Center.

Model of the synthesis of trisporic acid in Mucorales showing bistability.

PubMed

Werner, S; Schroeter, A; Schimek, C; Vlaic, S; Wöstemeyer, J; Schuster, S

2012-12-01

An important substance in the signalling between individuals of Mucor-like fungi is trisporic acid (TA). This compound, together with some of its precursors, serves as a pheromone in mating between (+)- and (-)-mating types. Moreover, intermediates of the TA pathway are exchanged between the two mating partners. Based on differential equations, mathematical models of the synthesis pathways of TA in the two mating types of an idealised Mucor-fungus are here presented. These models include the positive feedback of TA on its own synthesis. The authors compare three sub-models in view of bistability, robustness and the reversibility of transitions. The proposed modelling study showed that, in a system where intermediates are exchanged, a reversible transition between the two stable steady states occurs, whereas an exchange of the end product leads to an irreversible transition. The reversible transition is physiologically favoured, because the high-production state of TA must come to an end eventually. Moreover, the exchange of intermediates and TA is compared with the 3-way handshake widely used by computers linked in a network.

Top predators induce the evolutionary diversification of intermediate predator species.

PubMed

Zu, Jian; Yuan, Bo; Du, Jianqiang

2015-12-21

We analyze the evolutionary branching phenomenon of intermediate predator species in a tritrophic food chain model by using adaptive dynamics theory. Specifically, we consider the adaptive diversification of an intermediate predator species that feeds on a prey species and is fed upon by a top predator species. We assume that the intermediate predator׳s ability to forage on the prey can adaptively improve, but this comes at the cost of decreased defense ability against the top predator. First, we identify the general properties of trade-off relationships that lead to a continuously stable strategy or to evolutionary branching in the intermediate predator species. We find that if there is an accelerating cost near the singular strategy, then that strategy is continuously stable. In contrast, if there is a mildly decelerating cost near the singular strategy, then that strategy may be an evolutionary branching point. Second, we find that after branching has occurred, depending on the specific shape and strength of the trade-off relationship, the intermediate predator species may reach an evolutionarily stable dimorphism or one of the two resultant predator lineages goes extinct. Crown Copyright © 2015. Published by Elsevier Ltd. All rights reserved.

Cortical membrane potential signature of optimal states for sensory signal detection

PubMed Central

McGinley, Matthew J.; David, Stephen V.; McCormick, David A.

2015-01-01

The neural correlates of optimal states for signal detection task performance are largely unknown. One hypothesis holds that optimal states exhibit tonically depolarized cortical neurons with enhanced spiking activity, such as occur during movement. We recorded membrane potentials of auditory cortical neurons in mice trained on a challenging tone-in-noise detection task while assessing arousal with simultaneous pupillometry and hippocampal recordings. Arousal measures accurately predicted multiple modes of membrane potential activity, including: rhythmic slow oscillations at low arousal, stable hyperpolarization at intermediate arousal, and depolarization during phasic or tonic periods of hyper-arousal. Walking always occurred during hyper-arousal. Optimal signal detection behavior and sound-evoked responses, at both sub-threshold and spiking levels, occurred at intermediate arousal when pre-decision membrane potentials were stably hyperpolarized. These results reveal a cortical physiological signature of the classically-observed inverted-U relationship between task performance and arousal, and that optimal detection exhibits enhanced sensory-evoked responses and reduced background synaptic activity. PMID:26074005

A Native to Amyloidogenic Transition Regulated by a Backbone Trigger

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

Eakin,C.; Berman, A.; Miranker, A.

2006-01-01

Many polypeptides can self-associate into linear, aggregated assemblies termed amyloid fibers. High-resolution structural insights into the mechanism of fibrillogenesis are elusive owing to the transient and mixed oligomeric nature of assembly intermediates. Here, we report the conformational changes that initiate fiber formation by beta-2-microglobulin (beta2m) in dialysis-related amyloidosis. Access of beta2m to amyloidogenic conformations is catalyzed by selective binding of divalent cations. The chemical basis of this process was determined to be backbone isomerization of a conserved proline. On the basis of this finding, we designed a beta2m variant that closely adopts this intermediate state. The variant has kinetic, thermodynamicmore » and catalytic properties consistent with its being a fibrillogenic intermediate of wild-type beta2m. Furthermore, it is stable and folded, enabling us to unambiguously determine the initiating conformational changes for amyloid assembly at atomic resolution.« less

Bi-stable vocal fold adduction: a mechanism of modal-falsetto register shifts and mixed registration.

PubMed

Titze, Ingo R

2014-04-01

The origin of vocal registers has generally been attributed to differential activation of cricothyroid and thyroarytenoid muscles in the larynx. Register shifts, however, have also been shown to be affected by glottal pressures exerted on vocal fold surfaces, which can change with loudness, pitch, and vowel. Here it is shown computationally and with empirical data that intraglottal pressures can change abruptly when glottal adductory geometry is changed relatively smoothly from convergent to divergent. An intermediate shape between large convergence and large divergence, namely, a nearly rectangular glottal shape with almost parallel vocal fold surfaces, is associated with mixed registration. It can be less stable than either of the highly angular shapes unless transglottal pressure is reduced and upper stiffness of vocal fold tissues is balanced with lower stiffness. This intermediate state of adduction is desirable because it leads to a low phonation threshold pressure with moderate vocal fold collision. Achieving mixed registration consistently across wide ranges of F0, lung pressure, and vocal tract shapes appears to be a balancing act of coordinating laryngeal muscle activation with vocal tract pressures. Surprisingly, a large transglottal pressure is not facilitative in this process, exacerbating the bi-stable condition and the associated register contrast.

Bi-stable vocal fold adduction: A mechanism of modal-falsetto register shifts and mixed registration

PubMed Central

Titze, Ingo R.

2014-01-01

The origin of vocal registers has generally been attributed to differential activation of cricothyroid and thyroarytenoid muscles in the larynx. Register shifts, however, have also been shown to be affected by glottal pressures exerted on vocal fold surfaces, which can change with loudness, pitch, and vowel. Here it is shown computationally and with empirical data that intraglottal pressures can change abruptly when glottal adductory geometry is changed relatively smoothly from convergent to divergent. An intermediate shape between large convergence and large divergence, namely, a nearly rectangular glottal shape with almost parallel vocal fold surfaces, is associated with mixed registration. It can be less stable than either of the highly angular shapes unless transglottal pressure is reduced and upper stiffness of vocal fold tissues is balanced with lower stiffness. This intermediate state of adduction is desirable because it leads to a low phonation threshold pressure with moderate vocal fold collision. Achieving mixed registration consistently across wide ranges of F0, lung pressure, and vocal tract shapes appears to be a balancing act of coordinating laryngeal muscle activation with vocal tract pressures. Surprisingly, a large transglottal pressure is not facilitative in this process, exacerbating the bi-stable condition and the associated register contrast. PMID:25235006

Conformational relaxation dynamics in the excited electronic states of benzil in solution

NASA Astrophysics Data System (ADS)

Singh, Ajay K.; Palit, Dipak K.; Mittal, Jai P.

2002-07-01

Relaxation dynamics in the excited singlet (S1) state of benzil have been studied in solution using pico and subpicosecond transient absorption spectroscopic techniques. The triple exponential decay dynamics of the S1 state indicates that the process of conformational change from the cis-skewed to the trans-planar form takes place via the formation of a meta-stable intermediate conformer resulting the involvement of two consequent barrier crossing processes. The barrier crossing dynamics is governed by both the polarity of the solvent, which alters the barrier heights by `static' interactions, as well as the viscosity of the solvent via `dynamical' interactions.

Use of 2,5-dimethyl-2,5-hexane diamine as a curing agent for epoxy resins. [Patent application

DOEpatents

Rinde, J.A.; Newey, H.A.

Primary diamines are prepared for use as a curing agent for epoxy resins. These curing agents can be used to form epoxy resin mixtures useful in filament winding and preimpregnated fiber molding and in formulating film adhesives, powder coatings and molding powders. The epoxy mixtures form for such uses a room temperature non-reacting, intermediate stable state which has a latent cross-linking capability.

Photoregeneration of bovine rhodopsin from its signaling state.

PubMed

Arnis, S; Hofmann, K P

1995-07-25

In rhodopsin, 11-cis-retinal is bound by a protonated Schiff base and acts as a strong antagonist, which holds the receptor in its inactive ground state conformation. Light induces cis-/trans-retinal isomerization and a sequence of thermal transitions through intermediates. The active conformation that catalyzes GDP/GTP exchange in the G-protein (Gt) is generated from the metarhodopsin II intermediate (MII) and mediated by Schiff base proton translocation and proton uptake from the aqueous phase. In the stable nucleotide-free MII-Gt complex, any thermal transition of MII into other forms of rhodopsin is blocked. We have now studied how Gt affects flash-induced photochemical conversions of MII. Difference spectra from measured absorption changes show that MII photolyzes through two parallel pathways, with fast (1 ms) and slow (50 ms) kinetics (12 degrees C, pH 6). The slow pathway regenerates rhodopsin (9- or 11-cis) via Schiff base reprotonation and proton release. We infer a cis-isomerized early photoproduct (reverted meta, RM) preceding these thermal transitions. When MII is photolyzed in the MII-Gt complex, the slow absorption change is abolished, indicating that Gt blocks the completion of the regeneration process. This is due to the formation of a stable RM-Gt complex, as shown by successive photolysis of MII, RM, and ground state rhodopsin, and the application of GTP gamma S at different stages. The complex dissociates with GTP gamma S, and rhodopsin relaxes to the ground state. The results indicate that cis-retinal and Gt can bind to the receptor at the same time. We discuss the result that the protonations in the meta II state uncouple retinal geometry from Gt interaction.

Overdamped Nb/Al-AlO{sub x}/Nb Josephson junctions

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

Lacquaniti, V.; Cagliero, C.; Maggi, S.

2005-01-24

We report the fabrication and characterization of overdamped Nb/Al-AlO{sub x}/Nb superconductor-insulator-superconductor Josephson junction whose fabrication process derives from that of the well-known hysteretic junctions. These junctions are an intermediate state between the superconductor-normal metal-superconductor and the superconductor-insulator-superconductor Josephson junctions. Stable and reproducible nonhysteretic current-voltage characteristics are obtained with a proper choice of the fabrication parameters. We have measured critical current densities J{sub C} from 10{sup 3} up to 2x10{sup 4} A/cm{sup 2}, with characteristic voltages from 80 to nearly 450 {mu}V. The junctions are stable against time and repeated thermal cycling.

Structural origins of pH and ionic strength effects on protein stability. Acid denaturation of sperm whale apomyoglobin.

PubMed

Yang, A S; Honig, B

1994-04-15

A recently developed approach to calculate the pH dependence of protein stability from three-dimensional structure information is applied to the analysis of acid denaturation of sperm whale apomyoglobin. The finite difference Poisson-Boltzmann method is used to calculate pKa values and these are used to obtain titration curves for the folded protein as well as for compact intermediates. The total electrostatic free energy change involved in apomyoglobin unfolding is then evaluated. Calculations are carried out of the unfolding free energy of the native (N) and the compact intermediate (I) of apomyoglobin relative to the unfolded state (U) over a range of pH at various ionic strengths. The contributions from key ionizable groups to the unfolding process are discussed. For the acid-induced partial unfolding of apomyoglobin near pH 5, the transition from N to I is found to be driven by three histidines that are exposed when the B, C, D and E helices unfold. Similarly, the unfolding of the compact intermediate I consisting of the A, G and H helices is driven primarily by a few carboxylic acids with low pKa values in the compact state. This picture is in contrast to the view which attributes acid denaturation to electrostatic repulsion resulting from the build up of positive charge. In fact, charge-charge interactions in myoglobin are found to be attractive at all pH values where the protein unfolds. pH-dependent changes in these interactions contribute to acid denaturation but other electrostatic effects, such as hydrogen bonding and solvation, are important as well. The effect of increasing ionic strength on unfolding is attributed to the decrease of attractive charge-charge interactions which destabilize the N state relative to I, but stabilize the I state relative to U by reducing the pKa shifts of a few critical carboxylic acids. The I state is found to be more stable than U at neutral pH thus accounting for its presence as an intermediate on the protein folding pathway. Our results have implications for the origins of compact intermediates or "molten globule" states.

Reaction pathways of photoexcited retinal in proteorhodopsin studied by pump-dump-probe spectroscopy.

PubMed

Rupenyan, Alisa; van Stokkum, Ivo H M; Arents, Jos C; van Grondelle, Rienk; Hellingwerf, Klaas J; Groot, Marie Louise

2009-12-17

Proteorhodopsin (pR) is a membrane-embedded proton pump from the microbial rhodopsin family. Light absorption by its retinal chromophore initiates a photocycle, driven by trans/cis isomerization on the femtosecond to picosecond time scales. Here, we report a study on the photoisomerization dynamics of the retinal chromophore of pR, using dispersed ultrafast pump-dump-probe spectroscopy. The application of a pump pulse initiates the photocycle, and with an appropriately tuned dump pulse applied at a time delay after the dump, the molecules in the initial stages of the photochemical process can be de-excited and driven back to the ground state. In this way, we were able to resolve an intermediate on the electronic ground state that represents chromophores that are unsuccessful in isomerization. In particular, the fractions of molecules that undergo slow isomerization (20 ps) have a high probability to enter this state rather than the isomerized K-state. On the ground state reaction surface, return to the stable ground state conformation via a structural or vibrational relaxation occurs in 2-3 ps. Inclusion of this intermediate in the kinetic scheme led to more consistent spectra of the retinal-excited state, and to a more accurate estimation of the quantum yield of isomerization (Phi = 0.4 at pH 6).

Hydroxyacetone production from C 3 Criegee intermediates

DOE PAGES

Taatjes, Craig A.; Liu, Fang; Rotavera, Brandon; ...

2016-12-21

Hydroxyacetone (CH 3C(O)CH 2OH) is observed as a stable end product from reactions of the (CH 3) 2COO Criegee intermediate, acetone oxide, in a flow tube coupled with multiplexed photoionization mass spectrometer detection. In the experiment, the isomers at m/z = 74 are distinguished by their different photoionization spectra and reaction times. Hydroxyacetone is observed as a persistent signal at longer reaction times at a higher photoionization threshold of ca. 9.7 eV than Criegee intermediate and definitively identified by comparison with the known photoionization spectrum. Complementary electronic structure calculations reveal multiple possible reaction pathways for hydroxyacetone formation, including unimolecular isomerizationmore » via hydrogen atom transfer and –OH group migration as well as self-reaction of Criegee intermediates. Varying the concentration of Criegee intermediates suggests contributions from both unimolecular and self-reaction pathways to hydroxyacetone. As a result, the hydroxyacetone end product can provide an effective, stable marker for the production of transient Criegee intermediates in future studies of alkene ozonolysis.« less

Reshaping the folding energy landscape by chloride salt: impact on molten-globule formation and aggregation behavior of carbonic anhydrase.

PubMed

Borén, Kristina; Grankvist, Hannah; Hammarström, Per; Carlsson, Uno

2004-05-21

During chemical denaturation different intermediate states are populated or suppressed due to the nature of the denaturant used. Chemical denaturation by guanidine-HCl (GuHCl) of human carbonic anhydrase II (HCA II) leads to a three-state unfolding process (Cm,NI=1.0 and Cm,IU=1.9 M GuHCl) with formation of an equilibrium molten-globule intermediate that is stable at moderate concentrations of the denaturant (1-2 M) with a maximum at 1.5 M GuHCl. On the contrary, urea denaturation gives rise to an apparent two-state unfolding transition (Cm=4.4 M urea). However, 8-anilino-1-naphthalene sulfonate (ANS) binding and decreased refolding capacity revealed the presence of the molten globule in the middle of the unfolding transition zone, although to a lesser extent than in GuHCl. Cross-linking studies showed the formation of moderate oligomer sized (300 kDa) and large soluble aggregates (>1000 kDa). Inclusion of 1.5 M NaCl to the urea denaturant to mimic the ionic character of GuHCl leads to a three-state unfolding behavior (Cm,NI=3.0 and Cm,IU=6.4 M urea) with a significantly stabilized molten-globule intermediate by the chloride salt. Comparisons between NaCl and LiCl of the impact on the stability of the various states of HCA II in urea showed that the effects followed what could be expected from the Hofmeister series, where Li+ is a chaotropic ion leading to decreased stability of the native state. Salt addition to the completely urea unfolded HCA II also led to an aggregation prone unfolded state, that has not been observed before for carbonic anhydrase. Refolding from this state only provided low recoveries of native enzyme.

QM/MM nonadiabatic dynamics simulations on photoinduced Wolff rearrangements of 1,2,3-thiadiazole

NASA Astrophysics Data System (ADS)

Liu, Xiang-Yang; Fang, Ye-Guang; Xie, Bin-Bin; Fang, Wei-Hai; Cui, Ganglong

2017-06-01

The photoinduced rearrangement reaction mechanism of 1,2,3-thiadiazole remains experimentally elusive. Two possible mechanisms have been proposed to date. The first is a stepwise mechanism via a thiocarbene intermediate; the second is an excited-state concerted rearrangement mechanism. Herein we have adopted both the electronic structure calculations and nonadiabatic dynamics simulations to study the photoinduced rearrangement reactions of 1,2,3-thiadiazole in the S2, S1, and S0 states in solution. On the basis of QM(CASPT2)/MM [quantum mechanics(complete active space self-consistent field second-order perturbation theory)/molecular mechanics] calculations, we have found that (1) the thiocarbene intermediate is not stable; thus, the stepwise mechanism should be unfavorable; (2) the excited-state decay from the S2 via S1 to S0 state is ultrafast and completed within ca. 200 fs; therefore, both the S2 and S1 states should not have a long enough time for the excited-state rearrangements. Instead, we have computationally proposed a modified photoinduced rearrangement mechanism. Upon irradiation, the S2 state is first populated (114.0 kcal/mol), followed by an ultrafast S2 → S1 → S0 excited-state decay along the S-N bond fission, which eventually leads to a very "hot" intermediate with the S-N bond broken (18.3 kcal/mol). Then, thermal rearrangements to thioketene, thiirene, and ethynethiol occur in a concerted asynchronous way. This mechanistic scenario has been verified by full-dimensional trajectory-based nonadiabatic dynamics simulations at the QM(CASPT2)/MM level. Finally, our present computational work provides experimentally interesting mechanistic insights into the photoinduced rearrangement reactions of cyclic and acyclic diazo compounds.

Molecular dynamics simulation of nanobubble nucleation on rough surfaces

NASA Astrophysics Data System (ADS)

Liu, Yawei; Zhang, Xianren

2017-04-01

Here, we study how nanobubbles nucleate on rough hydrophobic surfaces, using long-time standard simulations to directly observe the kinetic pathways and using constrained simulations combined with the thermodynamic integration approach to quantitatively evaluate the corresponding free energy changes. Both methods demonstrate that a two-step nucleation route involving the formation of an intermediate state is thermodynamically favorable: at first, the system transforms from the Wenzel state (liquid being in full contact with the solid surface) to the Cassie state (liquid being in contact with the peaks of the rough surface) after gas cavities occur in the grooves (i.e., the Wenzel-to-Cassie transition); then, the gas cavities coalesce and form a stable surface nanobubble with pinned contact lines (i.e., the Cassie-to-nanobubble transition). Additionally, the free energy barriers for the two transitions show opposing dependencies on the degree of surface roughness, indicating that the surfaces with moderate roughness are favorable for forming stable surface nanobubbles. Moreover, the simulation results also reveal the coexistence and transition between the Wenzel, Cassie, and nanobubble states on rough surfaces.

Towards deployable meta-implants.

PubMed

Bobbert, F S L; Janbaz, S; Zadpoor, A A

2018-06-07

Meta-biomaterials exhibit unprecedented or rare combinations of properties not usually found in nature. Such unusual mechanical, mass transport, and biological properties could be used to develop novel categories of orthopedic implants with superior performance, otherwise known as meta-implants. Here, we use bi-stable elements working on the basis of snap-through instability to design deployable meta-implants. Deployable meta-implants are compact in their retracted state, allowing them to be brought to the surgical site with minimum invasiveness. Once in place, they are deployed to take their full-size load-bearing shape. We designed five types of meta-implants by arranging bi-stable elements in such a way to obtain a radially-deployable structure, three types of auxetic structures, and an axially-deployable structure. The intermediate stable conditions ( i.e. multi-stability features), deployment force, and stiffness of the meta-implants were found to be strongly dependent on the geometrical parameters of the bi-stable elements as well as on their arrangement.

Response of Submerged Macrophyte Communities to External and Internal Restoration Measures in North Temperate Shallow Lakes.

PubMed

Hilt, Sabine; Alirangues Nuñez, Marta M; Bakker, Elisabeth S; Blindow, Irmgard; Davidson, Thomas A; Gillefalk, Mikael; Hansson, Lars-Anders; Janse, Jan H; Janssen, Annette B G; Jeppesen, Erik; Kabus, Timm; Kelly, Andrea; Köhler, Jan; Lauridsen, Torben L; Mooij, Wolf M; Noordhuis, Ruurd; Phillips, Geoff; Rücker, Jacqueline; Schuster, Hans-Heinrich; Søndergaard, Martin; Teurlincx, Sven; van de Weyer, Klaus; van Donk, Ellen; Waterstraat, Arno; Willby, Nigel; Sayer, Carl D

2018-01-01

Submerged macrophytes play a key role in north temperate shallow lakes by stabilizing clear-water conditions. Eutrophication has resulted in macrophyte loss and shifts to turbid conditions in many lakes. Considerable efforts have been devoted to shallow lake restoration in many countries, but long-term success depends on a stable recovery of submerged macrophytes. However, recovery patterns vary widely and remain to be fully understood. We hypothesize that reduced external nutrient loading leads to an intermediate recovery state with clear spring and turbid summer conditions similar to the pattern described for eutrophication. In contrast, lake internal restoration measures can result in transient clear-water conditions both in spring and summer and reversals to turbid conditions. Furthermore, we hypothesize that these contrasting restoration measures result in different macrophyte species composition, with added implications for seasonal dynamics due to differences in plant traits. To test these hypotheses, we analyzed data on water quality and submerged macrophytes from 49 north temperate shallow lakes that were in a turbid state and subjected to restoration measures. To study the dynamics of macrophytes during nutrient load reduction, we adapted the ecosystem model PCLake. Our survey and model simulations revealed the existence of an intermediate recovery state upon reduced external nutrient loading, characterized by spring clear-water phases and turbid summers, whereas internal lake restoration measures often resulted in clear-water conditions in spring and summer with returns to turbid conditions after some years. External and internal lake restoration measures resulted in different macrophyte communities. The intermediate recovery state following reduced nutrient loading is characterized by a few macrophyte species (mainly pondweeds) that can resist wave action allowing survival in shallow areas, germinate early in spring, have energy-rich vegetative propagules facilitating rapid initial growth and that can complete their life cycle by early summer. Later in the growing season these plants are, according to our simulations, outcompeted by periphyton, leading to late-summer phytoplankton blooms. Internal lake restoration measures often coincide with a rapid but transient colonization by hornworts, waterweeds or charophytes. Stable clear-water conditions and a diverse macrophyte flora only occurred decades after external nutrient load reduction or when measures were combined.

The Folding of de Novo Designed Protein DS119 via Molecular Dynamics Simulations.

PubMed

Wang, Moye; Hu, Jie; Zhang, Zhuqing

2016-04-26

As they are not subjected to natural selection process, de novo designed proteins usually fold in a manner different from natural proteins. Recently, a de novo designed mini-protein DS119, with a βαβ motif and 36 amino acids, has folded unusually slowly in experiments, and transient dimers have been detected in the folding process. Here, by means of all-atom replica exchange molecular dynamics (REMD) simulations, several comparably stable intermediate states were observed on the folding free-energy landscape of DS119. Conventional molecular dynamics (CMD) simulations showed that when two unfolded DS119 proteins bound together, most binding sites of dimeric aggregates were located at the N-terminal segment, especially residues 5-10, which were supposed to form β-sheet with its own C-terminal segment. Furthermore, a large percentage of individual proteins in the dimeric aggregates adopted conformations similar to those in the intermediate states observed in REMD simulations. These results indicate that, during the folding process, DS119 can easily become trapped in intermediate states. Then, with diffusion, a transient dimer would be formed and stabilized with the binding interface located at N-terminals. This means that it could not quickly fold to the native structure. The complicated folding manner of DS119 implies the important influence of natural selection on protein-folding kinetics, and more improvement should be achieved in rational protein design.

The Folding of de Novo Designed Protein DS119 via Molecular Dynamics Simulations

PubMed Central

Wang, Moye; Hu, Jie; Zhang, Zhuqing

2016-01-01

As they are not subjected to natural selection process, de novo designed proteins usually fold in a manner different from natural proteins. Recently, a de novo designed mini-protein DS119, with a βαβ motif and 36 amino acids, has folded unusually slowly in experiments, and transient dimers have been detected in the folding process. Here, by means of all-atom replica exchange molecular dynamics (REMD) simulations, several comparably stable intermediate states were observed on the folding free-energy landscape of DS119. Conventional molecular dynamics (CMD) simulations showed that when two unfolded DS119 proteins bound together, most binding sites of dimeric aggregates were located at the N-terminal segment, especially residues 5–10, which were supposed to form β-sheet with its own C-terminal segment. Furthermore, a large percentage of individual proteins in the dimeric aggregates adopted conformations similar to those in the intermediate states observed in REMD simulations. These results indicate that, during the folding process, DS119 can easily become trapped in intermediate states. Then, with diffusion, a transient dimer would be formed and stabilized with the binding interface located at N-terminals. This means that it could not quickly fold to the native structure. The complicated folding manner of DS119 implies the important influence of natural selection on protein-folding kinetics, and more improvement should be achieved in rational protein design. PMID:27128902

Bistability in cell signaling: How to make continuous processes discontinuous, and reversible processes irreversible

NASA Astrophysics Data System (ADS)

Ferrell, James E.; Xiong, Wen

2001-03-01

Xenopus oocyte maturation is an example of an all-or-none, irreversible cell fate induction process. In response to a submaximal concentration of the steroid hormone progesterone, a given oocyte may either mature or not mature, but it can exist in intermediate states only transiently. Moreover, once an oocyte has matured, it will remain arrested in the mature state even after the progesterone is removed. It has been hypothesized that the all-or-none character of oocyte maturation, and some aspects of the irreversibility of maturation, arise out of the bistability of the signal transduction system that triggers maturation. The bistability, in turn, is hypothesized to arise from the way the signal transducers are organized into a signaling circuit that includes positive feedback (which makes it so that the system cannot rest in intermediate states) and ultrasensitivity (which filters small stimuli out of the feedback loop, allowing the system to have a stable off-state). Here we review two simple graphical methods that are commonly used to analyze bistable systems, discuss the experimental evidence for bistability in oocyte maturation, and suggest that bistability may be a common means of producing all-or-none responses and a type of biochemical memory.

Selective predation and productivity jointly drive complex behavior in host-parasite systems.

PubMed

Hall, Spencer R; Duffy, Meghan A; Cáceres, Carla E

2005-01-01

Successful invasion of a parasite into a host population and resulting host-parasite dynamics can depend crucially on other members of a host's community such as predators. We do not fully understand how predation intensity and selectivity shape host-parasite dynamics because the interplay between predator density, predator foraging behavior, and ecosystem productivity remains incompletely explored. By modifying a standard susceptible-infected model, we show how productivity can modulate complex behavior induced by saturating and selective foraging behavior of predators in an otherwise stable host-parasite system. When predators strongly prefer parasitized hosts, the host-parasite system can oscillate, but predators can also create alternative stable states, Allee effects, and catastrophic extinction of parasites. In the latter three cases, parasites have difficulty invading and/or persisting in ecosystems. When predators are intermediately selective, these more complex behaviors become less important, but the host-parasite system can switch from stable to oscillating and then back to stable states along a gradient of predator control. Surprisingly, at higher productivity, predators that neutrally select or avoid parasitized hosts can catalyze extinction of both hosts and parasites. Thus, synergy between two enemies can end disastrously for the host. Such diverse outcomes underscore the crucial importance of the community and ecosystem context in which host-parasite interactions occur.

Synchrotron radiation circular dichroism spectroscopy study of recombinant T β4 folding

NASA Astrophysics Data System (ADS)

Huang, Yung-Chin; Chu, Hsueh-Liang; Chen, Peng-Jen; Chang, Chia-Ching

Thymosin beta 4 (T β4) is a 43-amino acid small peptide, has been demonstrated that it can promote cardiac repair, wound repair, tissue protection, and involve in the proliferation of blood cell precursor stem cells of bone marrow. Moreover, T β4 has been identified as a multifunction intrinsically disordered protein, which is lacking the stable tertiary structure. Owing to the small size and disordered character, the T β4 protein degrades rapidly and the storage condition is critical. Therefore, it is not easy to reveal its folding mechanism of native T β4. However, recombinant T β4 protein (rT β4), which fused with a 5-kDa peptide in its amino-terminal, is stable and possesses identical function of T β4. Therefore, rT β4 can be used to study its folding mechanism. By using over-critical folding process, stable folding intermediates of rT β4 can be obtained. Structure analysis of folding intermediates by synchrotron radiation circular dichroism (SRCD) and fluorescence spectroscopies indicate that rT β4 is a random coli major protein and its hydrophobic region becomes compact gradually. Moreover, the rT β4 folding is a two state transition. Thermal denaturation analysis indicates that rT β4 lacks stable tertiary structure. These results indicated that rT β4, similar to T β4, is an intrinsically disordered protein. Research is supported by MOST, Taiwan. MOST 103-2112-M-009-011-MY3. Corresponding author: Chia-Ching Chang; ccchang01@faculty.nctu.edu.tw.

Evolutionary Dynamics on Protein Bi-stability Landscapes can Potentially Resolve Adaptive Conflicts

PubMed Central

Sikosek, Tobias; Bornberg-Bauer, Erich; Chan, Hue Sun

2012-01-01

Experimental studies have shown that some proteins exist in two alternative native-state conformations. It has been proposed that such bi-stable proteins can potentially function as evolutionary bridges at the interface between two neutral networks of protein sequences that fold uniquely into the two different native conformations. Under adaptive conflict scenarios, bi-stable proteins may be of particular advantage if they simultaneously provide two beneficial biological functions. However, computational models that simulate protein structure evolution do not yet recognize the importance of bi-stability. Here we use a biophysical model to analyze sequence space to identify bi-stable or multi-stable proteins with two or more equally stable native-state structures. The inclusion of such proteins enhances phenotype connectivity between neutral networks in sequence space. Consideration of the sequence space neighborhood of bridge proteins revealed that bi-stability decreases gradually with each mutation that takes the sequence further away from an exactly bi-stable protein. With relaxed selection pressures, we found that bi-stable proteins in our model are highly successful under simulated adaptive conflict. Inspired by these model predictions, we developed a method to identify real proteins in the PDB with bridge-like properties, and have verified a clear bi-stability gradient for a series of mutants studied by Alexander et al. (Proc Nat Acad Sci USA 2009, 106:21149–21154) that connect two sequences that fold uniquely into two different native structures via a bridge-like intermediate mutant sequence. Based on these findings, new testable predictions for future studies on protein bi-stability and evolution are discussed. PMID:23028272

A Confirmation of the Quench-Cryoannealing Relaxation Protocol for Identifying Reduction States of Freeze-Trapped Nitrogenase Intermediates

PubMed Central

2015-01-01

We have advanced a mechanism for nitrogenase catalysis that rests on the identification of a low-spin EPR signal (S = 1/2) trapped during turnover of a MoFe protein as the E4 state, which has accumulated four reducing equivalents as two [Fe–H–Fe] bridging hydrides. Because electrons are delivered to the MoFe protein one at a time, with the rate-limiting step being the off-rate of oxidized Fe protein, it is difficult to directly control, or know, the degree of reduction, n, of a trapped intermediate, denoted En, n = 1–8. To overcome this previously intractable problem, we introduced a quench-cryoannealing relaxation protocol for determining n of an EPR-active trapped En turnover state. The trapped “hydride” state was allowed to relax to the resting E0 state in frozen medium, which prevents additional accumulation of reducing equivalents; binding of reduced Fe protein and release of oxidized protein from the MoFe protein both are abolished in a frozen solid. Relaxation of En was monitored by periodic EPR analysis at cryogenic temperature. The protocol rests on the hypothesis that an intermediate trapped in the frozen solid can relax toward the resting state only by the release of a stable reduction product from FeMo-co. In turnover under Ar, the only product that can be released is H2, which carries two reducing equivalents. This hypothesis implicitly predicts that states that have accumulated an odd number of electrons/protons (n = 1, 3) during turnover under Ar cannot relax to E0: E3 can relax to E1, but E1 cannot relax to E0 in the frozen state. The present experiments confirm this prediction and, thus, the quench-cryoannealing protocol and our assignment of E4, the foundation of the proposed mechanism for nitrogenase catalysis. This study further gives insights into the identity of the En intermediates with high-spin EPR signals, 1b and 1c, trapped under high electron flux. PMID:24635454

The disappearance and reformation of the accretion disc during a low state of FO Aquarii

NASA Astrophysics Data System (ADS)

Hameury, J.-M.; Lasota, J.-P.

2017-09-01

Context. FO Aquarii, an asynchronous magnetic cataclysmic variable (intermediate polar) went into a low state in 2016, from which it slowly and steadily recovered without showing dwarf nova outbursts. This requires explanation since in a low state, the mass-transfer rate is in principle too low for the disc to be fully ionised and the disc should be subject to the standard thermal and viscous instability observed in dwarf novae. Aims: We investigate the conditions under which an accretion disc in an intermediate polar could exhibit a luminosity drop of two magnitudes in the optical band without showing outbursts. Methods: We use our numerical code for the time evolution of accretion discs, including other light sources from the system (primary, secondary, hot spot). Results: We show that although it is marginally possible for the accretion disc in the low state to stay on the hot stable branch, the required mass-transfer rate in the normal state would then have to be extremely high, of the order of 1019 g s-1 or even larger. This would make the system so intrinsically bright that its distance should be much larger than allowed by all estimates. We show that observations of FO Aqr are well accounted for by the same mechanism that we have suggested as explaining the absence of outbursts during low states of VY Scl stars: during the decay, the magnetospheric radius exceeds the circularisation radius, so that the disc disappears before it enters the instability strip for dwarf nova outbursts. Conclusions: Our results are unaffected, and even reinforced, if accretion proceeds both via the accretion disc and directly via the stream during some intermediate stages; the detailed process through which the disc disappears still requires investigation.

Nucleation via an unstable intermediate phase.

PubMed

Sear, Richard P

2009-08-21

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

Development of technical solutions for securing stable operation of the intermediate separation and steam reheating system for the K-1000-60/3000 turbine unit

NASA Astrophysics Data System (ADS)

Trifonov, N. N.; Kovalenko, E. V.; Nikolaenkova, E. K.; Tren'kin, V. B.

2012-09-01

The intermediate separation and steam reheating system and its equipment are described. Problems concerned with the presence of condensate in the stack's lower chamber and in the removing chamber, with cavitation failure of the separated moisture pumps, with misalignment of heating steam flowrates, with unstable draining of heating steam condensate, with occurrence of self oscillations, etc. are considered. A procedure for determining the level in removing heating steam condensate from steam reheater elements is proposed. Technical solutions for ensuring stable operation of the intermediate separation and steam reheating system and for achieving smaller misalignment between the apparatuses are developed.

A novel intermediate in the reaction of seleno CYP119 with m-chloroperbenzoic acid.

PubMed

Sivaramakrishnan, Santhosh; Ouellet, Hugues; Du, Jing; McLean, Kirsty J; Medzihradszky, Katalin F; Dawson, John H; Munro, Andrew W; Ortiz de Montellano, Paul R

2011-04-12

Cytochrome P450-mediated monooxygenation generally proceeds via a reactive ferryl intermediate coupled to a ligand radical [Fe(IV)═O]+• termed Compound I (Cpd I). The proximal cysteine thiolate ligand is a critical determinant of the spectral and catalytic properties of P450 enzymes. To explore the effect of an increased level of donation of electrons by the proximal ligand in the P450 catalytic cycle, we recently reported successful incorporation of SeCys into the active site of CYP119, a thermophilic cytochrome P450. Here we report relevant physical properties of SeCYP119 and a detailed analysis of the reaction of SeCYP119 with m-chloroperbenzoic acid. Our results indicate that the selenolate anion reduces rather than stabilizes Cpd I and also protects the heme from oxidative destruction, leading to the generation of a new stable species with an absorbance maximum at 406 nm. This stable intermediate can be returned to the normal ferric state by reducing agents and thiols, in agreement with oxidative modification of the selenolate ligand itself. Thus, in the seleno protein, the oxidative damage shifts from the heme to the proximal ligand, presumably because (a) an increased level of donation of electrons more efficiently quenches reactive species such as Cpd I and (b) the protection of the thiolate ligand provided by the protein active site structure is insufficient to shield the more oxidizable selenolate ligand.

Electronic polarization stabilizes tertiary structure prediction of HP-36.

PubMed

Duan, Li L; Zhu, Tong; Zhang, Qing G; Tang, Bo; Zhang, John Z H

2014-04-01

Molecular dynamic (MD) simulations with both implicit and explicit solvent models have been carried out to study the folding dynamics of HP-36 protein. Starting from the extended conformation, the secondary structure of all three helices in HP-36 was formed in about 50 ns and remained stable in the remaining simulation. However, the formation of the tertiary structure was difficult. Although some intermediates were close to the native structure, the overall conformation was not stable. Further analysis revealed that the large structure fluctuation of loop and hydrophobic core regions was devoted mostly to the instability of the structure during MD simulation. The backbone root-mean-square deviation (RMSD) of the loop and hydrophobic core regions showed strong correlation with the backbone RMSD of the whole protein. The free energy landscape indicated that the distribution of main chain torsions in loop and turn regions was far away from the native state. Starting from an intermediate structure extracted from the initial AMBER simulation, HP-36 was found to generally fold to the native state under the dynamically adjusted polarized protein-specific charge (DPPC) simulation, while the peptide did not fold into the native structure when AMBER force filed was used. The two best folded structures were extracted and taken into further simulations in water employing AMBER03 charge and DPPC for 25 ns. Result showed that introducing polarization effect into interacting potential could stabilize the near-native protein structure.

Kinetic evidence for folding and unfolding intermediates in staphylococcal nuclease.

PubMed

Walkenhorst, W F; Green, S M; Roder, H

1997-05-13

The complex kinetic behavior commonly observed in protein folding studies suggests that a heterogeneous population of molecules exists in solution and that a number of discrete steps are involved in the conversion of unfolded molecules to the fully native form. A central issue in protein folding is whether any of these kinetic events represent conformational steps important for efficient folding rather than side reactions caused by slow steps such as proline isomerization or misfolding of the polypeptide chain. In order to address this question, we used stopped-flow fluorescence techniques to characterize the kinetic mechanism of folding and unfolding for a Pro- variant of SNase in which all six proline residues were replaced by glycines or alanines. Compared to the wild-type protein, which exhibits a series of proline-dependent slow folding phases, the folding kinetics of Pro- SNase were much simpler, which made quantitative kinetic analysis possible. Despite the absence of prolines or other complicating factors, the folding kinetics still contain several phases and exhibit a complex denaturant dependence. The GuHCl dependence of the major observable folding phase and a distinct lag in the appearance of the native state provide clear evidence for an early folding intermediate. The fluorescence of Trp140 in the alpha-helical domain is insensitive to the formation of this early intermediate, which is consistent with a partially folded state with a stable beta-domain and a largely disordered alpha-helical region. A second intermediate is required to model the kinetics of unfolding for the Pro- variant, which shows evidence for a denaturant-induced change in the rate-limiting unfolding step. With the inclusion of these two intermediates, we are able to completely model the major phase(s) in both folding and unfolding across a wide range of denaturant concentrations using a sequential four-state folding mechanism. In order to model the minor slow phase observed for the Pro- mutant, a six-state scheme containing a parallel pathway originating from a distinct unfolded state was required. The properties of this alternate unfolded conformation are consistent with those expected due to the presence of a non-prolyl cis peptide bond. To test the kinetic model, we used simulations based on the six-state scheme and were able to completely reproduce the folding kinetics for Pro- SNase across a range of denaturant concentrations.

Ionization cross section, pressure shift and isotope shift measurements of osmium

NASA Astrophysics Data System (ADS)

Hirayama, Yoshikazu; Mukai, Momo; Watanabe, Yutaka; Oyaizu, Michihiro; Ahmed, Murad; Kakiguchi, Yutaka; Kimura, Sota; Miyatake, Hiroari; Schury, Peter; Wada, Michiharu; Jeong, Sun-Chan

2017-11-01

In-gas-cell laser resonance ionization spectroscopy of neutral osmium atoms was performed with the use of a two-color two-step laser resonance ionization technique. Saturation curves for the ionization scheme were measured, and the ionization cross section was experimentally determined by solving the rate equations for the ground, intermediate and ionization continuum populations. The pressure shift and pressure broadening in the resonance spectra of the excitation transition were measured. The electronic factor {F}247 for the transition {λ }1=247.7583 nm to the intermediate state was deduced from the measured isotope shifts of stable {}{188,189,{190,192}}Os isotopes. The efficient ionization scheme, pressure shift, nuclear isotope shift and {F}247 are expected to be useful for applications of laser ion sources to unstable nuclei and for nuclear spectroscopy based on laser ionization techniques.

Plate-tectonic boundary formation by grain-damage and pinning

NASA Astrophysics Data System (ADS)

Bercovici, David

2015-04-01

Shear weakening in the lithosphere is an essential ingredient for understanding how and why plate tectonics is generated from mantle convection on terrestrial planets. I present continued work on a theoretical model for lithospheric shear-localization and plate generation through damage, grain evolution and Zener pinning in two-phase (polycrystalline) lithospheric rocks. Grain size evolves through the competition between coarsening, which drives grain-growth, with damage, which drives grain reduction. The interface between phases controls Zener pinning, which impedes grain growth. Damage to the interface enhances the Zener pinning effect, which then reduces grain-size, forcing the rheology into the grain-size-dependent diffusion creep regime. This process thus allows damage and rheological weakening to co-exist, providing a necessary shear-localizing feedback. Moreover, because pinning inhibits grain-growth it promotes shear-zone longevity and plate-boundary inheritance. This theory has been applied recently to the emergence of plate tectonics in the Archean by transient subduction and accumulation of plate boundaries over 1Gyr, as well as to rapid slab detachment and abrupt tectonic changes. New work explores the saturation of interface damage at low interface curvature (e.g., because it is associated with larger grains that take up more of the damage, and/or because interface area is reduced). This effect allows three possible equilibrium grain-sizes for a given stress; a small-grain-size high-shear state in diffusion creep, a large grain-size low shear state in dislocation creep, and an intermediate state (often near the deformation map phase-boundary). The low and high grain-size states are stable, while the intermediate one is unstable. This implies that a material deformed at a given stress can acquire two stable deformation regimes, a low- and high- shear state; these are indicative of plate-like flows, i.e, the coexistence of both slowly deforming plates and rapidly deforming plate boundaries.

Identifying Trajectories of Borderline Personality Features in Adolescence

PubMed Central

Haltigan, John D.

2016-01-01

Objective: To examine trajectories of adolescent borderline personality (BP) features in a normative-risk cohort (n = 566) of Canadian children assessed at ages 13, 14, 15, and 16 and childhood predictors of trajectory group membership assessed at ages 8, 10, 11, and 12. Method: Data were drawn from the McMaster Teen Study, an on-going study examining relations among bullying, mental health, and academic achievement. Participants and their parents completed a battery of mental health and peer relations questionnaires at each wave of the study. Academic competence was assessed at age 8 (Grade 3). Latent class growth analysis, analysis of variance, and logistic regression were used to analyze the data. Results: Three distinct BP features trajectory groups were identified: elevated or rising, intermediate or stable, and low or stable. Parent- and child-reported mental health symptoms, peer relations risk factors, and intra-individual risk factors were significant predictors of elevated or rising and intermediate or stable trajectory groups. Child-reported attention-deficit hyperactivity disorder (ADHD) and somatization symptoms uniquely predicted elevated or rising trajectory group membership, whereas parent-reported anxiety and child-reported ADHD symptoms uniquely predicted intermediate or stable trajectory group membership. Child-reported somatization symptoms was the only predictor to differentiate the intermediate or stable and elevated or rising trajectory groups (OR 1.15, 95% CI 1.04 to 1.28). Associations between child-reported reactive temperament and elevated BP features trajectory group membership were 10.23 times higher among children who were bullied, supporting a diathesis–stress pathway in the development of BP features for these youth. Conclusions: Findings demonstrate the heterogeneous course of BP features in early adolescence and shed light on the potential prodromal course of later borderline personality disorder. PMID:27254092

Identifying Trajectories of Borderline Personality Features in Adolescence: Antecedent and Interactive Risk Factors.

PubMed

Haltigan, John D; Vaillancourt, Tracy

2016-03-01

To examine trajectories of adolescent borderline personality (BP) features in a normative-risk cohort (n = 566) of Canadian children assessed at ages 13, 14, 15, and 16 and childhood predictors of trajectory group membership assessed at ages 8, 10, 11, and 12. Data were drawn from the McMaster Teen Study, an on-going study examining relations among bullying, mental health, and academic achievement. Participants and their parents completed a battery of mental health and peer relations questionnaires at each wave of the study. Academic competence was assessed at age 8 (Grade 3). Latent class growth analysis, analysis of variance, and logistic regression were used to analyze the data. Three distinct BP features trajectory groups were identified: elevated or rising, intermediate or stable, and low or stable. Parent- and child-reported mental health symptoms, peer relations risk factors, and intra-individual risk factors were significant predictors of elevated or rising and intermediate or stable trajectory groups. Child-reported attention-deficit hyperactivity disorder (ADHD) and somatization symptoms uniquely predicted elevated or rising trajectory group membership, whereas parent-reported anxiety and child-reported ADHD symptoms uniquely predicted intermediate or stable trajectory group membership. Child-reported somatization symptoms was the only predictor to differentiate the intermediate or stable and elevated or rising trajectory groups (OR 1.15, 95% CI 1.04 to 1.28). Associations between child-reported reactive temperament and elevated BP features trajectory group membership were 10.23 times higher among children who were bullied, supporting a diathesis-stress pathway in the development of BP features for these youth. Findings demonstrate the heterogeneous course of BP features in early adolescence and shed light on the potential prodromal course of later borderline personality disorder. © The Author(s) 2015.

SWIFT J1910.2-0546: A Possible Black Hole Binary with a Retrograde Spin or Truncated Disk

NASA Astrophysics Data System (ADS)

Reis, R. C.; Reynolds, M. T.; Miller, J. M.; Walton, D. J.; Maitra, D.; King, A.; Degenaar, N.

2013-12-01

We present the first results from a long (51 ks) XMM-Newton observation of the Galactic X-ray binary SWIFT J1910.2-0546 in an intermediate state, obtained during its 2012 outburst. A clear, asymmetric iron emission line is observed and physically motivated models are used to fully describe the emission-line profile. Unlike other sources in their intermediate spectral states, the inner accretion disk in SWIFT J1910.2-0546 appears to be truncated, with an inner radius of r in =9.4^{+1.7}_{-1.3} r g at a 90% confidence limit. Quasi-periodic oscillations are also found at approximately 4.5 and 6 Hz, which correlates well with the break frequency of the underlying broad-band noise. Assuming that the line emission traces the innermost stable circular orbit, as would generally be expected for an intermediate state, the current observation of SWIFT J1910.2-0546 may offer the best evidence for a possible retrograde stellar mass black hole with a spin parameter a < - 0.32cJ/GM2 (90% confidence). Although this is an intriguing possibility, there are also a number of alternative scenarios which do not require a retrograde spin. For example, the inner accretion disk may be truncated at an unusually high luminosity in this case, potentially suffering frequent evaporation/condensation, or it could instead be persistently evacuated through mass loss in a relativistic jet. Further observations are required to distinguish between these different interpretations.

Permanganate ion oxidations. IX. Manganese intermediates (complexes) in the oxidation of 2,4(1H,3H)-pyrimidinediones.

PubMed

Freeman, F; Karchefski, E M

1976-10-04

Uniquely stable manganese intermediates (complexes) are formed from the permanganate ion oxidation of the 5,6-carbon-carbon double bond in several 2,4(1H,3H)-pyrimidinediones [uracil, (compound 7), 5-methyluracil (thymine, compound 5), and 6-methyluracil (compound 8)]. These manganese complexes, which represent some of the most stable intermediate manganese species observed thus far in the oxidation of carbon-carbon double bonds, show absorption maxima in the 285-296 nm region (epsilon max approximately 4500). The relative reactivities of 6-methyluracil: uracil: thymine are 1: 23 : 194 and the bimolecular oxidation process is characterized by relatively small deltaH++ values and large negative deltaS++ values.

Stable isotope analysis of CO2 in breath indicates metabolic fuel shifts in torpid arctic ground squirrels.

PubMed

Lee, Trixie N; Richter, Melanie M; Williams, Cory T; Tøien, Øivind; Barnes, Brian M; O'Brien, Diane M; Buck, C Loren

2017-07-01

Stable carbon isotope ratios (δ 13 C) in breath show promise as an indicator of immediate metabolic fuel utilization in animals because tissue lipids have a lower δ 13 C value than carbohydrates and proteins. Metabolic fuel consumption is often estimated using the respiratory exchange ratio (RER), which has lipid and carbohydrate boundaries, but does not differentiate between protein and mixed fuel catabolism at intermediate values. Because lipids have relatively low δ 13 C values, measurements of stable carbon isotopes in breath may help distinguish between catabolism of protein and mixed fuel that includes lipid. We measured breath δ 13 C and RER concurrently in arctic ground squirrels (Urocitellus parryii) during steady-state torpor at ambient temperatures from -2 to -26°C. As predicted, we found a correlation between RER and breath δ 13 C values; however, the range of RER in this study did not reach intermediate levels to allow further resolution of metabolic substrate use with the addition of breath δ 13 C measurements. These data suggest that breath δ 13 C values are 1.1‰ lower than lipid tissue during pure lipid metabolism. From RER, we determined that arctic ground squirrels rely on nonlipid fuel sources for a significant portion of energy during torpor (up to 37%). The shift toward nonlipid fuel sources may be influenced by adiposity of the animals in addition to thermal challenge. Copyright © 2017 Elsevier Inc. All rights reserved.

Chemical Equilibrium Models for the S3 State of the Oxygen-Evolving Complex of Photosystem II.

PubMed

Isobe, Hiroshi; Shoji, Mitsuo; Shen, Jian-Ren; Yamaguchi, Kizashi

2016-01-19

We have performed hybrid density functional theory (DFT) calculations to investigate how chemical equilibria can be described in the S3 state of the oxygen-evolving complex in photosystem II. For a chosen 340-atom model, 1 stable and 11 metastable intermediates have been identified within the range of 13 kcal mol(-1) that differ in protonation, charge, spin, and conformational states. The results imply that reversible interconversion of these intermediates gives rise to dynamic equilibria that involve processes with relocations of protons and electrons residing in the Mn4CaO5 cluster, as well as bound water ligands, with concomitant large changes in the cluster geometry. Such proton tautomerism and redox isomerism are responsible for reversible activation/deactivation processes of substrate oxygen species, through which Mn-O and O-O bonds are transiently ruptured and formed. These results may allow for a tentative interpretation of kinetic data on substrate water exchange on the order of seconds at room temperature, as measured by time-resolved mass spectrometry. The reliability of the hybrid DFT method for the multielectron redox reaction in such an intricate system is also addressed.

Intermediate coating layer for high temperature rubbing seals for rotary regenerators

DOEpatents

Schienle, James L.; Strangman, Thomas E.

1995-01-01

A metallic regenerator seal is provided having multi-layer coating comprising a NiCrAlY bond layer, a yttria stabilized zirconia (YSZ) intermediate layer, and a ceramic high temperature solid lubricant surface layer comprising zinc oxide, calcium fluoride, and tin oxide. Because of the YSZ intermediate layer, the coating is thermodynamically stable and resists swelling at high temperatures.

Equilibrium folding of pro-HlyA from Escherichia coli reveals a stable calcium ion dependent folding intermediate.

PubMed

Thomas, Sabrina; Bakkes, Patrick J; Smits, Sander H J; Schmitt, Lutz

2014-09-01

HlyA from Escherichia coli is a member of the repeats in toxin (RTX) protein family, produced by a wide range of Gram-negative bacteria and secreted by a dedicated Type 1 Secretion System (T1SS). RTX proteins are thought to be secreted in an unfolded conformation and to fold upon secretion by Ca(2+) binding. However, the exact mechanism of secretion, ion binding and folding to the correct native state remains largely unknown. In this study we provide an easy protocol for high-level pro-HlyA purification from E. coli. Equilibrium folding studies, using intrinsic tryptophan fluorescence, revealed the well-known fact that Ca(2+) is essential for stability as well as correct folding of the whole protein. In the absence of Ca(2+), pro-HlyA adopts a non-native conformation. Such molecules could however be rescued by Ca(2+) addition, indicating that these are not dead-end species and that Ca(2+) drives pro-HlyA folding. More importantly, pro-HlyA unfolded via a two-state mechanism, whereas folding was a three-state process. The latter is indicative of the presence of a stable folding intermediate. Analysis of deletion and Trp mutants revealed that the first folding transition, at 6-7M urea, relates to Ca(2+) dependent structural changes at the extreme C-terminus of pro-HlyA, sensed exclusively by Trp914. Since all Trp residues of HlyA are located outside the RTX domain, our results demonstrate that Ca(2+) induced folding is not restricted to the RTX domain. Taken together, Ca(2+) binding to the pro-HlyA RTX domain is required to drive the folding of the entire protein to its native conformation. Copyright © 2014 Elsevier B.V. All rights reserved.

Time-resolved distance determination by tryptophan fluorescence quenching: probing intermediates in membrane protein folding.

PubMed

Kleinschmidt, J H; Tamm, L K

1999-04-20

The mechanism of insertion and folding of an integral membrane protein has been investigated with the beta-barrel forming outer membrane protein A (OmpA) of Escherichia coli. This work describes a new approach to this problem by combining structural information obtained from tryptophan fluorescence quenching at different depths in the lipid bilayer with the kinetics of the refolding process. Experiments carried out over a temperature range between 2 and 40 degrees C allowed us to detect, trap, and characterize previously unidentified folding intermediates on the pathway of OmpA insertion and folding into lipid bilayers. Three membrane-bound intermediates were found in which the average distances of the Trps were 14-16, 10-11, and 0-5 A, respectively, from the bilayer center. The first folding intermediate is stable at 2 degrees C for at least 1 h. A second intermediate has been isolated at temperatures between 7 and 20 degrees C. The Trps move 4-5 A closer to the center of the bilayer at this stage. Subsequently, in an intermediate that is observable at 26-28 degrees C, the Trps move another 5-10 A closer to the center of the bilayer. The final (native) structure is observed at higher temperatures of refolding. In this structure, the Trps are located on average about 9-10 A from the bilayer center. Monitoring the evolution of Trp fluorescence quenching by a set of brominated lipids during refolding at various temperatures therefore allowed us to identify and characterize intermediate states in the folding process of an integral membrane protein.

Solvent effects on the excited-state double proton transfer mechanism in the 7-azaindole dimer: a TDDFT study with the polarizable continuum model.

PubMed

Yu, Xue-Fang; Yamazaki, Shohei; Taketsugu, Tetsuya

2017-08-30

Solvent effects on the excited-state double proton transfer (ESDPT) mechanism in the 7-azaindole (7AI) dimer were investigated using the time-dependent density functional theory (TDDFT) method. Excited-state potential energy profiles along the reaction paths in a locally excited (LE) state and a charge transfer (CT) state were calculated using the polarizable continuum model (PCM) to include the solvent effect. A series of non-polar and polar solvents with different dielectric constants were used to examine the polarity effect on the ESDPT mechanism. The present results suggest that in a non-polar solvent and a polar solvent with a small dielectric constant, ESDPT follows a concerted mechanism, similar to the case in the gas phase. In a polar solvent with a relatively large dielectric constant, however, ESDPT is likely to follow a stepwise mechanism via a stable zwitterionic intermediate in the LE state on the adiabatic potential energy surface, although inclusion of zero-point vibrational energy (ZPE) corrections again suggests the concerted mechanism. In the meantime, the stepwise reaction path involving the CT state with neutral intermediates is also examined, and is found to be less competitive than the concerted or stepwise path in the LE state in both non-polar and polar solvents. The present study provides a new insight into the experimental controversy of the ESDPT mechanism of the 7AI dimer in a solution.

Sb-rich Si-Sb-Te phase change material for multilevel data storage: The degree of disorder in the crystalline state

NASA Astrophysics Data System (ADS)

Zhou, Xilin; Wu, Liangcai; Song, Zhitang; Rao, Feng; Cheng, Yan; Peng, Cheng; Yao, Dongning; Song, Sannian; Liu, Bo; Feng, Songlin; Chen, Bomy

2011-07-01

The phase change memory with monolayer chalcogenide film (Si18Sb52Te30) is investigated for the feasibility of multilevel data storage. During the annealing of the film, a relatively stable intermediate resistance can be obtained at an appropriate heating rate. The transmission electron microscopy in situ analysis reveals a conversion of crystallization mechanism from nucleation to crystal growth, which leads a continuous reduction in the degree of disorder. It is indicated from the electrical properties of the devices that the fall edge of the voltage pulse is the critical factor that determines a reliable triple-level resistance state of the phase change memory cell.

5-Hydroxymethylcytosine is a predominantly stable DNA modification

NASA Astrophysics Data System (ADS)

Bachman, Martin; Uribe-Lewis, Santiago; Yang, Xiaoping; Williams, Michael; Murrell, Adele; Balasubramanian, Shankar

2014-12-01

5-Hydroxymethylcytosine (hmC) is an oxidation product of 5-methylcytosine which is present in the deoxyribonucleic acid (DNA) of most mammalian cells. Reduction of hmC levels in DNA is a hallmark of cancers. Elucidating the dynamics of this oxidation reaction and the lifetime of hmC in DNA is fundamental to understanding hmC function. Using stable isotope labelling of cytosine derivatives in the DNA of mammalian cells and ultrasensitive tandem liquid-chromatography mass spectrometry, we show that the majority of hmC is a stable modification, as opposed to a transient intermediate. In contrast with DNA methylation, which occurs immediately during replication, hmC forms slowly during the first 30 hours following DNA synthesis. Isotopic labelling of DNA in mouse tissues confirmed the stability of hmC in vivo and demonstrated a relationship between global levels of hmC and cell proliferation. These insights have important implications for understanding the states of chemically modified DNA bases in health and disease.

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

Kan, Jimmy J.; Gottwald, Matthias; Fullerton, Eric E.

We describe low-temperature characterization of magnetic tunnel junctions (MTJs) patterned by reactive ion etching for spin-transfer-torque magnetic random access memory. Magnetotransport measurements of typical MTJs show increasing tunneling magnetoresistance (TMR) and larger coercive fields as temperature is decreased down to 10 K. However, MTJs selected from the high-resistance population of an MTJ array exhibit stable intermediate magnetic states when measured at low temperature and show TMR roll-off below 100 K. These non-ideal low-temperature behaviors arise from edge damage during the etch process and can have negative impacts on thermal stability of the MTJs.

Octupole Deformation Bands of πh11/2 in Neutron-Rich 145,147La Nuclei

NASA Astrophysics Data System (ADS)

Zhu, Sheng-jiang; S, Zhu J.; Wang, Mu-ge; J, Hamilton H.; A, Ramayya V.; B, Babu R. S.; W, Ma C.; Long, Gui-lu; Zhu, Ling-yan; Li, Ming; A, Sakhaee; Gan, Cui-yun; Yang, Li-ming; J, Komicki; J, Cole D.; R, Aryaeinejad; M, Drigert W.; J, Rasmussen O.; M, Stoyer A.; S, Chu Y.; K, Gregorich E.; M, Mohar F.; S, Prussin G.; I, Lee Y.; Yu, Oganessian Ts; G, Ter-Akopian M.; A, Daniel V.

1999-03-01

Octupole deformation bands built on πh11/2 orbital in neutron-rich odd-Z 145,147La nuclei have been investigated by measuring the prompt γ-rays emitted from the 252Cf source. The alternating parity band structures and strong E1 transitions observed between negative- and positive-parity bands in both nuclei indicate the octupole deformation enhanced by the h11/2 single proton coupling. According to observed energy displacements the octupole deformation becomes stable at the intermediate spin states.

Cyclobutanone Mimics of Intermediates in Metallo-β-Lactamase Catalysis.

PubMed

Abboud, Martine I; Kosmopoulou, Magda; Krismanich, Anthony P; Johnson, Jarrod W; Hinchliffe, Philip; Brem, Jürgen; Claridge, Timothy D W; Spencer, James; Schofield, Christopher J; Dmitrienko, Gary I

2018-04-17

The most important resistance mechanism to β-lactam antibiotics involves hydrolysis by two β-lactamase categories: the nucleophilic serine and the metallo-β-lactamases (SBLs and MBLs, respectively). Cyclobutanones are hydrolytically stable β-lactam analogues with potential to inhibit both SBLs and MBLs. We describe solution and crystallographic studies on the interaction of a cyclobutanone penem analogue with the clinically important MBL SPM-1. NMR experiments using 19 F-labeled SPM-1 imply the cyclobutanone binds to SPM-1 with micromolar affinity. A crystal structure of the SPM-1:cyclobutanone complex reveals binding of the hydrated cyclobutanone through interactions with one of the zinc ions, stabilisation of the hydrate by hydrogen bonding to zinc-bound water, and hydrophobic contacts with aromatic residues. NMR analyses using a 13 C-labeled cyclobutanone support assignment of the bound species as the hydrated ketone. The results inform on how MBLs bind substrates and stabilize tetrahedral intermediates. They support further investigations on the use of transition-state and/or intermediate analogues as inhibitors of all β-lactamase classes. © 2018 Die Autoren. Veröffentlicht von Wiley-VCH Verlag GmbH & Co. KGaA.

Cyclobutanone Mimics of Intermediates in Metallo‐β‐Lactamase Catalysis

PubMed Central

Abboud, Martine I.; Kosmopoulou, Magda; Krismanich, Anthony P.; Johnson, Jarrod W.; Hinchliffe, Philip; Brem, Jürgen; Claridge, Timothy D. W.

2018-01-01

Abstract The most important resistance mechanism to β‐lactam antibiotics involves hydrolysis by two β‐lactamase categories: the nucleophilic serine and the metallo‐β‐lactamases (SBLs and MBLs, respectively). Cyclobutanones are hydrolytically stable β‐lactam analogues with potential to inhibit both SBLs and MBLs. We describe solution and crystallographic studies on the interaction of a cyclobutanone penem analogue with the clinically important MBL SPM‐1. NMR experiments using 19F‐labeled SPM‐1 imply the cyclobutanone binds to SPM‐1 with micromolar affinity. A crystal structure of the SPM‐1:cyclobutanone complex reveals binding of the hydrated cyclobutanone through interactions with one of the zinc ions, stabilisation of the hydrate by hydrogen bonding to zinc‐bound water, and hydrophobic contacts with aromatic residues. NMR analyses using a 13C‐labeled cyclobutanone support assignment of the bound species as the hydrated ketone. The results inform on how MBLs bind substrates and stabilize tetrahedral intermediates. They support further investigations on the use of transition‐state and/or intermediate analogues as inhibitors of all β‐lactamase classes. PMID:29250863

Direct single-molecule dynamic detection of chemical reactions.

PubMed

Guan, Jianxin; Jia, Chuancheng; Li, Yanwei; Liu, Zitong; Wang, Jinying; Yang, Zhongyue; Gu, Chunhui; Su, Dingkai; Houk, Kendall N; Zhang, Deqing; Guo, Xuefeng

2018-02-01

Single-molecule detection can reveal time trajectories and reaction pathways of individual intermediates/transition states in chemical reactions and biological processes, which is of fundamental importance to elucidate their intrinsic mechanisms. We present a reliable, label-free single-molecule approach that allows us to directly explore the dynamic process of basic chemical reactions at the single-event level by using stable graphene-molecule single-molecule junctions. These junctions are constructed by covalently connecting a single molecule with a 9-fluorenone center to nanogapped graphene electrodes. For the first time, real-time single-molecule electrical measurements unambiguously show reproducible large-amplitude two-level fluctuations that are highly dependent on solvent environments in a nucleophilic addition reaction of hydroxylamine to a carbonyl group. Both theoretical simulations and ensemble experiments prove that this observation originates from the reversible transition between the reactant and a new intermediate state within a time scale of a few microseconds. These investigations open up a new route that is able to be immediately applied to probe fast single-molecule physics or biophysics with high time resolution, making an important contribution to broad fields beyond reaction chemistry.

Predicting unfolding thermodynamics and stable intermediates for alanine-rich helical peptides with the aid of coarse-grained molecular simulation.

PubMed

Calero-Rubio, Cesar; Paik, Bradford; Jia, Xinqiao; Kiick, Kristi L; Roberts, Christopher J

2016-10-01

This report focuses on the molecular-level processes and thermodynamics of unfolding of a series of helical peptides using a coarse-grained (CG) molecular model. The CG model was refined to capture thermodynamics and structural changes as a function of temperature for a set of published peptide sequences. Circular dichroism spectroscopy (CD) was used to experimentally monitor the temperature-dependent conformational changes and stability of published peptides and new sequences introduced here. The model predictions were quantitatively or semi-quantitatively accurate in all cases. The simulations and CD results showed that, as expected, in most cases the unfolding of helical peptides is well described by a simply 2-state model, and conformational stability increased with increased length of the helices. A notable exception in a 19-residue helix was when two Ala residues were each replaced with Phe. This stabilized a partly unfolded intermediate state via hydrophobic contacts, and also promoted aggregates at higher peptide concentrations. Copyright © 2016 Elsevier B.V. All rights reserved.

On the structure of the disordered Bi 2Te 4O 11 phase

NASA Astrophysics Data System (ADS)

Masson, O.; Thomas, P.; Durand, O.; Hansen, T.; Champarnaud, J. C.; Mercurio, D.

2004-06-01

The structure of the disordered metastable Bi 2Te 4O 11 phase has been investigated using both neutron powder diffraction and reverse Monte Carlo (RMC) modelling. The average structure, of fluorite-type (space group Fm 3¯m ), is characterized by very high Debye-Waller parameters, especially for oxygen. Whereas the cations form a fairly well-defined FCC lattice, the oxygen sublattice is very disordered. It is shown that the local order is similar to that present in the stable monoclinic Bi 2Te 4O 11 phase. Clear differences are observed for the intermediate range order. The present phase is analogous to the "anti-glass" phases reported by Trömel in other tellurium-based mixed oxides. However, whereas Trömel defines anti-glass as having long range order but no short range order, it is shown here that this phase is best described as an intermediate state between the amorphous and crystalline states, i.e. having short and medium range order similar to that of tellurite glasses and a premise of long range order with the cations only.

Direct single-molecule dynamic detection of chemical reactions

PubMed Central

Guan, Jianxin; Jia, Chuancheng; Li, Yanwei; Liu, Zitong; Wang, Jinying; Yang, Zhongyue; Gu, Chunhui; Su, Dingkai; Houk, Kendall N.; Zhang, Deqing; Guo, Xuefeng

2018-01-01

Single-molecule detection can reveal time trajectories and reaction pathways of individual intermediates/transition states in chemical reactions and biological processes, which is of fundamental importance to elucidate their intrinsic mechanisms. We present a reliable, label-free single-molecule approach that allows us to directly explore the dynamic process of basic chemical reactions at the single-event level by using stable graphene-molecule single-molecule junctions. These junctions are constructed by covalently connecting a single molecule with a 9-fluorenone center to nanogapped graphene electrodes. For the first time, real-time single-molecule electrical measurements unambiguously show reproducible large-amplitude two-level fluctuations that are highly dependent on solvent environments in a nucleophilic addition reaction of hydroxylamine to a carbonyl group. Both theoretical simulations and ensemble experiments prove that this observation originates from the reversible transition between the reactant and a new intermediate state within a time scale of a few microseconds. These investigations open up a new route that is able to be immediately applied to probe fast single-molecule physics or biophysics with high time resolution, making an important contribution to broad fields beyond reaction chemistry. PMID:29487914

Response of Submerged Macrophyte Communities to External and Internal Restoration Measures in North Temperate Shallow Lakes

PubMed Central

Hilt, Sabine; Alirangues Nuñez, Marta M.; Bakker, Elisabeth S.; Blindow, Irmgard; Davidson, Thomas A.; Gillefalk, Mikael; Hansson, Lars-Anders; Janse, Jan H.; Janssen, Annette B. G.; Jeppesen, Erik; Kabus, Timm; Kelly, Andrea; Köhler, Jan; Lauridsen, Torben L.; Mooij, Wolf M.; Noordhuis, Ruurd; Phillips, Geoff; Rücker, Jacqueline; Schuster, Hans-Heinrich; Søndergaard, Martin; Teurlincx, Sven; van de Weyer, Klaus; van Donk, Ellen; Waterstraat, Arno; Willby, Nigel; Sayer, Carl D.

2018-01-01

Submerged macrophytes play a key role in north temperate shallow lakes by stabilizing clear-water conditions. Eutrophication has resulted in macrophyte loss and shifts to turbid conditions in many lakes. Considerable efforts have been devoted to shallow lake restoration in many countries, but long-term success depends on a stable recovery of submerged macrophytes. However, recovery patterns vary widely and remain to be fully understood. We hypothesize that reduced external nutrient loading leads to an intermediate recovery state with clear spring and turbid summer conditions similar to the pattern described for eutrophication. In contrast, lake internal restoration measures can result in transient clear-water conditions both in spring and summer and reversals to turbid conditions. Furthermore, we hypothesize that these contrasting restoration measures result in different macrophyte species composition, with added implications for seasonal dynamics due to differences in plant traits. To test these hypotheses, we analyzed data on water quality and submerged macrophytes from 49 north temperate shallow lakes that were in a turbid state and subjected to restoration measures. To study the dynamics of macrophytes during nutrient load reduction, we adapted the ecosystem model PCLake. Our survey and model simulations revealed the existence of an intermediate recovery state upon reduced external nutrient loading, characterized by spring clear-water phases and turbid summers, whereas internal lake restoration measures often resulted in clear-water conditions in spring and summer with returns to turbid conditions after some years. External and internal lake restoration measures resulted in different macrophyte communities. The intermediate recovery state following reduced nutrient loading is characterized by a few macrophyte species (mainly pondweeds) that can resist wave action allowing survival in shallow areas, germinate early in spring, have energy-rich vegetative propagules facilitating rapid initial growth and that can complete their life cycle by early summer. Later in the growing season these plants are, according to our simulations, outcompeted by periphyton, leading to late-summer phytoplankton blooms. Internal lake restoration measures often coincide with a rapid but transient colonization by hornworts, waterweeds or charophytes. Stable clear-water conditions and a diverse macrophyte flora only occurred decades after external nutrient load reduction or when measures were combined. PMID:29515607

Augmenting the efficacy of anti-cocaine catalytic antibodies through chimeric hapten design and combinatorial vaccination.

PubMed

Wenthur, Cody J; Cai, Xiaoqing; Ellis, Beverly A; Janda, Kim D

2017-08-15

Given the need for further improvements in anti-cocaine vaccination strategies, a chimeric hapten (GNET) was developed that combines chemically-stable structural features from steady-state haptens with the hydrolytic functionality present in transition-state mimetic haptens. Additionally, as a further investigation into the generation of an improved bifunctional antibody pool, sequential vaccination with steady-state and transition-state mimetic haptens was undertaken. While GNET induced the formation of catalytically-active antibodies, it did not improve overall behavioral efficacy. In contrast, the resulting pool of antibodies from GNE/GNT co-administration demonstrated intermediate efficacy as compared to antibodies developed from either hapten alone. Overall, improved antibody catalytic efficiency appears necessary to achieve the synergistic benefits of combining cocaine hydrolysis with peripheral sequestration. Copyright © 2017 Elsevier Ltd. All rights reserved.

Solvent control of charge transfer excited state relaxation pathways in [Fe(2,2'-bipyridine)(CN) 4] 2-

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

Kjær, Kasper S.; Kunnus, Kristjan; Harlang, Tobias C. B.

The excited state dynamics of solvated [Fe(bpy)(CN) 4] 2-, where bpy = 2,2'-bipyridine, show significant sensitivity to the solvent Lewis acidity. Using a combination of optical absorption and X-ray emission transient spectroscopies, we have previously shown that the metal to ligand charge transfer (MLCT) excited state of [Fe(bpy)(CN) 4] 2- has a 19 picosecond lifetime and no discernable contribution from metal centered (MC) states in weak Lewis acid solvents, such as dimethyl sulfoxide and acetonitrile. Here, in the present work, we use the same combination of spectroscopic techniques to measure the MLCT excited state relaxation dynamics of [Fe(bpy)(CN) 4] 2-more » in water, a strong Lewis acid solvent. The charge-transfer excited state is now found to decay in less than 100 femtoseconds, forming a quasi-stable metal centered excited state with a 13 picosecond lifetime. We find that this MC excited state has triplet ( 3MC) character, unlike other reported six-coordinate Fe(II)-centered coordination compounds, which form MC quintet ( 5MC) states. The solvent dependent changes in excited state non-radiative relaxation for [Fe(bpy)(CN) 4] 2- allows us to infer the influence of the solvent on the electronic structure of the complex. Lastly, the robust characterization of the dynamics and optical spectral signatures of the isolated 3MC intermediate provides a strong foundation for identifying 3MC intermediates in the electronic excited state relaxation mechanisms of similar Fe-centered systems being developed for solar applications.« less

Solvent control of charge transfer excited state relaxation pathways in [Fe(2,2'-bipyridine)(CN) 4] 2-

DOE PAGES

Kjær, Kasper S.; Kunnus, Kristjan; Harlang, Tobias C. B.; ...

2018-01-19

The excited state dynamics of solvated [Fe(bpy)(CN) 4] 2-, where bpy = 2,2'-bipyridine, show significant sensitivity to the solvent Lewis acidity. Using a combination of optical absorption and X-ray emission transient spectroscopies, we have previously shown that the metal to ligand charge transfer (MLCT) excited state of [Fe(bpy)(CN) 4] 2- has a 19 picosecond lifetime and no discernable contribution from metal centered (MC) states in weak Lewis acid solvents, such as dimethyl sulfoxide and acetonitrile. Here, in the present work, we use the same combination of spectroscopic techniques to measure the MLCT excited state relaxation dynamics of [Fe(bpy)(CN) 4] 2-more » in water, a strong Lewis acid solvent. The charge-transfer excited state is now found to decay in less than 100 femtoseconds, forming a quasi-stable metal centered excited state with a 13 picosecond lifetime. We find that this MC excited state has triplet ( 3MC) character, unlike other reported six-coordinate Fe(II)-centered coordination compounds, which form MC quintet ( 5MC) states. The solvent dependent changes in excited state non-radiative relaxation for [Fe(bpy)(CN) 4] 2- allows us to infer the influence of the solvent on the electronic structure of the complex. Lastly, the robust characterization of the dynamics and optical spectral signatures of the isolated 3MC intermediate provides a strong foundation for identifying 3MC intermediates in the electronic excited state relaxation mechanisms of similar Fe-centered systems being developed for solar applications.« less

Cardiovascular events and mortality in patients with adrenal incidentalomas that are either non-secreting or associated with intermediate phenotype or subclinical Cushing's syndrome: a 15-year retrospective study.

PubMed

Di Dalmazi, Guido; Vicennati, Valentina; Garelli, Silvia; Casadio, Elena; Rinaldi, Eleonora; Giampalma, Emanuela; Mosconi, Cristina; Golfieri, Rita; Paccapelo, Alexandro; Pagotto, Uberto; Pasquali, Renato

2014-05-01

Incidental discovery of adrenal masses has increased over the past few years. Mild alterations in cortisol secretion without clinical signs of overt hypercortisolism (subclinical Cushing's syndrome) are a common finding in patients with these tumours. Although metabolic alterations and increased cardiovascular risk have been noted in patients with subclinical Cushing's syndrome, incidence of cardiovascular events and mortality in the long term have not been assessed. We aimed to ascertain the frequency of new cardiovascular events and mortality in patients with non-secreting adrenal incidentalomas, tumours of intermediate phenotype, or those causing subclinical Cushing's syndrome. From January, 1995, to September, 2010, consecutive outpatients with adrenal incidentalomas who were referred to the endocrinology unit of S Orsola-Malpighi Hospital, Bologna, Italy, were enrolled into our study. Individuals were assessed every 18-30 months for the first 5 years (mean follow-up 7·5 [SD 3·2] years, range 26 months to 15 years). Cortisol concentrations after the 1 mg dexamethasone suppression test (DST) were used to define non-secreting (+50 nmol/L) and intermediate phenotype (50-138 nmol/L) adrenal incidentalomas and subclinical Cushing's syndrome (+138 nmol/L). At the end of follow-up, patients were reclassified as having either unchanged or worsened secreting patterns from baseline. 198 outpatients were assessed; at the end of follow-up, 114 patients had stable non-secreting adrenal incidentalomas, 61 had either a stable intermediate phenotype or subclinical Cushing's syndrome, and 23 had a pattern of secretion that had worsened. By comparison with patients with stable non-secreting adrenal incidentalomas, the incidence of cardiovascular events was higher in individuals with a stable intermediate phenotype or subclinical Cushing's syndrome (6·7% vs 16·7%; p=0·04) and in those with worsened secreting patterns (6·7% vs 28·4%; p=0·02). Cardiovascular events were associated independently with a change (from baseline to the end of follow-up) in cortisol concentrations post DST (hazard ratio 1·13, 95% CI 1·05-1·21; p=0·001). Survival rates for all-cause mortality were lower in patients with either stable intermediate phenotype adrenal incidentalomas or subclinical Cushing's syndrome compared with those with stable non-secreting masses (57·0% vs 91·2%; p=0·005). Factors associated with mortality were age (hazard ratio 1·06, 95% CI 1·01-1·12; p=0·03) and mean concentrations of cortisol post DST (1·10, 1·01-1·19; p=0·04). Compared with patients with stable non-secreting adrenal incidentalomas, unadjusted survival for cardiovascular-specific mortality was lower in patients with either a stable intermediate phenotype or subclinical Cushing's syndrome (97·5% vs 78·4%; p=0·02) and in those with worsened secreting patterns (97·5% vs 60·0%; p=0·01). Cancer mortality did not differ between groups. Even when clinical signs of overt hypercortisolism are not present, patients with adrenal incidentalomas and mild hypercortisolism have an increased risk of cardiovascular events and mortality. None. Copyright © 2014 Elsevier Ltd. All rights reserved.

Competing Pathways and Multiple Folding Nuclei in a Large Multidomain Protein, Luciferase.

PubMed

Scholl, Zackary N; Yang, Weitao; Marszalek, Piotr E

2017-05-09

Proteins obtain their final functional configuration through incremental folding with many intermediate steps in the folding pathway. If known, these intermediate steps could be valuable new targets for designing therapeutics and the sequence of events could elucidate the mechanism of refolding. However, determining these intermediate steps is hardly an easy feat, and has been elusive for most proteins, especially large, multidomain proteins. Here, we effectively map part of the folding pathway for the model large multidomain protein, Luciferase, by combining single-molecule force-spectroscopy experiments and coarse-grained simulation. Single-molecule refolding experiments reveal the initial nucleation of folding while simulations corroborate these stable core structures of Luciferase, and indicate the relative propensities for each to propagate to the final folded native state. Both experimental refolding and Monte Carlo simulations of Markov state models generated from simulation reveal that Luciferase most often folds along a pathway originating from the nucleation of the N-terminal domain, and that this pathway is the least likely to form nonnative structures. We then engineer truncated variants of Luciferase whose sequences corresponded to the putative structure from simulation and we use atomic force spectroscopy to determine their unfolding and stability. These experimental results corroborate the structures predicted from the folding simulation and strongly suggest that they are intermediates along the folding pathway. Taken together, our results suggest that initial Luciferase refolding occurs along a vectorial pathway and also suggest a mechanism that chaperones may exploit to prevent misfolding. Copyright © 2017 Biophysical Society. Published by Elsevier Inc. All rights reserved.

The global extent and determinants of savanna and forest as alternative biome states.

PubMed

Staver, A Carla; Archibald, Sally; Levin, Simon A

2011-10-14

Theoretically, fire-tree cover feedbacks can maintain savanna and forest as alternative stable states. However, the global extent of fire-driven discontinuities in tree cover is unknown, especially accounting for seasonality and soils. We use tree cover, climate, fire, and soils data sets to show that tree cover is globally discontinuous. Climate influences tree cover globally but, at intermediate rainfall (1000 to 2500 millimeters) with mild seasonality (less than 7 months), tree cover is bimodal, and only fire differentiates between savanna and forest. These may be alternative states over large areas, including parts of Amazonia and the Congo. Changes in biome distributions, whether at the cost of savanna (due to fragmentation) or forest (due to climate), will be neither smooth nor easily reversible.

Structure and Mechanism of Styrene Monooxygenase Reductase: New Insight into the FAD–Transfer Reaction†

PubMed Central

Morrison, Eliot; Kantz, Auric; Gassner, George T.; Sazinsky, Matthew H.

2013-01-01

The two–component flavoprotein styrene monooxygenase (SMO) from Pseudomonas putida S12 catalyzes the NADH– and FAD–dependent epoxidation of styrene to styrene oxide. In this study we investigate the mechanism of flavin reduction and transfer from the reductase (SMOB) to epoxidase (NSMOA) component and report our findings in light of the 2.2–Å crystal structure of SMOB. Upon rapidly mixing with NADH, SMOB forms an NADH→FADox charge–transfer intermediate and catalyzes a hydride–transfer reaction from NADH to FAD, with a rate constant of 49.1 ± 1.4 s−1, in a step that is coupled to the rapid dissociation of NAD+. Electrochemical and equilibrium–binding studies indicate that NSMOA binds FADhq ~13–times more tightly than SMOB, which supports a vectoral transfer of FADhq from the reductase to the epoxidase. After binding to NSMOA, FADhq rapidly reacts with molecular oxygen to form a stable C(4a)–hydroperoxide intermediate. The half–life of apoSMOB generated in the FAD–transfer reaction is increased ~21–fold, supporting the model of a protein–protein interaction between apoSMOB and NSMOA with the peroxide intermediate. The mechanisms of FAD–dissociation and transport from SMOB to NSMOA were probed by monitoring the competitive reduction of cytochrome c in the presence and absence of pyridine nucleotides. Based on these studies, we propose a model in which reduced FAD binds to SMOB in equilibrium between an unreactive, sequestered state (S–state) and more reactive, transfer state (T–state). Dissociation of NAD+ after the hydride transfer–reaction transiently populates the T–state, promoting the transfer of FADhq to NSMOA. The binding of pyridine nucleotides to SMOB–FADhq shifts the FADhq–binding equilibrium from the T–state to the S–state. Additionally, the 2.2–Å crystal structure of SMOB–FADox reported in this work is discussed in light of the pyridine nucleotide–gated flavin–transfer and electron–transfer reactions. PMID:23909369

Role of intermediate phase for stable cycling of Na7V4(P2O7)4PO4 in sodium ion battery

PubMed Central

Lim, Soo Yeon; Kim, Heejin; Chung, Jaehoon; Lee, Ji Hoon; Kim, Byung Gon; Choi, Jeon-Jin; Chung, Kyung Yoon; Cho, Woosuk; Kim, Seung-Joo; Goddard, William A.; Jung, Yousung; Choi, Jang Wook

2014-01-01

Sodium ion batteries offer promising opportunities in emerging utility grid applications because of the low cost of raw materials, yet low energy density and limited cycle life remain critical drawbacks in their electrochemical operations. Herein, we report a vanadium-based ortho-diphosphate, Na7V4(P2O7)4PO4, or VODP, that significantly reduces all these drawbacks. Indeed, VODP exhibits single-valued voltage plateaus at 3.88 V vs. Na/Na+ while retaining substantial capacity (>78%) over 1,000 cycles. Electronic structure calculations reveal that the remarkable single plateau and cycle life originate from an intermediate phase (a very shallow voltage step) that is similar both in the energy level and lattice parameters to those of fully intercalated and deintercalated states. We propose a theoretical scheme in which the reaction barrier that arises from lattice mismatches can be evaluated by using a simple energetic consideration, suggesting that the presence of intermediate phases is beneficial for cell kinetics by buffering the differences in lattice parameters between initial and final phases. We expect these insights into the role of intermediate phases found for VODP hold in general and thus provide a helpful guideline in the further understanding and design of battery materials. PMID:24379365

Interactions of "bora-penicilloates" with serine β-lactamases and DD-peptidases.

PubMed

Dzhekieva, Liudmila; Adediran, S A; Pratt, R F

2014-10-21

Specific boronic acids are generally powerful tetrahedral intermediate/transition state analogue inhibitors of serine amidohydrolases. This group of enzymes includes bacterial β-lactamases and DD-peptidases where there has been considerable development of boronic acid inhibitors. This paper describes the synthesis, determination of the inhibitory activity, and analysis of the results from two α-(2-thiazolidinyl) boronic acids that are closer analogues of particular tetrahedral intermediates involved in β-lactamase and DD-peptidase catalysis than those previously described. One of them, 2-[1-(dihydroxyboranyl)(2-phenylacetamido)methyl]-5,5-dimethyl-1,3-thiazolidine-4-carboxylic acid, is a direct analogue of the deacylation tetrahedral intermediates of these enzymes. These compounds are micromolar inhibitors of class C β-lactamases but, very unexpectedly, not inhibitors of class A β-lactamases. We rationalize the latter result on the basis of a new mechanism of boronic acid inhibition of the class A enzymes. A stable inhibitory complex is not accessible because of the instability of an intermediate on its pathway of formation. The new boronic acids also do not inhibit bacterial DD-peptidases (penicillin-binding proteins). This result strongly supports a central feature of a previously proposed mechanism of action of β-lactam antibiotics, where deacylation of β-lactam-derived acyl-enzymes is not possible because of unfavorable steric interactions.

Role of intermediate phase for stable cycling of Na7V4(P2O7)4PO4 in sodium ion battery.

PubMed

Lim, Soo Yeon; Kim, Heejin; Chung, Jaehoon; Lee, Ji Hoon; Kim, Byung Gon; Choi, Jeon-Jin; Chung, Kyung Yoon; Cho, Woosuk; Kim, Seung-Joo; Goddard, William A; Jung, Yousung; Choi, Jang Wook

2014-01-14

Sodium ion batteries offer promising opportunities in emerging utility grid applications because of the low cost of raw materials, yet low energy density and limited cycle life remain critical drawbacks in their electrochemical operations. Herein, we report a vanadium-based ortho-diphosphate, Na7V4(P2O7)4PO4, or VODP, that significantly reduces all these drawbacks. Indeed, VODP exhibits single-valued voltage plateaus at 3.88 V vs. Na/Na(+) while retaining substantial capacity (>78%) over 1,000 cycles. Electronic structure calculations reveal that the remarkable single plateau and cycle life originate from an intermediate phase (a very shallow voltage step) that is similar both in the energy level and lattice parameters to those of fully intercalated and deintercalated states. We propose a theoretical scheme in which the reaction barrier that arises from lattice mismatches can be evaluated by using a simple energetic consideration, suggesting that the presence of intermediate phases is beneficial for cell kinetics by buffering the differences in lattice parameters between initial and final phases. We expect these insights into the role of intermediate phases found for VODP hold in general and thus provide a helpful guideline in the further understanding and design of battery materials.

Role of clusters in nonclassical nucleation and growth of protein crystals

PubMed Central

Sleutel, Mike; Van Driessche, Alexander E. S.

2014-01-01

The development of multistep nucleation theory has spurred on experimentalists to find intermediate metastable states that are relevant to the solidification pathway of the molecule under interest. A great deal of studies focused on characterizing the so-called “precritical clusters” that may arise in the precipitation process. However, in macromolecular systems, the role that these clusters might play in the nucleation process and in the second stage of the precipitation process, i.e., growth, remains to a great extent unknown. Therefore, using biological macromolecules as a model system, we have studied the mesoscopic intermediate, the solid end state, and the relationship that exists between them. We present experimental evidence that these clusters are liquid-like and stable with respect to the parent liquid and metastable compared with the emerging crystalline phase. The presence of these clusters in the bulk liquid is associated with a nonclassical mechanism of crystal growth and can trigger a self-purifying cascade of impurity-poisoned crystal surfaces. These observations demonstrate that there exists a nontrivial connection between the growth of the macroscopic crystalline phase and the mesoscopic intermediate which should not be ignored. On the other hand, our experimental data also show that clusters existing in protein solutions can significantly increase the nucleation rate and therefore play a relevant role in the nucleation process. PMID:24449867

An Iterative, Bimodular Nonribosomal Peptide Synthetase that Converts Anthranilate and Tryptophan into Tetracyclic Asperlicins

PubMed Central

Gao, Xue; Jiang, Wei; Jiménez-Osés, Gonzalo; Choi, Moon Seok; Houk, Kendall N.; Tang, Yi; Walsh, Christopher T.

2013-01-01

The bimodular 276 kDa nonribosomal peptide synthetase AspA from Aspergillus alliaceus, heterologously expressed in Saccharomyces cerevisiae, converts tryptophan and two molecules of the aromatic β-amino acid anthranilate (Ant) into a pair of tetracyclic peptidyl alkaloids asperlicin C and D in a ratio of 10:1. The first module of AspA activates and processes two molecules of Ant iteratively to generate a tethered Ant-Ant-Trp-S-enzyme intermediate on module two. Release is postulated to involve tandem cyclizations, in which the first step is the macrocyclization of the linear tripeptidyl-S-enzyme, by the terminal condensation (CT) domain to generate the regioisomeric tetracyclic asperlicin scaffolds. Computational analysis of the transannular cyclization of the 11-membered macrocyclic intermediate shows that asperlicin C is the kinetically favored product due to the high stability of a conformation resembling the transition state for cyclization, while asperlicin D is thermodynamically more stable. PMID:23890005

Novel aminobenzyl and imidobenzyl benzenes

NASA Technical Reports Server (NTRS)

Bell, V. L.; Pratt, J. R.; Stump, B. L.

1976-01-01

Compounds are useful as intermediates for several classes of polymers. Amines can function as cross-linking agents for epoxide and urethane polymers, as well as intermediates for synthesis of thermally-stable addition-type polyimides. Imide derivatives can be obtained by reacting amines with certain monoanhydrides containing olefinic unsaturation.

Main Design Principles of the Cold Beam Pipe in the FastRamped Superconducting Accelerator Magnets for Heavy Ion Synchrotron SIS100

NASA Astrophysics Data System (ADS)

Mierau, A.; Schnizer, P.; Fischer, E.; Macavei, J.; Wilfert, S.; Koch, S.; Weiland, T.; Kurnishov, R.; Shcherbakov, P.

SIS100, the world second large scale heavy ion synchrotron using fast ramped superconducting magnets, is to be built at FAIR. Its high current operation of intermediate charge state ions requires stable vacuum pressures < 10-12 mbar under dynamic machine conditions which are only achievable when the whole beam pipe is used as an huge cryopump. In order to find technological feasible design solutions, three opposite requirements have to be met: minimum magnetic field distortion caused by AC losses, mechanical stability and low and stable wall temperatures of the beam pipe. We present the possible design versions of the beam pipe for the high current curved dipole. The pros and cons of these proposed designs were studied using simplified analytical models, FEM calculations and tests on models.

Time-resolved x-ray diffraction and calorimetric studies at low scan rates

PubMed Central

Yao, Haruhiko; Hatta, Ichiro; Koynova, Rumiana; Tenchov, Boris

1992-01-01

The phase transitions of dipalmitoylphosphatidylethanolamine (DPPE) in excess water have been examined by low-angle time-resolved x-ray diffraction and calorimetry at low scan rates. The lamellar subgel/lamellar liquid-crystalline (Lc → Lα), lamellar gel/lamellar liquid-crystalline (Lβ → Lα), and lamellar liquid-crystalline/lamellar gel (Lα → Lβ) phase transitions proceed via coexistence of the initial and final phases with no detectable intermediates at scan rates 0.1 and 0.5°C/min. At constant temperature within the region of the Lβ → Lα transition the ratio of the two coexisting phases was found to be stable for over 30 min. The state of stable phase coexistence was preceded by a 150-s relaxation taking place at constant temperature after termination of the heating scan in the transition region. While no intermediate structures were present in the coexistence region, a well reproducible multipeak pattern, with at least four prominent heat capacity peaks separated in temperature by 0.4-0.5°C, has been observed in the cooling transition (Lα → Lβ) by calorimetry. The multipeak pattern became distinct with an increase of incubation time in the liquid-crystalline phase. It was also clearly resolved in the x-ray diffraction intensity versus temperature plots recorded at slow cooling rates. These data suggest that the equilibrium state of the Lα phase of hydrated DPPE is represented by a mixture of domains that differ in thermal behavior, but cannot be distinguished structurally by x-ray scattering. Imagesp689-aFIGURE 9 PMID:19431820

Folding Free Energy Landscape of the Decapeptide Chignolin

NASA Astrophysics Data System (ADS)

Dou, Xianghua; Wang, Jihua

Chignolin is an artificially designed ten-residue (GYDPETGTWG) folded peptide, which is the smallest protein and provides a good template for protein folding. In this work, we completed four explicit water molecular dynamics simulations of Chignolin folding using GROMOS and OPLS-AA force fields from extended initial states without any experiment informations. The four-folding free energy landscapes of the peptide has been drawn. The folded state of Chignolin has been successfully predicated based on the free energy landscapes. The four independent simulations gave similar results. (i) The four free energy landscapes have common characters. They are fairly smooth, barrierless, funnel-like and downhill without intermediate state, which consists with the experiment. (ii) The different extended initial structures converge at similar folded structures with the lowest free energy under GROMOS and OPLS-AA force fields. In the GROMOS force field, the backbone RMSD of the folded structures from the NMR native structure of Chignolin is only 0.114 nm, which is a stable structure in this force field. In the OPLS-AA force field, the similar results have been obtained. In addition, the smallest RMSD structure is in better agreement with the NMR native structure but unlikely stable in the force field.

cis-β-Bromostyrene derivatives from cinnamic acids via a tandem substitutive bromination-decarboxylation sequence.

PubMed

Tang, Khanh G; Kent, Greggory T; Erden, Ihsan; Wu, Weiming

2017-10-04

cis -β-Bromostyrene derivatives were synthesized stereospecifically from cinnamic acids through β-lactone intermediates. The synthetic sequence did not require the purification of the β-lactone intermediates although they were found to be stable and readily purified in most cases.

ESIPT and photodissociation of 3-hydroxychromone in solution: photoinduced processes studied by static and time-resolved UV/Vis, fluorescence, and IR spectroscopy.

PubMed

Chevalier, Katharina; Grün, Anneken; Stamm, Anke; Schmitt, Yvonne; Gerhards, Markus; Diller, Rolf

2013-11-07

The spectral properties of fluorescence sensors such as 3-hydroxychromone (3-HC) and its derivatives are sensitive to interaction with the surrounding medium as well as to substitution. 3-HC is a prototype system for other derivatives because it is the basic unit of all flavonoides undergoing ESIPT and is not perturbed by a substituent. In this study, the elementary processes and intermediate states in the photocycle of 3-HC as well as its anion were identified and characterized by the use of static and femtosecond time-resolved spectroscopy in different solvents (methylcyclohexane, acetonitrile, ethanol, and water at different pH). Electronic absorption and fluorescence spectra and lifetimes of the intermediate states were obtained for the normal, tautomer and anionic excited state, while mid-IR vibrational spectra yielded structural information on ground and excited states of 3-HC. A high sensitivity on hydrogen-bonding perturbations was observed, leading to photoinduced anion formation in water, while in organic solvents, different processes are suggested, including slow picosecond ESIPT and contribution of the trans-structure excited state or a different stable solvation state with different direction of OH. The formation of the latter could be favored by the lack of a substituent increasing contact points for specific solute-solvent interactions at the hydroxyl group compared to substituted derivatives. The effect of substituents has to be considered for the design of future fluorescence sensors based on 3-HC.

Tree cover in sub-Saharan Africa: rainfall and fire constrain forest and savanna as alternative stable states.

PubMed

Staver, A Carla; Archibald, Sally; Levin, Simon

2011-05-01

Savannas are known as ecosystems with tree cover below climate-defined equilibrium values. However, a predictive framework for understanding constraints on tree cover is lacking. We present (a) a spatially extensive analysis of tree cover and fire distribution in sub-Saharan Africa, and (b) a model, based on empirical results, demonstrating that savanna and forest may be alternative stable states in parts of Africa, with implications for understanding savanna distributions. Tree cover does not increase continuously with rainfall, but rather is constrained to low (<50%, "savanna") or high tree cover (>75%, "forest"). Intermediate tree cover rarely occurs. Fire, which prevents trees from establishing, differentiates high and low tree cover, especially in areas with rainfall between 1000 mm and 2000 mm. Fire is less important at low rainfall (<1000 mm), where rainfall limits tree cover, and at high rainfall (>2000 mm), where fire is rare. This pattern suggests that complex interactions between climate and disturbance produce emergent alternative states in tree cover. The relationship between tree cover and fire was incorporated into a dynamic model including grass, savanna tree saplings, and savanna trees. Only recruitment from sapling to adult tree varied depending on the amount of grass in the system. Based on our empirical analysis and previous work, fires spread only at tree cover of 40% or less, producing a sigmoidal fire probability distribution as a function of grass cover and therefore a sigmoidal sapling to tree recruitment function. This model demonstrates that, given relatively conservative and empirically supported assumptions about the establishment of trees in savannas, alternative stable states for the same set of environmental conditions (i.e., model parameters) are possible via a fire feedback mechanism. Integrating alternative stable state dynamics into models of biome distributions could improve our ability to predict changes in biome distributions and in carbon storage under climate and global change scenarios.

Evidence for a Stable Intermediate in Leukemia Virus Activation in AKR Mouse Embryo Cells

PubMed Central

Ihle, James N.; Kenney, Francis T.; Tennant, Raymond W.

1974-01-01

Analysis of the requirement for serum in the activation of the endogenous leukemia virus expression in AKR mouse embryo cells by 5-iododeoxyuridine shows that activation can be dissociated into two discrete serum-dependent events. The first involves incorporation of 5-iododeoxyuridine into DNA and results in the formation of a stable “activation intermediate” resembling the provirus formed during infection of stationary mouse embryo cells with exogenous leukemia virus. The second event, resulting in expression of the activation intermediate as synthesis of virus proteins, requires DNA replication but not 5-iododeoxyuridine. PMID:4604455

An animated landscape representation of CD4+ T-cell differentiation, variability, and plasticity: Insights into the behavior of populations versus cells

PubMed Central

Rebhahn, Jonathan A; Deng, Nan; Sharma, Gaurav; Livingstone, Alexandra M; Huang, Sui; Mosmann, Tim R

2014-01-01

Recent advances in understanding CD4+ T-cell differentiation suggest that previous models of a few distinct, stable effector phenotypes were too simplistic. Although several well-characterized phenotypes are still recognized, some states display plasticity, and intermediate phenotypes exist. As a framework for reexamining these concepts, we use Waddington's landscape paradigm, augmented with explicit consideration of stochastic variations. Our animation program “LAVA” visualizes T-cell differentiation as cells moving across a landscape of hills and valleys, leading to attractor basins representing stable or semistable differentiation states. The model illustrates several principles, including: (i) cell populations may behave more predictably than individual cells; (ii) analogous to reticulate evolution, differentiation may proceed through a network of interconnected states, rather than a single well-defined pathway; (iii) relatively minor changes in the barriers between attractor basins can change the stability or plasticity of a population; (iv) intrapopulation variability of gene expression may be an important regulator of differentiation, rather than inconsequential noise; (v) the behavior of some populations may be defined mainly by the behavior of outlier cells. While not a quantitative representation of actual differentiation, our model is intended to provoke discussion of T-cell differentiation pathways, particularly highlighting a probabilistic view of transitions between states. PMID:24945794

Evaluation of accelerated stability test conditions for medicated chewing gums.

PubMed

Maggi, Lauretta; Conte, Ubaldo; Nhamias, Alain; Grenier, Pascal; Vergnault, Guy

2013-10-01

The overall stability of medicated chewing gums is investigated under different storage conditions. Active substances with different chemical stabilities in solid state are chosen as model drugs. The dosage form is a three layer tablet obtained by direct compression. The gum core contains the active ingredient while the external layers are formulated to prevent gum adhesion to the punches of the tableting machine. Two accelerated test conditions (40°C/75% RH and 30°C/65% RH) are performed for 6 months. Furthermore, a long-term stability test at room conditions is conducted to verify the predictability of the results obtained from the stress tests. Some drugs are stable in all the conditions tested, but other drugs, generally considered stable in solid dosage forms, have shown relevant stability problems particularly when stress test conditions are applied to this particular semi-solid dosage forms. For less stable drugs, the stress conditions of 40°C/75% RH are not always predictable of chewing gum stability at room temperature and may produce false negative; intermediate conditions, 30°C/65% RH, are more predictive for this purpose, the results of drug content found after 6 months at intermediate stress conditions and 12 months at room conditions are generally comparable. But the results obtained show that only long-term conditions stability tests gave consistent results. During aging, the semi solid nature of the gum base itself, may also influence the drug delivery rate during chewing and great attention should be given also to the dissolution stability.

Structural basis of urea-induced unfolding: Unraveling the folding pathway of hemochromatosis factor E.

PubMed

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

2016-10-01

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

Mitochondrial genomes and avian phylogeny: complex characters and resolvability without explosive radiations.

PubMed

Gibb, Gillian C; Kardailsky, Olga; Kimball, Rebecca T; Braun, Edward L; Penny, David

2007-01-01

We improve the taxon sampling for avian phylogeny by analyzing 7 new mitochondrial genomes (a toucan, woodpecker, osprey, forest falcon, American kestrel, heron, and a pelican). This improves inference of the avian tree, and it supports 3 major conclusions. The first is that some birds (including a parrot, a toucan, and an osprey) exhibit a complete duplication of the control region (CR) meaning that there are at least 4 distinct gene orders within birds. However, it appears that there are regions of continued gene conversion between the duplicate CRs, resulting in duplications that can be stable for long evolutionary periods. Because of this stable duplicated state, gene order can eventually either revert to the original order or change to the new gene order. The existence of this stable duplicate state explains how an apparently unlikely event (finding the same novel gene order) can arise multiple times. Although rare genomic changes have theoretical advantages for tree reconstruction, they can be compromised if these apparently rare events have a stable intermediate state. Secondly, the toucan and woodpecker improve the resolution of the 6-way split within Neoaves that has been called an "explosive radiation." An explosive radiation implies that normal microevolutionary events are insufficient to explain the observed macroevolution. By showing the avian tree is, in principle, resolvable, we demonstrate that the radiation of birds is amenable to standard evolutionary analysis. Thirdly, and as expected from theory, additional taxa breaking up long branches stabilize the position of some problematic taxa (like the falcon). In addition, we report that within the birds of prey and allies, we did not find evidence pairing New World vultures with storks or accipitrids (hawks, eagles, and osprey) with Falconids.

Glutamate Induced Thermal Equilibrium Intermediate and Counteracting Effect on Chemical Denaturation of Proteins.

PubMed

Anumalla, Bramhini; Prabhu, N Prakash

2018-01-25

When organisms are subjected to stress conditions, one of their adaptive responses is accumulation of small organic molecules called osmolytes. These osmolytes affect the structure and stability of the biological macromolecules including proteins. The present study examines the effect of a negatively charged amino acid osmolyte, glutamate (Glu), on two model proteins, ribonuclease A (RNase A) and α-lactalbumin (α-LA), which have positive and negative surface charges at pH 7, respectively. These proteins follow two-state unfolding transitions during both heat and chemical induced denaturation processes. The addition of Glu stabilizes the proteins against temperature and induces an early equilibrium intermediate during unfolding. The stability is found to be enthalpy-driven, and the free energy of stabilization is more for α-LA compared to RNase A. The decrease in the partial molar volume and compressibility of both of the proteins in the presence of Glu suggests that the proteins attain a more compact state through surface hydration which could provide a more stable conformation. This is also supported by molecule dynamic simulation studies which demonstrate that the water density around the proteins is increased upon the addition of Glu. Further, the intermediates could be completely destabilized by lower concentrations (∼0.5 M) of guanidinium chloride and salt. However, urea subverts the Glu-induced intermediate formed by α-LA, whereas it only slightly destabilizes in the case of RNase A which has a positive surface charge and could possess charge-charge interactions with Glu. This suggests that, apart from hydration, columbic interactions might also contribute to the stability of the intermediate. Gdm-induced denaturation of RNase A and α-LA in the absence and the presence of Glu at different temperatures was carried out. These results also show the Glu-induced stabilization of both of the proteins; however, all of the unfolding transitions followed two-state transitions during chemical denaturation. The extent of stability exerted by Glu is higher for RNase A at higher temperature, whereas it provides more stability for α-LA at lower temperature. Thus, the experiments indicate that Glu induces a thermal equilibrium intermediate and increases the thermodynamic stability of proteins irrespective of their surface charges. The extent of stability varies between the proteins in a temperature-dependent manner.

Use of 2,5-dimethyl-2,5-hexane diamine as a curing agent for epoxy resins

DOEpatents

Rinde, J.A.; Newey, H.A.

1981-02-24

Primary diamines are disclosed of the formula shown in a diagram wherein R is a straight chain saturated hydrocarbon of 2 to 4 carbons, a disubstituted benzene ring, or disubstituted dibenzomethane for use as a curing agent for epoxy resins. These curing agents can be used to form epoxy resin mixtures useful in filament winding and pre-impregnated fiber molding and in formulating film adhesives, powder coatings and molding powders. The epoxy mixtures form for such uses as room temperature non-reacting, intermediate stable state which has a latent cross-linking capability.

Use of 2,5-dimethyl-2,5-hexane diamine as a curing agent for epoxy resins

DOEpatents

Rinde, James A. [Livermore, CA; Newey, Herbert A. [Lafayette, CA

1981-02-24

Primary diamines of the formula ##STR1## wherein R is a straight chain saturated hydrocarbon of 2 to 4 carbons, a disubstituted benzene ring, or disubstituted dibenzo methane for use as a curing agent for epoxy resins. These curing agents can be used to form epoxy resin mixtures useful in filament winding and pre-impregnated fiber molding and in formulating film adhesives, powder coatings and molding powders. The epoxy mixtures form for such uses as room temperature non-reacting, intermediate stable state which has a latent cross-linking capability.

The Role of High-Dimensional Diffusive Search, Stabilization, and Frustration in Protein Folding

PubMed Central

Rimratchada, Supreecha; McLeish, Tom C.B.; Radford, Sheena E.; Paci, Emanuele

2014-01-01

Proteins are polymeric molecules with many degrees of conformational freedom whose internal energetic interactions are typically screened to small distances. Therefore, in the high-dimensional conformation space of a protein, the energy landscape is locally relatively flat, in contrast to low-dimensional representations, where, because of the induced entropic contribution to the full free energy, it appears funnel-like. Proteins explore the conformation space by searching these flat subspaces to find a narrow energetic alley that we call a hypergutter and then explore the next, lower-dimensional, subspace. Such a framework provides an effective representation of the energy landscape and folding kinetics that does justice to the essential characteristic of high-dimensionality of the search-space. It also illuminates the important role of nonnative interactions in defining folding pathways. This principle is here illustrated using a coarse-grained model of a family of three-helix bundle proteins whose conformations, once secondary structure has formed, can be defined by six rotational degrees of freedom. Two folding mechanisms are possible, one of which involves an intermediate. The stabilization of intermediate subspaces (or states in low-dimensional projection) in protein folding can either speed up or slow down the folding rate depending on the amount of native and nonnative contacts made in those subspaces. The folding rate increases due to reduced-dimension pathways arising from the mere presence of intermediate states, but decreases if the contacts in the intermediate are very stable and introduce sizeable topological or energetic frustration that needs to be overcome. Remarkably, the hypergutter framework, although depending on just a few physically meaningful parameters, can reproduce all the types of experimentally observed curvature in chevron plots for realizations of this fold. PMID:24739172

State transitions of actin cortices in vitro and in vivo

NASA Astrophysics Data System (ADS)

Tan, Tzer Han; Keren, Kinneret; Mackintosh, Fred; Schmidt, Christoph; Fakhri, Nikta

Most animal cells are enveloped by a thin layer of actin cortex which governs the cell mechanics. A functional cortex must be rigid to provide mechanical support while being flexible to allow for rapid restructuring events such as cell division. To satisfy these requirements, the actin cortex is highly dynamic with fast actin turnover and myosin-driven contractility. The regulatory mechanism responsible for the transition between a mechanically stable state and a restructuring state is not well understood. Here, we develop a technique to map the dynamics of reconstituted actin cortices in emulsion droplets using IR fluorescent single-walled carbon nanotubes (SWNTs). By increasing crosslinker concentration, we find that a homogeneous cortex transitions to an intermediate state with broken rotational symmetry and a globally contractile state which further breaks translational symmetry. We apply this new dynamic mapping technique to cortices of live starfish oocytes in various developmental stages. To identify the regulatory mechanism for steady state transitions, we subject the oocytes to actin and myosin disrupting drugs.

Role of Tryptophan Side Chain Dynamics on the Trp-Cage Mini-Protein Folding Studied by Molecular Dynamics Simulations

PubMed Central

Kannan, Srinivasaraghavan; Zacharias, Martin

2014-01-01

The 20 residue Trp-cage mini-protein is one of smallest proteins that adopt a stable folded structure containing also well-defined secondary structure elements. The hydrophobic core is arranged around a single central Trp residue. Despite several experimental and simulation studies the detailed folding mechanism of the Trp-cage protein is still not completely understood. Starting from fully extended as well as from partially folded Trp-cage structures a series of molecular dynamics simulations in explicit solvent and using four different force fields was performed. All simulations resulted in rapid collapse of the protein to on average relatively compact states. The simulations indicate a significant dependence of the speed of folding to near-native states on the side chain rotamer state of the central Trp residue. Whereas the majority of intermediate start structures with the central Trp side chain in a near-native rotameric state folded successfully within less than 100 ns only a fraction of start structures reached near-native folded states with an initially non-native Trp side chain rotamer state. Weak restraining of the Trp side chain dihedral angles to the state in the folded protein resulted in significant acceleration of the folding both starting from fully extended or intermediate conformations. The results indicate that the side chain conformation of the central Trp residue can create a significant barrier for controlling transitions to a near native folded structure. Similar mechanisms might be of importance for the folding of other protein structures. PMID:24563686

The acceleration rate of cosmic rays at cosmic ray modified shocks

NASA Astrophysics Data System (ADS)

Saito, Tatsuhiko; Hoshino, Masahiro; Amano, Takanobu

It is a still controversial matter whether the production efficiency of cosmic rays (CRs) is relatively efficient or inefficient (e.g. Helder et al. 2009; Hughes et al. 2000; Fukui 2013). In upstream region of SNR shocks (the interstellar medium), the energy density of CRs is comparable to a substantial fraction of that of the thermal plasma (e.g. Ferriere 2001). In such a situation, CRs can possibly exert a back-reaction to the shocks and modify the global shock structure. These shocks are called cosmic ray modified shocks (CRMSs). In CRMSs, as a result of the nonlinear feedback, there are almost always up to three steady-state solutions for given upstream parameters, which are characterized by CR production efficiencies (efficient, intermediate and inefficient branch). We evaluate qualitatively the efficiency of the CR production in SNR shocks by considering the stability of CRMS, under the effects of i) magnetic fields and ii) injection, which play significant roles in efficiency of acceleration. By adopting two-fluid model (Drury & Voelk, 1981), we investigate the stability of CRMSs by means of time-dependent numerical simulations. As a result, we show explicitly the bi-stable feature of these multiple solutions, i.e., the efficient and inefficient branches are stable and the intermediate branch is unstable, and the intermediate branch transit to the inefficient one. This feature is independent of the effects of i) shock angles and ii) injection. Furthermore, we investigate the evolution from a hydrodynamic shock to CRMS in a self-consistent manner. From the results, we suggest qualitatively that the CR production efficiency at SNR shocks may be the least efficient.

Investigation of Unexpected Reaction Intermediates in the Alkaline Hydrolysis of Methyl 3,5-Dinitrobenzoate

ERIC Educational Resources Information Center

Silva, Clesia C.; Silva, Ricardo O.; Navarro, Daniela M. A. F.; Navarro, Marcelo

2009-01-01

An experimental project aimed at identifying stable reaction intermediates is described. Initially, the studied reaction appears to involve the simple hydrolysis, by aqueous sodium hydroxide, of methyl 3,5-dinitrobenzoate dissolved in dimethyl sulfoxide. On mixing the substrates, however, the reaction mixture unexpectedly turns an intense red in…

Relative stability of radicals derived from artemisinin: A semiempirical and DFT study

NASA Astrophysics Data System (ADS)

Arantes, C.; de Araujo, M. T.; Taranto, A. G.; de M. Carneiro, J. W.

The semiempirical AM1 and PM3 methods, as well as the density functional (DFT/B3LYP) approach using the 6-31g(d) basis set, were employed to calculate the relative stability of intermediate radicals derived from artemisinin, a sesquiterpene lactone having an endoperoxide bridge that is essential for its antimalarial activity. The compounds studied have their nonperoxidic oxygen atom of the trioxane ring and/or the carbonyl group replaced by a CH2 unit. Relative stabilities were calculated by means of isodesmic equations using artemisinin as reference. It was found that replacement of oxygen atoms decreases the relative stability of the anionic radical intermediates. In contrast, for compounds with inverted stereochemistry the intermediate radicals were found to be more stable than those with the artemisinin-like stereochemistry. These relative stabilities may modulate the antimalarial potency. Radicals centered on carbon are always more stable than the corresponding radicals centered on oxygen.

Expected distributions of root-mean-square positional deviations in proteins.

PubMed

Pitera, Jed W

2014-06-19

The atom positional root-mean-square deviation (RMSD) is a standard tool for comparing the similarity of two molecular structures. It is used to characterize the quality of biomolecular simulations, to cluster conformations, and as a reaction coordinate for conformational changes. This work presents an approximate analytic form for the expected distribution of RMSD values for a protein or polymer fluctuating about a stable native structure. The mean and maximum of the expected distribution are independent of chain length for long chains and linearly proportional to the average atom positional root-mean-square fluctuations (RMSF). To approximate the RMSD distribution for random-coil or unfolded ensembles, numerical distributions of RMSD were generated for ensembles of self-avoiding and non-self-avoiding random walks. In both cases, for all reference structures tested for chains more than three monomers long, the distributions have a maximum distant from the origin with a power-law dependence on chain length. The purely entropic nature of this result implies that care must be taken when interpreting stable high-RMSD regions of the free-energy landscape as "intermediates" or well-defined stable states.

Insights into reaction mechanisms in heterogeneous catalysis revealed by in situ NMR spectroscopy.

PubMed

Blasco, Teresa

2010-12-01

This tutorial review intends to show the possibilities of in situ solid state NMR spectroscopy in the elucidation of reaction mechanisms and the nature of the active sites in heterogeneous catalysis. After a brief overview of the more usual experimental devices used for in situ solid state NMR spectroscopy measurements, some examples of applications taken from the recent literature will be presented. It will be shown that in situ NMR spectroscopy allows: (i) the identification of stable intermediates and transient species using indirect methods, (ii) to prove shape selectivity in zeolites, (iii) the study of reaction kinetics, and (iv) the determination of the nature and the role played by the active sites in a catalytic reaction. The approaches and methodology used to get this information will be illustrated here summarizing the most relevant contributions on the investigation of the mechanisms of a series of reactions of industrial interest: aromatization of alkanes on bifunctional catalysts, carbonylation reaction of methanol with carbon monoxide, ethylbenzene disproportionation, and the Beckmann rearrangement reaction. Special attention is paid to the research carried out on the role played by carbenium ions and alkoxy as intermediate species in the transformation of hydrocarbon molecules on solid acid catalysts.

Unexpected tautomeric equilibria of the carbanion-enamine intermediate in pyruvate oxidase highlight unrecognized chemical versatility of thiamin

PubMed Central

Meyer, Danilo; Neumann, Piotr; Koers, Eline; Sjuts, Hanno; Lüdtke, Stefan; Sheldrick, George M.; Ficner, Ralf; Tittmann, Kai

2012-01-01

Thiamin diphosphate, the vitamin B1 coenzyme, plays critical roles in fundamental metabolic pathways that require acyl carbanion equivalents. Studies on chemical models and enzymes had suggested that these carbanions are resonance-stabilized as enamines. A crystal structure of this intermediate in pyruvate oxidase at 1.1 Å resolution now challenges this paradigm by revealing that the enamine does not accumulate. Instead, the intermediate samples between the ketone and the carbanion both interlocked in a tautomeric equilibrium. Formation of the keto tautomer is associated with a loss of aromaticity of the cofactor. The alternate confinement of electrons to neighboring atoms rather than π-conjugation seems to be of importance for the enzyme-catalyzed, redox-coupled acyl transfer to phosphate, which requires a dramatic inversion of polarity of the reacting substrate carbon in two subsequent catalytic steps. The ability to oscillate between a nucleophilic (carbanion) and an electrophilic (ketone) substrate center highlights a hitherto unrecognized versatility of the thiamin cofactor. It remains to be studied whether formation of the keto tautomer is a general feature of all thiamin enzymes, as it could provide for stable storage of the carbanion state, or whether this feature represents a specific trait of thiamin oxidases. In addition, the protonation state of the two-electron reduced flavin cofactor can be fully assigned, demonstrating the power of high-resolution cryocrystallography for elucidation of enzymatic mechanisms. PMID:22730460

Reshaping the folding energy landscape of human carbonic anhydrase II by a single point genetic mutation Pro237His.

PubMed

Jiang, Yan; Su, Jing-Tan; Zhang, Jun; Wei, Xiang; Yan, Yong-Bin; Zhou, Hai-Meng

2008-01-01

Human carbonic anhydrase (HCA) II participates in a variety of important biological processes, and it has long been known that genetic mutations of HCA II are closely correlated to human disease. In this research, we investigated the effects of a genetic single point mutation P237, which is located on the surface of the molecule and does not participate in the HCA II catalysis, on HCA II activity, stability and folding. Spectroscopic studies revealed that the mutation caused more buried Trp residues to become accessible by solvent and caused the NMR signals to become less dispersed, but did not affect the secondary structure or the hydrophobic exposure of the protein. The mutant was less stable than the wild type enzyme against heat- and GdnHCl-induced inactivation, but its pH adaptation was similar to the wild type. The mutation slightly decreased the stability of the molten globular intermediate, but gradually affected the stability of the native state by a 10-fold reduction of the Gibbs free energy for the transition from the native state to the intermediate. This might have led to an accumulation of the aggregation-prone molten globular intermediate, which further trapped the proteins into the off-pathway aggregates during refolding and reduced the levels of active enzyme in vivo. The results herein suggested that the correct positioning of the long loop around P237 might be crucial to the folding of HCA II, particularly the formation of the active site.

Electronic and magnetic properties of RMnO3/AMnO3 heterostructures

NASA Astrophysics Data System (ADS)

Yu, Rong; Yunoki, Seiji; Dong, Shuai; Dagotto, Elbio

2009-09-01

The ground-state properties of RMnO3/AMnO3 (RMO/AMO) heterostructures (with R=La,Pr,… , a trivalent rare-earth cation and A=Sr,Ca,… , a divalent alkaline cation) are studied using a two-orbital double-exchange model including the superexchange coupling and Jahn-Teller lattice distortions. To describe the charge transfer across the interface, the long-range Coulomb interaction is taken into account at the mean-field level, by self-consistently solving the Poisson’s equation. The calculations are carried out numerically on finite clusters. We find that the state stabilized near the interface of the heterostructure is similar to the state of the bulk compound (R,A)MO at electronic density close to 0.5. For instance, a charge and orbitally ordered CE state is found at the interface if the corresponding bulk (R,A)MO material is a narrow-to-intermediate bandwidth manganite. But instead the interface regime accommodates an A-type antiferromagnetic state with a uniform x2-y2 orbital order, if the bulk (R,A)MO corresponds to a wide bandwidth manganite. We argue that these results explain some of the properties of long-period (RMO)m/(AMO)n superlattices, such as (PrMnO3)m/(CaMnO3)n and (LaMnO3)m/(SrMnO3)n . We also remark that the intermediate states in between the actual interface and the bulklike regimes of the heterostructure are dependent on the bandwidth and the screening of the Coulomb interaction. In these regions of the heterostructures, states are found that do not have an analog in experimentally known bulk phase diagrams. These new states of the heterostructures provide a natural interpolation between magnetically ordered states that are stable in the bulk at different electronic densities.

A Free Energy Barrier Caused by the Refolding of an Oligomeric Intermediate Controls the Lag Time of Amyloid Formation by hIAPP.

PubMed

Serrano, Arnaldo L; Lomont, Justin P; Tu, Ling-Hsien; Raleigh, Daniel P; Zanni, Martin T

2017-11-22

Transiently populated oligomers formed en route to amyloid fibrils may constitute the most toxic aggregates associated with many amyloid-associated diseases. Most nucleation theories used to describe amyloid aggregation predict low oligomer concentrations and do not take into account free energy costs that may be associated with structural rearrangements between the oligomer and fiber states. We have used isotope labeling and two-dimensional infrared spectroscopy to spectrally resolve an oligomeric intermediate during the aggregation of the human islet amyloid protein (hIAPP or amylin), the protein associated with type II diabetes. A structural rearrangement includes the F 23 G 24 A 25 I 26 L 27 region of hIAPP, which starts from a random coil structure, evolves into ordered β-sheet oligomers containing at least 5 strands, and then partially disorders in the fibril structure. The supercritical concentration is measured to be between 150 and 250 μM, which is the thermodynamic parameter that sets the free energy of the oligomers. A 3-state kinetic model fits the experimental data, but only if it includes a concentration independent free energy barrier >3 kcal/mol that represents the free energy cost of refolding the oligomeric intermediate into the structure of the amyloid fibril; i.e., "oligomer activation" is required. The barrier creates a transition state in the free energy landscape that slows fibril formation and creates a stable population of oligomers during the lag phase, even at concentrations below the supercritical concentration. Largely missing in current kinetic models is a link between structure and kinetics. Our experiments and modeling provide evidence that protein structural rearrangements during aggregation impact the populations and kinetics of toxic oligomeric species.

Stable isotopes of carbon and nitrogen in the study of avian and mammalian trophic ecology

Treesearch

Jeffrey F. Kelly

2000-01-01

Differential fractionation of stable isotopes of carbon during photosynthesis causes C4 plants and C3 plants to have distinct carbon-isotope signatures. In addition, marine C3 plants have stable-isotope ratios of carbon that are intermediate between C4 and terrestrial C3 plants. The direct incorporation of the carbon-isotope ratio (13C/12C) of plants into consumers...

Molecular and Silica-Supported Molybdenum Alkyne Metathesis Catalysts: Influence of Electronics and Dynamics on Activity Revealed by Kinetics, Solid-State NMR, and Chemical Shift Analysis.

PubMed

Estes, Deven P; Gordon, Christopher P; Fedorov, Alexey; Liao, Wei-Chih; Ehrhorn, Henrike; Bittner, Celine; Zier, Manuel Luca; Bockfeld, Dirk; Chan, Ka Wing; Eisenstein, Odile; Raynaud, Christophe; Tamm, Matthias; Copéret, Christophe

2017-12-06

Molybdenum-based molecular alkylidyne complexes of the type [MesC≡Mo{OC(CH 3 ) 3-x (CF 3 ) x } 3 ] (MoF 0 , x = 0; MoF 3 , x = 1; MoF 6 , x = 2; MoF 9 , x = 3; Mes = 2,4,6-trimethylphenyl) and their silica-supported analogues are prepared and characterized at the molecular level, in particular by solid-state NMR, and their alkyne metathesis catalytic activity is evaluated. The 13 C NMR chemical shift of the alkylidyne carbon increases with increasing number of fluorine atoms on the alkoxide ligands for both molecular and supported catalysts but with more shielded values for the supported complexes. The activity of these catalysts increases in the order MoF 0 < MoF 3 < MoF 6 before sharply decreasing for MoF 9 , with a similar effect for the supported systems (MoF 0 ≈ MoF 9 < MoF 6 < MoF 3 ). This is consistent with the different kinetic behavior (zeroth order in alkyne for MoF 9 derivatives instead of first order for the others) and the isolation of stable metallacyclobutadiene intermediates of MoF 9 for both molecular and supported species. Detailed solid-state NMR analysis of molecular and silica-supported metal alkylidyne catalysts coupled with DFT/ZORA calculations rationalize the NMR spectroscopic signatures and discernible activity trends at the frontier orbital level: (1) increasing the number of fluorine atoms lowers the energy of the π*(M≡C) orbital, explaining the more deshielded chemical shift values; it also leads to an increased electrophilicity and higher reactivity for catalysts up to MoF 6 , prior to a sharp decrease in reactivity for MoF 9 due to the formation of stable metallacyclobutadiene intermediates; (2) the silica-supported catalysts are less active than their molecular analogues because they are less electrophilic and dynamic, as revealed by their 13 C NMR chemical shift tensors.

Diffractive intermediate layer enables broadband light trapping for high efficiency ultrathin c-Si tandem cells

NASA Astrophysics Data System (ADS)

Li, Guijun; Ho, Jacob Y. L.; Li, He; Kwok, Hoi-Sing

2014-06-01

Light management through the intermediate reflector in the tandem cell configuration is of great practical importance for achieving high stable efficiency and also low cost production. So far, however, the intermediate reflectors employed currently are mainly focused on the light absorption enhancement of the top cell. Here, we present a diffractive intermediate layer that allows for light trapping over a broadband wavelength for the ultrathin c-Si tandem solar cell. Compared with the standard intermediate reflector, this nanoscale architectural intermediate layer results in a 35% and 21% remarkable enhancement of the light absorption in the top (400-800 nm) and bottom (800-1100 nm) cells simultaneously, and ultrathin c-Si tandem cells with impressive conversion efficiency of 13.3% are made on the glass substrate.

Theoretical investigation on the chemoselective N-heterocyclic carbene-catalyzed cross-benzoin reactions.

PubMed

Liu, Tao; Han, Shu-Min; Han, Ling-Li; Wang, Lu; Cui, Xiang-Yang; Du, Chong-Yang; Bi, Siwei

2015-03-28

A density functional theory study was performed to understand the detailed mechanisms of the cross-benzoin reactions catalyzed by N-heterocyclic carbene (NHC) species. Our theoretical study predicted that the first H-transfer operates with water in solution as a mediator, and the second H-transfer undergoes a concerted mechanism rather than a stepwise one. In addition, the chemoselectivity of the reactions studied in this work has been explored. P1 was obtained as a major product mainly due to the more stable intermediate formed by reaction of NHC with reactant R1. Different steric effects resulting from the fused six-membered ring in transition state TS7 and the fused five-membered ring in transition state TS13 are the origin leading to the chemoselectivity.

Crystal nucleation and metastable bcc phase in charged colloids: A molecular dynamics study

NASA Astrophysics Data System (ADS)

Ji, Xinqiang; Sun, Zhiwei; Ouyang, Wenze; Xu, Shenghua

2018-05-01

The dynamic process of homogenous nucleation in charged colloids is investigated by brute-force molecular dynamics simulation. To check if the liquid-solid transition will pass through metastable bcc, simulations are performed at the state points that definitely lie in the phase region of thermodynamically stable fcc. The simulation results confirm that, in all of these cases, the preordered precursors, acting as the seeds of nucleation, always have predominant bcc symmetry consistent with Ostwald's step rule and the Alexander-McTague mechanism. However, the polymorph selection is not straightforward because the crystal structures formed are not often determined by the symmetry of intermediate precursors but have different characters under different state points. The region of the state point where bcc crystal structures of large enough size are formed during crystallization is narrow, which gives a reasonable explanation as to why the metastable bcc phase in charged colloidal suspensions is rarely detected in macroscopic experiments.

Characterization of Folding Mechanisms of Trp-cage and WW-domain by Network Analysis of Simulations with a Hybrid-resolution Model

PubMed Central

Han, Wei; Schulten, Klaus

2013-01-01

In this study, we apply a hybrid-resolution model, namely PACE, to characterize the free energy surfaces (FESs) of trp-cage and a WW domain variant along with the respective folding mechanisms. Unbiased, independent simulations with PACE are found to achieve together multiple folding and unfolding events for both proteins, allowing us to perform network analysis of the FESs to identify folding pathways. PACE reproduces for both proteins expected complexity hidden in the folding FESs, in particular, meta-stable non-native intermediates. Pathway analysis shows that some of these intermediates are, actually, on-pathway folding intermediates and that intermediates kinetically closest to the native states can be either critical on-pathway or off-pathway intermediates, depending on the protein. Apart from general insights into folding, specific folding mechanisms of the proteins are resolved. We find that trp-cage folds via a dominant pathway in which hydrophobic collapse occurs before the N-terminal helix forms; full incorporation of Trp6 into the hydrophobic core takes place as the last step of folding, which, however, may not be the rate-limiting step. For the WW domain variant studied we observe two main folding pathways with opposite orders of formation of the two hairpins involved in the structure; for either pathway, formation of hairpin 1 is more likely to be the rate-limiting step. Altogether, our results suggest that PACE combined with network analysis is a computationally efficient and valuable tool for the study of protein folding. PMID:23915394

Computational Chemistry-Based Identification of Ultra-Low Temperature Water-Gas-Shift Catalysts

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

Manos Mavrikakis

2008-08-31

The current work seeks to identify novel, catalytically-active, stable, poison-resistant LWGS catalysts that retain the superior activity typical of conventional Cu catalysts but can be operated at similar or lower temperatures. A database for the Binding Energies (BEs) of the LWGS relevant species, namely CO, O and OH on the most-stable, close-packed facets of a set of 17 catalytically relevant transition metals was established. This BE data and a database of previously established segregation energies was utilized to predict the stability of bimetallic NSAs that could be synthesized by combinations of the 17 parent transition metals. NSAs that were potentiallymore » stable both in vacuo and under the influence of strong-binding WGS intermediates were then selected for adsorption studies. A set of 40 NSAs were identified that satisfied all three screener criteria and the binding energies of CO, O and OH were calculated on a set of 66, 43 and 79 NSA candidates respectively. Several NSAs were found that bound intermediates weaker than the monometallic catalysts and were thus potentially poison-resistant. Finally, kinetic studies were performed and resulted in the discovery of a specific NSA-based bimetallic catalyst Cu/Pt that is potentially a promising LWGS catalyst. This stable Cu/Pt subsurface alloy is expected to provide facile H{sub 2}O activation and remain relatively resistant from the poisoning by CO, S and formate intermediates.« less

Conformational properties of glucose-based disaccharides investigated using molecular dynamics simulations with local elevation umbrella sampling.

PubMed

Perić-Hassler, Lovorka; Hansen, Halvor S; Baron, Riccardo; Hünenberger, Philippe H

2010-08-16

Explicit-solvent molecular dynamics (MD) simulations of the 11 glucose-based disaccharides in water at 300K and 1bar are reported. The simulations were carried out with the GROMOS 45A4 force-field and the sampling along the glycosidic dihedral angles phi and psi was artificially enhanced using the local elevation umbrella sampling (LEUS) method. The trajectories are analyzed in terms of free-energy maps, stable and metastable conformational states (relative free energies and estimated transition timescales), intramolecular H-bonds, single molecule configurational entropies, and agreement with experimental data. All disaccharides considered are found to be characterized either by a single stable (overwhelmingly populated) state ((1-->n)-linked disaccharides with n=1, 2, 3, or 4) or by two stable (comparably populated and differing in the third glycosidic dihedral angle omega ; gg or gt) states with a low interconversion barrier ((1-->6)-linked disaccharides). Metastable (anti-phi or anti-psi) states are also identified with relative free energies in the range of 8-22 kJ mol(-1). The 11 compounds can be classified into four families: (i) the alpha(1-->1)alpha-linked disaccharide trehalose (axial-axial linkage) presents no metastable state, the lowest configurational entropy, and no intramolecular H-bonds; (ii) the four alpha(1-->n)-linked disaccharides (n=1, 2, 3, or 4; axial-equatorial linkage) present one metastable (anti-psi) state, an intermediate configurational entropy, and two alternative intramolecular H-bonds; (iii) the four beta(1-->n)-linked disaccharides (n=1, 2, 3, or 4; equatorial-equatorial linkage) present two metastable (anti-phi and anti-psi) states, an intermediate configurational entropy, and one intramolecular H-bond; (iv) the two (1-->6)-linked disaccharides (additional glycosidic dihedral angle) present no (isomaltose) or a pair of (gentiobiose) metastable (anti-phi) states, the highest configurational entropy, and no intramolecular H-bonds. The observed conformational preferences appear to be dictated by four main driving forces (ring conformational preferences, exo-anomeric effect, steric constraints, and possible presence of a third glycosidic dihedral angle), leaving a secondary role to intramolecular H-bonding and specific solvation effects. In spite of the weak conformational driving force attributed to solvent-exposed H-bonds in water (highly polar protic solvent), intramolecular H-bonds may still have a significant influence on the physico-chemical properties of the disaccharide by decreasing its hydrophilicity. Along with previous work, the results also complete the suggestion of a spectrum of approximate transition timescales for carbohydrates up to the disaccharide level, namely: approximately 30 ps (hydroxyl groups), approximately 1 ns (free lactol group, free hydroxymethyl groups, glycosidic dihedral angleomega in (1-->6)-linked disaccharides), approximately 10 ns to 2 micros (ring conformation, glycosidic dihedral angles phi and psi). The calculated average values of the glycosidic torsional angles agree well with the available experimental data, providing validation for the force-field and simulation methodology employed. Copyright 2010 Elsevier Ltd. All rights reserved.

Paramagnetic colloids: Chaotic routes to clusters and molecules

NASA Astrophysics Data System (ADS)

Abdi, Hamed; Soheilian, Rasam; Erb, Randall M.; Maloney, Craig E.

2018-03-01

We present computer simulations and experiments on dilute suspensions of superparamagnetic particles subject to rotating magnetic fields. We focus on chains of four particles and their decay routes to stable structures. At low rates, the chains track the external field. At intermediate rates, the chains break up but perform a periodic (albeit complex) motion. At sufficiently high rates, the chains generally undergo chaotic motion at short times and decay to either closely packed clusters or more dispersed, colloidal molecules at long times. We show that the transition out of the chaotic states can be described as a Poisson process in both simulation and experiment.

Risk, resources and state-dependent adaptive behavioural syndromes

PubMed Central

Luttbeg, Barney; Sih, Andrew

2010-01-01

Many animals exhibit behavioural syndromes—consistent individual differences in behaviour across two or more contexts or situations. Here, we present adaptive, state-dependent mathematical models for analysing issues about behavioural syndromes. We find that asset protection (where individuals with more ‘assets’ tend be more cautious) and starvation avoidance, two state-dependent mechanisms, can explain short-term behavioural consistency, but not long-term stable behavioural types (BTs). These negative-feedback mechanisms tend to produce convergence in state and behaviour over time. In contrast, a positive-feedback mechanism, state-dependent safety (where individuals with higher energy reserves, size, condition or vigour are better at coping with predators), can explain stable differences in personality over the long term. The relative importance of negative- and positive-feedback mechanisms in governing behavioural consistency depends on environmental conditions (predation risk and resource availability). Behavioural syndromes emerge more readily in conditions of intermediate ecological favourability (e.g. medium risk and medium resources, or high risk and resources, or low risk and resources). Under these conditions, individuals with higher initial state maintain a tendency to be bolder than individuals that start with low initial state; i.e. later BT is determined by state during an early ‘developmental window’. In contrast, when conditions are highly favourable (low risk, high resources) or highly unfavourable (high risk, low resources), individuals converge to be all relatively bold or all relatively cautious, respectively. In those circumstances, initial differences in BT are not maintained over the long term, and there is no early developmental window where initial state governs later BT. The exact range of ecological conditions favouring behavioural syndromes depends also on the strength of state-dependent safety. PMID:21078650

Prediction of serious complications in patients with seemingly stable febrile neutropenia: validation of the Clinical Index of Stable Febrile Neutropenia in a prospective cohort of patients from the FINITE study.

PubMed

Carmona-Bayonas, Alberto; Jiménez-Fonseca, Paula; Virizuela Echaburu, Juan; Antonio, Maite; Font, Carme; Biosca, Mercè; Ramchandani, Avinash; Martínez, Jerónimo; Hernando Cubero, Jorge; Espinosa, Javier; Martínez de Castro, Eva; Ghanem, Ismael; Beato, Carmen; Blasco, Ana; Garrido, Marcelo; Bonilla, Yaiza; Mondéjar, Rebeca; Arcusa Lanza, María Ángeles; Aragón Manrique, Isabel; Manzano, Aránzazu; Sevillano, Elena; Castañón, Eduardo; Cardona, Mercé; Gallardo Martín, Elena; Pérez Armillas, Quionia; Sánchez Lasheras, Fernando; Ayala de la Peña, Francisco

2015-02-10

To validate a prognostic score predicting major complications in patients with solid tumors and seemingly stable episodes of febrile neutropenia (FN). The definition of clinical stability implies the absence of organ dysfunction, abnormalities in vital signs, and major infections. We developed the Clinical Index of Stable Febrile Neutropenia (CISNE), with six explanatory variables associated with serious complications: Eastern Cooperative Oncology Group performance status ≥ 2 (2 points), chronic obstructive pulmonary disease (1 point), chronic cardiovascular disease (1 point), mucositis of grade ≥ 2 (National Cancer Institute Common Toxicity Criteria; 1 point), monocytes < 200 per μL (1 point), and stress-induced hyperglycemia (2 points). We integrated these factors into a score ranging from 0 to 8, which classifies patients into three prognostic classes: low (0 points), intermediate (1 to 2 points), and high risk (≥ 3 points). We present a multicenter validation of CISNE. We prospectively recruited 1,133 patients with seemingly stable FN from 25 hospitals. Complication rates in the training and validation subsets, respectively, were 1.1% and 1.1% in low-, 6.1% and 6.2% in intermediate-, and 32.5% and 36% in high-risk patients; mortality rates within each class were 0% in low-, 1.6% and 0% in intermediate-, and 4.3% and 3.1% in high-risk patients. Areas under the receiver operating characteristic curves in the validation subset were 0.652 (95% CI, 0.598 to 0.703) for Talcott, 0.721 (95% CI, 0.669 to 0.768) for Multinational Association for Supportive Care in Cancer (MASCC), and 0.868 (95% CI, 0.827 to 0.903) for CISNE (P = .002 for comparison between CISNE and MASCC). CISNE is a valid model for accurately classifying patients with cancer with seemingly stable FN episodes. © 2015 by American Society of Clinical Oncology.

Theoretical characterization of stable eta1-N2O-, eta2-N2O-, eta1-N2-, and eta2-N2-bound species: intermediates in the addition reactions of nitrogen hydrides with the pentacyanonitrosylferrate(II) ion.

PubMed

Olabe, José A; Estiú, Guillermina L

2003-08-11

The addition of nitrogen hydrides (hydrazine, hydroxylamine, ammonia, azide) to the pentacyanonitrosylferrate(II) ion has been analyzed by means of density functional calculations, focusing on the identification of stable intermediates along the reaction paths. Initial reversible adduct formation and further decomposition lead to the eta(1)- and eta(2)-linkage isomers of N(2)O and N(2), depending on the nucleophile. The intermediates (adducts and gas-releasing precursors) have been characterized at the B3LYP/6-31G level of theory through the calculation of their structural and spectroscopic properties, modeling the solvent by means of a continuous approach. The eta(2)-N(2)O isomer is formed at an initial stage of adduct decompositions with the hydrazine and azide adducts. Further conversion to the eta(1)-N(2)O isomer is followed by Fe-N(2)O dissociation. Only the eta(1)-N(2)O isomer is predicted for the reaction with hydroxylamine, revealing a kinetically controlled N(2)O formation. eta(1)-N(2) and eta(2)-N(2) isomers are also predicted as stable species.

Young driver licensing: examination of population-level rates using New Jersey's state licensing database.

PubMed

Curry, Allison E; Pfeiffer, Melissa R; Durbin, Dennis R; Elliott, Michael R; Kim, Konny H

2015-03-01

Recent surveys have provided insight on the primary reasons why US teens delay licensure but are limited in their ability to estimate licensing rates and trends. State administrative licensing data are the ideal source to provide this information but have not yet been analyzed for this purpose. Our objective was to analyze New Jersey's (NJ) licensing database to: (1) describe population-based rates of licensure among 17- to 20-year-olds, overall and by gender and zip code level indicators of household income, population density, and race/ethnicity; and (2) examine recent trends in licensure. We obtained records on all licensed NJ drivers through June 2012 from the NJ Motor Vehicle Commission's licensing database and determined each young driver's age at the time of intermediate and full licensure. Data from the US Census and American Community Survey were used to estimate a fixed cohort of NJ residents who turned 17 years old in 2006-2007 (n=255,833). Licensing data were used to estimate the number of these drivers who obtained an intermediate license by each month of age (numerators) and, among those who obtained an intermediate license, time to graduation to full licensure. Overall, 40% of NJ residents-and half of those who ultimately obtained a license by age 21-were licensed within a month of NJ's minimum licensing age of 17, 64% by their 18th birthday, and 81% by their 21st birthday. Starkly different patterns of licensure were observed by socioeconomic indicators; for example, 65% of 17-year-olds residing in the highest-income zip codes were licensed in the first month of eligibility compared with 13% of residents living in the lowest-income zip codes. The younger an individual obtained their intermediate license, the earlier they graduated to a full license. Finally, the rate and timing of licensure in NJ has been relatively stable from 2006 to 2012, with at most a 1-3% point decline in rates. These findings support the growing body of literature suggesting that teens delay licensure primarily for economic reasons and that a substantial proportion of potentially high-risk teens may be obtaining licenses outside the auspices of a graduated driver licensing system. Finally, our finding of a relatively stable trend in licensure in recent years is in contrast to national-level reports of a substantial decline in licensure rates. Copyright © 2015 Elsevier Ltd. All rights reserved.

Rotationally resolved fluorescence spectroscopy of molecular iodine

NASA Astrophysics Data System (ADS)

Lemon, Christopher; Canagaratna, Sebastian; Gray, Jeffrey

2008-03-01

Vibration-electronic spectroscopy of I2 vapor is a common, important experiment in physical chemistry lab courses. We use narrow bandwidth diode-pumped solid state (DPSS) lasers to excite specific rotational levels; these lasers are surprisingly stable and are now available at low cost. We also use efficient miniature fiber-optic spectrometers to resolve rotational fluorescence patterns in a vibrational progression. The resolution enables thorough and accurate analysis of spectroscopic constants for the ground electronic state. The high signal-to-noise ratio, which is easily achieved, also enables students to precisely measure fluorescence band intensities, providing further insight into vibrational wavefunctions and the molecular potential function. We will provide a detailed list of parts for the apparatus as well as modeling algorithms with statistical evaluation to facilitate widespread adoption of these experimental improvements by instructors of intermediate and advanced lab courses.

Elucidating quantitative stability/flexibility relationships within thioredoxin and its fragments using a distance constraint model.

PubMed

Jacobs, Donald J; Livesay, Dennis R; Hules, Jeremy; Tasayco, Maria Luisa

2006-05-05

Numerous quantitative stability/flexibility relationships, within Escherichia coli thioredoxin (Trx) and its fragments are determined using a minimal distance constraint model (DCM). A one-dimensional free energy landscape as a function of global flexibility reveals Trx to fold in a low-barrier two-state process, with a voluminous transition state. Near the folding transition temperature, the native free energy basin is markedly skewed to allow partial unfolded forms. Under native conditions the skewed shape is lost, and the protein forms a compact structure with some flexibility. Predictions on ten Trx fragments are generally consistent with experimental observations that they are disordered, and that complementary fragments reconstitute. A hierarchical unfolding pathway is uncovered using an exhaustive computational procedure of breaking interfacial cross-linking hydrogen bonds that span over a series of fragment dissociations. The unfolding pathway leads to a stable core structure (residues 22-90), predicted to act as a kinetic trap. Direct connection between degree of rigidity within molecular structure and non-additivity of free energy is demonstrated using a thermodynamic cycle involving fragments and their hierarchical unfolding pathway. Additionally, the model provides insight about molecular cooperativity within Trx in its native state, and about intermediate states populating the folding/unfolding pathways. Native state cooperativity correlation plots highlight several flexibly correlated regions, giving insight into the catalytic mechanism that facilitates access to the active site disulfide bond. Residual native cooperativity correlations are present in the core substructure, suggesting that Trx can function when it is partly unfolded. This natively disordered kinetic trap, interpreted as a molten globule, has a wide temperature range of metastability, and it is identified as the "slow intermediate state" observed in kinetic experiments. These computational results are found to be in overall agreement with a large array of experimental data.

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

Gupta, Preeti; Deep, Shashank, E-mail: sdeep@chemistry.iitd.ac.in

Highlights: • HCAII forms amyloid-like aggregates at moderate concentration of trifluoroethanol. • Protein adopts a state between β-sheet and α-helix at moderate % of TFE. • Hydrophobic surface(s) of partially structured conformation forms amyloid. • High % of TFE induces stable α-helical state preventing aggregation. - Abstract: In the present work, we examined the correlation between 2,2,2-trifluoroethanol (TFE)-induced conformational transitions of human carbonic anhydrase II (HCAII) and its aggregation propensity. Circular dichroism data indicates that protein undergoes a transition from β-sheet to α-helix on addition of TFE. The protein was found to aggregate maximally at moderate concentration of TFE atmore » which it exists somewhere between β-sheet and α-helix, probably in extended non-native β-sheet conformation. Thioflavin-T (ThT) and Congo-Red (CR) assays along with fluorescence microscopy and transmission electron microscopy (TEM) data suggest that the protein aggregates induced by TFE possess amyloid-like features. Anilino-8-naphthalene sulfonate (ANS) binding studies reveal that the exposure of hydrophobic surface(s) was maximum in intermediate conformation. Our study suggests that the exposed hydrophobic surface and/or the disruption of the structural features protecting a β-sheet protein might be the major reason(s) for the high aggregation propensity of non-native intermediate conformation of HCAII.« less

Thermal inactivation of alkali phosphatases under various conditions

NASA Astrophysics Data System (ADS)

Atyaksheva, L. F.; Tarasevich, B. N.; Chukhrai, E. S.; Poltorak, O. M.

2009-02-01

The thermal inactivation of alkali phosphatases from bacteria Escherichia coli (ECAP), bovine intestines (bovine IAP), and chicken intestines (chicken IAP) was studied in different buffer solutions and in the solid state. The conclusion was made that these enzymes had maximum stability in the solid state, and, in a carbonate buffer solution, their activity decreased most rapidly. It was found that the bacterial enzyme was more stable than animal phosphatases. It was noted that, for ECAP, four intermediate stages preceded the loss of enzyme activity, and, for bovine and chicken IAPs, three intermediate stages were observed. The activation energy of thermal inactivation of ECAP over the range 25-70°C was determined to be 80 kJ/mol; it corresponded to the dissociation of active dimers into inactive monomers. Higher activation energies (˜200 kJ/mol) observed at the initial stage of thermal inactivation of animal phosphatases resulted from the simultaneous loss of enzyme activity caused by dimer dissociation and denaturation. It was shown that the activation energy of denaturation of monomeric animal alkali phosphatases ranged from 330 to 380 kJ/mol depending on buffer media. It was concluded that the inactivation of solid samples of alkali phosphatases at 95°C was accompanied by an about twofold decrease in the content of β structures in protein molecules.

Programed dynamical ordering in self-organization processes of a nanocube: a molecular dynamics study.

PubMed

Harada, Ryuhei; Mashiko, Takako; Tachikawa, Masanori; Hiraoka, Shuichi; Shigeta, Yasuteru

2018-04-04

Self-organization processes of a gear-shaped amphiphile molecule (1) to form a hexameric structure (nanocube, 16) were inferred from sequential dissociation processes by using molecular dynamics (MD) simulations. Our MD study unveiled that programed dynamic ordering exists in the dissociation processes of 16. According to the dissociation processes, it is proposed that triple π-stacking among three 3-pyridyl groups and other weak molecular interactions such as CH-π and van der Waals interactions, some of which arise from the solvophobic effect, were sequentially formed in stable and transient oligomeric states in the self-organization processes, i.e.12, 13, 14, and 15. By subsequent analyses on structural stabilities, it was found that 13 and 14 are stable intermediate oligomers, whereas 12 and 15 are transient ones. Thus, the formation of 13 from three monomers and of 16 from 14 and two monomers via corresponding transients is time consuming in the self-assembly process.

Localization and Symmetry Breaking in the Quantum Quasiperiodic Ising Glass

NASA Astrophysics Data System (ADS)

Chandran, A.; Laumann, C. R.

2017-07-01

Quasiperiodic modulation can prevent isolated quantum systems from equilibrating by localizing their degrees of freedom. In this article, we show that such systems can exhibit dynamically stable long-range orders forbidden in equilibrium. Specifically, we show that the interplay of symmetry breaking and localization in the quasiperiodic quantum Ising chain produces a quasiperiodic Ising glass stable at all energy densities. The glass order parameter vanishes with an essential singularity at the melting transition with no signatures in the equilibrium properties. The zero-temperature phase diagram is also surprisingly rich, consisting of paramagnetic, ferromagnetic, and quasiperiodically alternating ground-state phases with extended, localized, and critically delocalized low-energy excitations. The system exhibits an unusual quantum Ising transition whose properties are intermediate between those of the clean and infinite randomness Ising transitions. Many of these results follow from a geometric generalization of the Aubry-André duality that we develop. The quasiperiodic Ising glass may be realized in near-term quantum optical experiments.

Remote Laser Welding of Zinc Coated Steel Sheets in an Edge Lap Configuration with Zero Gap

NASA Astrophysics Data System (ADS)

Roos, Christian; Schmidt, Michael

Remote Laser Welding (RLW) of zinc-coated steel sheets is a great challenge for the automotive industry but offers high potentials with respect to flexibility and costs. In state of the art applications, sheets are joined in overlap configuration with a preset gap for a stable zinc degassing. This paper investigates RLW of fillets without a preset gap and conditions for a stable process. The influence of process parameters on weld quality and process stability is shown. Experimental data give evidence, that the degassing of zinc through the capillary and the rear melt pool are the major degassing mechanisms. Furthermore the paper gives experimental validation of the zinc degassing in advance of the process zone to the open side of the fillet. Chemical analysis of the hot-dip galvanized zinc coating proof the iron-zinc-alloys to be the reason for a limited effectiveness of this mechanism in comparison to pure zinc as intermediate.

Comparative reactivity of different types of stable cyclic and acyclic mono- and diamino carbenes with simple organic substrates.

PubMed

Martin, David; Canac, Yves; Lavallo, Vincent; Bertrand, Guy

2014-04-02

A series of stable carbenes, featuring a broad range of electronic properties, were reacted with simple organic substrates. The N,N-dimesityl imidazolylidene (NHC) does not react with isocyanides, whereas anti-Bredt di(amino)carbene (pyr-NHC), cyclic (alkyl)(amino)carbene (CAAC), acyclic di(amino)carbene (ADAC), and acyclic (alkyl)(amino)carbene (AAAC) give rise to the corresponding ketenimines. NHCs are known to promote the benzoin condensation, and we found that the CAAC, pyr-NHC, and ADAC react with benzaldehyde to give the ketone tautomer of the Breslow intermediate, whereas the AAAC first gives the corresponding epoxide and ultimately the Breslow intermediate, which can be isolated. Addition of excess benzaldehyde to the latter does not lead to benzoin but to a stable 1,3-dioxolane. Depending on the electronic properties of carbenes, different products are also obtained with methyl acrylate as a substrate. The critical role of the carbene electrophilicity on the outcome of reactions is discussed.

Edge states in the climate system: exploring global instabilities and critical transitions

NASA Astrophysics Data System (ADS)

Lucarini, Valerio; Bódai, Tamás

2017-07-01

Multistability is a ubiquitous feature in systems of geophysical relevance and provides key challenges for our ability to predict a system’s response to perturbations. Near critical transitions small causes can lead to large effects and—for all practical purposes—irreversible changes in the properties of the system. As is well known, the Earth climate is multistable: present astronomical and astrophysical conditions support two stable regimes, the warm climate we live in, and a snowball climate characterized by global glaciation. We first provide an overview of methods and ideas relevant for studying the climate response to forcings and focus on the properties of critical transitions in the context of both stochastic and deterministic dynamics, and assess strengths and weaknesses of simplified approaches to the problem. Following an idea developed by Eckhardt and collaborators for the investigation of multistable turbulent fluid dynamical systems, we study the global instability giving rise to the snowball/warm multistability in the climate system by identifying the climatic edge state, a saddle embedded in the boundary between the two basins of attraction of the stable climates. The edge state attracts initial conditions belonging to such a boundary and, while being defined by the deterministic dynamics, is the gate facilitating noise-induced transitions between competing attractors. We use a simplified yet Earth-like intermediate complexity climate model constructed by coupling a primitive equations model of the atmosphere with a simple diffusive ocean. We refer to the climatic edge states as Melancholia states and provide an extensive analysis of their features. We study their dynamics, their symmetry properties, and we follow a complex set of bifurcations. We find situations where the Melancholia state has chaotic dynamics. In these cases, we have that the basin boundary between the two basins of attraction is a strange geometric set with a nearly zero codimension, and relate this feature to the time scale separation between instabilities occurring on weather and climatic time scales. We also discover a new stable climatic state that is similar to a Melancholia state and is characterized by non-trivial symmetry properties.

Phase behavior and reactive transport of partial melt in heterogeneous mantle model

NASA Astrophysics Data System (ADS)

Jordan, J.; Hesse, M. A.

2013-12-01

The reactive transport of partial melt is the key process that leads to the chemical and physical differentiation of terrestrial planets and smaller celestial bodies. The essential role of the lithological heterogeneities during partial melting of the mantle is increasingly recognized. How far can enriched melts propagate while interacting with the ambient mantle? Can the melt flow emanating from a fertile heterogeneity be localized through a reactive infiltration feedback in a model without exogenous factors or contrived initial conditions? A full understanding of the role of heterogeneities requires reactive melt transport models that account for the phase behavior of major elements. Previous work on reactive transport in the mantle focuses on trace element partitioning; we present the first nonlinear chromatographic analysis of reactive melt transport in systems with binary solid solution. Our analysis shows that reactive melt transport in systems with binary solid solution leads to the formation of two separate reaction fronts: a slow melting/freezing front along which enthalpy change is dominant and a fast dissolution/precipitation front along which compositional changes are dominated by an ion-exchange process over enthalpy change. An intermediate state forms between these two fronts with a bulk-rock composition and enthalpy that are not necessarily bounded by the bulk-rock composition and enthalpy of either the enriched heterogeneity or the depleted ambient mantle. The formation of this intermediate state makes it difficult to anticipate the porosity changes and hence the stability of reaction fronts. Therefore, we develop a graphical representation for the solution that allows identification of the intermediate state by inspection, for all possible bulk-rock compositions and enthalpies of the heterogeneity and the ambient mantle. We apply the analysis to the partial melting of an enriched heterogeneity. This leads to the formation of moving precipitation front that followes a stationary melting front which creates low porosity intermediate states. Therefore, localization of the melt flow is not observed because the precipitation front is stable and the melting front is always stationary under these conditions. This analysis illustrates the counterintuitive behavior that can arise when the phase behavior is taken into account and is a first step to understanding reactive melt transport and the reactive constraints on channelization in partial melts. ¬¬

Unique surface adsorption behaviors of serum proteins on chemically uniform and alternating surfaces

NASA Astrophysics Data System (ADS)

Song, Sheng

With increasing interests of studying proteins adsorption on the surfaces with nanoscale features in biomedical field, it is crucial to have fundamental understandings on how the proteins are adsorbed on such a surface and what factors contribute to the driving forces of adsorption. Besides, exploring more available nanoscale templates would greatly offer more possibilities one could design surface bio-detection methods with favorable protein-surface interactions. Thus, to fulfill the purpose, the work in this dissertation has been made into three major sections. First, to probe the intermediate states which possibly exist between stable and unstable phases described in mean-field theory diagram, a solvent vapor annealing method is chosen to slowly induce the copolymer polystyrene-block-polyvinylpyridine (PS-b-PVP)'s both blocks undergoing micro-phase separations from initial spherical nanodomains into terminal cylindrical nanodomains. During this process, real time atomic force microscopy (AFM) has been conducted to capture other six intermediate states with different morphologies on the polymeric film surfaces. Secondly, upon recognizing each intermediate state, the solution of immunoglobulin gamma (IgG) proteins has been deposited on the surface and been rinsed off with buffer solution before the protein-bounded surface is imaged by AFM. It has been found IgG showing a strong adsorption preference on PS over P4VP block. Among all the six intermediate states, the proteins are almost exclusively adsorbed on PS nanodomains regardless the concentration and deposition time. Thirdly, a trinodular shape protein fibrinogen (Fg) is selected for investigating how geometry and surface charge of proteins would interplay with cylindrical nanodomains on a surface developed from Polystyrene -block-Poly-(methyl methacrylate) PS-b-PMMA. Also, Fg adsorptions on chemically homogeneous surfaces are included here to have a better contrast of showing how much difference it can make by using it on a nanoscale surface. Interestingly, higher concentration of protein solution promotes the occurrences of single phase packed Fg on the PS domain. The densely packed network has formed where each Fg keeps its main body in PS domain and leaves its two alpha C chains on nearby PMMA domain. We believe this conformation and orientation would maximize both the hydrophobic and electrostatic interactions between Fg and the underlying surface.

Formation of a quinoneimine intermediate of 4-fluoro-N-methylaniline by FMO1: carbon oxidation plus defluorination.

PubMed

Driscoll, James P; Aliagas, Ignacio; Harris, Jennifer J; Halladay, Jason S; Khatib-Shahidi, Sheerin; Deese, Alan; Segraves, Nathaniel; Khojasteh-Bakht, S Cyrus

2010-05-17

Here, we report on the mechanism by which flavin-containing monooxygenase 1 (FMO1) mediates the formation of a reactive intermediate of 4-fluoro-N-methylaniline. FMO1 catalyzed a carbon oxidation reaction coupled with defluorination that led to the formation of 4-N-methylaminophenol, which was a reaction first reported by Boersma et al. (Boersma et al. (1993) Drug Metab. Dispos. 21 , 218 - 230). We propose that a labile 1-fluoro-4-(methylimino)cyclohexa-2,5-dienol intermediate was formed leading to an electrophilic quinoneimine intermediate. The identification of N-acetylcysteine adducts by LC-MS/MS and NMR further supports the formation of a quinoneimine intermediate. Incubations containing stable labeled oxygen (H(2)(18)O or (18)O(2)) and ab initio calculations were performed to support the proposed reaction mechanism.

Forest Canopy Water Cycling Responses to an Intermediate Disturbance Revealed Through Stable Water Vapor Isotopes

NASA Astrophysics Data System (ADS)

Fiorella, R.; Poulsen, C. J.; Matheny, A. M.; Rey Sanchez, C.; Fotis, A. T.; Morin, T. H.; Vogel, C. S.; Gough, C. M.; Aron, P.; Bohrer, G.

2016-12-01

Forest structure, age, and species composition modulate fluxes of carbon and water between the land surface and the atmosphere. The response of forests to intermediate disturbances such as ecological succession, species-specific insect invasion, or selective logging that disrupt the canopy but do not promote complete stand replacement, shape how these fluxes evolve through time. We investigate the impact of an intermediate disturbance to water cycling processes by comparing vertical profiles of stable water isotopes in two closely located forest canopies in the northern lower peninsula of Michigan using cavity ring-down spectroscopy. In one of the canopies, an intermediate disturbance was prescribed in 2008 by inducing mortality in all canopy-dominant early successional species. Isotopic compositions of atmospheric water vapor are measured at six heights during two time periods (summer and early fall) at two flux towers and compared with local meteorology and calculated atmospheric back-trajectories. Disturbance has little impact on low-frequency changes in isotopic composition (e.g., >1 day); at these timescales, isotopic composition is strongly related to large-scale moisture transport. In contrast, disturbance has substantial impacts on the vertical distribution of water isotopes throughout the canopy when transpiration rates are high during the summer, but impact is muted during early fall. Sub-diurnal differences in canopy water vapor cycling are likely related to differences in species composition and response to disturbance and changes in canopy structure. Predictions of transpiration fluxes by land-surface models that do not account species-specific relationships and canopy structure are unlikely to capture these relationships, but addition of stable isotopes to land surface models may provide a useful parameter to improve these predictions.

Phase transitions in the sdg interacting boson model

NASA Astrophysics Data System (ADS)

Van Isacker, P.; Bouldjedri, A.; Zerguine, S.

2010-05-01

A geometric analysis of the sdg interacting boson model is performed. A coherent state is used in terms of three types of deformation: axial quadrupole ( β), axial hexadecapole ( β) and triaxial ( γ). The phase-transitional structure is established for a schematic sdg Hamiltonian which is intermediate between four dynamical symmetries of U(15), namely the spherical U(5)⊗U(9), the (prolate and oblate) deformed SU(3) and the γ-soft SO(15) limits. For realistic choices of the Hamiltonian parameters the resulting phase diagram has properties close to what is obtained in the sd version of the model and, in particular, no transition towards a stable triaxial shape is found.

Emergence and stability of intermediate open vesicles in disk-to-vesicle transitions.

PubMed

Li, Jianfeng; Zhang, Hongdong; Qiu, Feng; Shi, An-Chang

2013-07-01

The transition between two basic structures, a disk and an enclosed vesicle, of a finite membrane is studied by examining the minimum energy path (MEP) connecting these two states. The MEP is constructed using the string method applied to continuum elastic membrane models. The results reveal that, besides the commonly observed disk and vesicle, open vesicles (bowl-shaped vesicles or vesicles with a pore) can become stable or metastable shapes. The emergence, stability, and probability distribution of these open vesicles are analyzed. It is demonstrated that open vesicles can be stabilized by higher-order elastic energies. The estimated probability distribution of the different structures is in good agreement with available experiments.

Magic angle spinning nuclear magnetic resonance apparatus and process for high-resolution in situ investigations

DOEpatents

Hu, Jian Zhi; Sears, Jr., Jesse A.; Hoyt, David W.; Mehta, Hardeep S.; Peden, Charles H. F.

2015-11-24

A continuous-flow (CF) magic angle sample spinning (CF-MAS) NMR rotor and probe are described for investigating reaction dynamics, stable intermediates/transition states, and mechanisms of catalytic reactions in situ. The rotor includes a sample chamber of a flow-through design with a large sample volume that delivers a flow of reactants through a catalyst bed contained within the sample cell allowing in-situ investigations of reactants and products. Flow through the sample chamber improves diffusion of reactants and products through the catalyst. The large volume of the sample chamber enhances sensitivity permitting in situ .sup.13C CF-MAS studies at natural abundance.

Manipulation of double-stranded DNA melting by force

NASA Astrophysics Data System (ADS)

Singh, Amit Raj; Granek, Rony

2017-09-01

By integrating elasticity—as described by the Gaussian network model—with bond binding energies that distinguish between different base-pair identities and stacking configurations, we study the force induced melting of a double-stranded DNA (dsDNA). Our approach is a generalization of our previous study of thermal dsDNA denaturation [J. Chem. Phys. 145, 144101 (2016), 10.1063/1.4964285] to that induced by force at finite temperatures. It allows us to obtain semimicroscopic information about the opening of the chain, such as whether the dsDNA opens from one of the ends or from the interior, forming an internal bubble. We study different types of force manipulation: (i) "end unzipping," with force acting at a single end base pair perpendicular to the helix, (ii) "midunzipping," with force acting at a middle base pair perpendicular to the helix, and (iii) "end shearing," where the force acts at opposite ends along the helix. By monitoring the free-energy landscape and probability distribution of intermediate denaturation states, we show that different dominant intermediate states are stabilized depending on the type of force manipulation used. In particular, the bubble state of the sequence L60B36, which we have previously found to be a stable state during thermal denaturation, is absent for end unzipping and end shearing, whereas very similar bubbles are stabilized by midunzipping, or when the force location is near the middle of the chain. Ours results offer a simple tool for stabilizing bubbles and loops using force manipulations at different temperatures, and may implicate on the mechanism in which DNA enzymes or motors open regions of the chain.

Cooperative alpha-helix formation of beta-lactoglobulin induced by sodium n-alkyl sulfates.

PubMed

Chamani, J; Moosavi-Movahedi, A A; Rajabi, O; Gharanfoli, M; Momen-Heravi, M; Hakimelahi, G H; Neamati-Baghsiah, A; Varasteh, A R

2006-01-01

It is generally assumed that folding intermediates contain partially formed native-like secondary structures. However, if we consider the fact that the conformational stability of the intermediate state is simpler than that of the native state, it would be expected that the secondary structures in a folding intermediate would not necessarily be similar to those of the native state. beta-Lactoglobulin is a predominantly beta-sheet protein, although it has a markedly high intrinsic preference for alpha-helical structure. The formation of non-native alpha-helical intermediate of beta-lactoglobulin was induced by n-alkyl sulfates including sodium octyl sulfate, SOS; sodium decyl sulfate, SDeS; sodium dodecyl sulfate, SDS; and sodium tetradecyl sulfate, STS at special condition. The effect of n-alkyl sulfates on the structure of native beta-lactoglobulin at pH 2 was utilized to investigate the contribution of hydrophobic interactions to the stability of non-native alpha-helical intermediate. The addition of various concentrations of n-alkyl sulfates to the native state of beta-lactoglobulin (pH 2) appears to support the stabilized form of non-native alpha-helical intermediate at pH 2. The m values of the intermediate state of beta-lactoglobulin by SOS, SDeS, SDS and STS showed substantial variation. The enhancement of m values as the stability criterion of non-native alpha-helical intermediate state corresponded with increasing chain length of the cited n-alkyl sulfates. The present results suggest that the folding reaction of beta-lactoglobulin follows a non-hierarchical mechanism and hydrophobic interactions play important roles in stabilizing the non-native alpha-helical intermediate state.

An overlapping region between the two terminal folding units of the outer surface protein A (OspA) controls its folding behavior.

PubMed

Makabe, Koki; Nakamura, Takashi; Dhar, Debanjan; Ikura, Teikichi; Koide, Shohei; Kuwajima, Kunihiro

2018-04-27

Although many naturally occurring proteins consist of multiple domains, most studies on protein folding to date deal with single-domain proteins or isolated domains of multi-domain proteins. Studies of multi-domain protein folding are required for further advancing our understanding of protein folding mechanisms. Borrelia outer surface protein A (OspA) is a β-rich two-domain protein, in which two globular domains are connected by a rigid and stable single-layer β-sheet. Thus, OspA is particularly suited as a model system for studying the interplays of domains in protein folding. Here, we studied the equilibria and kinetics of the urea-induced folding-unfolding reactions of OspA probed with tryptophan fluorescence and ultraviolet circular dichroism. Global analysis of the experimental data revealed compelling lines of evidence for accumulation of an on-pathway intermediate during kinetic refolding and for the identity between the kinetic intermediate and a previously described equilibrium unfolding intermediate. The results suggest that the intermediate has the fully native structure in the N-terminal domain and the single layer β-sheet, with the C-terminal domain still unfolded. The observation of the productive on-pathway folding intermediate clearly indicates substantial interactions between the two domains mediated by the single-layer β-sheet. We propose that a rigid and stable intervening region between two domains creates an overlap between two folding units and can energetically couple their folding reactions. Copyright © 2018. Published by Elsevier Ltd.

The effects of internal heating and large scale climate variations on tectonic bi-stability in terrestrial planets

NASA Astrophysics Data System (ADS)

Weller, M. B.; Lenardic, A.; O'Neill, C.

2015-06-01

We use 3D mantle convection and planetary tectonics models to explore the links between tectonic regimes and the level of internal heating within the mantle of a planet (a proxy for thermal age), planetary surface temperature, and lithosphere strength. At both high and low values of internal heating, for moderate to high lithospheric yield strength, hot and cold stagnant-lid (single plate planet) states prevail. For intermediate values of internal heating, multiple stable tectonic states can exist. In these regions of parameter space, the specific evolutionary path of the system has a dominant role in determining its tectonic state. For low to moderate lithospheric yield strength, mobile-lid behavior (a plate tectonic-like mode of convection) is attainable for high degrees of internal heating (i.e., early in a planet's thermal evolution). However, this state is sensitive to climate driven changes in surface temperatures. Relatively small increases in surface temperature can be sufficient to usher in a transition from a mobile- to a stagnant-lid regime. Once a stagnant-lid mode is initiated, a return to mobile-lid is not attainable by a reduction of surface temperatures alone. For lower levels of internal heating, the tectonic regime becomes less sensitive to surface temperature changes. Collectively our results indicate that terrestrial planets can alternate between multiple tectonic states over giga-year timescales. Within parameter space regions that allow for bi-stable behavior, any model-based prediction as to the current mode of tectonics is inherently non-unique in the absence of constraints on the geologic and climatic histories of a planet.

Pathogenic Roles for Fungal Melanins

PubMed Central

Jacobson, Eric S.

2000-01-01

Melanins represent virulence factors for several pathogenic fungi; the number of examples is growing. Thus, albino mutants of several genera (in one case, mutated precisely in the melanizing enzyme) exhibit decreased virulence in mice. We consider the phenomenon in relation to known chemical properties of melanin, beginning with biosynthesis from ortho-hydroquinone precursors which, when oxidized enzymatically to quinones, polymerize spontaneously to melanin. It follows that melanizing intermediates are cross-linking reagents; melanization stabilizes the external cell wall against hydrolysis and is thought to determine semipermeability in the osmotic ram (the appressorium) of certain plant pathogens. Polymeric melanins undergo reversible oxidation-reduction reactions between cell wall-penetrating quinone and hydroquinone oxidation states and thus represent polymeric redox buffers; using strong oxidants, it is possible to titrate the melanin on living cells and thereby demonstrate protection conferred by melanin in several species. The amount of buffering per cell approximately neutralizes the amount of oxidant generated by a single macrophage. Moreover, the intermediate oxidation state, the semiquinone, is a very stable free radical and is thought to trap unpaired electrons. We have suggested that the oxidation state of external melanin may be regulated by external Fe(II). An independent hypothesis holds that in Cryptococcus neoformans, an important function of the melanizing enzyme (apart from melanization) is the oxidation of Fe(II) to Fe(III), thereby forestalling generation of the harmful hydroxyl radical from H2O2. Thus, problems in fungal pathogenesis have led to evolving hypotheses regarding melanin functioning. PMID:11023965

A Kinetic Model of Trp-Cage Folding from Multiple Biased Molecular Dynamics Simulations

PubMed Central

Marinelli, Fabrizio; Pietrucci, Fabio; Laio, Alessandro; Piana, Stefano

2009-01-01

Trp-cage is a designed 20-residue polypeptide that, in spite of its size, shares several features with larger globular proteins. Although the system has been intensively investigated experimentally and theoretically, its folding mechanism is not yet fully understood. Indeed, some experiments suggest a two-state behavior, while others point to the presence of intermediates. In this work we show that the results of a bias-exchange metadynamics simulation can be used for constructing a detailed thermodynamic and kinetic model of the system. The model, although constructed from a biased simulation, has a quality similar to those extracted from the analysis of long unbiased molecular dynamics trajectories. This is demonstrated by a careful benchmark of the approach on a smaller system, the solvated Ace-Ala3-Nme peptide. For the Trp-cage folding, the model predicts that the relaxation time of 3100 ns observed experimentally is due to the presence of a compact molten globule-like conformation. This state has an occupancy of only 3% at 300 K, but acts as a kinetic trap. Instead, non-compact structures relax to the folded state on the sub-microsecond timescale. The model also predicts the presence of a state at of 4.4 Å from the NMR structure in which the Trp strongly interacts with Pro12. This state can explain the abnormal temperature dependence of the and chemical shifts. The structures of the two most stable misfolded intermediates are in agreement with NMR experiments on the unfolded protein. Our work shows that, using biased molecular dynamics trajectories, it is possible to construct a model describing in detail the Trp-cage folding kinetics and thermodynamics in agreement with experimental data. PMID:19662155

Two-Electron Transfer Pathways.

PubMed

Lin, Jiaxing; Balamurugan, D; Zhang, Peng; Skourtis, Spiros S; Beratan, David N

2015-06-18

The frontiers of electron-transfer chemistry demand that we develop theoretical frameworks to describe the delivery of multiple electrons, atoms, and ions in molecular systems. When electrons move over long distances through high barriers, where the probability for thermal population of oxidized or reduced bridge-localized states is very small, the electrons will tunnel from the donor (D) to acceptor (A), facilitated by bridge-mediated superexchange interactions. If the stable donor and acceptor redox states on D and A differ by two electrons, it is possible that the electrons will propagate coherently from D to A. While structure-function relations for single-electron superexchange in molecules are well established, strategies to manipulate the coherent flow of multiple electrons are largely unknown. In contrast to one-electron superexchange, two-electron superexchange involves both one- and two-electron virtual intermediate states, the number of virtual intermediates increases very rapidly with system size, and multiple classes of pathways interfere with one another. In the study described here, we developed simple superexchange models for two-electron transfer. We explored how the bridge structure and energetics influence multielectron superexchange, and we compared two-electron superexchange interactions to single-electron superexchange. Multielectron superexchange introduces interference between singly and doubly oxidized (or reduced) bridge virtual states, so that even simple linear donor-bridge-acceptor systems have pathway topologies that resemble those seen for one-electron superexchange through bridges with multiple parallel pathways. The simple model systems studied here exhibit a richness that is amenable to experimental exploration by manipulating the multiple pathways, pathway crosstalk, and changes in the number of donor and acceptor species. The features that emerge from these studies may assist in developing new strategies to deliver multiple electrons in condensed-phase redox systems, including multiple-electron redox species, multimetallic/multielectron redox catalysts, and multiexciton excited states.

A kinetic model of trp-cage folding from multiple biased molecular dynamics simulations.

PubMed

Marinelli, Fabrizio; Pietrucci, Fabio; Laio, Alessandro; Piana, Stefano

2009-08-01

Trp-cage is a designed 20-residue polypeptide that, in spite of its size, shares several features with larger globular proteins.Although the system has been intensively investigated experimentally and theoretically, its folding mechanism is not yet fully understood. Indeed, some experiments suggest a two-state behavior, while others point to the presence of intermediates. In this work we show that the results of a bias-exchange metadynamics simulation can be used for constructing a detailed thermodynamic and kinetic model of the system. The model, although constructed from a biased simulation, has a quality similar to those extracted from the analysis of long unbiased molecular dynamics trajectories. This is demonstrated by a careful benchmark of the approach on a smaller system, the solvated Ace-Ala3-Nme peptide. For theTrp-cage folding, the model predicts that the relaxation time of 3100 ns observed experimentally is due to the presence of a compact molten globule-like conformation. This state has an occupancy of only 3% at 300 K, but acts as a kinetic trap.Instead, non-compact structures relax to the folded state on the sub-microsecond timescale. The model also predicts the presence of a state at Calpha-RMSD of 4.4 A from the NMR structure in which the Trp strongly interacts with Pro12. This state can explain the abnormal temperature dependence of the Pro12-delta3 and Gly11-alpha3 chemical shifts. The structures of the two most stable misfolded intermediates are in agreement with NMR experiments on the unfolded protein. Our work shows that, using biased molecular dynamics trajectories, it is possible to construct a model describing in detail the Trp-cage folding kinetics and thermodynamics in agreement with experimental data.

A study of the nucleus-nucleus total reaction cross section of stable systems at intermediate energies: An application to 12C

NASA Astrophysics Data System (ADS)

Hu, Liyuan; Song, Yushou; Hou, Yingwei; Liu, Huilan; Li, Hui

2018-07-01

A semi-microscopic analytical expression of the nucleus-nucleus total reaction cross section (σR) was proposed based on the strong absorption model. It is suitable for stable nuclei at intermediate energies. The matter density distributions of nuclei and the nucleon-nucleon total cross section were both considered. Particularly, the Fermi motion effect of the nucleons in a nucleus was also taken into account. The parametrization of σR was applied to the colliding systems including 12C. The experimental data at energies from 30 to 1000 MeV/nucleon were well reproduced, according to which an approach of deriving σR without adjustable parameters was developed. The necessity of considering the Fermi motion effect in the parametrization was discussed.

OH-initiated transformation and hydrolysis of aspirin in AOPs system: DFT and experimental studies.

PubMed

He, Lin; Sun, Xiaomin; Zhu, Fanping; Ren, Shaojie; Wang, Shuguang

2017-08-15

Advanced oxidation processes (AOPs) are widely used in wastewater treatment of pharmaceutical and personal care products (PPCPs). In this work, the OH-initiated transformation as well as the hydrolysis of a typical PPCPs, aspirin, was investigated using density functional theory (DFT) calculations and laboratory experiments. For DFT calculations, the frontier electron densities and bond dissociation energies were analyzed. Profiles of the potential energy surface were constructed, and all the possible pathways were discussed. Additionally, rate constants for each pathway were calculated with transition state theory (TST) method. UV/H 2 O 2 experiments of aspirin were performed and degradation intermediates were identified by UPLC-MS-MS analysis. Different findings from previous experimental works were reported that the H-abstraction pathways at methyl position were dominated and OH-addition pathways on benzene ring were also favored. Meantime, hydroxyl ASA was confirmed as the main stable intermediate. Moreover, it was the first time to use DFT method to investigate the hydrolysis mechanisms of organic ester compound. Copyright © 2017 Elsevier B.V. All rights reserved.

Use of stable carbon and nitrogen isotopes to trace the larval striped bass food chain in the Sacramento-San Joaquin Estuary, California, April to September 1985

USGS Publications Warehouse

Rast, Walter; Sutton, J.E.

1989-01-01

To assess one potential cause for the decline of the striped bass fishery in the Sacramento-San Joaquin Estuary, stable carbon and nitrogen isotope ratios were used to examine the trophic structures of the larval striped bass food chain, and to trace the flux of these elements through the food chain components. Study results generally confirm a food chain consisting of the elements, phytoplankton/detritus-->zooplankton/Neomysis shrimp-->larval striped bass. The stable isotope ratios generally become more positive as one progresses from the lower to the higher trophic level food chain components, and no unusual trophic structure was found in the food chain. However, the data indicate an unidentified consumer organism occupying an intermediate position between the lower and higher trophic levels of the larval striped bass food chain. Based on expected trophic interactions, this unidentified consumer would have a stable carbon isotope ratio of about 28/mil and a stable nitrogen isotope ratio of about 8/mi. Three possible feeding stages for larval striped bass also were identified, based on their lengths. The smallest length fish seem to subsist on their yolk sac remnants, and the largest length fish subsist on Neomysis shrimp and zooplankton. The intermediate-length fish represent a transition stage between primary food sources and/or use of a mixture of food sources. (USGS)

Two states or not two states: Single-molecule folding studies of protein L

NASA Astrophysics Data System (ADS)

Aviram, Haim Yuval; Pirchi, Menahem; Barak, Yoav; Riven, Inbal; Haran, Gilad

2018-03-01

Experimental tools of increasing sophistication have been employed in recent years to study protein folding and misfolding. Folding is considered a complex process, and one way to address it is by studying small proteins, which seemingly possess a simple energy landscape with essentially only two stable states, either folded or unfolded. The B1-IgG binding domain of protein L (PL) is considered a model two-state folder, based on measurements using a wide range of experimental techniques. We applied single-molecule fluorescence resonance energy transfer (FRET) spectroscopy in conjunction with a hidden Markov model analysis to fully characterize the energy landscape of PL and to extract the kinetic properties of individual molecules of the protein. Surprisingly, our studies revealed the existence of a third state, hidden under the two-state behavior of PL due to its small population, ˜7%. We propose that this minority intermediate involves partial unfolding of the two C-terminal β strands of PL. Our work demonstrates that single-molecule FRET spectroscopy can be a powerful tool for a comprehensive description of the folding dynamics of proteins, capable of detecting and characterizing relatively rare metastable states that are difficult to observe in ensemble studies.

Early warning signals of Atlantic Meridional Overturning Circulation collapse in a fully coupled climate model

NASA Astrophysics Data System (ADS)

Boulton, Chris A.; Allison, Lesley C.; Lenton, Timothy M.

2014-12-01

The Atlantic Meridional Overturning Circulation (AMOC) exhibits two stable states in models of varying complexity. Shifts between alternative AMOC states are thought to have played a role in past abrupt climate changes, but the proximity of the climate system to a threshold for future AMOC collapse is unknown. Generic early warning signals of critical slowing down before AMOC collapse have been found in climate models of low and intermediate complexity. Here we show that early warning signals of AMOC collapse are present in a fully coupled atmosphere-ocean general circulation model, subject to a freshwater hosing experiment. The statistical significance of signals of increasing lag-1 autocorrelation and variance vary with latitude. They give up to 250 years warning before AMOC collapse, after ~550 years of monitoring. Future work is needed to clarify suggested dynamical mechanisms driving critical slowing down as the AMOC collapse is approached.

Early warning signals of Atlantic Meridional Overturning Circulation collapse in a fully coupled climate model

PubMed Central

Boulton, Chris A.; Allison, Lesley C.; Lenton, Timothy M.

2014-01-01

The Atlantic Meridional Overturning Circulation (AMOC) exhibits two stable states in models of varying complexity. Shifts between alternative AMOC states are thought to have played a role in past abrupt climate changes, but the proximity of the climate system to a threshold for future AMOC collapse is unknown. Generic early warning signals of critical slowing down before AMOC collapse have been found in climate models of low and intermediate complexity. Here we show that early warning signals of AMOC collapse are present in a fully coupled atmosphere-ocean general circulation model, subject to a freshwater hosing experiment. The statistical significance of signals of increasing lag-1 autocorrelation and variance vary with latitude. They give up to 250 years warning before AMOC collapse, after ~550 years of monitoring. Future work is needed to clarify suggested dynamical mechanisms driving critical slowing down as the AMOC collapse is approached. PMID:25482065

Early warning signals of Atlantic Meridional Overturning Circulation collapse in a fully coupled climate model.

PubMed

Boulton, Chris A; Allison, Lesley C; Lenton, Timothy M

2014-12-08

The Atlantic Meridional Overturning Circulation (AMOC) exhibits two stable states in models of varying complexity. Shifts between alternative AMOC states are thought to have played a role in past abrupt climate changes, but the proximity of the climate system to a threshold for future AMOC collapse is unknown. Generic early warning signals of critical slowing down before AMOC collapse have been found in climate models of low and intermediate complexity. Here we show that early warning signals of AMOC collapse are present in a fully coupled atmosphere-ocean general circulation model, subject to a freshwater hosing experiment. The statistical significance of signals of increasing lag-1 autocorrelation and variance vary with latitude. They give up to 250 years warning before AMOC collapse, after ~550 years of monitoring. Future work is needed to clarify suggested dynamical mechanisms driving critical slowing down as the AMOC collapse is approached.

Cooperative Tertiary Interaction Network Guides RNA Folding

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

Behrouzi, Reza; Roh, Joon Ho; Kilburn, Duncan

2013-04-08

Noncoding RNAs form unique 3D structures, which perform many regulatory functions. To understand how RNAs fold uniquely despite a small number of tertiary interaction motifs, we mutated the major tertiary interactions in a group I ribozyme by single-base substitutions. The resulting perturbations to the folding energy landscape were measured using SAXS, ribozyme activity, hydroxyl radical footprinting, and native PAGE. Double- and triple-mutant cycles show that most tertiary interactions have a small effect on the stability of the native state. Instead, the formation of core and peripheral structural motifs is cooperatively linked in near-native folding intermediates, and this cooperativity depends onmore » the native helix orientation. The emergence of a cooperative interaction network at an early stage of folding suppresses nonnative structures and guides the search for the native state. We suggest that cooperativity in noncoding RNAs arose from natural selection of architectures conducive to forming a unique, stable fold.« less

Conformational stability and thermodynamic characterization of the lipoic acid bearing domain of human mitochondrial branched chain α-ketoacid dehydrogenase

PubMed Central

Naik, Mandar T.; Huang, Tai-Huang

2004-01-01

The lipoic acid bearing domain (hbLBD) of human mitochondrial branched chain α-ketoacid dehydrogenase (BCKD) plays important role of substrate channeling in oxidative decarboxylation of the branched chain α-ketoacids. Recently hbLBD has been found to follow two-step folding mechanism without detectable presence of stable or kinetic intermediates. The present study describes the conformational stability underlying the folding of this small β-barrel domain. Thermal denaturation in presence of urea and isothermal urea denaturation titrations are used to evaluate various thermodynamic parameters defining the equilibrium unfolding. The linear extrapolation model successfully describes the two-step; native state ↔denatured state unfolding transition of hbLBD. The average temperature of maximum stability of hbLBD is estimated as 295.6 ± 0.9 K. Cold denaturation of hbLBD is also predicted and discussed. PMID:15322287

Evidence for a Shared Mechanism in the Formation of Urea-Induced Kinetic and Equilibrium Intermediates of Horse Apomyoglobin from Ultrarapid Mixing Experiments.

PubMed

Mizukami, Takuya; Abe, Yukiko; Maki, Kosuke

2015-01-01

In this study, the equivalence of the kinetic mechanisms of the formation of urea-induced kinetic folding intermediates and non-native equilibrium states was investigated in apomyoglobin. Despite having similar structural properties, equilibrium and kinetic intermediates accumulate under different conditions and via different mechanisms, and it remains unknown whether their formation involves shared or distinct kinetic mechanisms. To investigate the potential mechanisms of formation, the refolding and unfolding kinetics of horse apomyoglobin were measured by continuous- and stopped-flow fluorescence over a time range from approximately 100 μs to 10 s, along with equilibrium unfolding transitions, as a function of urea concentration at pH 6.0 and 8°C. The formation of a kinetic intermediate was observed over a wider range of urea concentrations (0-2.2 M) than the formation of the native state (0-1.6 M). Additionally, the kinetic intermediate remained populated as the predominant equilibrium state under conditions where the native and unfolded states were unstable (at ~0.7-2 M urea). A continuous shift from the kinetic to the equilibrium intermediate was observed as urea concentrations increased from 0 M to ~2 M, which indicates that these states share a common kinetic folding mechanism. This finding supports the conclusion that these intermediates are equivalent. Our results in turn suggest that the regions of the protein that resist denaturant perturbations form during the earlier stages of folding, which further supports the structural equivalence of transient and equilibrium intermediates. An additional folding intermediate accumulated within ~140 μs of refolding and an unfolding intermediate accumulated in <1 ms of unfolding. Finally, by using quantitative modeling, we showed that a five-state sequential scheme appropriately describes the folding mechanism of horse apomyoglobin.

Kinetics of the benzyl + O(3P) reaction: a quantum chemical/statistical reaction rate theory study.

PubMed

da Silva, Gabriel; Bozzelli, Joseph W

2012-12-14

The resonance stabilized benzyl radical is an important intermediate in the combustion of aromatic hydrocarbons and in polycyclic aromatic hydrocarbon (PAH) formation in flames. Despite being a free radical, benzyl is relatively stable in thermal, oxidizing environments, and is predominantly removed through bimolecular reactions with open-shell species other than O(2). In this study the reaction of benzyl with ground-state atomic oxygen, O((3)P), is examined using quantum chemistry and statistical reaction rate theory. C(7)H(7)O energy surfaces are generated at the G3SX level, and include several novel pathways. Transition state theory is used to describe elementary reaction kinetics, with canonical variational transition state theory applied for barrierless O atom association with benzyl. Apparent rate constants and branching ratios to different product sets are obtained as a function of temperature and pressure from solving the time-dependent master equation, with RRKM theory for microcanonical k(E). These simulations indicate that the benzyl + O reaction predominantly forms the phenyl radical (C(6)H(5)) plus formaldehyde (HCHO), with lesser quantities of the C(7)H(6)O products benzaldehyde, ortho-quinone methide, and para-quinone methide (+H), along with minor amounts of the formyl radical (HCO) + benzene. Addition of O((3)P) to the methylene site in benzyl produces a highly vibrationally excited C(7)H(7)O* adduct, the benzoxyl radical, which can β-scission to benzaldehyde + H and phenyl + HCHO. In order to account for the experimental observation of benzene as the major reaction product, a roaming radical mechanism is proposed that converts the nascent products phenyl and HCHO to benzene + HCO. Oxygen atom addition at the ortho and para ring sites in benzyl, which has not been previously considered, is shown to lead to the quinone methides + H; these species are less-stable isomers of benzaldehyde that are proposed as important combustion intermediates, but are yet to be identified experimentally. Franck-Condon simulations of the benzaldehyde, o-quinone methide, and p-quinone methide photoelectron spectra suggest that these C(7)H(6)O isomers could be distinguished using tunable VUV photoionization mass spectrometry.

Structural Evolution of Iron Antimonides from Amorphous Precursors to Crystalline Products Studied by Total Scattering Techniques.

PubMed

Bauers, Sage R; Wood, Suzannah R; Jensen, Kirsten M Ø; Blichfeld, Anders B; Iversen, Bo B; Billinge, Simon J L; Johnson, David C

2015-08-05

Homogeneous reaction precursors may be used to form several solid-state compounds inaccessible by traditional synthetic routes, but there has been little development of techniques that allow for a priori prediction of what may crystallize in a given material system. Here, the local structures of FeSbx designed precursors are determined and compared with the structural motifs of their crystalline products. X-ray total scattering and atomic pair distribution function (PDF) analysis are used to show that precursors that first nucleate a metastable FeSb3 compound share similar local structure to the product. Interestingly, precursors that directly crystallize to thermodynamically stable FeSb2 products also contain local structural motifs of the metastable phase, despite their compositional disagreement. While both crystalline phases consist of distorted FeSb6 octahedra with Sb shared between either two or three octahedra as required for stoichiometry, a corner-sharing arrangement indicative of AX3-type structures is the only motif apparent in the PDF of either precursor. Prior speculation was that local composition controlled which compounds nucleate from amorphous intermediates, with different compositions favoring different local arrangements and hence different products. This data suggests that local environments in these amorphous intermediates may not be very sensitive to overall composition. This can provide insight into potential metastable phases which may form in a material system, even with a precursor that does not crystallize to the kinetically stabilized product. Determination of local structure in homogeneous amorphous reaction intermediates from techniques such as PDF can be a valuable asset in the development of systematic methods to prepare targeted solid-state compounds from designed precursors.

Exquisite Modulation of the Active Site of Methanocaldococcus jannaschii Adenylosuccinate Synthetase in Forward Reaction Complexes.

PubMed

Karnawat, Vishakha; Mehrotra, Sonali; Balaram, Hemalatha; Puranik, Mrinalini

2016-05-03

In enzymes that conduct complex reactions involving several substrates and chemical transformations, the active site must reorganize at each step to complement the transition state of that chemical step. Adenylosuccinate synthetase (ADSS) utilizes a molecule each of guanosine 5'-monophosphate (GTP) and aspartate to convert inosine 5'-monophosphate (IMP) into succinyl adenosine 5'-monophosphate (sAMP) through several kinetic intermediates. Here we followed catalysis by ADSS through high-resolution vibrational spectral fingerprints of each substrate and intermediate involved in the forward reaction. Vibrational spectra show differential ligand distortion at each step of catalysis, and band positions of substrates are influenced by binding of cosubstrates. We found that the bound IMP is distorted toward its N1-deprotonated form even in the absence of any other ligands. Several specific interactions between GTP and active-site amino acid residues result in large Raman shifts and contribute substantially to intrinsic binding energy. When both IMP and GTP are simultaneously bound to ADSS, IMP is converted into an intermediate 6-phosphoryl inosine 5'-monophosphate (6-pIMP). The 6-pIMP·ADSS complex was found to be stable upon binding of the third ligand, hadacidin (HDA), an analogue of l-aspartate. We find that in the absence of HDA, 6-pIMP is quickly released from ADSS, is unstable in solution, and converts back into IMP. HDA allosterically stabilizes ADSS through local conformational rearrangements. We captured this complex and determined the spectra and structure of 6-pIMP in its enzyme-bound state. These results provide important insights into the exquisite tuning of active-site interactions with changing substrate at each kinetic step of catalysis.

An investigation into the applicability of the semiempirical method PM7 for modeling the catalytic mechanism in the enzyme chymotrypsin.

PubMed

Stewart, James J P

2017-05-01

The catalytic cycle for the serine protease α-chymotrypsin was investigated in an attempt to determine the suitability of using the semiempirical method PM7 in the program MOPAC for investigating enzyme-catalyzed reactions. All six classical intermediates were modeled using standard methods, and were characterized as stable minima on the potential energy surface. Using a modified saddle point optimization method, five transition states were located and verified both by vibrational and by intrinsic reaction coordinate analysis. Some individual features, such as the hydrogen bonds in the oxyanion hole, the nature of various electrostatic interactions, and the role of Met192, were examined. This involved designing and running computational experiments to model mutations that would allow features of interest, in particular the energies involved, to be isolated. Three features within the enzyme were examined in detail: the reaction site itself, where covalent bonds were made and broken, the electrostatic effects of the buried aspartate anion, a passive but essential component of the catalytic triad, and the oxyanion hole, where hydrogen bonds help stabilize charged intermediates. With one minor exception, all phenomena investigated agreed with previously-reported descriptions. This result, along with the fact that all the techniques used were relatively straightforward, leads to the recommendation that PM7 and related methods, such as PM6-D3H4, are appropriate for modeling similar enzyme-catalyzed reactions. Graphical abstract Fifth of six transition states, showing water splitting into hydroxyl anion and a proton, to form the second tetrahedral intermediate and histidinium ion. Atoms of the water molecule involved in the hydrolysis are indicated by halos.

Structural and Mechanical Properties of Intermediate Filaments under Extreme Conditions and Disease

NASA Astrophysics Data System (ADS)

Qin, Zhao

Intermediate filaments are one of the three major components of the cytoskeleton in eukaryotic cells. It was discovered during the recent decades that intermediate filament proteins play key roles to reinforce cells subjected to large-deformation as well as participate in signal transduction. However, it is still poorly understood how the nanoscopic structure, as well as the biochemical properties of these protein molecules contribute to their biomechanical functions. In this research we investigate the material function of intermediate filaments under various extreme mechanical conditions as well as disease states. We use a full atomistic model and study its response to mechanical stresses. Learning from the mechanical response obtained from atomistic simulations, we build mesoscopic models following the finer-trains-coarser principles. By using this multiple-scale model, we present a detailed analysis of the mechanical properties and associated deformation mechanisms of intermediate filament network. We reveal the mechanism of a transition from alpha-helices to beta-sheets with subsequent intermolecular sliding under mechanical force, which has been inferred previously from experimental results. This nanoscale mechanism results in a characteristic nonlinear force-extension curve, which leads to a delocalization of mechanical energy and prevents catastrophic fracture. This explains how intermediate filament can withstand extreme mechanical deformation of > 1 00% strain despite the presence of structural defects. We combine computational and experimental techniques to investigate the molecular mechanism of Hutchinson-Gilford progeria syndrome, a premature aging disease. We find that the mutated lamin tail .domain is more compact and stable than the normal one. This altered structure and stability may enhance the association of intermediate filaments with the nuclear membrane, providing a molecular mechanism of the disease. We study the nuclear membrane association with intermediate filaments by focusing on the effect of calcium on the maturation process of lamin A. Our result shows that calcium plays a regulatory role in the post-translational processing of lam in A by tuning its molecular conformation and mechanics. Based on these findings we demonstrate that multiple-scale computational modeling provides a useful tool in understanding the biomechanical property and disease mechanism of intermediate filaments. We provide a perspective on research opportunities to improve the foundation for engineering the mechanical and biochemical functions of biomaterials. (Copies available exclusively from MIT Libraries, libraries.mit.edu/docs - docs@mit.edu)

Time-dependent evolution of cosmic-ray-modified shock structure: Transition to steady state

NASA Astrophysics Data System (ADS)

Donohue, D. J.; Zank, G. P.; Webb, G. M.

1994-03-01

Steady state solutions to the two-fluid equations of cosmic-ray-modified shock structure were investigated first by Drury and Volk (1981). Their analysis revealed, among other properties, that there exist regions of upstream parameter space where the equations possess three different downstream solutions for a given upstream state. In this paper we investigate whether or not all these solutions can occur as time-asymptotic states in a physically realistic evolution. To do this, we investigate the time-dependent evolution of the two-fluid cosmic-ray equations in going from a specified initial condition to a steady state. Our results indicate that the time-asymptotic solution is strictly single-valued, and it undergoes a transition from weakly to strongly cosmic-ray-modified at a critical value of the upstream cosmic ray energy density. The expansion of supernova remnant shocks is considered as an example, and it is shown that the strong to weak transition is in fact more likely. The third intermediate solution is shown to influence the time-dependent evolution of the shock, but it is not found to be a stable time-asymptotic state. Timescales for convergence to these states and their implications for the efficiency of shock acceleration are considered. We also investigate the effects of a recently introduced model for the injection of seed particles into the shock accelerated cosmic-ray population. The injection is found to result in a more strongly cosmic-ray-dominated shock, which supports our conclusion that for most classes of intermediate and strong cosmic-ray-modified shocks, the downstream cosmic-ray pressure component is at least as large as the thermal gas pressure, independent of the upstream state. As a result, cosmic rays almost always play a significant role in determining the shock structure and dissipation and they cannot be regarded as test particles.

Time-dependent evolution of cosmic-ray-modified shock structure: Transition to steady state

NASA Technical Reports Server (NTRS)

Donohue, D. J.; Zank, G. P.; Webb, G. M.

1994-01-01

Steady state solutions to the two-fluid equations of cosmic-ray-modified shock structure were investigated first by Drury and Volk (1981). Their analysis revealed, among other properties, that there exist regions of upstream parameter space where the equations possess three different downstream solutions for a given upstream state. In this paper we investigate whether or not all these solutions can occur as time-asymptotic states in a physically realistic evolution. To do this, we investigate the time-dependent evolution of the two-fluid cosmic-ray equations in going from a specified initial condition to a steady state. Our results indicate that the time-asymptotic solution is strictly single-valued, and it undergoes a transition from weakly to strongly cosmic-ray-modified at a critical value of the upstream cosmic ray energy density. The expansion of supernova remnant shocks is considered as an example, and it is shown that the strong to weak transition is in fact more likely. The third intermediate solution is shown to influence the time-dependent evolution of the shock, but it is not found to be a stable time-asymptotic state. Timescales for convergence to these states and their implications for the efficiency of shock acceleration are considered. We also investigate the effects of a recently introduced model for the injection of seed particles into the shock accelerated cosmic-ray population. The injection is found to result in a more strongly cosmic-ray-dominated shock, which supports our conclusion that for most classes of intermediate and strong cosmic-ray-modified shocks, the downstream cosmic-ray pressure component is at least as large as the thermal gas pressure, independent of the upstream state. As a result, cosmic rays almost always play a significant role in determining the shock structure and dissipation and they cannot be regarded as test particles.

Analysis of the gas phase reactivity of chlorosilanes.

PubMed

Ravasio, Stefano; Masi, Maurizio; Cavallotti, Carlo

2013-06-27

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

Deciphering the kinetic mechanisms controlling selected plant ADP-glucose pyrophosphorylases.

PubMed

Boehlein, Susan K; Shaw, Janine R; Hwang, Seon K; Stewart, Jon D; Curtis Hannah, L

2013-07-15

ADP-Glc pyrophosphorylase (AGPase), a rate-limiting enzyme in starch biosynthesis, is controlled by thermostability and allosteric regulation. Previous studies suggested that redox affects turnover number and heat stability of AGPases. Here, we investigated how allostery and redox state affect kinetic mechanisms of the reduced, heat labile and the oxidized, heat stable potato tuber enzymes; the heat labile maize endosperm enzyme and a chimeric maize/potato heat stable enzyme that lacks the cysteine responsible for redox changes. With 3-PGA, all AGPases followed a Theorell-Chance Bi Bi mechanism with ATP binding first and ADP-Glc releasing last. 3-PGA increases the binding affinity for both substrates with little effect on velocity for the maize and MP isoforms. By contrast, 3-PGA increases the velocity and the affinity for G-1-P for the potato enzymes. Redox state does not affect kcat of the two potato isoforms. Without 3-PGA the oxidized potato enzyme exhibits a rapid equilibrium random Bi Bi mechanism with a dead end ternary complex. This fundamental change from rapid, ordered binding with little buildup of intermediates to a mechanism featuring relatively slow, random binding is unique to the oxidized potato tuber enzyme. Finally, ADP-Glc the physiologically relevant product of this enzyme has complex, isoform-specific effects on catalysis. Copyright © 2013 Elsevier Inc. All rights reserved.

Structural stability of vault particles.

PubMed

Esfandiary, Reza; Kickhoefer, Valerie A; Rome, Leonard H; Joshi, Sangeeta B; Middaugh, C Russell

2009-04-01

Vaults, at 13 MDa, are the largest ribonucleoprotein particles known. In vitro, expression of the major vault protein (MVP) alone in Sf9 insect cells results in the production of recombinant particles with characteristic vault structure. With the ultimate goal of using recombinant vaults as nanocapsules for the delivery of biomolecules, we have employed a variety of spectroscopic techniques (i.e., circular dichroism, fluorescence spectroscopy, and light scattering) along with electron microscopy, to characterize the structural stability of vaults over a wide range of pH (3-8) and temperature (10-90 degrees C). Ten different conformational states of the vaults were identified over the pH and temperature range studied with the most stable region at pH 6-8 below 40 degrees C and least stable at pH 4-6 above 60 degrees C. A unique intermediate molten globulelike state was also identified at pH 6 and approximately 55 degrees C. EM imaging showed the opening of intact vaults into flowerlike structures when transitioning from neutral to acidic pH. This information has potential use in the development of recombinant vaults into nanocapsules for drug delivery since one mechanism by which therapeutic agents entrapped in vaults could be released is through an opening of the intact vault structure.

Study of thermal annealing effect on Bragg gratings photo-inscribed in step-index polymer optical fibers

NASA Astrophysics Data System (ADS)

Hu, X.; Kinet, D.; Mégret, P.; Caucheteur, C.

2016-04-01

In this paper, both non-annealed and annealed trans-4-stilbenemethanol-doped step-index polymer optical fibers were photo-inscribed using a 325 nm HeCd laser with two different beam power densities reaching the fiber core. In the high density regime where 637 mW/mm2 are used, the grating reflectivity is stable over time after the photo-writing process but the reflected spectrum is of limited quality, as the grating physical length is limited to 1.2 mm. To produce longer gratings exhibiting more interesting spectral features, the beam is enlarged to 6 mm, decreasing the power density to 127 mW/mm2. In this second regime, the grating reflectivity is not stable after the inscription process but tends to decay for both kinds of fibers. A fortunate property in this case results from the possibility to fully recover the initial reflectivity using a post-inscription thermal annealing, where the gratings are annealed at 80 °C during 2 days. The observed evolutions for both regimes are attributed to the behavior of the excited intermediate states between the excited singlet and the ground singlet state of trans- and cis-isomers as well as the temperature-dependent glassy polymer matrix.

42 CFR 456.401 - State plan UR requirements and options; UR plan required for intermediate care facility services.

Code of Federal Regulations, 2012 CFR

2012-10-01

... required for intermediate care facility services. 456.401 Section 456.401 Public Health CENTERS FOR...: General Requirement § 456.401 State plan UR requirements and options; UR plan required for intermediate care facility services. (a) The State plan must provide that— (1) UR is performed for each ICF that...

42 CFR 456.401 - State plan UR requirements and options; UR plan required for intermediate care facility services.

Code of Federal Regulations, 2010 CFR

2010-10-01

... required for intermediate care facility services. 456.401 Section 456.401 Public Health CENTERS FOR...: General Requirement § 456.401 State plan UR requirements and options; UR plan required for intermediate care facility services. (a) The State plan must provide that— (1) UR is performed for each ICF that...

42 CFR 456.401 - State plan UR requirements and options; UR plan required for intermediate care facility services.

Code of Federal Regulations, 2013 CFR

2013-10-01

... required for intermediate care facility services. 456.401 Section 456.401 Public Health CENTERS FOR...: General Requirement § 456.401 State plan UR requirements and options; UR plan required for intermediate care facility services. (a) The State plan must provide that— (1) UR is performed for each ICF that...

Physics of intermediate shocks: A review

NASA Technical Reports Server (NTRS)

Karimabadi, H.

1995-01-01

Intermediate shocks (ISs) lead to a transition from super-Alfvenic to sub-Alfvenic flow and are different from slow and fast shocks in that an IS rotates the component of the magnetic field tangent to the shock plane by 180 deg. Another peculiarity of ISs is that for the same upstream conditions an IS can have two different downstream states. There also exist a second class of ISs which rotate the magnetic field by an angle other than 180 deg. Due to their noncoplanar nature they cannot be time-stationary and are referred to as time-dependent intermediate shocks (TDIS). The existence of ISs has been the subject of much controversy over the years. Early studies questioned the physical reality of ISs. However, the studies of ISs found a new impetus when C.C. Wu showed that ISs do exist and are stable within the resistive MHD framework. In this paper, after a brief historical overview of the subject, we will review the latest developments in the study of ISs. In particular, we will address the questions of stability and structure of ISs and the relationship between ISs and other discontinuities. One of the recent developments has been the finding that ISs can be unsteady, reforming in time. Details of this process will be discussed. Finally, we examine the effect of anisotropy on the resolutions and discuss the relevance of ISs to the observed field rotations at the Earth's magnetopause.

Structural basis for the appearance of a molten globule state in chimeric molecules derived from lysozyme and alpha-lactalbumin.

PubMed

Joniau, M; Haezebrouck, P; Noyelle, K; Van Dael, H

2001-07-01

The problem as to why alpha-lactalbumin, in the absence of Ca(2+), forms a molten globule intermediate, in contrast to its structural homologue lysozyme, has been addressed by the construction of chimeras of human lysozyme in which either the Ca(2+)-binding loop or a part of helix C of bovine alpha-lactalbumin were transplanted. Previously, we have shown that the introduction of both structural elements together in the lysozyme matrix causes the apo form of the resulting chimera to display molten globule behavior during the course of thermal denaturation. In this article, we demonstrate that this molten globule character is not correlated with the Ca(2+)-binding loop. Also, the Del 101 mutant in which Arg101 was deleted to simulate the alpha-lactalbumin conformation of the connecting loop between helix C and helix D, does not show a stable equilibrium intermediate. Rather, the molten globule character of the chimeras has to be related with a specific part of helix C. More particularly, attention is drawn to the four hydrophobic side-chains I93, V96, I99, and L100, the lysozyme counterparts of which are constituted of less bulky valines and alanine. Our observations are discussed in terms of decreased stability of the native form and increased stability of the intermediate molten globule. Copyright 2001 Wiley-Liss, Inc.

Methane formation from the hydrogenation of carbon dioxide on Ni(110) surface--a density functional theoretical study.

PubMed

Bothra, Pallavi; Periyasamy, Ganga; Pati, Swapan K

2013-04-21

The complete hydrogenation mechanisms of CO2 are explored on Ni(110) surface catalyst using density functional theory. We have studied the possible hydrogenation mechanism to form product methane from the stable adsorption-co-adsorption intermediates of CO2 and H2 on Ni(110) surface. Our computations clearly elucidate that the mechanism for the formation of methyl, methoxy and methane moieties from carbon dioxide on the nickel catalyst. Moreover, our studies clearly show that the methane formation via hydroxyl carbonyl intermediate requires a lower energy barrier than via carbon monoxide and formate intermediates on the Ni(110) surface.

M-aminophenyltrialkylstannane

DOEpatents

Kassis, Amin I.; Khawli, Leslie A.

1990-01-01

m-Radiohalo-aniline is a stable intermediate for preparing biotin-m-radiohalo-anilide to be used as an imaging agent or therapeutic agent. The invention also contemplates m-aminophenyltrialkylstannane which can be radiohalogenated and linked to biotin.

Characterization of a transient +2 sulfur oxidation state intermediate from the oxidation of aqueous sulfide

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

Vairavmurthy, M.A.; Zhou, Weiqing

1995-04-01

The oxidation H{sub 2}S to sulfate involves a net transfer of eight electrons and occurs through the formation of several partially oxidized intermediates with oxidation states ranging from {minus}1 to +5. Known intermediates include elemental sulfur (oxidation state 0), polysulfides (outer sulfur: {minus}1, inner sulfur: 0), sulfite (+4) and thiosulfate (outer sulfur: {minus}1, inner sulfur: +5). A noticeable gap in this series of intermediates is that of a +2 sulfur oxidation state oxoacid/oxoanion species, which was never detected experimentally. Here, we present evidence of the transient existence of +2 oxidation state intermediate in the Ni(II)-catalyzed oxidation of aqueous sulfide. X-raymore » absorption near-edge structure (XANES) spectroscopy and Fourier-transform-infrared (FT-IR) spectroscopy were used to characterize this species; they suggest that it has a sulfoxylate ion (SO{sub 2}{sup 2{minus}}) structure.« less

Analysis of membrane fusion as a two-state sequential process: evaluation of the stalk model.

PubMed

Weinreb, Gabriel; Lentz, Barry R

2007-06-01

We propose a model that accounts for the time courses of PEG-induced fusion of membrane vesicles of varying lipid compositions and sizes. The model assumes that fusion proceeds from an initial, aggregated vesicle state ((A) membrane contact) through two sequential intermediate states (I(1) and I(2)) and then on to a fusion pore state (FP). Using this model, we interpreted data on the fusion of seven different vesicle systems. We found that the initial aggregated state involved no lipid or content mixing but did produce leakage. The final state (FP) was not leaky. Lipid mixing normally dominated the first intermediate state (I(1)), but content mixing signal was also observed in this state for most systems. The second intermediate state (I(2)) exhibited both lipid and content mixing signals and leakage, and was sometimes the only leaky state. In some systems, the first and second intermediates were indistinguishable and converted directly to the FP state. Having also tested a parallel, two-intermediate model subject to different assumptions about the nature of the intermediates, we conclude that a sequential, two-intermediate model is the simplest model sufficient to describe PEG-mediated fusion in all vesicle systems studied. We conclude as well that a fusion intermediate "state" should not be thought of as a fixed structure (e.g., "stalk" or "transmembrane contact") of uniform properties. Rather, a fusion "state" describes an ensemble of similar structures that can have different mechanical properties. Thus, a "state" can have varying probabilities of having a given functional property such as content mixing, lipid mixing, or leakage. Our data show that the content mixing signal may occur through two processes, one correlated and one not correlated with leakage. Finally, we consider the implications of our results in terms of the "modified stalk" hypothesis for the mechanism of lipid pore formation. We conclude that our results not only support this hypothesis but also provide a means of analyzing fusion time courses so as to test it and gauge the mechanism of action of fusion proteins in the context of the lipidic hypothesis of fusion.

Independent of Their Localization in Protein the Hydrophobic Amino Acid Residues Have No Effect on the Molten Globule State of Apomyoglobin and the Disulfide Bond on the Surface of Apomyoglobin Stabilizes This Intermediate State

PubMed Central

Melnik, Tatiana N.; Majorina, Maria A.; Larina, Daria S.; Kashparov, Ivan A.; Samatova, Ekaterina N.; Glukhov, Anatoly S.; Melnik, Bogdan S.

2014-01-01

At present it is unclear which interactions in proteins reveal the presence of intermediate states, their stability and formation rate. In this study, we have investigated the effect of substitutions of hydrophobic amino acid residues in the hydrophobic core of protein and on its surface on a molten globule type intermediate state of apomyoglobin. It has been found that independent of their localization in protein, substitutions of hydrophobic amino acid residues do not affect the stability of the molten globule state of apomyoglobin. It has been shown also that introduction of a disulfide bond on the protein surface can stabilize the molten globule state. However in the case of apomyoglobin, stabilization of the intermediate state leads to relative destabilization of the native state of apomyoglobin. The result obtained allows us not only to conclude which mutations can have an effect on the intermediate state of the molten globule type, but also explains why the introduction of a disulfide bond (which seems to “strengthen” the protein) can result in destabilization of the protein native state of apomyoglobin. PMID:24892675

Independent of their localization in protein the hydrophobic amino acid residues have no effect on the molten globule state of apomyoglobin and the disulfide bond on the surface of apomyoglobin stabilizes this intermediate state.

PubMed

Melnik, Tatiana N; Majorina, Maria A; Larina, Daria S; Kashparov, Ivan A; Samatova, Ekaterina N; Glukhov, Anatoly S; Melnik, Bogdan S

2014-01-01

At present it is unclear which interactions in proteins reveal the presence of intermediate states, their stability and formation rate. In this study, we have investigated the effect of substitutions of hydrophobic amino acid residues in the hydrophobic core of protein and on its surface on a molten globule type intermediate state of apomyoglobin. It has been found that independent of their localization in protein, substitutions of hydrophobic amino acid residues do not affect the stability of the molten globule state of apomyoglobin. It has been shown also that introduction of a disulfide bond on the protein surface can stabilize the molten globule state. However in the case of apomyoglobin, stabilization of the intermediate state leads to relative destabilization of the native state of apomyoglobin. The result obtained allows us not only to conclude which mutations can have an effect on the intermediate state of the molten globule type, but also explains why the introduction of a disulfide bond (which seems to "strengthen" the protein) can result in destabilization of the protein native state of apomyoglobin.

Evidence against Stable Protein S-Nitrosylation as a Widespread Mechanism of Post-translational Regulation.

PubMed

Wolhuter, Kathryn; Whitwell, Harry J; Switzer, Christopher H; Burgoyne, Joseph R; Timms, John F; Eaton, Philip

2018-02-01

S-nitrosation, commonly referred to as S-nitrosylation, is widely regarded as a ubiquitous, stable post-translational modification that directly regulates many proteins. Such a widespread role would appear to be incompatible with the inherent lability of the S-nitroso bond, especially its propensity to rapidly react with thiols to generate disulfide bonds. As anticipated, we observed robust and widespread protein S-nitrosation after exposing cells to nitrosocysteine or lipopolysaccharide. Proteins detected using the ascorbate-dependent biotin switch method are typically interpreted to be directly regulated by S-nitrosation. However, these S-nitrosated proteins are shown to predominantly comprise transient intermediates leading to disulfide bond formation. These disulfides are likely to be the dominant end effectors resulting from elevations in nitrosating cellular nitric oxide species. We propose that S-nitrosation primarily serves as a transient intermediate leading to disulfide formation. Overall, we conclude that the current widely held perception that stable S-nitrosation directly regulates the function of many proteins is significantly incorrect. Copyright © 2017 The Author(s). Published by Elsevier Inc. All rights reserved.

M-aminophenyltrialkylstannane

DOEpatents

Kassis, A.I.; Khawli, L.A.

1990-12-11

m-Radiohalo-aniline is a stable intermediate for preparing biotin-m-radiohalo-anilide to be used as an imaging agent or therapeutic agent. The invention also contemplates m-aminophenyltrialkylstannane which can be radiohalogenated and linked to biotin. No Drawings

Simulating the multicellular homeostasis with a cell-based discrete receptor dynamics model: The non-mutational origin of cancer and aging.

PubMed

Lou, Yuting; Chen, Yu

2016-09-07

The purpose of the study is to investigate the multicellular homeostasis in epithelial tissues over very large timescales. Inspired by the receptor dynamics of IBCell model proposed by Rejniak et al. an on-grid agent-based model for multicellular system is constructed. Instead of observing the multicellular architectural morphologies, the diversity of homeostatic states is quantitatively analyzed through a substantial number of simulations by measuring three new order parameters, the phenotypic population structure, the average proliferation age and the relaxation time to stable homeostasis. Nearby the interfaces of distinct homeostatic phases in 3D phase diagrams of the three order parameters, intermediate quasi-stable phases of slow dynamics that features quasi-stability with a large spectrum of relaxation timescales are found. A further exploration on the static and dynamic correlations among the three order parameters reveals that the quasi-stable phases evolve towards two terminations, tumorigenesis and degeneration, which are respectively accompanied by rejuvenation and aging. With the exclusion of the environmental impact and the mutational strategies, the results imply that cancer and aging may share the non-mutational origin in the intrinsic slow dynamics of the multicellular systems. Copyright © 2016 Elsevier Ltd. All rights reserved.

Crystal structures of different substrates of bacteriorhodopsin's M intermediate at various pH levels.

PubMed

Yamamoto, Masataka; Hayakawa, Naoki; Murakami, Midori; Kouyama, Tsutomu

2009-10-30

The hexagonal P622 crystal of bacteriorhodopsin, which is made up of stacked membranes, is stable provided that the precipitant concentration in the soaking solution is higher than a critical value (i.e., 1.5 M ammonium sulfate). Diffraction data showed that the crystal lattice shrank linearly with increasing precipitant concentration, due primarily to narrowing of intermembrane spaces. Although the crystal shrinkage did not affect the rate of formation of the photoreaction M intermediate, its lifetime increased exponentially with the precipitant concentration. It was suggested that the energetic barrier of the M-to-N transition becomes higher when the motional freedom of the EF loop is reduced by crystal lattice force. As a result of this property, the M state accumulated predominantly when the crystal that was soaked at a high precipitant concentration was illuminated at room temperature. Structural data obtained at various pH levels showed that the overall structure of M is not strongly dependent on pH, except that Glu194 and Glu204 in the proton release complex are more separated at pH 7 than at pH 4.4. This result suggests that light-induced disruption of the paired structure of Glu194 and Glu204 is incomplete when external pH is lower than the pK(a) value of the proton release group in the M state.

Field Theoretic Study of Bilayer Membrane Fusion. I. Hemifusion Mechanism

PubMed Central

Katsov, K.; Müller, M.; Schick, M.

2004-01-01

Self-consistent field theory is used to determine structural and energetic properties of metastable intermediates and unstable transition states involved in the standard stalk mechanism of bilayer membrane fusion. A microscopic model of flexible amphiphilic chains dissolved in hydrophilic solvent is employed to describe these self-assembled structures. We find that the barrier to formation of the initial stalk is much smaller than previously estimated by phenomenological theories. Therefore its creation it is not the rate-limiting process. The relevant barrier is associated with the rather limited radial expansion of the stalk into a hemifusion diaphragm. It is strongly affected by the architecture of the amphiphile, decreasing as the effective spontaneous curvature of the amphiphile is made more negative. It is also reduced when the tension is increased. At high tension the fusion pore, created when a hole forms in the hemifusion diaphragm, expands without bound. At very low membrane tension, small fusion pores can be trapped in a flickering metastable state. Successful fusion is severely limited by the architecture of the lipids. If the effective spontaneous curvature is not sufficiently negative, fusion does not occur because metastable stalks, whose existence is a seemingly necessary prerequisite, do not form at all. However if the spontaneous curvature is too negative, stalks are so stable that fusion does not occur because the system is unstable either to a phase of stable radial stalks, or to an inverted-hexagonal phase induced by stable linear stalks. Our results on the architecture and tension needed for successful fusion are summarized in a phase diagram. PMID:15326031

A Theoretical Probe for Excitation Mechanisms of Sun-like and Mira-like Oscillations of Stars

NASA Astrophysics Data System (ADS)

Xiong, Da-run; Deng, Li-cai

2013-01-01

The linear nonadiabatic oscillations for evolutionary models of 0.6- 3M8 stars are calculated by using a nonlocal and time-dependent convection theory. The results show that in the HR diagram the pulsation-unstable low- temperature stars on the right side of instability strip can be divided into two groups. One group indicates the Sun-like oscillation stars composed of the main- sequence dwarfs, sub-giants and red giants (RGs) of low and intermediate lu- minosities, which are unstable in the intermediate- and high-order (n ≥ 12) p- modes, and stable in the low-order (n ≤ 5) p-modes. Another group indicates the Mira-like stars composed of the bright RGs and asymptotic giant branch (AGB) stars, which are just contrary to Sun-like stars, unstable in low-order (n ≤ 5) p-modes and stable in the intermediate- and high-order (n ≥ 12) p-modes. The oscillations for the red edge of Cepheid (δ Scuti) instability strip, Sun-like and Mira-like stars can be explained uniformly by the coupling between convection and oscillation (CCO). For the low-temperature stars on the right side of in- stability strip, CCO is the dominant excitation and damping mechanism of the oscillations of low- and intermediate-order p-modes, and the turbulent stochas- tic excitation becomes important only for the high-order p-modes of Sun-like oscillations.

Theoretical studies to understand surface chemistry on carbon anodes for lithium-ion batteries: how does vinylene carbonate play its role as an electrolyte additive?

PubMed

Wang, Yixuan; Nakamura, Shinichiro; Tasaki, Ken; Balbuena, Perla B

2002-04-24

To elucidate the role of vinylene carbonate (VC) as a solvent additive in organic polar solutions for lithium-ion batteries, reductive decompositions for vinylene carbonate (VC) and ethylene carbonate (EC) molecules have been comprehensively investigated both in the gas phase and in solution by means of density functional theory calculations. The salt and solvent effects are incorporated with the clusters (EC)nLi+(VC) (n = 0-3), and further corrections that account for bulk solvent effects are added using the polarized continuum model (PCM). The electron affinities of (EC)nLi+(VC) (n = 0-3) monotonically decrease when the number of EC molecules increases; a sharp decrease of about 20.0 kcal/mol is found from n = 0 to 1 and a more gentle variation for n > 1. For (EC)nLi+(VC) (n = 1-3), the reduction of VC brings about more stable ion-pair intermediates than those due to reduction of the EC molecule by 3.1, 6.1, and 5.3 kcal/mol, respectively. This finding qualitatively agrees with the experimental fact that the reduction potential of VC in the presence of Li salt is more negative than that of EC. The calculated reduction potentials corresponding to radical anion formation are close to the experimental potentials determined with cyclic voltammetry on a gold electrode surface (-2.67, -3.19 eV on the physical scale for VC and EC respectively vs experimental values -2.96 and -2.94 eV). Regarding the decomposition mechanisms, the VC and EC moieties undergo homolytic ring opening from their respective reduction intermediates, and the energy barrier of VC is about one time higher than that of EC (e.g., 20.1 vs 8.8 kcal/mol for (EC)2Li+(VC)); both are weakly affected by the explicit solvent molecules and by a bulk solvent represented by a continuum model. Alternatively, starting from the VC-reduction intermediate, the ring opening of the EC moiety via an intramolecular electron-transfer transition state has also been located; its barrier lies between those of EC and VC (e.g., 17.2 kcal/mol for (EC)2Li+(VC)). On the basis of these results, we suggest the following explanation about the role that VC may play as additive in EC-based lithium-ion battery electrolytes; VC is initially reduced to a more stable intermediate than that from EC reduction. One possibility then is that the reduced VC decomposes to form a radical anion via a barrier of about 20 kcal/mol, which undergoes a series of reactions to give rise to more active film-forming products than those resulting from EC reduction, such as lithium divinylene dicarbonate, Li-C carbides, lithium vinylene dicarbonate, R-O-Li compound, and even oligomers with repeated vinylene and carbonate-vinylene units. Another possibility starting from the VC-reduction intermediate is that the ring opening occurs on the unreduced EC moiety instead of being on the reduced VC, via an intramolecular electron transfer transition state, the energy barrier of which is lower than that of the former, in which VC just helps the intermediate formation and is not consumed. The factors that determine the additive functioning mechanism are briefly discussed, and consequently a general rule for the selection of electrolyte additive is proposed.

Low-Temperature Synthesis of New Ternary Chalcogenide Compounds of Copper, Gold, and Mercury Using Alkali Metal Polychalcogenide Fluxes

NASA Astrophysics Data System (ADS)

Park, Younbong

In last two decades great efforts have been exerted to find new materials with interesting optical, electrical, and catalytic properties. Metal chalcogenides have been studied extensively because of their interesting physical properties and rich structural chemistry, among the potential materials. Prior to this work, most known metal chalcogenides had been synthesized at high temperature (T > 500^circC). Intermediate temperature synthesis in solid state chemistry was seldom pursued because of the extremely slow diffusion rates between reactants. This intermediate temperature regime could be a new synthesis condition if one looks for new materials with unusual structural features and properties. Metastable or kinetically stable compounds can be stabilized in this intermediate temperature regime, in contrast to the thermodynamically stable high temperature compounds. Molten salts, especially alkali metal polychalcogenide fluxes, can provide a route for exploring new chalcogenide materials at intermediate temperatures. These fluxes are very reactive and melt as low as 145^circC (mp of K_2S_4). Using these fluxes as reaction media, we have encountered many novel chalcogenide compounds with unusual structures and interesting electrical properties (semiconductors to metallic conductors). Low-dimensional polychalcogenide compounds of alpha-ACuQ_4 (A = K, Cs; Q = S, Se), beta -KCuS_4, KAuQ_5 (Q = S, Se), K_3AuSe_ {13}, Na_3AuSe _8, and CsAuSe_3 exhibit the beautiful structural diversity and bonding flexibility of the polychalcogenide ligands. In addition, many novel chalcogenide compounds of Cu, Hg, and Au with low-dimensional structures. The preparation of novel mixed -valence Cu compounds, K_2Cu _5Te_5, Cs _3Cu_8Te_ {10}, Na_3Cu _4Se_4, K _3Cu_8S_4 Te_2, and KCu_4 S_2Te, which show interesting metallic properties, especially underscores the enormous potential of the molten salt method for the synthesis of new chalcogenide materials with interesting physical properties. The materials prepared in this study can be classified as a new class of chalcogenide compounds due to their unique structures. In this dissertation the synthesis, characterization with emphasis on structures, charge transport properties, and magnetic susceptibilities of the materials will be illustrated.

Differentiation among Multiple Sources of Anthropogenic Nitrate in a Complex Groundwater System using Dual Isotope Systematics: A case study from Mortandad Canyon, New Mexico

NASA Astrophysics Data System (ADS)

Larson, T. E.; Perkins, G.; Longmire, P.; Heikoop, J. M.; Fessenden, J. E.; Rearick, M.; Fabyrka-Martin, J.; Chrystal, A. E.; Dale, M.; Simmons, A. M.

2009-12-01

The groundwater system beneath Los Alamos National Laboratory has been affected by multiple sources of anthropogenic nitrate contamination. Average NO3-N concentrations of up to 18.2±1.7 mg/L have been found in wells in the perched intermediate aquifer beneath one of the more affected sites within Mortandad Canyon. Sources of nitrate potentially reaching the alluvial and intermediate aquifers include: (1) sewage effluent, (2) neutralized nitric acid, (3) neutralized 15N-depleted nitric acid (treated waste from an experiment enriching nitric acid in 15N), and (4) natural background nitrate. Each of these sources is unique in δ18O and δ15N space. Using nitrate stable isotope ratios, a mixing model for the three anthropogenic sources of nitrate was established, after applying a linear subtraction of the background component. The spatial and temporal variability in nitrate contaminant sources through Mortandad Canyon is clearly shown in ternary plots. While microbial denitrification has been shown to change groundwater nitrate stable isotope ratios in other settings, the redox potential, relatively high dissolved oxygen content, increasing nitrate concentrations over time, and lack of observed NO2 in these wells suggest minimal changes to the stable isotope ratios have occurred. Temporal trends indicate that the earliest form of anthropogenic nitrate in this watershed was neutralized nitric acid. Alluvial wells preserve a trend of decreasing nitrate concentrations and mixing models show decreasing contributions of 15N-depleted nitric acid. Nearby intermediate wells show increasing nitrate concentrations and mixing models indicate a larger component derived from 15N-depleted nitric acid. These data indicate that the pulse of neutralized 15N-depleted nitric acid that was released into Mortandad Canyon between 1986 and 1989 has infiltrated through the alluvial aquifer and is currently affecting two intermediate wells. This hypothesis is consistent with previous research suggesting that the perched intermediate aquifers in the Mortandad Canyon watershed are recharged locally from the overlying alluvial aquifers.

Electron doped layered nickelates: Spanning the phase diagram of the cuprates

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

Botana, Antia S.; Pardo, Victor; Norman, Michael R.

2017-07-01

Pr4Ni3O8 is an overdoped analog of hole-doped layered cuprates. Here we show via ab initio calculations that Ce-doped Pr4Ni3O8 (Pr3CeNi3O8) has the same electronic structure as the antiferromagnetic insulating phase of parent cuprates.We find that substantial Ce doping should be thermodynamically stable and that other 4+ cations would yield a similar antiferromagnetic insulating state, arguing this configuration is robust for layered nickelates of low-enough valence. The analogies with cuprates at different d fillings suggest that intermediate Ce-doping concentrations near 1/8 should be an appropriate place to search for superconductivity in these low-valence Ni oxides.

Mineralogical maturity in dunefields of North America, Africa and Australia

USGS Publications Warehouse

Muhs, D.R.

2004-01-01

Studies of dunefields in central and western North America show that mineralogical maturity can provide new insights into the origin and evolution of aeolian sand bodies. Many of the world's great sand seas in Africa, Asia and Australia are quartz-dominated and thus can be considered to be mineralogically mature. The Algodones (California) and Parker (Arizona) dunes in the southwestern United States are also mature, but have inherited a high degree of mineralogical maturity from quartz-rich sedimentary rocks drained by the Colorado River. In Libya, sediments of the Zallaf sand sea, which are almost pure quartz, may have originated in a similar fashion. The Fort Morgan (Colorado) and Casper (Wyoming) dunefields in the central Great Plains of North America, and the Namib sand sea of southern Africa have an intermediate degree of mineralogical maturity because their sources are large rivers that drained both unweathered plutonic and metamorphic rocks and mature sedimentary rocks. Mojave Desert dunefields in the southwestern United States are quite immature because they are in basins adjacent to plutonic rocks that were their sources. Other dunefields in the Great Plains of North America (those in Nebraska and Texas) are more mature than any possible source sediments and therefore reflect mineralogical evolution over time. Such changes in composition can occur because of either of two opposing long-term states of the dunefield. In one state, dunes are stable for long periods of time and chemical weathering depletes feldspars and other weatherable minerals in the sediment body. In the other state, which is most likely for the Great Plains, abrasion and ballistic impacts deplete the carbonate minerals and feldspars because the dunes are active for longer periods than they are stable. ?? 2003 Elsevier B.V. All rights reserved.

Evidence for a Shared Mechanism in the Formation of Urea-Induced Kinetic and Equilibrium Intermediates of Horse Apomyoglobin from Ultrarapid Mixing Experiments

PubMed Central

Mizukami, Takuya; Abe, Yukiko; Maki, Kosuke

2015-01-01

In this study, the equivalence of the kinetic mechanisms of the formation of urea-induced kinetic folding intermediates and non-native equilibrium states was investigated in apomyoglobin. Despite having similar structural properties, equilibrium and kinetic intermediates accumulate under different conditions and via different mechanisms, and it remains unknown whether their formation involves shared or distinct kinetic mechanisms. To investigate the potential mechanisms of formation, the refolding and unfolding kinetics of horse apomyoglobin were measured by continuous- and stopped-flow fluorescence over a time range from approximately 100 μs to 10 s, along with equilibrium unfolding transitions, as a function of urea concentration at pH 6.0 and 8°C. The formation of a kinetic intermediate was observed over a wider range of urea concentrations (0–2.2 M) than the formation of the native state (0–1.6 M). Additionally, the kinetic intermediate remained populated as the predominant equilibrium state under conditions where the native and unfolded states were unstable (at ~0.7–2 M urea). A continuous shift from the kinetic to the equilibrium intermediate was observed as urea concentrations increased from 0 M to ~2 M, which indicates that these states share a common kinetic folding mechanism. This finding supports the conclusion that these intermediates are equivalent. Our results in turn suggest that the regions of the protein that resist denaturant perturbations form during the earlier stages of folding, which further supports the structural equivalence of transient and equilibrium intermediates. An additional folding intermediate accumulated within ~140 μs of refolding and an unfolding intermediate accumulated in <1 ms of unfolding. Finally, by using quantitative modeling, we showed that a five-state sequential scheme appropriately describes the folding mechanism of horse apomyoglobin. PMID:26244984

Fatal attraction in glycolysis: how Saccharomyces cerevisiae manages sudden transitions to high glucose

PubMed Central

Heerden, Johan H. v.; Wortel, Meike T.; Bruggeman, Frank J.; Heijnen, Joseph J.; Bollen, Yves J.; Planqué, Robert; Hulshof, Josephus; O’Toole, Tom G.; Wahl, S. A.; Teusink, Bas

2014-01-01

In the model eukaryote Saccharomyces cerevisiae, it has long been known that a functional trehalose pathway is indispensable for transitions to high glucose conditions. Upon addition of glucose, cells with a defect in trehalose 6-phosphate synthase (Tps1), the first committed step in the trehalose pathway, display what we have termed an imbalanced glycolytic state; in this state the flux through the upper part of glycolysis outpaces that through the lower part of glycolysis. As a consequence, the intermediate fructose 1,6-bisphosphate (FBP) accumulates at low concentrations of ATP and inorganic phosphate (Pi). Despite significant research efforts, a satisfactory understanding of the regulatory role that trehalose metabolism plays during such transitions has remained infamously unresolved. In a recent study, we demonstrate that the startup of glycolysis exhibits two dynamic fates: a proper, functional, steady state or the imbalanced state described above. Both states are stable, attracting states, and the probability distribution of initial states determines the fate of a yeast cell exposed to glucose. Trehalose metabolism steers the dynamics of glycolysis towards the proper functional state through its ATP hydrolysis activity; a mechanism that ensures that the demand and supply of ATP is balanced with Pi availability under dynamic conditions. [van Heerden et al. Science (2014), DOI: 10.1126/science.1245114.] PMID:28357229

29 CFR 452.123 - Elections of intermediate body officers.

Code of Federal Regulations, 2011 CFR

2011-07-01

... 29 Labor 2 2011-07-01 2011-07-01 false Elections of intermediate body officers. 452.123 Section... intermediate body officers. Section 401(d) states that officers of intermediate bodies shall be elected either... intermediate bodies. Such delegates may therefore participate in the election of officers of intermediate...

29 CFR 452.123 - Elections of intermediate body officers.

Code of Federal Regulations, 2010 CFR

2010-07-01

... 29 Labor 2 2010-07-01 2010-07-01 false Elections of intermediate body officers. 452.123 Section... intermediate body officers. Section 401(d) states that officers of intermediate bodies shall be elected either... intermediate bodies. Such delegates may therefore participate in the election of officers of intermediate...

Multi-shell spherical GaAs /AlxGa1-x As quantum dot shells-size distribution as a mechanism to generate intermediate band energy levels

NASA Astrophysics Data System (ADS)

Rodríguez-Magdaleno, K. A.; Pérez-Álvarez, R.; Martínez-Orozco, J. C.; Pernas-Salomón, R.

2017-04-01

In this work the generation of an intermediate band of energy levels from multi-shell spherical GaAs /AlxGa1-x As quantum dot shells-size distribution is reported. Within the effective mass approximation the electronic structure of a GaAs spherical quantum-dot surrounded by one, two and three shells is studied in detail using a numerically stable transfer matrix method. We found that a shells-size distribution characterized by continuously wider GaAs domains is a suitable mechanism to generate the intermediate band whose width is also dependent on the Aluminium concentration x. Our results suggest that this effective mechanism can be used for the design of wider intermediate band than reported in other quantum systems with possible solar cells enhanced performance.

Coherence resonance in low-density jets

NASA Astrophysics Data System (ADS)

Zhu, Yuanhang; Gupta, Vikrant; Li, Larry K. B.

2017-11-01

Coherence resonance is a phenomenon in which the response of a stable nonlinear system to noise exhibits a peak in coherence at an intermediate noise amplitude. We report the first experimental evidence of coherence resonance in a purely hydrodynamic system, a low-density jet whose variants can be found in many natural and engineering systems. This evidence comprises four parts: (i) the jet's response amplitude increases as the Reynolds number approaches the instability boundary under a constant noise amplitude; (ii) as the noise amplitude increases, the amplitude distribution of the jet response first becomes unimodal, then bimodal, and finally unimodal again; (iii) a distinct peak emerges in the coherence factor at an intermediate noise amplitude; and (iv) for a subcritical Hopf bifurcation, the decay rate of the autocorrelation function exhibits a maximum at an intermediate noise amplitude, but for a supercritical Hopf bifurcation, the decay rate decreases monotonically with increasing noise amplitude. It is clear that coherence resonance can provide valuable information about a system's nonlinearity even in the unconditionally stable regime, opening up new possibilities for its use in system identification and flow control. This work was supported by the Research Grants Council of Hong Kong (Project No. 16235716 and 26202815).

New observations concerning the chloroacetaldehyde reaction with some tRNA constituents. Stable intermediates, kinetics and selectivity of the reaction.

PubMed Central

Biernat, J; Ciesiołka, J; Górnicki, P; Adamiak, R W; Kryzosiak, W J; Wiewiórowski, M

1978-01-01

The stable intermediates formed in the reaction of cytosine, cytidine and adenosine with chloracetaldehyde were isolated. The -CH2CH/OH/- bridge between the exo and endo nitrogen atoms of the parent base was found in these compounds by means of PMR spectroscopy. Their acid-induced dehydration resulted in formation of appropriate ethenoderivatives. The rate constants of the intermediate formation and its dehydration were found to be 38x10(-4) and 47x10(-4) /min-1/ for adenosine, and 33x10(-4) and 10x10(-4) /min-1/ for cytidine. The PH range of 4.5--5.0 was found to be optimum for both adenosine and cytidine reactions. The quantitative modification of these two nucleosides in the presence of guanosine may be achieved with high selectivity only at a low pH of 3.0--4.0 N6-methyladenosine and N4-methylcytidine react quantitatively with chloroacetaldehyde and the reaction rate is higher than in the case of the parent nucleosides. The structure of the reaction products was assigned on the basis of PMR spectroscopy. PMID:25420

Triggering the approach of an arene or heteroarene towards an aldehyde via Lewis acid-aldehyde communication.

PubMed

Pratihar, Sanjay

2016-03-14

The present work reports a combined experimental/computational study of the Lewis acid promoted hydroxyalkylation reaction involving aldehyde and arene/heteroarene and reveals a mechanism in which the rate determining aldehyde to alcohol formation via a four-member cyclic transition state (TS) involves a transfer of hydrogen from arene/heteroarene C-H to aldehyde oxygen with the breaking of the C-H bond and formation of C-C and O-H bonds. The effect of different Sn(iv) derivatives on the hydroxyalkylation reaction from different in situ NMR and computational studies reveals that although the exergonic formation of the intermediate and its gained electrophilicity at the carbonyl carbon drive the reaction in SnCl4 compared to other Sn(iv) derivatives, the overall reaction is low yielding because of its stable intermediate. With respect to different aldehydes, LA promoted hydroxylation was found to be more feasible for an electron withdrawing aldehyde compared to electron rich aldehyde because of lower stability, enhanced electrophilicity gained at the aldehyde center, and a lower activation barrier between its intermediate and TS in the former as compared to the latter. The relative stability of the LA-aldehyde adduct decreases in the order SnCl4 > AlCl3 > InCl3 > BF3 > ZnCl2 > TiCl4 > SiCl4, while the activation barrier (ΔG(#)) between intermediate and transition states increases in the order AlCl3 < SnCl4 < InCl3 < BF3 < TiCl4 < ZnCl2 < SiCl4. On the other hand, the activation barriers in the case of different arenes/heteroarenes are in the order of indole < furan < anisole < thiophene < toluene < benzene < chlorobenzene < cyanobenzene, which suggests a facile reaction in the case of indole and the most difficult reaction in the case of cyanobenzene. The ease of formation of the corresponding diaryl methyl carbocation from the alcohol-LA intermediate is responsible for the determination of the undesired product and is found to be more viable in the case of strong LAs like AlCl3, InCl3 and SnCl4 because they have negative free energy of formation (ΔG) for alcohol to the corresponding diaryl methyl carbocation.

Two-photon absorption by spectrally shaped entangled photons

NASA Astrophysics Data System (ADS)

Oka, Hisaki

2018-03-01

We theoretically investigate two-photon excitation by spectrally shaped entangled photons with energy anticorrelation in terms of how the real excitation of an intermediate state affects two-photon absorption by entangled photons. Spectral holes are introduced in the entangled photons around the energy levels of an intermediate state so that two-step excitation via the real excitation of the intermediated state can be suppressed. Using a three-level atomic system as an example, we show that the spectral holes well suppress the real excitation of the intermediate state and recover two-photon absorption via a virtual state. Furthermore, for a short pulse close to a monocycle, we show that the excitation efficiency by the spectrally shaped entangled photons can be enhanced a thousand times as large as that by uncorrelated photons.

How Does Your Protein Fold? Elucidating the Apomyoglobin Folding Pathway

PubMed Central

Dyson, H. Jane; Wright, Peter E.

2017-01-01

Conspectus Although each type of protein fold and in some cases individual proteins within a fold classification can have very different mechanisms of folding, the underlying biophysical and biochemical principles that operate to cause a linear polypeptide chain to fold into a globular structure must be the same. In an aqueous solution, the protein takes up the thermodynamically most stable structure, but the pathway along which the polypeptide proceeds in order to reach that structure is a function of the amino acid sequence, which must be the final determining factor, not only in shaping the final folded structure, but in dictating the folding pathway. A number of groups have focused on a single protein or group of proteins, to determine in detail the factors that influence the rate and mechanism of folding in a defined system, with the hope that hypothesis-driven experiments can elucidate the underlying principles governing the folding process. Our research group has focused on the folding of the globin family of proteins, and in particular on the monomeric protein apomyoglobin. Apomyoglobin (apoMb) folds relatively slowly (~2 seconds) via an ensemble of obligatory intermediates that form rapidly after the initiation of folding. The folding pathway can be dissected using rapid-mixing techniques, which can probe processes in the millisecond time range. Stopped-flow measurements detected by circular dichroism (CD) or fluorescence spectroscopy give information on the rates of folding events. Quench-flow experiments utilize the differential rates of hydrogen-deuterium exchange of amide protons protected in parts of the structure that are folded early; protection of amides can be detected by mass spectrometry or proton nuclear magnetic resonance spectroscopy (NMR). In addition, apoMb forms an intermediate at equilibrium at pH ~ 4, which is sufficiently stable for it to be structurally characterized by solution methods such as CD, fluorescence and NMR spectroscopies, and the conformational ensembles formed in the presence of denaturing agents and low pH can be characterized as models for the unfolded states of the protein. Newer NMR techniques such as measurement of residual dipolar couplings in the various partly folded states, and relaxation dispersion measurements to probe invisible states present at low concentrations, have contributed to providing a detailed picture of the apomyoglobin folding pathway. The research summarized in this review was aimed at characterizing and comparing the equilibrium and kinetic intermediates both structurally and dynamically, as well as delineating the complete folding pathway at a residue-specific level, in order to answer the question “What is it about the amino acid sequence that causes each molecule in the unfolded protein ensemble to start folding, and, once started, to proceed towards the formation of the correctly folded three-dimensional structure?” PMID:28032989

Grain-damage hysteresis and plate tectonic states

NASA Astrophysics Data System (ADS)

Bercovici, David; Ricard, Yanick

2016-04-01

Shear localization in the lithosphere is an essential ingredient for understanding how and why plate tectonics is generated from mantle convection on terrestrial planets. The theoretical model for grain-damage and pinning in two-phase polycrystalline rocks provides a frame-work for understanding lithospheric shear weakening and plate-generation, and is consistent with laboratory and field observations of mylonites. Grain size evolves through the competition between coarsening, which drives grain-growth, and damage, which drives grain reduction. The interface between crystalline phases controls Zener pinning, which impedes grain growth. Damage to the interface enhances the Zener pinning effect, which then reduces grain-size, forcing the rheology into the grain-size-dependent diffusion creep regime. This process thus allows damage and rheological weakening to co-exist, providing a necessary positive self-weakening feedback. Moreover, because pinning inhibits grain-growth it promotes shear-zone longevity and plate-boundary inheritance. However, the suppression of interface damage at low interface curvature (wherein inter-grain mixing is inefficient and other energy sinks of deformational work are potentially more facile) causes a hysteresis effect, in which three possible equilibrium grain-sizes for a given stress coexist: (1) a stable, large-grain, weakly-deforming state, (2) a stable, small-grain, rapidly-deforming state analogous to ultramylonites, and (3) an unstable, intermediate grain-size state perhaps comparable to protomylonites. A comparison of the model to field data suggests that shear-localized zones of small-grain mylonites and ultra-mylonites exist at a lower stress than the co-existing large-grain porphyroclasts, rather than, as predicted by paleopiezometers or paleowattmeters, at a much higher stress; this interpretation of field data thus allows localization to relieve instead of accumulate stress. The model also predicts that a lithosphere that deforms at a given stress can acquire two stable deformation regimes indicative of plate-like flows, i.e., it permits the coexistence of both slowly deforming plate interiors, and rapidly deforming plate boundaries. Earth seems to exist squarely inside the hysteresis loop and thus can have coexisting deformation states, while Venus appears to straddle the end of the loop where only the weakly deforming branch exists.

Structure of photosystem II and substrate binding at room temperature.

PubMed

Young, Iris D; Ibrahim, Mohamed; Chatterjee, Ruchira; Gul, Sheraz; Fuller, Franklin; Koroidov, Sergey; Brewster, Aaron S; Tran, Rosalie; Alonso-Mori, Roberto; Kroll, Thomas; Michels-Clark, Tara; Laksmono, Hartawan; Sierra, Raymond G; Stan, Claudiu A; Hussein, Rana; Zhang, Miao; Douthit, Lacey; Kubin, Markus; de Lichtenberg, Casper; Long Vo, Pham; Nilsson, Håkan; Cheah, Mun Hon; Shevela, Dmitriy; Saracini, Claudio; Bean, Mackenzie A; Seuffert, Ina; Sokaras, Dimosthenis; Weng, Tsu-Chien; Pastor, Ernest; Weninger, Clemens; Fransson, Thomas; Lassalle, Louise; Bräuer, Philipp; Aller, Pierre; Docker, Peter T; Andi, Babak; Orville, Allen M; Glownia, James M; Nelson, Silke; Sikorski, Marcin; Zhu, Diling; Hunter, Mark S; Lane, Thomas J; Aquila, Andy; Koglin, Jason E; Robinson, Joseph; Liang, Mengning; Boutet, Sébastien; Lyubimov, Artem Y; Uervirojnangkoorn, Monarin; Moriarty, Nigel W; Liebschner, Dorothee; Afonine, Pavel V; Waterman, David G; Evans, Gwyndaf; Wernet, Philippe; Dobbek, Holger; Weis, William I; Brunger, Axel T; Zwart, Petrus H; Adams, Paul D; Zouni, Athina; Messinger, Johannes; Bergmann, Uwe; Sauter, Nicholas K; Kern, Jan; Yachandra, Vittal K; Yano, Junko

2016-12-15

Light-induced oxidation of water by photosystem II (PS II) in plants, algae and cyanobacteria has generated most of the dioxygen in the atmosphere. PS II, a membrane-bound multi-subunit pigment protein complex, couples the one-electron photochemistry at the reaction centre with the four-electron redox chemistry of water oxidation at the Mn 4 CaO 5 cluster in the oxygen-evolving complex (OEC). Under illumination, the OEC cycles through five intermediate S-states (S 0 to S 4 ), in which S 1 is the dark-stable state and S 3 is the last semi-stable state before O-O bond formation and O 2 evolution. A detailed understanding of the O-O bond formation mechanism remains a challenge, and will require elucidation of both the structures of the OEC in the different S-states and the binding of the two substrate waters to the catalytic site. Here we report the use of femtosecond pulses from an X-ray free electron laser (XFEL) to obtain damage-free, room temperature structures of dark-adapted (S 1 ), two-flash illuminated (2F; S 3 -enriched), and ammonia-bound two-flash illuminated (2F-NH 3 ; S 3 -enriched) PS II. Although the recent 1.95 Å resolution structure of PS II at cryogenic temperature using an XFEL provided a damage-free view of the S 1 state, measurements at room temperature are required to study the structural landscape of proteins under functional conditions, and also for in situ advancement of the S-states. To investigate the water-binding site(s), ammonia, a water analogue, has been used as a marker, as it binds to the Mn 4 CaO 5 cluster in the S 2 and S 3 states. Since the ammonia-bound OEC is active, the ammonia-binding Mn site is not a substrate water site. This approach, together with a comparison of the native dark and 2F states, is used to discriminate between proposed O-O bond formation mechanisms.

Urinary functional outcomes and toxicity five years after proton therapy for low- and intermediate-risk prostate cancer: Results of two prospective trials

PubMed Central

2013-01-01

Background. To assess genitourinary (GU) function and toxicity in patients treated with image-guided proton therapy (PT) for early- and intermediate-risk prostate cancer and to analyze the impact of pretreatment urinary obstructive symptoms on urinary function after PT. Material and methods. Two prospective trials accrued 171 prostate cancer patients from August 2006 to September 2007. Low-risk patients received 78 cobalt gray equivalent (CGE) in 39 fractions and intermediate-risk patients received 78–82 CGE. Median follow-up was five years. The International Prostate Symptom Score (IPSS) and GU toxicities (per CTCAE v3.0 and v4.0) were documented prospectively. Results. Five transient GU events were scored Gr 3 per CTCAE v4.0, for a cumulative late GU toxicity rate of 2.9% at five years. There were no Gr 4 or 5 events. On multivariate analysis (MVA), the only factor predictive of Gr 2 + GU toxicity was pretreatment GU symptom management (p = 0.0058). Patients with pretreatment IPSS of 15–25 had a decline (clinical improvement) in median IPSS from 18 before treatment to 10 at their 60-month follow-up. At last follow-up, 18 (54.5%) patients had a > 5-point decline, 14 (42.5%) remained stable, and two patients (3%) had a > 5-point rise (deterioration) in IPSS. Patients with IPSS < 15 had a stable median IPSS of 6 before treatment and at 60 months. Conclusion. Urologic toxicity at five years with image-guided PT has been uncommon and transient. Patients with pretreatment IPSS of < 15 had stable urinary function five years after PT, but patients with 15–25 showed substantial improvement (decline) in median IPSS, a finding not explained by initiation or dose adjustment of alpha blockers. This suggests that PT provides a minimally toxic and effective treatment for low and intermediate prostate cancer patients, including those with significant pretreatment GU dysfunction (IPSS 15–25). PMID:23477359

Transient intermediates are populated in the folding pathways of single-domain two-state folding protein L

NASA Astrophysics Data System (ADS)

Maity, Hiranmay; Reddy, Govardhan

2018-04-01

Small single-domain globular proteins, which are believed to be dominantly two-state folders, played an important role in elucidating various aspects of the protein folding mechanism. However, recent single molecule fluorescence resonance energy transfer experiments [H. Y. Aviram et al. J. Chem. Phys. 148, 123303 (2018)] on a single-domain two-state folding protein L showed evidence for the population of an intermediate state and it was suggested that in this state, a β-hairpin present near the C-terminal of the native protein state is unfolded. We performed molecular dynamics simulations using a coarse-grained self-organized-polymer model with side chains to study the folding pathways of protein L. In agreement with the experiments, an intermediate is populated in the simulation folding pathways where the C-terminal β-hairpin detaches from the rest of the protein structure. The lifetime of this intermediate structure increased with the decrease in temperature. In low temperature conditions, we also observed a second intermediate state, which is globular with a significant fraction of the native-like tertiary contacts satisfying the features of a dry molten globule.

Tri-state resistive switching characteristics of MnO/Ta2O5 resistive random access memory device by a controllable reset process

NASA Astrophysics Data System (ADS)

Lee, N. J.; Kang, T. S.; Hu, Q.; Lee, T. S.; Yoon, T.-S.; Lee, H. H.; Yoo, E. J.; Choi, Y. J.; Kang, C. J.

2018-06-01

Tri-state resistive switching characteristics of bilayer resistive random access memory devices based on manganese oxide (MnO)/tantalum oxide (Ta2O5) have been studied. The current–voltage (I–V) characteristics of the Ag/MnO/Ta2O5/Pt device show tri-state resistive switching (RS) behavior with a high resistance state (HRS), intermediate resistance state (IRS), and low resistance state (LRS), which are controlled by the reset process. The MnO/Ta2O5 film shows bipolar RS behavior through the formation and rupture of conducting filaments without the forming process. The device shows reproducible and stable RS both from the HRS to the LRS and from the IRS to the LRS. In order to elucidate the tri-state RS mechanism in the Ag/MnO/Ta2O5/Pt device, transmission electron microscope (TEM) images are measured in the LRS, IRS and HRS. White lines like dendrites are observed in the Ta2O5 film in both the LRS and the IRS. Poole–Frenkel conduction, space charge limited conduction, and Ohmic conduction are proposed as the dominant conduction mechanisms for the Ag/MnO/Ta2O5/Pt device based on the obtained I–V characteristics and TEM images.

Analysis of heat recovery of diesel engine using intermediate working fluid

NASA Astrophysics Data System (ADS)

Jin, Lei; Zhang, Jiang; Tan, Gangfeng; Liu, Huaming

2017-07-01

The organic Rankine cycle (ORC) is an effective way to recovery the engine exhaust heat. The thermal stability of the evaporation system is significant for the stable operation of the ORC system. In this paper, the performance of the designed evaporation system which combines with the intermediate fluid for recovering the exhaust waste heat from a diesel engine is evaluated. The thermal characteristics of the target diesel engine exhaust gas are evaluated based on the experimental data firstly. Then, the mathematical model of the evaporation system is built based on the geometrical parameters and the specific working conditions of ORC. Finally, the heat transfer characteristics of the evaporation system are estimated corresponding to three typical operating conditions of the diesel engine. The result shows that the exhaust temperature at the evaporator outlet increases slightly with the engine speed and load. In the evaporator, the heat transfer coefficient of the Rankine working fluid is slightly larger than the intermediate fluid. However, the heat transfer coefficient of the intermediate fluid in the heat exchanger is larger than the exhaust side. The heat transfer areas of the evaporator in both the two-phase zone and the preheated zone change slightly along with the engine working condition while the heat transfer areas of the overheated zone has changed obviously. The maximum heat transfer rate occurs in the preheating zone while the minimum value occurs in the overheating zone. In addition, the Rankine working fluid temperature at the evaporator outlet is not sensitively affected by the torque and speed of the engine and the organic fluid flow is relatively stable. It is concluded that the intermediate fluid could effectively reduce the physical changes of Rankine working fluid in the evaporator outlet due to changes in engine operating conditions.

HIV-1 Env trimer opens through an asymmetric intermediate in which individual protomers adopt distinct conformations.

PubMed

Ma, Xiaochu; Lu, Maolin; Gorman, Jason; Terry, Daniel S; Hong, Xinyu; Zhou, Zhou; Zhao, Hong; Altman, Roger B; Arthos, James; Blanchard, Scott C; Kwong, Peter D; Munro, James B; Mothes, Walther

2018-03-21

HIV-1 entry into cells requires binding of the viral envelope glycoprotein (Env) to receptor CD4 and coreceptor. Imaging of individual Env molecules on native virions shows Env trimers to be dynamic, spontaneously transitioning between three distinct well-populated conformational states: a pre-triggered Env (State 1), a default intermediate (State 2) and a three-CD4-bound conformation (State 3), which can be stabilized by binding of CD4 and coreceptor-surrogate antibody 17b. Here, using single-molecule Fluorescence Resonance Energy Transfer (smFRET), we show the default intermediate configuration to be asymmetric, with individual protomers adopting distinct conformations. During entry, this asymmetric intermediate forms when a single CD4 molecule engages the trimer. The trimer can then transition to State 3 by binding additional CD4 molecules and coreceptor.

Combustion chemistry of ethanol: Ignition and speciation studies in a rapid compression facility [On the combustion chemistry of ethanol: Ignition and speciation studies in a rapid compression facility

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

Barraza-Botet, Cesar L.; Wagnon, Scott W.; Wooldridge, Margaret S.

Here, ethanol remains the most important alternative fuel for the transportation sector. This work presents new experimental data on ethanol ignition, including stable species measurements, obtained with the University of Michigan rapid compression facility. Ignition delay times were determined from pressure histories of ignition experiments with stoichiometric ethanol–air mixtures at pressures of ~3–10 atm. Temperatures (880–1150 K) were controlled by varying buffer gas composition (Ar, N 2, CO 2). High-speed imaging was used to record chemiluminescence during the experiments, which showed homogeneous ignition events. The results for ignition delay time agreed well with trends on the basis of previous experimentalmore » measurements. Speciation experiments were performed using fast gas sampling and gas chromatography to identify and quantify ethanol and 11 stable intermediate species formed during the ignition delay period. Simulations were carried out using a chemical kinetic mechanism available in the literature, and the agreement with the experimental results for ignition delay time and the intermediate species measured was excellent for the majority of the conditions studied. From the simulation results, ethanol + HO 2 was identified as an important reaction at the experimental conditions for both the ignition delay time and intermediate species measurements. Further studies to improve the accuracy of the rate coefficient for ethanol + HO 2 would improve the predictive understanding of intermediate and low-temperature ethanol combustion.« less

Combustion chemistry of ethanol: Ignition and speciation studies in a rapid compression facility [On the combustion chemistry of ethanol: Ignition and speciation studies in a rapid compression facility

DOE PAGES

Barraza-Botet, Cesar L.; Wagnon, Scott W.; Wooldridge, Margaret S.

2016-08-31

Here, ethanol remains the most important alternative fuel for the transportation sector. This work presents new experimental data on ethanol ignition, including stable species measurements, obtained with the University of Michigan rapid compression facility. Ignition delay times were determined from pressure histories of ignition experiments with stoichiometric ethanol–air mixtures at pressures of ~3–10 atm. Temperatures (880–1150 K) were controlled by varying buffer gas composition (Ar, N 2, CO 2). High-speed imaging was used to record chemiluminescence during the experiments, which showed homogeneous ignition events. The results for ignition delay time agreed well with trends on the basis of previous experimentalmore » measurements. Speciation experiments were performed using fast gas sampling and gas chromatography to identify and quantify ethanol and 11 stable intermediate species formed during the ignition delay period. Simulations were carried out using a chemical kinetic mechanism available in the literature, and the agreement with the experimental results for ignition delay time and the intermediate species measured was excellent for the majority of the conditions studied. From the simulation results, ethanol + HO 2 was identified as an important reaction at the experimental conditions for both the ignition delay time and intermediate species measurements. Further studies to improve the accuracy of the rate coefficient for ethanol + HO 2 would improve the predictive understanding of intermediate and low-temperature ethanol combustion.« less

A molten globule-like intermediate state detected in the thermal transition of cytochrome c under low salt concentration.

PubMed

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

2007-04-01

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

Trends in initial management of prostate cancer in New Hampshire.

PubMed

Ingimarsson, Johann P; Celaya, Maria O; Laviolette, Michael; Rees, Judy R; Hyams, Elias S

2015-06-01

Prostate cancer management strategies are evolving with increased understanding of the disease. Specifically, there is emerging evidence that "low-risk" cancer is best treated with observation, while localized "high-risk" cancer requires aggressive curative therapy. In this study, we evaluated trends in management of prostate cancer in New Hampshire to determine adherence to evidence-based practice. From the New Hampshire State Cancer Registry, cases of clinically localized prostate cancer diagnosed in 2004-2011 were identified and classified according to D'Amico criteria. Initial treatment modality was recorded as surgery, radiation therapy, expectant management, or hormone therapy. Temporal trends were assessed by Chi-square for trend. Of 6,203 clinically localized prostate cancers meeting inclusion criteria, 34, 30, and 28% were low-, intermediate-, and high-risk disease, respectively. For low-risk disease, use of expectant management (17-42%, p < 0.001) and surgery (29-39%, p < 0.001) increased, while use of radiation therapy decreased (49-19 %, p < 0.001). For intermediate-risk disease, use of surgery increased (24-50%, p < 0.001), while radiation decreased (58-34%, p < 0.001). Hormonal therapy alone was rarely used for low- and intermediate-risk disease. For high-risk patients, surgery increased (38-47%, p = 0.003) and radiation decreased (41-38%, p = 0.026), while hormonal therapy and expectant management remained stable. There are encouraging trends in the management of clinically localized prostate cancer in New Hampshire, including less aggressive treatment of low-risk cancer and increasing surgical treatment of high-risk disease.

High-pressure behavior of intermediate scapolite: compressibility, structure deformation and phase transition

NASA Astrophysics Data System (ADS)

Lotti, Paolo; Comboni, Davide; Merlini, Marco; Hanfland, Michael

2018-05-01

Scapolites are common volatile-bearing minerals in metamorphic rocks. In this study, the high-pressure behavior of an intermediate member of the scapolite solid solution series (Me47), chemical formula (Na1.86Ca1.86K0.23Fe0.01)(Al4.36Si7.64)O24[Cl0.48(CO3)0.48(SO4)0.01], has been investigated up to 17.79 GPa, by means of in situ single-crystal synchrotron X-ray diffraction. The isothermal elastic behavior of the studied scapolite has been described by a III-order Birch-Murnaghan equation of state, which provided the following refined parameters: V 0 = 1110.6(7) Å3, {K_{{V_0}}} = 70(2) GPa ({β _{{V_0}}} = 0.0143(4) GPa-1) and {K_{{V}}^' = 4.8(7). The refined bulk modulus is intermediate between those previously reported for Me17 and Me68 scapolite samples, confirming that the bulk compressibility among the solid solution increases with the Na content. A discussion on the P-induced structure deformation mechanisms of tetragonal scapolite at the atomic scale is provided, along with the implications of the reported results for the modeling of scapolite stability. In addition, a single-crystal to single-crystal phase transition, which is displacive in character, has been observed toward a triclinic polymorph at 9.87 GPa. The high-pressure triclinic polymorph was found to be stable up to the highest pressure investigated.

Ultrathin dendrimer-graphene oxide composite film for stable cycling lithium-sulfur batteries.

PubMed

Liu, Wen; Jiang, Jianbing; Yang, Ke R; Mi, Yingying; Kumaravadivel, Piranavan; Zhong, Yiren; Fan, Qi; Weng, Zhe; Wu, Zishan; Cha, Judy J; Zhou, Henghui; Batista, Victor S; Brudvig, Gary W; Wang, Hailiang

2017-04-04

Lithium-sulfur batteries (Li-S batteries) have attracted intense interest because of their high specific capacity and low cost, although they are still hindered by severe capacity loss upon cycling caused by the soluble lithium polysulfide intermediates. Although many structure innovations at the material and device levels have been explored for the ultimate goal of realizing long cycle life of Li-S batteries, it remains a major challenge to achieve stable cycling while avoiding energy and power density compromises caused by the introduction of significant dead weight/volume and increased electrochemical resistance. Here we introduce an ultrathin composite film consisting of naphthalimide-functionalized poly(amidoamine) dendrimers and graphene oxide nanosheets as a cycling stabilizer. Combining the dendrimer structure that can confine polysulfide intermediates chemically and physically together with the graphene oxide that renders the film robust and thin (<1% of the thickness of the active sulfur layer), the composite film is designed to enable stable cycling of sulfur cathodes without compromising the energy and power densities. Our sulfur electrodes coated with the composite film exhibit very good cycling stability, together with high sulfur content, large areal capacity, and improved power rate.

Metal-deficient SOD1 in amyotrophic lateral sclerosis.

PubMed

Hilton, James B; White, Anthony R; Crouch, Peter J

2015-05-01

Mutations to the ubiquitous antioxidant enzyme Cu/Zn superoxide dismutase (SOD1) were the first established genetic cause of the fatal, adult-onset neurodegenerative disease amyotrophic lateral sclerosis (ALS). It is widely accepted that these mutations do not cause ALS via a loss of antioxidant function, but elucidating the alternate toxic gain of function has proven to be elusive. Under physiological conditions, SOD1 binds one copper ion and one zinc ion per monomer to form a highly stable and functional homodimer, but there is now ample evidence to indicate aberrant persistence of SOD1 in an intermediate metal-deficient state may contribute to the protein's involvement in ALS. This review briefly discusses some of the data to support a role for metal-deficient SOD1 in the development of ALS and some of the outcomes from drug development studies that have aimed to modify the symptoms of ALS by targeting the metal state of SOD1. The implications for the metal state of SOD1 in cases of sporadic ALS that do not involve mutant SOD1 are also discussed.

Folding 19 proteins to their native state and stability of large proteins from a coarse-grained model.

PubMed

Kapoor, Abhijeet; Travesset, Alex

2014-03-01

We develop an intermediate resolution model, where the backbone is modeled with atomic resolution but the side chain with a single bead, by extending our previous model (Proteins (2013) DOI: 10.1002/prot.24269) to properly include proline, preproline residues and backbone rigidity. Starting from random configurations, the model properly folds 19 proteins (including a mutant 2A3D sequence) into native states containing β sheet, α helix, and mixed α/β. As a further test, the stability of H-RAS (a 169 residue protein, critical in many signaling pathways) is investigated: The protein is stable, with excellent agreement with experimental B-factors. Despite that proteins containing only α helices fold to their native state at lower backbone rigidity, and other limitations, which we discuss thoroughly, the model provides a reliable description of the dynamics as compared with all atom simulations, but does not constrain secondary structures as it is typically the case in more coarse-grained models. Further implications are described. Copyright © 2013 Wiley Periodicals, Inc.

Method for producing metal oxide aerogels

DOEpatents

Tillotson, Thomas M.; Poco, John F.; Hrubesh, Lawrence W.; Thomas, Ian M.

1995-01-01

A two-step hydrolysis-condensation method was developed to form metal oxide aerogels of any density, including densities of less than 0.003g/cm.sup.3 and greater than 0.27g/cm.sup.3. High purity metal alkoxide is reacted with water, alcohol solvent, and an additive to form a partially condensed metal intermediate. All solvent and reaction-generated alcohol is removed, and the intermediate is diluted with a nonalcoholic solvent. The intermediate can be stored for future use to make aerogels of any density. The aerogels are formed by reacting the intermediate with water, nonalcoholic solvent, and a catalyst, and extracting the nonalcoholic solvent directly. The resulting monolithic aerogels are hydrophobic and stable under atmospheric conditions, and exhibit good optical transparency, high clarity, and homogeneity. The aerogels have high thermal insulation capacity, high porosity, mechanical strength and stability, and require shorter gelation times than aerogels formed by conventional methods.

Method for producing metal oxide aerogels

DOEpatents

Tillotson, T.M.; Poco, J.F.; Hrubesh, L.W.; Thomas, I.M.

1995-04-25

A two-step hydrolysis-condensation method was developed to form metal oxide aerogels of any density, including densities of less than 0.003g/cm{sup 3} and greater than 0.27g/cm{sup 3}. High purity metal alkoxide is reacted with water, alcohol solvent, and an additive to form a partially condensed metal intermediate. All solvent and reaction-generated alcohol is removed, and the intermediate is diluted with a nonalcoholic solvent. The intermediate can be stored for future use to make aerogels of any density. The aerogels are formed by reacting the intermediate with water, nonalcoholic solvent, and a catalyst, and extracting the nonalcoholic solvent directly. The resulting monolithic aerogels are hydrophobic and stable under atmospheric conditions, and exhibit good optical transparency, high clarity, and homogeneity. The aerogels have high thermal insulation capacity, high porosity, mechanical strength and stability, and require shorter gelation times than aerogels formed by conventional methods. 8 figs.

Unique Proton Transportation Pathway in a Robust Inorganic Coordination Polymer Leading to Intrinsically High and Sustainable Anhydrous Proton Conductivity.

PubMed

Gui, Daxiang; Dai, Xing; Tao, Zetian; Zheng, Tao; Wang, Xiangxiang; Silver, Mark A; Shu, Jie; Chen, Lanhua; Wang, Yanlong; Zhang, Tiantian; Xie, Jian; Zou, Lin; Xia, Yuanhua; Zhang, Jujia; Zhang, Jin; Zhao, Ling; Diwu, Juan; Zhou, Ruhong; Chai, Zhifang; Wang, Shuao

2018-05-16

Although comprehensive progress has been made in the area of coordination polymer (CP)/metal-organic framework (MOF)-based proton-conducting materials over the past decade, searching for a CP/MOF with stable, intrinsic, high anhydrous proton conductivity that can be directly used as a practical electrolyte in an intermediate-temperature proton-exchange membrane fuel cell assembly for durable power generation remains a substantial challenge. Here, we introduce a new proton-conducting CP, (NH 4 ) 3 [Zr(H 2/3 PO 4 ) 3 ] (ZrP), which consists of one-dimensional zirconium phosphate anionic chains and fully ordered charge-balancing NH 4 + cations. X-ray crystallography, neutron powder diffraction, and variable-temperature solid-state NMR spectroscopy suggest that protons are disordered within an inherent hydrogen-bonded infinite chain of acid-base pairs (N-H···O-P), leading to a stable anhydrous proton conductivity of 1.45 × 10 -3 S·cm -1 at 180 °C, one of the highest values among reported intermediate-temperature proton-conducting materials. First-principles and quantum molecular dynamics simulations were used to directly visualize the unique proton transport pathway involving very efficient proton exchange between NH 4 + and phosphate pairs, which is distinct from the common guest encapsulation/dehydration/superprotonic transition mechanisms. ZrP as the electrolyte was further assembled into a H 2 /O 2 fuel cell, which showed a record-high electrical power density of 12 mW·cm -2 at 180 °C among reported cells assembled from crystalline solid electrolytes, as well as a direct methanol fuel cell for the first time to demonstrate real applications. These cells were tested for over 15 h without notable power loss.

Structure of Mandelate Racemase with Bound Intermediate Analogues Benzohydroxamate and Cupferron†

PubMed Central

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

2012-01-01

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

The synthesis of a tritium, carbon-14, and stable isotope-labeled cathepsin C inhibitors.

PubMed

Allen, Paul; Bragg, Ryan A; Caffrey, Moya; Ericsson, Cecilia; Hickey, Michael J; Kingston, Lee P; Elmore, Charles S

2017-02-01

As part of a medicinal chemistry program aimed at developing a highly potent and selective cathepsin C inhibitor, tritium, carbon-14, and stable isotope-labeled materials were required. The synthesis of tritium-labeled methanesulfonate 5 was achieved via catalytic tritiolysis of a chloro precursor, albeit at a low radiochemical purity of 67%. Tritium-labeled AZD5248 was prepared via a 3-stage synthesis, utilizing amide-directed hydrogen isotope exchange. Carbon-14 and stable isotope-labeled AZD5248 were successfully prepared through modifications of the medicinal chemistry synthetic route, enabling the use of available labeled intermediates. Copyright © 2016 John Wiley & Sons, Ltd.

Shellwise Mackay transformation in iron nanoclusters.

PubMed

Rollmann, Georg; Gruner, Markus E; Hucht, Alfred; Meyer, Ralf; Entel, Peter; Tiago, Murilo L; Chelikowsky, James R

2007-08-24

Structure and magnetism of iron clusters with up to 641 atoms have been investigated by means of density functional theory calculations including full geometric optimizations. Body-centered cubic (bcc) isomers are found to be lowest in energy when the clusters contain more than about 100 atoms. In addition, another stable conformation has been identified for magic-number clusters, which lies well within the range of thermal energies as compared to the bcc isomers. Its structure is characterized by a close-packed particle core and an icosahedral surface, while intermediate shells are partially transformed along the Mackay path between icosahedral and cuboctahedral geometry. The gradual transformation results in a favorable bcc environment for the subsurface atoms. For Fe55, the shellwise Mackay-transformed morphology is a promising candidate for the ground state.

Evolution of learning in fluctuating environments: when selection favors both social and exploratory individual learning.

PubMed

Borenstein, Elhanan; Feldman, Marcus W; Aoki, Kenichi

2008-03-01

Cumulative cultural change requires organisms that are capable of both exploratory individual learning and faithful social learning. In our model, an organism's phenotype is initially determined innately (by its genotypic value) or by social learning (copying a phenotype from the parental generation), and then may or may not be modified by individual learning (exploration around the initial phenotype). The environment alternates periodically between two states, each defined as a certain range of phenotypes that can survive. These states may overlap, in which case the same phenotype can survive in both states, or they may not. We find that a joint social and exploratory individual learning strategy-the strategy that supports cumulative culture-is likely to spread when the environmental states do not overlap. In particular, when the environmental states are contiguous and mutation is allowed among the genotypic values, this strategy will spread in either moderately or highly stable environments, depending on the exact nature of the individual learning applied. On the other hand, natural selection often favors a social learning strategy without exploration when the environmental states overlap. We find only partial support for the "consensus" view, which holds that individual learning, social learning, and innate determination of behavior will evolve at short, intermediate, and long environmental periodicities, respectively.

JANUS - A setup for low-energy Coulomb excitation at ReA3

NASA Astrophysics Data System (ADS)

Lunderberg, E.; Belarge, J.; Bender, P. C.; Bucher, B.; Cline, D.; Elman, B.; Gade, A.; Liddick, S. N.; Longfellow, B.; Prokop, C.; Weisshaar, D.; Wu, C. Y.

2018-03-01

A new experimental setup for low-energy Coulomb excitation experiments was constructed in a collaboration between the National Superconducting Cyclotron Laboratory (NSCL), Lawrence Livermore National Laboratory (LLNL), and the University of Rochester and was commissioned at the general purpose beam line of NSCL's ReA3 reaccelerator facility. The so-called JANUS setup combines γ-ray detection with the Segmented Ge Array (SeGA) and scattered particle detection using a pair of segmented double-sided Si detectors (Bambino 2). The low-energy Coulomb excitation program that JANUS enables will complement intermediate-energy Coulomb excitation studies that have long been performed at NSCL by providing access to observables that quantify collectivity beyond the first excited state, including the sign and magnitude of excited-state quadrupole moments. In this work, the setup and its performance will be described based on the commissioning run that used stable 78Kr impinging onto a 1.09 mg/cm2208Pb target at a beam energy of 3.9 MeV/u.

High temperature unfolding of a truncated hemoglobin by molecular dynamics simulation.

PubMed

Sharma, Ravi Datta; Kanwal, Rajnee; Lynn, Andrew M; Singh, Prerna; Pasha, Syed Tazeen; Fatma, Tasneem; Jawaid, Safdar

2013-09-01

Heme containing proteins are associated with peroxidase activity. The proteins like hemoglobin, myoglobins, cytochrome c and micro-peroxidase other than peroxidases have been shown to exhibit weak peroxidase-like activity. This weak peroxidase-like activity in hemoglobin-like molecules is due to heme moiety. We conducted molecular dynamics (MD) studies to decipher the unfolding path of Ba-Glb (a truncated hemoglobin from Bacillus anthracis) and the role of heme moiety to its unfolding path. The similar unfolding path is also observed in vitro by UV/VIS spectroscopy. The data confirmed that the unfolding of Ba-Glb follows a three state process with a meta-stable (intermediate) state between the native and unfolded conformations. The present study is supported by several unfolding parameters like root-mean-square-deviation (RMSD), dictionary of protein secondary structure (DSSP), and free energy landscape. Understanding the structure of hemoglobin like proteins in unicellular dreaded pathogens like B. anthracis will pave way for newer drug discovery targets and in the disease management of anthrax.

Phosphodiester Cleavage in Ribonuclease H Occurs via an Associative Two-Metal-Aided Catalytic Mechanism

PubMed Central

De Vivo, Marco; Dal Peraro, Matteo; Klein, Michael L.

2009-01-01

Ribonuclease H (RNase H) belongs to the nucleotidyl-transferase (NT) superfamily and hydrolyzes the phosphodiester linkages that form the backbone of the RNA strand in RNA·DNA hybrids. This enzyme is implicated in replication initiation and DNA topology restoration and represents a very promising target for anti-HIV drug design. Structural information has been provided by high-resolution crystal structures of the complex RNase H/RNA·DNA from Bacillus halodurans (Bh), which reveals that two metal ions are required for formation of a catalytic active complex. Here, we use classical force field-based and quantum mechanics/molecular mechanics calculations for modeling the nucleotidyl transfer reaction in RNase H, clarifying the role of the metal ions and the nature of the nucleophile (water versus hydroxide ion). During the catalysis, the two metal ions act cooperatively, facilitating nucleophile formation and stabilizing both transition state and leaving group. Importantly, the two Mg2+ metals also support the formation of a meta-stable phosphorane intermediate along the reaction, which resembles the phosphorane intermediate structure obtained only in the debated β-phosphoglucomutase crystal. The nucleophile formation (i.e., water deprotonation) can be achieved in situ, after migration of one proton from the water to the scissile phosphate in the transition state. This proton transfer is actually mediated by solvation water molecules. Due to the highly conserved nature of the enzymatic bimetal motif, these results might also be relevant for structurally similar enzymes belonging to the NT superfamily. PMID:18662000

Effect of mammalian kidney osmolytes on the folding pathway of sheep serum albumin.

PubMed

Dar, Mohammad Aasif; Islam, Asimul; Hassan, Md Imtaiyaz; Ahmad, Faizan

2017-04-01

Recently, we had published that urea-induced denaturation curves of optical properties of sheep serum albumin (SSA) are biphasic with a stable intermediate that has characteristics of molten globule (MG) state. In this study, we have extended the work by carrying out urea- and guanidinium chloride (GdmCl)-induced denaturations of SSA in the presence of naturally occurring mammalian kidney osmolytes, namely, sorbitol, myo-inositol and glycine betaine. We have observed that all these osmolytes (i) transform this biphasic transition into a co-operative, two-state transition and (ii) increase the stability of the protein in terms of midpoint of denaturation (C m ) and Gibbs free energy change in the absence of both denaturants (ΔG D 0 ). The relative effectiveness of different osmolytes on the stability of SSA follows the order: glycine betaine>myo-inositol>sorbitol. In this paper, we also report that kidney osmolytes destabilize MG state by shifting the equilibrium, native state↔MG state toward the left. This study will be helpful in understanding the existence of osmolytes in kidney and their role in folding of kidney proteins soaked with urea. Copyright © 2017 Elsevier B.V. All rights reserved.

Direct synthesis of anti-1,3-diols through nonclassical reaction of aryl Grignard reagents with isopropenyl acetate.

PubMed

Jiao, Yinchun; Cao, Chenzhong; Zhou, Zaichun

2011-01-21

A series of symmetrical aromatic 1,3-diols were efficiently synthesized from substituted aryl Grignard reagents and isopropenyl acetate in a one-step reaction that formed anti products as the major species. Both experimental and theoretical studies suggested that the reaction involves the formation of a relatively stable intermediate E containing a six-membered ring from intermediate A. The stereoselectivity of the reactions and the molecular structure of the products were confirmed by NMR spectroscopy, X-ray diffraction, and gas chromatography.

Magnetism and the spin state in cubic perovskite CaCo O3 synthesized under high pressure

NASA Astrophysics Data System (ADS)

Xia, Hailiang; Dai, Jianhong; Xu, Yuanji; Yin, Yunyu; Wang, Xiao; Liu, Zhehong; Liu, Min; McGuire, Michael A.; Li, Xiang; Li, Zongyao; Jin, Changqing; Yang, Yifeng; Zhou, Jianshi; Long, Youwen

2017-07-01

Cubic SrCo O3 with an intermediate spin state can only be stabilized by high pressure and high temperature (HPHT) treatment. It is metallic and ferromagnetic with the highest Curie temperature of the transition-metal perovskites. The chemical substitution by Ca on Sr sites would normally lower crystal symmetry from cubic to orthorhombic as seen in the perovskite family of Ca M O3 (M =M4 + of transition metals, G e4 + , S n4 + , and Z r4 + ) at room temperature. This structural change narrows the bandwidth, so as to further enhance the Curie temperature as the crossover to the localized electronic state is approached. We report a successful synthesis of the perovskite CaCo O3 with a HPHT treatment. Surprisingly, CaCo O3 crystallizes in a simple cubic structure that remains stable down to 20 K, the lowest temperature in the structural study. The new perovskite has been thoroughly characterized by a suite of measurements including transport, magnetization, specific heat, thermal conductivity, and thermoelectric power. Metallic CaCo O3 undergoes two successive magnetic transitions at 86 K and 54 K as temperature decreases. The magnetization at 5 K is compatible with the intermediate spin state t4e1 of C o4 + at the octahedral site. The thermal expansion of the Co-O bond length indicates that the population of high spin state t3e2 increases for T >100 K . The shortest Co-O bond length in cubic CaCo O3 is responsible for delocalizing electrons in the π*-band and itinerant-electron ferromagnetism at T <54 K . A comprehensive comparison between SrCo O3 and CaCo O3 and the justification of their physical properties by first-principles calculation have also been made in this report. Partially filled π* and σ* bands would make CaCo O3 suitable to study the Hund's coupling effect in a metal.

Impact of ambient gases on the mechanism of [Cs8Nb6O19]-promoted nerve-agent decomposition† †Dedicated to the memory of Prof. Keiji Morokuma. ‡ ‡Electronic supplementary information (ESI) available: (1) The calculated transition states, intermediates and products of the GB hydrolysis and their important geometry parameters (in Å) for X = SO2, (2) the calculated adsorption energies (in kcal mol–1) of NO2 radicals to Cs8Nb6O19, (3) Cartesian coordinates for all reported structures in xyz format. (structure.xyz). See DOI: 10.1039/c7sc04997h

PubMed Central

Kaledin, Alexey L.; Driscoll, Darren M.; Troya, Diego; Collins-Wildman, Daniel L.

2018-01-01

The impact of ambient gas molecules (X), NO2, CO2 and SO2 on the structure, stability and decontamination activity of Cs8Nb6O19 polyoxometalate was studied computationally and experimentally. It was found that Cs8Nb6O19 absorbs these molecules more strongly than it adsorbs water and Sarin (GB) and that these interactions hinder nerve agent decontamination. The impacts of diamagnetic CO2 and SO2 molecules on polyoxoniobate Cs8Nb6O19 were fundamentally different from that of NO2 radical. At ambient temperatures, weak coordination of the first NO2 radical to Cs8Nb6O19 conferred partial radical character on the polyoxoniobate and promoted stronger coordination of the second NO2 adsorbent to form a stable diamagnetic Cs8Nb6O19/(NO2)2 species. Moreover, at low temperatures, NO2 radicals formed stable dinitrogen tetraoxide (N2O4) that weakly interacted with Cs8Nb6O19. It was found that both in the absence and presence of ambient gas molecules, GB decontamination by the Cs8Nb6O19 species proceeds via general base hydrolysis involving: (a) the adsorption of water and the nerve agent on Cs8Nb6O19/(X), (b) concerted hydrolysis of a water molecule on a basic oxygen atom of the polyoxoniobate and nucleophilic addition of the nascent OH group to the phosphorus center of Sarin, and (c) rapid reorganization of the formed pentacoordinated-phosphorus intermediate, followed by dissociation of either HF or isopropanol and formation of POM-bound isopropyl methyl phosphonic acid (i-MPA) or methyl phosphonofluoridic acid (MPFA), respectively. The presence of the ambient gas molecules increases the energy of the intermediate stationary points relative to the asymptote of the reactants and slightly increases the hydrolysis barrier. These changes closely correlate with the Cs8Nb6O19–X complexation energy. The most energetically stable intermediates of the GB hydrolysis and decontamination reaction were found to be Cs8Nb6O19/X-MPFA-(i-POH) and Cs8Nb6O19/X-(i-MPA)-HF both in the absence and presence of ambient gas molecules. The high stability of these intermediates is due to, in part, the strong hydrogen bonding between the adsorbates and the protonated [Cs8Nb6O19/X/H]+-core. Desorption of HF or/and (i-POH) and regeneration of the catalyst required deprotonation of the [Cs8Nb6O19/X/H]+-core and protonation of the phosphonic acids i-MPA and MPFA. This catalyst regeneration is shown to be a highly endothermic process, which is the rate-limiting step of the GB hydrolysis and decontamination reaction both in the absence and presence of ambient gas molecules. PMID:29719688

Equation of state of dense nuclear matter and neutron star structure from nuclear chiral interactions

NASA Astrophysics Data System (ADS)

Bombaci, Ignazio; Logoteta, Domenico

2018-02-01

Aims: We report a new microscopic equation of state (EOS) of dense symmetric nuclear matter, pure neutron matter, and asymmetric and β-stable nuclear matter at zero temperature using recent realistic two-body and three-body nuclear interactions derived in the framework of chiral perturbation theory (ChPT) and including the Δ(1232) isobar intermediate state. This EOS is provided in tabular form and in parametrized form ready for use in numerical general relativity simulations of binary neutron star merging. Here we use our new EOS for β-stable nuclear matter to compute various structural properties of non-rotating neutron stars. Methods: The EOS is derived using the Brueckner-Bethe-Goldstone quantum many-body theory in the Brueckner-Hartree-Fock approximation. Neutron star properties are next computed solving numerically the Tolman-Oppenheimer-Volkov structure equations. Results: Our EOS models are able to reproduce the empirical saturation point of symmetric nuclear matter, the symmetry energy Esym, and its slope parameter L at the empirical saturation density n0. In addition, our EOS models are compatible with experimental data from collisions between heavy nuclei at energies ranging from a few tens of MeV up to several hundreds of MeV per nucleon. These experiments provide a selective test for constraining the nuclear EOS up to 4n0. Our EOS models are consistent with present measured neutron star masses and particularly with the mass M = 2.01 ± 0.04 M⊙ of the neutron stars in PSR J0348+0432.

Understanding and Mitigating the Effects of Stable Dodecahydro- closo -dodecaborate Intermediates on Hydrogen-Storage Reactions

DOE PAGES

White, James L.; Newhouse, Rebecca J.; Zhang, Jin Z.; ...

2016-10-25

Alkali metal borohydrides can reversibly store hydrogen; however, the materials display poor cyclability, often times linked to occurrence of stable closo-polyborate intermediate species. In an effort to understand the role of such intermediates on the hydrogen storage properties of metal borohydrides, several alkali metal dodecahydro-closo-dodecaborate salts were isolated in anhydrous form and characterized by diffraction and spectroscopic techniques. Mixtures of Li 2B 12H 12, Na 2B 12H 12, and K 2B 12H 12 with the corresponding alkali metal hydrides were subjected to hydrogenation conditions known to favor partial or full reversibility in metal borohydrides. The stoichiometric mixtures of MH andmore » M 2B 12H 12 salts form the corresponding metal borohydrides MBH 4 (M=Li, Na, K) in almost quantitative yield at 100 MPa H 2 and 500 °C. In addition, stoichiometric mixtures of Li 2B 12H 12 and MgH 2 were found to form MgB 2 at 500 °C and above upon desorption in vacuum. The two destabilization strategies outlined above suggest that metal polyhydro-closo-polyborate species can be converted into the corresponding metal borohydrides or borides, albeit under rather harsh conditions of hydrogen pressure and temperature.« less

The oxygenase-peroxidase theory of Bach and Chodat and its modern equivalents: change and permanence in scientific thinking as shown by our understanding of the roles of water, peroxide, and oxygen in the functioning of redox enzymes.

PubMed

Nicholls, P

2007-10-01

Alexander Bach was both revolutionary politician and biochemist. His earliest significant publication, "Tsar-golod" ("The Tsar of Hunger"), introduced Marxist thought to Russian workers. In exile for 30 years, he moved to study the dialectic of the oxidases. When his theory of oxidases as combinations of oxygenases and peroxidases was developed (circa 1900) the enzyme concept was not fully formulated, and the enzyme/substrate distinction not yet made. Peroxides however were then and remain now significant intermediates, when either free or bound, in oxidase catalyses. The aerobic dehydrogenase/peroxidase/catalase coupled systems which were studied slightly later clarified the Bach model and briefly became an oxidase paradigm. Identification of peroxidase as a metalloprotein, a key step in understanding oxidase and peroxidase mechanisms, postdated Bach's major work. Currently we recognize catalytic organic peroxides in flavoprotein oxygenases; such organic peroxides are also involved in lipid oxidation and tryptophan radical decay. But most physiologically important peroxides are now known to be bound to transition metals (either Fe or Cu) and formed both directly and indirectly (from oxygen). The typical stable metalloprotein peroxide product is the ferryl state. When both peroxide oxidizing equivalents are retained the second equivalent is held as a protein or porphyrin radical. True metal peroxide complexes are unstable. But often water molecules mark the spot where the original peroxide decayed. The cytochrome c oxidase Fe-Cu center can react with either peroxide or oxygen to form the intermediate higher oxidation states P and F. In its resting state water molecules and hydroxyl ions can be seen marking the original location of the oxygen or peroxide molecule.

Folding of the RNA Recognition Motif (RRM) Domains of the Amyotrophic Lateral Sclerosis (ALS)-linked Protein TDP-43 Reveals an Intermediate State*

PubMed Central

Mackness, Brian C.; Tran, Meme T.; McClain, Shannan P.; Matthews, C. Robert; Zitzewitz, Jill A.

2014-01-01

Pathological alteration of TDP-43 (TAR DNA-binding protein-43), a protein involved in various RNA-mediated processes, is a hallmark feature of the neurodegenerative diseases amyotrophic lateral sclerosis and frontotemporal lobar degeneration. Fragments of TDP-43, composed of the second RNA recognition motif (RRM2) and the disordered C terminus, have been observed in cytoplasmic inclusions in sporadic amyotrophic lateral sclerosis cases, suggesting that conformational changes involving RRM2 together with the disordered C terminus play a role in aggregation and toxicity. The biophysical data collected by CD and fluorescence spectroscopies reveal a three-state equilibrium unfolding model for RRM2, with a partially folded intermediate state that is not observed in RRM1. Strikingly, a portion of RRM2 beginning at position 208, which mimics a cleavage site observed in patient tissues, increases the population of this intermediate state. Mutually stabilizing interactions between the domains in the tethered RRM1 and RRM2 construct reduce the population of the intermediate state and enhance DNA/RNA binding. Despite the high sequence homology of the two domains, a network of large hydrophobic residues in RRM2 provides a possible explanation for the increased stability of RRM2 compared with RRM1. The cluster analysis suggests that the intermediate state may play a functional role by enhancing access to the nuclear export signal contained within its sequence. The intermediate state may also serve as a molecular hazard linking productive folding and function with pathological misfolding and aggregation that may contribute to disease. PMID:24497641

The catalytic mechanism of mouse renin studied with QM/MM calculations.

PubMed

Brás, Natércia F; Ramos, Maria J; Fernandes, Pedro A

2012-09-28

Hypertension is a chronic condition that affects nearly 25% of adults worldwide. As the Renin-Angiotensin-Aldosterone System is implicated in the control of blood pressure and body fluid homeostasis, its combined blockage is an attractive therapeutic strategy currently in use for the treatment of several cardiovascular conditions. We have performed QM/MM calculations to study the mouse renin catalytic mechanism in atomistic detail, using the N-terminal His6-Asn14 segment of angiotensinogen as substrate. The enzymatic reaction (hydrolysis of the peptidic bond between residues in the 10th and 11th positions) occurs through a general acid/base mechanism and, surprisingly, it is characterized by three mechanistic steps: it begins with the creation of a first very stable tetrahedral gem-diol intermediate, followed by protonation of the peptidic bond nitrogen, giving rise to a second intermediate. In a final step the peptidic bond is completely cleaved and both gem-diol hydroxyl protons are transferred to the catalytic dyad (Asp32 and Asp215). The final reaction products are two separate peptides with carboxylic acid and amine extremities. The activation energy for the formation of the gem-diol intermediate was calculated as 23.68 kcal mol(-1), whereas for the other steps the values were 15.51 kcal mol(-1) and 14.40 kcal mol(-1), respectively. The rate limiting states were the reactants and the first transition state. The associated barrier (23.68 kcal mol(-1)) is close to the experimental values for the angiotensinogen substrate (19.6 kcal mol(-1)). We have also tested the influence of the density functional on the activation and reaction energies. All eight density functionals tested (B3LYP, B3LYP-D3, X3LYP, M06, B1B95, BMK, mPWB1K and B2PLYP) gave very similar results.

Noble gases, stable isotopes, and radiocarbon as tracers of flow in the Dakota aquifer, Colorado and Kansas

USGS Publications Warehouse

Clark, J.F.; Davisson, M.L.; Hudson, G.B.; Macfarlane, P.A.

1998-01-01

A suite of chemical and isotope tracers (dissolved noble gases, stable isotopes of water, radiocarbon, and CI) have been analyzed along a flow path in the Dakota aquifer system to determine likely recharge sources, ground water residence times, and the extent of mixing between local and intermediate flow systems, presumably caused by large well screens. Three water types were distinguished with the tracers, each having a very different history. Two of the water types were found in south-eastern Colorado where the Dakota is poorly confined. The tracer data suggest that the first group recharged locally during the last few thousand years and the second group was composed of ground water that recharged earlier during a cooler climate, presumably during the last glacial period (LGP) and mixed aged water. The paleotemperature record archived in this groundwater system indicates that south-eastern Colorado was about 5??C cooler during the LGP than during the late Holocene. Similar temperature changes derived from dissolved noble gases in other aquifer systems have been reported earlier for the south-western United States. The third water type was located down gradient of the first two in the confined Dakota in western and central Kansas. Groundwater residence time of this water mass is on the order of 104-105 yrs and its recharge location is near the Colorado and Kansas border down gradient of the other water types. The study shows the importance of using multiple tracers when investigating ground water systems.A suite of chemical and isotope tracers (dissolved noble gases, stable isotopes of water, radiocarbon, and CL) were analyzed along a flow path in the Dakota aquifer system to determine likely recharge sources, ground water residence times, and the extent of mixing between local and intermediate flow systems. Three water types were distinguished with the tracers, each having a very different history. Two of the water types were located in south-eastern Colorado where the Dakota is poorly confined. The third water type was located down gradient of the first two in the confined Dakota in western and central Kansas.

Intermediate introns in nuclear genes of euglenids - are they a distinct type?

PubMed

Milanowski, Rafał; Gumińska, Natalia; Karnkowska, Anna; Ishikawa, Takao; Zakryś, Bożena

2016-02-29

Nuclear genes of euglenids contain two major types of introns: conventional spliceosomal and nonconventional introns. The latter are characterized by variable non-canonical borders, RNA secondary structure that brings intron ends together, and an unknown mechanism of removal. Some researchers also distinguish intermediate introns, which combine features of both types. They form a stable RNA secondary structure and are classified into two subtypes depending on whether they contain one (intermediate/nonconventional subtype) or both (conventional/intermediate subtype) canonical spliceosomal borders. However, it has been also postulated that most introns classified as intermediate could simply be special cases of conventional or nonconventional introns. Sequences of tubB, hsp90 and gapC genes from six strains of Euglena agilis were obtained. They contain four, six, and two or three introns, respectively (the third intron in the gapC gene is unique for just one strain). Conventional introns were present at three positions: two in the tubB gene (at one position conventional/intermediate introns were also found) and one in the gapC gene. Nonconventional introns are present at ten positions: two in the tubB gene (at one position intermediate/nonconventional introns were also found), six in hsp90 (at four positions intermediate/nonconventional introns were also found), and two in the gapC gene. Sequence and RNA secondary structure analyses of nonconventional introns confirmed that their most strongly conserved elements are base pairing nucleotides at positions +4, +5 and +6/ -8, -7 and -6 (in most introns CAG/CTG nucleotides were observed). It was also confirmed that the presence of the 5' GT/C end in intermediate/nonconventional introns is not the result of kinship with conventional introns, but is due to evolutionary pressure to preserve the purine at the 5' end. However, an example of a nonconventional intron with GC-AG ends was shown, suggesting the possibility of intron type conversion between nonconventional and conventional. Furthermore, an analysis of conventional introns revealed that the ability to form a stable RNA secondary structure by some introns is probably not a result of their relationship with nonconventional introns. It was also shown that acquisition of new nonconventional introns is an ongoing process and can be observed at the level of a single species. In the recently acquired intron in the gapC gene an extended direct repeats at the intron-exon junctions are present, suggesting that double-strand break repair process could be the source of new nonconventional introns.

Intergenerational educational mobility is associated with cardiovascular disease risk behaviours in a cohort of young Australian adults: The Childhood Determinants of Adult Health (CDAH) Study

PubMed Central

2010-01-01

Background Although educational disparity has been linked to single risk behaviours, it has not previously been studied as a predictor of overall lifestyle. We examined if current education, parental education or educational mobility between generations was associated with healthy lifestyles in young Australian adults. Methods In 2004-06, participant and parental education (high [bachelor degree or higher], intermediate [vocational training], low [secondary school only]) were assessed. Educational mobility was defined as: stable high (participant and parent in high group), stable intermediate (participant and parent in intermediate group), stable low (participant and parent in low group), downwardly (lower group than parent) and upwardly (higher group than parent) mobile. We derived a lifestyle score from 10 healthy behaviours (BMI, non-smoking, alcohol consumption, leisure time physical activity and six components of diet). Scores >4 indicated a high healthy lifestyle score. We estimated the likelihood of having a high healthy lifestyle score by education (participant and parent) and educational mobility. Results Complete data were available for 1973 participants (53% female, age range 26 to 36 years). Those with lower education were less likely to have healthy lifestyles. Parental education was not associated with having a high healthy lifestyle score after adjustment for participant's education. Those who moved upward or downward were as likely to have a high healthy lifestyle score as those in the group they attained. Conclusions We found clear disparities in health behaviour by participant education and intergenerational educational mobility. People attaining a higher level of education than their parents appeared protected from developing an unhealthy lifestyle suggesting that population-wide improvements in education may be important for health. PMID:20122282

Hydrogeological and hydrochemical investigation of groundwater using environmental isotopes (18O, 2H, 3H, 14C) and chemical tracers: a case study of the intermediate aquifer, Sfax, southeastern Tunisia

NASA Astrophysics Data System (ADS)

Ayadi, Rahma; Trabelsi, Rim; Zouari, Kamel; Saibi, Hakim; Itoi, Ryuichi; Khanfir, Hafedh

2018-06-01

Major element concentrations and stable (δ18O and δ2H) and radiogenic (3H and 14C) isotopes in groundwater have proved useful tracers for understanding the geochemical processes that control groundwater mineralization and for identifying recharge sources in the semi-arid region of Sfax (southeastern Tunisia). Major-ion chemical data indicate that the origins of the salinity in the groundwater are the water-rock interactions, mainly the dissolution of evaporitic minerals, as well as the cation exchange with clay minerals. The δ18O and δ2H relationships suggest variations in groundwater recharge mechanisms. Strong evaporation during recharge with limited rapid water infiltration is evident in the groundwater of the intermediate aquifer. The mixing with old groundwater in some areas explains the low stable isotope values of some groundwater samples. Groundwaters from the intermediate aquifer are classified into two main water types: Ca-Na-SO4 and Ca-Na-Cl-SO4. The high nitrate concentrations suggest an anthropogenic source of nitrogen contamination caused by intensive agricultural activities in the area. The stable isotopic signatures reveal three water groups: non-evaporated waters that indicate recharge by recent infiltrated water; evaporated waters that are characterized by relatively enriched δ18O and δ2H contents; and mixed groundwater (old/recent) or ancient groundwater, characterized by their depleted isotopic composition. Tritium data support the existence of recent limited recharge; however, other low tritium values are indicative of pre-nuclear recharge and/or mixing between pre-nuclear and contemporaneous recharge. The carbon-14 activities indicate that the groundwaters were mostly recharged under different climatic conditions during the cooler periods of the late Pleistocene and Holocene.

Hydrogeological and hydrochemical investigation of groundwater using environmental isotopes (18O, 2H, 3H, 14C) and chemical tracers: a case study of the intermediate aquifer, Sfax, southeastern Tunisia

NASA Astrophysics Data System (ADS)

Ayadi, Rahma; Trabelsi, Rim; Zouari, Kamel; Saibi, Hakim; Itoi, Ryuichi; Khanfir, Hafedh

2017-12-01

Major element concentrations and stable (δ18O and δ2H) and radiogenic (3H and 14C) isotopes in groundwater have proved useful tracers for understanding the geochemical processes that control groundwater mineralization and for identifying recharge sources in the semi-arid region of Sfax (southeastern Tunisia). Major-ion chemical data indicate that the origins of the salinity in the groundwater are the water-rock interactions, mainly the dissolution of evaporitic minerals, as well as the cation exchange with clay minerals. The δ18O and δ2H relationships suggest variations in groundwater recharge mechanisms. Strong evaporation during recharge with limited rapid water infiltration is evident in the groundwater of the intermediate aquifer. The mixing with old groundwater in some areas explains the low stable isotope values of some groundwater samples. Groundwaters from the intermediate aquifer are classified into two main water types: Ca-Na-SO4 and Ca-Na-Cl-SO4. The high nitrate concentrations suggest an anthropogenic source of nitrogen contamination caused by intensive agricultural activities in the area. The stable isotopic signatures reveal three water groups: non-evaporated waters that indicate recharge by recent infiltrated water; evaporated waters that are characterized by relatively enriched δ18O and δ2H contents; and mixed groundwater (old/recent) or ancient groundwater, characterized by their depleted isotopic composition. Tritium data support the existence of recent limited recharge; however, other low tritium values are indicative of pre-nuclear recharge and/or mixing between pre-nuclear and contemporaneous recharge. The carbon-14 activities indicate that the groundwaters were mostly recharged under different climatic conditions during the cooler periods of the late Pleistocene and Holocene.

Unfolding mechanism of thrombin-binding aptamer revealed by molecular dynamics simulation and Markov State Model

NASA Astrophysics Data System (ADS)

Zeng, Xiaojun; Zhang, Liyun; Xiao, Xiuchan; Jiang, Yuanyuan; Guo, Yanzhi; Yu, Xinyan; Pu, Xuemei; Li, Menglong

2016-04-01

Thrombin-binding aptamer (TBA) with the sequence 5‧GGTTGGTGTGGTTGG3‧ could fold into G-quadruplex, which correlates with functionally important genomic regionsis. However, unfolding mechanism involved in the structural stability of G-quadruplex has not been satisfactorily elucidated on experiments so far. Herein, we studied the unfolding pathway of TBA by a combination of molecular dynamics simulation (MD) and Markov State Model (MSM). Our results revealed that the unfolding of TBA is not a simple two-state process but proceeds along multiple pathways with multistate intermediates. One high flux confirms some observations from NMR experiment. Another high flux exhibits a different and simpler unfolding pathway with less intermediates. Two important intermediate states were identified. One is similar to the G-triplex reported in the folding of G-quadruplex, but lack of H-bonding between guanines in the upper plane. More importantly, another intermediate state acting as a connector to link the folding region and the unfolding one, was the first time identified, which exhibits higher population and stability than the G-triplex-like intermediate. These results will provide valuable information for extending our understanding the folding landscape of G-quadruplex formation.

Lifetime enhancement for multiphoton absorption in intermediate band solar cells

NASA Astrophysics Data System (ADS)

Bezerra, Anibal T.; Studart, Nelson

2017-08-01

A semiconductor structure consisting of two coupled quantum wells embedded into the intrinsic region of a p-i-n junction is proposed as an intermediate band solar cell with a photon ratchet state, which would lead to increasing the cell efficiency. The conduction subband of the right-hand side quantum well works as the intermediated band, whereas the excited conduction subband of the left-hand side quantum well operates as the ratchet state. The photoelectrons in the intermediate band are scattered through the thin wells barrier and accumulated into the ratchet subband. A rate equation model for describing the charge transport properties is presented. The efficiency of the current generation is analyzed by studying the occupation of the wells subbands, taking into account the charge dynamic behavior provided by the electrical contacts connected to the cell. The current generation efficiency depends essentially from the relations between the generation, recombination rates and the scattering rate to the ratchet state. The inclusion of the ratchet states led to both an increase and a decrease in the cell current depending on the transition rates. This suggests that the coupling between the intermediate band and the ratchet state is a key point in developing an efficient solar cell.

Control of Synchronization Regimes in Networks of Mobile Interacting Agents

NASA Astrophysics Data System (ADS)

Perez-Diaz, Fernando; Zillmer, Ruediger; Groß, Roderich

2017-05-01

We investigate synchronization in a population of mobile pulse-coupled agents with a view towards implementations in swarm-robotics systems and mobile sensor networks. Previous theoretical approaches dealt with range and nearest-neighbor interactions. In the latter case, a synchronization-hindering regime for intermediate agent mobility is found. We investigate the robustness of this intermediate regime under practical scenarios. We show that synchronization in the intermediate regime can be predicted by means of a suitable metric of the phase response curve. Furthermore, we study more-realistic K -nearest-neighbor and cone-of-vision interactions, showing that it is possible to control the extent of the synchronization-hindering region by appropriately tuning the size of the neighborhood. To assess the effect of noise, we analyze the propagation of perturbations over the network and draw an analogy between the response in the hindering regime and stable chaos. Our findings reveal the conditions for the control of clock or activity synchronization of agents with intermediate mobility. In addition, the emergence of the intermediate regime is validated experimentally using a swarm of physical robots interacting with cone-of-vision interactions.

Nitrate denitrification with nitrite or nitrous oxide as intermediate products: Stoichiometry, kinetics and dynamics of stable isotope signatures.

PubMed

Vavilin, V A; Rytov, S V

2015-09-01

A kinetic analysis of nitrate denitrification by a single or two species of denitrifying bacteria with glucose or ethanol as a carbon source and nitrite or nitrous oxide as intermediate products was performed using experimental data published earlier (Menyailo and Hungate, 2006; Vidal-Gavilan et al., 2013). Modified Monod kinetics was used in the dynamic biological model. The special equations were added to the common dynamic biological model to describe how isotopic fractionation between N species changes. In contrast to the generally assumed first-order kinetics, in this paper, the traditional Rayleigh equation describing stable nitrogen and oxygen isotope fractionation in nitrate was derived from the dynamic isotopic equations for any type of kinetics. In accordance with the model, in Vidal-Gavilan's experiments, the maximum specific rate of nitrate reduction was proved to be less for ethanol compared to glucose. Conversely, the maximum specific rate of nitrite reduction was proved to be much less for glucose compared to ethanol. Thus, the intermediate nitrite concentration was negligible for the ethanol experiment, while it was significant for the glucose experiment. In Menyailo's and Hungate's experiments, the low value of maximum specific rate of nitrous oxide reduction gives high intermediate value of nitrous oxide concentration. The model showed that the dynamics of nitrogen and oxygen isotope signatures are responding to the biological dynamics. Two microbial species instead of single denitrifying bacteria are proved to be more adequate to describe the total process of nitrate denitrification to dinitrogen. Copyright © 2015 Elsevier Ltd. All rights reserved.

Alloying effect on bright-dark exciton states in ternary monolayer Mo x W1-x Se2

NASA Astrophysics Data System (ADS)

Liu, Yanping; Tom, Kyle; Zhang, Xiaowei; Lou, Shuai; Liu, Yin; Yao, Jie

2017-07-01

Binary transition metal dichalcogenides (TMDCs) in the class MX2 (M = Mo, W; X = S, Se) have been widely investigated for potential applications in optoelectronics and nanoelectronics. Recently, alloy-based monolayers of TMDCs have provided a stable and versatile technique to tune the physical properties and optimize them for potential applications. Here, we present experimental evidence for the existence of an intermediate alloy state between the MoSe2-like and the WSe2-like behavior of the neutral exciton (X 0) using temperature-dependent photoluminescence (PL) of the monolayer Mo x W1-x Se2 alloy. The existence of a maximum PL intensity around 120 K can be explained by the competition between the thermally activated bright states and the non-radiative quenching of the bright states. Moreover, we also measured localized exciton (XB ) PL peak in the alloy and the observed behavior agrees well with a model previously proposed for the 3D case, which indicates the theory also applies to 2D systems. Our results not only shed light on bright-dark states and localized exciton physics of 2D semiconductors, but also offer a new route toward the control of the bright-dark transition and tailoring optical properties of 2D semiconductors through defect engineering.

Isomerization Intermediates In Solution Phase Photochemistry Of Stilbenes

NASA Astrophysics Data System (ADS)

Doany, F. E.; Hochstrasser, R. M.; Greene, B. I.

1985-04-01

Picosecond and subpicosecond spectroscopic studies have revealed evidence for an isomerization intermediate between cis and trans in the photoinduced isomerism of both stilbene and biindanyledene ("stiff" stilbene). In stiff stilbene, a transient absorption at 351 nm displays time evolution and viscosity dependence consistent with absorption by a twisted intermediate ("phantom" state) with a lOps lifetime. An analagous bottleneck state with a life-time of 4ps is also consistent with the ground state recovery dynamics of t-stilbene following excitation of c-stilbene when monitored with 0.1ps resolution.

42 CFR 54.12 - Treatment of intermediate organizations.

Code of Federal Regulations, 2010 CFR

2010-10-01

... 42 Public Health 1 2010-10-01 2010-10-01 false Treatment of intermediate organizations. 54.12... intermediate organizations. If a nongovernmental organization (referred to here as an “intermediate organization”), acting under a contract or other agreement with the Federal Government or a State or local...

Characterization and photochemistry of 13-desmethyl bacteriorhodopsin.

PubMed

Gillespie, Nathan B; Ren, Lei; Ramos, Lavoisier; Daniell, Heather; Dews, Deborah; Utzat, Karissa A; Stuart, Jeffrey A; Buck, Charles H; Birge, Robert R

2005-08-25

The photochemistry of the 13-desmethyl (DM) analogue of bacteriorhodopsin (BR) is examined by using spectroscopy, molecular orbital theory, and chromophore extraction followed by conformational analysis. The removal of the 13-methyl group permits the direct photochemical formation of a thermally stable, photochemically reversible state, P1(DM) (lambda(max) = 525 nm), which can be generated efficiently by exciting the resting state, bR(DM) with yellow or red light (lambda > 590 nm). Chromophore extraction analysis reveals that the retinal configuration in P1(DM) is 9-cis, identical to that of the retinal configuration in the native BR P1 state. Fourier transform infrared and Raman experiments on P1(DM) indicate an anti configuration around the C15=N bond, as would be expected of an O-state photoproduct. However, low-temperature spectroscopy and ambient, time-resolved studies indicate that the P1(DM) state forms primarily via thermal relaxation from the L(D)(DM) state. Theoretical studies on the BR binding site show that 13-dm retinal is capable of isomerizing into a 9-cis configuration with minimal steric hindrance from surrounding residues, in contrast to the native chromophore in which surrounding residues significantly obstruct the corresponding motion. Analysis of the photokinetic experiments indicates that the Arrhenius activation energy of the bR(DM) --> P1(DM) transition in 13-dm-BR is less than 0.6 kcal/mol (vs 22 +/-5 kcal/mol measured for the bR --> P (P1 and P2) reaction in 85:15 glycerol:water suspensions of wild type). Consequently, the P1(DM) state in 13-dm-BR can form directly from all-trans, 15-anti intermediates (bR(DM) and O(DM)) or all-trans, 15-syn (K(D)(DM)/L(D)(DM)) intermediates. This study demonstrates that the 13-methyl group, and its interactions with nearby binding site residues, is primarily responsible for channeling one-photon photochemical and thermal reactions and is limited to the all-trans and 13-cis species interconversions in the native protein.

Transition state analogue imprinted polymers as artificial amidases for amino acid p-nitroanilides: morphological effects of polymer network on catalytic efficiency.

PubMed

Mathew, Divya; Thomas, Benny; Devaky, K S

2017-11-13

The morphology of the polymer network - porous/less porous - plays predominant role in the amidase activities of the polymer catalysts in the hydrolytic reactions of amino acid p-nitroanilides. Polymers with the imprints of stable phosphonate analogue of the intermediate of hydrolytic reactions were synthesized as enzyme mimics. Molecular imprinting was carried out in thermodynamically stable porogen dimethyl sulphoxide and unstable porogen chloroform, to investigate the morphological effects of polymers on catalytic amidolysis. It was found that the medium of polymerization has vital influence in the amidase activities of the enzyme mimics. The morphological studies of the polymer catalysts were carried out by scanning electron microscopy and Bruner-Emmett-Teller analysis. The morphology of the polymer catalysts and their amidase activities are found to be dependent on the composition of reaction medium. The polymer catalyst prepared in dimethyl sulphoxide is observed to be efficient in 1:9 acetonitrile (ACN)-Tris HCl buffer and that prepared in chloroform is noticed to be stereo specifically and shape-selectively effective in 9:1 ACN-Tris HCl buffer. The solvent memory effect in catalytic amidolysis was investigated using the polymer prepared in acetonitrile.

A lithium-oxygen battery based on lithium superoxide.

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

Lu, Jun; Lee, Yun Jung; Luo, Xiangyi

Although the superoxide of lithium (LiO2) is believed to be a key intermediate in Li-O2 batteries leading to the formation of lithium peroxide, LiO2 has never been observed in its pure state. In this work, we provide evidence that use of a cathode based on a reduced graphene oxide with Ir nanoparticles in a Li-O2 battery results in a LiO2 discharge product formed by single electron transfer without further electron transfer or disproportionation to form Li2O2. High energy X-ray diffraction (HE-XRD) patterns indicates the presence of crystalline LiO2 with no evidence of Li2O2 or Li2O. The HEXRD studies as amore » function of time also show that LiO2 can be stable in its crystalline form after one week of aging in the presence of electrolyte. The results provide evidence that LiO2 is stable enough that it can be repeatedly charged and discharged with a very low charge potential (~3.2 V) and may open the avenue for a lithium superoxide-based battery.« less

A Broad Stability Investigation of Nb-Doped SrCoO 2.5+δ as a Reversible Oxygen Electrode for Intermediate-Temperature Solid Oxide Fuel Cells

DOE PAGES

Wang, Jie; Jiang, Long; Xiong, Xiaolei; ...

2016-06-10

The present work reports a systematic study on the structural, thermal, electrical and electrochemical stability of SrCo 1–xNb xO 2.5+δ series as a potential reversible oxygen-electrode for intermediate-temperature solid oxide fuel cells. The identified best composition is x = 0.10, which exhibits a stable pseudo primitive cubic structure at <700°C and a reversible oxygen redox reaction at 350°C. The conductivity of this material is p-type and also exhibits a peak at 350°C, implying that the electron hole conduction is closely associated with the oxygen nonstoichiometry. Electrochemical impedance spectroscopy analysis indicates a low polarization resistance rate-limited by a slower surface Omore » 2 dissociation step. Altogether, the material is thermally stable and oxygen redox reversible below 700°C, above which a catalytically less active brownmillerite SrCoO 2.5 is formed.« less

Concentrated dispersions of equilibrium protein nanoclusters that reversibly dissociate into active monomers

NASA Astrophysics Data System (ADS)

Truskett, Thomas M.; Johnston, Keith; Maynard, Jennifer; Borwankar, Ameya; Miller, Maria; Wilson, Brian; Dinin, Aileen; Khan, Tarik; Kaczorowski, Kevin

2012-02-01

Stabilizing concentrated protein solutions is of wide interest in drug delivery. However, a major challenge is how to reliably formulate concentrated, low viscosity (i.e., syringeable) solutions of biologically active proteins. Unfortunately, proteins typically undergo irreversible aggregation at intermediate concentrations of 100-200 mg/ml. In this talk, I describe how they can effectively avoid these intermediate concentrations by reversibly assembling into nanoclusters. Nanocluster assembly is achieved by balancing short-ranged, cosolute-induced attractions with weak, longer-ranger electrostatic repulsions near the isoelectric point. Theory predicts that native proteins are stabilized by a self-crowding mechanism within the concentrated environment of the nanoclusters, while weak cluster-cluster interactions can result in colloidally-stable dispersions with moderate viscosities. I present experimental results where this strategy is used to create concentrated antibody dispersions (up to 260 mg/ml) comprising nanoclusters of proteins [monoclonal antibody 1B7, polyclonal sheep Immunoglobin G and bovine serum albumin], which upon dilution in vitro or administration in vivo, are conformationally stable and retain activity.

Migrating Myeloid Cells Sense Temporal Dynamics of Chemoattractant Concentrations.

PubMed

Petrie Aronin, Caren E; Zhao, Yun M; Yoon, Justine S; Morgan, Nicole Y; Prüstel, Thorsten; Germain, Ronald N; Meier-Schellersheim, Martin

2017-11-21

Chemoattractant-mediated recruitment of hematopoietic cells to sites of pathogen growth or tissue damage is critical to host defense and organ homeostasis. Chemotaxis is typically considered to rely on spatial sensing, with cells following concentration gradients as long as these are present. Utilizing a microfluidic approach, we found that stable gradients of intermediate chemokines (CCL19 and CXCL12) failed to promote persistent directional migration of dendritic cells or neutrophils. Instead, rising chemokine concentrations were needed, implying that temporal sensing mechanisms controlled prolonged responses to these ligands. This behavior was found to depend on G-coupled receptor kinase-mediated negative regulation of receptor signaling and contrasted with responses to an end agonist chemoattractant (C5a), for which a stable gradient led to persistent migration. These findings identify temporal sensing as a key requirement for long-range myeloid cell migration to intermediate chemokines and provide insights into the mechanisms controlling immune cell motility in complex tissue environments. Published by Elsevier Inc.

Full Kinetics from First Principles of the Chlorine Evolution Reaction over a RuO2 (110) Model Electrode.

PubMed

Exner, Kai S; Anton, Josef; Jacob, Timo; Over, Herbert

2016-06-20

Current progress in modern electrocatalysis research is spurred by theory, frequently based on ab initio thermodynamics, where the stable reaction intermediates at the electrode surface are identified, while the actual energy barriers are ignored. This approach is popular in that a simple tool is available for searching for promising electrode materials. However, thermodynamics alone may be misleading to assess the catalytic activity of an electrochemical reaction as we exemplify with the chlorine evolution reaction (CER) over a RuO2 (110) model electrode. The full procedure is introduced, starting from the stable reaction intermediates, computing the energy barriers, and finally performing microkinetic simulations, all performed under the influence of the solvent and the electrode potential. Full kinetics from first-principles allows the rate-determining step in the CER to be identified and the experimentally observed change in the Tafel slope to be explained. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Solvent-dependent activation of intermediate excited states in the energy relaxation pathways of spheroidene.

PubMed

Maiuri, Margherita; Polli, Dario; Brida, Daniele; Lüer, Larry; LaFountain, Amy M; Fuciman, Marcel; Cogdell, Richard J; Frank, Harry A; Cerullo, Giulio

2012-05-14

In carotenoids internal conversion between the allowed (S(2)) and forbidden (S(1)) excited states occurs on a sub-picosecond timescale; the involvement of an intermediate excited state(s) (S(x)) mediating the process is controversial. Here we use high time resolution (sub-20 fs) broadband (1.2-2.5 eV) pump-probe spectroscopy to study the solvent dependence of excited state dynamics of spheroidene, a naturally-occurring carotenoid with ten conjugated double bonds. In the high polarizability solvent, CS(2), we find no evidence of an intermediate state, and the traditional three-level (S(0), S(1), S(2)) model fully accounts for the S(2)→ S(1) process. On the other hand, in the low polarizability solvent, cyclohexane, we find that rapid (~30 fs) relaxation to an intermediate state, S(x), lying between S(1) and S(2) is required to account for the data. We interpret these results as due to a shift of the S(2) energy, which positions the state above or below the energy of S(x) in response to changes in solvent polarizability. This journal is © the Owner Societies 2012

Excitation of photosystem I by 760 nm femtosecond laser pulses: transient absorption spectra and intermediates

NASA Astrophysics Data System (ADS)

Cherepanov, Dmitry A.; Shelaev, Ivan V.; Gostev, Fedor E.; Mamedov, Mahir D.; Petrova, Anastasia A.; Aybush, Arseniy V.; Shuvalov, Vladimir A.; Semenov, Alexey Yu; Nadtochenko, Victor A.

2017-09-01

Excitation of photosystem I (PS I) by a femtosecond 760 nm pump leads to one- and two-photon absorption. The one-photon excitation produces intermediates with transient absorption spectra similar to the spectra of the primary [{{{P}}700}+{{{A}}0}-{{A}}1] and secondary [{{{P}}700}+{{A}}0{{{A}}1}-] ion-radical pairs in the PS I reaction center. The two-photon absorption generates the upper level excited states of chlorophyll (Chl) and carotenoid molecules in the antenna. These excited states are converted into the long-lived intermediates and can be tentatively attributed to the excited and charge-transfer ion-radical states of Chl molecules and to the excited states of carotenoids in the antenna. The transient spectra of intermediates generated by two-photon excitation differ from the transient one-photon spectra of the primary and secondary ion-radical pairs.

Fluorescence lifetime components reveal kinetic intermediate states upon equilibrium denaturation of carbonic anhydrase II

NASA Astrophysics Data System (ADS)

Nemtseva, Elena V.; Lashchuk, Olesya O.; Gerasimova, Marina A.; Melnik, Tatiana N.; Nagibina, Galina S.; Melnik, Bogdan S.

2018-01-01

In most cases, intermediate states of multistage folding proteins are not ‘visible’ under equilibrium conditions but are revealed in kinetic experiments. Time-resolved fluorescence spectroscopy was used in equilibrium denaturation studies. The technique allows for detecting changes in the conformation and environment of tryptophan residues in different structural elements of carbonic anhydrase II which in its turn has made it possible to study the intermediate states of carbonic anhydrase II under equilibrium conditions. The results of equilibrium and kinetic experiments using wild-type bovine carbonic anhydrase II and its mutant form with the substitution of leucine for alanine at position 139 (L139A) were compared. The obtained lifetime components of intrinsic tryptophan fluorescence allowed for revealing that, the same as in kinetic experiments, under equilibrium conditions the unfolding of carbonic anhydrase II ensues through formation of intermediate states.

Fluorescence lifetime components reveal kinetic intermediate states upon equilibrium denaturation of carbonic anhydrase II.

PubMed

Nemtseva, Elena V; Lashchuk, Olesya O; Gerasimova, Marina A; Melnik, Tatiana N; Nagibina, Galina S; Melnik, Bogdan S

2017-12-21

In most cases, intermediate states of multistage folding proteins are not 'visible' under equilibrium conditions but are revealed in kinetic experiments. Time-resolved fluorescence spectroscopy was used in equilibrium denaturation studies. The technique allows for detecting changes in the conformation and environment of tryptophan residues in different structural elements of carbonic anhydrase II which in its turn has made it possible to study the intermediate states of carbonic anhydrase II under equilibrium conditions. The results of equilibrium and kinetic experiments using wild-type bovine carbonic anhydrase II and its mutant form with the substitution of leucine for alanine at position 139 (L139A) were compared. The obtained lifetime components of intrinsic tryptophan fluorescence allowed for revealing that, the same as in kinetic experiments, under equilibrium conditions the unfolding of carbonic anhydrase II ensues through formation of intermediate states.

Refolding of urea-denatured α-chymotrypsin by protein-folding liquid chromatography.

PubMed

Congyu, Ke; Wujuan, Sun; Qunzheng, Zhang; Xindu, Geng

2013-04-01

An approach for re-folding denatured proteins during proteome research by protein folding liquid chromatography (PFLC) is presented. Standard protein, α-chymotrypsin (α-Chy), was selected as a model protein and hydrophobic interaction chromatography was performed as a typical PFLC; the three different α-Chy states - urea-denatured (U state), its folded intermediates (M state) and nature state (N state) - were studied during protein folding. Based on the test by matrix-assisted laser desorption/ionization time of flight mass spectrometry and bioactivity, only one stable M state of the α-Chy was identified and then it was prepared for further investigation. The specific bioactivity of the refolded α-Chy was found to be higher than that of commercial α-Chy as the urea concentration in the sample solution ranged from 1.0 to 3.0 m; the highest specific bioactivity at urea concentration was 1.0 m, indicating the possibility for re-folding some proteins that have partially or completely lost their bioactivity, as a dilute urea solution was employed for dissolving the sample. The experiment showed that the peak height of its M state increased with increasing urea concentration, and correspondingly decreased in the amount of the refolded α-Chy. When the urea concentration reached 6.0 m, the unfolded α-Chy could not be refolded at all. Copyright © 2012 John Wiley & Sons, Ltd.

Chemical degradation and morphological instabilities during focused ion beam prototyping of polymers.

PubMed

Orthacker, A; Schmied, R; Chernev, B; Fröch, J E; Winkler, R; Hobisch, J; Trimmel, G; Plank, H

2014-01-28

Focused ion beam processing of low melting materials, such as polymers or biological samples, often leads to chemical and morphological instabilities which prevent the straight-forward application of this versatile direct-write structuring method. In this study the behaviour of different polymer classes under ion beam exposure is investigated using different patterning parameters and strategies with the aim of (i) correlating local temperatures with the polymers' chemistry and its morphological consequences; and (ii) finding a way of processing sensitive polymers with lowest chemical degradation while maintaining structuring times. It is found that during processing of polymers three temperature regimes can be observed: (1) at low temperatures all polymers investigated show stable chemical and morphological behaviour; (2) very high temperatures lead to strong chemical degradation which entails unpredictable morphologies; and (3) in the intermediate temperature regime the behaviour is found to be strongly material dependent. A detailed look reveals that polymers which rather cross-link in the proximity of the beam show stable morphologies in this intermediate regime, while polymers that rather undergo chain scission show tendencies to develop a creeping phase, where material follows the ion beam movement leading to instable and unpredictable morphologies. Finally a simple, alternative patterning strategy is suggested, which allows stable processing conditions with lowest chemical damage even for challenging polymers undergoing chain scission.

Method and reaction pathway for selectively oxidizing organic compounds

DOEpatents

Camaioni, Donald M.; Lilga, Michael A.

1998-01-01

A method of selectively oxidizing an organic compound in a single vessel comprises: a) combining an organic compound, an acid solution in which the organic compound is soluble, a compound containing two oxygen atoms bonded to one another, and a metal ion reducing agent capable of reducing one of such oxygen atoms, and thereby forming a mixture; b) reducing the compound containing the two oxygen atoms by reducing one of such oxygen atoms with the metal ion reducing agent to, 1) oxidize the metal ion reducing agent to a higher valence state, and 2) produce an oxygen containing intermediate capable of oxidizing the organic compound; c) reacting the oxygen containing intermediate with the organic compound to oxidize the organic compound into an oxidized organic intermediate, the oxidized organic intermediate having an oxidized carbon atom; d) reacting the oxidized organic intermediate with the acid counter ion and higher valence state metal ion to bond the acid counter ion to the oxidized carbon atom and thereby produce a quantity of an ester incorporating the organic intermediate and acid counter ion; and e) reacting the oxidized organic intermediate with the higher valence state metal ion and water to produce a quantity of alcohol which is less than the quantity of ester, the acid counter ion incorporated in the ester rendering the carbon atom bonded to the counter ion less reactive with the oxygen containing intermediate in the mixture than is the alcohol with the oxygen containing intermediate.

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

Zarkevich, N. A.; Johnson, D. D.

NiTi is the most used shape-memory alloy, nonetheless, a lack of understanding remains regarding the associated structures and transitions, including their barriers. Using a generalized solid-state nudge elastic band (GSSNEB) method implemented via density-functional theory, we detail the structural transformations in NiTi relevant to shape memory: those between body-centered orthorhombic (BCO) groundstate and a newly identified stable austenite (“glassy” B2-like) structure, including energy barriers (hysteresis) and intermediate structures (observed as a kinetically limited R-phase), and between martensite variants (BCO orientations). All results are in good agreement with available experiment. We contrast the austenite results to those from the often-assumed, butmore » unstable B2. Furthermore, these high- and low-temperature structures and structural transformations provide much needed atomic-scale detail for transitions responsible for NiTi shape-memory effects.« less

Negative ion electrospray ionization mass spectrometry of nucleoside phosphoramidate monoesters: elucidation of novel rearrangement mechanisms by multistage mass spectrometry incorporating in-source deuterium labelling.

PubMed

Xu, Peng-Xiang; Hu, An-Fu; Hu, Dan; Gao, Xiang; Zhao, Yu-Fen

2008-10-01

Several O-2',3'-isopropylideneuridine-O-5'-phosphoramidate monoesters were synthesized and analyzed by negative ion electrospray ionization tandem mass spectrometry (ESI-MS(n)). Two kinds of novel rearrangement reactions were observed due to the difference in the amino acid in the nucleoside phosphoramidate monoesters, and possible mechanisms were proposed. One involves a five-membered cyclic transition state. The other is formation of a stable five-membered ring intermediate by Michael addition. Results were confirmed by tandem mass spectrometry and isotopically labeled hydrogen atoms. Furthermore, the internal hydrogen exchange between active hydrogen and methyl acrylate in the heated capillary of the mass spectrometer was found. The characteristic fragmentation behavior in ESI-MS may be used to monitor this kind of compounds in the biological metabolism.

Do planetary seasons play a role in attaining stable climates?

NASA Astrophysics Data System (ADS)

Olsen, Kasper Wibeck; Bohr, Jakob

2018-05-01

A simple phenomenological account for planetary climate instabilities is presented. The description is based on the standard model where the balance of incoming stellar radiation and outward thermal radiation is described by the effective planet temperature. Often, it is found to have three different points, or temperatures, where the influx of radiation is balanced with the out-flux, even with conserved boundary conditions. Two of these points are relatively long-term stable, namely the point corresponding to a cold climate and the point corresponding to a hot climate. In a classical sense these points are equilibrium balance points. The hypothesis promoted in this paper is the possibility that the intermediate third point can become long-term stable by being driven dynamically. The initially unstable point is made relatively stable over a long period by the presence of seasonal climate variations.

The Synthesis and Chemiluminescence of a Stable 1,2-Dioxetane.

ERIC Educational Resources Information Center

Meijer, E. W.; Wynberg, Hans

1982-01-01

Background information, laboratory procedures, and discussion of results are provided for the synthesis and chemiluminescence of adamantylideneadamantane-1,2-dioxetane (I). Results provided were obtained during a normal junior level organic laboratory course. All intermediates and products were identified using routine spectroscopic analysis.…

Understanding the hydrolysis mechanism of ethyl acetate catalyzed by an aqueous molybdocene: a computational chemistry investigation.

PubMed

Tílvez, Elkin; Cárdenas-Jirón, Gloria I; Menéndez, María I; López, Ramón

2015-02-16

A thoroughly mechanistic investigation on the [Cp2Mo(OH)(OH2)](+)-catalyzed hydrolysis of ethyl acetate has been performed using density functional theory methodology together with continuum and discrete-continuum solvation models. The use of explicit water molecules in the PCM-B3LYP/aug-cc-pVTZ (aug-cc-pVTZ-PP for Mo)//PCM-B3LYP/aug-cc-pVDZ (aug-cc-pVDZ-PP for Mo) computations is crucial to show that the intramolecular hydroxo ligand attack is the preferred mechanism in agreement with experimental suggestions. Besides, the most stable intermediate located along this mechanism is analogous to that experimentally reported for the norbornenyl acetate hydrolysis catalyzed by molybdocenes. The three most relevant steps are the formation and cleavage of the tetrahedral intermediate immediately formed after the hydroxo ligand attack and the acetic acid formation, with the second one being the rate-determining step with a Gibbs energy barrier of 36.7 kcal/mol. Among several functionals checked, B3LYP-D3 and M06 give the best agreement with experiment as the rate-determining Gibbs energy barrier obtained only differs 0.2 and 0.7 kcal/mol, respectively, from that derived from the experimental kinetic constant measured at 296.15 K. In both cases, the acetic acid elimination becomes now the rate-determining step of the overall process as it is 0.4 kcal/mol less stable than the tetrahedral intermediate cleavage. Apart from clarifying the identity of the cyclic intermediate and discarding the tetrahedral intermediate formation as the rate-determining step for the mechanism of the acetyl acetate hydrolysis catalyzed by molybdocenes, the small difference in the Gibbs energy barrier found between the acetic acid formation and the tetrahedral intermediate cleavage also uncovers that the rate-determining step could change when studying the reactivity of carboxylic esters other than ethyl acetate substrate specific toward molybdocenes or other transition metal complexes. Therefore, in general, the information reported here could be of interest in designing new catalysts and understanding the reaction mechanism of these and other metal-catalyzed hydrolysis reactions.

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

PubMed

Palenik, Mark C; Rodriguez, Jorge H

2014-07-07

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

Large Eddy Simulations of Transverse Combustion Instability in a Multi-Element Injector

DTIC Science & Technology

2016-07-27

Instability in a Multi- Element Injector 5a. CONTRACT NUMBER 5b. GRANT NUMBER 5c. PROGRAM ELEMENT NUMBER 6. AUTHOR(S) Matthew Harvazinski, Yogin...Simulations of Transverse  Combustion Instability in a Multi‐ Element  Injector 2 History Damaged engine injector  faceplate caused by combustion...Clearance #16346 3 Single  Element  Studies Short Post Marginally Stable Intermediate Post Unstable Long Post Stable Long Post Unstable CVRC Experiment

Microsecond Unfolding Kinetics of Sheep Prion Protein Reveals an Intermediate that Correlates with Susceptibility to Classical Scrapie

PubMed Central

Chen, Kai-Chun; Xu, Ming; Wedemeyer, William J.; Roder, Heinrich

2011-01-01

The microsecond folding and unfolding kinetics of ovine prion proteins (ovPrP) were measured under various solution conditions. A fragment comprising residues 94–233 of the full-length ovPrP was studied for four variants with differing susceptibilities to classical scrapie in sheep. The observed biexponential unfolding kinetics of ovPrP provides evidence for an intermediate species. However, in contrast to previous results for human PrP, there is no evidence for an intermediate under refolding conditions. Global analysis of the kinetic data, based on a sequential three-state mechanism, quantitatively accounts for all folding and unfolding data as a function of denaturant concentration. The simulations predict that an intermediate accumulates under both folding and unfolding conditions, but is observable only in unfolding experiments because the intermediate is optically indistinguishable from the native state. The relative population of intermediates in two ovPrP variants, both transiently and under destabilizing equilibrium conditions, correlates with their propensities for classical scrapie. The variant susceptible to classical scrapie has a larger population of the intermediate state than the resistant variant. Thus, the susceptible variant should be favored to undergo the PrPC to PrPSc conversion and oligomerization. PMID:21889460

Mitochondrial 3β-Hydroxysteroid Dehydrogenase Enzyme Activity Requires Reversible pH-dependent Conformational Change at the Intermembrane Space*

PubMed Central

Prasad, Manoj; Thomas, James L.; Whittal, Randy M.; Bose, Himangshu S.

2012-01-01

The inner mitochondrial membrane protein 3β-hydroxysteroid dehydrogenase 2 (3βHSD2) synthesizes progesterone and androstenedione through its dehydrogenase and isomerase activities. This bifunctionality requires 3βHSD2 to undergo a conformational change. Given its proximity to the proton pump, we hypothesized that pH influences 3βHSD2 conformation and thus activity. Circular dichroism (CD) showed that between pH 7.4 and 4.5, 3βHSD2 retained its primarily α-helical character with a decrease in α-helical content at lower pH values, whereas the β-sheet content remained unchanged throughout. Titrating the pH back to 7.4 restored the original conformation within 25 min. Metabolic conversion assays indicated peak 3βHSD2 activity at pH 4.5 with ∼2-fold more progesterone synthesized at pH 4.5 than at pH 3.5 and 7.4. Increasing the 3βHSD2 concentration from 1 to 40 μg resulted in a 7-fold increase in progesterone at pH 4.5, but no change at pH 7.4. Incubation with guanidinum hydrochloride (GdmHCl) showed a three-step cooperative unfolding of 3βHSD2 from pH 7.4 to 4.5, possibly due to the native state unfolding to the intermediate ion core state. With further decreases in pH, increasing concentrations of GdmHCl led to rapid two-step unfolding that may represent complete loss of structure. Between pH 4 and 5, the two intermediate states appeared stable. Stopped-flow kinetics showed slower unfolding at around pH 4, where the protein is in a pseudostable state. Based on our data, we conclude that at pH 4–5, 3βHSD2 takes on a molten globule conformation that promotes the dual functionality of the enzyme. PMID:22262841

Evolution of dispersal in spatially and temporally variable environments: The importance of life cycles.

PubMed

Massol, François; Débarre, Florence

2015-07-01

Spatiotemporal variability of the environment is bound to affect the evolution of dispersal, and yet model predictions strongly differ on this particular effect. Recent studies on the evolution of local adaptation have shown that the life cycle chosen to model the selective effects of spatiotemporal variability of the environment is a critical factor determining evolutionary outcomes. Here, we investigate the effect of the order of events in the life cycle on the evolution of unconditional dispersal in a spatially heterogeneous, temporally varying landscape. Our results show that the occurrence of intermediate singular strategies and disruptive selection are conditioned by the temporal autocorrelation of the environment and by the life cycle. Life cycles with dispersal of adults versus dispersal of juveniles, local versus global density regulation, give radically different evolutionary outcomes that include selection for total philopatry, evolutionary bistability, selection for intermediate stable states, and evolutionary branching points. Our results highlight the importance of accounting for life-cycle specifics when predicting the effects of the environment on evolutionarily selected trait values, such as dispersal, as well as the need to check the robustness of model conclusions against modifications of the life cycle. © 2015 The Author(s). Evolution © 2015 The Society for the Study of Evolution.

Coiled-coil intermediate filament stutter instability and molecular unfolding.

PubMed

Arslan, Melis; Qin, Zhao; Buehler, Markus J

2011-05-01

Intermediate filaments (IFs) are the key components of cytoskeleton in eukaryotic cells and are critical for cell mechanics. The building block of IFs is a coiled-coil alpha-helical dimer, consisting of several domains that include linkers and other structural discontinuities. One of the discontinuities in the dimer's coiled-coil region is the so-called 'stutter' region. The stutter is a region where a variation of the amino acid sequence pattern from other parts of the alpha-helical domains of the protein is found. It was suggested in earlier works that due to this sequence variation, the perfect coiled-coil arrangement ceases to exist. Here, we show using explicit water molecular dynamics and well-tempered metadynamics that for the coil2 domain of vimentin IFs the stutter is more stable in a non-alpha-helical, unfolded state. This causes a local structural disturbance in the alpha helix, which has a global effect on the nanomechanics of the structure. Our analysis suggests that the stutter features an enhanced tendency to unfolding even under the absence of external forces, implying a much greater structural instability than previously assumed. As a result it features a smaller local bending stiffness than other segments and presents a seed for the initiation of molecular bending and unfolding at large deformation.

The Alkaline Hydrolysis of Sulfonate Esters: Challenges in Interpreting Experimental and Theoretical Data

PubMed Central

2013-01-01

Sulfonate ester hydrolysis has been the subject of recent debate, with experimental evidence interpreted in terms of both stepwise and concerted mechanisms. In particular, a recent study of the alkaline hydrolysis of a series of benzene arylsulfonates (Babtie et al., Org. Biomol. Chem.10, 2012, 8095) presented a nonlinear Brønsted plot, which was explained in terms of a change from a stepwise mechanism involving a pentavalent intermediate for poorer leaving groups to a fully concerted mechanism for good leaving groups and supported by a theoretical study. In the present work, we have performed a detailed computational study of the hydrolysis of these compounds and find no computational evidence for a thermodynamically stable intermediate for any of these compounds. Additionally, we have extended the experimental data to include pyridine-3-yl benzene sulfonate and its N-oxide and N-methylpyridinium derivatives. Inclusion of these compounds converts the Brønsted plot to a moderately scattered but linear correlation and gives a very good Hammett correlation. These data suggest a concerted pathway for this reaction that proceeds via an early transition state with little bond cleavage to the leaving group, highlighting the care that needs to be taken with the interpretation of experimental and especially theoretical data. PMID:24279349

Effect of Loading History on Airway Smooth Muscle Cell-Matrix Adhesions.

PubMed

Irons, Linda; Owen, Markus R; O'Dea, Reuben D; Brook, Bindi S

2018-06-05

Integrin-mediated adhesions between airway smooth muscle (ASM) cells and the extracellular matrix (ECM) regulate how contractile forces generated within the cell are transmitted to its external environment. Environmental cues are known to influence the formation, size, and survival of cell-matrix adhesions, but it is not yet known how they are affected by dynamic fluctuations associated with tidal breathing in the intact airway. Here, we develop two closely related theoretical models to study adhesion dynamics in response to oscillatory loading of the ECM, representing the dynamic environment of ASM cells in vivo. Using a discrete stochastic-elastic model, we simulate individual integrin binding and rupture events and observe two stable regimes in which either bond formation or bond rupture dominate, depending on the amplitude of the oscillatory loading. These regimes have either a high or low fraction of persistent adhesions, which could affect the level of strain transmission between contracted ASM cells and the airway tissue. For intermediate loading, we observe a region of bistability and hysteresis due to shared loading between existing bonds; the level of adhesion depends on the loading history. These findings are replicated in a related continuum model, which we use to investigate the effect of perturbations mimicking deep inspirations (DIs). Because of the bistability, a DI applied to the high adhesion state could either induce a permanent switch to a lower adhesion state or allow a return of the system to the high adhesion state. Transitions between states are further influenced by the frequency of oscillations, cytoskeletal or ECM stiffnesses, and binding affinities, which modify the magnitudes of the stable adhesion states as well as the region of bistability. These findings could explain (in part) the transient bronchodilatory effect of a DI observed in asthmatics compared to a more sustained effect in normal subjects. Copyright © 2018 Biophysical Society. Published by Elsevier Inc. All rights reserved.

Crystallographic and spectroscopic snapshots reveal a dehydrogenase in action

DOE PAGES

Huo, Lu; Davis, Ian; Liu, Fange; ...

2015-01-07

Aldehydes are ubiquitous intermediates in metabolic pathways and their innate reactivity can often make them quite unstable. There are several aldehydic intermediates in the metabolic pathway for tryptophan degradation that can decay into neuroactive compounds that have been associated with numerous neurological diseases. An enzyme of this pathway, 2-aminomuconate-6-semialdehyde dehydrogenase, is responsible for ‘disarming’ the final aldehydic intermediate. Here we show the crystal structures of a bacterial analogue enzyme in five catalytically relevant forms: resting state, one binary and two ternary complexes, and a covalent, thioacyl intermediate. We also report the crystal structures of a tetrahedral, thiohemiacetal intermediate, a thioacylmore » intermediate and an NAD +-bound complex from an active site mutant. These covalent intermediates are characterized by single-crystal and solution-state electronic absorption spectroscopy. The crystal structures reveal that the substrate undergoes an E/Z isomerization at the enzyme active site before an sp 3-to-sp 2 transition during enzyme-mediated oxidation.« less

Intermediate and deep water mass distribution in the Pacific during the Last Glacial Maximum inferred from oxygen and carbon stable isotopes

NASA Astrophysics Data System (ADS)

Herguera, J. C.; Herbert, T.; Kashgarian, M.; Charles, C.

2010-05-01

Intermediate ocean circulation changes during the last Glacial Maximum (LGM) in the North Pacific have been linked with Northern Hemisphere climate through air-sea interactions, although the extent and the source of the variability of the processes forcing these changes are still not well resolved. The ventilated volumes and ages in the upper wind driven layer are related to the wind stress curl and surface buoyancy fluxes at mid to high latitudes in the North Pacific. In contrast, the deeper thermohaline layers are more effectively ventilated by direct atmosphere-sea exchange during convective formation of Subantarctic Mode Waters (SAMW) and Antarctic Intermediate Waters (AAIW) in the Southern Ocean, the precursors of Pacific Intermediate Waters (PIW) in the North Pacific. Results reported here show a fundamental change in the carbon isotopic gradient between intermediate and deep waters during the LGM in the eastern North Pacific indicating a deepening of nutrient and carbon rich waters. These observations suggest changes in the source and nature of intermediate waters of Southern Ocean origin that feed PIW and enhanced ventilation processes in the North Pacific, further affecting paleoproductivity and export patters in this basin. Furthermore, oxygen isotopic results indicate these changes may have been accomplished in part by changes in circulation affecting the intermediate depths during the LGM.

Information encoded in non-native states drives substrate-chaperone pairing.

PubMed

Mapa, Koyeli; Tiwari, Satyam; Kumar, Vignesh; Jayaraj, Gopal Gunanathan; Maiti, Souvik

2012-09-05

Many proteins refold in vitro through kinetic folding intermediates that are believed to be by-products of native-state centric evolution. These intermediates are postulated to play only minor roles, if any, in vivo because they lack any information related to translation-associated vectorial folding. We demonstrate that refolding intermediate of a test protein, generated in vitro, is able to find its cognate chaperone, from the whole complement of Escherichia coli soluble chaperones. Cognate chaperone-binding uniquely alters the conformation of non-native substrate. Importantly, precise chaperone targeting of substrates are maintained as long as physiological molar ratios of chaperones remain unaltered. Using a library of different chaperone substrates, we demonstrate that kinetically trapped refolding intermediates contain sufficient structural features for precise targeting to cognate chaperones. We posit that evolution favors sequences that, in addition to coding for a functional native state, encode folding intermediates with higher affinity for cognate chaperones than noncognate ones. Copyright © 2012 Elsevier Ltd. All rights reserved.

Intermediate-valence state of the Sm and Eu in SmB6 and EuCu2Si2: neutron spectroscopy data and analysis

NASA Astrophysics Data System (ADS)

Savchenkov, P. S.; Alekseev, P. A.; Podlesnyak, A.; Kolesnikov, A. I.; Nemkovski, K. S.

2018-02-01

Magnetic neutron scattering data for Sm (SmB6, Sm(Y)S) and Eu (EuCu2Si2-x Ge x ) intermediate-valence compounds have been analysed in terms of a generalized model of the intermediate-radius exciton. Special attention is paid to the correlation between the average ion’s valence and parameters of the low-energy excitation in the neutron spectra, such as the resonance mode, including its magnetic form factor. Along with specific features of the formation of the intermediate-valence state for Sm and Eu ions, common physical mechanisms have been revealed for systems based on these elements from the middle of the rare-earth series. A consistent description of the existing experimental data has been obtained by using the concept of a loosely bound hole for the Eu f-electron shell in the intermediate-valence state, in analogy with the previously established loosely bound electron model for the Sm ion.

Structure of photosystem II and substrate binding at room temperature

PubMed Central

Gul, Sheraz; Fuller, Franklin; Koroidov, Sergey; Brewster, Aaron S.; Tran, Rosalie; Alonso-Mori, Roberto; Kroll, Thomas; Michels-Clark, Tara; Laksmono, Hartawan; Sierra, Raymond G.; Stan, Claudiu A.; Hussein, Rana; Zhang, Miao; Douthit, Lacey; Kubin, Markus; de Lichtenberg, Casper; Long Vo, Pham; Nilsson, Håkan; Cheah, Mun Hon; Shevela, Dmitriy; Saracini, Claudio; Bean, Mackenzie A.; Seuffert, Ina; Sokaras, Dimosthenis; Weng, Tsu-Chien; Pastor, Ernest; Weninger, Clemens; Fransson, Thomas; Lassalle, Louise; Bräuer, Philipp; Aller, Pierre; Docker, Peter T.; Andi, Babak; Orville, Allen M.; Glownia, James M.; Nelson, Silke; Sikorski, Marcin; Zhu, Diling; Hunter, Mark S.; Lane, Thomas J.; Aquila, Andy; Koglin, Jason E.; Robinson, Joseph; Liang, Mengning; Boutet, Sébastien; Lyubimov, Artem Y.; Uervirojnangkoorn, Monarin; Moriarty, Nigel W.; Liebschner, Dorothee; Afonine, Pavel V.; Waterman, David G.; Evans, Gwyndaf; Wernet, Philippe; Dobbek, Holger; Weis, William I.; Brunger, Axel T.; Zwart, Petrus H.; Adams, Paul D.; Zouni, Athina; Messinger, Johannes; Bergmann, Uwe; Sauter, Nicholas K.; Kern, Jan; Yachandra, Vittal K.; Yano, Junko

2016-01-01

Light-induced oxidation of water by photosystem II (PS II) in plants, algae and cyanobacteria has generated most of the dioxygen in the atmosphere. PS II, a membrane-bound multi-subunit pigment-protein complex, couples the one-electron photochemistry at the reaction center with the four-electron redox chemistry of water oxidation at the Mn4CaO5 cluster in the oxygen-evolving complex (OEC) (Fig. 1a, Extended Data Fig. 1). Under illumination, the OEC cycles through five intermediate S-states (S0 to S4)1, where S1 is the dark stable state and S3 is the last semi-stable state before O-O bond formation and O2 evolution2,3. A detailed understanding of the O-O bond formation mechanism remains a challenge, and elucidating the structures of the OEC in the different S-states, as well as the binding of the two substrate waters to the catalytic site4-6, is a prerequisite for this purpose. Here we report the use of femtosecond pulses from an X-ray free electron laser (XFEL) to obtain damage free, room temperature (RT) structures of dark-adapted (S1), two-flash illuminated (2F; S3-enriched), and ammonia-bound two-flash illuminated (2F-NH3; S3-enriched) PS II. Although the recent 1.95 Å structure of PS II7 at cryogenic temperature using an XFEL provided a damage-free view of the S1 state, RT measurements are required to study the structural landscape of proteins under functional conditions8,9, and also for in situ advancement of the S-states. To investigate the water-binding site(s), ammonia, a water analog, has been used as a marker, as it binds to the Mn4CaO5 cluster in the S2 and S3 states10. Since the ammonia-bound OEC is active, the ammonia-binding Mn site is not a substrate water site10-13. Thus, this approach, together with a comparison of the native dark and 2F states, is used to discriminate between proposed O-O bond formation mechanisms. PMID:27871088

Intensive Care Unit Utilization Among Medicare Patients Hospitalized with Non-ST-Segment Elevation Myocardial Infarction

PubMed Central

Fanaroff, Alexander C; Peterson, Eric D; Chen, Anita Y; Thomas, Laine; Doll, Jacob D; Fordyce, Christopher B; Newby, L Kristin; Amsterdam, Ezra A; Kosiborod, Mikhail N; de Lemos, James A; Wang, Tracy Y

2018-01-01

Importance Intensive care unit (ICU) utilization may have important implications for the care and outcomes of patients with non-ST-segment elevation myocardial infarction (NSTEMI). Objectives To examine inter-hospital variation in ICU utilization in the United States for older adults with hemodynamically stable NSTEMI and outcomes associated with ICU utilization among patients with at low, moderate, or high mortality risk. Design, Settings and Participants Retrospective analysis of 28,018 Medicare patients ≥65 years old admitted with NSTEMI to 346 hospitals participating in ACTION Registry-GWTG between April 1, 2011 and December 31, 2012. Patients with cardiogenic shock or cardiac arrest on presentation were excluded. Exposure Hospitals with high (>70% NSTEMI patients treated in an ICU during the index hospitalization), intermediate (30–70%), or low (< 30%) ICU utilization rates Main Outcome and Measure 30-day mortality Results Of NSTEMI patients ≥ 65 years old, 11,934 (43%) had an ICU stay. The proportion of NSTEMI patients treated in the ICU varied across hospitals (median 38% [26%, 54%]), but there were no significant differences in hospital characteristics or NSTEMI patient characteristics between hospitals with high, intermediate, or low ICU utilization rates. Compared with high ICU utilization hospitals, hospitals with low or intermediate ICU utilizations rates were only marginally more selective of higher risk patients, as determined by ACTION in-hospital mortality risk score or initial troponin level. Thirty-day mortality rates did not significantly differ based on hospital ICU utilization (high vs. low: 8.7% vs. 8.7%, adjusted OR 0.91, 95% CI 0.76–1.08; intermediate vs. low: 9.6% vs. 8.7%, adjusted OR 1.06, 95% CI 0.94–1.20). The relationship between hospital ICU utilization and mortality was similar in analyses stratified by low, moderate, or high ACTION risk score categories (adjusted interaction p 0.86). Conclusions and Relevance ICU utilization for older NSTEMI patients varied significantly among hospitals. This variability was not explained by hospital characteristics nor driven by patient risk. Post-MI mortality did not significantly differ among hospitals with high, intermediate, or low ICU utilization. PMID:27806171

Probing the Self-Assembly and the Accompanying Structural Changes of Hydrophobin SC3 on a Hydrophobic Surface by Mass Spectrometry

PubMed Central

Wang, X.; Permentier, H. P.; Rink, R.; Kruijtzer, J. A. W.; Liskamp, R. M. J.; Wösten, H. A. B.; Poolman, B.; Robillard, G. T.

2004-01-01

The fungal class I hydrophobin SC3 self-assembles into an amphipathic membrane at hydrophilic-hydrophobic interfaces such as the water-air and water-Teflon interface. During self-assembly, the water-soluble state of SC3 proceeds via the intermediate α-helical state to the stable end form called the β-sheet state. Self-assembly of the hydrophobin at the Teflon surface is arrested in the α-helical state. The β-sheet state can be induced at elevated temperature in the presence of detergent. The structural changes of SC3 were monitored by various mass spectrometry techniques. We show that the so-called second loop of SC3 (C39–S72) has a high affinity for Teflon. Binding of this part of SC3 to Teflon was accompanied by the formation of α-helical structure and resulted in low solvent accessibility. The solvent-protected region of the second loop extended upon conversion to the β-sheet state. In contrast, the C-terminal part of SC3 became more exposed to the solvent. The results indicate that the second loop of class I hydrophobins plays a pivotal role in self-assembly at the hydrophilic-hydrophobic interface. Of interest, this loop is much smaller in case of class II hydrophobins, which may explain the differences in their assembly. PMID:15345568

Modulation of frustration in folding by sequence permutation.

PubMed

Nobrega, R Paul; Arora, Karunesh; Kathuria, Sagar V; Graceffa, Rita; Barrea, Raul A; Guo, Liang; Chakravarthy, Srinivas; Bilsel, Osman; Irving, Thomas C; Brooks, Charles L; Matthews, C Robert

2014-07-22

Folding of globular proteins can be envisioned as the contraction of a random coil unfolded state toward the native state on an energy surface rough with local minima trapping frustrated species. These substructures impede productive folding and can serve as nucleation sites for aggregation reactions. However, little is known about the relationship between frustration and its underlying sequence determinants. Chemotaxis response regulator Y (CheY), a 129-amino acid bacterial protein, has been shown previously to populate an off-pathway kinetic trap in the microsecond time range. The frustration has been ascribed to premature docking of the N- and C-terminal subdomains or, alternatively, to the formation of an unproductive local-in-sequence cluster of branched aliphatic side chains, isoleucine, leucine, and valine (ILV). The roles of the subdomains and ILV clusters in frustration were tested by altering the sequence connectivity using circular permutations. Surprisingly, the stability and buried surface area of the intermediate could be increased or decreased depending on the location of the termini. Comparison with the results of small-angle X-ray-scattering experiments and simulations points to the accelerated formation of a more compact, on-pathway species for the more stable intermediate. The effect of chain connectivity in modulating the structures and stabilities of the early kinetic traps in CheY is better understood in terms of the ILV cluster model. However, the subdomain model captures the requirement for an intact N-terminal domain to access the native conformation. Chain entropy and aliphatic-rich sequences play crucial roles in biasing the early events leading to frustration in the folding of CheY.

Disturbance Regimes Predictably Alter Diversity in an Ecologically Complex Bacterial System

PubMed Central

Scholz, Monika; Hutchison, Alan L.; Dinner, Aaron R.; Gilbert, Jack A.; Coleman, Maureen L.

2016-01-01

ABSTRACT Diversity is often associated with the functional stability of ecological communities from microbes to macroorganisms. Understanding how diversity responds to environmental perturbations and the consequences of this relationship for ecosystem function are thus central challenges in microbial ecology. Unimodal diversity-disturbance relationships, in which maximum diversity occurs at intermediate levels of disturbance, have been predicted for ecosystems where life history tradeoffs separate organisms along a disturbance gradient. However, empirical support for such peaked relationships in macrosystems is mixed, and few studies have explored these relationships in microbial systems. Here we use complex microbial microcosm communities to systematically determine diversity-disturbance relationships over a range of disturbance regimes. We observed a reproducible switch between community states, which gave rise to transient diversity maxima when community states were forced to mix. Communities showed reduced compositional stability when diversity was highest. To further explore these dynamics, we formulated a simple model that reveals specific regimes under which diversity maxima are stable. Together, our results show how both unimodal and non-unimodal diversity-disturbance relationships can be observed as a system switches between two distinct microbial community states; this process likely occurs across a wide range of spatially and temporally heterogeneous microbial ecosystems. PMID:27999158

Preparation of certain m-aminophenols and the use thereof for preparation of laser dyes

DOEpatents

Hammond, P.R.

1983-12-29

Methods are provided for making certain m-aminophenols using a sulfonation/alkali fusion procedure. The aminophenols are key intermediates in the synthesis of dyes, particularly efficient, stable dyes for laser application. Preparations of some rhodamine and phenoxazone dyes from the m-aminophenols are described.

Shape transformation of viral capsids and HIV

NASA Astrophysics Data System (ADS)

Nguyen, Toan

2005-03-01

We present a continuum description of the shape transformation of viral capsids. The cone-like HIV virus is shown to be an thermodynamic stable shape, intermediate between icosahedral and sphero-cylinder capsid shapes. A generalized Caspar-Klug classification is introduced to describe spherical, conical and cylinderical shapes of virus.

Preparation of certain m-aminophenols and the use thereof for preparation of laser dyes

DOEpatents

Hammond, Peter R.

1986-01-01

Methods are provided for making certain m-aminophenols using a sulfonation/alkali fusion procedure. The aminophenols are key intermediates in the synthesis of dyes, particularly efficient, stable dyes for laser application. Preparations of some rhodamine and phenoxazone dyes from the m-aminophenols are described.

Modifying a known gelator scaffold for nitrite detection.

PubMed

Zurcher, Danielle M; Adhia, Yash J; Romero, Julián Díaz; McNeil, Anne J

2014-07-25

The process of selecting and modifying a known gelator scaffold to develop a new nitrite-based sensor is described. Five new azo-sulfonate gelators were discovered and characterized. The most promising scaffold exhibits a stable diazonium intermediate, proceeds in a high yield, and gels nitrite-spiked tap, river, and pond water.

Photochemistry in a 3D metal-organic framework (MOF): monitoring intermediates and reactivity of the fac-to-mer photoisomerization of Re(diimine)(CO)3Cl incorporated in a MOF.

PubMed

Easun, Timothy L; Jia, Junhua; Calladine, James A; Blackmore, Danielle L; Stapleton, Christopher S; Vuong, Khuong Q; Champness, Neil R; George, Michael W

2014-03-03

The mechanism and intermediates in the UV-light-initiated ligand rearrangement of fac-Re(diimine)(CO)3Cl to form the mer isomer, when incorporated into a 3D metal-organic framework (MOF), have been investigated. The structure hosting the rhenium diimine complex is a 3D network with the formula {Mn(DMF)2[LRe(CO)3Cl]}∞ (ReMn; DMF = N,N-dimethylformamide), where the diimine ligand L, 2,2'-bipyridine-5,5'-dicarboxylate, acts as a strut of the MOF. The incorporation of ReMn into a KBr disk allows spatial distribution of the mer-isomer photoproduct in the disk to be mapped and spectroscopically characterized by both Fourier transform infrared and Raman microscopy. Photoisomerization has been monitored by IR spectroscopy and proceeds via dissociation of a CO to form more than one dicarbonyl intermediate. The dicarbonyl species are stable in the solid state at 200 K. The photodissociated CO ligand appears to be trapped within the crystal lattice and, upon warming above 200 K, readily recombines with the dicarbonyl intermediates to form both the fac-Re(diimine)(CO)3Cl starting material and the mer-Re(diimine)(CO)3Cl photoproduct. Experiments over a range of temperatures (265-285 K) allow estimates of the activation enthalpy of recombination for each process of ca. 16 (±6) kJ mol(-1) (mer formation) and 23 (±4) kJ mol(-1) (fac formation) within the MOF. We have compared the photochemistry of the ReMn MOF with a related alkane-soluble Re(dnb)(CO)3Cl complex (dnb = 4,4'-dinonyl-2,2'-bipyridine). Time-resolved IR measurements clearly show that, in an alkane solution, the photoinduced dicarbonyl species again recombines with CO to both re-form the fac-isomer starting material and form the mer-isomer photoproduct. Density functional theory calculations of the possible dicarbonyl species aids the assignment of the experimental data in that the ν(CO) IR bands of the CO loss intermediate are, as expected, shifted to lower energy when the metal is bound to DMF rather than to an alkane and both solution data and calculations suggest that the ν(CO) band positions in the photoproduced dicarbonyl intermediates of ReMn are consistent with DMF binding.

Cost-effectiveness of anatomical and functional test strategies for stable chest pain: public health perspective from a middle-income country.

PubMed

Bertoldi, Eduardo G; Stella, Steffen F; Rohde, Luis Eduardo P; Polanczyk, Carisi A

2017-05-04

The aim of this research is to evaluate the relative cost-effectiveness of functional and anatomical strategies for diagnosing stable coronary artery disease (CAD), using exercise (Ex)-ECG, stress echocardiogram (ECHO), single-photon emission CT (SPECT), coronary CT angiography (CTA) or stress cardiacmagnetic resonance (C-MRI). Decision-analytical model, comparing strategies of sequential tests for evaluating patients with possible stable angina in low, intermediate and high pretest probability of CAD, from the perspective of a developing nation's public healthcare system. Hypothetical cohort of patients with pretest probability of CAD between 20% and 70%. The primary outcome is cost per correct diagnosis of CAD. Proportion of false-positive or false-negative tests and number of unnecessary tests performed were also evaluated. Strategies using Ex-ECG as initial test were the least costly alternatives but generated more frequent false-positive initial tests and false-negative final diagnosis. Strategies based on CTA or ECHO as initial test were the most attractive and resulted in similar cost-effectiveness ratios (I$ 286 and I$ 305 per correct diagnosis, respectively). A strategy based on C-MRI was highly effective for diagnosing stable CAD, but its high cost resulted in unfavourable incremental cost-effectiveness (ICER) in moderate-risk and high-risk scenarios. Non-invasive strategies based on SPECT have been dominated. An anatomical diagnostic strategy based on CTA is a cost-effective option for CAD diagnosis. Functional strategies performed equally well when based on ECHO. C-MRI yielded acceptable ICER only at low pretest probability, and SPECT was not cost-effective in our analysis. © Article author(s) (or their employer(s) unless otherwise stated in the text of the article) 2017. All rights reserved. No commercial use is permitted unless otherwise expressly granted.

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

McCammon, C.; Dubrovinsky, L.; Narygina, O.

We investigated the spin state of iron in Mg{sub 0.82}Fe{sub 0.18}SiO{sub 3} silicate perovskite using Moessbauer spectroscopy and nuclear forward scattering (NFS) at pressures up to 130 GPa and temperatures up to 1000 K. Majorite starting material was loaded into diamond anvil cells in three separate experiments, and transformed to silicate perovskite through laser heating. We found, in agreement with previous work, the predominance of a component with high isomer shift ({approx}1 mm/s relative to {alpha}-Fe) and high-quadrupole splitting (QS) (>4 mm/s) in Moessbauer and NFS spectra up to 115 GPa at room temperature, and in accordance with previous workmore » this component was assigned to intermediate-spin Fe{sup 2+}. At higher pressures, the intensity of the high QS component in the silicate perovskite spectrum decreased, while the intensity of a new component with low isomer shift ({approx}0 mm/s relative to {alpha}-Fe) and low quadrupole splitting (<0.5 mm/s) increased. This new component was assigned to low-spin Fe{sup 2+}, and its intensity increased with both increasing pressure and increasing temperature: at 120 GPa and 1000 K all Fe{sup 2+} was in the low-spin state. X-ray diffraction data showed well crystallized perovskite in all runs, and although the stable phase above 110 GPa is expected to be post-perovskite, sluggish transition kinetics likely preserved the perovskite phase in a metastable state. Our results combined with data in the literature and thermodynamic and topological considerations suggest that there may be a region where silicate perovskite containing low-spin Fe{sup 2+} is stable, which coincides with predicted pressure-temperature conditions near the D{double_prime} layer.« less

Deconvoluting Protein (Un)folding Structural Ensembles Using X-Ray Scattering, Nuclear Magnetic Resonance Spectroscopy and Molecular Dynamics Simulation

PubMed Central

Nasedkin, Alexandr; Marcellini, Moreno; Religa, Tomasz L.; Freund, Stefan M.; Menzel, Andreas; Fersht, Alan R.; Jemth, Per; van der Spoel, David; Davidsson, Jan

2015-01-01

The folding and unfolding of protein domains is an apparently cooperative process, but transient intermediates have been detected in some cases. Such (un)folding intermediates are challenging to investigate structurally as they are typically not long-lived and their role in the (un)folding reaction has often been questioned. One of the most well studied (un)folding pathways is that of Drosophila melanogaster Engrailed homeodomain (EnHD): this 61-residue protein forms a three helix bundle in the native state and folds via a helical intermediate. Here we used molecular dynamics simulations to derive sample conformations of EnHD in the native, intermediate, and unfolded states and selected the relevant structural clusters by comparing to small/wide angle X-ray scattering data at four different temperatures. The results are corroborated using residual dipolar couplings determined by NMR spectroscopy. Our results agree well with the previously proposed (un)folding pathway. However, they also suggest that the fully unfolded state is present at a low fraction throughout the investigated temperature interval, and that the (un)folding intermediate is highly populated at the thermal midpoint in line with the view that this intermediate can be regarded to be the denatured state under physiological conditions. Further, the combination of ensemble structural techniques with MD allows for determination of structures and populations of multiple interconverting structures in solution. PMID:25946337

Deconvoluting Protein (Un)folding Structural Ensembles Using X-Ray Scattering, Nuclear Magnetic Resonance Spectroscopy and Molecular Dynamics Simulation.

PubMed

Nasedkin, Alexandr; Marcellini, Moreno; Religa, Tomasz L; Freund, Stefan M; Menzel, Andreas; Fersht, Alan R; Jemth, Per; van der Spoel, David; Davidsson, Jan

2015-01-01

The folding and unfolding of protein domains is an apparently cooperative process, but transient intermediates have been detected in some cases. Such (un)folding intermediates are challenging to investigate structurally as they are typically not long-lived and their role in the (un)folding reaction has often been questioned. One of the most well studied (un)folding pathways is that of Drosophila melanogaster Engrailed homeodomain (EnHD): this 61-residue protein forms a three helix bundle in the native state and folds via a helical intermediate. Here we used molecular dynamics simulations to derive sample conformations of EnHD in the native, intermediate, and unfolded states and selected the relevant structural clusters by comparing to small/wide angle X-ray scattering data at four different temperatures. The results are corroborated using residual dipolar couplings determined by NMR spectroscopy. Our results agree well with the previously proposed (un)folding pathway. However, they also suggest that the fully unfolded state is present at a low fraction throughout the investigated temperature interval, and that the (un)folding intermediate is highly populated at the thermal midpoint in line with the view that this intermediate can be regarded to be the denatured state under physiological conditions. Further, the combination of ensemble structural techniques with MD allows for determination of structures and populations of multiple interconverting structures in solution.

Heterogeneity of Equilibrium Molten Globule State of Cytochrome c Induced by Weak Salt Denaturants under Physiological Condition

PubMed Central

Rahaman, Hamidur; Alam Khan, Md. Khurshid; Hassan, Md. Imtaiyaz; Islam, Asimul; Moosavi-Movahedi, Ali Akbar; Ahmad, Faizan

2015-01-01

While many proteins are recognized to undergo folding via intermediate(s), the heterogeneity of equilibrium folding intermediate(s) along the folding pathway is less understood. In our present study, FTIR spectroscopy, far- and near-UV circular dichroism (CD), ANS and tryptophan fluorescence, near IR absorbance spectroscopy and dynamic light scattering (DLS) were used to study the structural and thermodynamic characteristics of the native (N), denatured (D) and intermediate state (X) of goat cytochorme c (cyt-c) induced by weak salt denaturants (LiBr, LiCl and LiClO4) at pH 6.0 and 25°C. The LiBr-induced denaturation of cyt-c measured by Soret absorption (Δε 400) and CD ([θ]409), is a three-step process, N ↔ X ↔ D. It is observed that the X state obtained along the denaturation pathway of cyt-c possesses common structural and thermodynamic characteristics of the molten globule (MG) state. The MG state of cyt-c induced by LiBr is compared for its structural and thermodynamic parameters with those found in other solvent conditions such as LiCl, LiClO4 and acidic pH. Our observations suggest: (1) that the LiBr-induced MG state of cyt-c retains the native Met80-Fe(III) axial bond and Trp59-propionate interactions; (2) that LiBr-induced MG state of cyt-c is more compact retaining the hydrophobic interactions in comparison to the MG states induced by LiCl, LiClO4 and 0.5 M NaCl at pH 2.0; and (3) that there exists heterogeneity of equilibrium intermediates along the unfolding pathway of cyt-c as highly ordered (X1), classical (X2) and disordered (X3), i.e., D ↔ X3 ↔ X2 ↔ X1 ↔ N. PMID:25849212

Heterogeneity of equilibrium molten globule state of cytochrome c induced by weak salt denaturants under physiological condition.

PubMed

Rahaman, Hamidur; Alam Khan, Md Khurshid; Hassan, Md Imtaiyaz; Islam, Asimul; Moosavi-Movahedi, Ali Akbar; Ahmad, Faizan

2015-01-01

While many proteins are recognized to undergo folding via intermediate(s), the heterogeneity of equilibrium folding intermediate(s) along the folding pathway is less understood. In our present study, FTIR spectroscopy, far- and near-UV circular dichroism (CD), ANS and tryptophan fluorescence, near IR absorbance spectroscopy and dynamic light scattering (DLS) were used to study the structural and thermodynamic characteristics of the native (N), denatured (D) and intermediate state (X) of goat cytochorme c (cyt-c) induced by weak salt denaturants (LiBr, LiCl and LiClO4) at pH 6.0 and 25°C. The LiBr-induced denaturation of cyt-c measured by Soret absorption (Δε400) and CD ([θ]409), is a three-step process, N ↔ X ↔ D. It is observed that the X state obtained along the denaturation pathway of cyt-c possesses common structural and thermodynamic characteristics of the molten globule (MG) state. The MG state of cyt-c induced by LiBr is compared for its structural and thermodynamic parameters with those found in other solvent conditions such as LiCl, LiClO4 and acidic pH. Our observations suggest: (1) that the LiBr-induced MG state of cyt-c retains the native Met80-Fe(III) axial bond and Trp59-propionate interactions; (2) that LiBr-induced MG state of cyt-c is more compact retaining the hydrophobic interactions in comparison to the MG states induced by LiCl, LiClO4 and 0.5 M NaCl at pH 2.0; and (3) that there exists heterogeneity of equilibrium intermediates along the unfolding pathway of cyt-c as highly ordered (X1), classical (X2) and disordered (X3), i.e., D ↔ X3 ↔ X2 ↔ X1 ↔ N.

Single-molecule studies of the Im7 folding landscape.

PubMed

Pugh, Sara D; Gell, Christopher; Smith, D Alastair; Radford, Sheena E; Brockwell, David J

2010-04-23

Under appropriate conditions, the four-helical Im7 (immunity protein 7) folds from an ensemble of unfolded conformers to a highly compact native state via an on-pathway intermediate. Here, we investigate the unfolded, intermediate, and native states populated during folding using diffusion single-pair fluorescence resonance energy transfer by measuring the efficiency of energy transfer (or proximity or P ratio) between pairs of fluorophores introduced into the side chains of cysteine residues placed in the center of helices 1 and 4, 1 and 3, or 2 and 4. We show that while the native states of each variant give rise to a single narrow distribution with high P values, the distributions of the intermediates trapped at equilibrium (denoted I(eqm)) are fitted by two Gaussian distributions. Modulation of the folding conditions from those that stabilize the intermediate to those that destabilize the intermediate enabled the distribution of lower P value to be assigned to the population of the unfolded ensemble in equilibrium with the intermediate state. The reduced stability of the I(eqm) variants allowed analysis of the effect of denaturant concentration on the compaction and breadth of the unfolded state ensemble to be quantified from 0 to 6 M urea. Significant compaction is observed as the concentration of urea is decreased in both the presence and absence of sodium sulfate, as previously reported for a variety of proteins. In the presence of Na(2)SO(4) in 0 M urea, the P value of the unfolded state ensemble approaches that of the native state. Concurrent with compaction, the ensemble displays increased peak width of P values, possibly reflecting a reduction in the rate of conformational exchange among iso-energetic unfolded, but compact conformations. The results provide new insights into the initial stages of folding of Im7 and suggest that the unfolded state is highly conformationally constrained at the outset of folding. (c) 2010 Elsevier Ltd. All rights reserved.

Single-Molecule Studies of the Im7 Folding Landscape

PubMed Central

Pugh, Sara D.; Gell, Christopher; Smith, D. Alastair; Radford, Sheena E.; Brockwell, David J.

2010-01-01

Under appropriate conditions, the four-helical Im7 (immunity protein 7) folds from an ensemble of unfolded conformers to a highly compact native state via an on-pathway intermediate. Here, we investigate the unfolded, intermediate, and native states populated during folding using diffusion single-pair fluorescence resonance energy transfer by measuring the efficiency of energy transfer (or proximity or P ratio) between pairs of fluorophores introduced into the side chains of cysteine residues placed in the center of helices 1 and 4, 1 and 3, or 2 and 4. We show that while the native states of each variant give rise to a single narrow distribution with high P values, the distributions of the intermediates trapped at equilibrium (denoted Ieqm) are fitted by two Gaussian distributions. Modulation of the folding conditions from those that stabilize the intermediate to those that destabilize the intermediate enabled the distribution of lower P value to be assigned to the population of the unfolded ensemble in equilibrium with the intermediate state. The reduced stability of the Ieqm variants allowed analysis of the effect of denaturant concentration on the compaction and breadth of the unfolded state ensemble to be quantified from 0 to 6 M urea. Significant compaction is observed as the concentration of urea is decreased in both the presence and absence of sodium sulfate, as previously reported for a variety of proteins. In the presence of Na2SO4 in 0 M urea, the P value of the unfolded state ensemble approaches that of the native state. Concurrent with compaction, the ensemble displays increased peak width of P values, possibly reflecting a reduction in the rate of conformational exchange among iso-energetic unfolded, but compact conformations. The results provide new insights into the initial stages of folding of Im7 and suggest that the unfolded state is highly conformationally constrained at the outset of folding. PMID:20211187

Revascularization decisions in patients with stable angina and intermediate lesions: results of the international survey on interventional strategy.

PubMed

Toth, Gabor G; Toth, Balint; Johnson, Nils P; De Vroey, Frederic; Di Serafino, Luigi; Pyxaras, Stylianos; Rusinaru, Dan; Di Gioia, Giuseppe; Pellicano, Mariano; Barbato, Emanuele; Van Mieghem, Carlos; Heyndrickx, Guy R; De Bruyne, Bernard; Wijns, William

2014-12-01

Fractional flow reserve (FFR) measurement of intermediate coronary stenoses is recommended by guidelines when demonstration of ischemia by noninvasive testing is unavailable. The study aims to evaluate the penetration of this recommendation into current thinking about revascularization strategies for stable coronary artery disease. International Survey on Interventional Strategy was conducted via a web-based platform. First, participants' experiences in interventional cardiology were queried. Second, 5 complete angiograms were provided, presenting only focal intermediate stenoses. FFR and quantitative coronary angiography values were known; however, remained undisclosed. Determination of stenosis significance was asked for each lesion. In cases of uncertainty, the most appropriate adjunctive invasive diagnostic method among quantitative coronary angiography, intravascular ultrasound, optical coherence tomography, or FFR needed to be selected. International Survey on Interventional Strategy was taken by 495 participants who provided 4421 lesion evaluations. In 3158 (71%) decisions, participants relied solely on angiographic appearance that was discordant in 47% with the known FFR, using 0.80 as cutoff value. The use of FFR and imaging modalities was requested in 21% and 8%, respectively. Comparing 4 groups of participants according to the experience in FFR, angiogram-based decisions were less frequent with increasing experience (77% versus 72% versus 69% versus 67%, respectively; P<0.001). As a result, requests for FFR were more frequent (14% versus 19% versus 24% versus 28%, respectively; P<0.001) and rates of discordant decisions decreased (51% versus 49% versus 47% versus 43%, respectively; P<0.022). The findings confirm that, even when all potential external constraints are virtually eliminated, visual estimation continues to dominate the treatment decisions for intermediate stenoses, indicative of a worrisome disconnect between recommendations and current practice. © 2014 American Heart Association, Inc.

Cell differentiation modeled via a coupled two-switch regulatory network

NASA Astrophysics Data System (ADS)

Schittler, D.; Hasenauer, J.; Allgöwer, F.; Waldherr, S.

2010-12-01

Mesenchymal stem cells can give rise to bone and other tissue cells, but their differentiation still escapes full control. In this paper we address this issue by mathematical modeling. We present a model for a genetic switch determining the cell fate of progenitor cells which can differentiate into osteoblasts (bone cells) or chondrocytes (cartilage cells). The model consists of two switch mechanisms and reproduces the experimentally observed three stable equilibrium states: a progenitor, an osteogenic, and a chondrogenic state. Conventionally, the loss of an intermediate (progenitor) state and the entailed attraction to one of two opposite (differentiated) states is modeled as a result of changing parameters. In our model in contrast, we achieve this by distributing the differentiation process to two functional switch parts acting in concert: one triggering differentiation and the other determining cell fate. Via stability and bifurcation analysis, we investigate the effects of biochemical stimuli associated with different system inputs. We employ our model to generate differentiation scenarios on the single cell as well as on the cell population level. The single cell scenarios allow to reconstruct the switching upon extrinsic signals, whereas the cell population scenarios provide a framework to identify the impact of intrinsic properties and the limiting factors for successful differentiation.

Incoherent manipulation of the photoactive yellow protein photocycle with dispersed pump-dump-probe spectroscopy.

PubMed

Larsen, Delmar S; van Stokkum, Ivo H M; Vengris, Mikas; van Der Horst, Michael A; de Weerd, Frank L; Hellingwerf, Klaas J; van Grondelle, Rienk

2004-09-01

Photoactive yellow protein is the protein responsible for initiating the "blue-light vision" of Halorhodospira halophila. The dynamical processes responsible for triggering the photoactive yellow protein photocycle have been disentangled with the use of a novel application of dispersed ultrafast pump-dump-probe spectroscopy, where the photocycle can be started and interrupted with appropriately tuned and timed laser pulses. This "incoherent" manipulation of the photocycle allows for the detailed spectroscopic investigation of the underlying photocycle dynamics and the construction of a fully self-consistent dynamical model. This model requires three kinetically distinct excited-state intermediates, two (ground-state) photocycle intermediates, I(0) and pR, and a ground-state intermediate through which the protein, after unsuccessful attempts at initiating the photocycle, returns to the equilibrium ground state. Also observed is a previously unknown two-photon ionization channel that generates a radical and an ejected electron into the protein environment. This second excitation pathway evolves simultaneously with the pathway containing the one-photon photocycle intermediates.

Incoherent Manipulation of the Photoactive Yellow Protein Photocycle with Dispersed Pump-Dump-Probe Spectroscopy

PubMed Central

Larsen, Delmar S.; van Stokkum, Ivo H. M.; Vengris, Mikas; van der Horst, Michael A.; de Weerd, Frank L.; Hellingwerf, Klaas J.; van Grondelle, Rienk

2004-01-01

Photoactive yellow protein is the protein responsible for initiating the “blue-light vision” of Halorhodospira halophila. The dynamical processes responsible for triggering the photoactive yellow protein photocycle have been disentangled with the use of a novel application of dispersed ultrafast pump-dump-probe spectroscopy, where the photocycle can be started and interrupted with appropriately tuned and timed laser pulses. This “incoherent” manipulation of the photocycle allows for the detailed spectroscopic investigation of the underlying photocycle dynamics and the construction of a fully self-consistent dynamical model. This model requires three kinetically distinct excited-state intermediates, two (ground-state) photocycle intermediates, I0 and pR, and a ground-state intermediate through which the protein, after unsuccessful attempts at initiating the photocycle, returns to the equilibrium ground state. Also observed is a previously unknown two-photon ionization channel that generates a radical and an ejected electron into the protein environment. This second excitation pathway evolves simultaneously with the pathway containing the one-photon photocycle intermediates. PMID:15345564

[Alternative stable states in coastal intertidal wetland ecosystems of Yangtze estuary, China].

PubMed

Li, Hui; Yuan, Lin; Zhang, Li Quan; Li, Wei; Li, Shi Hua; Zhao, Zhi Yuan

2017-01-01

Alternative stable states phenomenon widely exists in a variety of ecosystems and is closely related to ecosystem health and sustainable development. Although alternative stable states research has become the focus and hotspot of the ecology researches, only a few empirical evidences supported its behavior and mechanisms in coastal wetland ecosystems up to now. In our study, ta-king the intertidal wetland ecosystem in Chongming Dongtan Nature Reserve as study area, we aimed to: 1) test the existence of alternative stable states based on judgment conditions (bimodal characteristic and threshold effect) and determine the relative stable state types; 2) explore the formation mechanisms of alternative stable states by monitoring hydrological conditions, sediment accretion dynamics as well as vegetation growth parameters and analyzing the positive feedbacks between saltmarsh vegetation and sedimentary geomorphology. Our results showed that: 1) Normalized difference vegetation index (NDVI) frequentness distribution revealed obvious bimodality at saltmarsh pioneer zone. Propagule biomass threshold limited the establishment of plant patches representing the "saltmarsh" state. The presence of bimodality and biomass threshold demonstrated there are "mudflat" stable state and "saltmarsh" stable state with distinct structure and function in intertidal wetland ecosystem. 2) Current velocities, turbidities and direction perpendicular to the vegetation zone were the most important factors responsible for the sediments rapid accretion at saltmarsh pioneer zone in spring and summer. Sediments accretion significantly promoted the growth of saltmarsh plant. The positive feedbacks between plant growth and sediments accretion resulted in the formation of alternative stable states. 3) The expansion pattern of saltmarshes in the Chongming Dongtan intertidal wetland ecosystem also suggested that increases of sediments accretion could trigger the formation of "mudflat" stable state and "saltmarsh" stable state on landscape scale. The results from this study could enrich regime shift mechanisms researches and provide the scientific supports for coastal zone protection, restoration and comprehensive management, which could have important theoretical and practical meaning.

Two-colour dip spectroscopy of jet-cooled molecules

NASA Astrophysics Data System (ADS)

Ito, Mitsuo

In optical-optical double resonance spectroscopy, the resonance transition from an intermediate state to a final state can be detected by a dip of the signal (fluorescence or ion) associated with the intermediate state. This method probing the signal of the intermediate state may be called `two-colour dip spectroscopy'. Various kinds of two-colour dip spectroscopy such as two-colour fluorescence/ion dip spectroscopy, two-colour ionization dip spectroscopy employing stimulated emission, population labelling spectroscopy and mass-selected ion dip spectroscopy with dissociation were briefly described, paying special attention to their characteristics in excitation, detection and application. They were extensively and successfully applied to jet-cooled large molecules and provided us with new useful information on the energy and dynamics of excited molecules.

Laser-induced breakup of helium 3S 1s2s with intermediate doubly excited states

NASA Astrophysics Data System (ADS)

Simonsen, A. S.; Bachau, H.; Førre, M.

2014-02-01

Solving the time-dependent Schrödinger equation in full dimensionality for two electrons, it is found that in the XUV regime the two-photon double ionization dynamics of He(1s2s) is predominantly dictated by the process of resonance enhanced multiphoton ionization via doubly excited states (DESs). We have studied a pump-probe scenario where the full laser-driven breakup of the 3S 1s2s metastable state is dominated by intermediate quasiresonant excitation to doubly excited (autoionizing) states in the 3Po series. Clear evidence of multipath interference effects is revealed in the resulting angular distributions of the ejected electrons in cases where more than one intermediate DES is populated in the process.

Group additivity-Pourbaix diagrams advocate thermodynamically stable nanoscale clusters in aqueous environments

PubMed Central

Wills, Lindsay A.; Qu, Xiaohui; Chang, I-Ya; Mustard, Thomas J. L.; Keszler, Douglas A.; Persson, Kristin A.; Cheong, Paul Ha-Yeon

2017-01-01

The characterization of water-based corrosion, geochemical, environmental and catalytic processes rely on the accurate depiction of stable phases in a water environment. The process is aided by Pourbaix diagrams, which map the equilibrium solid and solution phases under varying conditions of pH and electrochemical potential. Recently, metastable or possibly stable nanometric aqueous clusters have been proposed as intermediate species in non-classical nucleation processes. Herein, we describe a Group Additivity approach to obtain Pourbaix diagrams with full consideration of multimeric cluster speciation from computations. Comparisons with existing titration results from experiments yield excellent agreement. Applying this Group Additivity-Pourbaix approach to Group 13 elements, we arrive at a quantitative evaluation of cluster stability, as a function of pH and concentration, and present compelling support for not only metastable but also thermodynamically stable multimeric clusters in aqueous solutions. PMID:28643782

Group additivity-Pourbaix diagrams advocate thermodynamically stable nanoscale clusters in aqueous environments

NASA Astrophysics Data System (ADS)

Wills, Lindsay A.; Qu, Xiaohui; Chang, I.-Ya; Mustard, Thomas J. L.; Keszler, Douglas A.; Persson, Kristin A.; Cheong, Paul Ha-Yeon

2017-06-01

The characterization of water-based corrosion, geochemical, environmental and catalytic processes rely on the accurate depiction of stable phases in a water environment. The process is aided by Pourbaix diagrams, which map the equilibrium solid and solution phases under varying conditions of pH and electrochemical potential. Recently, metastable or possibly stable nanometric aqueous clusters have been proposed as intermediate species in non-classical nucleation processes. Herein, we describe a Group Additivity approach to obtain Pourbaix diagrams with full consideration of multimeric cluster speciation from computations. Comparisons with existing titration results from experiments yield excellent agreement. Applying this Group Additivity-Pourbaix approach to Group 13 elements, we arrive at a quantitative evaluation of cluster stability, as a function of pH and concentration, and present compelling support for not only metastable but also thermodynamically stable multimeric clusters in aqueous solutions.

Effect of doping on room temperature carrier escape mechanisms in InAs/GaAs quantum dot p-i-n junction photovoltaic cells

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

Sellers, D. G.; Chen, E. Y.; Doty, M. F.

2016-05-21

We investigate the effect of doping on the mechanisms of carrier escape from intermediate states in delta-doped InAs/GaAs intermediate band solar cells. The intermediate states arise from InAs quantum dots embedded in a GaAs p-i-n junction cell. We find that doping the sample increases the number of excited-state carriers participating in a cycle of trapping and carrier escape via thermal, optical, and tunneling mechanisms. However, we find that the efficiency of the optically-driven carrier escape mechanism is independent of doping and remains small.

A multi-hop teleportation protocol of arbitrary four-qubit states through intermediate nodes

NASA Astrophysics Data System (ADS)

Choudhury, Binayak S.; Samanta, Soumen

Teleportation processes over long distances become affected by the almost inevitable existence of noise which interferes with the entangled quantum channels. In view of this, intermediate nodes are introduced in the scheme. These nodes are connected in series through quantum entanglement. In this paper, we present a protocol for transferring an entangled four-particle cluster-type state in an integrated manner through the intermediate nodes. Its efficiency and advantage over the corresponding part by part teleportation process is discussed.

On the Generation of Intermediate Number Squeezed State of the Quantized Radiation Field

NASA Astrophysics Data System (ADS)

Baseia, B.; de Lima, A. F.; Bagnato, V. S.

Recently, a new state of the quantized radiation field — the intermediate number squeezed state (INSS) — has been introduced in the literature: it interpolates between the number state |n> and the squeezed state |z, α>=Ŝ(z)|α>, and exhibits interesting nonclassical properties as antibunching, sub-Poissonian statistics and squeezing. Here we introduce a slight modification in the previous definition allowing us a proposal to generate the INSS. Nonclassical properties using a new set of parameters are also studied.

JANUS — A setup for low-energy Coulomb excitation at ReA3

DOE PAGES

Lunderberg, E.; Belarge, J.; Bender, P. C.; ...

2017-12-21

We report that a new experimental setup for low-energy Coulomb excitation experiments was constructed in a collaboration between the National Superconducting Cyclotron Laboratory (NSCL), Lawrence Livermore National Laboratory (LLNL), and the University of Rochester and was commissioned at the general purpose beam line of NSCL's ReA3 reaccelerator facility. The so-called JANUS setup combines γ-ray detection with the Segmented Ge Array (SeGA) and scattered particle detection using a pair of segmented double-sided Si detectors (Bambino 2). The low-energy Coulomb excitation program that JANUS enables will complement intermediate-energy Coulomb excitation studies that have long been performed at NSCL by providing access tomore » observables that quantify collectivity beyond the first excited state, including the sign and magnitude of excited-state quadrupole moments. Here, in this work, the setup and its performance will be described based on the commissioning run that used stable 78Kr impinging onto a 1.09 mg/cm 2 208Pb target at a beam energy of 3.9 MeV/u.« less

Evidence for close side-chain packing in an early protein folding intermediate previously assumed to be a molten globule

PubMed Central

Rosen, Laura E.; Connell, Katelyn B.; Marqusee, Susan

2014-01-01

The molten globule, a conformational ensemble with significant secondary structure but only loosely packed tertiary structure, has been suggested to be a ubiquitous intermediate in protein folding. However, it is difficult to assess the tertiary packing of transiently populated species to evaluate this hypothesis. Escherichia coli RNase H is known to populate an intermediate before the rate-limiting barrier to folding that has long been thought to be a molten globule. We investigated this hypothesis by making mimics of the intermediate that are the ground-state conformation at equilibrium, using two approaches: a truncation to generate a fragment mimic of the intermediate, and selective destabilization of the native state using point mutations. Spectroscopic characterization and the response of the mimics to further mutation are consistent with studies on the transient kinetic intermediate, indicating that they model the early intermediate. Both mimics fold cooperatively and exhibit NMR spectra indicative of a closely packed conformation, in contrast to the hypothesis of molten tertiary packing. This result is important for understanding the nature of the subsequent rate-limiting barrier to folding and has implications for the assumption that many other proteins populate molten globule folding intermediates. PMID:25258414

Evidence for close side-chain packing in an early protein folding intermediate previously assumed to be a molten globule.

PubMed

Rosen, Laura E; Connell, Katelyn B; Marqusee, Susan

2014-10-14

The molten globule, a conformational ensemble with significant secondary structure but only loosely packed tertiary structure, has been suggested to be a ubiquitous intermediate in protein folding. However, it is difficult to assess the tertiary packing of transiently populated species to evaluate this hypothesis. Escherichia coli RNase H is known to populate an intermediate before the rate-limiting barrier to folding that has long been thought to be a molten globule. We investigated this hypothesis by making mimics of the intermediate that are the ground-state conformation at equilibrium, using two approaches: a truncation to generate a fragment mimic of the intermediate, and selective destabilization of the native state using point mutations. Spectroscopic characterization and the response of the mimics to further mutation are consistent with studies on the transient kinetic intermediate, indicating that they model the early intermediate. Both mimics fold cooperatively and exhibit NMR spectra indicative of a closely packed conformation, in contrast to the hypothesis of molten tertiary packing. This result is important for understanding the nature of the subsequent rate-limiting barrier to folding and has implications for the assumption that many other proteins populate molten globule folding intermediates.

NMR analysis of a kinetically trapped intermediate of a disulfide-deficient mutant of the starch-binding domain of glucoamylase.

PubMed

Sugimoto, Hayuki; Noda, Yasuo; Segawa, Shin-ichi

2011-09-16

A thermally unfolded disulfide-deficient mutant of the starch-binding domain of glucoamylase refolds into a kinetically trapped metastable intermediate when subjected to a rapid lowering of temperature. We attempted to characterise this intermediate using multidimensional NMR spectroscopy. The (1)H-(15)N heteronuclear single quantum coherence spectrum after a rapid temperature decrease (the spectrum of the intermediate) showed good chemical shift dispersion but was significantly different from that of the native state, suggesting that the intermediate adopts a nonnative but well-structured conformation. Large chemical shift changes for the backbone amide protons between the native and the intermediate states were observed for residues in the β-sheet consisting of strands 2, 3, 5, 6, and 7 as well as in the C-terminal region. These residues were found to be in close proximity to aromatic residues, suggesting that the chemical shift changes are mainly due to ring current shifts caused by the aromatic residues. The two-dimensional nuclear Overhauser enhancement (NOE) spectroscopy experiments showed that the intermediate contained substantial, native-like NOE connectivities, although there were fewer cross peaks in the spectrum of the intermediate compared with that of the native state. It was also shown that there were native-like interresidue NOEs for residues buried in the protein, whereas many of the NOE cross peaks were lost for the residues involved in a surface-exposed aromatic cluster. These results suggest that, in the intermediate, the aromatic cluster at the surface is structurally less organised, whereas the interior of the protein has relatively rigid, native-like side-chain packing. Copyright © 2011 Elsevier Ltd. All rights reserved.

Discrete structure of an RNA folding intermediate revealed by cryo-electron microscopy.

PubMed

Baird, Nathan J; Ludtke, Steven J; Khant, Htet; Chiu, Wah; Pan, Tao; Sosnick, Tobin R

2010-11-24

RNA folding occurs via a series of transitions between metastable intermediate states. It is unknown whether folding intermediates are discrete structures folding along defined pathways or heterogeneous ensembles folding along broad landscapes. We use cryo-electron microscopy and single-particle image reconstruction to determine the structure of the major folding intermediate of the specificity domain of a ribonuclease P ribozyme. Our results support the existence of a discrete conformation for this folding intermediate.

Intermediate-valence state of the Sm and Eu in SmB 6 and EuCu 2 Si 2 : neutron spectroscopy data and analysis

DOE PAGES

Savchenkov, P. S.; Alekseev, P. A.; Podlesnyak, A.; ...

2018-01-11

For this study, magnetic neutron scattering data for Sm (SmB 6, Sm(Y)S) and Eu (EuCu 2Si 2- x Ge x ) intermediate-valence compounds have been analysed in terms of a generalized model of the intermediate-radius exciton. Special attention is paid to the correlation between the average ion's valence and parameters of the low-energy excitation in the neutron spectra, such as the resonance mode, including its magnetic form factor. Along with specific features of the formation of the intermediate-valence state for Sm and Eu ions, common physical mechanisms have been revealed for systems based on these elements from the middle ofmore » the rare-earth series. A consistent description of the existing experimental data has been obtained by using the concept of a loosely bound hole for the Eu f-electron shell in the intermediate-valence state, in analogy with the previously established loosely bound electron model for the Sm ion.« less

Intermediate-valence state of the Sm and Eu in SmB 6 and EuCu 2 Si 2 : neutron spectroscopy data and analysis

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

Savchenkov, P. S.; Alekseev, P. A.; Podlesnyak, A.

For this study, magnetic neutron scattering data for Sm (SmB 6, Sm(Y)S) and Eu (EuCu 2Si 2- x Ge x ) intermediate-valence compounds have been analysed in terms of a generalized model of the intermediate-radius exciton. Special attention is paid to the correlation between the average ion's valence and parameters of the low-energy excitation in the neutron spectra, such as the resonance mode, including its magnetic form factor. Along with specific features of the formation of the intermediate-valence state for Sm and Eu ions, common physical mechanisms have been revealed for systems based on these elements from the middle ofmore » the rare-earth series. A consistent description of the existing experimental data has been obtained by using the concept of a loosely bound hole for the Eu f-electron shell in the intermediate-valence state, in analogy with the previously established loosely bound electron model for the Sm ion.« less

X-ray Free Electron Laser Determination of Crystal Structures of Dark and Light States of a Reversibly Photoswitching Fluorescent Protein at Room Temperature

PubMed Central

Hutchison, Christopher D. M.; Cordon-Preciado, Violeta; Morgan, Rhodri M. L.; Dorlhiac, Gabriel; Sanchez-Gonzalez, Alvaro; Fitzpatrick, Ann; Fare, Clyde; Marangos, Jon P.; Hunter, Mark S.; DePonte, Daniel P.; Boutet, Sébastien; Owada, Shigeki; Tanaka, Rie; Tono, Kensuke; Iwata, So; van Thor, Jasper J.

2017-01-01

The photochromic fluorescent protein Skylan-NS (Nonlinear Structured illumination variant mEos3.1H62L) is a reversibly photoswitchable fluorescent protein which has an unilluminated/ground state with an anionic and cis chromophore conformation and high fluorescence quantum yield. Photo-conversion with illumination at 515 nm generates a meta-stable intermediate with neutral trans-chromophore structure that has a 4 h lifetime. We present X-ray crystal structures of the cis (on) state at 1.9 Angstrom resolution and the trans (off) state at a limiting resolution of 1.55 Angstrom from serial femtosecond crystallography experiments conducted at SPring-8 Angstrom Compact Free Electron Laser (SACLA) at 7.0 keV and 10.5 keV, and at Linac Coherent Light Source (LCLS) at 9.5 keV. We present a comparison of the data reduction and structure determination statistics for the two facilities which differ in flux, beam characteristics and detector technologies. Furthermore, a comparison of droplet on demand, grease injection and Gas Dynamic Virtual Nozzle (GDVN) injection shows no significant differences in limiting resolution. The photoconversion of the on- to the off-state includes both internal and surface exposed protein structural changes, occurring in regions that lack crystal contacts in the orthorhombic crystal form. PMID:28880248

INTEGRAL SPI Observations of Cygnus X-1 in the Soft State: What about the Jet Contribution in Hard X-Rays?

NASA Astrophysics Data System (ADS)

Jourdain, E.; Roques, J. P.; Chauvin, M.

2014-07-01

During the first 7 yr of the INTEGRAL mission (2003-2009), Cyg X-1 has essentially been detected in its hard state (HS), with some incursions in intermediate HSs. This long, spectrally stable period allowed in particular the measurement of the polarization of the high-energy component that has long been observed above 200 keV in this peculiar object. This result strongly suggests that here we see the contribution of the jet, known to emit a strong synchrotron radio emission. In 2010 June, Cyg X-1 underwent a completed transition toward a soft state (SS). It gave us the unique opportunity to study in detail the corona emission in this spectral state, and to investigate in particular the behavior of the jet contribution. Indeed, during the SS, the hard X-ray emission decreases drastically, with its maximum energy shifted toward lower energy and its flux divided by a factor of ~5-10. Interestingly, the radio emission follows a similar drop, supporting the correlation between the jet emission and the hard component, even though the flux is too low to quantify the polarization characteristics. Based on observations with INTEGRAL, an ESA project with instruments and science data center funded by ESA member states (especially the PI countries: Denmark, France, Germany, Italy, Spain, and Switzerland), the Czech Republic and Poland with the participation of Russia and USA.

Long-Range Interactions Restrict Water Transport in Pyrophyllite Interlayers

DOE PAGES

Zarzycki, Piotr; Gilbert, Benjamin

2016-04-27

Water diffusion within smectite clay interlayers is reduced by confinement and hence is highly determined by the interlayer spacings that are adopted during swelling. However, a molecular understanding of the short-and long-range forces governing interlayer water structure and dynamics is lacking. Using molecular dynamics simulations of water intercalated between pyrophyllite (smectite prototype) layers we provide a detailed picture of the variation of interlayered water mobility accompanying smectite expansion. Subtle changes in hydrogen bond network structure cause significant changes in water mobility that is greater for stable hydration states and reduced for intermediate separations. By studying pyrophyllite with and without externalmore » water we reveal that long-range electrostatic forces apply a restraining effect upon interlayer water mobility. Our findings are relevant for broad range of confining nanostructures with walls thin enough to permit long-range interactions that could affect the mobility of confined solvent molecules and solute species.« less

New insights into structural determinants of prion protein folding and stability.

PubMed

Benetti, Federico; Legname, Giuseppe

2015-01-01

Prions are the etiological agent of fatal neurodegenerative diseases called prion diseases or transmissible spongiform encephalopathies. These maladies can be sporadic, genetic or infectious disorders. Prions are due to post-translational modifications of the cellular prion protein leading to the formation of a β-sheet enriched conformer with altered biochemical properties. The molecular events causing prion formation in sporadic prion diseases are still elusive. Recently, we published a research elucidating the contribution of major structural determinants and environmental factors in prion protein folding and stability. Our study highlighted the crucial role of octarepeats in stabilizing prion protein; the presence of a highly enthalpically stable intermediate state in prion-susceptible species; and the role of disulfide bridge in preserving native fold thus avoiding the misfolding to a β-sheet enriched isoform. Taking advantage from these findings, in this work we present new insights into structural determinants of prion protein folding and stability.

Methanol partial oxidation on Ag(111) from first principles

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

Aljama, Hassan; Yoo, Jong Suk; Nørskov, Jens K.

In this work, we examine the thermochemistry and kinetics of the partial oxidation of methanol to formaldehyde on silver surfaces. Periodic density functional theory calculations employing the BEEF-vdW functional are used to identify the most stable phases of the silver surface under relevant reaction conditions and the reaction energetics are obtained on these surfaces. The calculated binding energies and transition state energies are used as input in a mean-field microkinetic model providing the reaction kinetics on silver surfaces under different reaction conditions. Our results show that, under conditions pertaining to methanol partial oxidation, oxygen is present at low concentrations andmore » it plays a critical role in the catalytic reaction. Surface oxygen promotes the reaction by activating the OH bond in methanol, thus forming a methoxy intermediate, which can react further to form formaldehyde. Finally, the dissociation of molecular oxygen is identified as the most critical step.« less

Methanol partial oxidation on Ag(111) from first principles

DOE PAGES

Aljama, Hassan; Yoo, Jong Suk; Nørskov, Jens K.; ...

2016-10-26

In this work, we examine the thermochemistry and kinetics of the partial oxidation of methanol to formaldehyde on silver surfaces. Periodic density functional theory calculations employing the BEEF-vdW functional are used to identify the most stable phases of the silver surface under relevant reaction conditions and the reaction energetics are obtained on these surfaces. The calculated binding energies and transition state energies are used as input in a mean-field microkinetic model providing the reaction kinetics on silver surfaces under different reaction conditions. Our results show that, under conditions pertaining to methanol partial oxidation, oxygen is present at low concentrations andmore » it plays a critical role in the catalytic reaction. Surface oxygen promotes the reaction by activating the OH bond in methanol, thus forming a methoxy intermediate, which can react further to form formaldehyde. Finally, the dissociation of molecular oxygen is identified as the most critical step.« less

Degradation chemistry of gemcitabine hydrochloride, a new antitumor agent.

PubMed

Anliker, S L; McClure, M S; Britton, T C; Stephan, E A; Maple, S R; Cooke, G G

1994-05-01

The anti-tumor agent gemcitabine hydrochloride, a beta-difluoronucleoside, is remarkably stable in the solid state. In 0.1 N HCI solution at 40 degrees C, deamination of gemcitabine occurs, yielding its uridine analogue. Approximately 86% of the initial gemcitabine remains after 4 weeks under these conditions. Cleavage of the N-glycosidic bond of gemcitabine or conversion to its alpha-anomer in 0.1 N HCI solution is not observed over a 4-week period. However, this work has shown that gemcitabine hydrochloride anomerizes in 0.1 N NaOH at 40 degrees C. Approximately 72% of the initial gemcitabine remains after 4 weeks under the basic conditions used. Uridine hydrolysis products are also formed under these conditions. The anormerization reaction, which is unusual under basic conditions, has been confirmed by characterization of the chromatographically isolated alpha-anomer by NMR and mass spectrometry. A mechanism involving an acyclic intermediate is proposed.

Thermal and Electrical Stability of Sr 0.9Y 0.1CoO 2.5+δ as a Promising Cathode for Intermediate-Temperature Solid Oxide Fuel Cells

DOE PAGES

Jiang, Long; Wang, Jie; Xiong, Xiaolei; ...

2016-01-21

Here, the present study reports thermal and electrical properties of Sr 1-xYxCoO 2.5+δ (x = 0–0.40) as a promising cathode for intermediatetemperature solid oxide fuel cells. The results show that x = 0.10 is the best composition possessing a single primitive cubic perovskite structure, stable conductivity and the lowest polarization resistance. Thermogravimetric analysis indicates an oxygen intake from RT to ~375°C, above which oxygen loss occurs. The oxygen gain-loss behavior corresponds well with the conductivity increase-decrease trending, reflecting that oxygen-nonstoichiometry controls the hole-concentration (or oxidation-state of Co-ions). Electrochemical impedance spectroscopy analysis further reveals that the overall ORR polarization consists ofmore » a faster charge-transfer and a slower surface oxygen exchange.« less

Thermal and Electrical Stability of Sr 0.9Y 0.1CoO 2.5+δ as a Promising Cathode for Intermediate-Temperature Solid Oxide Fuel Cells

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

Jiang, Long; Wang, Jie; Xiong, Xiaolei

Here, the present study reports thermal and electrical properties of Sr 1-xYxCoO 2.5+δ (x = 0–0.40) as a promising cathode for intermediatetemperature solid oxide fuel cells. The results show that x = 0.10 is the best composition possessing a single primitive cubic perovskite structure, stable conductivity and the lowest polarization resistance. Thermogravimetric analysis indicates an oxygen intake from RT to ~375°C, above which oxygen loss occurs. The oxygen gain-loss behavior corresponds well with the conductivity increase-decrease trending, reflecting that oxygen-nonstoichiometry controls the hole-concentration (or oxidation-state of Co-ions). Electrochemical impedance spectroscopy analysis further reveals that the overall ORR polarization consists ofmore » a faster charge-transfer and a slower surface oxygen exchange.« less

Reactivity and reaction intermediates for acetic acid adsorbed on CeO 2(111)

DOE PAGES

Calaza, Florencia C.; Chen, Tsung -Liang; Mullins, David R.; ...

2015-05-02

Adsorption and reaction of acetic acid on a CeO 2(1 1 1) surface was studied by a combination of ultra-highvacuum based methods including temperature desorption spectroscopy (TPD), soft X-ray photoelectronspectroscopy (sXPS), near edge X-ray absorption spectroscopy (NEXAFS) and reflection absorption IRspectroscopy (RAIRS), together with density functional theory (DFT) calculations. TPD shows that thedesorption products are strongly dependent upon the initial oxidation state of the CeO 2 surface, includingselectivity between acetone and acetaldehyde products. The combination of sXPS and NEXAFS demon-strate that acetate forms upon adsorption at low temperature and is stable to above 500 K, above whichpoint ketene, acetone andmore » acetic acid desorb. Furthermore, DFT and RAIRS show that below 500 K, bridge bondedacetate coexists with a moiety formed by adsorption of an acetate at an oxygen vacancy, formed bywater desorption.« less

Long-Range Interactions Restrict Water Transport in Pyrophyllite Interlayers

PubMed Central

Zarzycki, Piotr; Gilbert, Benjamin

2016-01-01

Water diffusion within smectite clay interlayers is reduced by confinement and hence is highly determined by the interlayer spacings that are adopted during swelling. However, a molecular understanding of the short- and long-range forces governing interlayer water structure and dynamics is lacking. Using molecular dynamics simulations of water intercalated between pyrophyllite (smectite prototype) layers we provide a detailed picture of the variation of interlayered water mobility accompanying smectite expansion. Subtle changes in hydrogen bond network structure cause significant changes in water mobility that is greater for stable hydration states and reduced for intermediate separations. By studying pyrophyllite with and without external water we reveal that long-range electrostatic forces apply a restraining effect upon interlayer water mobility. Our findings are relevant for broad range of confining nanostructures with walls thin enough to permit long-range interactions that could affect the mobility of confined solvent molecules and solute species. PMID:27118164

Room-Temperature C-H Functionalization Sequence under Benchtop Conditions for the Undergraduate Chemistry Laboratory

ERIC Educational Resources Information Center

Chen, Shuming

2018-01-01

An iridium(III)-mediated C-H functionalization sequence involving a concerted cyclometalation-deprotonation/migratory insertion pathway is reported for the undergraduate chemistry laboratory. The air- and water-stable iridacycle intermediates are readily isolated and characterized by NMR spectroscopy. Both steps of the experiment are performed at…

Soil and water conservation in the Pacific Northwest through no-tillage and intensified crop rotations

USDA-ARS?s Scientific Manuscript database

The winter wheat (Triticum aestivum L.) summer fallow rotation typically practiced in the intermediate precipitation zone [300-450 mm (12-18 in)] of the inland Pacific Northwest has proven to be economically stable for producers in this region. However multiple tillage operations are used to control...

Incomplete Combustion of Hydrogen: Trapping a Reaction Intermediate

ERIC Educational Resources Information Center

Mattson, Bruce; Hoette, Trisha

2007-01-01

The combustion of hydrogen in air is quite complex with at least 28 mechanistic steps and twelve reaction species. Most of the species involved are radicals (having unpaired electrons) in nature. Among the various species generated, a few are stable, including hydrogen peroxide. In a normal hydrogen flame, the hydrogen peroxide goes on to further…

Seasonal variations in optimized applications of intermediate stable alpha-amylase in raw sugar manufacture

USDA-ARS?s Scientific Manuscript database

In recent years, starch being delivered to and processed in U.S. factories has risen markedly because of the increased production of green (unburnt) and combine-harvested (billeted) sugarcane and the introduction of new sugarcane varieties with higher starch content. To prevent carry-over alpha-amy...

THERMALLY STABLE PERFLUORINATED POLYMERS

DTIC Science & Technology

this system has been found which involves addition of perfluoroalkyl - dihydrazides to perfluoroalkyldinitriles in a highly polar solvent. Inactivation...formation of an intermediate poly( perfluorodiacyl hydrazine) from the reaction of perfluorodiacyl chlorides with perfluoroalkyldihydrazides ....Work on the poly( perfluoroalkylene -1,2,4,4H-triazole system has been continued with the objectives of increasing the polymer molecular weights

THERMALLY STABLE PERFLUORINATED POLYMERS.

DTIC Science & Technology

Ring closure of the N ( perfluoroacylimidoyl ) perfluoroalkyl amidine by acylation with perfluoroacyl chloride was apparently hindered by formation of...quantitatively. The reaction of perfluoroadiphydrazidine with perfluoroadiponitrile produced the intermediate polyimidoylhydrazidine as a step in a... perfluoroalkyltriazole polymer synthesis. Reaction of perfluoroglutaronitrile with N2H4 produced a cyclic compound which may be useful as a single monomer for

Unexpected dependence on pH of NO release from Paracoccus pantotrophus cytochrome cd1.

PubMed

Sam, Katharine A; Tolland, John D; Fairhurst, Shirley A; Higham, Christopher W; Lowe, David J; Thorneley, Roger N F; Allen, James W A; Ferguson, Stuart J

2008-07-11

A previous study of nitrite reduction by Paracoccus pantotrophus cytochrome cd(1) at pH 7.0 identified early reaction intermediates. The c-heme rapidly oxidised and nitrite was reduced to NO at the d(1)-heme. A slower equilibration of electrons followed, forming a stable complex assigned as 55% cFe(III)d(1)Fe(II)-NO and 45% cFe(II)d(1)Fe(II)-NO(+). No catalytically competent NO release was observed. Here we show that at pH 6.0, a significant proportion of the enzyme undergoes turnover and releases NO. An early intermediate, which was previously overlooked, is also identified; enzyme immediately following product release is a candidate. However, even at pH 6.0 a considerable fraction of the enzyme remains bound to NO so another component is required for full product release. The kinetically stable product formed at the end of the reaction differs significantly at pH 6.0 and 7.0, as does its rate of formation; thus the reaction is critically dependent on pH.

A Pictet-Spengler ligation for protein chemical modification

PubMed Central

Agarwal, Paresh; van der Weijden, Joep; Sletten, Ellen M.; Rabuka, David; Bertozzi, Carolyn R.

2013-01-01

Aldehyde- and ketone-functionalized proteins are appealing substrates for the development of chemically modified biotherapeutics and protein-based materials. Their reactive carbonyl groups are typically conjugated with α-effect nucleophiles, such as substituted hydrazines and alkoxyamines, to generate hydrazones and oximes, respectively. However, the resulting C=N linkages are susceptible to hydrolysis under physiologically relevant conditions, which limits the utility of such conjugates in biological systems. Here we introduce a Pictet-Spengler ligation that is based on the classic Pictet-Spengler reaction of aldehydes and tryptamine nucleophiles. The ligation exploits the bioorthogonal reaction of aldehydes and alkoxyamines to form an intermediate oxyiminium ion; this intermediate undergoes intramolecular C–C bond formation with an indole nucleophile to form an oxacarboline product that is hydrolytically stable. We used the reaction for site-specific chemical modification of glyoxyl- and formylglycine-functionalized proteins, including an aldehyde-tagged variant of the therapeutic monoclonal antibody Herceptin. In conjunction with techniques for site-specific introduction of aldehydes into proteins, the Pictet-Spengler ligation offers a means to generate stable bioconjugates for medical and materials applications. PMID:23237853

Unraveling the structure and chemical mechanisms of highly oxygenated intermediates in oxidation of organic compounds

PubMed Central

Popolan-Vaida, Denisia M.; Chen, Bingjie; Moshammer, Kai; Mohamed, Samah Y.; Wang, Heng; Sioud, Salim; Raji, Misjudeen A.; Kohse-Höinghaus, Katharina; Hansen, Nils; Dagaut, Philippe; Leone, Stephen R.

2017-01-01

Decades of research on the autooxidation of organic compounds have provided fundamental and practical insights into these processes; however, the structure of many key autooxidation intermediates and the reactions leading to their formation still remain unclear. This work provides additional experimental evidence that highly oxygenated intermediates with one or more hydroperoxy groups are prevalent in the autooxidation of various oxygenated (e.g., alcohol, aldehyde, keto compounds, ether, and ester) and nonoxygenated (e.g., normal alkane, branched alkane, and cycloalkane) organic compounds. These findings improve our understanding of autooxidation reaction mechanisms that are routinely used to predict fuel ignition and oxidative stability of liquid hydrocarbons, while also providing insights relevant to the formation mechanisms of tropospheric aerosol building blocks. The direct observation of highly oxygenated intermediates for the autooxidation of alkanes at 500–600 K builds upon prior observations made in atmospheric conditions for the autooxidation of terpenes and other unsaturated hydrocarbons; it shows that highly oxygenated intermediates are stable at conditions above room temperature. These results further reveal that highly oxygenated intermediates are not only accessible by chemical activation but also by thermal activation. Theoretical calculations on H-atom migration reactions are presented to rationalize the relationship between the organic compound’s molecular structure (n-alkane, branched alkane, and cycloalkane) and its propensity to produce highly oxygenated intermediates via extensive autooxidation of hydroperoxyalkylperoxy radicals. Finally, detailed chemical kinetic simulations demonstrate the influence of these additional reaction pathways on the ignition of practical fuels. PMID:29183984

SU(2) slave-boson formulation of spin nematic states in S=(1)/(2) frustrated ferromagnets

NASA Astrophysics Data System (ADS)

Shindou, Ryuichi; Momoi, Tsutomu

2009-08-01

An SU(2) slave-boson formulation of bond-type spin nematic orders is developed in frustrated ferromagnets, where the spin nematic states are described as the resonating spin-triplet valence bond (RVB) states. The d vectors of spin-triplet pairing ansatzes play the role of the directors in the bond-type spin-quadrupolar states. The low-energy excitations around such spin-triplet RVB ansatzes generally comprise the (potentially massless) gauge bosons, massless Goldstone bosons, and spinon individual excitations. Extending the projective symmetry-group argument to the spin-triplet ansatzes, we show how to identify the number of massless gauge bosons efficiently. Applying this formulation, we next (i) enumerate possible mean-field solutions for the S=(1)/(2) ferromagnetic J1-J2 Heisenberg model on the square lattice, with ferromagnetic nearest neighbor J1 and competing antiferromagnetic next-nearest neighbor J2 and (ii) argue their stability against small gauge fluctuations. As a result, two stable spin-triplet RVB ansatzes are found in the intermediate coupling regime around J1:J2≃1:0.4 . One is the Z2 Balian-Werthamer (BW) state stabilized by the Higgs mechanism and the other is the SU(2) chiral p -wave (Anderson-Brinkman-Morel) state stabilized by the Chern-Simon mechanism. The former Z2 BW state in fact shows the same bond-type spin-quadrupolar order as found in the previous exact diagonalization study [Shannon , Phys. Rev. Lett. 96, 027213 (2006)].

Photoinduced Reductive Elimination of H2 from the Nitrogenase Dihydride (Janus) State Involves a FeMo-cofactor-H2 Intermediate.

PubMed

Lukoyanov, Dmitriy; Khadka, Nimesh; Dean, Dennis R; Raugei, Simone; Seefeldt, Lance C; Hoffman, Brian M

2017-02-20

N 2 reduction by nitrogenase involves the accumulation of four reducing equivalents at the active site FeMo-cofactor to form a state with two [Fe-H-Fe] bridging hydrides (denoted E 4 (4H), the Janus intermediate), and we recently demonstrated that the enzyme is activated to cleave the N≡N triple bond by the reductive elimination (re) of H 2 from this state. We are exploring a photochemical approach to obtaining atomic-level details of the re activation process. We have shown that, when E 4 (4H) at cryogenic temperatures is subjected to 450 nm irradiation in an EPR cavity, it cleanly undergoes photoinduced re of H 2 to give a reactive doubly reduced intermediate, denoted E 4 (2H)*, which corresponds to the intermediate that would form if thermal dissociative re loss of H 2 preceded N 2 binding. Experiments reported here establish that photoinduced re primarily occurs in two steps. Photolysis of E 4 (4H) generates an intermediate state that undergoes subsequent photoinduced conversion to [E 4 (2H)* + H 2 ]. The experiments, supported by DFT calculations, indicate that the trapped intermediate is an H 2 complex on the ground adiabatic potential energy suface that connects E 4 (4H) with [E 4 (2H)* + H 2 ]. We suggest that this complex, denoted E 4 (H 2 ; 2H), is a thermally populated intermediate in the catalytically central re of H 2 by E 4 (4H) and that N 2 reacts with this complex to complete the activated conversion of [E 4 (4H) + N 2 ] into [E 4 (2N2H) + H 2 ].

Photoinduced Reductive Elimination of H 2 from the Nitrogenase Dihydride (Janus) State Involves a FeMo-cofactor-H 2 Intermediate

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

Lukoyanov, Dmitriy; Khadka, Nimesh; Dean, Dennis R.

N2 reduction by nitrogenase involves the accumulation of four reducing equivalents at the active site FeMo-cofactor to form a state with two [Fe-H-Fe] bridging hydrides (denoted E4(4H), the Janus intermediate), and we recently demonstrated that the enzyme is activated to cleave the N≡N triple bond by the reductive elimination (re) of H2 from this state. We are exploring a photochemical approach to obtaining atomic-level details of the re activation process. We have shown that when E4(4H) at cryogenic temperatures is subjected to 450 nm irradiation in an EPR cavity, it cleanly undergoes photoinduced re of H2 to give a reactivemore » doubly-reduced intermediate, denoted E4(2H)*, which corresponds to the intermediate that would form if thermal dissociative re loss of H2 preceded N2 binding. Experiments reported here establish that photoinduced re occurs in two steps. Photolysis of E4(4H) generates an intermediate state that undergoes subsequent photoinduced conversion to [E4(2H)* + H2]. The experiments, supported by DFT calculation, indicate that the trapped intermediate is an H2 complex on the ground adiabatic potential energy suface that connects E4(4H) with [E4(2H)* + H2]. We suggest this complex, denoted E4(H2; 2H), is a thermally populated intermediate in the catalytically central re of H2 by E4(4H), and that N2 reacts with this complex to complete the activated conversion of [E4(4H) + N2] into [E4(2N2H) + H2].« less

Identification and Spectroscopic Characterization of Nonheme Iron(III) Hypochlorite Intermediates.

PubMed

Draksharapu, Apparao; Angelone, Davide; Quesne, Matthew G; Padamati, Sandeep K; Gómez, Laura; Hage, Ronald; Costas, Miquel; Browne, Wesley R; de Visser, Sam P

2015-03-27

Fe III -hypohalite complexes have been implicated in a wide range of important enzyme-catalyzed halogenation reactions including the biosynthesis of natural products and antibiotics and post-translational modification of proteins. The absence of spectroscopic data on such species precludes their identification. Herein, we report the generation and spectroscopic characterization of nonheme Fe III -hypohalite intermediates of possible relevance to iron halogenases. We show that Fe III -OCl polypyridylamine complexes can be sufficiently stable at room temperature to be characterized by UV/Vis absorption, resonance Raman and EPR spectroscopies, and cryo-ESIMS. DFT methods rationalize the pathways to the formation of the Fe III -OCl, and ultimately Fe IV =O, species and provide indirect evidence for a short-lived Fe II -OCl intermediate. The species observed and the pathways involved offer insight into and, importantly, a spectroscopic database for the investigation of iron halogenases.

Identification and Spectroscopic Characterization of Nonheme Iron(III) Hypochlorite Intermediates**

PubMed Central

Draksharapu, Apparao; Angelone, Davide; Quesne, Matthew G; Padamati, Sandeep K; Gómez, Laura; Hage, Ronald; Costas, Miquel; Browne, Wesley R; de Visser, Sam P

2015-01-01

FeIII–hypohalite complexes have been implicated in a wide range of important enzyme-catalyzed halogenation reactions including the biosynthesis of natural products and antibiotics and post-translational modification of proteins. The absence of spectroscopic data on such species precludes their identification. Herein, we report the generation and spectroscopic characterization of nonheme FeIII–hypohalite intermediates of possible relevance to iron halogenases. We show that FeIII-OCl polypyridylamine complexes can be sufficiently stable at room temperature to be characterized by UV/Vis absorption, resonance Raman and EPR spectroscopies, and cryo-ESIMS. DFT methods rationalize the pathways to the formation of the FeIII-OCl, and ultimately FeIV=O, species and provide indirect evidence for a short-lived FeII-OCl intermediate. The species observed and the pathways involved offer insight into and, importantly, a spectroscopic database for the investigation of iron halogenases. PMID:25663379

Nature of electrogenerated intermediates in nitro-substituted nor-β-lapachones: the structure of radical species during successive electron transfer in multiredox centers.

PubMed

Armendáriz-Vidales, Georgina; Hernández-Muñoz, Lindsay S; González, Felipe J; de Souza, Antonio A; de Abreu, Fabiane C; Jardim, Guilherme A M; da Silva, Eufrânio N; Goulart, Marilia O F; Frontana, Carlos

2014-06-06

Electrochemical, spectroelectrochemical, and theoretical studies of the reduction reactions in nor-β-lapachone derivatives including a nitro redox center showed that reduction of the compounds involves the formation of several radical intermediates, including a biradical dianion resultant from the separate reduction of the quinone and nitro groups in the molecules. Theoretical descriptions of the corresponding Fukui functions f(αα)⁺ and f(ββ)⁺(r) and LUMO densities considering finite differences and frozen core approximations for describing the changes in electron and spin densities of the system allowed us to confirm these results. A description of the potential relationship with the obtained results and biological activity selectivity indexes suggests that both the formation of stable biradical dianion species and the stability of the semiquinone intermediates during further reduction are determining factors in the description of their biological activity.

Examination of the Mechanism of Human Brain Aspartoacylase through the Binding of an Intermediate Analogue†‡

PubMed Central

Le Coq, Johanne; Pavlovsky, Alexander; Malik, Radhika; Sanishvili, Ruslan; Xu, Chengfu; Viola, Ronald E.

2009-01-01

Canavan disease is a fatal neurological disorder caused by the malfunctioning of a single metabolic enzyme, aspartoacylase, that catalyzes the deacetylation of N-acetyl-l-aspartate to produce l-aspartate and acetate. The structure of human brain aspartoacylase has been determined in complex with a stable tetrahedral intermediate analogue, N-phosphonomethyl-l-aspartate. This potent inhibitor forms multiple interactions between each of its heteroatoms and the substrate binding groups arrayed within the active site. The binding of the catalytic intermediate analogue induces the conformational ordering of several substrate binding groups, thereby setting up the active site for catalysis. The highly ordered binding of this inhibitor has allowed assignments to be made for substrate binding groups and provides strong support for a carboxypeptidase-type mechanism for the hydrolysis of the amide bond of the substrate, N-acetyl-l-aspartate. PMID:18293939

Examination of the mechanism of human brain aspartoacylase through the binding of an intermediate analogue.

PubMed

Le Coq, Johanne; Pavlovsky, Alexander; Malik, Radhika; Sanishvili, Ruslan; Xu, Chengfu; Viola, Ronald E

2008-03-18

Canavan disease is a fatal neurological disorder caused by the malfunctioning of a single metabolic enzyme, aspartoacylase, that catalyzes the deacetylation of N-acetyl-L-aspartate to produce L-aspartate and acetate. The structure of human brain aspartoacylase has been determined in complex with a stable tetrahedral intermediate analogue, N-phosphonomethyl-L-aspartate. This potent inhibitor forms multiple interactions between each of its heteroatoms and the substrate binding groups arrayed within the active site. The binding of the catalytic intermediate analogue induces the conformational ordering of several substrate binding groups, thereby setting up the active site for catalysis. The highly ordered binding of this inhibitor has allowed assignments to be made for substrate binding groups and provides strong support for a carboxypeptidase-type mechanism for the hydrolysis of the amide bond of the substrate, N-acetyl- l-aspartate.

ECUT: Energy Conversion and Utilization Technologies program. Heterogeneous catalysis modeling program concept

NASA Technical Reports Server (NTRS)

Voecks, G. E.

1983-01-01

Insufficient theoretical definition of heterogeneous catalysts is the major difficulty confronting industrial suppliers who seek catalyst systems which are more active, selective, and stable than those currently available. In contrast, progress was made in tailoring homogeneous catalysts to specific reactions because more is known about the reaction intermediates promoted and/or stabilized by these catalysts during the course of reaction. However, modeling heterogeneous catalysts on a microscopic scale requires compiling and verifying complex information on reaction intermediates and pathways. This can be achieved by adapting homogeneous catalyzed reaction intermediate species, applying theoretical quantum chemistry and computer technology, and developing a better understanding of heterogeneous catalyst system environments. Research in microscopic reaction modeling is now at a stage where computer modeling, supported by physical experimental verification, could provide information about the dynamics of the reactions that will lead to designing supported catalysts with improved selectivity and stability.

Magnetism and the spin state in cubic perovskite CaCo O 3 synthesized under high pressure

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

Xia, Hailiang; Dai, Jianhong; Xu, Yuanji

Cubic SrCo O 3 with an intermediate spin state can only be stabilized by high pressure and high temperature (HPHT) treatment. It is metallic and ferromagnetic with the highest Curie temperature of the transition-metal perovskites. The chemical substitution by Ca on Sr sites would normally lower crystal symmetry from cubic to orthorhombic as seen in the perovskite family of Ca M O 3 ( M = M 4 + of transition metals, G e 4 + , S n 4 + , and Z r 4 +) at room temperature. This structural change narrows the bandwidth, so as to furthermore » enhance the Curie temperature as the crossover to the localized electronic state is approached. Here, we report a successful synthesis of the perovskite CaCo O 3 with a HPHT treatment. Surprisingly, CaCo O 3 crystallizes in a simple cubic structure that remains stable down to 20 K, the lowest temperature in the structural study. The new perovskite has been thoroughly characterized by a suite of measurements including transport, magnetization, specific heat, thermal conductivity, and thermoelectric power. Furthermore, metallic CaCo O 3 undergoes two successive magnetic transitions at 86 K and 54 K as temperature decreases. The magnetization at 5 K is compatible with the intermediate spin state t 4 e 1 of C o 4 + at the octahedral site. The thermal expansion of the Co-O bond length indicates that the population of high spin state t 3 e 2 increases for T > 100 K . The shortest Co-O bond length in cubic CaCo O 3 is responsible for delocalizing electrons in the π * -band and itinerant-electron ferromagnetism at T < 54 K . In our comprehensive comparison between SrCo O 3 and CaCo O 3 and the justification of their physical properties by first-principles calculation were made in this report. Partially filled π * and σ * bands would make CaCo O 3 suitable to study the Hund's coupling effect in a metal.« less

Magnetism and the spin state in cubic perovskite CaCo O 3 synthesized under high pressure

DOE PAGES

Xia, Hailiang; Dai, Jianhong; Xu, Yuanji; ...

2017-07-17

Cubic SrCo O 3 with an intermediate spin state can only be stabilized by high pressure and high temperature (HPHT) treatment. It is metallic and ferromagnetic with the highest Curie temperature of the transition-metal perovskites. The chemical substitution by Ca on Sr sites would normally lower crystal symmetry from cubic to orthorhombic as seen in the perovskite family of Ca M O 3 ( M = M 4 + of transition metals, G e 4 + , S n 4 + , and Z r 4 +) at room temperature. This structural change narrows the bandwidth, so as to furthermore » enhance the Curie temperature as the crossover to the localized electronic state is approached. Here, we report a successful synthesis of the perovskite CaCo O 3 with a HPHT treatment. Surprisingly, CaCo O 3 crystallizes in a simple cubic structure that remains stable down to 20 K, the lowest temperature in the structural study. The new perovskite has been thoroughly characterized by a suite of measurements including transport, magnetization, specific heat, thermal conductivity, and thermoelectric power. Furthermore, metallic CaCo O 3 undergoes two successive magnetic transitions at 86 K and 54 K as temperature decreases. The magnetization at 5 K is compatible with the intermediate spin state t 4 e 1 of C o 4 + at the octahedral site. The thermal expansion of the Co-O bond length indicates that the population of high spin state t 3 e 2 increases for T > 100 K . The shortest Co-O bond length in cubic CaCo O 3 is responsible for delocalizing electrons in the π * -band and itinerant-electron ferromagnetism at T < 54 K . In our comprehensive comparison between SrCo O 3 and CaCo O 3 and the justification of their physical properties by first-principles calculation were made in this report. Partially filled π * and σ * bands would make CaCo O 3 suitable to study the Hund's coupling effect in a metal.« less

The KIM-family protein-tyrosine phosphatases use distinct reversible oxidation intermediates: Intramolecular or intermolecular disulfide bond formation.

PubMed

Machado, Luciana E S F; Shen, Tun-Li; Page, Rebecca; Peti, Wolfgang

2017-05-26

The kinase interaction motif (KIM) family of protein-tyrosine phosphatases (PTPs) includes hematopoietic protein-tyrosine phosphatase (HePTP), striatal-enriched protein-tyrosine phosphatase (STEP), and protein-tyrosine phosphatase receptor type R (PTPRR). KIM-PTPs bind and dephosphorylate mitogen-activated protein kinases (MAPKs) and thereby critically modulate cell proliferation and differentiation. PTP activity can readily be diminished by reactive oxygen species (ROS), e.g. H 2 O 2 , which oxidize the catalytically indispensable active-site cysteine. This initial oxidation generates an unstable sulfenic acid intermediate that is quickly converted into either a sulfinic/sulfonic acid (catalytically dead and irreversible inactivation) or a stable sulfenamide or disulfide bond intermediate (reversible inactivation). Critically, our understanding of ROS-mediated PTP oxidation is not yet sufficient to predict the molecular responses of PTPs to oxidative stress. However, identifying distinct responses will enable novel routes for PTP-selective drug design, important for managing diseases such as cancer and Alzheimer's disease. Therefore, we performed a detailed biochemical and molecular study of all KIM-PTP family members to determine their H 2 O 2 oxidation profiles and identify their reversible inactivation mechanism(s). We show that despite having nearly identical 3D structures and sequences, each KIM-PTP family member has a unique oxidation profile. Furthermore, we also show that whereas STEP and PTPRR stabilize their reversibly oxidized state by forming an intramolecular disulfide bond, HePTP uses an unexpected mechanism, namely, formation of a reversible intermolecular disulfide bond. In summary, despite being closely related, KIM-PTPs significantly differ in oxidation profiles. These findings highlight that oxidation protection is critical when analyzing PTPs, for example, in drug screening. © 2017 by The American Society for Biochemistry and Molecular Biology, Inc.

Sn Cation Valency Dependence in Cation Exchange Reactions Involving Cu2-xSe Nanocrystals

PubMed Central

2014-01-01

We studied cation exchange reactions in colloidal Cu2-xSe nanocrystals (NCs) involving the replacement of Cu+ cations with either Sn2+ or Sn4+ cations. This is a model system in several aspects: first, the +2 and +4 oxidation states for tin are relatively stable; in addition, the phase of the Cu2-xSe NCs remains cubic regardless of the degree of copper deficiency (that is, “x”) in the NC lattice. Also, Sn4+ ions are comparable in size to the Cu+ ions, while Sn2+ ones are much larger. We show here that the valency of the entering Sn ions dictates the structure and composition not only of the final products but also of the intermediate steps of the exchange. When Sn4+ cations are used, alloyed Cu2–4ySnySe NCs (with y ≤ 0.33) are formed as intermediates, with almost no distortion of the anion framework, apart from a small contraction. In this exchange reaction the final stoichiometry of the NCs cannot go beyond Cu0.66Sn0.33Se (that is Cu2SnSe3), as any further replacement of Cu+ cations with Sn4+ cations would require a drastic reorganization of the anion framework, which is not possible at the reaction conditions of the experiments. When instead Sn2+ cations are employed, SnSe NCs are formed, mostly in the orthorhombic phase, with significant, albeit not drastic, distortion of the anion framework. Intermediate steps in this exchange reaction are represented by Janus-type Cu2-xSe/SnSe heterostructures, with no Cu–Sn–Se alloys. PMID:25340627

Propylene oxidation mechanisms and intermediates using in situ soft X-ray fluorescence methods on the Pt(111) surface

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

Gabelnick, A.M.; Capitano, A.T.; Kane, S.M.

2000-01-12

The oxidation of propylene preabsorbed on the Pt(111) surface has been characterized in oxygen pressures up to 0.02 Torr using fluorescence yield near-edge spectroscopy (FYNES) and temperature-programmed fluorescence yield near-edge spectroscopy (TP-FYNES) above the carbon K edge. During oxidation of adsorbed propylene, a stable intermediate was observed and characterized using these soft X-ray methods. A general in situ method for determining the stoichiometry of carbon-containing reaction intermediate species has been developed and demonstrated for the first time. Total carbon concentration measured during temperature-programmed reaction studies clearly indicates a reaction intermediate is formed in the 300 K temperature range with amore » surface concentration of 0.55 x 10{sup 15} carbon atoms/cm{sup 2}. By comparing the intensity of the C-H {sigma}* resonance at the magic angle with the intensity in the carbon continuum, the stoichiometry of this intermediate can be determined unambiguously. Based on calibration with molecular propylene (C{sub 3}H{sub 6}) and propylidyne (C{sub 3}H{sub 5}), the intermediate has a C{sub 3}H{sub 5} stoichiometry for oxygen pressures up to 0.02 Torr. A set of normal and glancing angle FYNES spectra above the carbon K edge was used to characterize the bonding and structure of this intermediate. Spectra of known coverages of adsorbed propylene and propylidyne served as standards. The spectra of di-{sigma} propylene, propylidyne, and the intermediate were curve fit as a group with consistent energies and widths of all primary features. Based on this procedure, the intermediate is 1,1,2-tri-{sigma} 1-methylvinyl. The stoichiometry and temperature stability range of the 1-methylvinyl intermediate formed in oxygen pressures up to 0.02 Torr is identical with the stoichiometry and stability of the same intermediate formed during oxidation of preadsorbed propylene by excess coadsorbed atomic oxygen.« less

Seismic variability of subduction thrust faults: Insights from laboratory models

NASA Astrophysics Data System (ADS)

Corbi, F.; Funiciello, F.; Faccenna, C.; Ranalli, G.; Heuret, A.

2011-06-01

Laboratory models are realized to investigate the role of interface roughness, driving rate, and pressure on friction dynamics. The setup consists of a gelatin block driven at constant velocity over sand paper. The interface roughness is quantified in terms of amplitude and wavelength of protrusions, jointly expressed by a reference roughness parameter obtained by their product. Frictional behavior shows a systematic dependence on system parameters. Both stick slip and stable sliding occur, depending on driving rate and interface roughness. Stress drop and frequency of slip episodes vary directly and inversely, respectively, with the reference roughness parameter, reflecting the fundamental role for the amplitude of protrusions. An increase in pressure tends to favor stick slip. Static friction is a steeply decreasing function of the reference roughness parameter. The velocity strengthening/weakening parameter in the state- and rate-dependent dynamic friction law becomes negative for specific values of the reference roughness parameter which are intermediate with respect to the explored range. Despite the simplifications of the adopted setup, which does not address the problem of off-fault fracturing, a comparison of the experimental results with the depth distribution of seismic energy release along subduction thrust faults leads to the hypothesis that their behavior is primarily controlled by the depth- and time-dependent distribution of protrusions. A rough subduction fault at shallow depths, unable to produce significant seismicity because of low lithostatic pressure, evolves into a moderately rough, velocity-weakening fault at intermediate depths. The magnitude of events in this range is calibrated by the interplay between surface roughness and subduction rate. At larger depths, the roughness further decreases and stable sliding becomes gradually more predominant. Thus, although interplate seismicity is ultimately controlled by tectonic parameters (velocity of the plates/trench and the thermal regime), the direct control is exercised by the resulting frictional properties of the plate interface.

Proton elastic scattering from stable and unstable nuclei - Extraction of nuclear densities

NASA Astrophysics Data System (ADS)

Sakaguchi, H.; Zenihiro, J.

2017-11-01

Progress in proton elastic scattering at intermediate energies to determine nuclear density distributions is reviewed. After challenges of about 15 years to explain proton elastic scattering and associated polarization phenomena at intermediate energies, we have reached to some conclusions regarding proton elastic scattering as a means of obtaining nuclear densities. During this same period, physics of unstable nuclei has become of interest, and the density distributions of protons and neutrons play more important roles in unstable nuclei, since the differences in proton and neutron numbers and densities are expected to be significant. As such, proton elastic scattering experiments at intermediate energies using the inverse kinematic method have started to determine density distributions of unstable nuclei. In the region of unstable nuclei, we are confronted with a new problem when attempting to find proton and neutron densities separately from elastic proton scattering data, since electron scattering data for unstable nuclei are not presently available. We introduce a new means of determining proton and neutron densities separately by double-energy proton elastic scattering at intermediate energies.

42 CFR 54a.12 - Treatment of intermediate organizations.

Code of Federal Regulations, 2010 CFR

2010-10-01

... 42 Public Health 1 2010-10-01 2010-10-01 false Treatment of intermediate organizations. 54a.12... CHARITABLE CHOICE REGULATIONS APPLICABLE TO STATES, LOCAL GOVERNMENTS AND RELIGIOUS ORGANIZATIONS RECEIVING... ABUSE PREVENTION AND TREATMENT SERVICES § 54a.12 Treatment of intermediate organizations. If a...

Photon ratchet intermediate band solar cells

NASA Astrophysics Data System (ADS)

Yoshida, M.; Ekins-Daukes, N. J.; Farrell, D. J.; Phillips, C. C.

2012-06-01

In this paper, we propose an innovative concept for solar power conversion—the "photon ratchet" intermediate band solar cell (IBSC)—which may increase the photovoltaic energy conversion efficiency of IBSCs by increasing the lifetime of charge carriers in the intermediate state. The limiting efficiency calculation for this concept shows that the efficiency can be increased by introducing a fast thermal transition of carriers into a non-emissive state. At 1 sun, the introduction of a "ratchet band" results in an increase of efficiency from 46.8% to 48.5%, due to suppression of entropy generation.

Effect of NO2(-) on stable isotope fractionation during bacterial sulfate reduction.

PubMed

Einsiedl, Florian

2009-01-01

The effects of low NO2(-) concentrations on stable isotope fractionation during dissimilatory sulfate reduction by strain Desulfovibrio desulfuricans were investigated. Nitrite, formed as an intermediate during nitrification and denitrification processes in marine and freshwater habitats, inhibits the reduction of the sulfuroxy intermediate SO3(2-) to H2S even at low concentrations. To gain an understanding of the inhibition effect of the reduction of the sulfuroxy intermediate on stable isotope fractionation in sulfur and oxygen during bacterial sulfate reduction, nitrite was added in the form of short pulses. In the batch experiments that contained 0.02, 0.05, and 0.1 mM nitrite, sulfur enrichment factors epsilon of -12 +/- 1.6, -15 +/- 1.1, and -26 +/- 1.3 per thousand, respectively were observed. In the control experiment (no addition of nitrite) a sulfur enrichment factor epsilon of around -11 per thousand was calculated. In the experiments that contained no 18O enriched water (delta18O: -10 per thousand) and nitrite concentrations of 0.02, 0.05, and 0.1 mM, delta18O values in the remaining sulfate were fairly constant during the experiments (delta18O sulfate: approximately equal to 10 per thousand) and were similar to those obtained from the control experiment (no nitrite and no enriched water). However, in the batch experiments that contained 18O enriched water (+700 per thousand) and nitrite concentrations of 0.05 and 0.1 mM increasing delta18O values in the remaining sulfate from around 15 per thousand to approximately 65 and 85 per thousand, respectively, were found. Our experiments that contained isotopic enriched water and nitrite show clear evidence that the ratio of forward and backward fluxes regulated by adenosine-5'-phosphosulfate reductase (APSR) controls the extent of sulfur isotope fractionation during bacterial sulfate reduction in strain Desulfovibrio desulfuricans. Since the metabolic sulfuroxy intermediate SO3(2-) exchanges with water, evidence of 18O enriched water in the remaining sulfate in the experiments that contained nitrite also demonstrates that SO3(2-) recycling to sulfate affects sulfur and oxygen isotope fractionation during bacterial sulfate reduction to some extent. Even though reduction of adenosine-5'-phosphosulfate (APS) to sulfite of -25 per thousand was not fully expressed, SO3(2-) was recycled to SO4(2-). On the basis of the results of this study a sulfur isotope fractionation for APSR of upto approximately -30 per thousand can be assumed. However, reported NO2(-) concentrations of up to 20 microM in freshwater and marine habitats may not significantly impact the ability to use stable isotope analysis in assessing bacterial sulfate reduction.

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

Aromí, G.; Beavers, C. M.; Sánchez Costa, J.

Crystal-to-crystal transformations have been crucial in the understanding of solid-state processes, since these may be studied in detail by means of single crystal X-ray diffraction (SCXRD) techniques. The description of the mechanisms and potential intermediates of those processes remains very challenging. In fact, solid-state transient states have rarely been observed, at least to a sufficient level of detail. We have investigated the process of guest extrusion from the non-porous molecular material [Fe(bpp)(H 2L)](ClO 4) 2·1.5C 3H 6O (bpp = 2,6-bis(pyrazol-3-yl)pyridine; H 2L = 2,6-bis(5-(2-methoxyphenyl)-pyrazol-3-yl)pyridine; C 3H 6O = acetone), which occurs through ordered diffusion of acetone in a crystal-to-crystal manner,more » leading to dramatic structural changes. The slow kinetics of the transition allows thermal trapping of the system at various intermediate stages. The transiting single crystal can be then examined at these points through synchrotron SCXRD, offering a window upon the mechanism of the transformation at the molecular scale. These experiments have unveiled the development of an ordered intermediate phase, distinct from the initial and the final states, coexisting as the process advances with either of these two phases or, at a certain moment with both of them. The new intermediate phase has been structurally characterized in full detail by SCXRD, providing insights into the mechanism of this diffusion triggered solid-state phenomenon. Lastly, the process has been also followed by calorimetry, optical microscopy, local Raman spectroscopy and powder X-ray diffraction. The discovery and description of an intermediate ordered state in a molecular solid-state transformation is of great interest and will help to understand the mechanistic details and reaction pathways underlying these transformations.« less

Non-invasive assessment of low- and intermediate-risk patients with chest pain

PubMed Central

Balfour, Pelbreton C.; Gonzalez, Jorge A.; Kramer, Christopher M.

2016-01-01

Coronary artery disease (CAD) remains a significant global public health burden despite advancements in prevention and therapeutic strategies. Common non-invasive imaging modalities, anatomic and functional, are available for the assessment of patients with stable chest pain. Exercise electrocardiography is a long-standing method for evaluation for CAD and remains the initial test for the majority of patients who can exercise adequately with a baseline interpretable electrocardiogram. The addition of cardiac imaging to exercise testing provides incremental benefit for accurate diagnosis for CAD and is particularly useful in patients who are unable to exercise adequately and/or have uninterpretable electrocardiograms. Radionuclide myocardial perfusion imaging and echocardiography with exercise or pharmacological stress provide high sensitivity and specificity in the detection and further risk stratification of patients with CAD. Recently, coronary computed tomography angiography has demonstrated its growing role to rule out significant CAD given its high negative predictive value. Although less available, stress cardiac magnetic resonance provides a comprehensive assessment of cardiac structure and function and provides a high diagnostic accuracy in the detection of CAD. The utilization of non-invasive testing is complex due to various advantages and limitations, particularly in the assessment of low- and intermediate-risk patients with chest pain, where no single study is suitable for all patients. This review will describe currently available non-invasive modalities, along with current evidence-based guidelines and appropriate use criteria in the assessment of low- and intermediate-risk patients with suspected, stable CAD. PMID:27717538

34 CFR 403.113 - How does a State allocate funds under the Secondary School Vocational Education Program to area...

Code of Federal Regulations, 2010 CFR

2010-07-01

... School Vocational Education Program to area vocational education schools and intermediate educational... TECHNOLOGY EDUCATION PROGRAM What Kinds of Activities Does the Secretary Assist Under the Basic Programs... intermediate educational agencies? (a) A State shall distribute funds reserved under § 403.112(a) directly to...

Time-resolved vibrational spectroscopy detects protein-based intermediates in the photosynthetic oxygen-evolving cycle.

PubMed

Barry, Bridgette A; Cooper, Ian B; De Riso, Antonio; Brewer, Scott H; Vu, Dung M; Dyer, R Brian

2006-05-09

Photosynthetic oxygen production by photosystem II (PSII) is responsible for the maintenance of aerobic life on earth. The production of oxygen occurs at the PSII oxygen-evolving complex (OEC), which contains a tetranuclear manganese (Mn) cluster. Photo-induced electron transfer events in the reaction center lead to the accumulation of oxidizing equivalents on the OEC. Four sequential photooxidation reactions are required for oxygen production. The oxidizing complex cycles among five oxidation states, called the S(n) states, where n refers to the number of oxidizing equivalents stored. Oxygen release occurs during the S(3)-to-S(0) transition from an unstable intermediate, known as the S(4) state. In this report, we present data providing evidence for the production of an intermediate during each S state transition. These protein-derived intermediates are produced on the microsecond to millisecond time scale and are detected by time-resolved vibrational spectroscopy on the microsecond time scale. Our results suggest that a protein-derived conformational change or proton transfer reaction precedes Mn redox reactions during the S(2)-to-S(3) and S(3)-to-S(0) transitions.

The Protective Antigen Component of Anthrax Toxin Forms Functional Octameric Complexes

PubMed Central

Kintzer, Alexander F.; Thoren, Katie L.; Sterling, Harry J.; Dong, Ken C.; Feld, Geoffrey K.; Tang, Iok I.; Zhang, Teri T.; Williams, Evan R.; Berger, James M.; Krantz, Bryan A.

2009-01-01

The assembly of bacterial toxins and virulence factors is critical to their function, but the regulation of assembly during infection has not been studied. We begin to address this question using anthrax toxin as a model. The protective antigen (PA) component of the toxin assembles into ring-shaped homooligomers that bind the two other enzyme components of the toxin, lethal factor (LF) and edema factor (EF), to form toxic complexes. To disrupt the host, these toxic complexes are endocytosed, such that the PA oligomer forms a membrane-spanning channel that LF and EF translocate through to enter the cytosol. We show using single-channel electrophysiology that PA channels contain two populations of conductance states, which correspond with two different PA pre-channel oligomers observed by electron microscopy—the well-described heptamer and a novel octamer. Mass spectrometry demonstrates that the PA octamer binds four LFs, and assembly routes leading to the octamer are populated with even-numbered, dimeric and tetrameric, PA intermediates. Both heptameric and octameric PA complexes can translocate LF and EF with similar rates and efficiencies. Here we also report a 3.2-Å crystal structure of the PA octamer. The octamer comprises ∼20−30% of the oligomers on cells, but outside of the cell, the octamer is more stable than the heptamer under physiological pH. Thus the PA octamer is a physiological, stable, and active assembly state capable of forming lethal toxins that may withstand the hostile conditions encountered in the bloodstream. This assembly mechanism may provide a novel means to control cytotoxicity. PMID:19627991

Traveling waves in an optimal velocity model of freeway traffic.

PubMed

Berg, P; Woods, A

2001-03-01

Car-following models provide both a tool to describe traffic flow and algorithms for autonomous cruise control systems. Recently developed optimal velocity models contain a relaxation term that assigns a desirable speed to each headway and a response time over which drivers adjust to optimal velocity conditions. These models predict traffic breakdown phenomena analogous to real traffic instabilities. In order to deepen our understanding of these models, in this paper, we examine the transition from a linear stable stream of cars of one headway into a linear stable stream of a second headway. Numerical results of the governing equations identify a range of transition phenomena, including monotonic and oscillating travelling waves and a time- dependent dispersive adjustment wave. However, for certain conditions, we find that the adjustment takes the form of a nonlinear traveling wave from the upstream headway to a third, intermediate headway, followed by either another traveling wave or a dispersive wave further downstream matching the downstream headway. This intermediate value of the headway is selected such that the nonlinear traveling wave is the fastest stable traveling wave which is observed to develop in the numerical calculations. The development of these nonlinear waves, connecting linear stable flows of two different headways, is somewhat reminiscent of stop-start waves in congested flow on freeways. The different types of adjustments are classified in a phase diagram depending on the upstream and downstream headway and the response time of the model. The results have profound consequences for autonomous cruise control systems. For an autocade of both identical and different vehicles, the control system itself may trigger formations of nonlinear, steep wave transitions. Further information is available [Y. Sugiyama, Traffic and Granular Flow (World Scientific, Singapore, 1995), p. 137].

Traveling waves in an optimal velocity model of freeway traffic

NASA Astrophysics Data System (ADS)

Berg, Peter; Woods, Andrew

2001-03-01

Car-following models provide both a tool to describe traffic flow and algorithms for autonomous cruise control systems. Recently developed optimal velocity models contain a relaxation term that assigns a desirable speed to each headway and a response time over which drivers adjust to optimal velocity conditions. These models predict traffic breakdown phenomena analogous to real traffic instabilities. In order to deepen our understanding of these models, in this paper, we examine the transition from a linear stable stream of cars of one headway into a linear stable stream of a second headway. Numerical results of the governing equations identify a range of transition phenomena, including monotonic and oscillating travelling waves and a time- dependent dispersive adjustment wave. However, for certain conditions, we find that the adjustment takes the form of a nonlinear traveling wave from the upstream headway to a third, intermediate headway, followed by either another traveling wave or a dispersive wave further downstream matching the downstream headway. This intermediate value of the headway is selected such that the nonlinear traveling wave is the fastest stable traveling wave which is observed to develop in the numerical calculations. The development of these nonlinear waves, connecting linear stable flows of two different headways, is somewhat reminiscent of stop-start waves in congested flow on freeways. The different types of adjustments are classified in a phase diagram depending on the upstream and downstream headway and the response time of the model. The results have profound consequences for autonomous cruise control systems. For an autocade of both identical and different vehicles, the control system itself may trigger formations of nonlinear, steep wave transitions. Further information is available [Y. Sugiyama, Traffic and Granular Flow (World Scientific, Singapore, 1995), p. 137].

Russian Compliance with the Intermediate Range Nuclear Forces (INF) Treaty: Background and Issues for Congress

DTIC Science & Technology

2017-01-27

Russian Compliance with the Intermediate Range Nuclear Forces (INF) Treaty: Background and Issues for Congress Amy F. Woolf Specialist in... Nuclear Weapons Policy January 27, 2017 Congressional Research Service 7-5700 www.crs.gov R43832 Russian Compliance with the Intermediate Range... Nuclear Forces (INF) Treaty Congressional Research Service Summary The United States and Soviet Union signed the Intermediate-Range Nuclear Forces

Characterization of two distinct beta2-microglobulin unfolding intermediates that may lead to amyloid fibrils of different morphology.

PubMed

Armen, Roger S; Daggett, Valerie

2005-12-13

The self-assembly of beta(2)-microglobulin into fibrils leads to dialysis-related amyloidosis. pH-mediated partial unfolding is required for the formation of the amyloidogenic intermediate that then self-assembles into amyloid fibrils. Two partially folded intermediates of beta(2)-microglobulin have been identified experimentally and linked to the formation of fibrils of distinct morphology, yet it remains difficult to characterize these partially unfolded states at high resolution using experimental approaches. Consequently, we have performed molecular dynamics simulations at neutral and low pH to determine the structures of these partially unfolded amyloidogenic intermediates. In the low-pH simulations, we observed the formation of alpha-sheet structure, which was first proposed by Pauling and Corey. Multiple simulations were performed, and two distinct intermediate state ensembles were identified that may account for the different fibril morphologies. The predominant early unfolding intermediate was nativelike in structure, in agreement with previous NMR studies. The late unfolding intermediate was significantly disordered, but it maintained an extended elongated structure, with hydrophobic clusters and residual alpha-extended chain strands in specific regions of the sequence that map to amyloidogenic peptides. We propose that the formation of alpha-sheet facilitates self-assembly into partially unfolded prefibrillar amyloidogenic intermediates.

On the Structure Sensitivity of Formic Acid Decomposition on Cu Catalysts

DOE PAGES

Li, Sha; Scaranto, Jessica; Mavrikakis, Manos

2016-08-03

Catalytic decomposition of formic acid (HCOOH) has attracted substantial attention since HCOOH is a major by-product in biomass reforming, a promising hydrogen carrier, and also a potential low temperature fuel cell feed. Despite the abundance of experimental studies for vapor-phase HCOOH decomposition on Cu catalysts, the reaction mechanism and its structure sensitivity is still under debate. In this work, self-consistent, periodic density functional theory calculations were performed on three model surfaces of copper—Cu(111), Cu(100) and Cu(211), and both the HCOO (formate)-mediated and COOH (carboxyl)-mediated pathways were investigated for HCOOH decomposition. The energetics of both pathways suggest that the HCOO-mediated routemore » is more favorable than the COOH-mediated route on all three surfaces, and that HCOOH decomposition proceeds through two consecutive dehydrogenation steps via the HCOO intermediate followed by the recombinative desorption of H 2. On all three surfaces, HCOO dehydrogenation is the likely rate determining step since it has the highest transition state energy and also the highest activation energy among the three catalytic steps in the HCOO pathway. The reaction is structure sensitive on Cu catalysts since the examined three Cu facets have dramatically different binding strengths for the key intermediate HCOO and varied barriers for the likely rate determining step—HCOO dehydrogenation. Cu(100) and Cu(211) bind HCOO much more strongly than Cu(111), and they are also characterized by potential energy surfaces that are lower in energy than that for the Cu(111) facet. Coadsorbed HCOO and H represents the most stable state along the reaction coordinate, indicating that, under reaction conditions, there might be a substantial surface coverage of the HCOO intermediate, especially at under-coordinated step, corner or defect sites. Therefore, under reaction conditions, HCOOH decomposition is predicted to occur most readily on the terrace sites of Cu nanoparticles. Finally, as a result, we hereby present an example of a fundamentally structure-sensitive reaction, which may present itself as structure-insensitive in typical varied particle-size experiments.« less

Carbonyl Activation by Borane Lewis Acid Complexation: Transition States of H2 Splitting at the Activated Carbonyl Carbon Atom in a Lewis Basic Solvent and the Proton-Transfer Dynamics of the Boroalkoxide Intermediate.

PubMed

Heshmat, Mojgan; Privalov, Timofei

2017-07-06

By using transition-state (TS) calculations, we examined how Lewis acid (LA) complexation activates carbonyl compounds in the context of hydrogenation of carbonyl compounds by H 2 in Lewis basic (ethereal) solvents containing borane LAs of the type (C 6 F 5 ) 3 B. According to our calculations, LA complexation does not activate a ketone sufficiently enough for the direct addition of H 2 to the O=C unsaturated bond; but, calculations indicate a possibly facile heterolytic cleavage of H 2 at the activated and thus sufficiently Lewis acidic carbonyl carbon atom with the assistance of the Lewis basic solvent (i.e., 1,4-dioxane or THF). For the solvent-assisted H 2 splitting at the carbonyl carbon atom of (C 6 F 5 ) 3 B adducts with different ketones, a number of TSs are computed and the obtained results are related to insights from experiment. By using the Born-Oppenheimer molecular dynamics with the DFT for electronic structure calculations, the evolution of the (C 6 F 5 ) 3 B-alkoxide ionic intermediate and the proton transfer to the alkoxide oxygen atom were investigated. The results indicate a plausible hydrogenation mechanism with a LA, that is, (C 6 F 5 ) 3 B, as a catalyst, namely, 1) the step of H 2 cleavage that involves a Lewis basic solvent molecule plus the carbonyl carbon atom of thermodynamically stable and experimentally identifiable (C 6 F 5 ) 3 B-ketone adducts in which (C 6 F 5 ) 3 B is the "Lewis acid promoter", 2) the transfer of the solvent-bound proton to the oxygen atom of the (C 6 F 5 ) 3 B-alkoxide intermediate giving the (C 6 F 5 ) 3 B-alcohol adduct, and 3) the S N 2-style displacement of the alcohol by a ketone or a Lewis basic solvent molecule. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Stable amplitude chimera states in a network of locally coupled Stuart-Landau oscillators

NASA Astrophysics Data System (ADS)

Premalatha, K.; Chandrasekar, V. K.; Senthilvelan, M.; Lakshmanan, M.

2018-03-01

We investigate the occurrence of collective dynamical states such as transient amplitude chimera, stable amplitude chimera, and imperfect breathing chimera states in a locally coupled network of Stuart-Landau oscillators. In an imperfect breathing chimera state, the synchronized group of oscillators exhibits oscillations with large amplitudes, while the desynchronized group of oscillators oscillates with small amplitudes, and this behavior of coexistence of synchronized and desynchronized oscillations fluctuates with time. Then, we analyze the stability of the amplitude chimera states under various circumstances, including variations in system parameters and coupling strength, and perturbations in the initial states of the oscillators. For an increase in the value of the system parameter, namely, the nonisochronicity parameter, the transient chimera state becomes a stable chimera state for a sufficiently large value of coupling strength. In addition, we also analyze the stability of these states by perturbing the initial states of the oscillators. We find that while a small perturbation allows one to perturb a large number of oscillators resulting in a stable amplitude chimera state, a large perturbation allows one to perturb a small number of oscillators to get a stable amplitude chimera state. We also find the stability of the transient and stable amplitude chimera states and traveling wave states for an appropriate number of oscillators using Floquet theory. In addition, we also find the stability of the incoherent oscillation death states.

Stable amplitude chimera states in a network of locally coupled Stuart-Landau oscillators.

PubMed

Premalatha, K; Chandrasekar, V K; Senthilvelan, M; Lakshmanan, M

2018-03-01

We investigate the occurrence of collective dynamical states such as transient amplitude chimera, stable amplitude chimera, and imperfect breathing chimera states in a locally coupled network of Stuart-Landau oscillators. In an imperfect breathing chimera state, the synchronized group of oscillators exhibits oscillations with large amplitudes, while the desynchronized group of oscillators oscillates with small amplitudes, and this behavior of coexistence of synchronized and desynchronized oscillations fluctuates with time. Then, we analyze the stability of the amplitude chimera states under various circumstances, including variations in system parameters and coupling strength, and perturbations in the initial states of the oscillators. For an increase in the value of the system parameter, namely, the nonisochronicity parameter, the transient chimera state becomes a stable chimera state for a sufficiently large value of coupling strength. In addition, we also analyze the stability of these states by perturbing the initial states of the oscillators. We find that while a small perturbation allows one to perturb a large number of oscillators resulting in a stable amplitude chimera state, a large perturbation allows one to perturb a small number of oscillators to get a stable amplitude chimera state. We also find the stability of the transient and stable amplitude chimera states and traveling wave states for an appropriate number of oscillators using Floquet theory. In addition, we also find the stability of the incoherent oscillation death states.

Atmospheric blocking as a traffic jam in the jet stream

NASA Astrophysics Data System (ADS)

Nakamura, N.; Huang, S. Y.

2017-12-01

It is demonstrated using the ERA-Interim product that synoptic to intraseasonal variabilities of extratropical circulation in the boreal storm track regions are strongly affected by the zonal convergence of the column-integrated eastward flux of local wave activity (LWA). In particular, from the multi-year daily samples of LWA fluxes, we find that the wintertime zonal LWA flux in the jet exit regions tends to maximize for an intermediate value of column-averaged LWA. This is because an increasing LWA decelerates the zonal flow, eventually weakening the eastward advection of LWA. From theory we argue that large wave events on the decreasing side of the flux curve with increasing LWA cannot be maintained as a stable steady state. Consistent with this argument, observed states corresponding to that side of flux curve often exhibit local wave breaking and blocking events. A close parallelism exists for the traffic flow problem, in which the traffic flux (traffic density times traffic speed) is often observed to maximize for an intermediate value of traffic density. This is because the traffic speed is controlled not only by the imposed speed limit but also by the traffic density — an increasingly heavy traffic slows down the flow naturally and eventually decreases the flux. Once the flux starts to decrease with an increasing traffic density, a traffic jam kicks in suddenly (Lighthill and Whitham 1955, Richards 1956). The above idea is demonstrated by a simple conceptual model based on the equivalent barotropic PV contour design (Nakamura and Huang 2017, JAS), which predicts a threshold of blocking onset. The idea also suggests that the LWA that gives the `flux capacity,' i.e., the maximum LWA flux at a given location, is a useful predictor of local wave breaking/block formation.

An A-train climatology of extratropical cyclone clouds and precipitation

NASA Astrophysics Data System (ADS)

Naud, C. M.; Booth, J.; Del Genio, A. D.; van den Heever, S. C.; Posselt, D. J.

2016-12-01

It is demonstrated using the ERA-Interim product that synoptic to intraseasonal variabilities of extratropical circulation in the boreal storm track regions are strongly affected by the zonal convergence of the column-integrated eastward flux of local wave activity (LWA). In particular, from the multi-year daily samples of LWA fluxes, we find that the wintertime zonal LWA flux in the jet exit regions tends to maximize for an intermediate value of column-averaged LWA. This is because an increasing LWA decelerates the zonal flow, eventually weakening the eastward advection of LWA. From theory we argue that large wave events on the decreasing side of the flux curve with increasing LWA cannot be maintained as a stable steady state. Consistent with this argument, observed states corresponding to that side of flux curve often exhibit local wave breaking and blocking events. A close parallelism exists for the traffic flow problem, in which the traffic flux (traffic density times traffic speed) is often observed to maximize for an intermediate value of traffic density. This is because the traffic speed is controlled not only by the imposed speed limit but also by the traffic density — an increasingly heavy traffic slows down the flow naturally and eventually decreases the flux. Once the flux starts to decrease with an increasing traffic density, a traffic jam kicks in suddenly (Lighthill and Whitham 1955, Richards 1956). The above idea is demonstrated by a simple conceptual model based on the equivalent barotropic PV contour design (Nakamura and Huang 2017, JAS), which predicts a threshold of blocking onset. The idea also suggests that the LWA that gives the `flux capacity,' i.e., the maximum LWA flux at a given location, is a useful predictor of local wave breaking/block formation.

Solvent and α-secondary kinetic isotope effects on β-glucosidase.

PubMed

Xie, Miaomiao; Byers, Larry D

2015-11-01

β-Glucosidase from sweet almond is a retaining, family 1, glycohydrolase. It is known that glycosylation of the enzyme by aryl glucosides occurs with little, if any, acid catalysis. For this reaction both the solvent and α-secondary kinetic isotope effects are 1.0. However, for the deglucosylation reaction (e.g., kcat for 2,4-dinitrophenyl-β-D-glucopyranoside) there is a small solvent deuterium isotope effect of 1.50 (±0.06) and an α-secondary kinetic isotope effect of 1.12 (±0.03). For aryl glucosides, kcat/KM is very sensitive to the pKa of the phenol leaving group [βlg≈-1; Dale et al., Biochemistry25 (1986) 2522-2529]. With alkyl glucosides the βlg is smaller (between -0.2 and -0.3) but still negative. This, coupled with the small solvent isotope effect on the pH-independent second-order rate constant for the glucosylation of the enzyme with 2,2,2-trifluoroethyl-β-glucoside [D2O(kcat/KM)=1.23 (±0.04)] suggests that there is more glycone-aglycone bond fission than aglycone oxygen protonation in the transition state for alkyl glycoside hydrolysis. The kinetics constants for the partitioning (between water and various alcohols) of the glucosyl-enzyme intermediate, coupled with the rate constants for the forward (hydrolysis) reaction provide an estimate of the stability of the glucosyl-enzyme intermediate. This is a relatively stable species with an energy about 2 to 4 kcal/mol higher than that of the ES complex. This article is part of a Special Issue entitled: Enzyme Transition States from Theory and Experiment. Copyright © 2015 Elsevier B.V. All rights reserved.

Observing a late folding intermediate of Ubiquitin at atomic resolution by NMR

PubMed Central

Surana, Parag

2016-01-01

Abstract The study of intermediates in the protein folding pathway provides a wealth of information about the energy landscape. The intermediates also frequently initiate pathogenic fibril formations. While observing the intermediates is difficult due to their transient nature, extreme conditions can partially unfold the proteins and provide a glimpse of the intermediate states. Here, we observe the high resolution structure of a hydrophobic core mutant of Ubiquitin at an extreme acidic pH by nuclear magnetic resonance (NMR) spectroscopy. In the structure, the native secondary and tertiary structure is conserved for a major part of the protein. However, a long loop between the beta strands β3 and β5 is partially unfolded. The altered structure is supported by fluorescence data and the difference in free energies between the native state and the intermediate is reflected in the denaturant induced melting curves. The unfolded region includes amino acids that are critical for interaction with cofactors as well as for assembly of poly‐Ubiquitin chains. The structure at acidic pH resembles a late folding intermediate of Ubiquitin and indicates that upon stabilization of the protein's core, the long loop converges on the core in the final step of the folding process. PMID:27111887

GFP's Mechanical Intermediate States

PubMed Central

Saeger, John; Hytönen, Vesa P.; Klotzsch, Enrico; Vogel, Viola

2012-01-01

Green fluorescent protein (GFP) mutants have become the most widely used fluorescence markers in the life sciences, and although they are becoming increasingly popular as mechanical force or strain probes, there is little direct information on how their fluorescence changes when mechanically stretched. Here we derive high-resolution structural models of the mechanical intermediate states of stretched GFP using steered molecular dynamics (SMD) simulations. These structures were used to produce mutants of EGFP and EYFP that mimic GFP's different mechanical intermediates. A spectroscopic analysis revealed that a population of EGFP molecules with a missing N-terminal α-helix was significantly dimmed, while the fluorescence lifetime characteristic of the anionic chromophore state remained unaffected. This suggests a mechanism how N-terminal deletions can switch the protonation state of the chromophore, and how the fluorescence of GFP molecules in response to mechanical disturbance might be turned off. PMID:23118864

The population density of Lymnaea columella (Say, 1817) (Mollusca, Lymnaeidae) an intermediate host of Fasciola hepatica (Linnaeus, 1758), in the Caparaó microregion, ES, Brazil.

PubMed

D'Almeida, S C G; Freitas, D F; Carneiro, M B; Camargo, P F; Azevedo, J C; Martins, I V F

2016-06-01

The aim of this study was to monitor the population density of Lymnaea columella, an intermediate host of Fasciola hepatica, in various aquatic habitats and in drinking water in the area of the Instituto Federal de Educação, Ciência e Tecnologia do Espírito Santo, on Caparaó Microregion, municipality of Alegre, state of Espírito Santo, Brazil. Monthly samplings were performed at certain points between drainage areas and drinking water in cattle and goat production systems during the years 2010 to 2013. The mean temperature, precipitation and the frequency of samples of L. columella were analysed graphically according the monthly average during the study period. A total of 2,038 molluscs were collected, 1558 of which were L. columella, that predominated in all sampled points. The highest average of specimens observed for L. columella was in the years 2010 and 2013 (51.0), and occurred decreased in 2011 (19.8). The temperature and precipitation averaged is 23.7 °C and 141 mm/year, respectively. Rainfall peak occurred in March (2011, 2013) and November (2012), during these periods the population of L. columella growth. There was no significant difference in the relationship between the specimens observed with seasons (dry-wet), thus the population of L. columella remained stable and can be found throughout the year.

Thermal and urea-induced unfolding in T7 RNA polymerase: Calorimetry, circular dichroism and fluorescence study

PubMed Central

Griko, Yuri; Sreerama, Narasimha; Osumi-Davis, Patricia; Woody, Robert W.; Woody, A-Young Moon

2001-01-01

Structural changes in T7 RNA polymerase (T7RNAP) induced by temperature and urea have been studied over a wide range of conditions to obtain information about the structural organization and the stability of the enzyme. T7RNAP is a large monomeric enzyme (99 kD). Calorimetric studies of the thermal transitions in T7RNAP show that the enzyme consists of three cooperative units that may be regarded as structural domains. Interactions between these structural domains and their stability strongly depend on solvent conditions. The unfolding of T7RNAP under different solvent conditions induces a highly stable intermediate state that lacks specific tertiary interactions, contains a significant amount of residual secondary structure, and undergoes further cooperative unfolding at high urea concentrations. Circular dichroism (CD) studies show that thermal unfolding leads to an intermediate state that has increased β-sheet and reduced α-helix content relative to the native state. Urea-induced unfolding at 25°C reveals a two-step process. The first transition centered near 3 M urea leads to a plateau from 3.5 to 5.0 M urea, followed by a second transition centered near 6.5 M urea. The CD spectrum of the enzyme in the plateau region, which is similar to that of the enzyme thermally unfolded in the absence of urea, shows little temperature dependence from 15° to 60°C. The second transition leads to a mixture of poly(Pro)II and unordered conformations. As the temperature increases, the ellipticity at 222 nm becomes more negative because of conversion of poly(Pro)II to the unordered conformation. Near-ultraviolet CD spectra at 25°C at varying concentrations of urea are consistent with this picture. Both thermal and urea denaturation are irreversible, presumably because of processes that follow unfolding. PMID:11274475

Intermediate regime and a phase diagram of red blood cell dynamics in a linear flow.

PubMed

Levant, Michael; Steinberg, Victor

2016-12-01

In this paper we investigate the in vitro dynamics of a single rabbit red blood cell (RBC) in a planar linear flow as a function of a shear stress σ and the dynamic viscosity of outer fluid η_{o}. A linear flow is a generalization of previous studies dynamics of soft objects including RBC in shear flow and is realized in the experiment in a microfluidic four-roll mill device. We verify that the RBC stable orientation dynamics is found in the experiment being the in-shear-plane orientation and the RBC dynamics is characterized by observed three RBC dynamical states, namely tumbling (TU), intermediate (INT), and swinging (SW) [or tank-treading (TT)] on a single RBC. The main results of these studies are the following. (i) We completely characterize the RBC dynamical states and reconstruct their phase diagram in the case of the RBC in-shear-plane orientation in a planar linear flow and find it in a good agreement with that obtained in early experiments in a shear flow for human RBCs. (ii) The value of the critical shear stress σ_{c} of the TU-TT(SW) transition surprisingly coincides with that found in early experiments in spite of a significant difference in the degree of RBC shape deformations in both the SW and INT states. (iii) We describe the INT regime, which is stationary, characterized by strong RBC shape deformations and observed in a wide range of the shear stresses. We argue that our observations cast doubts on the main claim of the recent numerical simulations that the only RBC spheroidal stress-free shape is capable to explain the early experimental data. Finally, we suggest that the amplitude dependence of both θ and the shape deformation parameter D on σ can be used as the quantitative criterion to determine the RBC stress-free shape.

NHC-catalyzed cleavage of vicinal diketones and triketones followed by insertion of enones and ynones.

PubMed

Takaki, Ken; Hino, Makoto; Ohno, Akira; Komeyama, Kimihiro; Yoshida, Hiroto; Fukuoka, Hiroshi

2017-01-01

Thiazolium carbene-catalyzed reactions of 1,2-diketones and 1,2,3-triketones with enones and ynones have been investigated. The diketones gave α,β-double acylation products via unique Breslow intermediates isolable as acid salts, whereas the triketones formed stable adducts with the NHC instead of the coupling products.

NHC-catalyzed cleavage of vicinal diketones and triketones followed by insertion of enones and ynones

PubMed Central

Hino, Makoto; Ohno, Akira; Komeyama, Kimihiro; Yoshida, Hiroto; Fukuoka, Hiroshi

2017-01-01

Thiazolium carbene-catalyzed reactions of 1,2-diketones and 1,2,3-triketones with enones and ynones have been investigated. The diketones gave α,β-double acylation products via unique Breslow intermediates isolable as acid salts, whereas the triketones formed stable adducts with the NHC instead of the coupling products. PMID:28904625

Difluoromethyl 2-pyridyl sulfone: a new gem-difluoroolefination reagent for aldehydes and ketones.

PubMed

Zhao, Yanchuan; Huang, Weizhou; Zhu, Lingui; Hu, Jinbo

2010-04-02

Difluoromethyl 2-pyridyl sulfone, a previously unknown compound, was found to act as a novel and efficient gem-difluoroolefination reagent for both aldehydes and ketones. It was found that the fluorinated sulfinate intermediate in the reaction is relatively stable, which can be observed by (19)F NMR and trapped with CH(3)I.

Chemotherapy of colorectal liver metastases induces a rapid rise in intermediate blood monocytes which predicts treatment response

PubMed Central

Schauer, Dominic; Starlinger, Patrick; Alidzanovic, Lejla; Zajc, Philipp; Maier, Thomas; Feldman, Alexandra; Padickakudy, Robin; Buchberger, Elisabeth; Elleder, Vanessa; Spittler, Andreas; Stift, Judith; Pop, Lorand; Gruenberger, Birgit; Gruenberger, Thomas; Brostjan, Christine

2016-01-01

ABSTRACT We have previously reported that intermediate monocytes (CD14++/CD16+) were increased in colorectal cancer (CRC) patients, while the subset of pro-angiogenic TIE2-expressing monocytes (TEMs) was not significantly elevated. This study was designed to evaluate changes in frequency and function of intermediate monocytes and TEMs during chemotherapy and anti-angiogenic cancer treatment and their relation to treatment response. Monocyte populations were determined by flow cytometry in 60 metastasized CRC (mCRC) patients who received neoadjuvant chemotherapy with or without bevacizumab. Blood samples were taken before treatment, after two therapy cycles, at the end of neoadjuvant therapy and immediately before surgical resection of liver metastases. Neoadjuvant treatment resulted in a significant increase in circulating intermediate monocytes which was most pronounced after two cycles and positively predicted tumor response (AUC = 0.875, p = 0.005). With a cut-off value set to 1% intermediate monocytes of leukocytes, this parameter showed a predictive sensitivity and specificity of 75% and 88%. Anti-angiogenic therapy with bevacizumab had no impact on monocyte populations including TEMs. In 15 patients and six healthy controls, the gene expression profile and the migratory behavior of monocyte subsets was evaluated. The profile of intermediate monocytes suggested functions in antigen presentation, inflammatory cytokine production, chemotaxis and was remarkably stable during chemotherapy. Intermediate monocytes showed a preferential migratory response to tumor-derived signals in vitro and correlated with the level of CD14+/CD16+ monocytic infiltrates in the resected tumor tissue. In conclusion, the rapid rise of intermediate monocytes during chemotherapy may offer a simple marker for response prediction and a timely change in regimen. PMID:27471631

Use of CAS in Secondary School: A Factor Influencing the Transition to University-Level Mathematics?

ERIC Educational Resources Information Center

Varsavsky, Cristina

2012-01-01

Australian secondary school systems offer three levels of senior (year 12) mathematics studies, none of them compulsory: elementary, intermediate and advanced. The intermediate and advanced studies prepare students for further mathematics studies at university level. In the state of Victoria, there are two versions of intermediate mathematics: one…

Unraveling the structure and chemical mechanisms of highly oxygenated intermediates in oxidation of organic compounds.

PubMed

Wang, Zhandong; Popolan-Vaida, Denisia M; Chen, Bingjie; Moshammer, Kai; Mohamed, Samah Y; Wang, Heng; Sioud, Salim; Raji, Misjudeen A; Kohse-Höinghaus, Katharina; Hansen, Nils; Dagaut, Philippe; Leone, Stephen R; Sarathy, S Mani

2017-12-12

Decades of research on the autooxidation of organic compounds have provided fundamental and practical insights into these processes; however, the structure of many key autooxidation intermediates and the reactions leading to their formation still remain unclear. This work provides additional experimental evidence that highly oxygenated intermediates with one or more hydroperoxy groups are prevalent in the autooxidation of various oxygenated (e.g., alcohol, aldehyde, keto compounds, ether, and ester) and nonoxygenated (e.g., normal alkane, branched alkane, and cycloalkane) organic compounds. These findings improve our understanding of autooxidation reaction mechanisms that are routinely used to predict fuel ignition and oxidative stability of liquid hydrocarbons, while also providing insights relevant to the formation mechanisms of tropospheric aerosol building blocks. The direct observation of highly oxygenated intermediates for the autooxidation of alkanes at 500-600 K builds upon prior observations made in atmospheric conditions for the autooxidation of terpenes and other unsaturated hydrocarbons; it shows that highly oxygenated intermediates are stable at conditions above room temperature. These results further reveal that highly oxygenated intermediates are not only accessible by chemical activation but also by thermal activation. Theoretical calculations on H-atom migration reactions are presented to rationalize the relationship between the organic compound's molecular structure ( n -alkane, branched alkane, and cycloalkane) and its propensity to produce highly oxygenated intermediates via extensive autooxidation of hydroperoxyalkylperoxy radicals. Finally, detailed chemical kinetic simulations demonstrate the influence of these additional reaction pathways on the ignition of practical fuels. Copyright © 2017 the Author(s). Published by PNAS.

Unraveling the structure and chemical mechanisms of highly oxygenated intermediates in oxidation of organic compounds

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

Wang, Zhandong; Popolan-Vaida, Denisia M.; Chen, Bingjie

Decades of research on the autooxidation of organic compounds have provided fundamental and practical insights into these processes; however, the structure of many key autooxidation intermediates and the reactions leading to their formation still remain unclear. This work provides additional experimental evidence that highly oxygenated intermediates with one or more hydroperoxy groups are prevalent in the autooxidation of various oxygenated (e.g., alcohol, aldehyde, keto compounds, ether, and ester) and nonoxygenated (e.g., normal alkane, branched alkane, and cycloalkane) organic compounds. These findings improve our understanding of autooxidation reaction mechanisms that are routinely used to predict fuel ignition and oxidative stability ofmore » liquid hydrocarbons, while also providing insights relevant to the formation mechanisms of tropospheric aerosol building blocks. The direct observation of highly oxygenated intermediates for the autooxidation of alkanes at 500–600 K builds upon prior observations made in atmospheric conditions for the autooxidation of terpenes and other unsaturated hydrocarbons; it shows that highly oxygenated intermediates are stable at conditions above room temperature. These results further reveal that highly oxygenated intermediates are not only accessible by chemical activation but also by thermal activation. Theoretical calculations on H-atom migration reactions are presented to rationalize the relationship between the organic compound’s molecular structure (n-alkane, branched alkane, and cycloalkane) and its propensity to produce highly oxygenated intermediates via extensive autooxidation of hydroperoxyalkylperoxy radicals. In conclusion, detailed chemical kinetic simulations demonstrate the influence of these additional reaction pathways on the ignition of practical fuels.« less

Unraveling the structure and chemical mechanisms of highly oxygenated intermediates in oxidation of organic compounds

DOE PAGES

Wang, Zhandong; Popolan-Vaida, Denisia M.; Chen, Bingjie; ...

2017-11-28

Decades of research on the autooxidation of organic compounds have provided fundamental and practical insights into these processes; however, the structure of many key autooxidation intermediates and the reactions leading to their formation still remain unclear. This work provides additional experimental evidence that highly oxygenated intermediates with one or more hydroperoxy groups are prevalent in the autooxidation of various oxygenated (e.g., alcohol, aldehyde, keto compounds, ether, and ester) and nonoxygenated (e.g., normal alkane, branched alkane, and cycloalkane) organic compounds. These findings improve our understanding of autooxidation reaction mechanisms that are routinely used to predict fuel ignition and oxidative stability ofmore » liquid hydrocarbons, while also providing insights relevant to the formation mechanisms of tropospheric aerosol building blocks. The direct observation of highly oxygenated intermediates for the autooxidation of alkanes at 500–600 K builds upon prior observations made in atmospheric conditions for the autooxidation of terpenes and other unsaturated hydrocarbons; it shows that highly oxygenated intermediates are stable at conditions above room temperature. These results further reveal that highly oxygenated intermediates are not only accessible by chemical activation but also by thermal activation. Theoretical calculations on H-atom migration reactions are presented to rationalize the relationship between the organic compound’s molecular structure (n-alkane, branched alkane, and cycloalkane) and its propensity to produce highly oxygenated intermediates via extensive autooxidation of hydroperoxyalkylperoxy radicals. In conclusion, detailed chemical kinetic simulations demonstrate the influence of these additional reaction pathways on the ignition of practical fuels.« less

Comparisons of switching characteristics between Ti/Al2O3/Pt and TiN/Al2O3/Pt RRAM devices with various compliance currents

NASA Astrophysics Data System (ADS)

Qi, Yanfei; Zhao, Ce Zhou; Liu, Chenguang; Fang, Yuxiao; He, Jiahuan; Luo, Tian; Yang, Li; Zhao, Chun

2018-04-01

In this study, the influence of the Ti and TiN top electrodes on the switching behaviors of the Al2O3/Pt resistive random access memory devices with various compliance currents (CCs, 1-15 mA) has been compared. Based on the similar statistical results of the resistive switching (RS) parameters such as V set/V reset, R HRS/R LRS (measured at 0.10 V) and resistance ratio with various CCs for both devices, the Ti/Al2O3/Pt device differs from the TiN/Al2O3/Pt device mainly in the forming process rather than in the following switching cycles. Apart from the initial isolated state, the Ti/Al2O3/Pt device has the initial intermediate state as well. In addition, its forming voltage is relatively lower. The conduction mechanisms of the ON and OFF state for both devices are demonstrated as ohmic conduction and Frenkel-Poole emission, respectively. Therefore, with the combined modulations of the CCs and the stop voltages, the TiN/Al2O3/Pt device is more stable for nonvolatile memory applications to further improve the RS performance.

Forming Rb(+) snowballs in the center of He nanodroplets.

PubMed

Theisen, Moritz; Lackner, Florian; Ernst, Wolfgang E

2010-12-07

Helium nanodroplets doped with rubidium atoms are ionized by applying a resonant two-step ionization scheme. Subsequent immersion of rubidium ions is observed in time-of-flight mass spectra. While alkali-metal atoms usually desorb from the surface of a helium nanodroplet upon electronic excitation, rubidium in its excited 5(2)P(1/2) state provides an exception from this rule (Auböck et al., Phys. Rev. Lett., 2008, 101, 35301). In our new experiment, Rb atoms are selectively excited either to the 5(2)P(1/2) or to the 5(2)P(3/2) state. From there they are ionized by a laser pulse. Time-of-flight mass spectra of the ionization products reveal that the intermediate population of the 5(2)P(1/2) state does not only make the ionization process Rb-monomer selective, but also gives rise to a very high yield of Rb(+)-He(N) complexes. Ions with masses of up to several thousand amu have been monitored, which can be explained by an immersion of the single Rb ion into the He nanodroplet, where most likely a snowball is formed in the center of the He nanodroplet. As the most stable position for an ion is in the center of a He nanodroplet, our results agree well with theory.

Ab initio simulations of water splitting on hematite

NASA Astrophysics Data System (ADS)

Seriani, Nicola

2017-11-01

In recent years, hematite has attracted great interest as a photocatalyst for water splitting, but many questions remain unanswered about the mechanisms and the main limiting factors. For this reason, density functional theory has been used to understand the optical, electronic and chemical properties of this material at an atomistic level. Bulk doping can be used to reduce the band gap, and to increase photoabsorption and charge mobility. Charge transport takes place through adiabatic polaron hopping. The stable (0 0 0 1) surface has a stoichiometric termination when exposed to oxygen, it becomes hydroxylated in water, and it has an oxygen-rich termination under illumination in a photoelectrochemical setup. On the oxygen-rich termination, surface states are present that might act as recombination centres for electrons and holes. On the contrary, on the hydroxylated termination surface states appear only on reaction intermediates. The intrinsic surface states disappear in the presence of an overlayer of gallium oxide. The reaction of water oxidation is assumed to proceed by four proton-coupled electron transfers and it is shown to involve a nucleophilic attack with the formation of an OOH group. Calculated overpotentials are in the range of 0.5-0.6 V. Open questions and future research directions are briefly discussed.

Contour integration impairment in schizophrenia and first episode psychosis: state or trait?

PubMed

Feigenson, Keith A; Keane, Brian P; Roché, Matthew W; Silverstein, Steven M

2014-11-01

Contour integration is a fundamental visual process that recovers object structure by representing spatially separated edge elements as a continuous contour or shape boundary. Clinically stable persons with schizophrenia have repeatedly been shown to be impaired at contour integration but it is unclear whether this process varies with clinical state or whether it arises as early as the first episode of psychosis. To consider these issues, we administered a contour integration test to persons with chronic schizophrenia and to those with a first episode of psychosis. The test was administered twice-once at admission to short term psychiatric hospitalization and once again at discharge. A well-matched healthy control group was also tested across the same time points. We found that contour integration performance improved to the same degree in all groups over time, indicating that there were no recovery effects over and above normal practice effects. Moreover, the schizophrenia group demonstrated poorer contour integration than the control group and the first episode group exhibited intermediate performance that could not be distinguished from the other groups. These results suggest that contour integration ability does not vary as a function of short-term changes in clinical state, and that it may become further impaired with an increased number of psychotic episodes. Copyright © 2014 Elsevier B.V. All rights reserved.

Generalized Stone-Wales transformation as the possible origin of ferromagnetism in polymeric C60: a density-functional theory study.

PubMed

Ribas-Ariño, J; Novoa, Juan J

2006-11-07

Recently, there has been a proposal [Y.-H. Kim et al., Phys. Rev. B 68, 125420 (2003)] suggesting that ferromagnetic interactions in compressed and heated polymeric-C(60) solids could be due to the existence of triplet open cages resulting from successive generalized Stone-Wales transformations within the C(60) cage. Here, by performing B3LYP3-21G and B3LYP6-31G(d) optimizations, we carried out a systematic investigation of the thermodynamics and kinetics of the mechanism of generation of these open cages in their closed-shell singlet, open-shell singlet, and triplet states. We also computed the magnetic interactions induced by the open cages presenting a triplet ground state. Our results indicate that this mechanism is not appropriate to explain the ferromagnetism found in compressed and heated polymeric C(60) for the following reasons: (a) the formation of the only open cage presenting a triplet ground state requires overpassing a highest energy point of 318 kcal/mol, well above other competitive mechanisms reported in the literature; the triplet open cages formed are not stable against their transformation into a diamagnetic intermediate; (c) the magnetic interactions between two adjacent triplet open cages are antiferromagnetic.

Porphyrinoids as a platform of stable radicals

PubMed Central

Shimizu, Daiki

2018-01-01

The non-innocent ligand nature of porphyrins was observed for compound I in enzymatic cycles of cytochrome P450. Such porphyrin radicals were first regarded as reactive intermediates in catabolism, but recent studies have revealed that porphyrinoids, including porphyrins, ring-contracted porphyrins, and ring-expanded porphyrins, display excellent radical-stabilizing abilities to the extent that radicals can be handled like usual closed-shell organic molecules. This review surveys four types of stable porphyrinoid radical and covers their synthetic methods and properties such as excellent redox properties, NIR absorption, and magnetic properties. The radical-stabilizing abilities of porphyrinoids stem from their unique macrocyclic conjugated systems with high electronic and structural flexibilities. PMID:29675188

Video- Demonstrations of Stable and Unstable Solid Body Rotation on the International Space Station

NASA Technical Reports Server (NTRS)

2003-01-01

Saturday Morning Science, the science of opportunity series of applied experiments and demonstrations, performed aboard the International Space Station (ISS) by Expedition 6 astronaut Dr. Don Pettit, revealed some remarkable findings. In this video clip, Pettit demonstrates stable and unstable modes for solid body rotation on the ISS. Using a hard cover textbook, he demonstrates that it will rotate stably about the longest and shortest axis, which represent the maximum and minimum movements of Inertia. Trying to rotate the book around an intermediate axis results in an unstable rotation in which the book appears to flip-flop while it rotates.

Mechanistic Significance of the Si–O–Pd Bond in the Palladium-Catalyzed Cross-Coupling Reactions of Arylsilanolates

PubMed Central

2016-01-01

Through the combination of reaction kinetics (both stoichiometric and catalytic), solution- and solid-state characterization of arylpalladium(II) arylsilanolates, and computational analysis, the intermediacy of covalent adducts containing Si–O–Pd linkages in the cross-coupling reactions of arylsilanolates has been unambiguously established. Two mechanistically distinct pathways have been demonstrated: (1) transmetalation via a neutral 8-Si-4 intermediate that dominates in the absence of free silanolate (i.e., stoichiometric reactions of arylpalladium(II) arylsilanolate complexes), and (2) transmetalation via an anionic 10-Si-5 intermediate that dominates in the cross-coupling under catalytic conditions (i.e., in the presence of free silanolate). Arylpalladium(II) arylsilanolate complexes bearing various phosphine ligands have been isolated, fully characterized, and evaluated for their kinetic competence under thermal (stoichiometric) and anionic (catalytic) conditions. Comparison of the rates for thermal and anionic activation suggested, but did not prove, that intermediates containing the Si–O–Pd linkage were involved in the cross-coupling process. The isolation of a coordinatively unsaturated, T-shaped arylpalladium(II) arylsilanolate complex ligated with t-Bu3P allowed the unambiguous demonstration of the operation of both pathways involving 8-Si-4 and 10-Si-5 intermediates. Three kinetic regimes were identified: (1) with 0.5–1.0 equiv of added silanolate (with respect to arylpalladium bromide), thermal transmetalation via a neutral 8-Si-4 intermediate; (2) with 1.0–5.0 equiv of added silanolate, activated transmetalation via an anionic 10-Si-5 intermediate; and (3) with >5.0 equiv of added silanolate, concentration-independent (saturation) activated transmetalation via an anionic 10-Si-5 intermediate. Transition states for the intramolecular transmetalation of neutral (8-Si-4) and anionic (10-Si-5) intermediates have been located computationally, and the anionic pathway is favored by 1.8 kcal/mol. The energies of all intermediates and transition states are highly dependent on the configuration around the palladium atom. PMID:25945516

Snapshots of a solid-state transformation: coexistence of three phases trapped in one crystal

DOE PAGES

Aromí, G.; Beavers, C. M.; Sánchez Costa, J.; ...

2016-01-05

Crystal-to-crystal transformations have been crucial in the understanding of solid-state processes, since these may be studied in detail by means of single crystal X-ray diffraction (SCXRD) techniques. The description of the mechanisms and potential intermediates of those processes remains very challenging. In fact, solid-state transient states have rarely been observed, at least to a sufficient level of detail. We have investigated the process of guest extrusion from the non-porous molecular material [Fe(bpp)(H 2L)](ClO 4) 2·1.5C 3H 6O (bpp = 2,6-bis(pyrazol-3-yl)pyridine; H 2L = 2,6-bis(5-(2-methoxyphenyl)-pyrazol-3-yl)pyridine; C 3H 6O = acetone), which occurs through ordered diffusion of acetone in a crystal-to-crystal manner,more » leading to dramatic structural changes. The slow kinetics of the transition allows thermal trapping of the system at various intermediate stages. The transiting single crystal can be then examined at these points through synchrotron SCXRD, offering a window upon the mechanism of the transformation at the molecular scale. These experiments have unveiled the development of an ordered intermediate phase, distinct from the initial and the final states, coexisting as the process advances with either of these two phases or, at a certain moment with both of them. The new intermediate phase has been structurally characterized in full detail by SCXRD, providing insights into the mechanism of this diffusion triggered solid-state phenomenon. Lastly, the process has been also followed by calorimetry, optical microscopy, local Raman spectroscopy and powder X-ray diffraction. The discovery and description of an intermediate ordered state in a molecular solid-state transformation is of great interest and will help to understand the mechanistic details and reaction pathways underlying these transformations.« less

Ligand Docking to Intermediate and Close-To-Bound Conformers Generated by an Elastic Network Model Based Algorithm for Highly Flexible Proteins

PubMed Central

Kurkcuoglu, Zeynep; Doruker, Pemra

2016-01-01

Incorporating receptor flexibility in small ligand-protein docking still poses a challenge for proteins undergoing large conformational changes. In the absence of bound structures, sampling conformers that are accessible by apo state may facilitate docking and drug design studies. For this aim, we developed an unbiased conformational search algorithm, by integrating global modes from elastic network model, clustering and energy minimization with implicit solvation. Our dataset consists of five diverse proteins with apo to complex RMSDs 4.7–15 Å. Applying this iterative algorithm on apo structures, conformers close to the bound-state (RMSD 1.4–3.8 Å), as well as the intermediate states were generated. Dockings to a sequence of conformers consisting of a closed structure and its “parents” up to the apo were performed to compare binding poses on different states of the receptor. For two periplasmic binding proteins and biotin carboxylase that exhibit hinge-type closure of two dynamics domains, the best pose was obtained for the conformer closest to the bound structure (ligand RMSDs 1.5–2 Å). In contrast, the best pose for adenylate kinase corresponded to an intermediate state with partially closed LID domain and open NMP domain, in line with recent studies (ligand RMSD 2.9 Å). The docking of a helical peptide to calmodulin was the most challenging case due to the complexity of its 15 Å transition, for which a two-stage procedure was necessary. The technique was first applied on the extended calmodulin to generate intermediate conformers; then peptide docking and a second generation stage on the complex were performed, which in turn yielded a final peptide RMSD of 2.9 Å. Our algorithm is effective in producing conformational states based on the apo state. This study underlines the importance of such intermediate states for ligand docking to proteins undergoing large transitions. PMID:27348230

S-acylation of SOD1, CCS, and a stable SOD1-CCS heterodimer in human spinal cords from ALS and non-ALS subjects.

PubMed

Antinone, Sarah E; Ghadge, Ghanashyam D; Ostrow, Lyle W; Roos, Raymond P; Green, William N

2017-01-25

Previously, we found that human Cu, Zn-superoxide dismutase (SOD1) is S-acylated (palmitoylated) in vitro and in amyotrophic lateral sclerosis (ALS) mouse models, and that S-acylation increased for ALS-causing SOD1 mutants relative to wild type. Here, we use the acyl resin-assisted capture (acyl-RAC) assay to demonstrate S-acylation of SOD1 in human post-mortem spinal cord homogenates from ALS and non-ALS subjects. Acyl-RAC further revealed that endogenous copper chaperone for SOD1 (CCS) is S-acylated in both human and mouse spinal cords, and in vitro in HEK293 cells. SOD1 and CCS formed a highly stable heterodimer in human spinal cord homogenates that was resistant to dissociation by boiling, denaturants, or reducing agents and was not observed in vitro unless both SOD1 and CCS were overexpressed. Cysteine mutations that attenuate SOD1 maturation prevented the SOD1-CCS heterodimer formation. The degree of S-acylation was highest for SOD1-CCS heterodimers, intermediate for CCS monomers, and lowest for SOD1 monomers. Given that S-acylation facilitates anchoring of soluble proteins to cell membranes, our findings suggest that S-acylation and membrane localization may play an important role in CCS-mediated SOD1 maturation. Furthermore, the highly stable S-acylated SOD1-CCS heterodimer may serve as a long-lived maturation intermediate in human spinal cord.

S-acylation of SOD1, CCS, and a stable SOD1-CCS heterodimer in human spinal cords from ALS and non-ALS subjects

PubMed Central

Antinone, Sarah E.; Ghadge, Ghanashyam D.; Ostrow, Lyle W.; Roos, Raymond P.; Green, William N.

2017-01-01

Previously, we found that human Cu, Zn-superoxide dismutase (SOD1) is S-acylated (palmitoylated) in vitro and in amyotrophic lateral sclerosis (ALS) mouse models, and that S-acylation increased for ALS-causing SOD1 mutants relative to wild type. Here, we use the acyl resin-assisted capture (acyl-RAC) assay to demonstrate S-acylation of SOD1 in human post-mortem spinal cord homogenates from ALS and non-ALS subjects. Acyl-RAC further revealed that endogenous copper chaperone for SOD1 (CCS) is S-acylated in both human and mouse spinal cords, and in vitro in HEK293 cells. SOD1 and CCS formed a highly stable heterodimer in human spinal cord homogenates that was resistant to dissociation by boiling, denaturants, or reducing agents and was not observed in vitro unless both SOD1 and CCS were overexpressed. Cysteine mutations that attenuate SOD1 maturation prevented the SOD1-CCS heterodimer formation. The degree of S-acylation was highest for SOD1-CCS heterodimers, intermediate for CCS monomers, and lowest for SOD1 monomers. Given that S-acylation facilitates anchoring of soluble proteins to cell membranes, our findings suggest that S-acylation and membrane localization may play an important role in CCS-mediated SOD1 maturation. Furthermore, the highly stable S-acylated SOD1-CCS heterodimer may serve as a long-lived maturation intermediate in human spinal cord. PMID:28120938

An integrated analysis of social stress in laying hens: The interaction between physiology, behaviour, and hierarchy.

PubMed

Carvalho, Renata Rezende; Palme, Rupert; da Silva Vasconcellos, Angélica

2018-04-01

Livestock is the category of animals that suffers the most severe welfare problems. Among these, physical, physiological, and behavioural distress caused by artificial grouping are some of the challenges faced by these animals. Groups whose members are frequently changed have been reported as socially unstable, which could jeopardise the welfare of animals. Here, we assessed the effect of social instability on aggression, stress, and productivity in groups of laying hens (Gallus gallus domesticus). We studied 36 females, distributed into three stable groups (without group membership change) and three unstable groups (where the dominant member was rotated every week) over the course of 10 weeks. We evaluated the frequency of agonistic interactions, glucocorticoid metabolites (GCM) concentrations, and egg production. In both treatments, dominant hens produced more eggs compared to intermediate and subordinates, and intermediate hens had the highest GCM concentrations. Socially unstable groups had lower productivity and higher frequencies of agonistic interactions than stable groups. Social instability also affected GCM of the animals: in stable groups, subordinate hens had higher concentrations than dominants; in unstable groups, this pattern was reversed. Our results point to a social destabilisation in groups whose members were alternated, and suggest the welfare of individuals in unstable groups was compromised. Our results pointed to a complex relationship between hierarchy, productivity, physiological stress and aggression in laying hens, and have implications for their husbandry and management and, consequently, for their welfare levels. Copyright © 2018 Elsevier B.V. All rights reserved.

Unfolding Kinetics of β-Lactoglobulin Induced by Surfactant and Denaturant: A Stopped-Flow/Fluorescence Study

PubMed Central

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

2007-01-01

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

High-level QM/MM calculations support the concerted mechanism for Michael addition and covalent complex formation in thymidylate synthase.

PubMed

Kaiyawet, Nopporn; Lonsdale, Richard; Rungrotmongkol, Thanyada; Mulholland, Adrian J; Hannongbua, Supot

2015-02-10

Thymidylate synthase (TS) is a promising cancer target, due to its crucial function in thymine synthesis. It performs the reductive methylation of 2'-deoxyuridine-5'-phosphate (dUMP) to thymidine-5'-phosphate (dTMP), using N-5,10-methylene-5,6,7,8-tetrahydrofolate (mTHF) as a cofactor. After the formation of the dUMP/mTHF/TS noncovalent complex, and subsequent conformational activation, this complex has been proposed to react via nucleophilic attack (Michael addition) by Cys146, followed by methylene-bridge formation to generate the ternary covalent intermediate. Herein, QM/MM (B3LYP-D/6-31+G(d)-CHARMM27) methods are used to model the formation of the ternary covalent intermediate. A two-dimensional potential energy surface reveals that the methylene-bridged intermediate is formed via a concerted mechanism, as indicated by a single transition state on the minimum energy pathway and the absence of a stable enolate intermediate. A range of different QM methods (B3LYP, MP2 and SCS-MP2, and different basis sets) are tested for the calculation of the activation energy barrier for the formation of the methylene-bridged intermediate. We test convergence of the QM/MM results with respect to size of the QM region. Inclusion of Arg166, which interacts with the nucleophilic thiolate, in the QM region is important for reliable results; the MM model apparently does not reproduce energies for distortion of the guanidinium side chain correctly. The spin component scaled-Møller-Plessett perturbation theory (SCS-MP2) approach was shown to be in best agreement (within 1.1 kcal/mol) while the results obtained with MP2 and B3LYP also yielded acceptable values (deviating by less than 3 kcal/mol) compared with the barrier derived from experiment. Our results indicate that using a dispersion-corrected DFT method, or a QM method with an accurate treatment of electron correlation, increases the agreement between the calculated and experimental activation energy barriers, compared with the semiempirical AM1 method. These calculations provide important insight into the reaction mechanism of TS and may be useful in the design of new TS inhibitors.

Unfolding and melting of DNA (RNA) hairpins: the concept of structure-specific 2D dynamic landscapes.

PubMed

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

2008-08-07

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

Analysis of steady-state flow and advective transport in the eastern Snake River Plain aquifer system, Idaho

USGS Publications Warehouse

Ackerman, D.J.

1995-01-01

Quantitative estimates of ground-water flow directions and traveltimes for advective flow were developed for the regional aquifer system of the eastern Snake River Plain, Idaho. The work included: (1) descriptions of compartments in the aquifer that function as intermediate and regional flow systems, (2) descriptions of pathlines for flow originating at or near the water table, and (3) quantitative estimates of traveltimes for advective transport originating at or near the water table. A particle-tracking postprocessing program was used to compute pathlines on the basis of output from an existing three-dimensional steady-state flow model. The flow model uses 1980 conditions to approximate average annual conditions for 1950-80. The advective transport model required additional information about the nature of flow across model boundaries, aquifer thickness, and porosity. Porosity of two types of basalt strata has been reported for more than 1,500 individual cores from test holes, wells, and outcrops near the south side of the Idaho National Engineering Laboratory. The central 80 percent of samples had porosities of 0.08 to 0.25, the central 50 percent of samples, O. 11 to 0.21. Calibration of the model involved choosing a value for porosity that yielded the best solution. Two radiologic contaminants, iodine-129 and tritium, both introduced to the flow system about 40 years ago, are relatively conservative tracers. Iodine- 129 was considered to be more useful because of a lower analytical detection limit, longer half-life, and longer flow path. The calibration value for porosity was 0.21. Most flow in the aquifer is contained within a regional-scale compartment and follows paths that discharge to the Snake River downstream from Milner Dam. Two intermediate-scale compartments exist along the southeast side of the aquifer and near Mud Lake.One intermediate-scale compartment along the southeast side of the aquifer discharges to the Snake River near American Fails Reservoir and covers an area of nearly 1,000 square miles. This compartment, which receives recharge from an area of intensive surface-water irrigation, is apparently fairly stable. The other intermediate-scale compartment near Mud Lake covers an area of 300 square miles. The stability and size of this compartment are uncertain, but are assumed to be in a state of change. Traveltimes for advective flow from the water table to discharge points in the regional compartment ranged from 12 to 350 years for 80 percent of the particles; in the intermediate-scale flow compartment near American Falls Reservoir, from 7 to 60 years for 80 percent of the particles; and in the intermediate-scale compartment near Mud Lake, from 25 to 100 years for 80 percent of the particles. Traveltimes are sensitive to porosity and assumptions regarding the importance of the strength of internal sinks, which represent ground-water pumpage. A decrease in porosity results in shorter traveltimes but not a uniform decrease in traveltime, because the porosity and thickness is different in each model layer. Most flow was horizontal and occurred in the top 500 feet of the aquifer. An important limitation of the model is the assumption of steady-state flow. The most recent trend in the flow system has been a decrease in recharge since 1987 because of an extended drought and changes in land use. A decrease in flow through the system will result in longer traveltimes than those predicted for a greater flow. Because the interpretation of the model was limited to flow on a larger scale, and did not consider individual wells or well fields, the interpretations were not seriously limited by the discretization of well discharge. The interpretations made from this model also were limited by the discretization of the major discharge areas. Near discharge areas, pathlines might not be representative at the resolution of the grid. Most improvement in the estimates of ground-waterflow directions and travelt

A Study of the Curricular Organization of Intermediate Sciences in a County in New York State

ERIC Educational Resources Information Center

Nettuno, Thomas

2012-01-01

This study of a County in New York State gathered information about the means for teaching the intermediate science curriculum in middle schools. The study collected 43 surveys and conducted ten follow-up interviews with administrators responsible for curriculum. Data included the division of content among grade level, starting grade level,…

42 CFR 456.401 - State plan UR requirements and options; UR plan required for intermediate care facility services.

Code of Federal Regulations, 2011 CFR

2011-10-01

... 42 Public Health 4 2011-10-01 2011-10-01 false State plan UR requirements and options; UR plan required for intermediate care facility services. 456.401 Section 456.401 Public Health CENTERS FOR MEDICARE & MEDICAID SERVICES, DEPARTMENT OF HEALTH AND HUMAN SERVICES (CONTINUED) MEDICAL ASSISTANCE PROGRAMS UTILIZATION CONTROL Utilization Control:...

42 CFR 456.401 - State plan UR requirements and options; UR plan required for intermediate care facility services.

Code of Federal Regulations, 2014 CFR

2014-10-01

... 42 Public Health 4 2014-10-01 2014-10-01 false State plan UR requirements and options; UR plan required for intermediate care facility services. 456.401 Section 456.401 Public Health CENTERS FOR MEDICARE & MEDICAID SERVICES, DEPARTMENT OF HEALTH AND HUMAN SERVICES (CONTINUED) MEDICAL ASSISTANCE PROGRAMS UTILIZATION CONTROL Utilization Control:...

Serial Femtosecond Crystallography and Ultrafast Absorption Spectroscopy of the Photoswitchable Fluorescent Protein IrisFP.

PubMed

Colletier, Jacques-Philippe; Sliwa, Michel; Gallat, François-Xavier; Sugahara, Michihiro; Guillon, Virginia; Schirò, Giorgio; Coquelle, Nicolas; Woodhouse, Joyce; Roux, Laure; Gotthard, Guillaume; Royant, Antoine; Uriarte, Lucas Martinez; Ruckebusch, Cyril; Joti, Yasumasa; Byrdin, Martin; Mizohata, Eiichi; Nango, Eriko; Tanaka, Tomoyuki; Tono, Kensuke; Yabashi, Makina; Adam, Virgile; Cammarata, Marco; Schlichting, Ilme; Bourgeois, Dominique; Weik, Martin

2016-03-03

Reversibly photoswitchable fluorescent proteins find growing applications in cell biology, yet mechanistic details, in particular on the ultrafast photochemical time scale, remain unknown. We employed time-resolved pump-probe absorption spectroscopy on the reversibly photoswitchable fluorescent protein IrisFP in solution to study photoswitching from the nonfluorescent (off) to the fluorescent (on) state. Evidence is provided for the existence of several intermediate states on the pico- and microsecond time scales that are attributed to chromophore isomerization and proton transfer, respectively. Kinetic modeling favors a sequential mechanism with the existence of two excited state intermediates with lifetimes of 2 and 15 ps, the second of which controls the photoswitching quantum yield. In order to support that IrisFP is suited for time-resolved experiments aiming at a structural characterization of these ps intermediates, we used serial femtosecond crystallography at an X-ray free electron laser and solved the structure of IrisFP in its on state. Sample consumption was minimized by embedding crystals in mineral grease, in which they remain photoswitchable. Our spectroscopic and structural results pave the way for time-resolved serial femtosecond crystallography aiming at characterizing the structure of ultrafast intermediates in reversibly photoswitchable fluorescent proteins.

Bifunctionality of the thiamin diphosphate cofactor: assignment of tautomeric/ionization states of the 4′-aminopyrimidine ring when various intermediates occupy the active sites during the catalysis of yeast pyruvate decarboxylase

PubMed Central

Balakrishnan, Anand; Gao, Yuhong; Moorjani, Prerna; Nemeria, Natalia S.; Tittmann, Kai; Jordan, Frank

2012-01-01

Thiamin diphosphate (ThDP) dependent enzymes perform crucial C-C bond forming and breaking reactions in sugar and amino acid metabolism and in biosynthetic pathways via a sequence of ThDP-bound covalent intermediates. A member of this superfamily, yeast pyruvate decarboxylase (YPDC) carries out the non-oxidative decarboxylation of pyruvate and is mechanistically a simpler ThDP enzyme. YPDC variants created by substitution at the active center (D28A, E51X, E477Q) and on the substrate activation pathway (E91D and C221E) display varying activity, suggesting that they stabilize different covalent intermediates. To test the role of both rings of ThDP in YPDC catalysis (the 4′-aminopyrimidine as acid-base, and thiazolium as electrophilic covalent catalyst), we applied a combination of steady state and time-resolved circular dichroism experiments (assessing the state of ionization and tautomerization of enzyme-bound ThDP-related intermediates), and chemical quench of enzymatic reaction mixtures followed by NMR characterization of the ThDP-bound intermediates released from YPDC (assessing occupancy of active centers by these intermediates and rate-limiting steps). Results suggest that: (1) Pyruvate and analogs induce active site asymmetry in YPDC and variants. (2) The rare 1′,4′-iminopyrimidine ThDP tautomer participates in formation of ThDP-bound intermediates. (3) Propionylphosphinate also binds at the regulatory site and its binding is reflected by catalytic events at the active site 20Å away. (4) YPDC stabilizes an electrostatic model for the 4′-aminopyrimidinium ionization state, an important contribution of the protein to catalysis. The combination of tools used provides time-resolved details about individual events during ThDP catalysis; the methods are transferable to other ThDP superfamily members. PMID:22300533

Assessing the Comparative Effectiveness of Teaching Undergraduate Intermediate Accounting in the Online Classroom Format

ERIC Educational Resources Information Center

Rich, Anne J.; Dereshiwsky, Mary I.

2011-01-01

This paper presents the results of a study assessing the comparative effectiveness of teaching an undergraduate intermediate accounting course in the online classroom format. Students in a large state university were offered an opportunity to complete the first course in intermediate accounting either online or on-campus. Students were required to…

19. VIEW SOUTHWEST OF INTERMEDIATE VERTICAL PENNSYLVANIA PETIT TRUSS WITH ...

Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

19. VIEW SOUTHWEST OF INTERMEDIATE VERTICAL PENNSYLVANIA PETIT TRUSS WITH CASTLE ROCK IN BACKGROUND. JUNCTION OF INTERMEDIATE VERTICAL AND TOP CHORD WITH STABILIZING LATERAL STRUT ABOVE AND SWAY STRUT BELOW. ORIGINAL PAIRED DIAGONAL EYE BARS LATER REINFORCED WITH TIE ROD - New River Bridge, Spanning New River at State Route 623, Pembroke, Giles County, VA

Structural analysis of kinetic folding intermediates for a TIM barrel protein, indole-3-glycerol phosphate synthase, by hydrogen exchange mass spectrometry and Gō-model simulation

PubMed Central

Gu, Zhenyu; Rao, Maithreyi K.; Forsyth, William R.

2009-01-01

The structures of partially-folded states appearing during the folding of a (βα)8 TIM barrel protein, the indole-3-glycerol phosphate synthase from S. solfataricus (sIGPS), was assessed by hydrogen exchange mass spectrometry (HX-MS) and Gō-model simulations. HX-MS analysis of the peptic peptides derived from the pulse-labeled product of the sub-millisecond folding reaction from the urea-denatured state revealed strong protection in the (βα)4 region, modest protection in the neighboring (βα)1–3 and (βα)5β6 segments and no significant protection in the remaining N- and C-terminal segments. These results demonstrate that this species is not a collapsed form of the unfolded state under native-favoring conditions nor is it the native state formed via fast-track folding. However, the striking contrast of these results with the strong protection observed in the (βα)2–5β6 region after 5 s of folding demonstrates that these species represent kinetically-distinct folding intermediates that are not identical as previously thought. A re-examination of the kinetic folding mechanism by chevron analysis of fluorescence data confirmed distinct roles for these two species: the burst-phase intermediate is predicted to be a misfolded, off-pathway intermediate while the subsequent 5 s intermediate corresponds to an on-pathway equilibrium intermediate. Comparison with the predictions using a Cα Gō-model simulation of the kinetic folding reaction for sIGPS shows good agreement with the core of structure offering protection against exchange in the on-pathway intermediate(s). Because the native-centric Gō-model simulations do not explicitly include sequence-specific information, the simulation results support the hypothesis that the topology of TIM barrel proteins is a primary determinant of the folding free energy surface for the productive folding reaction. The early misfolding reaction must involve aspects of non-native structure not detected by the Gō-model simulation. PMID:17942114

Quantitative analysis of autophagic flux by confocal pH-imaging of autophagic intermediates

PubMed Central

Maulucci, Giuseppe; Chiarpotto, Michela; Papi, Massimiliano; Samengo, Daniela; Pani, Giovambattista; De Spirito, Marco

2015-01-01

Although numerous techniques have been developed to monitor autophagy and to probe its cellular functions, these methods cannot evaluate in sufficient detail the autophagy process, and suffer limitations from complex experimental setups and/or systematic errors. Here we developed a method to image, contextually, the number and pH of autophagic intermediates by using the probe mRFP-GFP-LC3B as a ratiometric pH sensor. This information is expressed functionally by AIPD, the pH distribution of the number of autophagic intermediates per cell. AIPD analysis reveals how intermediates are characterized by a continuous pH distribution, in the range 4.5–6.5, and therefore can be described by a more complex set of states rather than the usual biphasic one (autophagosomes and autolysosomes). AIPD shape and amplitude are sensitive to alterations in the autophagy pathway induced by drugs or environmental states, and allow a quantitative estimation of autophagic flux by retrieving the concentrations of autophagic intermediates. PMID:26506895

Hydrophobic hydration driven self-assembly of curcumin in water: Similarities to nucleation and growth under large metastability, and an analysis of water dynamics at heterogeneous surfaces

NASA Astrophysics Data System (ADS)

Hazra, Milan Kumar; Roy, Susmita; Bagchi, Biman

2014-11-01

As the beneficial effects of curcumin have often been reported to be limited to its small concentrations, we have undertaken a study to find the aggregation properties of curcumin in water by varying the number of monomers. Our molecular dynamics simulation results show that the equilibrated structure is always an aggregated state with remarkable structural rearrangements as we vary the number of curcumin monomers from 4 to 16 monomers. We find that the curcumin monomers form clusters in a very definite pattern where they tend to aggregate both in parallel and anti-parallel orientation of the phenyl rings, often seen in the formation of β-sheet in proteins. A considerable enhancement in the population of parallel alignments is observed with increasing the system size from 12 to 16 curcumin monomers. Due to the prevalence of such parallel alignment for large system size, a more closely packed cluster is formed with maximum number of hydrophobic contacts. We also follow the pathway of cluster growth, in particular the transition from the initial segregated to the final aggregated state. We find the existence of a metastable structural intermediate involving a number of intermediate-sized clusters dispersed in the solution. We have constructed a free energy landscape of aggregation where the metatsable state has been identified. The course of aggregation bears similarity to nucleation and growth in highly metastable state. The final aggregated form remains stable with the total exclusion of water from its sequestered hydrophobic core. We also investigate water structure near the cluster surface along with their orientation. We find that water molecules form a distorted tetrahedral geometry in the 1st solvation layer of the cluster, interacting rather strongly with the hydrophilic groups at the surface of the curcumin. The dynamics of such quasi-bound water molecules near the surface of curcumin cluster is considerably slower than the bulk signifying a restricted motion as often found in protein hydration layer.

Relaxation mode analysis and Markov state relaxation mode analysis for chignolin in aqueous solution near a transition temperature

NASA Astrophysics Data System (ADS)

Mitsutake, Ayori; Takano, Hiroshi

2015-09-01

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

Unstable equilibrium behaviour in collapsible tubes.

PubMed

Bertram, C D

1986-01-01

Thick-walled silicone rubber tube connected to rigid pipes upstream and downstream was externally pressurised (pe) to cause collapse while aqueous fluid flowed through propelled by a constant upstream head. Three types of equilibrium were found: stable equilibria (steady flow) at high downstream flow resistance R2, self-excited oscillations at low R2, and 'unattainable' (by varying external pressure) or exponentially unstable equilibria at intermediate R2. The self-excited oscillations were highly non-linear and appeared in four, apparently discrete, frequency bands: 2.7 Hz, 3.8-5.0 Hz, 12-16 Hz and 60-63 Hz, suggesting that the possible oscillation modes may be harmonically related. Stable, intermediate 'two-in-every-three-beats' oscillation was also observed, with a repetition frequency in the 3.8-5.0 Hz band. As pe was increased, self-excited oscillations were eventually suppressed, leaving internal fluid pressure varying with no single dominant frequency as a result of turbulent jet dissipation at the downstream rigid pipe connection. Comparison of pressure-wave velocity calculated from the local pressure-area relation for the tube with fluid velocity indicated that supercritical velocities were attained in the course of the self-excited oscillations.

Unique fluorophores in the dimeric archaeal histones hMfB and hPyA1 reveal the impact of nonnative structure in a monomeric kinetic intermediate

PubMed Central

Stump, Matthew R.; Gloss, Lisa M.

2008-01-01

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

An unusual high-spin ground state of Co3+ in octahedral coordination in brownmillerite-type cobalt oxide.

PubMed

Istomin, S Ya; Tyablikov, O A; Kazakov, S M; Antipov, E V; Kurbakov, A I; Tsirlin, A A; Hollmann, N; Chin, Y Y; Lin, H-J; Chen, C T; Tanaka, A; Tjeng, L H; Hu, Z

2015-06-21

The crystal and magnetic structures of brownmillerite-like Sr(2)Co(1.2)Ga(0.8)O(5) with a stable Co(3+) oxidation state at both octahedral and tetrahedral sites are refined using neutron powder diffraction data collected at 2 K (S.G. Icmm, a = 5.6148(6) Å, b = 15.702(2) Å, c = 5.4543(6) Å; R(wp) = 0.0339, R(p) = 0.0443, χ(2) = 0.775). The very large tetragonal distortion of CoO(6) octahedra (1.9591(4) Å for Co-O(eq) and 2.257(6) Å for Co-O(ax)) could be beneficial for the stabilization of the long-sought intermediate-spin state of Co(3+) in perovskite-type oxides. However, the large magnetic moment of octahedral Co(3+) (3.82(7)μ(B)) indicates the conventional high-spin state of Co(3+) ions, which is further supported by the results of a combined theoretical and experimental soft X-ray absorption spectroscopy study at the Co-L(2,3) edges on Sr(2)Co(1.2)Ga(0.8)O(5). A high-spin ground state of Co(3+) in Sr(2)Co(1.2)Ga(0.8)O(5) resulted in much lower in comparison with a LaCoO(3) linear thermal expansion coefficient of 13.1 ppm K(-1) (298-1073 K) determined from high-temperature X-ray powder diffraction data collected in air.

Factors controlling soil organic carbon stability along a temperate forest altitudinal gradient

PubMed Central

Tian, Qiuxiang; He, Hongbo; Cheng, Weixin; Bai, Zhen; Wang, Yang; Zhang, Xudong

2016-01-01

Changes in soil organic carbon (SOC) stability may alter carbon release from the soil and, consequently, atmospheric CO2 concentration. The mean annual temperature (MAT) can change the soil physico-chemical characteristics and alter the quality and quantity of litter input into the soil that regulate SOC stability. However, the relationship between climate and SOC stability remains unclear. A 500-day incubation experiment was carried out on soils from an 11 °C-gradient mountainous system on Changbai Mountain in northeast China. Soil respiration during the incubation fitted well to a three-pool (labile, intermediate and stable) SOC decomposition model. A correlation analysis revealed that the MAT only influenced the labile carbon pool size and not the SOC stability. The intermediate carbon pool contributed dominantly to cumulative carbon release. The size of the intermediate pool was strongly related to the percentage of sand particle. The decomposition rate of the intermediate pool was negatively related to soil nitrogen availability. Because both soil texture and nitrogen availability are temperature independent, the stability of SOC was not associated with the MAT, but was heavily influenced by the intrinsic processes of SOC formation and the nutrient status. PMID:26733344

Dynein-ADP as a force-generating intermediate revealed by a rapid reactivation of flagellar axoneme.

PubMed Central

Tani, T; Kamimura, S

1999-01-01

Fragmented flagellar axonemes of sand dollar spermatozoa were reactivated by rapid photolysis of caged ATP. After a time lag of 10 ms, axonemes treated with protease started sliding disintegration. Axonemes without protease digestion started nanometer-scale high-frequency oscillation after a similar time lag. Force development in the sliding disintegration was measured with a flexible glass needle and its time course was corresponded well to that of the dynein-ADP intermediate production estimated using kinetic rates previously reported. However, with a high concentration ( approximately 80 microM) of vanadate, which binds to the dynein-ADP intermediate and forms a stable complex of dynein-ADP-vanadate, the time course of force development in sliding disintegration was not affected at all. In the case of high frequency oscillation, the time lag to start the oscillation, the initial amplitude, and the initial frequency were not affected by vanadate, though the oscillation once started was damped more quickly at higher concentrations of vanadate. These results suggest that during the initial turnover of ATP hydrolysis, force generation of dynein is not blocked by vanadate. A vanadate-insensitive dynein-ADP is postulated as a force-generating intermediate. PMID:10465762

Photoproduction of One-Electron Reducing Intermediates by Chromophoric Dissolved Organic Matter (CDOM): Relation to O2- and H2O2 Photoproduction and CDOM Photooxidation.

PubMed

Zhang, Yi; Blough, Neil V

2016-10-06

A molecular probe, 3-amino-2,2,5,5,-tetramethy-1-pyrrolydinyloxy (3ap), was employed to determine the formation rates of one-electron reducing intermediates generated photochemically from both untreated and borohydride-reduced Suwanee River fulvic and humic acids (SRFA and SRHA, respectively). This stable nitroxyl radical reacts rapidly with reducing radicals and other one-electron reductants to produce a relatively stable product, the hydroxylamine, which can be derivatized with fluorescamine, separated by HPLC and quantified fluorimetrically. We provide evidence that O 2 and 3ap compete for the same pool(s) of photoproduced reducing intermediates, and that under appropriate experimental conditions, the initial rate of hydroxylamine formation (R H ) can provide an estimate of the initial rate of superoxide (O 2 - ) formation. However, comparison of the initial rates of H 2 O 2 formation (R H2O2 ) to that of R H show far larger ratios of R H /R H2O2 (∼6-13) than be accounted for by simple O 2 - dismutation (R H /R H2O2 = 2), implying a significant oxidative sink of O 2 - (∼67-85%). Because of their high reactivity with O 2 - and their likely importance in the photochemistry of CDOM, we suggest that coproduced phenoxy radicals could represent a viable oxidative sink. Because O 2 - /phenoxy radical reactions can lead to more highly oxidized products, O 2 - could be playing a far more significant role in the photooxidation of CDOM than has been previously recognized.

Structure and Reactivity of a Thermostable Prokaryotic Nitric-oxide Synthase That Forms a Long-lived Oxy-Heme Complex

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

Sudhamsu,J.; Crane, B.

2006-01-01

In an effort to generate more stable reaction intermediates involved in substrate oxidation by nitric-oxide synthases (NOSs), we have cloned, expressed, and characterized a thermostable NOS homolog from the thermophilic bacterium Geobacillus stearothermophilus (gsNOS). As expected, gsNOS forms nitric oxide (NO) from L-arginine via the stable intermediate N-hydroxy L-arginine (NOHA). The addition of oxygen to ferrous gsNOS results in long-lived heme-oxy complexes in the presence (Soret peak 427 nm) and absence (Soret peak 413 nm) of substrates L-arginine and NOHA. The substrate-induced red shift correlates with hydrogen bonding between substrate and heme-bound oxygen resulting in conversion to a ferric heme-superoxymore » species. In single turnover experiments with NOHA, NO forms only in the presence of H4B. The crystal structure of gsNOS at 3.2 A Angstroms of resolution reveals great similarity to other known bacterial NOS structures, with the exception of differences in the distal heme pocket, close to the oxygen binding site. In particular, a Lys-356 (Bacillus subtilis NOS) to Arg-365 (gsNOS) substitution alters the conformation of a conserved Asp carboxylate, resulting in movement of an Ile residue toward the heme. Thus, a more constrained heme pocket may slow ligand dissociation and increase the lifetime of heme-bound oxygen to seconds at 4 degC. Similarly, the ferric-heme NO complex is also stabilized in gsNOS. The slow kinetics of gsNOS offer promise for studying downstream intermediates involved in substrate oxidation.« less

Deciphering excited state evolution in halorhodopsin with stimulated emission pumping.

PubMed

Bismuth, Oshrat; Komm, Pavel; Friedman, Noga; Eliash, Tamar; Sheves, Mordechai; Ruhman, Sanford

2010-03-04

The primary photochemical dynamics of Hb. pharaonis Halorhodopsin (pHR) are investigated by femtosecond visible pump-near IR dump-hyperspectral probe spectroscopy. The efficiency of excited state depletion is deduced from transient changes in absorption, recorded with and without stimulated emission pumping (SEP), as a function of the dump delay. The concomitant reduction of photocycle population is assessed by probing the "K" intermediate difference spectrum. Results show that the cross section for stimulating emission is nearly constant throughout the fluorescent state lifetime. Probing "K" demonstrates that dumping produces a proportionate reduction in photocycle yields. We conclude that, despite its nonexponential internal conversion (IC) kinetics, the fluorescent state in pHR constitutes a single intermediate in the photocycle. This contrasts with conclusions drawn from the study of primary events in the related chloride pump from Hb. salinarum (sHR), believed to produce the "K" intermediate from a distinct short-lived subpopulation in the excited state. Our discoveries concerning internal conversion dynamics in pHR are discussed in light of recent expectations for similar excited state dynamics in both proteins.

Attention doesn’t slide: spatiotopic updating after eye movements instantiates a new, discrete attentional locus

PubMed Central

Marino, Alexandria C.; Chun, Marvin M.

2011-01-01

During natural vision, eye movements can drastically alter the retinotopic (eye-centered) coordinates of locations and objects, yet the spatiotopic (world-centered) percept remains stable. Maintaining visuospatial attention in spatiotopic coordinates requires updating of attentional representations following each eye movement. However, this updating is not instantaneous; attentional facilitation temporarily lingers at the previous retinotopic location after a saccade, a phenomenon known as the retinotopic attentional trace. At various times after a saccade, we probed attention at an intermediate location between the retinotopic and spatiotopic locations to determine whether a single locus of attentional facilitation slides progressively from the previous retinotopic location to the appropriate spatiotopic location, or whether retinotopic facilitation decays while a new, independent spatiotopic locus concurrently becomes active. Facilitation at the intermediate location was not significant at any time, suggesting that top-down attention can result in enhancement of discrete retinotopic and spatiotopic locations without passing through intermediate locations. PMID:21258903

Biological Reactive Intermediates (BRIs) Formed from Botanical Dietary Supplements

PubMed Central

Dietz, Birgit M.; Bolton, Judy L.

2013-01-01

The use of botanical dietary supplements is increasingly popular, due to their natural origin and the perceived assumption that they are safer than prescription drugs. While most botanical dietary supplements can be considered safe, a few contain compounds, which can be converted to reactive biological reactive intermediates (BRIs) causing toxicity. For example, sassafras oil contains safrole, which can be converted to a reactive carbocation forming genotoxic DNA adducts. Alternatively, some botanical dietary supplements contain stable BRIs such as simple Michael acceptors that react with chemosensor proteins such as Keap1 resulting in induction of protective detoxification enzymes. Examples include curcumin from turmeric, xanthohumol from hops, and Z-ligustilide from dang gui. Quinones (sassafras, kava, black cohosh), quinone methides (sassafras), and epoxides (pennyroyal oil) represent BRIs of intermediate reactivity, which could generate both genotoxic and/or chemopreventive effects. The biological targets of BRIs formed from botanical dietary supplements and their resulting toxic and/or chemopreventive effects are closely linked to the reactivity of BRIs as well as dose and time of exposure. PMID:20970412

Lithium hydride doped intermediate connector for high-efficiency and long-term stable tandem organic light-emitting diodes.

PubMed

Ding, Lei; Tang, Xun; Xu, Mei-Feng; Shi, Xiao-Bo; Wang, Zhao-Kui; Liao, Liang-Sheng

2014-10-22

Lithium hydride (LiH) is employed as a novel n-dopant in the intermediate connector for tandem organic light-emitting diodes (OLEDs) because of its easy coevaporation with other electron transporting materials. The tandem OLEDs with two and three electroluminescent (EL) units connected by a combination of LiH doped 8-hydroxyquinoline aluminum (Alq3) and 1,4,5,8,9,11-hexaazatriphenylene-hexacarbonitrile (HAT-CN) demonstrate approximately 2-fold and 3-fold enhancement in current efficiency, respectively. In addition, no extra voltage drop across the intermediate connector is observed. Particularly, the lifetime (T75%) in the tandem OLED with two and three EL units is substantially improved by 3.8 times and 7.4 times, respectively. The doping effect of LiH into Alq3, the charge injection, and transport characteristics of LiH-doped Alq3 are further investigated by ultraviolet photoelectron spectroscopy (UPS) and X-ray photoemission spectroscopy (XPS).

From QCA (Quantum Cellular Automata) to Organocatalytic Reactions with Stabilized Carbenium Ions.

PubMed

Gualandi, Andrea; Mengozzi, Luca; Manoni, Elisabetta; Giorgio Cozzi, Pier

2016-06-01

What do quantum cellular automata (QCA), "on water" reactions, and SN 1-type organocatalytic transformations have in common? The link between these distant arguments is the practical access to useful intermediates and key products through the use of stabilized carbenium ions. Over 10 years, starting with a carbenium ion bearing a ferrocenyl group, to the 1,3-benzodithiolylium carbenium ion, our group has exploited the use of these intermediates in useful and practical synthetic transformations. In particular, we have applied the use of carbenium ions to stereoselective organocatalytic alkylation reactions, showing a possible solution for the "holy grail of organocatalysis". Examples of the use of these quite stabilized intermediates are now also considered in organometallic chemistry. On the other hand, the stable carbenium ions are also applied to tailored molecules adapted to quantum cellular automata, a new possible paradigm for computation. Carbenium ions are not a problem, they can be a/the solution! © 2016 The Chemical Society of Japan & Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Stereochemically probing the photo-Favorskii rearrangement: a mechanistic investigation.

PubMed

Givens, Richard S; Rubina, Marina; Stensrud, Kenneth F

2013-03-01

Using model (R)-2-acetyl-2-phenyl acetate esters of (S)- or (R)-α-substituted-p-hydroxybutyrophenones (S,R)-12a and (R,R)-12b, we have shown that a highly efficient photo-Favorskii rearrangement proceeds through a series of intermediates to form racemic rearrangement products. The stereogenic methine on the photoproduct, rac-2-(p-hydroxyphenyl)propanoic acid (rac-9), is formed by closure of a phenoxy-allyloxy intermediate 17 collapsing to a cyclopropanone, the "Favorskii" intermediate 18. These results quantify the intermediacy of a racemized triplet biradical (3)16 on the major rearrangement pathway elusively to the intermediate 18. Thus, intersystem crossing from the triplet biradical surface to the ground state generates a planar zwitterion prior to formation of a Favorskii cyclopropanone that retains no memory of its stereochemical origin. These results parallel the mechanism of Dewar and Bordwell for the ground state formation of cyclopropanone 3 that proceeds through an oxyallyl zwitterionic intermediate. The results are not consistent with the stereospecific S(N)2 ground state Favorskii mechanism observed by Stork, House, and Bernetti. Interconversion of the diastereomeric starting esters of (S,R)-12a and (R,R)-12b during photolysis did not occur, thus ruling out leaving group return prior to rearrangement.

Stereochemically Probing the photo-Favorskii Rearrangement: A Mechanistic Investigation

PubMed Central

Givens, Richard S.; Rubina, Marina; Stensrud, Kenneth F.

2012-01-01

Using model (R)-2-acetyl-2-phenyl acetate esters of (S)- or (R)-α-substituted-p-hydroxybutyrophenones (S,R)-12a and (R,R)-12b, we have shown that a highly efficient photo-Favorskii rearrangement proceeds through a series of intermediates to form racemic rearrangement products. The stereogenic methine on the photoproduct, rac-2-(p-hydroxyphenyl)propanoic acid (rac-9), is formed by closure of a phenoxy-allyloxy intermediate 17 collapsing to a cyclopropanone, the “Favorskii” intermediate 18. These results quantify the intermediacy of a racemized triplet biradical 316 on the major rearrangement pathway elusively to the intermediate 18. Thus, intersystem crossing from the triplet biradical surface to the ground state generates a planar zwitterion prior to formation of a Favorskii cyclopropanone that retains no memory of its stereochemical origin. These results parallel the mechanism of Dewar and Bordwell for the ground state formation of cyclopropanone 3 that proceed through an oxyallyl zwitterionic intermediate. The results are not consistent with the stereospecific SN2 ground state Favorskii mechanism observed by Stork, House, and Bernetti. Interconversion of the diastereomeric starting esters of (S,R)-12a and (R,R)-12b during photolysis did not occur thus ruling out leaving group return prior to rearrangement. PMID:23057737

Spectroscopic Characterization of the Water Oxidation Intermediates in the Blue Dimer Ru-Based Catalyst for Artificial Photosynthesis

NASA Astrophysics Data System (ADS)

Moonshiram, Dooshaye; Pushkar, Yulia; Jurss, Jonah; Concepcion, Javier; Meyer, Thomas; Zakharova, Taisiya; Alperovich, Igor

2012-02-01

Utilization of sunlight requires solar capture, light-to-energy conversion and storage. One effective way to store energy is to convert it into chemical energy by fuel-forming reactions, such as water splitting into hydrogen and oxygen. Ruthenium complexes are among few molecular-defined catalysts capable of water splitting. Mechanistic insights about such catalysts can be acquired by spectroscopic analysis of short-lived intermediates of catalytic water oxidation. Use of techniques such as EPR and X-ray absorption spectroscopy (XAS) are used to determine electronic requirements of catalytic water oxidation. About 30 years ago Meyer and coworkers reported first ruthenium-based catalyst for water oxidation, the ``blue dimer''. We performed EPR studies and characterized structures and electronic configurations of intermediates of water oxidation by the ``blue dimer''. Intermediates were prepared chemically by oxidation of Ru-complexes with defined number of Ce (IV) equivalents and freeze-quenched at controlled times. Changes in oxidation state of Ru atom were detected by XANES at Ru K-edges. K-edges are sensitive to changes in Ru oxidation state for Blue Dimer [3,3]^4+, [3,4]^4+, [3,4]'^4+ and [4,5]^3+ allowing a clear assignment of Ru oxidation state in intermediates. EXAFS demonstrated structural changes.

Structural and electronic properties of high pressure phases of lead chalcogenides

NASA Astrophysics Data System (ADS)

Petersen, John; Scolfaro, Luisa; Myers, Thomas

2012-10-01

Lead chalcogenides, most notably PbTe and PbSe, have become an active area of research due to their thermoelectric properties. The high figure of merit (ZT) of these materials has brought much attention to them, due to their ability to convert waste heat into electricity. Variation in synthesis conditions gives rise to a need for analysis of structural and thermoelectric properties of these materials at different pressures. In addition to the NaCl structure at ambient conditions, lead chalcogenides have a dynamic orthorhombic (Pnma) intermediate phase and a higher pressure yet stable CsCl phase. By altering the lattice constant, we simulate the application of external pressure; this has notable effects on ground state total energy, band gap, and structural phase. Using the General Gradient Approximation (GGA) in Density Functional Theory (DFT), we calculate the phase transition pressures by finding the differences in enthalpy from total energy calculations. For each phase, elastic constants, bulk modulus, shear modulus, Young's modulus, and hardness are calculated, using two different approaches. In addition to structural properties, we analyze the band structure and density of states at varying pressures, paying special note to thermoelectric implications.

Surprisal analysis characterizes the free energy time course of cancer cells undergoing epithelial-to-mesenchymal transition.

PubMed

Zadran, Sohila; Arumugam, Rameshkumar; Herschman, Harvey; Phelps, Michael E; Levine, R D

2014-09-09

The epithelial-to-mesenchymal transition (EMT) initiates the invasive and metastatic behavior of many epithelial cancers. Mechanisms underlying EMT are not fully known. Surprisal analysis of mRNA time course data from lung and pancreatic cancer cells stimulated to undergo TGF-β1-induced EMT identifies two phenotypes. Examination of the time course for these phenotypes reveals that EMT reprogramming is a multistep process characterized by initiation, maturation, and stabilization stages that correlate with changes in cell metabolism. Surprisal analysis characterizes the free energy time course of the expression levels throughout the transition in terms of two state variables. The landscape of the free energy changes during the EMT for the lung cancer cells shows a stable intermediate state. Existing data suggest this is the previously proposed maturation stage. Using a single-cell ATP assay, we demonstrate that the TGF-β1-induced EMT for lung cancer cells, particularly during the maturation stage, coincides with a metabolic shift resulting in increased cytosolic ATP levels. Surprisal analysis also characterizes the absolute expression levels of the mRNAs and thereby examines the homeostasis of the transcription system during EMT.

Quantum Kramers model: Corrections to the linear response theory for continuous bath spectrum

NASA Astrophysics Data System (ADS)

Rips, Ilya

2017-01-01

Decay of the metastable state is analyzed within the quantum Kramers model in the weak-to-intermediate dissipation regime. The decay kinetics in this regime is determined by energy exchange between the unstable mode and the stable modes of thermal bath. In our previous paper [Phys. Rev. A 42, 4427 (1990), 10.1103/PhysRevA.42.4427], Grabert's perturbative approach to well dynamics in the case of the discrete bath [Phys. Rev. Lett. 61, 1683 (1988), 10.1103/PhysRevLett.61.1683] has been extended to account for the second order terms in the classical equations of motion (EOM) for the stable modes. Account of the secular terms reduces EOM for the stable modes to those of the forced oscillator with the time-dependent frequency (TDF oscillator). Analytic expression for the characteristic function of energy loss of the unstable mode has been derived in terms of the generating function of the transition probabilities for the quantum forced TDF oscillator. In this paper, the approach is further developed and applied to the case of the continuous frequency spectrum of the bath. The spectral density functions of the bath of stable modes are expressed in terms of the dissipative properties (the friction function) of the original bath. They simplify considerably for the one-dimensional systems, when the density of phonon states is constant. Explicit expressions for the fourth order corrections to the linear response theory result for the characteristic function of the energy loss and its cumulants are obtained for the particular case of the cubic potential with Ohmic (Markovian) dissipation. The range of validity of the perturbative approach in this case is determined (γ /ωb<0.26 ), which includes the turnover region. The dominant correction to the linear response theory result is associated with the "work function" and leads to reduction of the average energy loss and its dispersion. This reduction increases with the increasing dissipation strength (up to ˜10 % ) within the range of validity of the approach. We have also calculated corrections to the depopulation factor and the escape rate for the quantum and for the classical Kramers models. Results for the classical escape rate are in very good agreement with the numerical simulations for high barriers. The results can serve as an additional proof of the robustness and accuracy of the linear response theory.

Quantum Kramers model: Corrections to the linear response theory for continuous bath spectrum.

PubMed

Rips, Ilya

2017-01-01

Decay of the metastable state is analyzed within the quantum Kramers model in the weak-to-intermediate dissipation regime. The decay kinetics in this regime is determined by energy exchange between the unstable mode and the stable modes of thermal bath. In our previous paper [Phys. Rev. A 42, 4427 (1990)PLRAAN1050-294710.1103/PhysRevA.42.4427], Grabert's perturbative approach to well dynamics in the case of the discrete bath [Phys. Rev. Lett. 61, 1683 (1988)PRLTAO0031-900710.1103/PhysRevLett.61.1683] has been extended to account for the second order terms in the classical equations of motion (EOM) for the stable modes. Account of the secular terms reduces EOM for the stable modes to those of the forced oscillator with the time-dependent frequency (TDF oscillator). Analytic expression for the characteristic function of energy loss of the unstable mode has been derived in terms of the generating function of the transition probabilities for the quantum forced TDF oscillator. In this paper, the approach is further developed and applied to the case of the continuous frequency spectrum of the bath. The spectral density functions of the bath of stable modes are expressed in terms of the dissipative properties (the friction function) of the original bath. They simplify considerably for the one-dimensional systems, when the density of phonon states is constant. Explicit expressions for the fourth order corrections to the linear response theory result for the characteristic function of the energy loss and its cumulants are obtained for the particular case of the cubic potential with Ohmic (Markovian) dissipation. The range of validity of the perturbative approach in this case is determined (γ/ω_{b}<0.26), which includes the turnover region. The dominant correction to the linear response theory result is associated with the "work function" and leads to reduction of the average energy loss and its dispersion. This reduction increases with the increasing dissipation strength (up to ∼10%) within the range of validity of the approach. We have also calculated corrections to the depopulation factor and the escape rate for the quantum and for the classical Kramers models. Results for the classical escape rate are in very good agreement with the numerical simulations for high barriers. The results can serve as an additional proof of the robustness and accuracy of the linear response theory.

A World Malaria Map: Plasmodium falciparum Endemicity in 2007

PubMed Central

Hay, Simon I; Guerra, Carlos A; Gething, Peter W; Patil, Anand P; Tatem, Andrew J; Noor, Abdisalan M; Kabaria, Caroline W; Manh, Bui H; Elyazar, Iqbal R. F; Brooker, Simon; Smith, David L; Moyeed, Rana A; Snow, Robert W

2009-01-01

Background Efficient allocation of resources to intervene against malaria requires a detailed understanding of the contemporary spatial distribution of malaria risk. It is exactly 40 y since the last global map of malaria endemicity was published. This paper describes the generation of a new world map of Plasmodium falciparum malaria endemicity for the year 2007. Methods and Findings A total of 8,938 P. falciparum parasite rate (PfPR) surveys were identified using a variety of exhaustive search strategies. Of these, 7,953 passed strict data fidelity tests for inclusion into a global database of PfPR data, age-standardized to 2–10 y for endemicity mapping. A model-based geostatistical procedure was used to create a continuous surface of malaria endemicity within previously defined stable spatial limits of P. falciparum transmission. These procedures were implemented within a Bayesian statistical framework so that the uncertainty of these predictions could be evaluated robustly. The uncertainty was expressed as the probability of predicting correctly one of three endemicity classes; previously stratified to be an informative guide for malaria control. Population at risk estimates, adjusted for the transmission modifying effects of urbanization in Africa, were then derived with reference to human population surfaces in 2007. Of the 1.38 billion people at risk of stable P. falciparum malaria, 0.69 billion were found in Central and South East Asia (CSE Asia), 0.66 billion in Africa, Yemen, and Saudi Arabia (Africa+), and 0.04 billion in the Americas. All those exposed to stable risk in the Americas were in the lowest endemicity class (PfPR2−10 ≤ 5%). The vast majority (88%) of those living under stable risk in CSE Asia were also in this low endemicity class; a small remainder (11%) were in the intermediate endemicity class (PfPR2−10 > 5 to < 40%); and the remaining fraction (1%) in high endemicity (PfPR2−10 ≥ 40%) areas. High endemicity was widespread in the Africa+ region, where 0.35 billion people are at this level of risk. Most of the rest live at intermediate risk (0.20 billion), with a smaller number (0.11 billion) at low stable risk. Conclusions High levels of P. falciparum malaria endemicity are common in Africa. Uniformly low endemic levels are found in the Americas. Low endemicity is also widespread in CSE Asia, but pockets of intermediate and very rarely high transmission remain. There are therefore significant opportunities for malaria control in Africa and for malaria elimination elsewhere. This 2007 global P. falciparum malaria endemicity map is the first of a series with which it will be possible to monitor and evaluate the progress of this intervention process. PMID:19323591

Identification and characterization of monomeric, volatile SiCl3NH2 as product of the reaction between SiCl4 and NH3: an important intermediate on the way to silicon nitride?

PubMed

Himmel, Hans-Jörg; Schiefenhövel, Nils; Binnewies, Michael

2003-03-17

We studied the reaction of SiCl(4) with NH(3) by mass spectrometry and IR spectroscopy. By means of mass spectrometry, SiCl(3)NH(2) was for the first time identified as an intermediate generated in significant amounts in the course of the reaction. In additional experiments, SiCl(3)NH(2) was formed as a stable gaseous product of the ammonolysis of SiCl(4), and the product was identified and characterized in detail by IR spectroscopic methods (gas phase and matrix isolation) in combination with quantum-chemical calculations. The calculations also gave access to important thermodynamical data.

Photochemical and radiation-chemical aspects of matrix acidity effects on some organic systems

NASA Astrophysics Data System (ADS)

Ambroz, H. B.; Przybytniak, G. K.; Wronska, T.; Kemp, T. J.

The role of matrix effects in radiolysis and photolysis is illustrated using two systems: organosulphur compounds and benzenediazonium salts. Their intermediates as detected by low temperature ESR and optical spectroscopy or FAB-MS give evidence that the main reaction pathways depend strongly on these effects. Changes in matrix acidity can control the formation of neutral radical, ion-radical or ionic species which are crucial to the character of the final products of irradiation of organosulphur compounds, which are of great importance in medicine, biology, ecology and industry. Microenvironmental influences determine whether the triplet aryl cation or radical species are detected as the principal or sole intermediates in the decomposition of diazonium salts, a process leading to different stable products with industrial application.

Capturing a flavivirus pre-fusion intermediate.

PubMed

Kaufmann, Bärbel; Chipman, Paul R; Holdaway, Heather A; Johnson, Syd; Fremont, Daved H; Kuhn, Richard J; Diamond, Michael S; Rossmann, Michael G

2009-11-01

During cell entry of flaviviruses, low endosomal pH triggers the rearrangement of the viral surface glycoproteins to a fusion-active state that allows the release of the infectious RNA into the cytoplasm. In this work, West Nile virus was complexed with Fab fragments of the neutralizing mAb E16 and was subsequently exposed to low pH, trapping the virions in a pre-fusion intermediate state. The structure of the complex was studied by cryo-electron microscopy and provides the first structural glimpse of a flavivirus fusion intermediate near physiological conditions. A radial expansion of the outer protein layer of the virion was observed compared to the structure at pH 8. The resulting approximately 60 A-wide shell of low density between lipid bilayer and outer protein layer is likely traversed by the stem region of the E glycoprotein. By using antibody fragments, we have captured a structural intermediate of a virus that likely occurs during cell entry. The trapping of structural transition states by antibody fragments will be applicable for other processes in the flavivirus life cycle and delineating other cellular events that involve conformational rearrangements.

Connecting nitrogenase intermediates with the kinetic scheme for N2 reduction by a relaxation protocol and identification of the N2 binding state

PubMed Central

Lukoyanov, Dmitriy; Barney, Brett M.; Dean, Dennis R.; Seefeldt, Lance C.; Hoffman, Brian M.

2007-01-01

A major obstacle to understanding the reduction of N2 to NH3 by nitrogenase has been the impossibility of synchronizing electron delivery to the MoFe protein for generation of specific enzymatic intermediates. When an intermediate is trapped without synchronous electron delivery, the number of electrons, n, it has accumulated is unknown. Consequently, the intermediate is untethered from kinetic schemes for reduction, which are indexed by n. We show that a trapped intermediate itself provides a “synchronously prepared” initial state, and its relaxation to the resting state at 253 K, conditions that prevent electron delivery to MoFe protein, can be analyzed to reveal n and the nature of the relaxation reactions. The approach is applied to the “H+/H− intermediate” (A) that appears during turnover both in the presence and absence of N2 substrate. A exhibits an S = ½ EPR signal from the active-site iron–molybdenum cofactor (FeMo-co) to which are bound at least two hydrides/protons. A undergoes two-step relaxation to the resting state (C): A → B → C, where B has an S = 3/2 FeMo-co. Both steps show large solvent kinetic isotope effects: KIE ≈ 3–4 (85% D2O). In the context of the Lowe–Thorneley kinetic scheme for N2 reduction, these results provide powerful evidence that H2 is formed in both relaxation steps, that A is the catalytically central state that is activated for N2 binding by the accumulation of n = 4 electrons, and that B has accumulated n = 2 electrons. PMID:17251348

Enhanced sampling molecular dynamics simulation captures experimentally suggested intermediate and unfolded states in the folding pathway of Trp-cage miniprotein.

PubMed

Shao, Qiang; Shi, Jiye; Zhu, Weiliang

2012-09-28

The ability of molecular dynamics simulation to capturing the transient states within the folding pathway of protein is important to the understanding of protein folding mechanism. In the present study, the integrated-tempering-sampling molecular dynamics (ITS-MD) simulation was performed to investigate the transient states including intermediate and unfolded ones in the folding pathway of a miniprotein, Trp-cage. Three force fields (FF03, FF99SB, and FF96) were tested, and both intermediate and unfolded states with their characteristics in good agreement with experiments were observed during the simulations, which supports the hypothesis that observable intermediates might present in the folding pathway of small polypeptides. In addition, it was demonstrated that FF03 force field as combined with ITS-MD is in overall a more proper force field than the others in reproducing experimentally recorded properties in UVRS, ECD, and NMR, Photo-CIDNP NMR, and IR T-jump experiments, and the folding∕unfolding thermodynamics parameters, such as ΔG(U), ΔC(p), and ΔH(U) (T(m)). In summary, the present study showed that using suitable force field and energy sampling method, molecular dynamics simulation could capture the transient states within the folding pathway of protein which are consistent with the experimental measurements, and thus provide information of protein folding mechanism and thermodynamics.

Binding mechanism and dynamic conformational change of C subunit of PKA with different pathways

PubMed Central

Chu, Wen-Ting; Chu, Xiakun; Wang, Jin

2017-01-01

The catalytic subunit of PKA (PKAc) exhibits three major conformational states (open, intermediate, and closed) during the biocatalysis process. Both ATP and substrate/inhibitor can effectively induce the conformational changes of PKAc from open to closed states. Aiming to explore the mechanism of this allosteric regulation, we developed a coarse-grained model and analyzed the dynamics of conformational changes of PKAc during binding by performing molecular dynamics simulations for apo PKAc, binary PKAc (PKAc with ATP, PKAc with PKI), and ternary PKAc (PKAc with ATP and PKI). Our results suggest a mixed binding mechanism of induced fit and conformational selection, with the induced fit dominant. The ligands can drive the movements of Gly-rich loop as well as some regions distal to the active site in PKAc and stabilize them at complex state. In addition, there are two parallel pathways (pathway with PKAc-ATP as an intermediate and pathway PKAc-PKI as an intermediate) during the transition from open to closed states. By molecular dynamics simulations and rate constant analyses, we find that the pathway through PKAc-ATP intermediate is the main binding route from open to closed state because of the fact that the bound PKI will hamper ATP from successful binding and significantly increase the barrier for the second binding subprocess. These findings will provide fundamental insights of the mechanisms of PKAc conformational change upon binding. PMID:28855336

Binding mechanism and dynamic conformational change of C subunit of PKA with different pathways.

PubMed

Chu, Wen-Ting; Chu, Xiakun; Wang, Jin

2017-09-19

The catalytic subunit of PKA (PKAc) exhibits three major conformational states (open, intermediate, and closed) during the biocatalysis process. Both ATP and substrate/inhibitor can effectively induce the conformational changes of PKAc from open to closed states. Aiming to explore the mechanism of this allosteric regulation, we developed a coarse-grained model and analyzed the dynamics of conformational changes of PKAc during binding by performing molecular dynamics simulations for apo PKAc, binary PKAc (PKAc with ATP, PKAc with PKI), and ternary PKAc (PKAc with ATP and PKI). Our results suggest a mixed binding mechanism of induced fit and conformational selection, with the induced fit dominant. The ligands can drive the movements of Gly-rich loop as well as some regions distal to the active site in PKAc and stabilize them at complex state. In addition, there are two parallel pathways (pathway with PKAc-ATP as an intermediate and pathway PKAc-PKI as an intermediate) during the transition from open to closed states. By molecular dynamics simulations and rate constant analyses, we find that the pathway through PKAc-ATP intermediate is the main binding route from open to closed state because of the fact that the bound PKI will hamper ATP from successful binding and significantly increase the barrier for the second binding subprocess. These findings will provide fundamental insights of the mechanisms of PKAc conformational change upon binding.

Structural Studies of E. coli Topoisomerase III-DNA Complexes Reveal A Novel Type IA Topoisomerase-DNA Conformational Intermediate

PubMed Central

Changela, Anita; DiGate, Russell J.; Mondragón, Alfonso

2007-01-01

Summary E. coli DNA topoisomerase III belongs to the type IA family of DNA topoisomerases, which transiently cleave single-stranded DNA (ssDNA) via a 5′ phosphotyrosine intermediate. We have solved crystal structures of wild-type E. coli topoisomerase III bound to an 8-base ssDNA molecule in three different pH environments. The structures reveal the enzyme in three distinct conformational states while bound to DNA. One conformation resembles the one observed previously with a DNA-bound, catalytically inactive mutant of topoisomerase III where DNA binding realigns catalytic residues to form a functional active site. Another conformation represents a novel intermediate in which DNA is bound along the ssDNA-binding groove but does not enter the active site, which remains in a catalytically inactive, closed state. A third conformation shows an intermediate state where the enzyme is still in a closed state, but the ssDNA is starting to invade the active site. For the first time, the active site region in the presence of both the catalytic tyrosine and ssDNA substrate is revealed for a type IA DNA topoisomerase, although there is no evidence of ssDNA cleavage. Comparative analysis of the various conformational states suggests a sequence of domain movements undertaken by the enzyme upon substrate binding. PMID:17331537

[Inhibiting properties of stable nitroxyl radicals in reactions of linoleic acid and linoleyl alcohol oxidation catalyzed by 5-lipoxygenase].

PubMed

Kharchenko, O V; Kharitonenko, A I; Vovk, A I; Kukhar', V P; Babiĭ, L V; Khil'chevskiĭ, A N; Mel'nik, A K

2005-01-01

The inhibiting effects of 2,2,6,6-tetramethylpiperidine-1-oxyl (TEMPO) and its 4-substituted derivatives in reactions of linoleyl acid or linoleyl alcohol oxidation catalyzed by potato tuber 5-lipoxygenase were investigated. Inhibiting properties of stable nitroxyl radicals in presence of lubrol and SDS were reduced at the transition from TEMPO to 4-hydroxy-TEMPO or 4-amino-TEMPO and increased at use of adamantane-1-carboxylic or 3-methyladamantane-1-carboxylic acid 1-oxyl-2,2,6,6-tetramethylpiperidine-4-yl esters. Enzyme activity at saturating concentrations of inhibitor was not suppressed completely, and decreased up to the certain level determined by the substrate nature. The dependence of partial inhibition efficiency on rotational correlation time of stable nitroxides in model micellar systems were analysed. It was supposed that 5-lipoxygenase inhibition includes the interaction of hydrophobic nitroxide with radical intermediate formed in enzymatic process.

Carbon-hydrogen vs. carbon-halogen oxidative addition of chlorobenzene by a neutral iridium complex explored by DFT.

PubMed

Wu, Hong; Hall, Michael B

2009-08-14

Density functional theory (DFT) is used to explore the competitive C-H and C-Cl oxidative additions (OA) of chlorobenzene to the neutral Ir(i) complex: (PNP)Ir(I) [PNP = bis(Z-2-(dimethylphosphino)vinyl)amino]. Consistent with experimental results, our calculation shows that C-H OA is kinetically favored with an activation free-energy barrier of DeltaG(double dagger) = 17.2 kcal mol(-1) that is significantly lower than that for the C-Cl activation at DeltaG(double dagger) = 24.2 kcal mol(-1). However, C-Cl OA is thermodynamically preferred and the C-Cl OA product is 22.6 kcal mol(-1) more stable than the most stable C-H OA product. The calculations also show that the lowest energy path for the conversion of the C-H OA product to the more stable C-Cl OA product is intramolecular through a "benzyne"-type intermediate.

Six-month trajectories of self-reported depressive symptoms in long-term care.

PubMed

McCusker, Jane; Cole, Martin G; Voyer, Philippe; Monette, Johanne; Champoux, Nathalie; Ciampi, Antonio; Vu, Minh; Belzile, Eric; Bai, Chun

2016-01-01

Depression is a common problem in long-term care (LTC) settings. We sought to characterize depression symptom trajectories over six months among older residents, and to identify resident characteristics at baseline that predict symptom trajectory. This study was a secondary analysis of data from a six-month prospective, observational, and multi-site study. Severity of depressive symptoms was assessed with the 15-item Geriatric Depression Scale (GDS) at baseline and with up to six monthly follow-up assessments. Participants were 130 residents with a Mini-Mental State Examination score of 15 or more at baseline and of at least two of the six monthly follow-up assessments. Individual resident GDS trajectories were grouped using hierarchical clustering. The baseline predictors of a more severe trajectory were identified using the Proportional Odds Model. Three clusters of depression symptom trajectory were found that described "lower," "intermediate," and "higher" levels of depressive symptoms over time (mean GDS scores for three clusters at baseline were 2.2, 4.9, and 9.0 respectively). The GDS scores in all groups were generally stable over time. Baseline predictors of a more severe trajectory were as follows: Initial GDS score of 7 or more, female sex, LTC residence for less than 12 months, and corrected visual impairment. The six-month course of depressive symptoms in LTC is generally stable. Most residents who experience a more severe symptom trajectory can be identified at baseline.

Uncoupling binding of substrate CO from turnover by vanadium nitrogenase.

PubMed

Lee, Chi Chung; Fay, Aaron W; Weng, Tsu-Chien; Krest, Courtney M; Hedman, Britt; Hodgson, Keith O; Hu, Yilin; Ribbe, Markus W

2015-11-10

Biocatalysis by nitrogenase, particularly the reduction of N2 and CO by this enzyme, has tremendous significance in environment- and energy-related areas. Elucidation of the detailed mechanism of nitrogenase has been hampered by the inability to trap substrates or intermediates in a well-defined state. Here, we report the capture of substrate CO on the resting-state vanadium-nitrogenase in a catalytically competent conformation. The close resemblance of this active CO-bound conformation to the recently described structure of CO-inhibited molybdenum-nitrogenase points to the mechanistic relevance of sulfur displacement to the activation of iron sites in the cofactor for CO binding. Moreover, the ability of vanadium-nitrogenase to bind substrate in the resting-state uncouples substrate binding from subsequent turnover, providing a platform for generation of defined intermediate(s) of both CO and N2 reduction.

The History of the Discovery of the Molybdenum Cofactor and Novel Aspects of its Biosynthesis in Bacteria

PubMed Central

Leimkühler, Silke; Wuebbens, Margot M.; Rajagopalan, K.V.

2010-01-01

Biosynthesis of the molybdenum cofactor in bacteria is described with a detailed analysis of each individual reaction leading to the formation of stable intermediates during the synthesis of molybdopterin from GTP. As a starting point, the discovery of molybdopterin and the elucidation of its structure through the study of stable degradation products are described. Subsequent to molybdopterin synthesis, the molybdenum atom is added to the molybdopterin dithiolene group to form the molybdenum cofactor. This cofactor is either inserted directly into specific molybdoenzymes or is further modified by the addition of nucleotides to the molybdopterin phosphate group or the replacement of ligands at the molybdenum center. PMID:21528011

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.

Pronounced chemical response of Subarctic lakes to climate-driven losses in surface area

USGS Publications Warehouse

Lewis, Tyler L.; Lindberg, Mark S.; Schmutz, Joel A.; Heglund, Patricia J.; Rover, Jennifer R.; Koch, Joshua C.; Bertram, Mark R.

2015-01-01

Losses in lake area have been observed for several Arctic and Subarctic regions in recent decades, with unknown consequences for lake ecosystems. These reductions are primarily attributed to two climate-sensitive mechanisms, both of which may also cause changes in water chemistry: (i) increased imbalance of evaporation relative to inflow, whereby increased evaporation and decreased inflow act to concentrate solutes into smaller volumes; and (ii) accelerated permafrost degradation, which enhances sublacustrine drainage while simultaneously leaching previously frozen solutes into lakes. We documented changes in nutrients [total nitrogen (TN), total phosphorus (TP)] and ions (calcium, chloride, magnesium, sodium) over a 25 year interval in shrinking, stable, and expanding Subarctic lakes of the Yukon Flats, Alaska. Concentrations of all six solutes increased in shrinking lakes from 1985–1989 to 2010–2012, while simultaneously undergoing little change in stable or expanding lakes. This created a present-day pattern, much weaker or absent in the 1980s, in which shrinking lakes had higher solute concentrations than their stable or expanding counterparts. An imbalanced evaporation-to-inflow ratio (E/I) was the most likely mechanism behind such changes; all four ions, which behave semiconservatively and are prone to evapoconcentration, increased in shrinking lakes and, along with TN and TP, were positively related to isotopically derived E/I estimates. Moreover, the most conservative ion, chloride, increased >500% in shrinking lakes. Conversely, only TP concentration was related to probability of permafrost presence, being highest at intermediate probabilities. Overall, the substantial increases of nutrients (TN >200%, TP >100%) and ions (>100%) may shift shrinking lakes towards overly eutrophic or saline states, with potentially severe consequences for ecosystems of northern lakes.

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.

Learning from adaptive neural dynamic surface control of strict-feedback systems.

PubMed

Wang, Min; Wang, Cong

2015-06-01

Learning plays an essential role in autonomous control systems. However, how to achieve learning in the nonstationary environment for nonlinear systems is a challenging problem. In this paper, we present learning method for a class of n th-order strict-feedback systems by adaptive dynamic surface control (DSC) technology, which achieves the human-like ability of learning by doing and doing with learned knowledge. To achieve the learning, this paper first proposes stable adaptive DSC with auxiliary first-order filters, which ensures the boundedness of all the signals in the closed-loop system and the convergence of tracking errors in a finite time. With the help of DSC, the derivative of the filter output variable is used as the neural network (NN) input instead of traditional intermediate variables. As a result, the proposed adaptive DSC method reduces greatly the dimension of NN inputs, especially for high-order systems. After the stable DSC design, we decompose the stable closed-loop system into a series of linear time-varying perturbed subsystems. Using a recursive design, the recurrent property of NN input variables is easily verified since the complexity is overcome using DSC. Subsequently, the partial persistent excitation condition of the radial basis function NN is satisfied. By combining a state transformation, accurate approximations of the closed-loop system dynamics are recursively achieved in a local region along recurrent orbits. Then, the learning control method using the learned knowledge is proposed to achieve the closed-loop stability and the improved control performance. Simulation studies are performed to demonstrate the proposed scheme can not only reuse the learned knowledge to achieve the better control performance with the faster tracking convergence rate and the smaller tracking error but also greatly alleviate the computational burden because of reducing the number and complexity of NN input variables.

Dynamically Stable Legged Locomotion

DTIC Science & Technology

1989-09-01

length during overground locomotion: task-specific modulation of the locomotor synergy. Journal of Experimental Psychology, 15(3). Raibert, M. I. 1986...energy conversions that intermediates between combus- tion of a fluid fuel such as gasoline , and the controlled delivery of force and power to the...question of this study: Can the extremely high energy density and rapid response of combustible fluid fuels such as gasoline be harnessed to produce

Pressure- and heat-induced inactivation of butyrylcholinesterase: evidence for multiple intermediates and the remnant inactivation process.

PubMed Central

Weingand-Ziade, A; Ribes, F; Renault, F; Masson, P

2001-01-01

The inactivation process of native (N) human butyrylcholinesterase (BuChE) by pressure and/or heat was found to be multi-step. It led to irreversible formation of an active intermediate (I) state and a denatured state. This series-inactivation process was described by expanding the Lumry-Eyring [Lumry, R. and Eyring, H. (1954) J. Phys. Chem. 58, 110-120] model. The intermediate state (I) was found to have a K(m) identical with that of the native state and a turnover rate (k(cat)) twofold higher than that of the native state with butyrylthiocholine as the substrate. The increased catalytic efficiency (k(cat)/K(m)) of I can be explained by a conformational change in the active-site gorge and/or restructuring of the water-molecule network in the active-site pocket, making the catalytic steps faster. However, a pressure/heat-induced covalent modification of native BuChE, affecting the catalytic machinery, cannot be ruled out. The inactivation process of BuChE induced by the combined action of pressure and heat was found to continue after interruption of pressure/temperature treatment. This secondary inactivation process was termed 'remnant inactivation'. We hypothesized that N and I were in equilibrium with populated metastable N' and I' states. The N' and I' states can either return to the active forms, N and I, or develop into inactive forms, N(')(in) and I(')(in). Both active N' and I' intermediate states displayed different rates of remnant inactivation depending on the pressure and temperature pretreatments and on the storage temperature. A first-order deactivation model describing the kinetics of the remnant inactivation of BuChE is proposed. PMID:11368776

Structural Properties of Human IAPP Dimer in Membrane Environment Studied by All-Atom Molecular Dynamics Simulations.

PubMed

Liu, Na; Duan, Mojie; Yang, Minghui

2017-08-11

The aggregation of human islet amyloid polypeptide (hIAPP) can damage the membrane of the β-cells in the pancreatic islets and induce type 2 diabetes (T2D). Growing evidences indicated that the major toxic species are small oligomers of IAPP. Due to the fast aggregation nature, it is hard to characterize the structures of IAPP oligomers by experiments, especially in the complex membrane environment. On the other side, molecular dynamics simulation can provide atomic details of the structure and dynamics of the aggregation of IAPP. In this study, all-atom bias-exchange metadynamics (BE-Meta) and unbiased molecular dynamics simulations were employed to study the structural properties of IAPP dimer in the membranes environments. A number of intermediates, including α-helical states, β-sheet states, and fully disordered states, are identified. The formation of N-terminal β-sheet structure is prior to the C-terminal β-sheet structure towards the final fibril-like structures. The α-helical intermediates have lower propensity in the dimeric hIAPP and are off-pathway intermediates. The simulations also demonstrate that the β-sheet intermediates induce more perturbation on the membrane than the α-helical and disordered states and thus pose higher disruption ability.

22. PIN CONNECTION AT JUNCTURE OF INTERMEDIATE VERTICAL WITH BOTTOM ...

Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

22. PIN CONNECTION AT JUNCTURE OF INTERMEDIATE VERTICAL WITH BOTTOM CHORD ON PENNSYLVANIA PETIT TRUSS. HYDRAULICALLY FORGED EYES ON ROLLED STOCK. - New River Bridge, Spanning New River at State Route 623, Pembroke, Giles County, VA

Simultaneous noncontact AFM and STM of Ag:Si(111)-(3×3)R30∘

NASA Astrophysics Data System (ADS)

Sweetman, Adam; Stannard, Andrew; Sugimoto, Yoshiaki; Abe, Masayuki; Morita, Seizo; Moriarty, Philip

2013-02-01

The Ag:Si(111)-(3×3)R30∘ surface structure has attracted considerable debate concerning interpretation of scanning tunneling microscope (STM) and noncontact atomic force microscope (NC-AFM) images. In particular, the accepted interpretation of atomic resolution images in NC-AFM has been questioned by theoretical and STM studies. In this paper, we use combined NC-AFM and STM to conclusively show that the inequivalent trimer (IET) configuration best describes the surface ground state. Thermal-averaging effects result in a honeycomb-chained-trimer (HCT) appearance at room temperature, in contrast to studies suggesting that the IET configuration remains stable at higher temperatures [Zhang, Gustafsson, and Johansson, Phys. Rev. BPRBMDO1098-012110.1103/PhysRevB.74.201304 74, 201304(R) (2006) and J. Phys.: Conf. Ser.1742-658810.1088/1742-6596/61/1/264 61, 1336 (2007)]. We also comment on results obtained at an intermediate temperature that suggest an intriguing difference between the imaging mechanisms of NC-AFM and STM on structurally fluctuating samples.

Quasifree (p, 2p) Reactions on Oxygen Isotopes: Observation of Isospin Independence of the Reduced Single-Particle Strength.

PubMed

Atar, L; Paschalis, S; Barbieri, C; Bertulani, C A; Díaz Fernández, P; Holl, M; Najafi, M A; Panin, V; Alvarez-Pol, H; Aumann, T; Avdeichikov, V; Beceiro-Novo, S; Bemmerer, D; Benlliure, J; Boillos, J M; Boretzky, K; Borge, M J G; Caamaño, M; Caesar, C; Casarejos, E; Catford, W; Cederkall, J; Chartier, M; Chulkov, L; Cortina-Gil, D; Cravo, E; Crespo, R; Dillmann, I; Elekes, Z; Enders, J; Ershova, O; Estrade, A; Farinon, F; Fraile, L M; Freer, M; Galaviz Redondo, D; Geissel, H; Gernhäuser, R; Golubev, P; Göbel, K; Hagdahl, J; Heftrich, T; Heil, M; Heine, M; Heinz, A; Henriques, A; Hufnagel, A; Ignatov, A; Johansson, H T; Jonson, B; Kahlbow, J; Kalantar-Nayestanaki, N; Kanungo, R; Kelic-Heil, A; Knyazev, A; Kröll, T; Kurz, N; Labiche, M; Langer, C; Le Bleis, T; Lemmon, R; Lindberg, S; Machado, J; Marganiec-Gałązka, J; Movsesyan, A; Nacher, E; Nikolskii, E Y; Nilsson, T; Nociforo, C; Perea, A; Petri, M; Pietri, S; Plag, R; Reifarth, R; Ribeiro, G; Rigollet, C; Rossi, D M; Röder, M; Savran, D; Scheit, H; Simon, H; Sorlin, O; Syndikus, I; Taylor, J T; Tengblad, O; Thies, R; Togano, Y; Vandebrouck, M; Velho, P; Volkov, V; Wagner, A; Wamers, F; Weick, H; Wheldon, C; Wilson, G L; Winfield, J S; Woods, P; Yakorev, D; Zhukov, M; Zilges, A; Zuber, K

2018-02-02

Quasifree one-proton knockout reactions have been employed in inverse kinematics for a systematic study of the structure of stable and exotic oxygen isotopes at the R^{3}B/LAND setup with incident beam energies in the range of 300-450  MeV/u. The oxygen isotopic chain offers a large variation of separation energies that allows for a quantitative understanding of single-particle strength with changing isospin asymmetry. Quasifree knockout reactions provide a complementary approach to intermediate-energy one-nucleon removal reactions. Inclusive cross sections for quasifree knockout reactions of the type ^{A}O(p,2p)^{A-1}N have been determined and compared to calculations based on the eikonal reaction theory. The reduction factors for the single-particle strength with respect to the independent-particle model were obtained and compared to state-of-the-art ab initio predictions. The results do not show any significant dependence on proton-neutron asymmetry.

Isolation and reversible dimerization of a selenium-selenium three-electron σ-bond.

PubMed

Zhang, Senwang; Wang, Xingyong; Su, Yuanting; Qiu, Yunfan; Zhang, Zaichao; Wang, Xinping

2014-06-11

Three-electron σ-bonding that was proposed by Linus Pauling in 1931 has been recognized as important in intermediates encountered in many areas. A number of three-electron bonding systems have been spectroscopically investigated in the gas phase, solution and solid matrix. However, X-ray diffraction studies have only been possible on simple noble gas dimer Xe∴Xe and cyclic framework-constrained N∴N radical cations. Here, we show that a diselena species modified with a naphthalene scaffold can undergo one-electron oxidation using a large and weakly coordinating anion, to afford a room-temperature-stable radical cation containing a Se∴Se three-electron σ-bond. When a small anion is used, a reversible dimerization with phase and marked colour changes is observed: radical cation in solution (blue) but diamagnetic dimer in the solid state (brown). These findings suggest that more examples of three-electron σ-bonds may be stabilized and isolated by using naphthalene scaffolds together with large and weakly coordinating anions.

Floquet prethermalization and regimes of heating in a periodically driven, interacting quantum system

NASA Astrophysics Data System (ADS)

Weidinger, Simon A.; Knap, Michael

2017-04-01

We study the regimes of heating in the periodically driven O(N)-model, which is a well established model for interacting quantum many-body systems. By computing the absorbed energy with a non-equilibrium Keldysh Green’s function approach, we establish three dynamical regimes: at short times a single-particle dominated regime, at intermediate times a stable Floquet prethermal regime in which the system ceases to absorb, and at parametrically late times a thermalizing regime. Our simulations suggest that in the thermalizing regime the absorbed energy grows algebraically in time with an exponent that approaches the universal value of 1/2, and is thus significantly slower than linear Joule heating. Our results demonstrate the parametric stability of prethermal states in a many-body system driven at frequencies that are comparable to its microscopic scales. This paves the way for realizing exotic quantum phases, such as time crystals or interacting topological phases, in the prethermal regime of interacting Floquet systems.

Integrated light and scanning electron microscopy of GFP-expressing cells.

PubMed

Peddie, Christopher J; Liv, Nalan; Hoogenboom, Jacob P; Collinson, Lucy M

2014-01-01

Integration of light and electron microscopes provides imaging tools in which fluorescent proteins can be localized to cellular structures with a high level of precision. However, until recently, there were few methods that could deliver specimens with sufficient fluorescent signal and electron contrast for dual imaging without intermediate staining steps. Here, we report protocols that preserve green fluorescent protein (GFP) in whole cells and in ultrathin sections of resin-embedded cells, with membrane contrast for integrated imaging. Critically, GFP is maintained in a stable and active state within the vacuum of an integrated light and scanning electron microscope. For light microscopists, additional structural information gives context to fluorescent protein expression in whole cells, illustrated here by analysis of filopodia and focal adhesions in Madin Darby canine kidney cells expressing GFP-Paxillin. For electron microscopists, GFP highlights the proteins of interest within the architectural space of the cell, illustrated here by localization of the conical lipid diacylglycerol to cellular membranes. © 2014 Elsevier Inc. All rights reserved.

Nonequilibrium self-organization of colloidal particles on substrates: adsorption, relaxation, and annealing.

PubMed

Araújo, Nuno A M; Dias, Cristóvão S; Telo da Gama, Margarida M

2017-01-11

Colloidal particles are considered ideal building blocks to produce materials with enhanced physical properties. The state-of-the-art techniques for synthesizing these particles provide control over shape, size, and directionality of the interactions. In spite of these advances, there is still a huge gap between the synthesis of individual components and the management of their spontaneous organization towards the desired structures. The main challenge is the control over the dynamics of self-organization. In their kinetic route towards thermodynamically stable structures, colloidal particles self-organize into intermediate (mesoscopic) structures that are much larger than the individual particles and become the relevant units for the dynamics. To follow the dynamics and identify kinetically trapped structures, one needs to develop new theoretical and numerical tools. Here we discuss the self-organization of functionalized colloids (also known as patchy colloids) on attractive substrates. We review our recent results on the adsorption and relaxation and explore the use of annealing cycles to overcome kinetic barriers and drive the relaxation towards the targeted structures.

Cavity transport effects in generator-collector electrochemical analysis of nitrobenzene.

PubMed

Lewis, Grace E M; Dale, Sara E C; Kasprzyk-Hordern, Barbara; Lubben, Anneke T; Barnes, Edward O; Compton, Richard G; Marken, Frank

2014-09-21

Two types of generator-collector electrode systems, (i) a gold-gold interdigitated microband array and (ii) a gold-gold dual-plate microtrench, are compared for nitrobenzene electroanalysis in aerated aqueous 0.1 M NaOH. The complexity of the nitrobenzene reduction in conjunction with the presence of ambient levels of oxygen in the analysis solution provide a challenging problem in which feedback-amplified generator-collector steady state currents provide the analytical signal. In contrast to the more openly accessible geometry of the interdigitated array electrode, where the voltammetric response for nitrobenzene is less well-defined and signals drift, the voltammetric response for the cavity-like microtrench electrode is stable and readily detectable at 1 μM level. Both types of electrode show oxygen-enhanced low concentration collector current responses due to additional feedback via reaction intermediates. The observations are rationalised in terms of a "cavity transport coefficient" which is beneficial in the dual-plate microtrench, where oxygen interference effects are suppressed and the analytical signal is amplified and stabilised.

Systematic Effect for an Ultralong Cycle Lithium-Sulfur Battery.

PubMed

Wu, Feng; Ye, Yusheng; Chen, Renjie; Qian, Ji; Zhao, Teng; Li, Li; Li, Wenhui

2015-11-11

Rechargeable lithium-sulfur (Li-S) batteries are attractive candidates for energy storage devices because they have five times the theoretical energy storage of state-of-the-art Li-ion batteries. The main problems plaguing Li-S batteries are poor cycle life and limited rate capability, caused by the insulating nature of S and the shuttle effect associated with the dissolution of intermediate lithium polysulfides. Here, we report the use of biocell-inspired polydopamine (PD) as a coating agent on both the cathode and separator to address these problems (the "systematic effects"). The PD-modified cathode and separator play key roles in facilitating ion diffusion and keeping the cathode structure stable, leading to uniform lithium deposition and a solid electrolyte interphase. As a result, an ultralong cycle performance of more than 3000 cycles, with a capacity fade of only 0.018% per cycle, was achieved at 2 C. It is believed that the systematic modification of the cathode and separator for Li-S batteries is a new strategy for practical applications.

Cu(In,Ga)Se2 surface treatment with Na and NaF: A combined photoelectron spectroscopy and surface photovoltage study in ultra-high vacuum

NASA Astrophysics Data System (ADS)

Parvan, V.; Mizrak, A.; Majumdar, I.; Ümsür, B.; Calvet, W.; Greiner, D.; Kaufmann, C. A.; Dittrich, T.; Avancini, E.; Lauermann, I.

2018-06-01

Either metallic Na or NaF were deposited onto Cu(In,Ga)Se2 surfaces and studied by photoelectron spectroscopy and surface photovoltage spectroscopy without breaking the ultra-high vacuum. The deposition of elemental Na at room temperature led to the formation of an intermediate Cu and Ga rich layer at the CIGSe surface, whereas for NaF the composition of the CIGSe surface remained unchanged. A metal like surface induced by an inverted near surface region with a reduced number of defect states was formed after the deposition of Na. Under the chosen experimental conditions, the near surface layer was independent on the amount of Na and stable in time. In contrast, the usage of NaF weakened the inversion and led to an increased band bending compared to the untreated CIGSe sample. The SPV signals decreased with proceeding time after the deposition of NaF.

Isoproturon Reappearance after Photosensitized Degradation in the Presence of Triplet Ketones or Fulvic Acids.

PubMed

Yuan, Chenyi; Chakraborty, Mrinal; Canonica, Silvio; Weavers, Linda K; Hadad, Christopher M; Chin, Yu-Ping

2016-11-15

Isoproturon (IPU) is a phenylurea herbicide used to control broad-leaf grasses on grain fields. Photosensitized transformation induced by excited triplet states of dissolved organic matter ( 3 DOM*) has been identified as an important degradation pathway for IPU in sunlit waters, but the reappearance of IPU in the absence of light is observed after the initial photolysis. In this study, we elucidate the kinetics of this photodegradation and dark-reappearance cycling of IPU in the presence of DOM proxies (aromatic ketones and reference fulvic acids). Using mass spectrometry and nuclear magnetic resonance spectroscopic techniques, a semi-stable intermediate (IPU int ) was found to be responsible for IPU reversion and was identified as a hydroperoxyl derivative of IPU. IPU int is photogenerated from incorporation of diatomic oxygen to IPU and is subjected to thermolysis whose rate depends on temperature, pH, the presence of DOM, and inorganic ions. These results are important to understand the overall aquatic fate of IPU and structurally similar compounds under diurnal conditions.

Uncleaved prefusion-optimized gp140 trimers derived from analysis of HIV-1 envelope metastability

NASA Astrophysics Data System (ADS)

Kong, Leopold; He, Linling; de Val, Natalia; Vora, Nemil; Morris, Charles D.; Azadnia, Parisa; Sok, Devin; Zhou, Bin; Burton, Dennis R.; Ward, Andrew B.; Wilson, Ian A.; Zhu, Jiang

2016-06-01

The trimeric HIV-1 envelope glycoprotein (Env) is critical for host immune recognition and neutralization. Despite advances in trimer design, the roots of Env trimer metastability remain elusive. Here we investigate the contribution of two Env regions to metastability. First, we computationally redesign a largely disordered bend in heptad region 1 (HR1) of SOSIP trimers that connects the long, central HR1 helix to the fusion peptide, substantially improving the yield of soluble, well-folded trimers. Structural and antigenic analyses of two distinct HR1 redesigns confirm that redesigned Env closely mimics the native, prefusion trimer with a more stable gp41. Next, we replace the cleavage site between gp120 and gp41 with various linkers in the context of an HR1 redesign. Electron microscopy reveals a potential fusion intermediate state for uncleaved trimers containing short but not long linkers. Together, these results outline a general approach for stabilization of Env trimers from diverse HIV-1 strains.

Inflammatory biomarkers are not predictive of intermediate-term risk of ventricular tachyarrhythmias in stable CHF patients.

PubMed

Konstantino, Yuval; Kusniec, Jairo; Reshef, Tamar; David-Zadeh, Ofer; Mazur, Alexander; Strasberg, Boris; Battler, Alexander; Haim, Moti

2007-08-01

Elevated levels of inflammatory biomarkers and brain natriuretic peptide (BNP) are associated with increased mortality in patients with heart failure (HF). : The aim of the current study was to assess the correlation between circulating biomarkers and ventricular tachyarrhythmias among patients with HF. Blood samples from 50 stable ambulatory HF patients with moderate to severe systolic left ventricular (LV) dysfunction and an implantable cardioverter defibrillator (ICD) were analyzed for interleukin 6 (IL-6), tumor necrosis factor-alpha (TNF-alpha), high-sensitivity C-reactive protein (hsCRP) and BNP. Thereafter, the patients were followed for a mean period of 152 +/- 44 days, during which ventricular tachyarrhythmias were recorded by the ICDs. Follow-up data were obtained from 47 patients. Of them, 45 (96%) had ischemic cardiomyopathy, 38 (81%) had New York Heart Association class I-II, 43 (91%) were males, and the mean age was 68.6 +/- 11.1 years. During follow-up, 5 patients (11%) had nonsustained ventricular tachycardia (NSVT), 6 patients (13%) had sustained ventricular tachycardia (VT) or ventricular fibrillation (VF) and 36 patients (76%) had no events. The circulating biomarkers' levels upon enrollment were not significantly different between patients who subsequently had NSVT or VT/VF and patients who were free of events. No correlation was found between plasma levels of IL-6, TNF-alpha, hsCRP and BNP and ventricular arrhythmic events among stable HF patients during an intermediate term follow-up of 5.1 months. Further studies are still required to assess the association between these biomarkers and long-term risk of ventricular tachyarrhythmia. (c) 2007 Wiley Periodicals, Inc.

A 400-solar-mass black hole in the galaxy M82.

PubMed

Pasham, Dheeraj R; Strohmayer, Tod E; Mushotzky, Richard F

2014-09-04

M82 X-1, the brightest X-ray source in the galaxy M82, has been thought to be an intermediate-mass black hole (100 to 10,000 solar masses) because of its extremely high luminosity and variability characteristics, although some models suggest that its mass may be only about 20 solar masses. The previous mass estimates were based on scaling relations that use low-frequency characteristic timescales which have large intrinsic uncertainties. For stellar-mass black holes, we know that the high-frequency quasi-periodic oscillations (100-450 hertz) in the X-ray emission that occur in a 3:2 frequency ratio are stable and scale in frequency inversely with black hole mass with a reasonably small dispersion. The discovery of such stable oscillations thus potentially offers an alternative and less ambiguous means of mass determination for intermediate-mass black holes, but has hitherto not been realized. Here we report stable, twin-peak (3:2 frequency ratio) X-ray quasi-periodic oscillations from M82 X-1 at frequencies of 3.32 ± 0.06 hertz and 5.07 ± 0.06 hertz. Assuming that we can extrapolate the inverse-mass scaling that holds for stellar-mass black holes, we estimate the black hole mass of M82 X-1 to be 428 ± 105 solar masses. In addition, we can estimate the mass using the relativistic precession model, from which we get a value of 415 ± 63 solar masses.

Effect of midgap defect states on the optical properties of Ge20Se70Te10 nano colloids

NASA Astrophysics Data System (ADS)

Cheruvalath, Ajina; Sebastian, Indu; Sebastian, Mathew; Nampoori, V. P. N.; Thomas, Sheenu

2017-10-01

In this work, we report the linear and nonlinear optical studies on a pseudo binary chalcogenide glass of composition Ge20 Se70 Te10 in its nano colloidal form. The possibility of tuning the band gap, nonlinear refractive index and nonlinear absorption of the material by changing the glass loading in the colloid has been revealed. A red shift in the band edge along with an intermediate peak in the band tail due to defect states is observed with increasing concentration. Photoluminescence studies confirm the existence of intermediate defect states in the bandgap. Nonlinear properties analyzed with open and closed aperture z scan technique reveal that the nonlinear refraction enhances due to resonant effects as the band gap of the colloid gets near the one photon absorption edge. The nonlinear absorption is prominent in the concentrated sample due to the presence of defect states which acts as an intermediate level in two step photon absorption.

Dynamic-load-enabled ultra-low power multiple-state RRAM devices.

PubMed

Yang, Xiang; Chen, I-Wei

2012-01-01

Bipolar resistance-switching materials allowing intermediate states of wide-varying resistance values hold the potential of drastically reduced power for non-volatile memory. To exploit this potential, we have introduced into a nanometallic resistance-random-access-memory (RRAM) device an asymmetric dynamic load, which can reliably lower switching power by orders of magnitude. The dynamic load is highly resistive during on-switching allowing access to the highly resistive intermediate states; during off-switching the load vanishes to enable switching at low voltage. This approach is entirely scalable and applicable to other bipolar RRAM with intermediate states. The projected power is 12 nW for a 100 × 100 nm(2) device and 500 pW for a 10 × 10 nm(2) device. The dynamic range of the load can be increased to allow power to be further decreased by taking advantage of the exponential decay of wave-function in a newly discovered nanometallic random material, reaching possibly 1 pW for a 10×10 nm(2) nanometallic RRAM device.

[Artificial Cysteine Bridges on the Surface of Green Fluorescent Protein Affect Hydration of Its Transition and Intermediate States].

PubMed

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

2018-01-01

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

Point Mutations in Membrane Proteins Reshape Energy Landscape and Populate Different Unfolding Pathways

PubMed Central

Sapra, K. Tanuj; Balasubramanian, G. Prakash; Labudde, Dirk; Bowie, James U.; Muller, Daniel J.

2009-01-01

Using single-molecule force spectroscopy, we investigated the effect of single point mutations on the energy landscape and unfolding pathways of the transmembrane protein bacteriorhodopsin. We show that the unfolding energy barriers in the energy landscape of the membrane protein followed a simple two-state behavior and represent a manifestation of many converging unfolding pathways. Although the unfolding pathways of wild-type and mutant bacteriorhodopsin did not change, indicating the presence of same ensemble of structural unfolding intermediates, the free energies of the rate-limiting transition states of the bacteriorhodopsin mutants decreased as the distance of those transition states to the folded intermediate states decreased. Thus, all mutants exhibited Hammond behavior and a change in the free energies of the intermediates along the unfolding reaction coordinate and, consequently, their relative occupancies. This is the first experimental proof showing that point mutations can reshape the free energy landscape of a membrane protein and force single proteins to populate certain unfolding pathways over others. PMID:18191146

Controlling the Chiral Inversion Reaction of the Metallopeptide Ni-Asparagine-Cysteine-Cysteine with Dioxygen

PubMed Central

Glass, Amanda M.; Krause, Mary E.; Laurence, Jennifer S.; Jackson, Timothy A.

2014-01-01

Synthetically generated metallopeptides have the potential to serve a variety of roles in biotechnology applications, but the use of such systems is often hampered by the inability to control secondary reactions. We have previously reported that the NiII complex of the tripeptide LLL-asparagine-cysteine-cysteine, LLL-NiII-NCC, undergoes metal-facilitated chiral inversion to DLD-NiII-NCC, which increases the observed superoxide scavenging activity. However, the mechanism for this process remained unexplored. Electronic absorption and circular dichroism studies of the chiral inversion reaction of NiII-NCC reveal a unique dependence on dioxygen. Specifically, in the absence of dioxygen, the chiral inversion is not observed, even at elevated pH, whereas the addition of O2 initiates this reactivity and concomitantly generates superoxide. Scavenging experiments using acetaldehyde are indicative of the formation of carbanion intermediates, demonstrating that inversion takes place by deprotonation of the alpha carbons of Asn1 and Cys3. Together, these data are consistent with the chiral inversion being dependent on the formation of a NiIII-NCC intermediate from NiII-NCC and O2. The data further suggest that the anionic thiolate and amide ligands in NiII-NCC inhibit Cα–H deprotonation for the NiII oxidation state, leading to a stable complex in the absence of O2. Together, these results offer insights into the factors controlling reactivity in synthetic metallopeptides. PMID:22928993

Reactive centre loop mutants of α-1-antitrypsin reveal position-specific effects on intermediate formation along the polymerization pathway

PubMed Central

Haq, Imran; Irving, James A.; Faull, Sarah V.; Dickens, Jennifer A.; Ordóñez, Adriana; Belorgey, Didier; Gooptu, Bibek; Lomas, David A.

2013-01-01

The common severe Z mutation (E342K) of α1-antitrypsin forms intracellular polymers that are associated with liver cirrhosis. The native fold of this protein is well-established and models have been proposed from crystallographic and biophysical data for the stable inter-molecular configuration that terminates the polymerization pathway. Despite these molecular ‘snapshots’, the details of the transition between monomer and polymer remain only partially understood. We surveyed the RCL (reactive centre loop) of α1-antitrypsin to identify sites important for progression, through intermediate states, to polymer. Mutations at P14P12 and P4, but not P10P8 or P2P1′, resulted in a decrease in detectable polymer in a cell model that recapitulates the intracellular polymerization of the Z variant, consistent with polymerization from a near-native conformation. We have developed a FRET (Förster resonance energy transfer)-based assay to monitor polymerization in small sample volumes. An in vitro assessment revealed the position-specific effects on the unimolecular and multimolecular phases of polymerization: the P14P12 region self-inserts early during activation, while the interaction between P6P4 and β-sheet A presents a kinetic barrier late in the polymerization pathway. Correspondingly, mutations at P6P4, but not P14P12, yield an increase in the overall apparent activation energy of association from ~360 to 550 kJ mol−1. PMID:23659468

Nuclear Resonance Vibrational Spectroscopic Definition of Peroxy Intermediates in Nonheme Iron Sites

DOE PAGES

Sutherlin, Kyle D.; Liu, Lei V.; Lee, Yong-Min; ...

2016-11-02

Fe III-(hydro)peroxy intermediates have been isolated in two classes of mononuclear nonheme Fe enzymes that are important in bioremediation: the Rieske dioxygenases and the extradiol dioxygenases. The binding mode and protonation state of the peroxide moieties in these intermediates are not well-defined, due to a lack of vibrational structural data. Nuclear resonance vibrational spectroscopy (NRVS) is an important technique for obtaining vibrational information on these and other intermediates, as it is sensitive to all normal modes with Fe displacement. Here in this paper, we present the NRVS spectra of side-on Fe III-peroxy and end-on Fe III-hydroperoxy model complexes and assignmore » these spectra using calibrated DFT calculations. We then use DFT calculations to define and understand the changes in the NRVS spectra that arise from protonation and from opening the Fe–O–O angle. This study identifies four spectroscopic handles that will enable definition of the binding mode and protonation state of Fe III-peroxy intermediates in mononuclear nonheme Fe enzymes. These structural differences are important in determining the frontier molecular orbitals available for reactivity.« less

Nuclear Resonance Vibrational Spectroscopic Definition of Peroxy Intermediates in Nonheme Iron Sites

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

Sutherlin, Kyle D.; Liu, Lei V.; Lee, Yong-Min

Fe III-(hydro)peroxy intermediates have been isolated in two classes of mononuclear nonheme Fe enzymes that are important in bioremediation: the Rieske dioxygenases and the extradiol dioxygenases. The binding mode and protonation state of the peroxide moieties in these intermediates are not well-defined, due to a lack of vibrational structural data. Nuclear resonance vibrational spectroscopy (NRVS) is an important technique for obtaining vibrational information on these and other intermediates, as it is sensitive to all normal modes with Fe displacement. Here in this paper, we present the NRVS spectra of side-on Fe III-peroxy and end-on Fe III-hydroperoxy model complexes and assignmore » these spectra using calibrated DFT calculations. We then use DFT calculations to define and understand the changes in the NRVS spectra that arise from protonation and from opening the Fe–O–O angle. This study identifies four spectroscopic handles that will enable definition of the binding mode and protonation state of Fe III-peroxy intermediates in mononuclear nonheme Fe enzymes. These structural differences are important in determining the frontier molecular orbitals available for reactivity.« less

Nuclear Resonance Vibrational Spectroscopic Definition of Peroxy Intermediates in Nonheme Iron Sites.

PubMed

Sutherlin, Kyle D; Liu, Lei V; Lee, Yong-Min; Kwak, Yeonju; Yoda, Yoshitaka; Saito, Makina; Kurokuzu, Masayuki; Kobayashi, Yasuhiro; Seto, Makoto; Que, Lawrence; Nam, Wonwoo; Solomon, Edward I

2016-11-02

Fe III -(hydro)peroxy intermediates have been isolated in two classes of mononuclear nonheme Fe enzymes that are important in bioremediation: the Rieske dioxygenases and the extradiol dioxygenases. The binding mode and protonation state of the peroxide moieties in these intermediates are not well-defined, due to a lack of vibrational structural data. Nuclear resonance vibrational spectroscopy (NRVS) is an important technique for obtaining vibrational information on these and other intermediates, as it is sensitive to all normal modes with Fe displacement. Here, we present the NRVS spectra of side-on Fe III -peroxy and end-on Fe III -hydroperoxy model complexes and assign these spectra using calibrated DFT calculations. We then use DFT calculations to define and understand the changes in the NRVS spectra that arise from protonation and from opening the Fe-O-O angle. This study identifies four spectroscopic handles that will enable definition of the binding mode and protonation state of Fe III -peroxy intermediates in mononuclear nonheme Fe enzymes. These structural differences are important in determining the frontier molecular orbitals available for reactivity.

Multi-Hop Teleportation of an Unknown Qubit State Based on W States

NASA Astrophysics Data System (ADS)

Zhou, Xiang-Zhen; Yu, Xu-Tao; Zhang, Zai-Chen

2018-04-01

Quantum teleportation is important in quantum communication networks. Considering that quantum state information is also transmitted between two distant nodes, intermediated nodes are employed and two multi-hop teleportation protocols based on W state are proposed. One is hop-by-hop teleportation protocol and the other is the improved multi-hop teleportation protocol with centralized unitary transformation. In hop-by-hop protocol, the transmitted quantum state needs to be recovered at every node on the route. In improved multi-hop teleportation protocol with centralized unitary transformation, intermediate nodes need not to recover the transmitted quantum state. Compared to the hop-by-hop protocol, the improved protocol can reduce the transmission delay and improve the transmission efficiency.

Intermediates detected by visible spectroscopy during the reaction of nitrite with deoxyhemoglobin: the effect of nitrite concentration and diphosphoglycerate.

PubMed

Nagababu, Enika; Ramasamy, Somasundaram; Rifkind, Joseph M

2007-10-16

The reaction of nitrite with deoxyhemoglobin (deoxyHb) results in the reduction of nitrite to NO, which binds unreacted deoxyHb forming Fe(II)-nitrosylhemoglobin (Hb(II)NO). The tight binding of NO to deoxyHb is, however, inconsistent with reports implicating this reaction with hypoxic vasodilation. This dilemma is resolved by the demonstration that metastable intermediates are formed in the course of the reaction of nitrite with deoxyHb. The level of intermediates is quantitated by the excess deoxyHb consumed over the concentrations of the final products formed. The dominant intermediate has a spectrum that does not correspond to that of Hb(III)NO formed when NO reacts with methemoglobin (MetHb), but is similar to metHb resulting in the spectroscopic determinations of elevated levels of metHb. It is a delocalized species involving the heme iron, the NO, and perhaps the beta-93 thiol. The putative role for red cell reacted nitrite on vasodilation is associated with reactions involving the intermediate. (1) The intermediate is less stable with a 10-fold excess of nitrite and is not detected with a 100-fold excess of nitrite. This observation is attributed to the reaction of nitrite with the intermediate producing N2O3. (2) The release of NO quantitated by the formation of Hb(II)NO is regulated by changes in the distal heme pocket as shown by the 4.5-fold decrease in the rate constant in the presence of 2,3-diphosphoglycerate. The regulated release of NO or N2O3 as well as the formation of the S-nitroso derivative of hemoglobin, which has also been reported to be formed from the intermediates generated during nitrite reduction, should be associated with any hypoxic vasodilation attributed to the RBC.

Folding of the four-helix bundle FF domain from a compact on-pathway intermediate state is governed predominantly by water motion.

PubMed

Sekhar, Ashok; Vallurupalli, Pramodh; Kay, Lewis E

2012-11-20

Friction plays a critical role in protein folding. Frictional forces originating from random solvent and protein fluctuations both retard motion along the folding pathway and activate protein molecules to cross free energy barriers. Studies of friction thus may provide insights into the driving forces underlying protein conformational dynamics. However, the molecular origin of friction in protein folding remains poorly understood because, with the exception of the native conformer, there generally is little detailed structural information on the other states participating in the folding process. Here, we study the folding of the four-helix bundle FF domain that proceeds via a transiently formed, sparsely populated compact on-pathway folding intermediate whose structure was elucidated previously. Because the intermediate is stabilized by both native and nonnative interactions, friction in the folding transition between intermediate and folded states is expected to arise from intrachain reorganization in the protein. However, the viscosity dependencies of rates of folding from or unfolding to the intermediate, as established by relaxation dispersion NMR spectroscopy, clearly indicate that contributions from internal friction are small relative to those from solvent, so solvent frictional forces drive the folding process. Our results emphasize the importance of solvent dynamics in mediating the interconversion between protein configurations, even those that are highly compact, and in equilibrium folding/unfolding fluctuations in general.

Characterization of Intermediate Oxidation States in CO2 Activation

NASA Astrophysics Data System (ADS)

Dodson, Leah G.; Thompson, Michael C.; Weber, J. Mathias

2018-04-01

Redox chemistry during the activation of carbon dioxide involves changing the charge state in a CO2 molecular unit. However, such changes are usually not well described by integer formal charges, and one can think of COO functional units as being in intermediate oxidation states. In this article, we discuss the properties of CO2 and CO2-based functional units in various charge states. Besides covering isolated CO2 and its ions, we describe the CO2-based ionic species formate, oxalate, and carbonate. Finally, we provide an overview of CO2-based functional groups and ligands in clusters and metal-organic complexes.

Multipulse spectroscopy on the wild-type and YM210W Bacterial Reaction Centre uncovers a new intermediate state in the special pair excited state

NASA Astrophysics Data System (ADS)

Cohen Stuart, T. A.; van Grondelle, R.

2009-06-01

The Bacterial Reaction Centre (BRC) has a complex electronic excited state, P ∗, that evolves into subsequent charge separated product states P +H - and P +B -. Pump-dump-probe spectroscopy on the wild-type BRC and on YM210W, a mutant with a stabilized, long-lived P ∗ excited state, has uncovered a new charge-separated state in both BRC's. When P ∗ is dumped, a fraction of its population is transferred to this state that has a strong Stark shift in the accessory bacteriochlorophyll (B M) region which serves as a signature for P + and a lifetime highly comparable to the slow phase of P ∗ decay. This lead us propose this intermediate to be P +/P -.

From stable to unstable anomaly-induced inflation

NASA Astrophysics Data System (ADS)

Netto, Tibério de Paula; Pelinson, Ana M.; Shapiro, Ilya L.; Starobinsky, Alexei A.

2016-10-01

Quantum effects derived through conformal anomaly lead to an inflationary model that can be either stable or unstable. The unstable version requires a large dimensionless coefficient of about 5× {10}^8 in front of the {R}^2 term that results in the inflationary regime in the R+{R}^2 ("Starobinsky") model being a generic intermediate attractor. In this case the non-local terms in the effective action are practically irrelevant, and there is a `graceful exit' to a low curvature matter-like dominated stage driven by high-frequency oscillations of R - scalarons, which later decay to pairs of all particles and antiparticles, with the amount of primordial scalar (density) perturbations required by observations. The stable version is a genuine generic attractor, so there is no exit from it. We discuss a possible transition from stable to unstable phases of inflation. It is shown that this transition is automatic if the sharp cut-off approximation is assumed for quantum corrections in the period of transition. Furthermore, we describe two different quantum mechanisms that may provide a required large {R}^2-term in the transition period.

Consequences of acid strength for isomerization and elimination catalysis on solid acids.

PubMed

Macht, Josef; Carr, Robert T; Iglesia, Enrique

2009-05-13

We address here the manner in which acid catalysis senses the strength of solid acids. Acid strengths for Keggin polyoxometalate (POM) clusters and zeolites, chosen because of their accurately known structures, are described rigorously by their deprotonation energies (DPE). Mechanistic interpretations of the measured dynamics of alkane isomerization and alkanol dehydration are used to obtain rate and equilibrium constants and energies for intermediates and transition states and to relate them to acid strength. n-Hexane isomerization rates were limited by isomerization of alkoxide intermediates on bifunctional metal-acid mixtures designed to maintain alkane-alkene equilibrium. Isomerization rate constants were normalized by the number of accessible protons, measured by titration with 2,6-di-tert-butylpyridine during catalysis. Equilibrium constants for alkoxides formed by protonation of n-hexene increased slightly with deprotonation energies (DPE), while isomerization rate constants decreased and activation barriers increased with increasing DPE, as also shown for alkanol dehydration reactions. These trends are consistent with thermochemical analyses of the transition states involved in isomerization and elimination steps. For all reactions, barriers increased by less than the concomitant increase in DPE upon changes in composition, because electrostatic stabilization of ion-pairs at the relevant transition states becomes more effective for weaker acids, as a result of their higher charge density at the anionic conjugate base. Alkoxide isomerization barriers were more sensitive to DPE than for elimination from H-bonded alkanols, the step that limits 2-butanol and 1-butanol dehydration rates; the latter two reactions showed similar DPE sensitivities, despite significant differences in their rates and activation barriers, indicating that slower reactions are not necessarily more sensitive to acid strength, but instead reflect the involvement of more unstable organic cations at their transition states. These compensating effects from electrostatic stabilization depend on how similar the charge density in these organic cations is to that in the proton removed. Cations with more localized charge favor strong electrostatic interactions with anions and form more stable ionic structures than do cations with more diffuse charges. Ion-pairs at elimination transition states contain cations with higher local charge density at the sp(2) carbon than for isomerization transition states; as a result, these ion-pairs recover a larger fraction of the deprotonation energy, and, consequently, their reactions become less sensitive to acid strength. These concepts lead us to conclude that the energetic difficulty of a catalytic reaction, imposed by gas-phase reactant proton affinities in transition state analogues, does not determine its sensitivity to the acid strength of solid catalysts.

The OH-Initiated Oxidation of CS2 in the Presence of NO: FTIR Matrix-Isolation and Theoretical Studies.

PubMed

Bil, A; Grzechnik, K; Sałdyka, M; Mielke, Z

2016-09-01

We studied the photochemistry of the carbon disulfide-nitrous acid system with the help of Fourier transform infrared (FTIR) matrix isolation spectroscopy and theoretical methods. The irradiation of the CS2···HONO complexes, isolated in solid argon, with the filtered output of the mercury lamp (λ > 345 nm) was found to produce OCS, SO2, and HNCS; HSCN was also tentatively identified. The (13)C, (15)N, and (2)H isotopic shifts as well as literature data were used for product identifications. The evolution of the measured FTIR spectra with irradiation time and the changes in the spectra after matrix annealing indicated that the identified molecules are the products of different reaction channels: OCS being a product of another reaction path than SO2 and HNCS or HSCN. The possible reaction channels between SC(OH)S/SCS(OH) radicals and NO were studied using DFT/B3LYP/aug-cc-pVTZ method. The SC(OH)S and/or SCS(OH) intermediates are formed when HONO attached to CS2 photodissociates into OH and NO. The calculations indicated that SC(OH)S radical can form with NO two stable adducts. The more stable SC(OH)S···NO structure is a reactant for a simple one-step process leading to OCS and HONS molecules. An alternative, less-stable complex formed between SC(OH)S and NO leads to formation of OCS and HSNO. The calculations predict only one stable complex between SCS(OH) radical and NO, which can dissociate along two channels leading to HNCS and SO2 or HSCN and SO2 as the end products. The identified photoproducts indicate that both SC(OH)S and SCS(OH) adducts are intermediates in the CS2 + OH + NO reaction leading to different reaction products.

δ18O water isotope in the iLOVECLIM model (version 1.0) - Part 3: A paleoperspective based on present-day data-model comparison for oxygen stable isotopes in carbonates

NASA Astrophysics Data System (ADS)

Caley, T.; Roche, D. M.

2013-03-01

Oxygen stable isotopes (18O) are among the most usual tools in paleoclimatology/paleoceanography. Simulation of oxygen stable isotopes allows testing how the past variability of these isotopes in water can be interpreted. By modelling the proxy directly in the model, the results can also be directly compared with the data. Water isotopes have been implemented in the global three-dimensional model of intermediate complexity iLOVECLIM allowing fully coupled atmosphere-ocean simulations. In this study, we present the validation of the model results for present day climate against global database for oxygen stable isotopes in carbonates. The limitation of the model together with the processes operating in the natural environment reveal the complexity of use the continental calcite 18O signal of speleothems for a data-model comparison exercise. On the contrary, the reconstructed surface ocean calcite δ18O signal in iLOVECLIM does show a very good agreement with late Holocene database (foraminifers) at the global and regional scales. Our results indicate that temperature and the isotopic composition of the seawater are the main control on the fossil δ18O signal recorded in foraminifer shells and that depth habitat and seasonality play a role but have secondary importance. We argue that a data-model comparison for surface ocean calcite δ18O in past climate, such as the last glacial maximum (≈21 000 yr), could constitute an interesting tool for mapping the potential shifts of the frontal systems and circulation changes throughout time. Similarly, the potential changes in intermediate oceanic circulation systems in the past could be documented by a data (benthic foraminifers)-model comparison exercise whereas future investigations are necessary in order to quantitatively compare the results with data for the deep ocean.

An Efficient Scheme of Quantum Wireless Multi-hop Communication using Coefficient Matrix

NASA Astrophysics Data System (ADS)

Zhao, Bei; Zha, Xin-Wei; Duan, Ya-Jun; Sun, Xin-Mei

2015-08-01

By defining the coefficient matrix, a new quantum teleportation scheme in quantum wireless multi-hop network is proposed. With the help of intermediate nodes, an unknown qubit state can be teleported between two distant nodes which do not share entanglement in advance. Arbitrary Bell pairs and entanglement swapping are utilized for establishing quantum channel among intermediate nodes. Using collapsed matrix, the initial quantum state can be perfectly recovered at the destination.

JPRS Report, China

DTIC Science & Technology

1987-12-31

inconsistent with Japan’s declared policy of opening up her markets. JPRS-CAR-87-061 31 December 1987 28 ECONOMIC 2. The "three lows "— low oil prices, the...intermediate- range warheads in Soviet Asia and the United States, respectively. But the United States and some Western European nations soon demanded...Union insisted on keeping 100 intermediate- range guided missiles in Asia while balking at the U.S. demand that it be allowed to deploy an equal