Toroidal modelling of resistive internal kink and fishbone instabilities

NASA Astrophysics Data System (ADS)

Wu, Tingting; He, Hongda; Liu, Yueqiang; Liu, Yue; Hao, G. Z.; Zhu, Jinxia

2018-05-01

The influence of energetic particles and plasma resistivity on the n =1 ( n is the toroidal mode number) internal kink and fishbone modes in tokamak plasmas is numerically investigated, using the full toroidal, resistive magnetohydrodynamic-kinetic hybrid stability code MARS-K [Liu et al., Phys. Plasmas 15 112503 (2008)]. The results show that energetic particles can either stabilize or destabilize the ideal internal kink mode, depending on the radial profiles of the particles' density and pressure. Resistive fishbones with and without an ideal wall are investigated. It is found that, in the presence of energetic particles as well as plasma resistivity, two branches of unstable roots exist, for a plasma which is ideally stable to the internal kink instability. One is the resistive internal kink mode. The other is the resistive fishbone mode. These two-branch solutions show similar behaviors, independent of whether the initial ideal kink stability is due to an ideal wall stabilization for high-beta plasmas, or due to a stable equilibrium below the Bussac pressure limit. For a realistic toroidal plasma, the resistive internal kink is the dominant instability, which grows much faster than the resistive fishbone. The plasma resistivity destabilizes the resistive internal kink while stabilizes the resistive fishbone. Systematic comparison with an analytic model qualitatively confirms the MARS-K results. Compared to analytic models based on the perturbative approach, MARS-K offers an improved physics model via self-consistent treatment of coupling between the fluid and kinetic effects due to energetic particles.

Making A D-Latch Sensitive To Alpha Particles

NASA Technical Reports Server (NTRS)

Buehler, Martin G.; Blaes, Brent R.; Nixon, Robert H.

1994-01-01

Standard complementary metal oxide/semiconductor (CMOS) D-latch integrated circuit modified to increase susceptibility to single-event upsets (SEU's) (changes in logic state) caused by impacts of energetic alpha particles. Suitable for use in relatively inexpensive bench-scale SEU tests of itself and of related integrated circuits like static random-access memories.

A model of energetic ion effects on pressure driven tearing modes in tokamaks

DOE PAGES

Halfmoon, M. R.; Brennan, D. P.

2017-06-05

Here, the effects that energetic trapped ions have on linear resistive magnetohydrodynamic (MHD) instabilities are studied in a reduced model that captures the essential physics driving or damping the modes through variations in the magnetic shear. The drift-kinetic orbital interaction of a slowing down distribution of trapped energetic ions with a resistive MHD instability is integrated to a scalar contribution to the perturbed pressure, and entered into an asymptotic matching formalism for the resistive MHD dispersion relation. Toroidal magnetic field line curvature is included to model trapping in the particle distribution, in an otherwise cylindrical model. The focus is onmore » a configuration that is driven unstable to the m/n = 2/1 mode by increasing pressure, where m is the poloidal mode number and n is the toroidal. The particles and pressure can affect the mode both in the core region where there can be low and reversed shear and outside the resonant surface in significant positive shear. The results show that the energetic ions damp and stabilize the mode when orbiting in significant positive shear, increasing the marginal stability boundary. However, the inner core region contribution with low and reversed shear can drive the mode unstable. This effect of shear on the energetic ion pressure contribution is found to be consistent with the literature. These results explain the observation that the 2/1 mode was found to be damped and stabilized by energetic ions in delta δf-MHD simulations of tokamak experiments with positive shear throughout, while the 2/1 mode was found to be driven unstable in simulations of experiments with weakly reversed shear in the core. This is also found to be consistent with related experimental observations of the stability of the 2/1 mode changing significantly with core shear.« less

A model of energetic ion effects on pressure driven tearing modes in tokamaks

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

Halfmoon, M. R.; Brennan, D. P.

Here, the effects that energetic trapped ions have on linear resistive magnetohydrodynamic (MHD) instabilities are studied in a reduced model that captures the essential physics driving or damping the modes through variations in the magnetic shear. The drift-kinetic orbital interaction of a slowing down distribution of trapped energetic ions with a resistive MHD instability is integrated to a scalar contribution to the perturbed pressure, and entered into an asymptotic matching formalism for the resistive MHD dispersion relation. Toroidal magnetic field line curvature is included to model trapping in the particle distribution, in an otherwise cylindrical model. The focus is onmore » a configuration that is driven unstable to the m/n = 2/1 mode by increasing pressure, where m is the poloidal mode number and n is the toroidal. The particles and pressure can affect the mode both in the core region where there can be low and reversed shear and outside the resonant surface in significant positive shear. The results show that the energetic ions damp and stabilize the mode when orbiting in significant positive shear, increasing the marginal stability boundary. However, the inner core region contribution with low and reversed shear can drive the mode unstable. This effect of shear on the energetic ion pressure contribution is found to be consistent with the literature. These results explain the observation that the 2/1 mode was found to be damped and stabilized by energetic ions in delta δf-MHD simulations of tokamak experiments with positive shear throughout, while the 2/1 mode was found to be driven unstable in simulations of experiments with weakly reversed shear in the core. This is also found to be consistent with related experimental observations of the stability of the 2/1 mode changing significantly with core shear.« less

Upper-Bound Estimates Of SEU in CMOS

NASA Technical Reports Server (NTRS)

Edmonds, Larry D.

1990-01-01

Theory of single-event upsets (SEU) (changes in logic state caused by energetic charged subatomic particles) in complementary metal oxide/semiconductor (CMOS) logic devices extended to provide upper-bound estimates of rates of SEU when limited experimental information available and configuration and dimensions of SEU-sensitive regions of devices unknown. Based partly on chord-length-distribution method.

Energetic Coupling between Ligand Binding and Dimerization in E. coli Phosphoglycerate Mutase

PubMed Central

Gardner, Nathan W.; Monroe, Lyman K.; Kihara, Daisuke; Park, Chiwook

2016-01-01

Energetic coupling of two molecular events in a protein molecule is ubiquitous in biochemical reactions mediated by proteins, such as catalysis and signal transduction. Here, we investigate energetic coupling between ligand binding and folding of a dimer using a model system that shows three-state equilibrium unfolding in an exceptional quality. The homodimeric E. coli cofactor-dependent phosphoglycerate mutase (dPGM) was found to be stabilized by ATP in a proteome-wide screen, although dPGM does not require or utilize ATP for enzymatic function. We investigated the effect of ATP on the thermodynamic stability of dPGM using equilibrium unfolding. In the absence of ATP, dPGM populates a partially unfolded, monomeric intermediate during equilibrium unfolding. However, addition of 1.0 mM ATP drastically reduces the population of the intermediate by selectively stabilizing the native dimer. Using a computational ligand docking method, we predicted ATP binds to the active site of the enzyme using the triphosphate group. By performing equilibrium unfolding and isothermal titration calorimetry with active-site variants of dPGM, we confirmed that active-site residues are involved in ATP binding. Our findings show that ATP promotes dimerization of the protein by binding to the active site, which is distal from the dimer interface. This cooperativity suggests an energetic coupling between the active-site and the dimer interface. We also propose a structural link to explain how ligand binding to the active site is energetically coupled with dimerization. PMID:26919584

The effects of the geosynchronous energetic particle radiation environment on spacecraft charging phenomena

NASA Technical Reports Server (NTRS)

Reagan, J. B.; Imhof, W. L.; Gaines, E. E.

1977-01-01

The energetic electron environment at the geosynchronous orbit is responsible for a variety of adverse charging effects on spacecraft components. The most serious of these is the degradation and failure of a complementary-metal-oxide-semiconductor (CMOS) electronic components as a result of internal charge-buildup induced by the energetic electrons. Efforts to accurately determine the expected lifetime of these components in this orbit are hampered by the lack of detailed knowledge of the electron spectrum and intensity, particularly of the more penetrating energies greater than 1.5 MeV. This problem is illustrated through the calculation of the dose received by a CMOS device from the energetic electrons and associated bremsstrahlung as a function of aluminum shielding thickness using the NASA AE-6 and the Aerospace measured electron environments. Two computational codes which were found to be in good agreement were used to perform the calculations. For a given shielding thickness the dose received with the two radiation environments differ by as much as a factor of seven with a corresponding variation in lifetime of the CMOS.

An evaluation of complementary approaches to elucidate fundamental interfacial phenomena driving adhesion of energetic materials

DOE PAGES

Hoss, Darby J.; Knepper, Robert; Hotchkiss, Peter J.; ...

2016-03-23

In this study, cohesive Hamaker constants of solid materials are measured via optical and dielectric properties (i.e., Lifshitz theory), inverse gas chromatography (IGC), and contact angle measurements. To date, however, a comparison across these measurement techniques for common energetic materials has not been reported. This has been due to the inability of the community to produce samples of energetic materials that are readily compatible with contact angle measurements. Here we overcome this limitation by using physical vapor deposition to produce thin films of five common energetic materials, and the contact angle measurement approach is applied to estimate the cohesive Hamakermore » constants and surface energy components of the materials. The cohesive Hamaker constants range from 85 zJ to 135 zJ across the different films. When these Hamaker constants are compared to prior work using Lifshitz theory and nonpolar probe IGC, the relative magnitudes can be ordered as follows: contact angle > Lifshitz > IGC. Furthermore, the dispersive surface energy components estimated here are in good agreement with those estimated by IGC. Due to these results, researchers and technologists will now have access to a comprehensive database of adhesion constants which describe the behavior of these energetic materials over a range of settings.« less

Temperature Dependence and Energetics of Single Ions at the Aqueous Liquid-Vapor Interface

PubMed Central

Ou, Shuching; Patel, Sandeep

2014-01-01

We investigate temperature-dependence of free energetics with two single halide anions, I− and Cl−, crossing the aqueous liquid-vapor interface through molecular dynamics simulations. The result shows that I− has a modest surface stability of 0.5 kcal/mol at 300 K and the stability decreases as the temperature increases, indicating the surface adsorption process for the anion is entropically disfavored. In contrast, Cl− shows no such surface state at all temperatures. Decomposition of free energetics reveals that water-water interactions provide a favorable enthalpic contribution, while the desolvation of ion induces an increase in free energy. Calculations of surface fluctuations demonstrate that I− generates significantly greater interfacial fluctuations compared to Cl−. The fluctuation is attributed to the malleability of the solvation shells, which allows for more long-ranged perturbations and solvent density redistribution induced by I− as the anion approaches the liquid-vapor interface. The increase in temperature of the solvent enhances the inherent thermally-excited fluctuations and consequently reduces the relative contribution from anion to surface fluctuations, which is consistent with the decrease in surface-stability of I−. Our results indicate a strong correlation with induced interfacial fluctuations and anion surface stability; moreover, resulting temperature dependent behavior of induced fluctuations suggests the possibility of a critical level of induced fluctuations associated with surface stability. PMID:23537166

Ordered and layered structure of liquid nitromethane within a graphene bilayer: toward stabilization of energetic materials through nanoscale confinement.

PubMed

Liu, Yingzhe; Yu, Tao; Lai, Weipeng; Kang, Ying; Ge, Zhongxue

2015-03-01

The structural characteristics involving thermal stabilities of liquid nitromethane (NM)—one of the simplest energetic materials—confined within a graphene (GRA) bilayer were investigated by means of all-atom molecular dynamics simulations and density functional theory calculations. The results show that ordered and layered structures are formed at the confinement of the GRA bilayer induced by the van der Waals attractions of NM with GRA and the dipole-dipole interactions of NM, which is strongly dependent on the confinement size, i.e., the GRA bilayer distance. These unique intermolecular arrangements and preferred orientations of confined NM lead to higher stabilities than bulk NM revealed by bond dissociation energy calculations.

Highly Anomalous Energetics of Protein Cold Denaturation Linked to Folding-Unfolding Kinetics

PubMed Central

Romero-Romero, M. Luisa; Inglés-Prieto, Alvaro; Ibarra-Molero, Beatriz; Sanchez-Ruiz, Jose M.

2011-01-01

Despite several careful experimental analyses, it is not yet clear whether protein cold-denaturation is just a “mirror image” of heat denaturation or whether it shows unique structural and energetic features. Here we report that, for a well-characterized small protein, heat denaturation and cold denaturation show dramatically different experimental energetic patterns. Specifically, while heat denaturation is endothermic, the cold transition (studied in the folding direction) occurs with negligible heat effect, in a manner seemingly akin to a gradual, second-order-like transition. We show that this highly anomalous energetics is actually an apparent effect associated to a large folding/unfolding free energy barrier and that it ultimately reflects kinetic stability, a naturally-selected trait in many protein systems. Kinetics thus emerges as an important factor linked to differential features of cold denaturation. We speculate that kinetic stabilization against cold denaturation may play a role in cold adaptation of psychrophilic organisms. Furthermore, we suggest that folding-unfolding kinetics should be taken into account when analyzing in vitro cold-denaturation experiments, in particular those carried out in the absence of destabilizing conditions. PMID:21829584

Distillation of multipartite entanglement by complementary stabilizer measurements.

PubMed

Miyake, Akimasa; Briegel, Hans J

2005-11-25

We propose a scheme of multipartite entanglement distillation driven by a complementary pair of stabilizer measurements to distill directly a wider range of states beyond the stabilizer code states (such as the Greenberger-Horne-Zeilinger states). We make our idea explicit by constructing a recurrence protocol for the 3-qubit state [formula: see text]. Noisy states resulting from typical decoherence can be directly purified in a few steps, if their initial fidelity is larger than a threshold. For general input mixed states, we observe distillations to hierarchical fixed points, i.e., not only to the state but also to the 2-qubit Bell pair, depending on their initial entanglement.

Toward a Molecular Understanding of Energetics in Li–S Batteries Using Nonaqueous Electrolytes: A High-Level Quantum Chemical Study

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

Assary, Rajeev S.; Curtiss, Larry A.; Moore, Jeffrey S.

2014-06-05

The Li-S battery (secondary cell or redox flow) technology is a promising future alternative to the present lithium intercalation-based energy storage and, therefore, a molecular level understanding of the chemical processes and properties such as stability of intermediates, reactivity of polysulfides and reactivity towards the non-aqueous electrolytes in the Li-S batteries is of great interest. In this paper, quantum chemical methods (G4MP2, MP2, and B3LYP) were utilized to compute reduction potentials of lithium polysulfides and polysulfide molecular clusters, energetics of disproportionation and association reactions of likely intermediates, and their reactions with ether-based electrolytes. Based on the computed reaction energetics inmore » solution, a probable mechanism during the discharge process for polysulfide anions and lithium polysulfides in solution is proposed and likely intermediates such as S42-,S32-, S22-, and S31- radical were identified. Additionally, the stability and reactivity of propylene carbonate and tetraglyme solvent molecules were assessed against the above-mentioned intermediates and other reactive species by computing the reaction energetics required to initiate the solvent decomposition reactions in solution. Calculations suggest that the propylene carbonate molecule is unstable against the polysulfide anions such as S22-, S32-, and S42- (ΔH† < 0.8 eV) and highly reactive towards Li2S2 and Li2S3. Even though the tetraglyme solvent molecule exhibits increased stability towards polysulfide anions compared to propylene carbonate, this molecule too is vulnerable to nucleophilic attack from Li2S2 and Li2S3 species in solutions. Hence, a long- term stability of the ether molecules is unlikely if high concentration of these reactive intermediates present in the Li-S energy storage systems.« less

Determining the Energetics of the Hydrogen Bond through FTIR: A Hands-On Physical Chemistry Lab Experiment

ERIC Educational Resources Information Center

Guerin, Abby C.; Riley, Kristi; Rupnik, Kresimir; Kuroda, Daniel G.

2016-01-01

Hydrogen bonds are very important chemical structures that are responsible for many unique and important properties of solvents, such as the solvation power of water. These distinctive features are directly related to the stabilization energy conferred by hydrogen bonds to the solvent. Thus, the characterization of hydrogen bond energetics has…

Pressure profiles of plasmas confined in the field of a dipole magnet

NASA Astrophysics Data System (ADS)

Davis, Matthew Stiles

Understanding the maintenance and stability of plasma pressure confined by a strong magnetic field is a fundamental challenge in both laboratory and space plasma physics. Using magnetic and X-ray measurements on the Levitated Dipole Experiment (LDX), the equilibrium plasma pressure has been reconstructed, and variations of the plasma pressure for different plasma conditions have been examined. The relationship of these profiles to the magnetohydrodynamic (MHD) stability limit, and to the enhanced stability limit that results from a fraction of energetic trapped electrons, has been analyzed. In each case, the measured pressure profiles and the estimated fractional densities of energetic electrons were qualitatively consistent with expectations of plasma stability. LDX confines high temperature and high pressure plasma in the field of a superconducting dipole magnet. The strong dipole magnet can be either mechanically supported or magnetically levitated. When the dipole was mechanically supported, the plasma density profile was generally uniform while the plasma pressure was highly peaked. The uniform density was attributed to the thermal plasma being rapidly lost along the field to the mechanical supports. In contrast, the strongly peaked plasma pressure resulted from a fraction of energetic, mirror trapped electrons created by microwave heating at the electron cyclotron resonance (ECRH). These hot electrons are known to be gyrokinetically stabilized by the background plasma and can adopt pressure profiles steeper than the MHD limit. X-ray measurements indicated that this hot electron population could be described by an energy distribution in the range 50-100 keV. Combining information from the magnetic reconstruction of the pressure profile, multi-chord interferometer measurements of the electron density profile, and X-ray measurements of the hot electron energy distribution, the fraction of energetic electrons at the pressure peak was estimated to be ˜ 35% of the total electron population. When the dipole was magnetically levitated the plasma density increased substantially because particle losses to the mechanical supports were eliminated so particles could only be lost via slower cross-field transport processes. The pressure profile was observed to be broader during levitated operation than it was during supported operation, and the pressure appeared to be contained in both a thermal population and an energetic electron population. X-ray spectra indicated that the X-rays came from a similar hot electron population during levitated and supported operation; however, the hot electron fraction was an order of magnitude smaller during levitated operation (<3% of the total electron population). Pressure gradients for both supported and levitated plasmas were compared to the MHD limit. Levitated plasmas had pressure profiles that were (i) steeper than, (ii) shallower than, or (iii) near the MHD limit dependent on plasma conditions. However, those profiles that exceeded the MHD limit were observed to have larger fractions of energetic electrons. When the dipole magnet was supported, high pressure plasmas always had profiles that exceeded the MHD interchange stability limit, but the high pressure in these plasmas appeared to arise entirely from a population of energetic trapped electrons.

Phase stabilities at a glance: Stability diagrams of nickel dipnictides

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

Bachhuber, F.; School of Chemical Sciences, The University of Auckland, Private Bag 92019, Auckland; Rothballer, J.

2013-12-07

In the course of the recent advances in chemical structure prediction, a straightforward type of diagram to evaluate phase stabilities is presented based on an expedient example. Crystal structures and energetic stabilities of dipnictides NiPn{sub 2} (Pn = N, P, As, Sb, Bi) are systematically investigated by first principles calculations within the framework of density functional theory using the generalized gradient approximation to treat exchange and correlation. These dipnictides show remarkable polymorphism that is not yet understood systematically and offers room for the discovery of new phases. Relationships between the concerned structures including the marcasite, the pyrite, the arsenopyrite/CoSb{sub 2},more » and the NiAs{sub 2} types are highlighted by means of common structural fragments. Electronic stabilities of experimentally known and related AB{sub 2} structure types are presented graphically in so-called stability diagrams. Additionally, competing binary phases are taken into consideration in the diagrams to evaluate the stabilities of the title compounds with respect to decomposition. The main purpose of the stability diagrams is the introduction of an image that enables the estimation of phase stabilities at a single glance. Beyond that, some of the energetically favored structure types can be identified as potential new phases.« less

Observation of runaway electron beams by visible color camera in the Experimental Advanced Superconducting Tokamak

NASA Astrophysics Data System (ADS)

Shi, Yuejiang; Fu, Jia; Li, Jiahong; Yang, Yu; Wang, Fudi; Li, Yingying; Zhang, Wei; Wan, Baonian; Chen, Zhongyong

2010-03-01

The synchrotron radiation originated from the energetic runaway electrons has been measured by a visible complementary metal oxide semiconductor camera working in the wavelength ranges of 380-750 nm in the Experimental Advanced Superconducting Tokamak [H. Q. Liu et al., Plasma Phys. Contr. Fusion 49, 995 (2007)]. With a tangential viewing into the plasma in the direction of electron approach on the equatorial plane, the synchrotron radiation from the energetic runaway electrons was measured in full poloidal cross section. The synchrotron radiation diagnostics provides a direct pattern of the runaway beam inside the plasma. The energy and pitch angle of runaway electrons have been obtained according to the synchrotron radiation pattern. A stable shell shape of synchrotron radiation has been observed in a few runaway discharges.

A combined calorimetric and computational study of the energetics of rare earth substituted UO 2 systems

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

Zhang, Lei; Solomon, Jonathan M.; Asta, Mark

2015-09-01

The energetics of rare earth substituted UO2 solid solutions (U1-xLnxO2-0.5x+y, where Ln = La, Y, and Nd) are investigated employing a combination of calorimetric measurements and density functional theory based computations. Calculated and measured formation enthalpies agree within 10 kJ/mol for stoichiometric oxygen/metal compositions. To better understand the factors governing the stability and defect binding in rare earth substituted urania solid solutions, systematic trends in the energetics are investigated based on the present results and previous computational and experimental thermochemical studies of rare earth substituted fluorite oxides (A1-xLnxO2-0.5x, where A = Hf, Zr, Ce, and Th). A consistent trend towardsmore » increased energetic stability with larger size mismatch between the smaller host tetravalent cation and the larger rare earth trivalent cation is found for both actinide and non-actinide fluorite oxide systems where aliovalent substitution of Ln cations is compensated by oxygen vacancies. However, the large exothermic oxidation enthalpy in the UO2 based systems favors oxygen rich compositions where charge compensation occurs through the formation of uranium cations with higher oxidation states.« less

Damping Rates of Energetic Particle Modes and Stability With Changing Equilibrium Conditions in the MST Reversed-Field Pinch

NASA Astrophysics Data System (ADS)

Sears, S. H.; Almagri, A. F.; Anderson, J. K.; Bonofiglo, P. J.; Capecchi, W.; Kim, J.

2016-10-01

The damping of Alfvenic waves is an important process, with implications varying from anomalous ion heating in laboratory and astrophysical plasmas to the stability of fusion alpha-driven modes in a burning plasma. With a 1 MW NBI on the MST, a controllable set of energetic particle modes (EPMs) and Alfvenic eigenmodes can be excited. We investigate the damping of these modes as a function of both magnetic and flow shear. Typical EPM damping rates are -104 s-1 in standard RFP discharges. Magnetic shear in the region of large energetic ion density is -2 cm-1 and can be increased up to -2.5 cm-1 by varying the boundary field. Continuum mode damping rates can be reduced up to 50%. New experiments use a bias probe to control the rotation profile. Accelerating the edge plasma relative to the rapidly rotating NBI-driven core decreases the flow shear, while decelerating the edge plasma increases the flow shear in the region of strong energetic ion population. Mode damping rates measured as a function of the local flow shear are compared to ideal MHD predictions. Work supported by US DOE.

Irmpd Action Spectroscopy and Computational Approaches to Elucidate Gas-Phase Structures and Energetics of 2'-DEOXYCYTIDINE and Cytidine Sodium Complexes

NASA Astrophysics Data System (ADS)

Zhu, Yanlong; Hamlow, Lucas; He, Chenchen; Gao, Juehan; Oomens, Jos; Rodgers, M. T.

2016-06-01

The local structures of DNA and RNA are influenced by protonation, deprotonation and noncovalent interactions with cations. In order to determine the effects of Na+ cationization on the gas-phase structures of 2'-deoxycytidine, [dCyd+Na]+, and cytidine, [Cyd+Na]+, infrared multiple photon dissociation (IRMPD) action spectra of these sodium cationized nucleosides are measured over the range extending from 500 to 1850 wn using the FELIX free electron laser. Complementary electronic structure calculations are performed to determine the stable low-energy conformations of these complexes. Geometry optimizations, frequency analyses, and IR spectra of these species are determined at the B3LYP/6-311+G(d,p) level of theory. Single-point energies are calculated at the B3LYP/6-311+G(2d,2p) level of theory to determine the relative stabilities of these conformations. Comparison of the measure IRMPD action spectra and computed linear IR spectra enable the conformations accessed in the experiments to be elucidated. For both cytosine nucleosides, tridentate binding of the Na+ cation to the O2, O4' and O5' atoms of the nucleobase and sugar is observed. Present results for the sodium cationized nucleosides are compared to results for the analogous protonated forms of these nucleosides to elucidate the effects of multiple chelating interactions with the sodium cation vs. hydrogen bonding interactions in the protonated systems on the structures and stabilities of these nucleosides.

Room-Temperature Micron-Scale Exciton Migration in a Stabilized Emissive Molecular Aggregate.

PubMed

Caram, Justin R; Doria, Sandra; Eisele, Dörthe M; Freyria, Francesca S; Sinclair, Timothy S; Rebentrost, Patrick; Lloyd, Seth; Bawendi, Moungi G

2016-11-09

We report 1.6 ± 1 μm exciton transport in self-assembled supramolecular light-harvesting nanotubes (LHNs) assembled from amphiphillic cyanine dyes. We stabilize LHNs in a sucrose glass matrix, greatly reducing light and oxidative damage and allowing the observation of exciton-exciton annihilation signatures under weak excitation flux. Fitting to a one-dimensional diffusion model, we find an average exciton diffusion constant of 55 ± 20 cm 2 /s, among the highest measured for an organic system. We develop a simple model that uses cryogenic measurements of static and dynamic energetic disorder to estimate a diffusion constant of 32 cm 2 /s, in agreement with experiment. We ascribe large exciton diffusion lengths to low static and dynamic energetic disorder in LHNs. We argue that matrix-stabilized LHNS represent an excellent model system to study coherent excitonic transport.

Molecular recognition of thiaclopride by Aplysia californica AChBP: new insights from a computational investigation

NASA Astrophysics Data System (ADS)

Alamiddine, Zakaria; Selvam, Balaji; Cerón-Carrasco, José P.; Mathé-Allainmat, Monique; Lebreton, Jacques; Thany, Steeve H.; Laurent, Adèle D.; Graton, Jérôme; Le Questel, Jean-Yves

2015-12-01

The binding of thiaclopride (THI), a neonicotinoid insecticide, with Aplysia californica acetylcholine binding protein ( Ac-AChBP), the surrogate of the extracellular domain of insects nicotinic acetylcholine receptors, has been studied with a QM/QM' hybrid methodology using the ONIOM approach (M06-2X/6-311G(d):PM6). The contributions of Ac-AChBP key residues for THI binding are accurately quantified from a structural and energetic point of view. The importance of water mediated hydrogen-bond (H-bond) interactions involving two water molecules and Tyr55 and Ser189 residues in the vicinity of the THI nitrile group, is specially highlighted. A larger stabilization energy is obtained with the THI- Ac-AChBP complex compared to imidacloprid (IMI), the forerunner of neonicotinoid insecticides. Pairwise interaction energy calculations rationalize this result with, in particular, a significantly more important contribution of the pivotal aromatic residues Trp147 and Tyr188 with THI through CH···π/CH···O and π-π stacking interactions, respectively. These trends are confirmed through a complementary non-covalent interaction (NCI) analysis of selected THI- Ac-AChBP amino acid pairs.

Nitrogen-rich salts based on the energetic [monoaquabis(N,N-bis(1H-tetrazol-5-yl)amine)-zinc(II)] anion: a promising design in the development of new energetic materials.

PubMed

Li, Fugang; Bi, Yangang; Zhao, Wenyuan; Zhang, Tonglai; Zhou, Zunning; Yang, Li

2015-02-16

Nitrogen-rich energetic salts involving various cations (lithium, 1; ammonium, 2; hydrazinium, 3; hydroxylammonium, 4; guanidinium, 5; aminoguanidinium, 6; diaminoguanidinium, 7; and triaminoguanidinium, 8) based on nitrogen-rich anion [Zn(BTA)2(H2O)](2-) (N% = 65.37, BTA = N,N-bis[1H-tetrazol-5-yl]amine anion) were synthesized with a simple method. The crystal structures of all compounds except 1, 2, and 6 were determined by single-crystal X-ray diffraction and fully characterized by elemental analysis and FT-IR spectroscopy. The thermal stabilities were investigated by differential scanning calorimetry (DSC). The DSC results show that all compounds exhibit high thermal stabilities (decomposition temperature >200 °C). Additionally, the heats of formation were calculated on the basis of the experimental constant-volume energies of combustion measured by using bomb calorimetry. Lastly, the sensitivities toward impact and friction were assessed according to Bundesamt für Materialforschung (BAM) standard methods.

Dynamics of energetic particle driven modes and MHD modes in wall-stabilized high-β plasmas on JT-60U and DIII-D

NASA Astrophysics Data System (ADS)

Matsunaga, G.; Okabayashi, M.; Aiba, N.; Boedo, J. A.; Ferron, J. R.; Hanson, J. M.; Hao, G. Z.; Heidbrink, W. W.; Holcomb, C. T.; In, Y.; Jackson, G. L.; Liu, Y. Q.; Luce, T. C.; McKee, G. R.; Osborne, T. H.; Pace, D. C.; Shinohara, K.; Snyder, P. B.; Solomon, W. M.; Strait, E. J.; Turnbull, A. D.; Van Zeeland, M. A.; Watkins, J. G.; Zeng, L.; the DIII-D Team; the JT-60 Team

2013-12-01

In the wall-stabilized high-β plasmas in JT-60U and DIII-D, interactions between energetic particle (EP) driven modes (EPdMs) and edge localized modes (ELMs) have been observed. The interaction between the EPdM and ELM are reproducibly observed. Many EP diagnostics indicate a strong correlation between the distorted waveform of the EPdM and the EP transport to the edge. The waveform distortion is composed of higher harmonics (n ⩾ 2) and looks like a density snake near the plasma edge. According to statistical analyses, ELM triggering by the EPdMs requires a finite level of waveform distortion and pedestal recovery. ELM pacing by the EPdMs occurs when the repetition frequency of the EPdMs is higher than the natural ELM frequency. EPs transported by EPdMs are thought to contribute to change the edge stability.

Optimal exploitation of spatially distributed trophic resources and population stability

USGS Publications Warehouse

Basset, A.; Fedele, M.; DeAngelis, D.L.

2002-01-01

The relationships between optimal foraging of individuals and population stability are addressed by testing, with a spatially explicit model, the effect of patch departure behaviour on individual energetics and population stability. A factorial experimental design was used to analyse the relevance of the behavioural factor in relation to three factors that are known to affect individual energetics; i.e. resource growth rate (RGR), assimilation efficiency (AE), and body size of individuals. The factorial combination of these factors produced 432 cases, and 1000 replicate simulations were run for each case. Net energy intake rates of the modelled consumers increased with increasing RGR, consumer AE, and consumer body size, as expected. Moreover, through their patch departure behaviour, by selecting the resource level at which they departed from the patch, individuals managed to substantially increase their net energy intake rates. Population stability was also affected by the behavioural factors and by the other factors, but with highly non-linear responses. Whenever resources were limiting for the consumers because of low RGR, large individual body size or low AE, population density at the equilibrium was directly related to the patch departure behaviour; on the other hand, optimal patch departure behaviour, which maximised the net energy intake at the individual level, had a negative influence on population stability whenever resource availability was high for the consumers. The consumer growth rate (r) and numerical dynamics, as well as the spatial and temporal fluctuations of resource density, which were the proximate causes of population stability or instability, were affected by the behavioural factor as strongly or even more strongly than by the others factors considered here. Therefore, patch departure behaviour can act as a feedback control of individual energetics, allowing consumers to optimise a potential trade-off between short-term individual fitness and long-term population stability. ?? 2002 Elsevier Science B.V. All rights reserved.

Energetic-Energetic Cocrystals of Diacetone Diperoxide (DADP): Dramatic and Divergent Sensitivity Modifications via Cocrystallization.

PubMed

Landenberger, Kira B; Bolton, Onas; Matzger, Adam J

2015-04-22

Here we report a series of energetic-energetic cocrystals that incorporate the primary explosive diacetone diperoxide (DADP) with a series of trihalotrinitrobenzene explosives: 1:1 DADP/1,3,5-trichloro-2,4,6-trinitrobenzene (TCTNB), 1:1 DADP/1,3,5-tribromo-2,4,6-trinitrobenzene (TBTNB), and 1:1 DADP/1,3,5-triiodo-2,4,6-trinitrobenzene (TITNB). Acetone peroxides are attractive for their inexpensive and facile synthesis, but undesirable properties such as poor stability, intractably high sensitivity and low density, an indicator for low explosive power, have limited their application. Here through cocrystallization the density, oxygen balance, and stability of DADP are dramatically improved. Regarding sensitivity, in the case of the DADP/TCTNB cocrystal, the high impact sensitivity of DADP is retained by the cocrystal, making it a denser and less volatile form of DADP that remains viable as a primary explosive. Conversely, the DADP/TITNB cocrystal features impact sensitivity that is greatly reduced relative to both pure DADP and pure TITNB, demonstrating for the first time an energetic cocrystal that is less sensitive to impact than either of its pure components. This dramatic difference in cocrystal sensitivities may stem from the significantly different halogen-peroxide interactions seen in each cocrystal structure. These results highlight how sensitivity is defined by complex relationships between inherent bond strengths and solid-state properties, and cocrystal series such as that presented here provide a powerful experimental platform to probe this relationship.

High-Pressure Structural Response of an Insensitive Energetic Crystal: Dihydroxylammonium 5,5'-Bistetrazole-1,1'-diolate (TKX-50)

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

Dreger, Zbigniew A.; Stash, Adam I.; Yu, Zhi-Gang

2017-03-06

The structural response of a novel, insensitive energetic crystal—dihydroxylammonium 5,5'-bistetrazole-1,1'-diolate (TKX-50)—was examined under high pressure. Using synchrotron single-crystal X-ray diffraction measurements, details of molecular, intermolecular, and crystal changes were determined to ~10 GPa to understand its structural stability. The experimental results showed that TKX-50 exhibits highly anisotropic compression and significantly lower volume compressibility than currently known energetic crystals. These results are found to be in general agreement with our previous predictions from the DFT calculations. Additionally, the experimental data revealed anomalous compression—an expansion of the unit cell along the a axis (negative linear compressibility, NLC) upon compression to ~3 GPa.more » The structural analyses demonstrated that this unusual effect, the first such observation in an energetic crystal, is a consequence of the highly anisotropic response of 3D motifs, comprised of two parallel anions [(C 2N 8O 2) 2–] linked with two cations [(NH 3OH) +] through four strong hydrogen bonds. The present results demonstrate that the structural stability of TKX-50 is controlled by the strong and highly anisotropic intermolecular interactions, and these may contribute to its shock insensitivity.« less

High-pressure structural response of an insensitive energetic crystal: Dihydroxylammonium 5,5'-bistetrazole-1,1'-diolate (TKX-50)

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

Dreger, Zbigniew A.; Stash, Adam I.; Yu, Zhi -Gang

The structural response of a novel, insensitive energetic crystal—dihydroxylammonium 5,5'-bistetrazole-1,1'-diolate (TKX-50)—was examined under high pressure. Using synchrotron single-crystal X-ray diffraction measurements, details of molecular, intermolecular, and crystal changes were determined to ~10 GPa to understand its structural stability. The experimental results showed that TKX-50 exhibits highly anisotropic compression and significantly lower volume compressibility than currently known energetic crystals. These results are found to be in general agreement with our previous predictions from the DFT calculations. Additionally, the experimental data revealed anomalous compression—an expansion of the unit cell along the a axis (negative linear compressibility, NLC) upon compression to ~3 GPa.more » The structural analyses demonstrated that this unusual effect, the first such observation in an energetic crystal, is a consequence of the highly anisotropic response of 3D motifs, comprised of two parallel anions [(C 2N 8O 2) 2–] linked with two cations [(NH 3OH) +] through four strong hydrogen bonds. Finally, the present results demonstrate that the structural stability of TKX-50 is controlled by the strong and highly anisotropic intermolecular interactions, and these may contribute to its shock insensitivity.« less

High-pressure structural response of an insensitive energetic crystal: Dihydroxylammonium 5,5'-bistetrazole-1,1'-diolate (TKX-50)

DOE PAGES

Dreger, Zbigniew A.; Stash, Adam I.; Yu, Zhi -Gang; ...

2017-02-28

The structural response of a novel, insensitive energetic crystal—dihydroxylammonium 5,5'-bistetrazole-1,1'-diolate (TKX-50)—was examined under high pressure. Using synchrotron single-crystal X-ray diffraction measurements, details of molecular, intermolecular, and crystal changes were determined to ~10 GPa to understand its structural stability. The experimental results showed that TKX-50 exhibits highly anisotropic compression and significantly lower volume compressibility than currently known energetic crystals. These results are found to be in general agreement with our previous predictions from the DFT calculations. Additionally, the experimental data revealed anomalous compression—an expansion of the unit cell along the a axis (negative linear compressibility, NLC) upon compression to ~3 GPa.more » The structural analyses demonstrated that this unusual effect, the first such observation in an energetic crystal, is a consequence of the highly anisotropic response of 3D motifs, comprised of two parallel anions [(C 2N 8O 2) 2–] linked with two cations [(NH 3OH) +] through four strong hydrogen bonds. Finally, the present results demonstrate that the structural stability of TKX-50 is controlled by the strong and highly anisotropic intermolecular interactions, and these may contribute to its shock insensitivity.« less

[The principle of the energy minimum in ontogeny and the channeling of developmental processes].

PubMed

Ozerniuk, N D

1989-01-01

The principle of minimum of energy in ontogenesis has been formulated on the basis of data concerning age changes in energetic metabolism, as well as the influence of ecological factors on this process. According to this principle the smallest expenditures of energy are observed in the zone of the most favorable developmental conditions. The minimal level of energetic metabolism at every developmental stage that corresponds to the most stable state of organism is treated as homeostasis and the developmental stability is treated as homeorrhesis. Regulation mechanisms of energetic metabolism during ontogenesis and under the influence of environmental factors are analyzed.

Reduction of Charge Traps and Stability Enhancement in Solution-Processed Organic Field-Effect Transistors Based on a Blended n-Type Semiconductor.

PubMed

Campos, Antonio; Riera-Galindo, Sergi; Puigdollers, Joaquim; Mas-Torrent, Marta

2018-05-09

Solution-processed n-type organic field-effect transistors (OFETs) are essential elements for developing large-area, low-cost, and all organic logic/complementary circuits. Nonetheless, the development of air-stable n-type organic semiconductors (OSCs) lags behind their p-type counterparts. The trapping of electrons at the semiconductor-dielectric interface leads to a lower performance and operational stability. Herein, we report printed small-molecule n-type OFETs based on a blend with a binder polymer, which enhances the device stability due to the improvement of the semiconductor-dielectric interface quality and a self-encapsulation. Both combined effects prevent the fast deterioration of the OSC. Additionally, a complementary metal-oxide semiconductor-like inverter is fabricated depositing p-type and n-type OSCs simultaneously.

BODY SIZE AND HAREM SIZE IN MALE RED-WINGED BLACKBIRDS: MANIPULATING SELECTION WITH SEX-SPECIFIC FEEDERS.

PubMed

Rohwer, Sievert; Langston, Nancy; Gori, Dave

1996-10-01

We experimentally manipulated the strength of selection in the field on red-winged blackbirds (Agelaius phoeniceus) to test hypotheses about contrasting selective forces that favor either large or small males in sexually size dimorphic birds. Selander (1972) argued that sexual selection favors larger males, while survival selection eventually stabilizes male size because larger males do not survive as well as smaller males during harsh winters. Searcy (1979a) proposed instead that sexual selection may be self limiting: male size might be stabilized not by overwinter mortality, but by breeding-season sexual selection that favors smaller males. Under conditions of energetic stress, smaller males should be able to display more and thus achieve higher reproductive success. Using feeders that provisioned males or females but not both, we produced conditions that mimicked the extremes of natural conditions. We found experimental support for the hypothesis that when food is abundant, sexual selection favors larger males. But even under conditions of severe energetic stress, smaller males did not gain larger harems, as the self-limiting hypothesis predicted. Larger males were more energetically stressed than smaller males, but in ways that affected their future reproductive output rather than their current reproductive performance. Stressed males that returned had smaller wings and tails than those that did not return; among returning stressed males, relative harem sizes were inversely related to wing and tail length. Thus, male body size may be stabilized not by survival costs during the non-breeding season, nor by energetic costs during the breeding season, but by costs of future reproduction that larger males pay for their increased breeding-season effort. © 1996 The Society for the Study of Evolution.

The solar radio corona: Manifestations of energetic electrons

NASA Technical Reports Server (NTRS)

Pick, M.

1986-01-01

Radio observations are powerful tools which are complementary to the space missions devoted to the physics of the flares, of the corona, or of the interplanetary medium. To undertake this task two multifrequency radioheliographs presently exist: the Nancay instrument (the multifrequency facility will be in operation by the end of 1985) observes the middle corona at decimeter-meter wavelengths, and the Clark Lake radioheliograph, operating at decameter wavelengths, is the only one in the world to have the ability of observing the outer corona above the disk.

Packing interface energetics in different crystal forms of the λ Cro dimer.

PubMed

Ahlstrom, Logan S; Miyashita, Osamu

2014-07-01

Variation among crystal structures of the λ Cro dimer highlights conformational flexibility. The structures range from a wild type closed to a mutant fully open conformation, but it is unclear if each represents a stable solution state or if one may be the result of crystal packing. Here we use molecular dynamics (MD) simulation to investigate the energetics of crystal packing interfaces and the influence of site-directed mutagenesis on them in order to examine the effect of crystal packing on wild type and mutant Cro dimer conformation. Replica exchange MD of mutant Cro in solution shows that the observed conformational differences between the wild type and mutant protein are not the direct consequence of mutation. Instead, simulation of Cro in different crystal environments reveals that mutation affects the stability of crystal forms. Molecular Mechanics Poisson-Boltzmann Surface Area binding energy calculations reveal the detailed energetics of packing interfaces. Packing interfaces can have diverse properties in strength, energetic components, and some are stronger than the biological dimer interface. Further analysis shows that mutation can strengthen packing interfaces by as much as ∼5 kcal/mol in either crystal environment. Thus, in the case of Cro, mutation provides an additional energetic contribution during crystal formation that may stabilize a fully open higher energy state. Moreover, the effect of mutation in the lattice can extend to packing interfaces not involving mutation sites. Our results provide insight into possible models for the effect of crystallization on Cro conformational dynamics and emphasize careful consideration of protein crystal structures. © 2013 Wiley Periodicals, Inc.

Packing Interface Energetics in Different Crystal Forms of the λ Cro Dimer

PubMed Central

Ahlstrom, Logan S.; Miyashita, Osamu

2014-01-01

Variation among crystal structures of the λ Cro dimer highlights conformational flexibility. The structures range from a wild type closed to a mutant fully open conformation, but it is unclear if each represents a stable solution state or if one may be the result of crystal packing. Here we use molecular dynamics (MD) simulation to investigate the energetics of crystal packing interfaces and the influence of site-directed mutagenesis on them, in order to examine the effect of crystal packing on wild type and mutant Cro dimer conformation. Replica exchange MD of mutant Cro in solution shows that the observed conformational differences between the wild type and mutant protein are not the direct consequence of mutation. Instead, simulation of Cro in different crystal environments reveals that mutation affects the stability of crystal forms. Molecular Mechanics Poisson-Boltzmann Surface Area binding energy calculations reveal the detailed energetics of packing interfaces. Packing interfaces can have diverse properties in strength, energetic components, and some are stronger than the biological dimer interface. Further analysis shows that mutation can strengthen packing interfaces by as much as ~5 kcal/mol in either crystal environment. Thus, in the case of Cro, mutation provides an additional energetic contribution during crystal formation that may stabilize a fully open higher energy state. Moreover, the effect of mutation in the lattice can extend to packing interfaces not involving mutation sites. Our results provide insight into possible models for the effect of crystallization on Cro conformational dynamics and emphasize careful consideration of protein crystal structures. PMID:24218107

Composition-dependent stability of the medium-range order responsible for metallic glass formation

DOE PAGES

Zhang, Feng; Ji, Min; Fang, Xiao-Wei; ...

2014-09-18

The competition between the characteristic medium-range order corresponding to amorphous alloys and that in ordered crystalline phases is central to phase selection and morphology evolution under various processing conditions. We examine the stability of a model glass system, Cu–Zr, by comparing the energetics of various medium-range structural motifs over a wide range of compositions using first-principles calculations. Furthermore, we focus specifically on motifs that represent possible building blocks for competing glassy and crystalline phases, and we employ a genetic algorithm to efficiently identify the energetically favored decorations of each motif for specific compositions. These results show that a Bergman-type motifmore » with crystallization-resisting icosahedral symmetry is energetically most favorable in the composition range 0.63 < xCu < 0.68, and is the underlying motif for one of the three optimal glass-forming ranges observed experimentally for this binary system (Li et al., 2008). This work establishes an energy-based methodology to evaluate specific medium-range structural motifs which compete with stable crystalline nuclei in deeply undercooled liquids.« less

Density functional studies of the defect-induced electronic structure modifications in bilayer boronitrene

NASA Astrophysics Data System (ADS)

Ukpong, A. M.; Chetty, N.

2012-05-01

The van der Waals interaction-corrected density functional theory is used in this study to investigate the formation, energetic stability, and inter-layer cohesion in bilayer hexagonal boronitrene. The effect of inter-layer separation on the electronic structure is systematically investigated. The formation and energetic stability of intrinsic defects are also investigated at the equilibrium inter-layer separation. It is found that nonstoichiometric defects, and their complexes, that induce excess nitrogen or excess boron, in each case, are relatively more stable in the atmosphere that corresponds to the excess atomic species. The modifications of the electronic structure due to formation of complexes are also investigated. It is shown that van der Waals density functional theory gives an improved description of the cohesive properties but not the electronic structure in bilayer boronitrene compared to other functionals. We identify energetically favourable topological defects that retain the energy gap in the electronic structure, and discuss their implications for band gap engineering in low-n layer boronitrene insulators. The relative strengths and weaknesses of the functionals in predicting the properties of bilayer boronitrene are also discussed.

InP and InAs nanowires hetero- and homojunctions: energetic stability and electronic properties.

PubMed

Dionízio Moreira, M; Venezuela, P; Miwa, R H

2010-07-16

We performed an ab initio total energy investigation, within the density functional theory, of the energetic stability and the electronic properties of hydrogenated InAs/InP nanowire (NW) heterojunctions, as well as InAs and InP homojunctions composed of different structural arrangements, zinc-blend (zb) and wurtzite (w). For InAs/InP NW heterojunctions our results indicate that w and zb NW heterojunctions are quite similar, energetically, for thin NWs. We also examined the robustness of the abrupt interface through an atomic <--> swap at the InAs/InP interface. Our results support the formation of abrupt (non-abrupt) interfaces in w (zb) InAs/InP heterojunctions. Concerning InAs/InP NW-SLs, our results indicate a type-I band alignment, with the energy barrier at the InP layers, in accordance with experimental works. For InAs or InP zb/w homojunctions, we also found a type-I band alignment for thin NWs, however, on increasing the NW diameter both InAs and InP homojunctions exhibit a type-II band alignment.

Interaction of high-energy beams with magnetized plasma: feasibility study for laboratory experiments

NASA Astrophysics Data System (ADS)

Roytershteyn, V.; Delzanno, G. L.; Dorfman, S. E.; Cattell, C. A.; Van Compernolle, B.

2017-12-01

We discuss plans for an experiment that will investigate interaction of energetic electron beam with magnetized plasma. The planned experiment will be conducted on the Large Plasma Device (LAPD) at UCLA and will utilize a variable-energy (0.1-1) MeV electron beam. Such energetic beams have recently attracted renewed attention as a basis for a number of active experiments in space, largely due to possibility of overcoming limitations imposed by spacecraft charging in low-density (e.g. magnetospheric) plasma. In this talk, we will discuss theoretical and computation studies of the plasma modes excited by the beam and beam stability. Energetic beams radiate both whistler and high-frequency R-X mode via Cherenkov resonances, with the relative efficiency of coupling to R-X mode increasing with beam energy. The stability of a finite-size, modulated beam (as produced by the available beam sources) is investigated and relative significance of instabilities and direct radiation is discussed. Special attention will be paid to discussing how laboratory experiments relate to conditions in space.

Closing loop base pairs in RNA loop-loop complexes: structural behavior, interaction energy and solvation analysis through molecular dynamics simulations.

PubMed

Golebiowski, Jérôme; Antonczak, Serge; Fernandez-Carmona, Juan; Condom, Roger; Cabrol-Bass, Daniel

2004-12-01

Nanosecond molecular dynamics using the Ewald summation method have been performed to elucidate the structural and energetic role of the closing base pair in loop-loop RNA duplexes neutralized by Mg2+ counterions in aqueous phases. Mismatches GA, CU and Watson-Crick GC base pairs have been considered for closing the loop of an RNA in complementary interaction with HIV-1 TAR. The simulations reveal that the mismatch GA base, mediated by a water molecule, leads to a complex that presents the best compromise between flexibility and energetic contributions. The mismatch CU base pair, in spite of the presence of an inserted water molecule, is too short to achieve a tight interaction at the closing-loop junction and seems to force TAR to reorganize upon binding. An energetic analysis has allowed us to quantify the strength of the interactions of the closing and the loop-loop pairs throughout the simulations. Although the water-mediated GA closing base pair presents an interaction energy similar to that found on fully geometry-optimized structure, the water-mediated CU closing base pair energy interaction reaches less than half the optimal value.

Stabilizing the boat conformation of cyclohexane rings

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

Dasgupta, S.; Goddard, W.A. III; Moldowan, J.M.

1995-06-21

In calculating the energetics for various conformers of the A, B, and C series of hopanoid hydrocarbons present in mature oil reservoirs, we find that the B series prefers the boat conformation (by 1.3-2.5 kcal/mol) for the D cyclohexane ring. We analyze the structural elements responsible for stabilizing this boat conformation, identify the key features, and illustrate how one might stabilize boat conformations of other systems. 5 refs., 3 figs., 2 tabs.

In-situ nano-crystal-to-crystal transformation synthesis of energetic materials based on three 5,5′-azotetrazolate Cr(III) salts

PubMed Central

Miao, Yu; Qiu, Yanxuan; Cai, Jiawei; Wang, Zizhou; Yu, Xinwei; Dong, Wen

2016-01-01

The in-situ nano-crystal-to-crystal transformation (SCCT) synthesis provides a powerful approach for tailoring controllable feature shapes and sizes of nano crystals. In this work, three nitrogen-rich energetic nano-crystals based on 5,5′-azotetrazolate(AZT2−) Cr(III) salts were synthesized by means of SCCT methodology. SEM and TEM analyses show that the energetic nano-crystals feature a composition- and structure-dependent together with size-dependent thermal stability. Moreover, nano-scale decomposition products can be obtained above 500 °C, providing a new method for preparing metallic oxide nano materials. PMID:27869221

Investigations of Novel Energetic Materials to Stabilize Rocket Motors

DTIC Science & Technology

2002-04-30

Delaware Thomas A. Litzinger Pennsylvania State University Vigor Yang Pennsylvania State University Gary A. Flandro University of Tennessee Space...Gas Dynamics ( Flandro ) ..........................192 3.3.1 Improved Motor Stability Calculations...phenomenon was initiated by Flandro prior to the MURI program and has continued to the present. Relative to other types of chemical propulsion, the solid

Three-dimensional instabilities of natural convection between two differentially heated vertical plates: Linear and nonlinear complementary approaches

NASA Astrophysics Data System (ADS)

Gao, Zhenlan; Podvin, Berengere; Sergent, Anne; Xin, Shihe; Chergui, Jalel

2018-05-01

The transition to the chaos of the air flow between two vertical plates maintained at different temperatures is studied in the Boussinesq approximation. After the first bifurcation at critical Rayleigh number Rac, the flow consists of two-dimensional (2D) corotating rolls. The stability of the 2D rolls is examined, confronting linear predictions with nonlinear integration. In all cases the 2D rolls are destabilized in the spanwise direction. Efficient linear stability analysis based on an Arnoldi method shows competition between two eigenmodes, corresponding to different spanwise wavelengths and different types of roll distortion. Nonlinear integration shows that the lower-wave-number mode is always dominant. A partial route to chaos is established through the nonlinear simulations. The flow becomes temporally chaotic for Ra =1.05 Rac , but remains characterized by the spatial patterns identified by linear stability analysis. This highlights the complementary role of linear stability analysis and nonlinear simulation.

Energetics analysis of interstitial loops in single-phase concentrated solid-solution alloys

NASA Astrophysics Data System (ADS)

Wang, Xin-Xin; Niu, Liang-Liang; Wang, Shaoqing

2018-04-01

Systematic energetics analysis on the shape preference, relative stability and radiation-induced segregation of interstitial loops in nickel-containing single-phase concentrated solid-solution alloys have been conducted using atomistic simulations. It is shown that the perfect loops prefer rhombus shape for its low potential energy, while the Frank faulted loops favor ellipse for its low potential energy and the possible large configurational entropy. The decrease of stacking fault energy with increasing compositional complexity provides the energetic driving force for the formation of faulted loops, which, in conjunction with the kinetic factors, explains the experimental observation that the fraction of faulted loops rises with increasing compositional complexity. Notably, the kinetics is primarily responsible for the absence of faulted loops in nickel-cobalt with a very low stacking fault energy. We further demonstrate that the simultaneous nickel enrichment and iron/chromium depletion on interstitial loops can be fully accounted for by their energetics.

Myocardial Energetics and Heart Failure: a Review of Recent Therapeutic Trials.

PubMed

Bhatt, Kunal N; Butler, Javed

2018-06-01

Several novel therapeutics being tested in patients with heart failure are based on myocardial energetics. This review will provide a summary of the recent trials in this area, including therapeutic options targeting various aspects of cellular and mitochondrial metabolism. Agents that improve the energetic balance in myocardial cells have the potential to improve clinical heart failure status. The most promising therapies currently under investigation in this arena include (1) elamipretide, a cardiolipin stabilizer; (2) repletion of iron deficiency with intravenous ferrous carboxymaltose; (3) coenzyme Q10; and (4) the partial adenosine receptor antagonists capadenoson and neladenosone. Myocardial energetics-based therapeutics are groundbreaking in that they utilize novel mechanisms of action to improve heart failure symptoms, without causing the adverse neurohormonal side effects associated with current guideline-based therapies. The drugs appear likely to be added to the heart failure therapy armamentarium as adjuncts to current regimens in the near future.

Biologically tunable reactivity of energetic nanomaterials using protein cages.

PubMed

Slocik, Joseph M; Crouse, Christopher A; Spowart, Jonathan E; Naik, Rajesh R

2013-06-12

The performance of aluminum nanomaterial based energetic formulations is dependent on the mass transport, diffusion distance, and stability of reactive components. Here we use a biologically inspired approach to direct the assembly of oxidizer loaded protein cages onto the surface of aluminum nanoparticles to improve reaction kinetics by reducing the diffusion distance between the reactants. Ferritin protein cages were loaded with ammonium perchlorate (AP) or iron oxide and assembled with nAl to create an oxidation-reduction based energetic reaction and the first demonstration of a nanoscale biobased thermite material. Both materials showed enhanced exothermic behavior in comparison to nanothermite mixtures of bulk free AP or synthesized iron oxide nanopowders prepared without the use of ferritin. In addition, by utilizing a layer-by-layer (LbL) process to build multiple layers of protein cages containing iron oxide and iron oxide/AP on nAl, stoichiometric conditions and energetic performance can be optimized.

The energetic basis of the DNA double helix: a combined microcalorimetric approach

PubMed Central

Vaitiekunas, Paulius; Crane-Robinson, Colyn; Privalov, Peter L.

2015-01-01

Microcalorimetric studies of DNA duplexes and their component single strands showed that association enthalpies of unfolded complementary strands into completely folded duplexes increase linearly with temperature and do not depend on salt concentration, i.e. duplex formation results in a constant heat capacity decrement, identical for CG and AT pairs. Although duplex thermostability increases with CG content, the enthalpic and entropic contributions of an AT pair to duplex formation exceed that of a CG pair when compared at the same temperature. The reduced contribution of AT pairs to duplex stabilization comes not from their lower enthalpy, as previously supposed, but from their larger entropy contribution. This larger enthalpy and particularly the greater entropy results from water fixed by the AT pair in the minor groove. As the increased entropy of an AT pair exceeds that of melting ice, the water molecule fixed by this pair must affect those of its neighbors. Water in the minor groove is, thus, orchestrated by the arrangement of AT groups, i.e. is context dependent. In contrast, water hydrating exposed nonpolar surfaces of bases is responsible for the heat capacity increment on dissociation and, therefore, for the temperature dependence of all thermodynamic characteristics of the double helix. PMID:26304541

Energetics of zirconia stabilized by cation and nitrogen substitution

NASA Astrophysics Data System (ADS)

Molodetsky, Irina

Tetragonal and cubic zirconia are used in advanced structural ceramics, fuel cells, oxygen sensors, nuclear waste ceramics and many other applications. These zirconia phases are stabilized at room temperature (relative to monoclinic phase for pure zirconia) by cation and nitrogen substitution. This work is aimed at a better understanding of the mechanisms of stabilization of the high-temperature zirconia. phases. Experimental data are produced on the energetics of zirconia stabilized by yttria and calcia, energetics of nitrogen-oxygen substitution in zirconia and cation doped zirconia, and energetics of x-ray amorphous zirconia. obtained by low-temperature synthesis. High-temperature oxide melt solution enables direct measurement of enthalpies of formation of these refractory oxides. The enthalpy of the monoclinic to cubic phase transition of zirconia is DeltaHm-c = 12.2 +/- 1.2 kJ/mol. For cubic phases of YSZ at low yttria contents, a straight line DeltaH f,YSZ = -(52.4 +/- 3.6)x + (12.2 +/- 1.2) approximates the enthalpy of formation as a function of the yttria content, x (0. 1 < x < 0.3). Use of the quadratic fit DeltaHf,YSZ = 126.36 x 2 - 81.29 x + 12.37 (0.1 ≲ x ≲ 0.53) indicates that yttria stabilizes the cubic phase in enthalpy at low dopant content and destabilizes the cubic phase as yttria content increases. Positive entropy of mixing in YSZ and small enthalpy of long range ordering in 0.47ZrO2-0.53YO1.5, DeltaHord = -2.4 +/- 3.0 kJ/mol, indicate presence of short range ordering in YSZ. The enthalpy of formation of calcia stabilized zirconia as a function of calcia content x, is approximated as DeltaHf,c = (-91.4 +/- 3.8) x + (13.5 +/- 1.7) kJ/mol. The enthalpy of oxygen-nitrogen substitution, DeltaHO-N, in zirconium oxynitrides is a linear function of nitrogen content. DeltaH O-N ˜ -500 kJ/mol N is for Ca (Y)-Zr-N-O and Zr-N-O oxynitrides and DeltaHO-N ˜ -950 kJ/mol N is for Mg-Zr-N-O oxynitrides. X-ray amorphous zirconia is 58.6 +/- 3.3 kJ/mol less stable in enthalpy than monoclinic zirconia. The difference between the surface energies of amorphous and tetragonal zirconia phases is ˜1.19 +/- 0.05 J/m2, with a lower surface energy for the amorphous material.

Synthesis and Characterization of Energetic Plasticizer AMDNNM

NASA Astrophysics Data System (ADS)

Schulze, Maxwell C.; Chavez, David E.

2016-04-01

The synthesis of room temperature liquid azidomethyl-dinitroxydimethyl-nitromethane (AMDNNM, 5) in 57% overall yield and its formulation with nitrocellulose (AMDNNM/NC) are described. The small-scale explosive sensitivity of neat AMDNNM was determined to be slightly more sensitive than PETN, whereas AMDNNM/NC is significantly less sensitive. Both neat AMDNNM and AMDNNM/NC have thermal stabilities similar to that of pentaerythritol tetranitrate (PETN). The explosive and chemical properties of this novel material make it a good candidate for an energetic plasticizer.

A review of advanced high performance, insensitive and thermally stable energetic materials emerging for military and space applications.

PubMed

Sikder, A K; Sikder, Nirmala

2004-08-09

Energetic materials used extensively both for civil and military applications. There are continuous research programmes worldwide to develop new materials with higher performance and enhanced insensitivity to thermal or shock insults than the existing ones in order to meet the requirements of future military and space applications. This review concentrates on recent advances in syntheses, potential formulations and space applications of potential compounds with respect to safety, performance and stability.

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

NASA Astrophysics Data System (ADS)

Adlakha, I.; Solanki, K. N.

2015-03-01

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

The Importance of Water for High Fidelity Information Processing and for Life

NASA Technical Reports Server (NTRS)

Hoehler, Tori M.; Pohorille, Andrew

2011-01-01

Is water an absolute prerequisite for life? Life depends on a variety of non-covalent interactions among molecules, the nature of which is determined as much by the solvent in which they occur as by the molecules themselves. Catalysis and information processing, two essential functions of life, require non-covalent molecular recognition with very high specificity. For example, to correctly reproduce a string consisting of 600,000 units of information (e.g ., 600 kilobases, equivalent to the genome of the smallest free living terrestrial organisms) with a 90% success rate requires specificity > 107 : 1 for the target molecule vs. incorrect alternatives. Such specificity requires (i) that the correct molecular association is energetically stabilized by at least 40 kJ/mol relative to alternatives, and (ii) that the system is able to sample among possible states (alternative molecular associations) rapidly enough to allow the system to fall under thermodynamic control and express the energetic stabilization. We argue that electrostatic interactions are required to confer the necessary energetic stabilization vs. a large library of molecular alternatives, and that a solvent with polarity and dielectric properties comparable to water is required for the system to sample among possible states and express thermodynamic control. Electrostatic associations can be made in non-polar solvents, but the resulting complexes are too stable to be "unmade" with sufficient frequency to confer thermodynamic control on the system. An electrostatic molecular complex representing 3 units of information (e.g., 3 base pairs) with specificity > 107 per unit has a stability in non-polar solvent comparable to that of a carbon-carbon bond at room temperature. These considerations suggest that water, or a solvent with properties very like water, is necessary to support high-fidelity information processing, and can therefore be considered a critical prerequisite for life.

When Is Ligand p Ka a Good Descriptor for Catalyst Energetics? In Search of Optimal CO2 Hydration Catalysts.

PubMed

Kim, Jeong Yun; Kulik, Heather J

2018-05-10

We present a detailed study of nearly 70 Zn molecular catalysts for CO 2 hydration from four diverse ligand classes ranging from well-studied carbonic anhydrase mimics (e.g., cyclen) to new structures we obtain by leveraging diverse hits from large organic libraries. Using microkinetic analysis and establishing linear free energy relationships, we confirm that turnover is sensitive to the relative thermodynamic stability of reactive hydroxyl and bound bicarbonate moieties. We observe a wide range of thermodynamic stabilities for these intermediates, showing up to 6 kcal/mol improvement over well-studied cyclen catalysts. We observe a good correlation between the p K a of the Zn-OH 2 moiety and the resulting relative stability of hydroxyl moieties over bicarbonate, which may be rationalized by the dominant effect of the difference in higher Zn-OH bond order in comparison to weaker bonding in bicarbonate and water. A direct relationship is identified between isolated organic ligand p K a and the p K a of a bound water molecule on the catalyst. Thus, organic ligand p K a , which is intuitive, easy to compute or tabulate, and much less sensitive to electronic structure method choice than whole-catalyst properties, is a good quantitative descriptor for predicting the effect of through-bond electronic effects on relative CO 2 hydration energetics. We expect this to be applicable to other reactions where is it essential to stabilize turnover-determining hydroxyl species with respect to more weakly bound moieties. Finally, we note exceptions for rigid ligands (e.g., porphyrins) that are observed to preferentially stabilize hydroxyl over bicarbonate without reducing p K a values as substantially. We expect the strategy outlined here, to (i) curate diverse ligands from large organic libraries and (ii) identify when ligand-only properties can determine catalyst energetics, to be broadly useful for both experimental and computational catalyst design.

Development of Capsular Adhesive Systems and Evaluation of Their Stability.

DTIC Science & Technology

1985-07-26

Adhesives; Microencapsulation processes, Epoxy resins, Anaerobic systems, Characterization, Microcapsules properties, Stability, Liquid Chromatography...II. TECHNICAL DISCUSSION ................... 5 A. Complementary microencapsulation stu- dies ............................... 5 1...initial phase of this program (1), studies on microencapsulation of adhesive systems were conducted in which the capsule shells are made from the

Energetics of cubic and hexagonal phases in Mn-doped GaN : First-principles pseudopotential calculations

NASA Astrophysics Data System (ADS)

Choi, Eun-Ae; Kang, Joongoo; Chang, K. J.

2006-12-01

We perform first-principles pseudopotential calculations to study the influence of Mn doping on the stability of two polytypes, wurtzite and zinc-blende, in GaN . In Mn δ -doped GaN and GaMnN alloys, we find similar critical concentrations of the Mn ions for stabilizing the zinc-blende phase against the wurtzite phase. Using a slab geometry of hexagonal lattices, we find that it is energetically unfavorable to form inversion domains with Mn exposure, in contrast to Mg doping. At the initial stage of epitaxial growth, a stacking fault that leads to the cubic bonds can be generated with the Mn exposure to the Ga-polar surface. However, the influence of the Mn δ -doped layer on the formation of the cubic phase is only effective for GaN layers deposited up to two monolayers. We find that the Mn ions are energetically more stable on the growth front than in the bulk, indicating that these ions act as a surfactant. Thus it is possible to grow cubic GaN if the Mn ions are periodically supplied or diffuse out from the Mn δ -doped layer to the growth front during the growth process.

Computational study of the energetics and defect clustering tendencies for Y- and La-doped UO 2

DOE PAGES

Solomon, J. M.; Alexandrov, V.; Sadigh, B.; ...

2014-07-24

The energetics and defect-ordering tendencies in solid solutions of uoritestructured UO 2 with trivalent rare earth cations (M 3+=Y, La) are investigated computationally using a combination of ionic-pair-potential and densityfunctional- theory (DFT) based methods. Calculated enthalpies of formation with respect to constituent oxides show higher energetic stability for La solid solutions relative to Y, consistent with the di erences in experimentally measured solubility limits for the two systems. Additionally, calculations performed for di erent atomic con gurations show a preference for reduced (increased) oxygen vacancy coordination around La (Y) dopants. The current results are shown to be qualitatively consistent withmore » related calculations and calorimetry measurements in other trivalent-doped uorite-structured oxides, which show a tendency for increasing stability and increasing preference for higher oxygen coordination with increasing size of the trivalent impurity. The implications of these results are discussed in the context of the e ect of trivalent impurities on oxygen-ion mobilities in UO 2, which are relevant to the understanding of experimental observations concerning the e ect of trivalent ssion products on oxidative corrosion rates of spent nuclear fuel.« less

The origin of excellent gate-bias stress stability in organic field-effect transistors employing fluorinated-polymer gate dielectrics.

PubMed

Kim, Jiye; Jang, Jaeyoung; Kim, Kyunghun; Kim, Haekyoung; Kim, Se Hyun; Park, Chan Eon

2014-11-12

Tuning of the energetic barriers to charge transfer at the semiconductor/dielectric interface in organic field-effect transistors (OFETs) is achieved by varying the dielectric functionality. Based on this, the correlation between the magnitude of the energy barrier and the gate-bias stress stability of the OFETs is demonstrated, and the origin of the excellent device stability of OFETs employing fluorinated dielectrics is revealed. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Energetic Analysis of Conjugated Hydrocarbons Using the Interacting Quantum Atoms Method.

PubMed

Jara-Cortés, Jesús; Hernández-Trujillo, Jesús

2018-07-05

A number of aromatic, antiaromatic, and nonaromatic organic molecules was analyzed in terms of the contributions to the electronic energy defined in the quantum theory of atoms in molecules and the interacting quantum atoms method. Regularities were found in the exchange and electrostatic interatomic energies showing trends that are closely related to those of the delocalization indices defined in the theory. In particular, the CC interaction energies between bonded atoms allow to rationalize the energetic stabilization associated with the bond length alternation in conjugated polyenes. This approach also provides support to Clar's sextet rules devised for aromatic systems. In addition, the H⋯H bonding found in some of the aromatic molecules studied was of an attractive nature, according to the stabilizing exchange interaction between the bonded H atoms. © 2017 Wiley Periodicals, Inc. © 2017 Wiley Periodicals, Inc.

ECUT (Energy Conversion and Utilization Technologies) program: Biocatalysis Project

NASA Technical Reports Server (NTRS)

1988-01-01

Fiscal year 1987 research activities and accomplishments for the Biocatalysis Project of the U.S. Department of Energy, Energy Conversion and Utilization Technologies (ECUT) Division are presented. The project's technical activities were organized into three work elements. The Molecular Modeling and Applied Genetics work element includes modeling and simulation studies to verify a dynamic model of the enzyme carboxypeptidase; plasmid stabilization by chromosomal integration; growth and stability characteristics of plasmid-containing cells; and determination of optional production parameters for hyper-production of polyphenol oxidase. The Bioprocess Engineering work element supports efforts in novel bioreactor concepts that are likely to lead to substantially higher levels of reactor productivity, product yields, and lower separation energetics. The Bioprocess Design and Assessment work element attempts to develop procedures (via user-friendly computer software) for assessing the economics and energetics of a given biocatalyst process.

Thermodynamics of cooperative binding of FAD to human NQO1: Implications to understanding cofactor-dependent function and stability of the flavoproteome.

PubMed

Clavería-Gimeno, Rafael; Velazquez-Campoy, Adrian; Pey, Angel Luis

2017-12-15

The stability of human flavoproteins strongly depends on flavin levels, although the structural and energetic basis of this relationship is poorly understood. Here, we report an in-depth analysis on the thermodynamics of FAD binding to one of the most representative examples of such relationship, NAD(P)H:quinone oxidoreductase 1 (NQO1). NQO1 is a dimeric enzyme that tightly binds FAD, which triggers large structural changes upon binding. A common cancer-associated polymorphism (P187S) severely compromises FAD binding. We show that FAD binding is described well by a thermodynamic model explicitly incorporating binding cooperativity when applied to different sets of calorimetric analyses and NQO1 variants, thus providing insight on the effects in vitro and in cells of cancer-associated P187S, its suppressor mutation H80R and the role of NQO1 C-terminal domain to modulate binding cooperativity and energetics. Furthermore, we show that FAD binding to NQO1 is very sensitive to physiologically relevant environmental conditions, such as the presence of phosphate buffer and salts. Overall, our results contribute to understanding at the molecular level the link between NQO1 stability and fluctuations of FAD levels intracellularly, and supports the notion that FAD binding energetics and cooperativity are fundamentally linked with the dynamic nature of apo-NQO1 conformational ensemble. Copyright © 2017 Elsevier Inc. All rights reserved.

Protein folding and misfolding: mechanism and principles

PubMed Central

Englander, S. Walter; Mayne, Leland; Krishna, Mallela M. G.

2012-01-01

Two fundamentally different views of how proteins fold are now being debated. Do proteins fold through multiple unpredictable routes directed only by the energetically downhill nature of the folding landscape or do they fold through specific intermediates in a defined pathway that systematically puts predetermined pieces of the target native protein into place? It has now become possible to determine the structure of protein folding intermediates, evaluate their equilibrium and kinetic parameters, and establish their pathway relationships. Results obtained for many proteins have serendipitously revealed a new dimension of protein structure. Cooperative structural units of the native protein, called foldons, unfold and refold repeatedly even under native conditions. Much evidence obtained by hydrogen exchange and other methods now indicates that cooperative foldon units and not individual amino acids account for the unit steps in protein folding pathways. The formation of foldons and their ordered pathway assembly systematically puts native-like foldon building blocks into place, guided by a sequential stabilization mechanism in which prior native-like structure templates the formation of incoming foldons with complementary structure. Thus the same propensities and interactions that specify the final native state, encoded in the amino-acid sequence of every protein, determine the pathway for getting there. Experimental observations that have been interpreted differently, in terms of multiple independent pathways, appear to be due to chance misfolding errors that cause different population fractions to block at different pathway points, populate different pathway intermediates, and fold at different rates. This paper summarizes the experimental basis for these three determining principles and their consequences. Cooperative native-like foldon units and the sequential stabilization process together generate predetermined stepwise pathways. Optional misfolding errors are responsible for 3-state and heterogeneous kinetic folding. PMID:18405419

Spectroscopic investigation of the electronic structure of yttria-stabilized zirconia

NASA Astrophysics Data System (ADS)

Götsch, Thomas; Bertel, Erminald; Menzel, Alexander; Stöger-Pollach, Michael; Penner, Simon

2018-03-01

The electronic structure and optical properties of yttria-stabilized zirconia are investigated as a function of the yttria content using multiple experimental and theoretical methods, including electron energy-loss spectroscopy, Kramers-Kronig analysis to obtain the optical parameters, photoelectron spectroscopy, and density functional theory. It is shown that many properties, including the band gaps, the crystal field splitting, the so-called defect gap between acceptor (YZr') and donor (VO••) states, as well as the index of refraction in the visible range exhibit the same "zig-zag-like" trend as the unit cell height does, showing the influence of an increased yttria content as well as of the tetragonal-cubic phase transition between 8 mol % and 20 mol %Y2O3 . Also, with Čerenkov spectroscopy (CS), a new technique is presented, providing information complementary to electron energy-loss spectroscopy. In CS, the Čerenkov radiation emitted inside the TEM is used to measure the onset of optical absorption. The apparent absorption edges in the Čerenkov spectra correspond to the energetic difference between the disorder states close to the valence band and the oxygen-vacancy-related electronic states within the band gap. Theoretical computations corroborate this assignment: they find both, the acceptor states and the donor states, at the expected energies in the band structures for diverse yttria concentrations. In the end, a schematic electronic structure diagram of the area around the band gap is constructed, including the chemical potential of the electrons obtained from photoelectron spectroscopy. The latter reveal that tetragonal YSZ corresponds to a p -type semiconductor, whereas the cubic samples exhibit n -type semiconductor properties.

Sequence-Selective Formation of Synthetic H-Bonded Duplexes

PubMed Central

2017-01-01

Oligomers equipped with a sequence of phenol and pyridine N-oxide groups form duplexes via H-bonding interactions between these recognition units. Reductive amination chemistry was used to synthesize all possible 3-mer sequences: AAA, AAD, ADA, DAA, ADD, DAD, DDA, and DDD. Pairwise interactions between the oligomers were investigated using NMR titration and dilution experiments in toluene. The measured association constants vary by 3 orders of magnitude (102 to 105 M–1). Antiparallel sequence-complementary oligomers generally form more stable complexes than mismatched duplexes. Mismatched duplexes that have an excess of H-bond donors are stabilized by the interaction of two phenol donors with one pyridine N-oxide acceptor. Oligomers that have a H-bond donor and acceptor on the ends of the chain can fold to form intramolecular H-bonds in the free state. The 1,3-folding equilibrium competes with duplex formation and lowers the stability of duplexes involving these sequences. As a result, some of the mismatch duplexes are more stable than some of the sequence-complementary duplexes. However, the most stable mismatch duplexes contain DDD and compete with the most stable sequence-complementary duplex, AAA·DDD, so in mixtures that contain all eight sequences, sequence-complementary duplexes dominate. Even higher fidelity sequence selectivity can be achieved if alternating donor–acceptor sequences are avoided. PMID:28857551

Creation of artificial skyrmions and antiskyrmions by anisotropy engineering

NASA Astrophysics Data System (ADS)

Zhang, S.; Petford-Long, A. K.; Phatak, C.

2016-08-01

Topologically non-trivial spin textures form a fundamental paradigm in solid-state physics and present unique opportunities to explore exciting phenomena such as the topological Hall effect. One such texture is a skyrmion, in which the spins can be mapped to point in all directions wrapping around a sphere. Understanding the formation of these spin textures, and their energetic stability, is crucial in order to control their behavior. In this work, we report on controlling the perpendicular anisotropy of continuous Co/Pt multilayer films with ion irradiation to form unique spin configurations of artificial skyrmions and antiskyrmions that are stabilized by their demagnetization energy. We elucidate their behavior using aberration-corrected Lorentz transmission electron microscopy. We also discuss the energetic stability of these structures studied through in-situ magnetizing experiments performed at room temperature, combined with micromagnetic simulations that successfully reproduce the spin textures and behavior. This research offers new opportunities towards creation of artificial skyrmion or antiskyrmion lattices that can be used to investigate not only fundamental properties of their interaction with electron currents but also technological applications such as artificial magnonic crystals.

A method for fast safety screening of explosives in terms of crystal packing and molecular stability.

PubMed

Hu, Xiaohua; Chen, Nana; Li, Weichen

2016-07-01

Safety prediction is crucial to the molecular design or the material design of explosives, and the predictions based on any single factor alone will cause much inaccuracy, leading to a desire for a method on multi-bases. The presented proposes an improved method for fast screening explosive safety by combining a crystal packing factor and a molecular one, that is, steric hindrance against shear slide in crystal and molecular stability, denoted by intermolecular friction symbol (IFS) and bond dissociation energy (BDE) of trigger linkage respectively. Employing this BDE-IFS combined method, we understand the impact sensitivities of 24 existing explosives, and predict those of two energetic-energetic cocrystals of the observed CL-20/BTF and the supposed HMX/TATB. As a result, a better understanding is implemented by the combined method relative to molecular stability alone, verifying its improvement of more accurate predictions and the feasibility of IFS to graphically reflect molecular stacking in crystals. Also, this work verifies that the explosive safety is strongly related with its crystal stacking, which determines steric hindrance and influences shear slide.

Computed Energetics of Nucleotides in Spatial Ribozyme Structures: An Accurate Identification of Functional Regions from Structure

PubMed Central

Torshin, Ivan Y.

2004-01-01

Ribozymes are functionally diverse RNA molecules with intrinsic catalytic activity. Multiple structural and biochemical studies are required to establish which nucleotide bases are involved in the catalysis. The relative energetic properties of the nucleotide bases have been analyzed in a set of the known ribozyme structures. It was found that many of the known catalytic nucleotides can be identified using only the structure without any additional biochemical data. The results of the calculations compare well with the available biochemical data on RNA stability. Extensive in silico mutagenesis suggests that most of the nucleotides in ribozymes stabilize the RNA. The calculations show that relative contribution of the catalytic bases to RNA stability observably differs from contributions of the noncatalytic bases. Distinction between the concepts of “relative stability” and “mutational stability” is suggested. As results of prediction for several models of ribozymes appear to be in agreement with the published data on the potential active site regions, the method can potentially be used for prediction of functional nucleotides from nucleic sequence. PMID:15105962

First-principles screening of structural properties of intermetallic compounds on martensitic transformation

NASA Astrophysics Data System (ADS)

Lee, Joohwi; Ikeda, Yuji; Tanaka, Isao

2017-11-01

Martensitic transformation with good structural compatibility between parent and martensitic phases are required for shape memory alloys (SMAs) in terms of functional stability. In this study, first-principles-based materials screening is systematically performed to investigate the intermetallic compounds with the martensitic phases by focusing on energetic and dynamical stabilities as well as structural compatibility with the parent phase. The B2, D03, and L21 crystal structures are considered as the parent phases, and the 2H and 6M structures are considered as the martensitic phases. In total, 3384 binary and 3243 ternary alloys with stoichiometric composition ratios are investigated. It is found that 187 alloys survive after the screening. Some of the surviving alloys are constituted by the chemical elements already widely used in SMAs, but other various metallic elements are also found in the surviving alloys. The energetic stability of the surviving alloys is further analyzed by comparison with the data in Materials Project Database (MPD) to examine the alloys whose martensitic structures may cause further phase separation or transition to the other structures.

Refining the treatment of membrane proteins by coarse-grained models.

PubMed

Vorobyov, Igor; Kim, Ilsoo; Chu, Zhen T; Warshel, Arieh

2016-01-01

Obtaining a quantitative description of the membrane proteins stability is crucial for understanding many biological processes. However the advance in this direction has remained a major challenge for both experimental studies and molecular modeling. One of the possible directions is the use of coarse-grained models but such models must be carefully calibrated and validated. Here we use a recent progress in benchmark studies on the energetics of amino acid residue and peptide membrane insertion and membrane protein stability in refining our previously developed coarse-grained model (Vicatos et al., Proteins 2014;82:1168). Our refined model parameters were fitted and/or tested to reproduce water/membrane partitioning energetics of amino acid side chains and a couple of model peptides. This new model provides a reasonable agreement with experiment for absolute folding free energies of several β-barrel membrane proteins as well as effects of point mutations on a relative stability for one of those proteins, OmpLA. The consideration and ranking of different rotameric states for a mutated residue was found to be essential to achieve satisfactory agreement with the reference data. © 2015 Wiley Periodicals, Inc.

Theoretical study of ANTO molecular systems: Causes of insensitivity of the energetic compound NTO

NASA Astrophysics Data System (ADS)

Liu, Min-Hsien; Chen, Cheng; Hong, Yaw-Shun

The ANTO molecular system, which comprises the energetic compound 3-nitro-1,2,4-triazole-5-one (NTO, with its two lowest-energy conformers L1 and L2), ammonia (NH3), and water (H2O) molecules, is introduced for a theoretical survey of corresponding geometrical structure and localized bonding character. With the medium (or solvent) of H2O and NH3, three intermolecular hydrogen bonds formed in the NTO + NH3 + H2O system would lower the overall molecular energy and stabilize.

Examining Energetic Particle Injections and the Effects on the Inner Magnetosphere with Multiple Spacecraft/Missions

NASA Astrophysics Data System (ADS)

Leonard, T. W.; Baker, D. N.; Blake, J. B.; Burch, J. L.; Cohen, I. J.; Ergun, R.; Fennell, J. F.; Gershman, D. J.; Giles, B. L.; Jaynes, A. N.; Le Contel, O.; Mauk, B.; Russell, C. T.; Strangeway, R. J.; Torbert, R. B.; Turner, D. L.; Wilder, F. D.

2017-12-01

The Magnetospheric Multiscale (MMS) Fly's Eye Energetic Particle Spectrometer (FEEPS) instrument has observed a multitude of particle injection events since its launch in 2014. These injections often lead to enhancements observed by the Van Allen Probes MagEIS instrument, as well as other elements of the modern-day Heliophysics System Observatory. The high spatial resolution and unprecedented time scales of the MMS observations provide a microscope view of the plasma physical properties in Earth's neighborhood while the combination with other missions in the Heliophysics System Observatory provides a telescope view of the larger Sun-Earth system. Past studies have found a relationship between substorm activity, which can be more powerful during high speed solar wind stream events, and enhancements of the outer radiation belt electrons. In this study, we examine several distinct particle injection events with dipolarization front characteristics observed by MMS and multiple complementary missions. In particular, cases involving multiple injection events are compared to singular injection events for their effectiveness of creating radiation belt enhancements.

Improving atomic displacement and replacement calculations with physically realistic damage models

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

Nordlund, Kai; Zinkle, Steven J.; Sand, Andrea E.

Atomic collision processes are fundamental to numerous advanced materials technologies such as electron microscopy, semiconductor processing and nuclear power generation. Extensive experimental and computer simulation studies over the past several decades provide the physical basis for understanding the atomic-scale processes occurring during primary displacement events. The current international standard for quantifying this energetic particle damage, the Norgett-Robinson-Torrens displacements per atom (NRT-dpa) model, has nowadays several well-known limitations. In particular, the number of radiation defects produced in energetic cascades in metals is only ~1/3 the NRT-dpa prediction, while the number of atoms involved in atomic mixing is about a factor ofmore » 30 larger than the dpa value. Here we propose two new complementary displacement production estimators (athermal recombination corrected dpa, arc-dpa) and atomic mixing (replacements per atom, rpa) functions that extend the NRT-dpa by providing more physically realistic descriptions of primary defect creation in materials and may become additional standard measures for radiation damage quantification.« less

Improving atomic displacement and replacement calculations with physically realistic damage models

DOE PAGES

Nordlund, Kai; Zinkle, Steven J.; Sand, Andrea E.; ...

2018-03-14

Atomic collision processes are fundamental to numerous advanced materials technologies such as electron microscopy, semiconductor processing and nuclear power generation. Extensive experimental and computer simulation studies over the past several decades provide the physical basis for understanding the atomic-scale processes occurring during primary displacement events. The current international standard for quantifying this energetic particle damage, the Norgett-Robinson-Torrens displacements per atom (NRT-dpa) model, has nowadays several well-known limitations. In particular, the number of radiation defects produced in energetic cascades in metals is only ~1/3 the NRT-dpa prediction, while the number of atoms involved in atomic mixing is about a factor ofmore » 30 larger than the dpa value. Here we propose two new complementary displacement production estimators (athermal recombination corrected dpa, arc-dpa) and atomic mixing (replacements per atom, rpa) functions that extend the NRT-dpa by providing more physically realistic descriptions of primary defect creation in materials and may become additional standard measures for radiation damage quantification.« less

Improving atomic displacement and replacement calculations with physically realistic damage models.

PubMed

Nordlund, Kai; Zinkle, Steven J; Sand, Andrea E; Granberg, Fredric; Averback, Robert S; Stoller, Roger; Suzudo, Tomoaki; Malerba, Lorenzo; Banhart, Florian; Weber, William J; Willaime, Francois; Dudarev, Sergei L; Simeone, David

2018-03-14

Atomic collision processes are fundamental to numerous advanced materials technologies such as electron microscopy, semiconductor processing and nuclear power generation. Extensive experimental and computer simulation studies over the past several decades provide the physical basis for understanding the atomic-scale processes occurring during primary displacement events. The current international standard for quantifying this energetic particle damage, the Norgett-Robinson-Torrens displacements per atom (NRT-dpa) model, has nowadays several well-known limitations. In particular, the number of radiation defects produced in energetic cascades in metals is only ~1/3 the NRT-dpa prediction, while the number of atoms involved in atomic mixing is about a factor of 30 larger than the dpa value. Here we propose two new complementary displacement production estimators (athermal recombination corrected dpa, arc-dpa) and atomic mixing (replacements per atom, rpa) functions that extend the NRT-dpa by providing more physically realistic descriptions of primary defect creation in materials and may become additional standard measures for radiation damage quantification.

Energetic electrons, hard x-ray emission and MHD activity studies in the IR-T1 tokamak.

PubMed

Agah, K Mikaili; Ghoranneviss, M; Elahi, A Salar

2015-01-01

Determinations of plasma parameters as well as the Magnetohydrodynamics (MHD) activity, energetic electrons energy and energy confinement time are essential for future fusion reactors experiments and optimized operation. Also some of the plasma information can be deduced from these parameters, such as plasma equilibrium, stability, and MHD instabilities. In this contribution we investigated the relation between energetic electrons, hard x-ray emission and MHD activity in the IR-T1 Tokamak. For this purpose we used the magnetic diagnostics and a hard x-ray spectroscopy in IR-T1 tokamak. A hard x-ray emission is produced by collision of the runaway electrons with the plasma particles or limiters. The mean energy was calculated from the slope of the energy spectrum of hard x-ray photons.

What Have We Learned From Decades of CRT, And Where Do We Go From Here?

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

Burnham, A K; Souers, P C; Gagliardi, F J

2006-09-11

The Chemical Reactivity Test, or CRT, has been the workhorse for determining short-to-medium term compatibility and thermal stability for energetic materials since the mid 1960s. The concept behind the CRT is quite simple. 0.25 g of material is heated in a 17 cm{sup 3} vessel for 22 hours at 80, 100, or 120 C, and the yield of gaseous products are analyzed by gas chromatography to determine its thermal stability. The instrumentation is shown in Figure 1, and the vessel configuration is shown in Figure 2. For compatibility purposes, two materials, normally 0.25 g of each, are analyzed as amore » mixture. Recently, data from the past 4 decades have been compiled in an Excel spreadsheet and inspected for reliability and internal consistency. The resulting processed data will be added this year to the LLNL HE Reference Guide. Also recently, we have begun to assess the suitability of the CRT to answer new compatibility issues, especially in view of more modern instrumentation now available commercially. One issue that needs to be addressed is the definition of thermal stability and compatibility from the CRT. Prokosch and Garcia (and the associated MIL-STD-1751A) state that the criterion for thermal stability is a gas yield of less than 4 cm{sup 3}/g for a single material for 22 hours at 120 C. The gases from energetic materials of interest ordinarily have an average molecular weight of about 36 g/mol, so this represents decomposition of 0.5-1.0% of the sample. This is a reasonable value, and a relatively unstable energetic material such as PETN has no problem passing. PBX 9404, which yields 1.5 to 2.0 cm{sup 3}/g historically, is used as a periodic check standard. This is interesting in itself, since the nitrocellulose in the 9404 is unstable and probably has partially decomposed over the decades. However, it is not clear whether this aging of the standard would lead to more or less gas, since the initial gaseous degradation products are captured by the DPA stabilizer. Clearly this is an issue that needs reconsideration. The criterion for compatibility is less clearly correct. Although some LLNL reports say that generation of gas in excess of the materials by themselves is an indication of incompatibility, LLNL reports invariably say that materials are compatible if they generate less than 1 cm{sup 3}/g of gas. There are two problems with this criterion. First, it is not stated whether the gas yield is per gram of energetic material or mixture. Second, a material that generates >2 cm{sup 3}/g by itself could never pass the compatibility tests as stated, because even a mixture of equal masses of that material with a completely inert material would generate >1 cm{sup 3}/g of gas per mixture. Furthermore, Prokosch states that a yield equal to or less than from the materials individually means that no reaction has occurred. Clearly, less gas can not be generated unless some type of interaction has occurred. An obvious example would be mixing CaO with a CO{sub 2}-generating energetic material. In the absence of any direct action of the CaO on the energetic material, the CO{sub 2} product would be captured by the CaO, thereby decreasing the gas yield and liberating considerable heat. In a large, closed volume, this could tip the balance to thermal runaway.« less

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

Howe, Joshua D.; Morelock, Cody R.; Jiao, Yang

We present a joint computational and experimental study of Mg–Ni-MOF-74 and Mg–Cd-MOF-74 to gain insight into the mixing of metals and understand how metal mixing affects the structure of the undercoordinated open-metal sites. Our calculations predict that metal mixing is energetically preferred in these materials. Recent experimental work has demonstrated that Mg–Ni-MOF-74 shows a much greater surface area retention in the presence of water than Mg-MOF-74. To probe this effect, we study H 2O adsorption in Mg–Ni-MOF-74, finding that the adsorption energetics and electronic structure do not change significantly at the metal sites when compared to Mg-MOF-74 and Ni-MOF-74, respectively.more » Lastly, we conclude that the increased stability of Mg–Ni-MOF-74 is a result of a M–O bond length distortion in mixed-metal MOF-74, consistent with recent work on the stability of MOF-74 under water exposure.« less

Hydrophobically stabilized open state for the lateral gate of the Sec translocon

PubMed Central

Zhang, Bin; Miller, Thomas F.

2010-01-01

The Sec translocon is a central component of cellular pathways for protein translocation and membrane integration. Using both atomistic and coarse-grained molecular simulations, we investigate the conformational landscape of the translocon and explore the role of peptide substrates in the regulation of the translocation and integration pathways. Inclusion of a hydrophobic peptide substrate in the translocon stabilizes the opening of the lateral gate for membrane integration, whereas a hydrophilic peptide substrate favors the closed lateral gate conformation. The relative orientation of the plug moiety and a peptide substrate within the translocon channel is similarly dependent on whether the substrate is hydrophobic or hydrophilic in character, and the energetics of the translocon lateral gate opening in the presence of a peptide substrate is governed by the energetics of the peptide interface with the membrane. Implications of these results for the regulation of Sec-mediated pathways for protein translocation vs. membrane integration are discussed. PMID:20203009

High pressure-high temperature phase diagram of an energetic crystal: Dihydroxylammonium 5,5'-bistetrazole-1,1'-diolate (TKX-50)

DOE PAGES

Dreger, Z. A.; Breshike, C. J.; Gupta, Y. M.

2017-05-08

Raman spectroscopy was used to examine the high pressure-high temperature structural and chemical stability of an insensitive, high-performance energetic crystal – dihydroxylammonium 5,5'-bistetrazole-1,1'-diolate (TKX-50). The phase diagram was determined over 8 GPa and (293-760) K. Under isobaric heating, the melting/decomposition of TKX-50 is preceded by a transformation to two consecutive high-temperature intermediates; a lower-temperature intermediate – diammonium 5,5’-bistetrazole-1,1'-diolate, and a higher-temperature intermediate – dihydroxylammonium 5,5'-bistetrazolate and/or diammonium 5,5'-bistetrazolate. Pressure strongly increases the transition temperatures for these transformations and subsequent decomposition. As a result, significant increase in the chemical stability of TKX-50 and intermediates with pressure was attributed to a suppressionmore » of hydrogen-transfer.« less

Toward an atomistic description of the urea-denatured state of proteins.

PubMed

Candotti, Michela; Esteban-Martín, Santiago; Salvatella, Xavier; Orozco, Modesto

2013-04-09

We present here the characterization of the structural, dynamics, and energetics of properties of the urea-denatured state of ubiquitin, a small prototypical soluble protein. By combining state-of-the-art molecular dynamics simulations with NMR and small-angle X-ray scattering data, we were able to: (i) define the unfolded state ensemble, (ii) understand the energetics stabilizing unfolded structures in urea, (iii) describe the dedifferential nature of the interactions of the fully unfolded proteins with urea and water, and (iv) characterize the early stages of protein refolding when chemically denatured proteins are transferred to native conditions. The results presented herein are unique in providing a complete picture of the chemically unfolded state of proteins and contribute to deciphering the mechanisms that stabilize the native state of proteins, as well as those that maintain them unfolded in the presence of urea.

Toward an atomistic description of the urea-denatured state of proteins

PubMed Central

Candotti, Michela; Esteban-Martín, Santiago; Salvatella, Xavier; Orozco, Modesto

2013-01-01

We present here the characterization of the structural, dynamics, and energetics of properties of the urea-denatured state of ubiquitin, a small prototypical soluble protein. By combining state-of-the-art molecular dynamics simulations with NMR and small-angle X-ray scattering data, we were able to: (i) define the unfolded state ensemble, (ii) understand the energetics stabilizing unfolded structures in urea, (iii) describe the dedifferential nature of the interactions of the fully unfolded proteins with urea and water, and (iv) characterize the early stages of protein refolding when chemically denatured proteins are transferred to native conditions. The results presented herein are unique in providing a complete picture of the chemically unfolded state of proteins and contribute to deciphering the mechanisms that stabilize the native state of proteins, as well as those that maintain them unfolded in the presence of urea. PMID:23536295

Structural and energetic consequences of mutations in a solvated hydrophobic cavity

NASA Technical Reports Server (NTRS)

Adamek, D. H.; Guerrero, L.; Blaber, M.; Caspar, D. L. D.

2005-01-01

The structural and energetic consequences of modifications to the hydrophobic cavity of interleukin 1-beta (IL-1beta) are described. Previous reports demonstrated that the entirely hydrophobic cavity of IL-1beta contains positionally disordered water. To gain a better understanding of the nature of this cavity and the water therein, a number of mutant proteins were constructed by site-directed mutagenesis, designed to result in altered hydrophobicity of the cavity. These mutations involve the replacement of specific phenylalanine residues, which circumscribe the cavity, with tyrosine, tryptophan, leucine and isoleucine. Using differential scanning calorimetry to determine the relative stabilities of the wild-type and mutant proteins, we found all of the mutants to be destabilizing. X-ray crystallography was used to identify the structural consequences of the mutations. No clear correlation between the hydrophobicities of the specific side-chains introduced and the resulting stabilities was found.

The Quest for Greater Chemical Energy Storage: A Deceiving Game of Nanometer Manipulation

NASA Astrophysics Data System (ADS)

Lindsay, C. Michael

2015-06-01

It is well known that modern energetic materials based on organic chemistry have nearly reached a plateau in performance with only ~ 40% improvement realized over the past half century. This fact has stimulated research on alternative chemical energy storage schema in various US government funded ``High Energy Density Materials'' (HEDM) programs since the 1950's. These efforts have examined a wide range of phenomena such as free radical stabilization, metallic hydrogen, metastable helium, polynitrogens, extended molecular solids, nanothermites, and others. In spite of the substantial research investments, significant improvements in energetic material performance have not been forthcoming. In this talk we will survey various fundamental modes of chemical energy storage, lesson's learned in the various HEDM programs, and areas that are being explored currently. A recurring theme in all of this work is the challenge to successfully manipulate and stabilize matter at the ~ 1 nm scale.

Boosting protein stability with the computational design of β-sheet surfaces.

PubMed

Kim, Doo Nam; Jacobs, Timothy M; Kuhlman, Brian

2016-03-01

β-sheets often have one face packed against the core of the protein and the other facing solvent. Mutational studies have indicated that the solvent-facing residues can contribute significantly to protein stability, and that the preferred amino acid at each sequence position is dependent on the precise structure of the protein backbone and the identity of the neighboring amino acids. This suggests that the most advantageous methods for designing β-sheet surfaces will be approaches that take into account the multiple energetic factors at play including side chain rotamer preferences, van der Waals forces, electrostatics, and desolvation effects. Here, we show that the protein design software Rosetta, which models these energetic factors, can be used to dramatically increase protein stability by optimizing interactions on the surfaces of small β-sheet proteins. Two design variants of the β-sandwich protein from tenascin were made with 7 and 14 mutations respectively on its β-sheet surfaces. These changes raised the thermal midpoint for unfolding from 45°C to 64°C and 74°C. Additionally, we tested an empirical approach based on increasing the number of potential salt bridges on the surfaces of the β-sheets. This was not a robust strategy for increasing stability, as three of the four variants tested were unfolded. © 2016 The Protein Society.

Stability of M 3S 3 complexes on fcc M(111) surfaces: M = Au, Ag, Cu, and Ni

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

Liu, Da-Jiang; Lee, Jiyoung; Windus, Theresa L.

Density Functional Theory is utilized to assess the stability of metal (M)-sulfur (S) complexes adsorbed on fcc M(111) surfaces, specifically considering S-decorated planar M trimers, M 3S 3. Scanning Tunneling Microscopy studies have identified structures proposed to be Ni 3S 3 on Ni(111), and Au 3S 3 on Au(111). In addition, Cu 3S 3 on Cu(111) has been suggested to facilitate enhanced Cu surface mass transport. Our analysis considers M 3S 3 complexes for M = Au, Ag, Cu, and Ni, assessing key measures of stability on surfaces, and also comparing behavior with trends in gas-phase stability. These surface andmore » gas-phase analyses are systematically related within the framework of Hess’s law, which allows elucidation of various contributions to the overall energetics. In all cases, the adsorbed complex is stable relative to its separated constituents adsorbed on the terrace. However, only for Ag does one find a negative energy of formation from excess S on terraces and M extracted from kink sites along step edges, implying spontaneous complex formation for this pathway. We interpret various experimental observations in the context of our results for energetics.« less

Stability of M 3S 3 complexes on fcc M(111) surfaces: M = Au, Ag, Cu, and Ni

DOE PAGES

Liu, Da-Jiang; Lee, Jiyoung; Windus, Theresa L.; ...

2018-02-08

Density Functional Theory is utilized to assess the stability of metal (M)-sulfur (S) complexes adsorbed on fcc M(111) surfaces, specifically considering S-decorated planar M trimers, M 3S 3. Scanning Tunneling Microscopy studies have identified structures proposed to be Ni 3S 3 on Ni(111), and Au 3S 3 on Au(111). In addition, Cu 3S 3 on Cu(111) has been suggested to facilitate enhanced Cu surface mass transport. Our analysis considers M 3S 3 complexes for M = Au, Ag, Cu, and Ni, assessing key measures of stability on surfaces, and also comparing behavior with trends in gas-phase stability. These surface andmore » gas-phase analyses are systematically related within the framework of Hess’s law, which allows elucidation of various contributions to the overall energetics. In all cases, the adsorbed complex is stable relative to its separated constituents adsorbed on the terrace. However, only for Ag does one find a negative energy of formation from excess S on terraces and M extracted from kink sites along step edges, implying spontaneous complex formation for this pathway. We interpret various experimental observations in the context of our results for energetics.« less

Handedness results from Complementary Hemispheric Dominance, not Global Hemispheric Dominance: Evidence from Mechanically Coupled Bilateral Movements.

PubMed

Woytowicz, Elizabeth J; Westlake, Kelly P; Whitall, Jill; Sainburg, Robert L

2018-05-09

Two contrasting views of handedness can be described as 1) complementary dominance, in which each hemisphere is specialized for different aspects of motor control, and 2) global dominance, in which the hemisphere contralateral to the dominant arm is specialized for all aspects of motor control. The present study sought to determine which motor lateralization hypothesis best predicts motor performance during common bilateral task of stabilizing an object (e.g. bread) with one hand while applying forces to the object (e.g. slicing) using the other hand. We designed an experimental equivalent of this task, performed in a virtual environment with the unseen arms supported by frictionless air-sleds. The hands were connected by a spring, and the task was to maintain the position of one hand, while moving the other hand to a target. Thus, the reaching hand was required to take account of the spring load to make smooth and accurate trajectories, while the stabilizer hand was required to impede the spring load to keep a constant position. Right-handed subjects performed two task sessions (right hand reach and left hand stabilize; left hand reach and right hand stabilize) with the order of the sessions counterbalanced between groups. Our results indicate a hand by task-component interaction, such that the right hand showed straighter reaching performance while the left showed more stable holding performance. These findings provide support for the complementary dominance hypothesis and suggest that the specializations of each cerebral hemisphere for impedance and dynamic control mechanisms are expressed during bilateral interactive tasks.

Optimization of DIII-D discharges to avoid AE destabilization

NASA Astrophysics Data System (ADS)

Varela, Jacobo; Spong, Donald; Garcia, Luis; Huang, Juan; Murakami, Masanori

2017-10-01

The aim of the study is to analyze the stability of Alfven Eigenmodes (AE) perturbed by energetic particles (EP) during DIII-D operation. We identify the optimal NBI operational regimes that avoid or minimize the negative effects of AE on the device performance. We use the reduced MHD equations to describe the linear evolution of the poloidal flux and the toroidal component of the vorticity in a full 3D system, coupled with equations of density and parallel velocity moments for the energetic particles, including the effect of the acoustic modes. We add the Landau damping and resonant destabilization effects using a closure relation. We perform parametric studies of the MHD and AE stability, taking into account the experimental profiles of the thermal plasma and EP, also using a range of values of the energetic particles β, density and velocity as well the effect of the toroidal couplings. We reproduce the AE activity observed in high poloidal β discharge at the pedestal and reverse shear discharges. This material based on work is supported both by the U.S. Department of Energy, Office of Science, under Contract DE-AC05-00OR22725 with UT-Battelle, LLC. Research sponsored in part by the Ministerio de Economia y Competitividad of Spain under the project.

The effect of the averaged structural and energetic features on the cohesive energy of nanocrystals

NASA Astrophysics Data System (ADS)

Ali Safaei

2010-03-01

The size dependency of the cohesive energy of nanocrystals is obtained in terms of their averaged structural and energetic properties, which are in direct proportion with their cohesive energies. The significance of the effect of the geometrical shape of nanoparticles on their thermal stability has been discussed. The model has been found to have good prediction for the case of Cu and Al nanoparticles, with sizes in the ranges of 1-22 nm and 2-22 nm, respectively. Defining a new parameter, named as the surface-to-volume energy-contribution ratio, the relative thermal stabilities of different nanoclusters and their different surface-crystalline faces are discussed and compared to the molecular dynamic (MD) simulation results of copper nanoclusters. Finally, based on the size dependency of the cohesive energy, a formula for the size-dependent diffusion coefficient has been presented which includes the structural and energetic effects. Using this formula, the faster-than-expected interdiffusion/alloying of Au(core)-Ag(shell) nanoparticles with the core-shell structure, the Au-core diameter of 20 nm and the Ag-shell thickness of 2.91 nm, has been discussed and the calculated diffusion coefficient has been found to be consistent with its corresponding experimental value.

Stability and Control of Burning Tokamak Plasmas with Resistive Walls: Final Technical Report

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

Miller, George; Brennan, Dylan; Cole, Andrew

This project is focused on theoretical and computational development for quantitative prediction of the stability and control of the equilibrium state evolution in toroidal burning plasmas, including its interaction with the surrounding resistive wall. The stability of long pulse burning plasmas is highly sensitive to the physics of resonant layers in the plasma, sources of momentum and flow, kinetic effects of energetic particles, and boundary conditions at the wall, including feedback control and error fields. In ITER in particular, the low toroidal flow equilibrium state, sustained primarily by energetic alpha particles from fusion reactions, will require the consideration of allmore » of these key elements to predict quantitatively the stability and evolution. The principal investigators on this project have performed theoretical and computational analyses, guided by analytic modeling, to address this physics in realistic configurations. The overall goal has been to understand the key physics mechanisms that describe stable toroidal burning plasmas under active feedback control. Several relevant achievements have occurred during this project, leading to publications and invited conference presentations. In theoretical efforts, with the physics of the resonant layers, resistive wall, and toroidal momentum transport included, this study has extended from cylindrical resistive plasma - resistive wall models with feedback control to toroidal geometry with strong shaping to study mode coupling effects on the stability. These results have given insight into combined tearing and resistive wall mode behavior in simulations and experiment, while enabling a rapid exploration of plasma parameter space, to identify possible domains of interest for large plasma codes to investigate in more detail. Resonant field amplification and quasilinear torques in the presence of error fields and velocity shear have also been investigated. Here it was found, surprisingly, that the Maxwell torque on resonant layers in the plasma which exhibit finite real frequencies ωr in their response is significantly different from the conventional results based on tearing layers with pure real growth (or damping) rates. This observation suggests the possibility that the torque on the tearing layers can lock the plasma rotation to this finite phase velocity, which may lead to locking in which velocity shear is maintained. More broadly, the sources of all torques driving flows in magnetic confinement experiments is not fully understood, and this theoretical work may shed light on puzzling experimental results. It was also found that real frequencies occur over a wide range of plasma response regimes, and are indeed the norm and not the exception, often leading to profound effects on the locking torque. Also, the influence of trapped energetic ions orbiting over the resistive plasma mode structure, a critical effect in burning plasmas, was investigated through analytic modeling and analysis of simulations and experiment. This effort has shown that energetic ions can drive the development of disruptive instabilities, but also damp and stabilize the instabilities, depending on the details of the shear in the equilibrium magnetic field. This finding could be critical to maintaining stable operations in burning plasmas. In the most recent work, a series of simulations have been conducted to study the effect of differential flow and energetic ion effects on entry to the onset of a disruptive instability in the most realistic conditions possible, with preexisting nonlinearly saturated benign instabilities. Throughout this work, the linear and quasilinear theory of resonant layers with differential flow between them, their interaction with resistive wall and error fields, and energetic ions effects, have been used to understand realistic simulations of mode onset and the experimental discharges they represent. These studies will continue to answer remaining questions about the relation between theoretical results obtained in this project and observations of the onset and evolution of disruptive instabilities in experiment.« less

Ferroelectricity emerging in strained (111)-textured ZrO{sub 2} thin films

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

Fan, Zhen, E-mail: a0082709@u.nus.edu, E-mail: msecj@nus.edu.sg; Deng, Jinyu; Liu, Ziyan

2016-01-04

(Anti-)ferroelectricity in complementary metal-oxide-semiconductor (CMOS)-compatible binary oxides have attracted considerable research interest recently. Here, we show that by using substrate-induced strain, the orthorhombic phase and the desired ferroelectricity could be achieved in ZrO{sub 2} thin films. Our theoretical analyses suggest that the strain imposed on the ZrO{sub 2} (111) film by the TiN/MgO (001) substrate would energetically favor the tetragonal (t) and orthorhombic (o) phases over the monoclinic (m) phase of ZrO{sub 2}, and the compressive strain along certain 〈11-2〉 directions may further stabilize the o-phase. Experimentally ZrO{sub 2} thin films are sputtered onto the MgO (001) substrates buffered bymore » epitaxial TiN layers. ZrO{sub 2} thin films exhibit t- and o-phases, which are highly (111)-textured and strained, as evidenced by X-ray diffraction and transmission electron microscopy. Both polarization-electric field (P-E) loops and corresponding current responses to voltage stimulations measured with appropriate applied fields reveal the ferroelectric sub-loop behavior of the ZrO{sub 2} films at certain thicknesses, confirming that the ferroelectric o-phase has been developed in the strained (111)-textured ZrO{sub 2} films. However, further increasing the applied field leads to the disappearance of ferroelectric hysteresis, the possible reasons of which are discussed.« less

Creation of energetic biothermite inks using ferritin liquid protein

NASA Astrophysics Data System (ADS)

Slocik, Joseph M.; McKenzie, Ruel; Dennis, Patrick B.; Naik, Rajesh R.

2017-04-01

Energetic liquids function mainly as fuels due to low energy densities and slow combustion kinetics. Consequently, these properties can be significantly increased through the addition of metal nanomaterials such as aluminium. Unfortunately, nanoparticle additives are restricted to low mass fractions in liquids because of increased viscosities and severe particle agglomeration. Nanoscale protein ionic liquids represent multifunctional solvent systems that are well suited to overcoming low mass fractions of nanoparticles, producing stable nanoparticle dispersions and simultaneously offering a source of oxidizing agents for combustion of reactive nanomaterials. Here, we use iron oxide-loaded ferritin proteins to create a stable and highly energetic liquid composed of aluminium nanoparticles and ferritin proteins for printing and forming 3D shapes and structures. In total, this bioenergetic liquid exhibits increased energy output and performance, enhanced dispersion and oxidation stability, lower activation temperatures, and greater processability and functionality.

Thermal degradation of Lewis acid complexed LDPE films

NASA Astrophysics Data System (ADS)

Sreelatha, K.; Predeep, P.

2017-06-01

The study highlights the thermal behavior of the semiconducting LDPE films synthesized by SbCl5 doping. The structural peculiarities and the responses of the structure to energetic modifications are studied. TGA and DTG curves are used to determine the thermal stability of the material. Degradation kinetics is elucidated. Activation energy and the entropy of activation for the degradation of the samples are calculated using Coats-Redfern plots and the samples show appreciable thermal stability.

Adaptive dynamics of competition for nutritionally complementary resources: character convergence, displacement, and parallelism.

PubMed

Vasseur, David A; Fox, Jeremy W

2011-10-01

Consumers acquire essential nutrients by ingesting the tissues of resource species. When these tissues contain essential nutrients in a suboptimal ratio, consumers may benefit from ingesting a mixture of nutritionally complementary resource species. We investigate the joint ecological and evolutionary consequences of competition for complementary resources, using an adaptive dynamics model of two consumers and two resources that differ in their relative content of two essential nutrients. In the absence of competition, a nutritionally balanced diet rarely maximizes fitness because of the dynamic feedbacks between uptake rate and resource density, whereas in sympatry, nutritionally balanced diets maximize fitness because competing consumers with different nutritional requirements tend to equalize the relative abundances of the two resources. Adaptation from allopatric to sympatric fitness optima can generate character convergence, divergence, and parallel shifts, depending not on the degree of diet overlap but on the match between resource nutrient content and consumer nutrient requirements. Contrary to previous verbal arguments that suggest that character convergence leads to neutral stability, coadaptation of competing consumers always leads to stable coexistence. Furthermore, we show that incorporating costs of consuming or excreting excess nonlimiting nutrients selects for nutritionally balanced diets and so promotes character convergence. This article demonstrates that resource-use overlap has little bearing on coexistence when resources are nutritionally complementary, and it highlights the importance of using mathematical models to infer the stability of ecoevolutionary dynamics.

Achieving a long-lived high-beta plasma state by energetic beam injection

NASA Astrophysics Data System (ADS)

Guo, H. Y.; Binderbauer, M. W.; Tajima, T.; Milroy, R. D.; Steinhauer, L. C.; Yang, X.; Garate, E. G.; Gota, H.; Korepanov, S.; Necas, A.; Roche, T.; Smirnov, A.; Trask, E.

2015-04-01

Developing a stable plasma state with high-beta (ratio of plasma to magnetic pressures) is of critical importance for an economic magnetic fusion reactor. At the forefront of this endeavour is the field-reversed configuration. Here we demonstrate the kinetic stabilizing effect of fast ions on a disruptive magneto-hydrodynamic instability, known as a tilt mode, which poses a central obstacle to further field-reversed configuration development, by energetic beam injection. This technique, combined with the synergistic effect of active plasma boundary control, enables a fully stable ultra-high-beta (approaching 100%) plasma with a long lifetime.

Off-pathway assembly of fimbria subunits is prevented by chaperone CfaA of CFA/I fimbriae from enterotoxigenic E. coli.

PubMed

Bao, Rui; Liu, Yang; Savarino, Stephen J; Xia, Di

2016-12-01

The assembly of the class 5 colonization factor antigen I (CFA/I) fimbriae of enterotoxigenic E. coli was proposed to proceed via the alternate chaperone-usher pathway. Here, we show that in the absence of the chaperone CfaA, CfaB, the major pilin subunit of CFA/I fimbriae, is able to spontaneously refold and polymerize into cyclic trimers. CfaA kinetically traps CfaB to form a metastable complex that can be stabilized by mutations. Crystal structure of the stabilized complex reveals distinctive interactions provided by CfaA to trap CfaB in an assembly competent state through donor-strand complementation (DSC) and cleft-mediated anchorage. Mutagenesis indicated that DSC controls the stability of the chaperone-subunit complex and the cleft-mediated anchorage of the subunit C-terminus additionally assist in subunit refolding. Surprisingly, over-stabilization of the chaperone-subunit complex led to delayed fimbria assembly, whereas destabilizing the complex resulted in no fimbriation. Thus, CfaA acts predominantly as a kinetic trap by stabilizing subunit to avoid its off-pathway self-polymerization that results in energetically favorable trimers and could serve as a driving force for CFA/I pilus assembly, representing an energetic landscape unique to class 5 fimbria assembly. Published 2016. This article is a U.S. Government work and is in the public domain in the USA. Molecular Microbiology published by John Wiley & Sons Ltd.

Brain size and thermoregulation during the evolution of the genus Homo.

PubMed

Naya, Daniel E; Naya, Hugo; Lessa, Enrique P

2016-01-01

Several hypotheses have been proposed to explain the evolution of an energetically costly brain in the genus Homo. Some of these hypotheses are based on the correlation between climatic factors and brain size recorded for this genus during the last millions of years. In this study, we propose a complementary climatic hypothesis that is based on the mechanistic connection between temperature, thermoregulation, and size of internal organs in endothermic species. We hypothesized that global cooling during the last 3.2 my may have imposed an increased energy expenditure for thermoregulation, which in the case of hominids could represent a driver for the evolution of an expanded brain, or at least, it could imply the relaxation of a negative selection pressure acting upon this costly organ. To test this idea, here we (1) assess variation in the energetic costs of thermoregulation and brain maintenance for the last 3.2 my, and (2) evaluate the relationship between Earth temperature and brain maintenance cost for the same period, taking into account the effects of body mass and fossil age. We found that: (1) the energetic cost associated with brain enlargement represents an important fraction (between 47.5% and 82.5%) of the increase in energy needed for thermoregulation; (2) fossil age is a better predictor of brain maintenance cost than Earth temperature, suggesting that (at least) another factor correlated with time was more relevant than ambient temperature in brain size evolution; and (3) there is a significant negative correlation between the energetic cost of brain and Earth temperature, even after accounting for the effect of body mass and fossil age. Thus, our results expand the current energetic framework for the study of brain size evolution in our lineage by suggesting that a fall in Earth temperature during the last millions of years may have facilitated brain enlargement. Copyright © 2015 Elsevier Inc. All rights reserved.

The Methionine-aromatic Motif Plays a Unique Role in Stabilizing Protein Structure*

PubMed Central

Valley, Christopher C.; Cembran, Alessandro; Perlmutter, Jason D.; Lewis, Andrew K.; Labello, Nicholas P.; Gao, Jiali; Sachs, Jonathan N.

2012-01-01

Of the 20 amino acids, the precise function of methionine (Met) remains among the least well understood. To establish a determining characteristic of methionine that fundamentally differentiates it from purely hydrophobic residues, we have used in vitro cellular experiments, molecular simulations, quantum calculations, and a bioinformatics screen of the Protein Data Bank. We show that approximately one-third of all known protein structures contain an energetically stabilizing Met-aromatic motif and, remarkably, that greater than 10,000 structures contain this motif more than 10 times. Critically, we show that as compared with a purely hydrophobic interaction, the Met-aromatic motif yields an additional stabilization of 1–1.5 kcal/mol. To highlight its importance and to dissect the energetic underpinnings of this motif, we have studied two clinically relevant TNF ligand-receptor complexes, namely TRAIL-DR5 and LTα-TNFR1. In both cases, we show that the motif is necessary for high affinity ligand binding as well as function. Additionally, we highlight previously overlooked instances of the motif in several disease-related Met mutations. Our results strongly suggest that the Met-aromatic motif should be exploited in the rational design of therapeutics targeting a range of proteins. PMID:22859300

Importance of many-body dispersion and temperature effects on gas-phase gold cluster (meta)stability

NASA Astrophysics Data System (ADS)

Goldsmith, Bryan R.; Gruene, Philipp; Lyon, Jonathan T.; Rayner, David M.; Fielicke, André; Scheffler, Matthias; Ghiringhelli, Luca M.

Gold clusters in the gas phase exhibit many structural isomers that are shown to intercovert frequently, even at room temperature. We performed ab initio replica-exchange molecular dynamics (REMD) calculations on gold clusters (of sizes 5-14 atoms) to identify metastable states and their relative populations at finite temperature, as well as to examine the importance of temperature and van der Waals (vdW) on their isomer energetic ordering. Free energies of the gold cluster isomers are optimally estimated using the Multistate Bennett Acceptance Ratio. The distribution of bond coordination numbers and radius of gyration are used to address the challenge of discriminating isomers along their dynamical trajectories. Dispersion effects are important for stabilizing three-dimensional structures relative to planar structures and brings isomer energetic predictions to closer quantitative agreement compared with RPA@PBE calculations. We find that higher temperatures typically stabilize metastable three-dimensional structures relative to planar/quasiplanar structures. Computed IR spectra of low free energy Au9, Au10, and Au12 isomers are in agreement with experimental spectra obtained by far-IR multiple photon dissociation in a molecular beam at 100 K.

Application of a parallel genetic algorithm to the global optimization of medium-sized Au-Pd sub-nanometre clusters

NASA Astrophysics Data System (ADS)

Hussein, Heider A.; Demiroglu, Ilker; Johnston, Roy L.

2018-02-01

To contribute to the discussion of the high activity and reactivity of Au-Pd system, we have adopted the BPGA-DFT approach to study the structural and energetic properties of medium-sized Au-Pd sub-nanometre clusters with 11-18 atoms. We have examined the structural behaviour and stability as a function of cluster size and composition. The study suggests 2D-3D crossover points for pure Au clusters at 14 and 16 atoms, whereas pure Pd clusters are all found to be 3D. For Au-Pd nanoalloys, the role of cluster size and the influence of doping were found to be extensive and non-monotonic in altering cluster structures. Various stability criteria (e.g. binding energies, second differences in energy, and mixing energies) are used to evaluate the energetics, structures, and tendency of segregation in sub-nanometre Au-Pd clusters. HOMO-LUMO gaps were calculated to give additional information on cluster stability and a systematic homotop search was used to evaluate the energies of the generated global minima of mono-substituted clusters and the preferred doping sites, as well as confirming the validity of the BPGA-DFT approach.

Quadrupedal locomotor simulation: producing more realistic gaits using dual-objective optimization

PubMed Central

Hirasaki, Eishi

2018-01-01

In evolutionary biomechanics it is often considered that gaits should evolve to minimize the energetic cost of travelling a given distance. In gait simulation this goal often leads to convincing gait generation. However, as the musculoskeletal models used get increasingly sophisticated, it becomes apparent that such a single goal can lead to extremely unrealistic gait patterns. In this paper, we explore the effects of requiring adequate lateral stability and show how this increases both energetic cost and the realism of the generated walking gait in a high biofidelity chimpanzee musculoskeletal model. We also explore the effects of changing the footfall sequences in the simulation so it mimics both the diagonal sequence walking gaits that primates typically use and also the lateral sequence walking gaits that are much more widespread among mammals. It is apparent that adding a lateral stability criterion has an important effect on the footfall phase relationship, suggesting that lateral stability may be one of the key drivers behind the observed footfall sequences in quadrupedal gaits. The observation that single optimization goals are no longer adequate for generating gait in current models has important implications for the use of biomimetic virtual robots to predict the locomotor patterns in fossil animals. PMID:29657790

Energetics and Kinetics of trans-SNARE Zippering

NASA Astrophysics Data System (ADS)

Rebane, Aleksander A.; Shu, Tong; Krishnakumar, Shyam; Rothman, James E.; Zhang, Yongli

Synaptic exocytosis relies on assembly of soluble N-ethylmaleimide-sensitive factor attachment protein receptor (SNARE) proteins into a four-helix bundle to drive membrane fusion. Complementary SNAREs anchored to the synaptic vesicle (v-SNARE) and the plasma membrane (t-SNARE) associate from their N-termini, transiting a half-assembled intermediate (trans-SNARE), and ending at their C-termini with a rapid power stroke that leads to membrane fusion. Although cytosolic SNARE assembly has been characterized, it remains unknown how membranes modulate the energetics and kinetics of SNARE assembly. Here, we present optical tweezers measurements on folding of single membrane proteins in phospholipid bilayers. To our knowledge, this is the first such report. We measured the energetics, kinetics, and assembly intermediates of trans-SNAREs formed between a t-SNARE inserted into a bead-supported bilayer and a v-SNARE in a nanodisc. We found that the repulsive force of the apposed membranes increases the lifetime of the half-assembled intermediate. Our findings provide a single-molecule platform to study the regulation of trans-SNARE assembly by proteins that act on the half-assembled state, and thus reveal the mechanistic basis of the speed and high fidelity of synaptic transmission. This work was supported by US National Institutes of Health Grants F31 GM119312-01 (to A.A.R) and R01 GM093341 (to Y.Z.).

Analysis of Alfvén eigenmode destabilization by energetic particles in Large Helical Device using a Landau-closure model

DOE PAGES

Varela, Jacobo Rodriguez; Spong, D. A.; Garcia, L.

2017-03-06

Here, energetic particle populations in nuclear fusion experiments can destabilize the Alfvén Eigenmodes through inverse Landau damping and couplings with gap modes in the shear Alfvén continua. We use the reduced MHD equations to describe the linear evolution of the poloidal flux and the toroidal component of the vorticity in a full 3D system, coupled with equations of density and parallel velocity moments for the energetic particles. We add the Landau damping and resonant destabilization effects using a closure relation. We apply the model to study the Alfvén mode stability in the inward-shifted configurations of the Large Helical Device (LHD), performing a parametric analysis of the energetic particle β (more » $${{\\beta}_{f}}$$ ) in a range of realistic values, the ratios of the energetic particle thermal/Alfvén velocities ($${{V}_{\\text{th}}}/{{V}_{A0}}$$ ), the magnetic Lundquist numbers (S) and the toroidal modes (n). The n = 1 and n = 2 TAEs are destabilized, although the n = 3 and n = 4 TAEs are weakly perturbed. The most unstable configurations are associated with the density gradients of energetic particles in the plasma core: the TAEs are destabilized, even for small energetic particle populations, if their thermal velocity is lower than 0.4 times the Alfvén velocity. The frequency range of MHD bursts measured in the LHD are 50–70 kHz for the n = 1 and 60–80 kHz for the n = 2 TAE, which is consistent with the model predictions.« less

First-principles study of the solid solution of hydrogen in lanthanum

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

Schoellhammer, Gunther; Herzig, Peter; Wolf, Walter

2011-09-01

Results from first-principles investigations of the energetical, structural, electronic, and vibrational properties of model structures probing the metal-rich region of the lanthanum-hydrogen system, i.e., the region of the solid solution of hydrogen in lanthanum, are presented. We have studied the site preference and the ordering tendency of hydrogen atoms interstitially bonded in close-packed lanthanum. Spatially separated hydrogen atoms have turned out to exhibit an energetical preference for the occupation of octahedral interstitial sites at low temperature. Indications for a reversal of the site preference in favor of the occupation of tetrahedral interstitial sites at elevated temperature have been found. Linearmore » arrangements consisting of pairs of octahedrally and/or tetrahedrally coordinated hydrogen atoms collinearly bonded to a central lanthanum atom have turned out to be energetically favorable structure elements. Further stabilization is achieved if such hydrogen pairs are in turn linked together so that extended chains of La-H bonds are formed. Pair formation and chain linking counteract the energetical preference for octahedral coordination observed for separated hydrogen atoms.« less

Effect of a strong-current ion ring on spheromak stability

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

Litwin, C.; Sudan, R.N.

The stability of a spheromak with an energetic ion ring, carrying a current comparable to the plasma current, to the tilt mode is considered. For small departures from sphericity a perturbative approach is applied to an appropriate energy principle in order to calculate the lowest nontrivial kinetic contribution of the ion ring. An analytic stability criterion is obtained. It is seen that the prolate configuration becomes more stable while the oblate one is less stable than in the absence of the ring. The prolomak becomes stable when the ring kinetic energy exceeds the magnetic energy within the separatrix.

Uncovering the determinants of a highly perturbed tyrosine pKa in the active site of ketosteroid isomerase.

PubMed

Schwans, Jason P; Sunden, Fanny; Gonzalez, Ana; Tsai, Yingssu; Herschlag, Daniel

2013-11-05

Within the idiosyncratic enzyme active-site environment, side chain and ligand pKa values can be profoundly perturbed relative to their values in aqueous solution. Whereas structural inspection of systems has often attributed perturbed pKa values to dominant contributions from placement near charged groups or within hydrophobic pockets, Tyr57 of a Pseudomonas putida ketosteroid isomerase (KSI) mutant, suggested to have a pKa perturbed by nearly 4 units to 6.3, is situated within a solvent-exposed active site devoid of cationic side chains, metal ions, or cofactors. Extensive comparisons among 45 variants with mutations in and around the KSI active site, along with protein semisynthesis, (13)C NMR spectroscopy, absorbance spectroscopy, and X-ray crystallography, was used to unravel the basis for this perturbed Tyr pKa. The results suggest that the origin of large energetic perturbations are more complex than suggested by visual inspection. For example, the introduction of positively charged residues near Tyr57 raises its pKa rather than lowers it; this effect, and part of the increase in the Tyr pKa from the introduction of nearby anionic groups, arises from accompanying active-site structural rearrangements. Other mutations with large effects also cause structural perturbations or appear to displace a structured water molecule that is part of a stabilizing hydrogen-bond network. Our results lead to a model in which three hydrogen bonds are donated to the stabilized ionized Tyr, with these hydrogen-bond donors, two Tyr side chains, and a water molecule positioned by other side chains and by a water-mediated hydrogen-bond network. These results support the notion that large energetic effects are often the consequence of multiple stabilizing interactions rather than a single dominant interaction. Most generally, this work provides a case study for how extensive and comprehensive comparisons via site-directed mutagenesis in a tight feedback loop with structural analysis can greatly facilitate our understanding of enzyme active-site energetics. The extensive data set provided may also be a valuable resource for those wishing to extensively test computational approaches for determining enzymatic pKa values and energetic effects.

Uncovering the Determinants of a Highly Perturbed Tyrosine pKa in the Active Site of Ketosteroid Isomerase†

PubMed Central

Schwans, Jason P.; Sunden, Fanny; Gonzalez, Ana; Tsai, Yingssu; Herschlag, Daniel

2013-01-01

Within the idiosyncratic enzyme active site environment, side chain and ligand pKa values can be profoundly perturbed relative to their values in aqueous solution. Whereas structural inspection of systems has often attributed perturbed pKa values to dominant contributions from placement near to charged groups or within hydrophobic pockets, Tyr57 of a P. putida ketosteroid isomerase (KSI) mutant, suggested to have a pKa perturbed by nearly 4 units to 6.3, is situated within a solvent-exposed active site devoid of cationic side chains, metal ions, or cofactors. Extensive comparisons among 45 variants with mutations in and around the KSI active site, along with protein semi-synthesis, 13C NMR spectroscopy, absorbance spectroscopy, and x-ray crystallography, was used to unravel the basis for this perturbed Tyr pKa. The results suggest that the origin of large energetic perturbations are more complex than suggested by visual inspection. For example, the introduction of positively charged residues near Tyr57 raises its pKa rather than lowers it; this effect, and part of the increase in the Tyr pKa from introduction of nearby anionic groups arise from accompanying active site structural rearrangements. Other mutations with large effects also cause structural perturbations or appear to displace a structured water molecule that is part of a stabilizing hydrogen bond network. Our results lead to a model in which three hydrogen bonds are donated to the stabilized ionized Tyr, with these hydrogen bond donors, two Tyr side chains and a water molecule, positioned by other side chains and by a water-mediated hydrogen bond network. These results support the notion that large energetic effects are often the consequence of multiple stabilizing interactions, rather than a single dominant interaction. Most generally, this work provides a case study for how extensive and comprehensive comparisons via site-directed mutagenesis in a tight feedback loop with structural analysis can greatly facilitate our understanding of enzyme active site energetics. The extensive dataset provided may also be a valuable resource for those wishing to extensively test computational approaches for determining enzymatic pKa values and energetic effects. PMID:24151972

Theoretical insight into the binding energy and detonation performance of ε-, γ-, β-CL-20 cocrystals with β-HMX, FOX-7, and DMF in different molar ratios, as well as electrostatic potential.

PubMed

Feng, Rui-Zhi; Zhang, Shu-Hai; Ren, Fu-de; Gou, Rui-Jun; Gao, Li

2016-06-01

Molecular dynamics method was employed to study the binding energies on the selected crystal planes of the ε-, γ-, β-conformation 2,4,6,8,10,12-hexanitrohexaazaisowurtzitane (ε-, γ-, β-CL-20) cocrystal explosives with 1,1-diamino-2,2-dinitroethylene (FOX-7), 1,3,5,7-tetranitro- 1,3,5,7-tetrazacyclooctane with β-conformation (β-HMX) and N,N-dimethylformamide (DMF) in different molar ratios. The oxygen balance, density, detonation velocity, detonation pressure, and surface electrostatic potential were analyzed. The results indicate that the binding energies E b (*) and stabilities are in the order of 1:1 > 2:1 > 3:1 > 5:1 > 8:1 (CL-20:FOX-7/β-HMX/DMF). The values of E b (*) and stabilities of the energetic-nonenergetic CL-20/DMF cocrystals are far larger than those of the energetic-energetic CL-20/FOX-7 and CL-20/β-HMX, and those of CL-20/β-HMX are the smallest. For CL-20/FOX-7 and CL-20/β-HMX, the largest E b (*) appears in the cocrystals with the 1:1, 1:2 or 1:3 molar ratio, and the stabilities of the cocrystals with the excess ratio of CL-20 are weaker than those in the cocrystals with the excess ratio of FOX-7 or β-HMX. In CL-20/FOX-7, CL-20 prefers adopting the γ-form, and ε-CL-20 is the preference in CL-20/β-HMX, and ε-CL-20 and β-CL-20 can be found in CL-20/DMF. The CL-20/FOX-7 and CL-20/β-HMX cocrystals with low molar ratios can meet the requirements of low sensitive high energetic materials. Surface electrostatic potential reveals the nature of the sensitivity change upon the cocrystal formation. Graphical Abstract MD method was employed to study the binding energies on the selected crystal planes in the ε-, γ-, β-CL-20 cocrystals with FOX-7, β-HMX and DMF in different molar ratios. Surface electrostatic potential reveals the nature of the sensitivity change in cocrystals.

Link between microstability and macrostability of plasmas

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

Litwin, C.

A mechanism linking high-frequency microinstabilities and the low-frequencymacrostability is proposed. The coupling is provided by the time-averagedforce, ponderomotive force, of unstable high-frequency waves. Two specificexamples of this phenomenon are discussed. It is shown that an..cap alpha..-particle loss-cone instability stabilizes the flute mode of anignited, axisymmetric mirror plasma. In tokamaks, the ion-whistler instability,driven by an anisotropic population of energetic particles, stabilizes theinternal kink mode for JET range of parameters.

β-armchair antimony nanotube: Structure, stability and electronic properties

NASA Astrophysics Data System (ADS)

Singh, Shilpa; Gupta, Sanjeev K.; Sonvane, Yogesh; Gajjar, P. N.

2018-05-01

In the present work, we have used density functional theory (DFT) to investigate the structure, stability and electronic properties of β-armchair antimony nanotube (ASbNT). We have calculated formation energy and found that β-armchair antimony nanotube (ASbNT) is energetically less stable than β-antimonene. The result shows that β-ASbNT of higher diameter are more stable than nanotubes of lower diameter while electronic band structure shows semiconducting nature of these nanotubes.

Fast ion stabilization of the ion temperature gradient driven modes in the Joint European Torus hybrid-scenario plasmas: a trigger mechanism for internal transport barrier formation

NASA Astrophysics Data System (ADS)

Romanelli, M.; Zocco, A.; Crisanti, F.; Contributors, JET-EFDA

2010-04-01

Understanding and modelling turbulent transport in thermonuclear fusion plasmas are crucial for designing and optimizing the operational scenarios of future fusion reactors. In this context, plasmas exhibiting state transitions, such as the formation of an internal transport barrier (ITB), are particularly interesting since they can shed light on transport physics and offer the opportunity to test different turbulence suppression models. In this paper, we focus on the modelling of ITB formation in the Joint European Torus (JET) [1] hybrid-scenario plasmas, where, due to the monotonic safety factor profile, magnetic shear stabilization cannot be invoked to explain the transition. The turbulence suppression mechanism investigated here relies on the increase in the plasma pressure gradient in the presence of a minority of energetic ions. Microstability analysis of the ion temperature gradient driven modes (ITG) in the presence of a fast-hydrogen minority shows that energetic ions accelerated by the ion cyclotron resonance heating (ICRH) system (hydrogen, nH,fast/nD,thermal up to 10%, TH,fast/TD,thermal up to 30) can increase the pressure gradient enough to stabilize the ITG modes driven by the gradient of the thermal ions (deuterium). Numerical analysis shows that, by increasing the temperature of the energetic ions, electrostatic ITG modes are gradually replaced by nearly electrostatic modes with tearing parity at progressively longer wavelengths. The growth rate of the microtearing modes is found to be lower than that of the ITG modes and comparable to the local E × B-velocity shearing rate. The above mechanism is proposed as a possible trigger for the formation of ITBs in this type of discharges.

Off-axis fishbone-like instability and excitation of resistive wall modes in JT-60U and DIII-D

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

Okabayashi, M.; Solomon, W. M.; Budny, R. V.

2011-05-15

An energetic-particle (EP)-driven ''off-axis-fishbone-like mode (OFM)'' often triggers a resistive wall mode (RWM) in JT-60U and DIII-D devices, preventing long-duration high-{beta}{sub N} discharges. In these experiments, the EPs are energetic ions (70-85 keV) injected by neutral beams to produce high-pressure plasmas. EP-driven bursting events reduce the EP density and the plasma rotation simultaneously. These changes are significant in high-{beta}{sub N} low-rotation plasmas, where the RWM stability is predicted to be strongly influenced by the EP precession drift resonance and by the plasma rotation near the q=2 surface (kinetic effects). Analysis of these effects on stability with a self-consistent perturbation tomore » the mode structure using the MARS-K code showed that the impact of EP losses and rotation drop is sufficient to destabilize the RWM in low-rotation plasmas, when the plasma rotation normalized by Alfven frequency is only a few tenths of a percent near the q=2 surface. The OFM characteristics are very similar in JT-60U and DIII-D, including nonlinear mode evolution. The modes grow initially like a classical fishbone, and then the mode structure becomes strongly distorted. The dynamic response of the OFM to an applied n=1 external field indicates that the mode retains its external kink character. These comparative studies suggest that an energetic particle-driven 'off-axis-fishbone-like mode' is a new EP-driven branch of the external kink mode in wall-stabilized plasmas, analogous to the relationship of the classical fishbone branch to the internal kink mode.« less

Multipoint Observations of Energetic Particle Injections and Substorm Activity During a Conjunction Between Magnetospheric Multiscale (MMS) and Van Allen Probes

NASA Astrophysics Data System (ADS)

Turner, D. L.; Fennell, J. F.; Blake, J. B.; Claudepierre, S. G.; Clemmons, J. H.; Jaynes, A. N.; Leonard, T.; Baker, D. N.; Cohen, I. J.; Gkioulidou, M.; Ukhorskiy, A. Y.; Mauk, B. H.; Gabrielse, C.; Angelopoulos, V.; Strangeway, R. J.; Kletzing, C. A.; Le Contel, O.; Spence, H. E.; Torbert, R. B.; Burch, J. L.; Reeves, G. D.

2017-11-01

This study examines multipoint observations during a conjunction between Magnetospheric Multiscale (MMS) and Van Allen Probes on 7 April 2016 in which a series of energetic particle injections occurred. With complementary data from Time History of Events and Macroscale Interactions during Substorms, Geotail, and Los Alamos National Laboratory spacecraft in geosynchronous orbit (16 spacecraft in total), we develop new insights on the nature of energetic particle injections associated with substorm activity. Despite this case involving only weak substorm activity (maximum AE <300 nT) during quiet geomagnetic conditions in steady, below-average solar wind, a complex series of at least six different electron injections was observed throughout the system. Intriguingly, only one corresponding ion injection was clearly observed. All ion and electron injections were observed at <600 keV only. MMS reveals detailed substructure within the largest electron injection. A relationship between injected electrons with energy <60 keV and enhanced whistler mode chorus wave activity is also established from Van Allen Probes and MMS. Drift mapping using a simplified magnetic field model provides estimates of the dispersionless injection boundary locations as a function of universal time, magnetic local time, and L shell. The analysis reveals that at least five electron injections, which were localized in magnetic local time, preceded a larger injection of both electrons and ions across nearly the entire nightside of the magnetosphere near geosynchronous orbit. The larger ion and electron injection did not penetrate to L < 6.6, but several of the smaller electron injections penetrated to L < 6.6. Due to the discrepancy between the number, penetration depth, and complexity of electron versus ion injections, this event presents challenges to the current conceptual models of energetic particle injections.

The bending stiffness of shoes is beneficial to running energetics if it does not disturb the natural MTP joint flexion.

PubMed

Oh, Keonyoung; Park, Sukyung

2017-02-28

A local minimum for running energetics has been reported for a specific bending stiffness, implying that shoe stiffness assists in running propulsion. However, the determinant of the metabolic optimum remains unknown. Highly stiff shoes significantly increase the moment arm of the ground reaction force (GRF) and reduce the leverage effect of joint torque at ground push-off. Inspired by previous findings, we hypothesized that the restriction of the natural metatarsophalangeal (MTP) flexion caused by stiffened shoes and the corresponding joint torque changes may reduce the benefit of shoe bending stiffness to running energetics. We proposed the critical stiffness, k cr , which is defined as the ratio of the MTP joint (MTPJ) torque to the maximal MTPJ flexion angle, as a possible threshold of the elastic benefit of shoe stiffness. 19 subjects participated in a running test while wearing insoles with five different bending stiffness levels. Joint angles, GRFs, and metabolic costs were measured and analyzed as functions of the shoe stiffness. No significant changes were found in the take-off velocity of the center of mass (CoM), but the horizontal ground push-offs were significantly reduced at different shoe stiffness levels, indicating that complementary changes in the lower-limb joint torques were introduced to maintain steady running. Slight increases in the ankle, knee, and hip joint angular impulses were observed at stiffness levels exceeding the critical stiffness, whereas the angular impulse at the MTPJ was significantly reduced. These results indicate that the shoe bending stiffness is beneficial to running energetics if it does not disturb the natural MTPJ flexion. Copyright © 2017 Elsevier Ltd. All rights reserved.

Multipoint Observations of Energetic Particle Injections and Substorm Activity During a Conjunction Between Magnetospheric Multiscale (MMS) and Van Allen Probes

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

Turner, Drew L.; Fennell, J. F.; Blake, J. B.

Here, this study examines multipoint observations during a conjunction between Magnetospheric Multiscale (MMS) and Van Allen Probes on 7 April 2016 in which a series of energetic particle injections occurred. With complementary data from Time History of Events and Macroscale Interactions during Substorms, Geotail, and Los Alamos National Laboratory spacecraft in geosynchronous orbit (16 spacecraft in total), we develop new insights on the nature of energetic particle injections associated with substorm activity. Despite this case involving only weak substorm activity (maximum AE <300 nT) during quiet geomagnetic conditions in steady, below-average solar wind, a complex series of at least sixmore » different electron injections was observed throughout the system. Intriguingly, only one corresponding ion injection was clearly observed. All ion and electron injections were observed at <600 keV only. MMS reveals detailed substructure within the largest electron injection. A relationship between injected electrons with energy <60 keV and enhanced whistler mode chorus wave activity is also established from Van Allen Probes and MMS. Drift mapping using a simplified magnetic field model provides estimates of the dispersionless injection boundary locations as a function of universal time, magnetic local time, and L shell. The analysis reveals that at least five electron injections, which were localized in magnetic local time, preceded a larger injection of both electrons and ions across nearly the entire nightside of the magnetosphere near geosynchronous orbit. The larger ion and electron injection did not penetrate to L < 6.6, but several of the smaller electron injections penetrated to L < 6.6. Due to the discrepancy between the number, penetration depth, and complexity of electron versus ion injections, this event presents challenges to the current conceptual models of energetic particle injections.« less

Multipoint Observations of Energetic Particle Injections and Substorm Activity During a Conjunction Between Magnetospheric Multiscale (MMS) and Van Allen Probes

DOE PAGES

Turner, Drew L.; Fennell, J. F.; Blake, J. B.; ...

2017-09-25

Here, this study examines multipoint observations during a conjunction between Magnetospheric Multiscale (MMS) and Van Allen Probes on 7 April 2016 in which a series of energetic particle injections occurred. With complementary data from Time History of Events and Macroscale Interactions during Substorms, Geotail, and Los Alamos National Laboratory spacecraft in geosynchronous orbit (16 spacecraft in total), we develop new insights on the nature of energetic particle injections associated with substorm activity. Despite this case involving only weak substorm activity (maximum AE <300 nT) during quiet geomagnetic conditions in steady, below-average solar wind, a complex series of at least sixmore » different electron injections was observed throughout the system. Intriguingly, only one corresponding ion injection was clearly observed. All ion and electron injections were observed at <600 keV only. MMS reveals detailed substructure within the largest electron injection. A relationship between injected electrons with energy <60 keV and enhanced whistler mode chorus wave activity is also established from Van Allen Probes and MMS. Drift mapping using a simplified magnetic field model provides estimates of the dispersionless injection boundary locations as a function of universal time, magnetic local time, and L shell. The analysis reveals that at least five electron injections, which were localized in magnetic local time, preceded a larger injection of both electrons and ions across nearly the entire nightside of the magnetosphere near geosynchronous orbit. The larger ion and electron injection did not penetrate to L < 6.6, but several of the smaller electron injections penetrated to L < 6.6. Due to the discrepancy between the number, penetration depth, and complexity of electron versus ion injections, this event presents challenges to the current conceptual models of energetic particle injections.« less

Entanglement is a costly life-history stage in large whales.

PubMed

van der Hoop, Julie; Corkeron, Peter; Moore, Michael

2017-01-01

Individuals store energy to balance deficits in natural cycles; however, unnatural events can also lead to unbalanced energy budgets. Entanglement in fishing gear is one example of an unnatural but relatively common circumstance that imposes energetic demands of a similar order of magnitude and duration of life-history events such as migration and pregnancy in large whales. We present two complementary bioenergetic approaches to estimate the energy associated with entanglement in North Atlantic right whales, and compare these estimates to the natural energetic life history of individual whales. Differences in measured blubber thicknesses and estimated blubber volumes between normal and entangled, emaciated whales indicate between 7.4 × 10 10  J and 1.2 × 10 11  J of energy are consumed during the course to death of a lethal entanglement. Increased thrust power requirements to overcome drag forces suggest that when entangled, whales require 3.95 × 10 9 to 4.08 × 10 10  J more energy to swim. Individuals who died from their entanglements performed significantly more work (energy expenditure × time) than those that survived; entanglement duration is therefore critical in determining whales' survival. Significant sublethal energetic impacts also occur, especially in reproductive females. Drag from fishing gear contributes up to 8% of the 4-year female reproductive energy budget, delaying time of energetic equilibrium (to restore energy lost by a particular entanglement) for reproduction by months to years. In certain populations, chronic entanglement in fishing gear can be viewed as a costly unnatural life-history stage, rather than a rare or short-term incident.

Bis(4-nitraminofurazanyl-3-azoxy)azofurazan and Derivatives: 1,2,5-Oxadiazole Structures and High-Performance Energetic Materials.

PubMed

Liu, Yuji; Zhang, Jiaheng; Wang, Kangcai; Li, Jinshan; Zhang, Qinghua; Shreeve, Jean'ne M

2016-09-12

Bis(4-nitraminofurazanyl-3-azoxy)azofurazan (1) and ten of its energetic salts were prepared and fully characterized. Computational analysis based on isochemical shielding surface and trigger bond dissociation enthalpy provide a better understanding of the thermal stabilities for nitramine-furazans. These energetic compounds exhibit good densities, high heats of formation, and excellent detonation velocity and pressure. Some representative compounds, for example, 1 (vD : 9541 m s(-1) ; P: 40.5 GPa), and 4 (vD : 9256 m s(-1) ; P: 38.0 GPa) exhibit excellent detonation performances, which are comparable with current high explosives such as RDX (vD : 8724 m s(-1) ; P: 35.2 GPa) and HMX (vD : 9059 m s(-1) ; P: 39.2 GPa). © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Creation of energetic biothermite inks using ferritin liquid protein

PubMed Central

Slocik, Joseph M.; McKenzie, Ruel; Dennis, Patrick B.; Naik, Rajesh R.

2017-01-01

Energetic liquids function mainly as fuels due to low energy densities and slow combustion kinetics. Consequently, these properties can be significantly increased through the addition of metal nanomaterials such as aluminium. Unfortunately, nanoparticle additives are restricted to low mass fractions in liquids because of increased viscosities and severe particle agglomeration. Nanoscale protein ionic liquids represent multifunctional solvent systems that are well suited to overcoming low mass fractions of nanoparticles, producing stable nanoparticle dispersions and simultaneously offering a source of oxidizing agents for combustion of reactive nanomaterials. Here, we use iron oxide-loaded ferritin proteins to create a stable and highly energetic liquid composed of aluminium nanoparticles and ferritin proteins for printing and forming 3D shapes and structures. In total, this bioenergetic liquid exhibits increased energy output and performance, enhanced dispersion and oxidation stability, lower activation temperatures, and greater processability and functionality. PMID:28447665

The Energetics of Transient Eddies in the Martian Northern Hemisphere

NASA Astrophysics Data System (ADS)

Battalio, Joseph Michael; Szunyogh, Istvan; Lemmon, Mark T.

2016-10-01

The energetics of northern hemisphere transient waves in the Mars Analysis Correction Data Assimilation is analyzed. Three periods between the fall and spring equinoxes (Ls=200°-230°, 255°-285°, and 330°-360°) during three Mars Years are selected to exemplify the fall, winter, and spring wave activity. Fall and spring eddy energetics is similar with some inter-annual and inter-seasonal variability, but winter eddy kinetic energy and its transport are strongly reduced in intensity as a result of the solsticial pause in eddy activity. Barotropic energy conversion acts as a sink of eddy kinetic energy throughout the northern hemisphere eddy period with little reduction in amplitude during the solsticial pause. Baroclinic energy conversion acts as a source in fall and spring but disappears during the winter period as a result of the stabilized vertical shear profile of the westerly jet around winter solstice.

N-type organic electrochemical transistors with stability in water

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

Giovannitti, Alexander; Nielsen, Christian B.; Sbircea, Dan -Tiberiu

Organic electrochemical transistors (OECTs) are receiving significant attention due to their ability to efficiently transduce biological signals. A major limitation of this technology is that only p-type materials have been reported, which precludes the development of complementary circuits, and limits sensor technologies. Here, we report the first ever n-type OECT, with relatively balanced ambipolar charge transport characteristics based on a polymer that supports both hole and electron transport along its backbone when doped through an aqueous electrolyte and in the presence of oxygen. This new semiconducting polymer is designed specifically to facilitate ion transport and promote electrochemical doping. Stability measurementsmore » in water show no degradation when tested for 2 h under continuous cycling. Furthermore, this demonstration opens the possibility to develop complementary circuits based on OECTs and to improve the sophistication of bioelectronic devices.« less

N-type organic electrochemical transistors with stability in water

DOE PAGES

Giovannitti, Alexander; Nielsen, Christian B.; Sbircea, Dan -Tiberiu; ...

2016-10-07

Organic electrochemical transistors (OECTs) are receiving significant attention due to their ability to efficiently transduce biological signals. A major limitation of this technology is that only p-type materials have been reported, which precludes the development of complementary circuits, and limits sensor technologies. Here, we report the first ever n-type OECT, with relatively balanced ambipolar charge transport characteristics based on a polymer that supports both hole and electron transport along its backbone when doped through an aqueous electrolyte and in the presence of oxygen. This new semiconducting polymer is designed specifically to facilitate ion transport and promote electrochemical doping. Stability measurementsmore » in water show no degradation when tested for 2 h under continuous cycling. Furthermore, this demonstration opens the possibility to develop complementary circuits based on OECTs and to improve the sophistication of bioelectronic devices.« less

Aerobic stability of distillers’ wet grains as influenced by temperature

USDA-ARS?s Scientific Manuscript database

Maximizing the storability of distillers’ wet grains (DWG) has great influence on the economic, energetic, and carbon balances of fuel ethanol production, yet there is little published data from controlled studies on the deterioration of DWG following its production. Under laboratory conditions, we...

Electronic Structure Principles and Aromaticity

ERIC Educational Resources Information Center

Chattaraj, P. K.; Sarkar, U.; Roy, D. R.

2007-01-01

The relationship between aromaticity and stability in molecules on the basis of quantities such as hardness and electrophilicity is explored. The findings reveal that aromatic molecules are less energetic, harder, less polarizable, and less electrophilic as compared to antiaromatic molecules, as expected from the electronic structure principles.

Semi-continuous anaerobic digestion of extruded OFMSW: Process performance and energetics evaluation.

PubMed

Mu, Lan; Zhang, Lei; Zhu, Kongyun; Ma, Jiao; Li, Aimin

2018-01-01

Recently, extrusion press treatment shows some promising advantages for effectively separating of organic fraction of municipal solid waste (OFMSW) from the mixed MSW, which is critical for their following high-efficiency treatment. In this study, an extruded OFMSW obtained from a demonstrated MSW treatment plant was characterized, and submitted to a series of semi-continuous anaerobic experiments to examine its biodegradability and process stability. The results indicated that the extruded OFMSW was a desirable substrate with a high biochemical methane potential (BMP), balanced nutrients and reliable stability. For increasing organic loading rates (OLRs), feeding higher volatile solid (VS) contents in feedstock was much better than shortening the hydraulic retention times (HRTs), while excessively high contents caused a low biodegradability due to the mass transfer limitation. For energetics evaluation, a high electricity output of 129.19-156.37kWh/ton raw MSW was obtained, which was further improved by co-digestion with food waste. Copyright © 2017 Elsevier Ltd. All rights reserved.

Understanding structure, metal distribution, and water adsorption in mixed-metal MOF-74

DOE PAGES

Howe, Joshua D.; Morelock, Cody R.; Jiao, Yang; ...

2016-11-30

We present a joint computational and experimental study of Mg–Ni-MOF-74 and Mg–Cd-MOF-74 to gain insight into the mixing of metals and understand how metal mixing affects the structure of the undercoordinated open-metal sites. Our calculations predict that metal mixing is energetically preferred in these materials. Recent experimental work has demonstrated that Mg–Ni-MOF-74 shows a much greater surface area retention in the presence of water than Mg-MOF-74. To probe this effect, we study H 2O adsorption in Mg–Ni-MOF-74, finding that the adsorption energetics and electronic structure do not change significantly at the metal sites when compared to Mg-MOF-74 and Ni-MOF-74, respectively.more » Lastly, we conclude that the increased stability of Mg–Ni-MOF-74 is a result of a M–O bond length distortion in mixed-metal MOF-74, consistent with recent work on the stability of MOF-74 under water exposure.« less

Ultra-fast self-assembly and stabilization of reactive nanoparticles in reduced graphene oxide films

PubMed Central

Chen, Yanan; Egan, Garth C.; Wan, Jiayu; Zhu, Shuze; Jacob, Rohit Jiji; Zhou, Wenbo; Dai, Jiaqi; Wang, Yanbin; Danner, Valencia A.; Yao, Yonggang; Fu, Kun; Wang, Yibo; Bao, Wenzhong; Li, Teng; Zachariah, Michael R.; Hu, Liangbing

2016-01-01

Nanoparticles hosted in conductive matrices are ubiquitous in electrochemical energy storage, catalysis and energetic devices. However, agglomeration and surface oxidation remain as two major challenges towards their ultimate utility, especially for highly reactive materials. Here we report uniformly distributed nanoparticles with diameters around 10 nm can be self-assembled within a reduced graphene oxide matrix in 10 ms. Microsized particles in reduced graphene oxide are Joule heated to high temperature (∼1,700 K) and rapidly quenched to preserve the resultant nano-architecture. A possible formation mechanism is that microsized particles melt under high temperature, are separated by defects in reduced graphene oxide and self-assemble into nanoparticles on cooling. The ultra-fast manufacturing approach can be applied to a wide range of materials, including aluminium, silicon, tin and so on. One unique application of this technique is the stabilization of aluminium nanoparticles in reduced graphene oxide film, which we demonstrate to have excellent performance as a switchable energetic material. PMID:27515900

Thermal stability and formation barrier of a high-energetic material N8 polymer nitrogen encapsulated in (5,5) carbon nanotube

NASA Astrophysics Data System (ADS)

Ji, Wei; Timoshevskii, V.; Guo, H.; Abou-Rachid, Hakima; Lussier, Louis-Simon

2009-07-01

We report the density functional theory total energy calculations of thermal stability and formation barrier of polymer nitrogen confined in carbon nanotubes (CNT). The analysis suggests that N8 polymer nitrogen encapsulated in (5,5) carbon nanotube [N8@CNT(5,5)] is thermally (meta)stable at a finite temperature up to energy scale of at least 5000 K, similar to nitrogen molecule gas phase confined in CNT [N2@CNT(5,5)]. The energetic difference between these two phases of N does not significantly change with temperature. A barrier of 1.07 eV was found for the formation of N8@CNT(5,5) from N2@CNT(5,5), while the dissociation barrier was found to be 0.2 eV. Snapshots of the reaction pathway show that the transition state is composed by a N2 and a N6 inside a CNT(5,5).

Oligonucleotides Containing Aminated 2'-Amino-LNA Nucleotides: Synthesis and Strong Binding to Complementary DNA and RNA.

PubMed

Lou, Chenguang; Samuelsen, Simone V; Christensen, Niels Johan; Vester, Birte; Wengel, Jesper

2017-04-19

Mono- and diaminated 2'-amino-LNA monomers were synthesized and introduced into oligonucleotides. Each modification imparts significant stabilization of nucleic acid duplexes and triplexes, excellent sequence selectivity, and significant nuclease resistance. Molecular modeling suggested that structural stabilization occurs via intrastrand electrostatic attraction between the protonated amino groups of the aminated 2'-amino-LNA monomers and the host oligonucleotide backbone.

Easy methods to study the smart energetic TNT/CL-20 co-crystal.

PubMed

Li, Huarong; Shu, Yuanjie; Gao, Shijie; Chen, Ling; Ma, Qing; Ju, Xuehai

2013-11-01

2,4,6,8,10,12-hexanitro-2,4,6,8,10,12-hexaazaisowurtzitane (CL-20) is a high-energy nitramine explosive with high mechanical sensitivity. 2,4,6-trinitrotoluene (TNT) is insensitive but by no means a high performance explosive. To reveal the significant importance and smart-material functionality of the energetic-energetic co-crystals, the stability, mechanical and explosive properties TNT/CL-20 co-crystal, TNT crystal and CL-20 crystal were studied. Non-hydrogen bonded non-covalent interactions govern the structures of energetic-energetic co-crystals. However, it is very difficult to accurately calculate the non-covalent intermolecular interaction energies. In this paper, the local conformation and the intricate non-covalent interactions were effectively mapped and analyzed from the electron density (ρ) and its derivatives. The results show that the two components TNT and CL-20 are connected mainly by nitro-aromatic interactions, and nitro-nitro interactions. The steric interactions in TNT/CL-20 could not be confronted with the attractive interactions. Moreover, the scatter graph of TNT crystal reveals the reason why TNT is brittle. The detailed electrostatic potential analysis predicted that the detonation velocities (D) and impact sensitivity for the compounds both increase in the sequence of CL-20 > TNT/CL-20 co-crystal > TNT. Additionally, TNT/CL-20 co-crystal has better malleability than its pure components. This demonstrates the capacity and the feasibility of realizing explosive smart materials by co-crystallization, even if strong hydrogen bonding schemes are generally lacking in energetic materials.

Gas-filled Rugby hohlraum energetics and implosions experiments on OMEGA

NASA Astrophysics Data System (ADS)

Casner, Alexis; Philippe, F.; Tassin, V.; Seytor, P.; Monteil, M. C.; Villette, B.; Reverdin, C.

2010-11-01

Recent experiments [1,2] have validated the x-ray drive enhancement provided by rugby-shaped hohlraums over cylinders in the indirect drive (ID) approach to inertial confinement fusion (ICF). This class of hohlraum is the baseline design for the Laser Mégajoule program, is also applicable to the National Ignition Facility and could therefore benefit ID Inertial Fusion Energy studies. We have carried out a serie of energetics and implosions experiments with OMEGA ``scale 1'' rugby hohlraums [1,2]. For empty hohlraums these experiments provide complementary measurements of backscattered light along 42 cone, as well as detailed drive history. In the case of gas-filled rugby hohlraums we have also study implosion performance (symmetry, yield, bangtime, hotspot spectra...) using a high contrast shaped pulse leading to a different implosion regime and for a range of capsule convergence ratios. These results will be compared with FCI2 hydrocodes calculations and future experimental campaigns will be suggested. [4pt] [1] F. Philippe et al., Phys. Rev. Lett. 104, 035004 (2010). [0pt] [2] H. Robey et al., Phys. Plasnas 17, 056313 (2010).

An energetic scale for equilibrium H/D fractionation factors illuminates hydrogen bond free energies in proteins

PubMed Central

Cao, Zheng; Bowie, James U

2014-01-01

Equilibrium H/D fractionation factors have been extensively employed to qualitatively assess hydrogen bond strengths in protein structure, enzyme active sites, and DNA. It remains unclear how fractionation factors correlate with hydrogen bond free energies, however. Here we develop an empirical relationship between fractionation factors and free energy, allowing for the simple and quantitative measurement of hydrogen bond free energies. Applying our empirical relationship to prior fractionation factor studies in proteins, we find: [1] Within the folded state, backbone hydrogen bonds are only marginally stronger on average in α-helices compared to β-sheets by ∼0.2 kcal/mol. [2] Charge-stabilized hydrogen bonds are stronger than neutral hydrogen bonds by ∼2 kcal/mol on average, and can be as strong as –7 kcal/mol. [3] Changes in a few hydrogen bonds during an enzyme catalytic cycle can stabilize an intermediate state by –4.2 kcal/mol. [4] Backbone hydrogen bonds can make a large overall contribution to the energetics of conformational changes, possibly playing an important role in directing conformational changes. [5] Backbone hydrogen bonding becomes more uniform overall upon ligand binding, which may facilitate participation of the entire protein structure in events at the active site. Our energetic scale provides a simple method for further exploration of hydrogen bond free energies. PMID:24501090

pH-dependent relationship between thermodynamic and kinetic stability in the denaturation of human phosphoglycerate kinase 1.

PubMed

Pey, Angel L

2014-08-01

Human phosphoglycerate kinase 1 (hPGK1) is a glycolytic enzyme essential for ATP synthesis, and it is implicated in different pathological conditions such as inherited diseases, oncogenesis and activation of drugs for cancer and viral treatments. Particularly, mutations in hPGK1 cause human PGK1 deficiency, a rate metabolic conformational disease. We have recently found that most of these mutations cause protein kinetic destabilization by significant changes in the structure/energetics of the transition state for irreversible denaturation. In this work, we explore the relationships between protein conformation, thermodynamic and kinetic stability in hPGK1 by performing comprehensive analyses in a wide pH range (2.5-8). hPGK1 remains in a native conformation at pH 5-8, but undergoes a conformational transition to a molten globule-like state at acidic pH. Interestingly, hPGK1 kinetic stability remains essentially constant at pH 6-8, but is significantly reduced when pH is decreased from 6 to 5. We found that this decrease in kinetic stability is caused by significant changes in the energetic/structural balance of the denaturation transition state, which diverge from those found for disease-causing mutations. We also show that protein kinetic destabilization by acidic pH is strongly linked to lower thermodynamic stability, while in disease-causing mutations seems to be linked to lower unfolding cooperativity. These results highlight the plasticity of the hPGK1 denaturation mechanism that responds differently to changes in pH and in disease-causing mutations. New insight is presented into the different factors contributing to hPGK1 thermodynamic and kinetic stability and the role of denaturation mechanisms in hPGK1 deficiency. Copyright © 2014 Elsevier Masson SAS. All rights reserved.

Influence of pendant chiral C(γ)-(alkylideneamino/guanidino) cationic side-chains of PNA backbone on hybridization with complementary DNA/RNA and cell permeability.

PubMed

Jain, Deepak R; Anandi V, Libi; Lahiri, Mayurika; Ganesh, Krishna N

2014-10-17

Intrinsically cationic and chiral C(γ)-substituted peptide nucleic acid (PNA) analogues have been synthesized in the form of γ(S)-ethyleneamino (eam)- and γ(S)-ethyleneguanidino (egd)-PNA with two carbon spacers from the backbone. The relative stabilization (ΔTm) of duplexes from modified cationic PNAs as compared to 2-aminoethylglycyl (aeg)-PNA is better with complementary DNA (PNA:DNA) than with complementary RNA (PNA:RNA). Inherently, PNA:RNA duplexes have higher stability than PNA:DNA duplexes, and the guanidino PNAs are superior to amino PNAs. The cationic PNAs were found to be specific toward their complementary DNA target as seen from their significantly lower binding with DNA having single base mismatch. The differential binding avidity of cationic PNAs was assessed by the displacement of DNA duplex intercalated ethidium bromide and gel electrophoresis. The live cell imaging of amino/guanidino PNAs demonstrated their ability to penetrate the cell membrane in 3T3 and MCF-7 cells, and cationic PNAs were found to be accumulated in the vicinity of the nuclear membrane in the cytoplasm. Fluorescence-activated cell sorter (FACS) analysis of cell permeability showed the efficiency to be dependent upon the nature of cationic functional group, with guanidino PNAs being better than the amino PNAs in both cell lines. The results are useful to design new biofunctional cationic PNA analogues that not only bind RNA better but also show improved cell permeability.

Layered reactive particles with controlled geometries, energies, and reactivities, and methods for making the same

DOEpatents

Fritz, Gregory M.; Weihs, Timothy P.; Grzyb, Justin A.

2016-07-05

An energetic composite having a plurality of reactive particles each having a reactive multilayer construction formed by successively depositing reactive layers on a rod-shaped substrate having a longitudinal axis, dividing the reactive-layer-deposited rod-shaped substrate into a plurality of substantially uniform longitudinal segments, and removing the rod-shaped substrate from the longitudinal segments, so that the reactive particles have a controlled, substantially uniform, cylindrically curved or otherwise rod-contoured geometry which facilitates handling and improves its packing fraction, while the reactant multilayer construction controls the stability, reactivity and energy density of the energetic composite.

Layered reactive particles with controlled geometries, energies, and reactivities, and methods for making the same

DOEpatents

Fritz, Gregory M; Knepper, Robert Allen; Weihs, Timothy P; Gash, Alexander E; Sze, John S

2013-04-30

An energetic composite having a plurality of reactive particles each having a reactive multilayer construction formed by successively depositing reactive layers on a rod-shaped substrate having a longitudinal axis, dividing the reactive-layer-deposited rod-shaped substrate into a plurality of substantially uniform longitudinal segments, and removing the rod-shaped substrate from the longitudinal segments, so that the reactive particles have a controlled, substantially uniform, cylindrically curved or otherwise rod-contoured geometry which facilitates handling and improves its packing fraction, while the reactant multilayer construction controls the stability, reactivity and energy density of the energetic composite.

Energy Level Alignment at the Interface between Linear-Structured Benzenediamine Molecules and Au(111) Surface

NASA Astrophysics Data System (ADS)

Li, Guo; Rangel, Tonatiuh; Liu, Zhenfei; Cooper, Valentino; Neaton, Jeffrey

Using density functional theory with model self-energy corrections, we calculate the adsorption energetics and geometry, and the energy level alignment of benzenediamine (BDA) molecules adsorbed on Au(111) surfaces. Our calculations show that linear structures of BDA, stabilized via hydrogen bonds between amine groups, are energetically more favorable than monomeric phases. Moreover, our self-energy-corrected calculations of energy level alignment show that the highest occupied molecular orbital energy of the BDA linear structure is deeper relative to the Fermi level relative to the isolated monomer and agrees well with the values measured with photoemission spectroscopy. This work supported by DOE.

Stability and refrigeration of magnet cryosystems near 1.8 K using the thermomechanical effect

NASA Technical Reports Server (NTRS)

Frederking, T. H. K.; Chen, W. E. W.; Caspi, S.

1987-01-01

Magnet cryosystem options utilizing the thermomechanical effect of He II and the mechano-caloric effect for refrigeration (referred to as vortex refrigeration) are examined. The performance of the existing He II magnet refrigeration system is briefly reviewed, with attention given to superleak properties, vortex shedding, heat input, and thermodynamic cycle. It is concluded that the possibilities of magnet heat leak use for energetics and stability improvements are promising when He II is selected as magnet coolant.

Analysis of Alfvén eigenmode destabilization by energetic particles in Large Helical Device using a Landau-closure model

NASA Astrophysics Data System (ADS)

Varela, J.; Spong, D. A.; Garcia, L.

2017-04-01

Energetic particle populations in nuclear fusion experiments can destabilize the Alfvén Eigenmodes through inverse Landau damping and couplings with gap modes in the shear Alfvén continua. We use the reduced MHD equations to describe the linear evolution of the poloidal flux and the toroidal component of the vorticity in a full 3D system, coupled with equations of density and parallel velocity moments for the energetic particles. We add the Landau damping and resonant destabilization effects using a closure relation. We apply the model to study the Alfvén mode stability in the inward-shifted configurations of the Large Helical Device (LHD), performing a parametric analysis of the energetic particle β ({βf} ) in a range of realistic values, the ratios of the energetic particle thermal/Alfvén velocities ({{V}\\text{th}}/{{V}A0} ), the magnetic Lundquist numbers (S) and the toroidal modes (n). The n  =  1 and n  =  2 TAEs are destabilized, although the n  =  3 and n  =  4 TAEs are weakly perturbed. The most unstable configurations are associated with the density gradients of energetic particles in the plasma core: the TAEs are destabilized, even for small energetic particle populations, if their thermal velocity is lower than 0.4 times the Alfvén velocity. The frequency range of MHD bursts measured in the LHD are 50-70 kHz for the n  =  1 and 60-80 kHz for the n  =  2 TAE, which is consistent with the model predictions. ).

Unstable solitary-wave solutions of the generalized Benjamin-Bona-Mahony equation

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

McKinney, W.R.; Restrepo, J.M.; Bona, J.L.

1994-06-01

The evolution of solitary waves of the gBBM equation is investigated computationally. The experiments confirm previously derived theoretical stability estimates and, more importantly, yield insights into their behavior. For example, highly energetic unstable solitary waves when perturbed are shown to evolve into several stable solitary waves.

Nanojets: Electrification, Energetics, Dynamics, Stability and Breakup

DTIC Science & Technology

2007-11-01

citations therein. This excellent review contains original material as well as a comprehensive discussion and list of references to earlier work on...Increasing E field, liquid state aspect ratio d =10 nm E > Ecritical + E=0.625 V/nm Decreasing E field after ordering; liquid-solid coexistence E=1.0 V

Elucidating the influence of praziquantel nanosuspensions on the in vivo metabolism of Taenia crassiceps cysticerci.

PubMed

Silva, Luciana Damacena; Arrúa, Eva Carolina; Pereira, Dayanne Amaral; Fraga, Carolina Miguel; Costa, Tatiane Luiza da; Hemphill, Andrew; Salomon, Claudio Javier; Vinaud, Marina Clare

2016-09-01

The aim of this work was to develop nanosuspensions of praziquantel (PZQ) and to evaluate their influence on the energetic metabolism of cysticerci inoculated in BALB/c mice. We analyzed metabolic alterations of glycolytic pathways and the tricarboxylic acid cycle in the parasite. The nanosuspensions were prepared by precipitation and polyvinyl alcohol (PVA), poloxamer 188 (P188) and poloxamer 407 (P407) were used as stabilizers. Nanosuspension prepared with PVA had a particle size of 100nm, while P188- and P407-based nanosuspensions had particle sizes of 74nm and 285nm, respectively. The zeta potential was -8.1, -8.6, and -13.2 for the formulations stabilized with PVA, P188 and P407, respectively. Treatments of T. crassiceps cysticerci-infected mice resulted in an increase in glycolysis organic acids, and enhanced the partial reversion of the tricarboxylic acid cycle, the urea cycle and the production of ketonic bodies in the parasites when compared to the groups treated with conventional PZQ. These data suggest that PZQ nanosuspensions greatly modified the energetic metabolism of cysticerci in vivo. Moreover, the remarkable metabolic alterations produced by the stabilizers indicate that further studies on nanoformulations are required to find potentially suitable nanomedicines. Copyright © 2016 Elsevier B.V. All rights reserved.

New chemical sources of energy: A theoretical study

NASA Astrophysics Data System (ADS)

Chaban, Galina

The research presented in this dissertation employs methods of quantum chemistry for the search of highly energetic chemical compounds that can have applications as possible energy sources. The areas of research include: (1) improvement of orbital optimization methods for different types of wavefunctions which leads to substantial savings of computer time and memory; (2) predicting new high energy isomers for singlet and triplet states of Nsb3F and their kinetic stability with respect to isomerisation and dissociation reactions; (3) estimation of minimum energy reaction paths for dissociation reactions of high energy isomers of Nsb2Osb2 including potential energy barriers and minimum energy crossing points between the closest singlet and triplet states; (4) investigation of thermodynamic and kinetic stability of Van der Waals complexes M-Hsb2 (M = Li, Be, B, C, Na, Mg, Al, Si) that can play an important role in improvement of energetic properties of hydrogen based rocket fuels; (5) mapping of the potential energy surface for AlHsb2 compound in the region of crossing between sp2Bsb2 and sp2Asb1 electronic states and predicting the kinetic stability of Al complex, which suggests that Al may be among the promising candidates for inclusion into solid hydrogen for the purpose of energy storage.

Energetics and Defect Interactions of Complex Oxides for Energy Applications

NASA Astrophysics Data System (ADS)

Solomon, Jonathan Michael

The goal of this dissertation is to employ computational methods to gain greater insights into the energetics and defect interactions of complex oxides that are relevant for today's energy challenges. To achieve this goal, the development of novel computational methodologies are required to handle complex systems, including systems containing nearly 650 ions and systems with tens of thousands of possible atomic configurations. The systems that are investigated in this dissertation are aliovalently doped lanthanum orthophosphate (LaPO4) due to its potential application as a proton conducting electrolyte for intermediate temperature fuel cells, and aliovalently doped uranium dioxide (UO2) due to its importance in nuclear fuel performance and disposal. First we undertake density-functional-theory (DFT) calculations on the relative energetics of pyrophosphate defects and protons in LaPO4, including their binding with divalent dopant cations. In particular, for supercell calculations with 1.85 mol% Sr doping, we investigate the dopant-binding energies for pyrophosphate defects to be 0.37 eV, which is comparable to the value of 0.34 eV calculated for proton-dopant binding energies in the same system. These results establish that dopant-defect interactions further stabilize proton incorporation, with the hydration enthalpies when the dopants are nearest and furthest from the protons and pyrophosphate defects being -1.66 eV and -1.37 eV, respectively. Even though our calculations show that dopant binding enhances the enthalpic favorability of proton incorporation, they also suggest that such binding is likely to substantially lower the kinetic rate of hydrolysis of pyrophosphate defects. We then shift our focus to solid solutions of fluorite-structured UO 2 with trivalent rare earth fission product cations (M3+=Y, La) using a combination of ionic pair potential and DFT based methods. Calculated enthalpies of formation with respect to constituent oxides show higher energetic stability for La solid solutions than for Y. Additionally, calculations performed for different atomic configurations show a preference for reduced (increased) oxygen vacancy coordination around La (Y) dopants. The current results are shown to be qualitatively consistent with related calculations and calorimetric measurements of heats of formation in other trivalent doped fluorite oxides, which show a tendency for increasing stability and increasing preference for higher oxygen coordination with increasing size of the trivalent impurity. We expand this investigation by considering a series of trivalent rare earth fission product cations, specifically, Y3+ (1.02 A, Shannon radius with eightfold coordination), Dy3+ (1.03 A), Gd 3+ (1.05 A), Eu3+ (1.07 A), Sm3+ (1.08 A), Pm3+ (1.09 A), Nd3+ (1.11 A), Pr3+ (1.13 A), Ce3+ (1.14 A) and La3+ (1.16 A). Compounds with ionic radius of the M3+ species smaller or larger than 1.09 A are found to have energetically preferred defect ordering arrangements. Systems with preferred defect ordering arrangements are suggestive of defect clustering in short range ordered solid solutions, which is expected to limit oxygen ion mobility and therefore the rate of oxidation of spent nuclear fuel. Finally, the energetics of rare earth substituted (M3+= La, Y, and Nd) UO2 solid solutions are investigated by employing a combination of calorimetric measurements and DFT based computations. The calorimetric studies are performed by Lei Zhang and Professor Alexandra Navrotsky at the University of Calfornia, Davis, as part of a joint computational/ experimental collaborative effort supported through the Materials Science of Actinides Energy Frontier Research Center. Calculated and measured formation enthalpies agree within 10 kJ/mol for stoichiometric oxygen/metal compositions. To better understand the factors governing the stability and defect binding in rare earth substituted urania solid solutions, systematic trends in the energetics are investigated based on the present results and previous computational and experimental thermochemical studies of rare earth substituted fluorite oxides. A consistent trend towards increased energetic stability with larger size mismatch between the smaller host tetravalent cation and the larger rare earth trivalent cation is found for both actinide and non-actinide fluorite oxide systems where aliovalent substitution of M cations is compensated by oxygen vacancies. However, the large exothermic oxidation enthalpy in the UO2 based systems favors compositions with higher oxygen-to-metal ratios where charge compensation occurs through the formation of uranium cations with higher oxidation states.

The Energetics of Oxide Multilayer Systems: SOFC Cathode and Electrolyte Materials

NASA Astrophysics Data System (ADS)

Kemik, Nihan

Complex oxides are evoking a surge of scientific and technological interest due to the unexpected properties of their interfaces which have been shown to differ from the constituent materials. Layered oxide structures have found wide use in applications ranging from electronic and magnetic devices to solid oxide fuel cells (SOFCs). For devices such as SOFCs which utilize multilayers at elevated temperatures, it is critical to know the relative stabilities of these interfaces since they directly influence the device performance. In this work, we explored the energetics of two oxide multilayer systems which are relevant for SOFCs components using high temperature solution calorimetry and differential scanning calorimetry (DSC). The fundamental understanding of the interfacial and structural properties of multilayers combined with the information about phase stabilities is essential in materials selection for components for intermediate temperature SOFC's. For cathode materials, we investigated the family of perovskite oxides, La0.7Sr0.3MO3, where M=Mn and Fe, as well as their solid solution phase. Manganites have been the most investigated cathode material, while the ferrites are also being considered for future use due to their thermodynamic stability and close thermal expansion coefficient with the commonly used electrolyte materials. For the bulk La0.7Sr0.3FexMn1-xO 3 solid solution, high temperature oxide melt drop solution calorimetry was performed to determine the enthalpies of formation from binary oxides and the enthalpy of mixing. It was shown that the symmetry of the perovskite structure, the valence of transition metal, and the energetics are highly interdependent and the balance between the different valence states of the Mn and Fe ions is the main factor in determining the energetics. The energetics of interfaces in multilayered structures was investigated by high temperature oxide melt solution calorimetry for the first time. The drop solution calorimetry results of La0.7Sr0.3MnO3(LSMO)/La0.7 Sr0.3FeO3(LSFO) multilayers and LSMO film are highly exothermic and differ from the bulk material with the same composition. The magnetic and electronic properties of LSMO/LSFO superlattices are highly dependent on the thickness and the structure of the individual layers. Resonant X-Ray reflectivity (XRR) technique was utilized to characterize the structure of the LSMO/LSFO superlattices. It was shown that the XRR spectra taken at the Mn and Fe absorption edges can provide more structural information than the spectra at the X-ray energy of a conventional Cu source. With this non-destructive technique, we demonstrated the ability to compare the intermixing behavior and thickness regularity throughout the thickness of different superlattice structures. For electrolyte materials, we studied the yttria stabilized zirconia (YSZ) /Al2O3 multilayer system. Differential scanning calorimetry (DSC) was used to study the crystallization of the YSZ layers to explore the effect of the interfaces on phase stabilities. It was observed that the crystallization temperature increased and the enthalpy became more exothermic as the interfacial area increased. This work demonstrated that DSC is a promising technique to study the thin film reactions and explore the interfacial enthalpies in oxide multilayer systems.

Quantum-Chemical ab initio Calculations on the Three Isomers of Diborabenzene (C4H4B2)

NASA Astrophysics Data System (ADS)

Singh, Jaswinder; Wang, Yuekui; Raabe, Gerhard

2010-01-01

Quantum-chemical ab initio calculations up to the ZPE+CCSD(T)/aug-cc-pVTZ//MP2/6- 311++G** level were performed on three possible structural isomers of diborabenzene (C4H4B2). All three molecules were found to be local minima on the C4H4B2 energy surface and to have closed shell singlet ground states. While the ground states of the 1,3- and 1,4-isomer are planar and of C2v and D2h symmetry, respectively, 1,2-diborabenzene is non-planar with a C2 axis passing through the center of the BB bond and the middle of the opposite carbon-carbon bond as the only symmetry element. The energetically most favourable 1,3-diborabenzene was found to be about 19 and 36 kcal/mol lower in energy than the 1,2- and the 1,4-isomer. Planar 1,3- and 1,4-diborabenzene have three doubly occupied π orbitals while non-planar 1,2-diborabenzene has also three doubly occupied orbitals which can be derived from the π orbitals of its 3.7 kcal/mol energetically less favourable planar form ("π-like" orbitals). The lowest unoccupied orbitals of all three isomers have σ symmetry with large coefficients at the two boron atoms. These orbitals are lower in energy than the lowest unoccupied molecular orbitals (LUMOs) of e. g. benzene and pyridine and might cause pronounced acceptor properties which could be one of the reasons for the elusiveness of the title compounds. The results of bond separation reactions show that cyclic conjugation stabilizes all three diborabenzenes relative to their isolated fragments. The most effective stabilization energy of about 24 kcal/mol was found for the energetically lowest 1,3-isomer. This value amounts to approximately one third of the experimental value for the bond separation energy of pyridine. In all cases the energetically lowest triplet states are significantly (16 - 24 kcal/mol) higher in energy than the singlet ground states. Also among the triplets the 1,3-isomer is the energetically most fabourable species.

Structural Modulation from 1D Chain to 3D Framework: Improved Thermostability, Insensitivity, and Energies of Two Nitrogen-Rich Energetic Coordination Polymers.

PubMed

Guo, Zhaoqi; Wu, Yunlong; Deng, Chongqing; Yang, Guoping; Zhang, Jiangong; Sun, Zhihua; Ma, Haixia; Gao, Chao; An, Zhongwei

2016-11-07

Two new energetic coordination polymers (CPs) [Pb(BT)(H 2 O) 3 ] n (1) and [Pb 3 (DOBT) 3 (H 2 O) 2 ] n ·(4H 2 O) n (2) with 1D and 3D structures were synthesized by employing two rational designed ligands, 1H,1'H-5,5'-bitetrazole (H 2 BT) and 1H,1'H-[5,5'-bitetrazole]-1,1'-diol ligands (DHBT), respectively. Thermal analyses and sensitivity tests show that the 3D architecture reinforces the network of 2 which has higher thermal stability and lower sensitivity than that of 1. Through oxygen-bomb combustion calorimetry the molar enthalpy of formation of 2 is derived to be much higher than that of 1 as well as the reported CPs. Herein, more importantly, the heats of detonation (ΔH det ) were calculated according to the decomposition products of TG-DSC-MS-FTIR simultaneous analyses for the first time. The calculated results show that ΔH det of 2 is 23% higher than that of 1. This research demonstrates that 3D energetic CP with outstanding energetic properties can be obtained through efficient and reasonable design.

Synchrotron based mass spectrometry to investigate the molecular properties of mineral-organic associations

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

Liu, Suet Yi; Kleber, Markus; Takahashi, Lynelle K.

2013-04-01

Soil organic matter (OM) is important because its decay drives life processes in the biosphere. Analysis of organic compounds in geological systems is difficult because of their intimate association with mineral surfaces. To date there is no procedure capable of quantitatively separating organic from mineral phases without creating artifacts or mass loss. Therefore, analytical techniques that can (a) generate information about both organic and mineral phases simultaneously and (b) allow the examination of predetermined high-interest regions of the sample as opposed to conventional bulk analytical techniques are valuable. Laser Desorption Synchrotron Postionization (synchrotron-LDPI) mass spectrometry is introduced as a novelmore » analytical tool to characterize the molecular properties of organic compounds in mineral-organic samples from terrestrial systems, and it is demonstrated that when combined with Secondary Ion Mass Spectrometry (SIMS), can provide complementary information on mineral composition. Mass spectrometry along a decomposition gradient in density fractions, verifies the consistency of our results with bulk analytical techniques. We further demonstrate that by changing laser and photoionization energies, variations in molecular stability of organic compounds associated with mineral surfaces can be determined. The combination of synchrotron-LDPI and SIMS shows that the energetic conditions involved in desorption and ionization of organic matter may be a greater determinant of mass spectral signatures than the inherent molecular structure of the organic compounds investigated. The latter has implications for molecular models of natural organic matter that are based on mass spectrometric information.« less

Time-of-flight mass spectrographs—From ions to neutral atoms

NASA Astrophysics Data System (ADS)

Möbius, E.; Galvin, A. B.; Kistler, L. M.; Kucharek, H.; Popecki, M. A.

2016-12-01

After their introduction to space physics in the mid 1980s time-of-flight (TOF) spectrographs have become a main staple in spaceborne mass spectrometry. They have largely replaced magnetic spectrometers, except when extremely high mass resolution is required to identify complex molecules, for example, in the vicinity of comets or in planetary atmospheres. In combination with electrostatic analyzers and often solid state detectors, TOF spectrographs have become key instruments to diagnose space plasma velocity distributions, mass, and ionic charge composition. With a variety of implementation schemes that also include isochronous electric field configurations, TOF spectrographs can respond to diverse science requirements. This includes a wide range in mass resolution to allow the separation of medium heavy isotopes or to simply provide distributions of the major species, such as H, He, and O, to obtain information on source tracers or mass fluxes. With a top-hat analyzer at the front end, or in combination with deflectors for three-axis stabilized spacecraft, the distribution function of ions can be obtained with good time resolution. Most recently, the reach of TOF ion mass spectrographs has been extended to include energetic neutral atoms. After selecting the arrival direction with mechanical collimation, followed by conversion to ions, adapted TOF sensors form a new branch of the spectrograph family tree. We review the requirements, challenges, and implementation schemes for ion and neutral atom spectrographs, including potential directions for the future, while largely avoiding overlap with complementary contributions in this special issue.

Substitutional carbon doping of free-standing and Ru-supported BN sheets: a first-principles study

NASA Astrophysics Data System (ADS)

Berseneva, N.; Komsa, H.-P.; Vierimaa, V.; Björkman, T.; Fan, Z.; Harju, A.; Todorović, M.; Krasheninnikov, A. V.; Nieminen, R. M.

2017-10-01

The development of spatially homogeneous mixed structures with boron (B), nitrogen (N) and carbon (C) atoms arranged in a honeycomb lattice is highly desirable, as they open the possibility of creating stable two-dimensional materials with tunable band gaps. However, at least in the free-standing form, the mixed BCN system is energetically driven towards phase segregation to graphene and hexagonal BN. It is possible to overcome the segregation when BCN material is grown on a particular metal substrate, for example Ru(0 0 0 1), but the stabilization mechanism is still unknown. With the use of density-functional theory we study the energetics of BN/Ru slabs, with different types of configurations of C substitutional defects introduced to the h-BN overlayer. The results are compared to the energetics of free-standing BCN materials. We found that the substrate facilitates the C substitution process in the h-BN overlayer. Thus, more homogeneous BCN material can be grown, overcoming the segregation into graphene and h-BN. In addition, we investigate the electronic and transport gaps in free-standing BCN structures, and assess their mechanical properties and stability. The band gap in mixed BCN free-standing material depends on the concentration of the constituent elements and ranges from zero in pristine graphene to nearly 5 eV in free-standing h-BN. This makes BCN attractive for application in modern electronics.

Impact of velocity space distribution on hybrid kinetic-magnetohydrodynamic simulation of the (1,1) mode

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

Kim, Charlson C.

2008-07-15

Numeric studies of the impact of the velocity space distribution on the stabilization of (1,1) internal kink mode and excitation of the fishbone mode are performed with a hybrid kinetic-magnetohydrodynamic model. These simulations demonstrate an extension of the physics capabilities of NIMROD[C. R. Sovinec et al., J. Comput. Phys. 195, 355 (2004)], a three-dimensional extended magnetohydrodynamic (MHD) code, to include the kinetic effects of an energetic minority ion species. Kinetic effects are captured by a modification of the usual MHD momentum equation to include a pressure tensor calculated from the {delta}f particle-in-cell method [S. E. Parker and W. W. Lee,more » Phys. Fluids B 5, 77 (1993)]. The particles are advanced in the self-consistent NIMROD fields. We outline the implementation and present simulation results of energetic minority ion stabilization of the (1,1) internal kink mode and excitation of the fishbone mode. A benchmark of the linear growth rate and real frequency is shown to agree well with another code. The impact of the details of the velocity space distribution is examined; particularly extending the velocity space cutoff of the simulation particles. Modestly increasing the cutoff strongly impacts the (1,1) mode. Numeric experiments are performed to study the impact of passing versus trapped particles. Observations of these numeric experiments suggest that assumptions of energetic particle effects should be re-examined.« less

Characterization of Complementary and Alternative Medicine-Related Consultations in an Academic Drug Information Service.

PubMed

Gregory, Philip J; Jalloh, Mohamed A; Abe, Andrew M; Hu, James; Hein, Darren J

2016-12-01

To characterize requests received through an academic drug information consultation service related to complementary and alternative medicines. A retrospective review and descriptive analysis of drug information consultations was conducted. A total of 195 consultations related to complementary and alternative medicine were evaluated. All consultation requests involved questions about dietary supplements. The most common request types were related to safety and tolerability (39%), effectiveness (38%), and therapeutic use (34%). Sixty-eight percent of the requests were from pharmacists. The most frequent consultation requests from pharmacists were questions related to drug interactions (37%), therapeutic use (37%), or stability/compatibility/storage (34%). Nearly 60% of complementary and alternative medicine-related consultation requests were able to be completely addressed using available resources. Among review sources, Natural Medicines Comprehensive Database, Clinical Pharmacology, Micromedex, and Pharmacist's Letter were the most common resources used to address consultations. Utilization of a drug information service may be a viable option for health care professionals to help answer a complementary and alternative medicine-related question. Additionally, pharmacists and other health care professionals may consider acquiring resources identified to consistently answering these questions. © The Author(s) 2015.

The quest for greater chemical energy storage in energetic materials: Grounding expectations

NASA Astrophysics Data System (ADS)

Lindsay, C. Michael; Fajardo, Mario E.

2017-01-01

It is well known that the performance of modern energetic materials based on organic chemistry has plateaued, with only ˜ 40% improvements realized over the past half century. This fact has stimulated research on alternative chemical energy storage schemes in various U.S. government funded "High Energy Density Materials" (HEDM) programs since the 1950's. These efforts have examined a wide range of phenomena such as free radical stabilization, metallic hydrogen, metastable helium, polynitrogens, extended molecular solids, nanothermites, and others. In spite of the substantial research investments, significant improvements in energetic material performance have not been forthcoming. This paper discusses the lessons learned in the various HEDM programs, the different degrees of freedom in which to store energy in materials, and the fundamental limitations and orders of magnitude of the energies involved. The discussion focuses almost exclusively on the topic of energy density and only mentions in passing other equally important properties of explosives and propellants such as gas generation and reaction rate.

Novel Energetic Compounds Based on 3-Methyl-1,2,5-Oxadiazole 2-Oxide

NASA Astrophysics Data System (ADS)

Xu, Zhen; Yang, Hongwei; Cheng, Guangbin

2018-01-01

Two derivatives of 3-methyl-1,2,5-oxadiazole 2-oxide, (E) 4-methyl-1,2,5-oxadiazole-3-carboxaldehyde 5-oxide (2,4,6-trinitrophenyl)hydrazone (1) and 2,2,2-trinitroethyl 4-methyl-1,2,5-oxadiazole-3-carboxylate 5-oxide (2), were designed, synthesized, and fully characterized. The structures of the new compounds were confirmed by single-crystal X-ray analysis. Physicochemical and energetic properties including density, thermal stability, and sensitivity were investigated, and energetic properties (e.g., detonation velocities and detonation pressures) were calculated using EXPLO5 code. The results indicated that compound 1 exhibits positive heat of formation of 448.0 kJ mol-1 and acceptable sensitivities (IS: 20 J, FS: 280 N). In addition, compound 2 possesses low melting point (99.92°C), moderate decomposition temperature (183.67°C), good detonation performances (D: 8430 m s-1; P: 31.5 GPa), and lower sensitivities (IS: 18 J; FS: 220 N), which suggest 2 has the potential to be melt-cast explosive.

Laser Diagnostics Study of Plasma Assisted Combustion for Scramjet Applications

DTIC Science & Technology

2011-12-01

stabilization. Therefore, most of the flowrates used in this study are conditions that are too high for unassisted stabilization; however, a few low power non...dramatically increased as highly reactive air interacts with the fuel. At powers exceeding 400 mA, the OH P re m ix ed F la m e S in gl e A ve ra ge N...energetic enhancement of the combustion chemistry as show in Figure 9. The plasma generation process can be achieved with minimal power , as a high electric

Nanoscale High Energetic Materials: A Polymeric Nitrogen Chain N8 Confined inside a Carbon Nanotube

NASA Astrophysics Data System (ADS)

Abou-Rachid, Hakima; Hu, Anguang; Timoshevskii, Vladimir; Song, Yanfeng; Lussier, Louis-Simon

2008-05-01

We present a theoretical study of a new hybrid material, nanostructured polymeric nitrogen, where a polymeric nitrogen chain is encapsulated in a carbon nanotube. The electronic and structural properties of the new system are studied by means of ab initio electronic structure and molecular dynamics calculations. Finite temperature simulations demonstrate the stability of this nitrogen phase at ambient pressure and room temperature using carbon nanotube confinement. This nanostructured confinement may open a new path towards stabilizing polynitrogen or polymeric nitrogen at ambient conditions.

Stability of disclination loop in pure twist nematic liquid crystals

NASA Astrophysics Data System (ADS)

Kadivar, Erfan

2018-04-01

In this work, the annihilations dynamics and stability of disclination loop in a bulk pure twist nematic liquid crystal are investigated. This work is based on the Frank free energy and the nematodynamics equations. The energy dissipation is calculated by using two methods. In the first method, the energy dissipation is obtained from the Frank free energy. In the second method, it is calculated by using the nematodynamics equations. Finally, we derive a critical radius of disclination loop that above this radius, loop creation is energetically forbidden.

Method of using triaxial magnetic fields for making particle structures

DOEpatents

Martin, James E.; Anderson, Robert A.; Williamson, Rodney L.

2005-01-18

A method of producing three-dimensional particle structures with enhanced magnetic susceptibility in three dimensions by applying a triaxial energetic field to a magnetic particle suspension and subsequently stabilizing said particle structure. Combinations of direct current and alternating current fields in three dimensions produce particle gel structures, honeycomb structures, and foam-like structures.

Oxygen disorder, a way to accommodate large epitaxial strains in oxides

DOE PAGES

Zhang, Yu Yang; Mishra, Rohan; Pennycook, Timothy J.; ...

2015-09-22

Density-functional calculations (total-energy comparisons) and checks for negative-frequency phonon modes are employed as a stability indicator to show that, in rutile- and fluorite-structure oxides, e.g., zirconia strained by a strontium titanate substrate, oxygen-sublattice disorder can be the energetically preferred way to accommodate strain.

Heterocyclic energetic materials: Synthesis, characterization and computational design

NASA Astrophysics Data System (ADS)

Tsyshevsky, Roman; Pagoria, Philip; Smirnov, Aleksander; Kuklja, Maija

2017-06-01

Achievement of the tailored properties (high performance, low sensitivity, etc.) in targeted new energetic materials (EM) remains a great challenge. Recently, attention of researchers has shifted from conventional nitroester-, nitramine-, and nitroaromatic-based explosives to new heterocyclic EM with oxygen- and nitrogenrich molecular structures. They have increased densities and formation enthalpies complemented by attractive performance and high stability to external stimuli. We will demonstrate that oxadiazol-containing heterocycles offer a convenient playground to probe specific chemical functional groups as building blocks for design of EM. We discuss a joint experimental and computational approach for design, characterization, synthesis, and modeling of novel heterocyclic EM. Combinatorically, we comprehensively analyzed how overall stability and performance of each material in the family (BNFF, LLM-172, LLM-175, LLM-191, LLM-192, LLM-200) depends upon their chemical composition and details of the molecular structure (such as a substitution of a nitro group by an amino group and 1,2,5-oxadiazole fragment by 1,2,3- or 1,2,4-oxadiazol ring). We will also discuss proposed new EM with predicted superior chemical and physical properties. P. Pagoria, R. Tsyshevsky, A. Smirnov.

Creation of artificial skyrmions and antiskyrmions by anisotropy engineering

DOE PAGES

Zhang, S.; Petford-Long, A. K.; Phatak, C.

2016-08-10

Topological spin textures form a fundamental paradigm in solid state physics and present unique opportunities to explore exciting phenomena such as the quantum Hall effect. One such non-trivial spin texture is a skyrmion, in which the spins can be mapped to point in all directions wrapping around a sphere. Understanding the formation of these spin textures, and their topological and energetic stability, is crucial in order to control their behavior. In this work, we report on controlling the anisotropy of continuous Co/Pt multilayer films with ion irradiation to form unique domain configurations of artificial skyrmions and antiskyrmions. We elucidate theirmore » behavior using aberration-corrected Lorentz transmission electron microscopy. We also discuss the energetic stability of these structures studied through in-situ magnetizing experiments performed at room temperature, combined with micromagnetic simulations that successfully reproduce the spin textures and behavior. As a result, this research offers new opportunities towards creation of artificial skyrmion or antiskyrmion lattices that can be used to investigate not only fundamental properties of their interaction with electron currents but also technological applications such as artificial magnonic crystals.« less

Electronic and energetics properties of oxygen defects in La2-xSrxCuO4 in relation to doping and strain

NASA Astrophysics Data System (ADS)

Park, Sohee; Park, Changwon; Yoon, Mina

The level of oxygen defects in La2-xSrxCuO4 (LSCO), a high temperature superconductor, is known to drastically change LSCO's structural and electronic properties. However, the atomistic understanding of the role of oxygen defects is far from being complete. Using first-principles calculations, we investigated the electronic and energetic properties of oxygen vacancies in LSCO in relation to external parameters such as degree of Sr doping amount and external strain. We find that the relative stabilities between the equatorial vacancy induced in the CuO2 layer and the apical vacancy in the LaO layer can be altered by strain. In addition, Sr doping plays a crucial role in their relative stabilities. Therefore, the complex interplay between those key parameters essentially determines the overall oxygen density. Our finding can be instrumental in the experimental development of LSCO with desired oxygen density. Work supported by the LDRD Program of ORNL managed by UT-Battle, LLC, for the U.S. DOE.

Surface modification of montmorillonite on surface Acid-base characteristics of clay and thermal stability of epoxy/clay nanocomposites.

PubMed

Park, Soo-Jin; Seo, Dong-Il; Lee, Jae-Rock

2002-07-01

In this work, the effect of surface treatments on smectitic clay was investigated in surface energetics and thermal behaviors of epoxy/clay nanocomposites. The pH values, X-ray diffraction (XRD), and Fourier transform infrared spectroscopy (FT-IR) were used to analyze the effect of cation exchange on clay surface and the exfoliation phenomenon of clay interlayer. The surface energetics of clay and thermal properties of epoxy/clay nanocomposites were investigated in contact angles and thermogravimetric analysis (TGA), respectively. From the experimental results, the surface modification of clay by dodecylammonium chloride led to the increases in both distance between silicate layers of about 8 A and surface acid values, as well as in the electron acceptor component (gamma(+)(s)) of surface free energy, resulting in improved interfacial adhesion between basic (or electron donor) epoxy resins and acidic (electron acceptor) clay interlayers. Also, the thermal stability of nanocomposites was highly superior to pure epoxy resin due to the presence of the well-dispersed clay nanolayer, which has a barrier property in a composite system.

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

Hoffman, D.M.; Jessop, E.S.; Swansiger, R.W.

Cast cure, extrusion cast, and paste extrudable explosives have not been designed for transferring through long tortuous paths or into fine three dimensional shapes. To allow the crystalline explosive to flow a lubricating fluid is required. The energetic liquid ethane trinitrate (TMETN) was used as the lubricant to maximize the explosive energy. TMETN is a liquid nitrate ester which requires stabilization with conventional free radical stabilizers such as 2- nitrodiphenylamine, methyl-nitroanaline, or ethyl centrylite. Since these injection moldable explosives are expected to cure in place, a polyesterurethane binder based on polymeric isocyanate of hexamethylene diisocyanate and polycaprolactone polyols is dissolvedmore » in TMETN. The solubility of the polymer precursors in TMETN also reduces the energetic liquids sensitivity. The latent cure catalyst Dabco T-131 was used to minimize shrinkage associated with thermal expansion, reduce cost associated with oven cures, to give 4-6 hour potlife and overnight cure to handling strength. The product RX-08-HD is a new, low-viscosity, injection moldable explosive that can be extruded into complex, void-free shapes. Combined with appropriate design and other aspects of weaponization, RX-08-HD has produced outstanding results.« less

Structure, thermodynamic and electronic properties of carbon-nitrogen cubanes and protonated polynitrogen cations

NASA Astrophysics Data System (ADS)

Chaban, Vitaly V.; Andreeva, Nadezhda A.

2017-12-01

Energy generation and storage are at the center of modern civilization. Energetic materials constitute quite a large class of compounds with a high amount of stored chemical energy that can be released. We hereby use a combination of quantum chemistry methods to investigate feasibility and properties of carbon-nitrogen cubanes and multi-charged polynitrogen cations in the context of their synthesis and application as unprecedented energetic materials. We show that the stored energy increases gradually with the nitrogen content increase. Nitrogen-poor cubanes retain their stabilities in vacuum, even at elevated temperatures. Such molecules will be probably synthesized at some point. In turn, polynitrogen cations are highly unstable, except N8H+, despite they are isoelectronic to all-carbon cubane. Kinetic stability of the cation decays drastically as its total charge increases. High-level thermodynamic calculations revealed that large amounts of energy are liberated upon decompositions of polynitrogen cations, which produce molecular nitrogen, acetylene, and protons. The present results bring a substantial insights to the design of novel high-energy compounds.

Cu doped diamond: Effect of charge state and defect aggregation on spin interactions in a 3d transition metal doped wide band-gap semiconductor

NASA Astrophysics Data System (ADS)

Benecha, E. M.; Lombardi, E. B.

2018-05-01

We present a first principles study of Cu in diamond using DFT+U electronic structure methods, by carefully considering the impact of co-doping, charge state, and Fermi level position on its stability, lattice location, spin states, and electronic properties. We show that the energetic stability and spin states of Cu are strongly dependent on the Fermi level position and the type of diamond co-doping, with Cu being energetically more favorable in n-type or p-type co-doped diamond compared to intrinsic diamond. Since Cu has been predicted to order magnetically in a number of other wide band-gap semiconductors, we have also evaluated this possibility for Cu doped diamond. We show that while Cu exhibits strong spin interactions at specific interatomic separations in diamond, a detailed consideration of the impact of Fermi level position and Cu aggregation precludes magnetic ordering, with Cu forming non-magnetic, antiferromagnetic, or paramagnetic clusters. These results have important implications in the understanding of the properties of transition metal dopants in diamond for device applications.

Creation of artificial skyrmions and antiskyrmions by anisotropy engineering

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

Zhang, S.; Petford-Long, A. K.; Phatak, C.

Topological spin textures form a fundamental paradigm in solid state physics and present unique opportunities to explore exciting phenomena such as the quantum Hall effect. One such non-trivial spin texture is a skyrmion, in which the spins can be mapped to point in all directions wrapping around a sphere. Understanding the formation of these spin textures, and their topological and energetic stability, is crucial in order to control their behavior. In this work, we report on controlling the anisotropy of continuous Co/Pt multilayer films with ion irradiation to form unique domain configurations of artificial skyrmions and antiskyrmions. We elucidate theirmore » behavior using aberration-corrected Lorentz transmission electron microscopy. We also discuss the energetic stability of these structures studied through in-situ magnetizing experiments performed at room temperature, combined with micromagnetic simulations that successfully reproduce the spin textures and behavior. As a result, this research offers new opportunities towards creation of artificial skyrmion or antiskyrmion lattices that can be used to investigate not only fundamental properties of their interaction with electron currents but also technological applications such as artificial magnonic crystals.« less

A random access memory immune to single event upset using a T-Resistor

DOEpatents

Ochoa, A. Jr.

1987-10-28

In a random access memory cell, a resistance ''T'' decoupling network in each leg of the cell reduces random errors caused by the interaction of energetic ions with the semiconductor material forming the cell. The cell comprises two parallel legs each containing a series pair of complementary MOS transistors having a common gate connected to the node between the transistors of the opposite leg. The decoupling network in each leg is formed by a series pair of resistors between the transistors together with a third resistor interconnecting the junction between the pair of resistors and the gate of the transistor pair forming the opposite leg of the cell. 4 figs.

Role of AGC1/aralar in the metabolic synergies between neuron and glia.

PubMed

Contreras, Laura

2015-09-01

Brain energetic requirements are elevated due to the high cost of impulse transmission and information storage, and are met mainly by glucose oxidation. The energy needs are closely matched by metabolic regulation, which requires the close cooperation of neurons and astrocytes and involves highly regulated fluxes of metabolites between cells. The metabolism in each type of cell is determined in part by its proteomic profile, which has been regarded as complementary. This review will consider the cellular distribution of the mitochondrial aspartate-glutamate carrier, aralar/AGC1/SLC25A12, and its role in the synergic metabolism between neurons and astrocytes. Copyright © 2015 Elsevier Ltd. All rights reserved.

Particle acceleration in step function shear flows - A microscopic analysis

NASA Technical Reports Server (NTRS)

Jokipii, J. R.; Morfill, G. E.

1990-01-01

The transport of energetic particles in a moving, scattering fluid, which has a large shear in its velocity over a distance small compared with the scattering mean free path is discussed. The analysis is complementary to an earlier paper by Earl, Jokipii, and Morfill (1988), which considered effects of more-gradual shear in the diffusion approximation. The case in which the scattering fluid undergoes a step function change in velocity, in the direction normal to the flow is considered. An analytical, approximate calculation and a Monte Carlo analysis of particle motion are presented. It is found that particles gain energy at a rate proportional to the square of the magnitude of the velocity change.

Random access memory immune to single event upset using a T-resistor

DOEpatents

Ochoa, Jr., Agustin

1989-01-01

In a random access memory cell, a resistance "T" decoupling network in each leg of the cell reduces random errors caused by the interaction of energetic ions with the semiconductor material forming the cell. The cell comprises two parallel legs each containing a series pair of complementary MOS transistors having a common gate connected to the node between the transistors of the opposite leg. The decoupling network in each leg is formed by a series pair of resistors between the transistors together with a third resistor interconnecting the junction between the pair of resistors and the gate of the transistor pair forming the opposite leg of the cell.

How electrostatic networks modulate specificity and stability of collagen.

PubMed

Zheng, Hongning; Lu, Cheng; Lan, Jun; Fan, Shilong; Nanda, Vikas; Xu, Fei

2018-06-12

One-quarter of the 28 types of natural collagen exist as heterotrimers. The oligomerization state of collagen affects the structure and mechanics of the extracellular matrix, providing essential cues to modulate biological and pathological processes. A lack of high-resolution structural information limits our mechanistic understanding of collagen heterospecific self-assembly. Here, the 1.77-Å resolution structure of a synthetic heterotrimer demonstrates the balance of intermolecular electrostatics and hydrogen bonding that affects collagen stability and heterospecificity of assembly. Atomistic simulations and mutagenesis based on the solved structure are used to explore the contributions of specific interactions to energetics. A predictive model of collagen stability and specificity is developed for engineering novel collagen structures.

Influence of osmolytes on protein and water structure: a step to understanding the mechanism of protein stabilization.

PubMed

Bruździak, Piotr; Panuszko, Aneta; Stangret, Janusz

2013-10-03

Results concerning the thermostability of hen egg white lysozyme in aqueous solutions with stabilizing osmolytes, trimethylamine-N-oxide (TMAO), glycine (Gly), and its N-methyl derivatives, N-methylglycine (NMG), N,N-dimethylglycine (DMG), and N,N,N-trimethylglycine (betaine, TMG), have been presented. The combination of spectroscopic (IR) and calorimetric (DSC) data allowed us to establish a link between osmolytes' influence on water structure and their ability to thermally stabilize protein molecule. Structural and energetic characteristics of stabilizing osmolytes' and lysozyme's hydration water appear to be very similar. The osmolytes increase lysozyme stabilization in the order bulk water < TMAO < TMG < Gly < DMG < NMG, which is consistent with the order corresponding to the value of the most probable oxygen-oxygen distance of water molecules affected by osmolytes in their surrounding. Obtained results verified the hypothesis concerning the role of water molecules in protein stabilization, explained the osmophobic effect, and finally helped to bring us nearer to the exact mechanism of protein stabilization by osmolytes.

Stacked-unstacked equilibrium at the nick site of DNA.

PubMed

Protozanova, Ekaterina; Yakovchuk, Peter; Frank-Kamenetskii, Maxim D

2004-09-17

Stability of duplex DNA with respect to separation of complementary strands is crucial for DNA executing its major functions in the cell and it also plays a central role in major biotechnology applications of DNA: DNA sequencing, polymerase chain reaction, and DNA microarrays. Two types of interaction are well known to contribute to DNA stability: stacking between adjacent base-pairs and pairing between complementary bases. However, their contribution into the duplex stability is yet to be determined. Now we fill this fundamental gap in our knowledge of the DNA double helix. We have prepared a series of 32, 300 bp-long DNA fragments with solitary nicks in the same position differing only in base-pairs flanking the nick. Electrophoretic mobility of these fragments in the gel has been studied. Assuming the equilibrium between stacked and unstacked conformations at the nick site, all 32 stacking free energy parameters have been obtained. Only ten of them are essential and they govern the stacking interactions between adjacent base-pairs in intact DNA double helix. A full set of DNA stacking parameters has been determined for the first time. From these data and from a well-known dependence of DNA melting temperature on G.C content, the contribution of base-pairing into duplex stability has been estimated. The obtained energy parameters of the DNA double helix are of paramount importance for understanding sequence-dependent DNA flexibility and for numerous biotechnology applications.

Heterogeneous Two-Phase Pillars in Epitaxial NiFe 2 O 4 -LaFeO 3 Nanocomposites

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

Comes, Ryan B.; Perea, Daniel E.; Spurgeon, Steven R.

2017-07-10

Self-assembled epitaxial oxide nanocomposites have been explored for a wide range of applications, including multiferroic and magnetoelectric properties, plasmonics, and catalysis. These so-called “vertically aligned nanocomposites” form spontaneously during the deposition process when segregation into two phases is energetically favorable as compared to a solid solution. However, there has been surprisingly little work understanding the driving forces that govern the synthesis of these materials, which can include point defect energetics, surface diffusion, and interfacial energies. To explore these factors, La-Ni-Fe-O films have been synthesized by molecular beam epitaxy and it is shown that these phase segregate into spinel-perovskite nanocomposites. Usingmore » complementary scanning transmission electron microscopy and atom-probe tomography, the elemental composition of each phase is examined and found that Ni ions are exclusively found in the spinel phase. From correlative analysis, a model for the relative favorability of the Ni2+ and Ni3+ valences under the growth conditions is developed. It is shown that multidimensional characterization techniques provide previously unobserved insight into the growth process and complex driving forces for phase segregation.« less

Progressing the analysis of Improvised Explosive Devices: Comparative study for trace detection of explosive residues in handprints by Raman spectroscopy and liquid chromatography.

PubMed

Zapata, Félix; de la Ossa, Mª Ángeles Fernández; Gilchrist, Elizabeth; Barron, Leon; García-Ruiz, Carmen

2016-12-01

Concerning the dreadful global threat of terrorist attacks, the detection of explosive residues in biological traces and marks is a current need in both forensics and homeland security. This study examines the potential of Raman microscopy in comparison to liquid chromatography (ion chromatography (IC) and reversed-phase high performance liquid chromatography (RP-HPLC)) to detect, identify and quantify residues in human handmarks of explosives and energetic salts commonly used to manufacture Improvised Explosive Devices (IEDs) including dynamite, ammonium nitrate, single- and double-smokeless gunpowders and black powder. Dynamite, ammonium nitrate and black powder were detected through the identification of the energetic salts by Raman spectroscopy, their respective anions by IC, and organic components by RP-HPLC. Smokeless gunpowders were not detected, either by Raman spectroscopy or the two liquid chromatography techniques. Several aspects of handprint collection, sample treatment and a critical comparison of the identification of compounds by both techniques are discussed. Raman microscopy and liquid chromatography were shown to be complementary to one another offering more comprehensive information for trace explosives analysis. Copyright © 2016 Elsevier B.V. All rights reserved.

C-5 Propynyl Modifications Enhance the Mechanical Stability of DNA.

PubMed

Aschenbrenner, Daniela; Baumann, Fabian; Milles, Lukas F; Pippig, Diana A; Gaub, Hermann E

2015-07-20

Increased thermal or mechanical stability of DNA duplexes is desired for many applications in nanotechnology or -medicine where DNA is used as a programmable building block. Modifications of pyrimidine bases are known to enhance thermal stability and have the advantage of standard base-pairing and easy integration during chemical DNA synthesis. Through single-molecule force spectroscopy experiments with atomic force microscopy and the molecular force assay we investigated the effect of pyrimidines harboring C-5 propynyl modifications on the mechanical stability of double-stranded DNA. Utilizing these complementary techniques, we show that propynyl bases significantly increase the mechanical stability if the DNA is annealed at high temperature. In contrast, modified DNA complexes formed at room temperature and short incubation times display the same stability as non-modified DNA duplexes. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Quantum Dot Nanobioelectronics and Selective Antimicrobial Redox Interventions

NASA Astrophysics Data System (ADS)

Goodman, Samuel Martin

The unique properties of nanomaterials have engendered a great deal of interest in applying them for applications ranging from solid state physics to bio-imaging. One class of nanomaterials, known collectively as quantum dots, are defined as semiconducting crystals which have a characteristic dimension smaller than the excitonic radius of the bulk material which leads to quantum confinement effects. In this size regime, excited charge carriers behave like prototypical particles in a box, with their energy levels defined by the dimensions of the constituent particle. This is the source of the tunable optical properties which have drawn a great deal of attention with regards to finding appropriate applications for these materials. This dissertation is divided into multiple sections grouped by the type of application explored. The first sectoin investigates the energetic interactions of physically-coupled quantum dots and DNA, with the goal of gaining insight into how self-assembled molecular wires can bridge the energetic states of physically separated nanocrystals. Chapter 1 begins with an introduction to the properties of quantum dots, the conductive properties of DNA, and the common characterization methods used to characterize materials on the nanoscale. In Chapter 2 scanning tunneling measurements of QD-DNA constructs on the single particle level are presented which show the tunable coupling between the two materials and their resulting hybrid electronic structure. This is expanded upon in Chapter 3 where the conduction of photogenerated charges in QD-DNA hybrid thin films are characterized, which exhibit different charge transfer pathways through the constituent nucleobases depending on the energy of the incident light and resulting electrons. Complementary investigations of energy transfer mediated through DNA are presented in Chapter 4, with confirmation of Dexter-like transfer being facilitated through the oligonucleotides. The second section quantifies the use of cadmium telluride quantum dots as light-activated therapeutics for treating multi-drug resistant bacterial infectoins. A review of the physiological effects of cadmium chalcogenide quantum dots is first presented in Chapter 5 which provides a foundation for understanding the inherent toxicity of these materials. The phototoxic effect induced by CdTe quantum dots is then introduced in Chapter 6 showing the reduction in growth of gram-negative bacteria. Additional insight is provided in Chapter 7 which discusses the therapeutic mechanism and the oxygen-centered radical species which are formed by the application of light in aqueous media. The section closes with Chapter 8 describing efforts to improve the stability and bio-compatibility of the dots using various surface treatments, and shows that stability can be improved by the passivation of the quantum dots' anionic facets, though at the cost of overall radical generation.

Salt bridge as a gatekeeper against partial unfolding.

PubMed

Hinzman, Mark W; Essex, Morgan E; Park, Chiwook

2016-05-01

Salt bridges are frequently observed in protein structures. Because the energetic contribution of salt bridges is strongly dependent on the environmental context, salt bridges are believed to contribute to the structural specificity rather than the stability. To test the role of salt bridges in enhancing structural specificity, we investigated the contribution of a salt bridge to the energetics of native-state partial unfolding in a cysteine-free version of Escherichia coli ribonuclease H (RNase H*). Thermolysin cleaves a protruding loop of RNase H(*) through transient partial unfolding under native conditions. Lys86 and Asp108 in RNase H(*) form a partially buried salt bridge that tethers the protruding loop. Investigation of the global stability of K86Q/D108N RNase H(*) showed that the salt bridge does not significantly contribute to the global stability. However, K86Q/D108N RNase H(*) is greatly more susceptible to proteolysis by thermolysin than wild-type RNase H(*) is. The free energy for partial unfolding determined by native-state proteolysis indicates that the salt bridge significantly increases the energy for partial unfolding by destabilizing the partially unfolded form. Double mutant cycles with single and double mutations of the salt bridge suggest that the partially unfolded form is destabilized due to a significant decrease in the interaction energy between Lys86 and Asp108 upon partial unfolding. This study demonstrates that, even in the case that a salt bridge does not contribute to the global stability, the salt bridge may function as a gatekeeper against partial unfolding that disturbs the optimal geometry of the salt bridge. © 2016 The Protein Society.

Density Functional Investigation of the Inclusion of Gold Clusters on a CH 3 S Self-Assembled Lattice on Au(111)

DOE PAGES

Allen, Darnel J.; Archibald, Wayne E.; Harper, John A.; ...

2016-01-01

We employ first-principles density functional theoretical calculations to address the inclusion of gold (Au) clusters in a well-packed CH 3 S self-assembled lattice. We compute CH 3 S adsorption energies to quantify the energetic stability of the self-assembly and gold adsorption and dissolution energies to characterize the structural stability of a series of Au clusters adsorbed at the SAM-Au interface. Our results indicate that the inclusion of Au clusters with less than four Au atoms in the SAM-Au interface enhances the binding of CH 3 S species. In contrast, larger Au clusters destabilize the self-assembly. We attribute this effect tomore » the low-coordinated gold atoms in the cluster. For small clusters, these low-coordinated sites have significantly different electronic properties compared to larger islands, which makes the binding with the self-assembly energetically more favorable. Our results further indicate that Au clusters in the SAM-Au interface are thermodynamically unstable and they will tend to dissolve, producing Au adatoms incorporated in the self-assembly in the form of CH 3 S-Au-SCH 3 species. This is due to the strong S-Au bond which stabilizes single Au adatoms in the self-assembly. Our results provide solid insight into the impact of adatom islands at the CH 3 S-Au interface.« less

Theoretical Design on a Series of Novel Bicyclic and Cage Nitramines as High Energy Density Compounds.

PubMed

Pan, Yong; Zhu, Weihua

2017-11-30

We designed four bicyclic nitramines and three cage nitramines by incorporating -N(NO 2 )-CH 2 -N(NO 2 )-, -N(NO 2 )-, and -O- linkages based on the HMX (1,3,5,7-tetranitro-1,3,5,7-tetrazocane) framework. Then, their electronic structure, heats of formation, energetic properties, strain energy, thermal stability, and impact sensitivity were systematically studied using density functional theory (DFT). Compared to the parent compound HMX, all the title compounds have much higher density, better detonation properties, and better oxygen balance. Among them, four compounds have extraordinary high detonation properties (D > 9.70 km/s and P > 44.30 GPa). Moreover, most of the title compounds exhibit better thermal stability and lower impact sensitivity than CL-20 2,4,6,8,10,12-hexanitro-2,4,6,8,10,12-hexaazaisowurtzitane) or HNHAA (hexanitrohexaazaadamantane). Thus, all of the seven new nitramine compounds are promising candidates for high energy density compounds. In particular, five compounds exhibit a best combination of better oxygen balance, good thermal stability, excellent detonation properties superior to or comparable to CL-20 or HNHAA, and lower impact sensitivity than CL-20 or HNHAA. The results indicate that our unusual design strategy that constructing bicyclic or cage nitramines based on the HMX framework by incorporating the intramolecular linkages is very useful for developing novel energetic compounds with excellent detonation performance and low sensitivity.

Conformational Preference and Spectroscopical Characteristics of the Active Pharmaceutical Ingredient Levetiracetam.

PubMed

Luchian, Raluca; Vinţeler, Emil; Chiş, Cosmina; Vasilescu, Mihai; Leopold, Nicolae; Prates Ramalho, João P; Chiş, Vasile

2017-12-01

The analysis of the possible conformers and the conformational change between solid and liquid states of a particular drug molecule are mandatory not only for describing reliably its spectroscopical properties but also for understanding the interaction with the receptor and its mechanism of action. Therefore, here we investigated the free-energy conformational landscape of levetiracetam (LEV) in gas phase as well as in water and ethanol, aiming to describe the 3-dimensional structure and energetic stability of its conformers. Twenty-two unique conformers were identified, and their energetic stability was determined at density functional theory B3LYP/6-31+G(2d,2p) level of theory. The 6 most stable monomers in water, within a relative free-energy window of 0.71 kcal mol -1 and clearly separated in energy from the remaining subset of 16 conformers, as well as the 3 most stable dimers were then used to compute the Boltzmann populations-averaged UV-Vis and NMR spectra of LEV. The conformational landscape in solution is distinctly different from that corresponding to gas phase, particularly due to the relative orientations of the butanamide group. Aiming to clarify the stability of the possible dimers of LEV, we also investigated computationally the structure of a set of 11 nonhydrated and hydrated homochiral hydrogen-bonded LEV dimers. Copyright © 2017 American Pharmacists Association®. Published by Elsevier Inc. All rights reserved.

GLOBAL ENERGETICS OF SOLAR FLARES. IV. CORONAL MASS EJECTION ENERGETICS

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

Aschwanden, Markus J., E-mail: aschwanden@lmsal.com

2016-11-01

This study entails the fourth part of a global flare energetics project, in which the mass m {sub cme}, kinetic energy E {sub kin}, and the gravitational potential energy E {sub grav} of coronal mass ejections (CMEs) is measured in 399 M and X-class flare events observed during the first 3.5 years of the Solar Dynamics Observatory (SDO) mission, using a new method based on the EUV dimming effect. EUV dimming is modeled in terms of a radial adiabatic expansion process, which is fitted to the observed evolution of the total emission measure of the CME source region. The modelmore » derives the evolution of the mean electron density, the emission measure, the bulk plasma expansion velocity, the mass, and the energy in the CME source region. The EUV dimming method is truly complementary to the Thomson scattering method in white light, which probes the CME evolution in the heliosphere at r ≳ 2 R {sub ⊙}, while the EUV dimming method tracks the CME launch in the corona. We compare the CME parameters obtained in white light with the LASCO/C2 coronagraph with those obtained from EUV dimming with the Atmospheric Imaging Assembly onboard the SDO for all identical events in both data sets. We investigate correlations between CME parameters, the relative timing with flare parameters, frequency occurrence distributions, and the energy partition between magnetic, thermal, nonthermal, and CME energies. CME energies are found to be systematically lower than the dissipated magnetic energies, which is consistent with a magnetic origin of CMEs.« less

Two species drag/diffusion model for energetic particle driven modes

NASA Astrophysics Data System (ADS)

Aslanyan, V.; Sharapov, S. E.; Spong, D. A.; Porkolab, M.

2017-12-01

A nonlinear bump-on-tail model for the growth and saturation of energetic particle driven plasma waves has been extended to include two populations of fast particles—one dominated by dynamical friction at the resonance and the other by velocity space diffusion. The resulting temporal evolution of the wave amplitude and frequency depends on the relative weight of the two populations. The two species model is applied to burning plasma with drag-dominated alpha particles and diffusion-dominated ICRH accelerated minority ions, showing the stabilization of bursting modes. The model also suggests an explanation for the recent observations on the TJ-II stellarator, where Alfvén Eigenmodes transition between steady state and bursting as the magnetic configuration varied.

Cardioprotection Resulting from Glucagon-Like Peptide-1 Administration Involves Shifting Metabolic Substrate Utilization to Increase Energy Efficiency in the Rat Heart.

PubMed

Aravindhan, Karpagam; Bao, Weike; Harpel, Mark R; Willette, Robert N; Lepore, John J; Jucker, Beat M

2015-01-01

Previous studies have shown that glucagon-like peptide-1 (GLP-1) provides cardiovascular benefits independent of its role on peripheral glycemic control. However, the precise mechanism(s) by which GLP-1 treatment renders cardioprotection during myocardial ischemia remain unresolved. Here we examined the role for GLP-1 treatment on glucose and fatty acid metabolism in normal and ischemic rat hearts following a 30 min ischemia and 24 h reperfusion injury, and in isolated cardiomyocytes (CM). Relative carbohydrate and fat oxidation levels were measured in both normal and ischemic hearts using a 1-13C glucose clamp coupled with NMR-based isotopomer analysis, as well as in adult rat CMs by monitoring pH and O2 consumption in the presence of glucose or palmitate. In normal heart, GLP-1 increased glucose uptake (↑64%, p<0.05) without affecting glycogen levels. In ischemic hearts, GLP-1 induced metabolic substrate switching by increasing the ratio of carbohydrate versus fat oxidation (↑14%, p<0.01) in the LV area not at risk, without affecting cAMP levels. Interestingly, no substrate switching occurred in the LV area at risk, despite an increase in cAMP (↑106%, p<0.05) and lactate (↑121%, p<0.01) levels. Furthermore, in isolated CMs GLP-1 treatment increased glucose utilization (↑14%, p<0.05) and decreased fatty acid oxidation (↓15%, p<0.05) consistent with in vivo finding. Our results show that this benefit may derive from distinct and complementary roles of GLP-1 treatment on metabolism in myocardial sub-regions in response to this injury. In particular, a switch to anaerobic glycolysis in the ischemic area provides a compensatory substrate switch to overcome the energetic deficit in this region in the face of reduced tissue oxygenation, whereas a switch to more energetically favorable carbohydrate oxidation in more highly oxygenated remote regions supports maintaining cardiac contractility in a complementary manner.

Toll-Like Receptor-9-Mediated Invasion in Breast Cancer

DTIC Science & Technology

2011-07-01

Molecular Dynamics Simulations. Theoretical structural models were obtained from molecular dynamics simulations using explicit solvation by...with AMBER by MARDIGRAS. The solution structure was then derived by coupling the resulting NMR distance restraints with a molecular dynamic ...Overlay of NMR restrained structure (red) with theoretical molecular dynamic simulated annealing structure (blue). Energetic stability of the 9-mer

Extrusion cast explosive

DOEpatents

Scribner, Kenneth J.

1985-01-01

Improved, multiphase, high performance, high energy, extrusion cast explosive compositions, comprising, a crystalline explosive material; an energetic liquid plasticizer; a urethane prepolymer, comprising a blend of polyvinyl formal, and polycaprolactone; a polyfunctional isocyanate; and a catalyst are disclosed. These new explosive compositions exhibit higher explosive content, a smooth detonation front, excellent stability over long periods of storage, and lower sensitivity to mechanical stimulants.

Duplex and triplex formation of mixed pyrimidine oligonucleotides with stacking of phenyl-triazole moieties in the major groove.

PubMed

Andersen, Nicolai Krog; Døssing, Holger; Jensen, Frank; Vester, Birte; Nielsen, Poul

2011-08-05

5-(1-Phenyl-1,2,3-triazol-4-yl)-2'-deoxycytidine was synthesized from a modified CuAAC protocol and incorporated into mixed pyrimidine oligonucleotide sequences together with the corresponding 5-(1-phenyl-1,2,3-triazol-4-yl)-2'-deoxyuridine. With consecutive incorporations of the two modified nucleosides, improved duplex formation with a complementary RNA and improved triplex formation with a complementary DNA duplex were observed. The improvement is due to π-π stacking of the phenyl-triazole moieties in the major groove. The strongest stacking and most pronounced positive influence on thermal stability was found in between the uridine analogues or with the cytidine analogue placed in the 3' direction to the uridine analogue. Modeling indicated a different orientation of the phenyl-triazole moieties in the major groove to account for the difference between the two nucleotides. The modified oligonucleotides were all found to be significantly stabilized toward nucleolytic degration.

Low-Temperature Bainite: A Thermal Stability Study

NASA Astrophysics Data System (ADS)

Santajuana, Miguel A.; Rementeria, Rosalia; Kuntz, Matthias; Jimenez, Jose A.; Caballero, Francisca G.; Garcia-Mateo, Carlos

2018-06-01

The thermal stability of nanobainitic structures obtained by heat treating two different high-carbon high-silicon steels at temperatures between 200 °C and 600 °C has been investigated by means of three complementary techniques, i.e., field emission gun-scanning electron microscopy, X-ray diffraction, and high-resolution dilatometry. Three main stages have been established, each of them characterized by a distinctive microstructure. Furthermore, the nanocrystalline structure generated by the bainite reaction confers the steel with an extraordinary tempering resistance.

Low-Temperature Bainite: A Thermal Stability Study

NASA Astrophysics Data System (ADS)

Santajuana, Miguel A.; Rementeria, Rosalia; Kuntz, Matthias; Jimenez, Jose A.; Caballero, Francisca G.; Garcia-Mateo, Carlos

2018-04-01

The thermal stability of nanobainitic structures obtained by heat treating two different high-carbon high-silicon steels at temperatures between 200 °C and 600 °C has been investigated by means of three complementary techniques, i.e., field emission gun-scanning electron microscopy, X-ray diffraction, and high-resolution dilatometry. Three main stages have been established, each of them characterized by a distinctive microstructure. Furthermore, the nanocrystalline structure generated by the bainite reaction confers the steel with an extraordinary tempering resistance.

The effects of disulfide bonds on the denatured state of barnase.

PubMed Central

Clarke, J.; Hounslow, A. M.; Bond, C. J.; Fersht, A. R.; Daggett, V.

2000-01-01

The effects of engineered disulfide bonds on protein stability are poorly understood because they can influence the structure, dynamics, and energetics of both the native and denatured states. To explore the effects of two engineered disulfide bonds on the stability of barnase, we have conducted a combined molecular dynamics and NMR study of the denatured state of the two mutants. As expected, the disulfide bonds constrain the denatured state. However, specific extended beta-sheet structure can also be detected in one of the mutant proteins. This mutant is also more stable than would be predicted. Our study suggests a possible cause of the very high stability conferred by this disulfide bond: the wild-type denatured ensemble is stabilized by a nonnative hydrophobic cluster, which is constrained from occurring in the mutant due to the formation of secondary structure. PMID:11206061

The Use of Healing Touch in Integrative Oncology

PubMed Central

Hart, Laura K.; Freel, Mildred I.; Haylock, Pam J.; Lutgendorf, Susan K.

2013-01-01

The use of complementary therapies by cancer patients has become so prevalent that nurses working in oncology are finding it necessary to understand these therapies and the evidence-based support for their use. The integrative use of the biofield therapy Healing Touch (HT) in conjunction with the chemoradiation received by patients with cervical cancer (stages 1B1 to IVA) during a recent research study is described. Findings indicated effects of HT on the immune response and on depression, in contrast to patients receiving relaxation or standard care. Specifically, HT patients demonstrated a minimal decrease in natural killer cell cytotoxicity (NKCC) over the course of treatment whereas NKCC of patients receiving relaxation therapy (RT) and standard care (SC) declined sharply during radiation (p = 0.018). HT patients also showed significant decreases in depressed mood compared to RT and SC (p < 0.05). These findings, as well as the energetic effects of chemoradiation that were observed, and the proposed mechanisms and potential contributions of biofield therapy are addressed. It is suggested that the appropriate integration of complementary modalities into oncology care has the potential to enhance the impact of conventional care by putting the patient in the best condition to use their innate healing resources. PMID:21951738

Asteroid models from photometry and complementary data sources

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

Kaasalainen, Mikko

I discuss inversion methods for asteroid shape and spin reconstruction with photometry (lightcurves) and complementary data sources such as adaptive optics or other images, occultation timings, interferometry, and range-Doppler radar data. These are essentially different sampling modes (generalized projections) of plane-of-sky images. An important concept in this approach is the optimal weighting of the various data modes. The maximum compatibility estimate, a multi-modal generalization of the maximum likelihood estimate, can be used for this purpose. I discuss the fundamental properties of lightcurve inversion by examining the two-dimensional case that, though not usable in our three-dimensional world, is simple to analyze,more » and it shares essentially the same uniqueness and stability properties as the 3-D case. After this, I review the main aspects of 3-D shape representations, lightcurve inversion, and the inclusion of complementary data.« less

Stability of hydrogenated graphene: a first-principles study

DOE PAGES

Yi, Ding; Yang, Liu; Xie, Shijie; ...

2015-02-10

In order to explain the disagreement between present theoretical and experimental investigations on the stability of hydrogenated graphene, we have systematically studied hydrogenated graphene with different configurations from the consideration of single-side and double-side adsorption using first-principles calculations. Both binding energy and formation energy are calculated to characterize the stability of the system. It is found that single-side hydrogenated graphene is always unstable. However, for double-side hydrogenation, some configurations are stable due to the increased carbon–carbon sp 3 hybridization compared to single-side hydrogenation. Furthermore, it is found that the system is energetically favorable when an equal number of hydrogen atomsmore » are adsorbed on each side of the graphene.« less

Magma oceanography. I - Thermal evolution. [of lunar surface

NASA Technical Reports Server (NTRS)

Solomon, S. C.; Longhi, J.

1977-01-01

Fractional crystallization and flotation of cumulate plagioclase in a cooling 'magma ocean' provides the simplest explanation for early emplacement of a thick feldspar-rich lunar crust. The complementary mafic cumulates resulting from the differentiation of such a magma ocean have been identified as the ultimate source of mare basalt liquids on the basis or rare-earth abundance patterns and experimental petrology studies. A study is conducted concerning the thermal evolution of the early differentiation processes. A range of models of increasing sophistication are considered. The models developed contain the essence of the energetics and the time scale for magma ocean differentiation. Attention is given to constraints on a magma ocean, modeling procedures, single-component magma oceans, fractionating magma oceans, and evolving magma oceans.

Structure of an energetic narrow discrete arc

NASA Technical Reports Server (NTRS)

Mcfadden, J. P.; Carlson, C. W.; Boehm, M. H.

1990-01-01

Particle distributions, waves, dc electric fields, and magnetic fields were measured by two sounding rockets at altitudes of 950 and 430 km through an energetic (greater than 5 keV) narrow (about 10 km) stable discrete arc. Although the payloads' magnetic footprints were separated by only 50 km, differences in the arc's structure were observed including the spatial width, peak energy, and characteristic spectra. The energetic electron precipitation included both slowly varying isotropic fluxes that formed an inverted-V energy-time signature and rapidly varying field-aligned fluxes at or below the isotropic spectral peak. The isotropic precipitation had a flux discontinuity inside the arc indicating the arc was present on a boundary between two different magnetospheric plasmas. Dispersive and nondispersive bursts of field-aligned electrons were measured throughout the arc, appearing over broad energy ranges or as monoenergetic beams. Dispersive bursts gave variable source distances less than 8000 km. Plateauing of some of the most intense bursts suggests that waves stabilized these electrons. During the lower altitude arc crossing, the field-aligned component formed a separate inverted-V energy-time signature whose peak energy was half the isotropic peak energy.

NIMROD Modeling of Sawtooth Modes Using Hot-Particle Closures

NASA Astrophysics Data System (ADS)

Kruger, Scott; Jenkins, T. G.; Held, E. D.; King, J. R.

2015-11-01

In DIII-D shot 96043, RF heating gives rise to an energetic ion population that alters the sawtooth stability boundary, replacing conventional sawtooth cycles by longer-period, larger-amplitude `giant sawtooth' oscillations. We explore the use of particle-in-cell closures within the NIMROD code to numerically represent the RF-induced hot-particle distribution, and investigate the role of this distribution in determining the altered mode onset threshold and subsequent nonlinear evolution. Equilibrium reconstructions from the experimental data are used to enable these detailed validation studies. Effects of other parameters on the sawtooth behavior, such as the plasma Lundquist number and hot-particle beta-fraction, are also considered. The fast energetic particles present many challenges for the PIC closure. We review new algorithm and performance improvements to address these challenges, and provide a preliminary assessment of the efficacy of the PIC closure versus a continuum model for energetic particle modeling. We also compare our results with those of, and discuss plans for a more complete validation campaign for this discharge. Supported by US Department of Energy via the SciDAC Center for Extended MHD Modeling (CEMM).

Thermodynamic analysis of cavity creating mutations in an engineered leucine zipper and energetics of glycerol-induced coiled coil stabilization.

PubMed

Dürr, E; Jelesarov, I

2000-04-18

Protein stability in vitro can be influenced either by introduction of mutations or by changes in the chemical composition of the solvent. Recently, we have characterized the thermodynamic stability and the rate of folding of the engineered dimeric leucine zipper A(2), which has a strengthened hydrophobic core [Dürr, E., Jelesarov, I., and Bosshard, H. R. (1999) Biochemistry 38, 870-880]. Here we report on the energetic consequences of a cavity introduced by Leu/Ala substitution at the tightly packed dimeric interface and how addition of 30% glycerol affects the folding thermodynamics of A(2) and the cavity mutants. Folding could be described by a two-state transition from two unfolded monomers to a coiled coil dimer. Removal of six methylene groups by Leu/Ala substitutions destabilized the dimeric coiled coil by 25 kJ mol(-1) at pH 3.5 and 25 degrees C in aqueous buffer. Destabilization was purely entropic at around room temperature and became increasingly enthalpic at elevated temperatures. Mutations were accompanied by a decrease of the unfolding heat capacity by 0.5 kJ K(-1) mol(-1). Addition of 30% glycerol increased the free energy of folding of A(2) and the cavity mutants by 5-10 kJ mol(-1) and lowered the unfolding heat capacity by 25% for A(2) and by 50% for the Leu/Ala mutants. The origin of the stabilizing effect of glycerol varied with temperature. Stabilization of the parent leucine zipper A(2) was enthalpic with an unfavorable entropic component between 0 and 100 degrees C. In the case of cavity mutants, glycerol induced enthalpic stabilization below 50 degrees C and entropic stabilization above 50 degrees C. The effect of glycerol could not be accounted for solely by the enthalpy and entropy of transfer or protein surface from water to glycerol/water mixture. We propose that in the presence of glycerol the folded coiled coil dimer is better packed and displays less intramolecular fluctuations, leading to enhanced enthalpic interactions and to an increase of the entropy of folding. This work demonstrates that mutational and solvent effects on protein stability can be thermodynamically complex and that it may not be sufficient to only analyze changes of enthalpy and entropy at the unfolding temperature (T(m)) to understand the mechanisms of protein stabilization.

Diaminoethane adsorption and water substitution on hydrated TiO2: a thermochemical study based on first-principles calculations.

PubMed

Hémeryck, Anne; Motta, Alessandro; Swiatowska, Jolanta; Pereira-Nabais, Catarina; Marcus, Philippe; Costa, Dominique

2013-07-14

Epoxy-amines are used as structural adhesives deposited on Ti. The amine adhesion to a Ti surface depends highly on the surface state (oxidation, hydroxylation). Amines may adsorb above preadsorbed water molecules or substitute them to bind directly to surface Ti(4+) Lewis acid sites. The adsorption of a model amine molecule, diaminoethane (DAE), on a model surface, hydrated TiO2-anatase (101) surface, is investigated using Density Functional Theory including Dispersive forces (DFT-D) calculations. DAE adsorption and water substitution by DAE are exothermic processes and turn nearly isoenergetic at high coverage with adsorption-substitution energies around -0.3 eV (including dispersion forces and ZPE). Complementary ab initio molecular dynamics studies also suggest that the formation of an amine-water interaction induces water desorption from the surface at room temperature, a preliminary step towards the amine-Ti bond formation. An atomistic thermodynamic approach is developed to evaluate the interfacial free energy balance of both processes (adsorption and substitution). The main contributions to the energetic balance are dispersive interactions between molecules and the surface on the exergonic side, translational and rotational entropic contributions on the endergonic one. The substitution process is stabilized by 0.55 eV versus the adsorption one when free solvation, rotational and vibrational energies are considered. The main contribution to this free energy gain is due to water solvation. The calculations suggest that in toluene solvent with a water concentration of 10(-4) M or less, a full DAE layer replaces a preadsorbed water layer for a threshold concentration of DAE ≥ 0.1 M.

Rainbow trout consume less oxygen in turbulence: the energetics of swimming behaviors at different speeds

PubMed Central

Taguchi, Masashige; Liao, James C.

2011-01-01

SUMMARY Measuring the rate of consumption of oxygen () during swimming reveals the energetics of fish locomotion. We show that rainbow trout have substantially different oxygen requirements for station holding depending on which hydrodynamic microhabitats they choose to occupy around a cylinder. We used intermittent flow respirometry to show that an energetics hierarchy, whereby certain behaviors are more energetically costly than others, exists both across behaviors at a fixed flow velocity and across speeds for a single behavior. At 3.5 L s–1 (L is total body length) entraining has the lowest , followed by Kármán gaiting, bow waking and then free stream swimming. As flow speed increases the costs associated with a particular behavior around the cylinder changes in unexpected ways compared with free stream swimming. At times, actually decreases as flow velocity increases. Entraining demands the least oxygen at 1.8 L s–1 and 3.5 L s–1, whereas bow waking requires the least oxygen at 5.0 L s–1. Consequently, a behavior at one speed may have a similar cost to another behavior at another speed. We directly confirm that fish Kármán gaiting in a vortex street gain an energetic advantage from vortices beyond the benefit of swimming in a velocity deficit. We propose that the ability to exploit velocity gradients as well as stabilization costs shape the complex patterns of oxygen consumption for behaviors around cylinders. Measuring for station holding in turbulent flows advances our attempts to develop ecologically relevant approaches to evaluating fish swimming performance. PMID:21490251

Extrusion cast explosive

DOEpatents

Scribner, K.J.

1985-01-29

Improved, multiphase, high performance, high energy, extrusion cast explosive compositions, comprising, a crystalline explosive material; an energetic liquid plasticizer; a urethane prepolymer, comprising a blend of polyvinyl formal, and polycaprolactone; a polyfunctional isocyanate; and a catalyst are disclosed. These new explosive compositions exhibit higher explosive content, a smooth detonation front, excellent stability over long periods of storage, and lower sensitivity to mechanical stimulants. 1 fig.

Extrusion cast explosive

DOEpatents

Scribner, K.J.

1985-11-26

Disclosed is an improved, multiphase, high performance, high energy, extrusion cast explosive compositions, comprising, a crystalline explosive material; an energetic liquid plasticizer; a urethane prepolymer, comprising a blend of polyvinyl formal, and polycaprolactone; a polyfunctional isocyanate; and a catalyst. These new explosive compositions exhibit higher explosive content, a smooth detonation front, excellent stability over long periods of storage, and lower sensitivity to mechanical stimulants. 1 fig.

On the upper bound of the thermodynamic stability of fullerenes from small to giant

NASA Astrophysics Data System (ADS)

Pankratyev, Evgeniy Yu; Khatymov, Rustem V.; Sabirov, Denis Sh; Yuldashev, Arthur V.

2018-07-01

From the large variety of C20sbnd C720 fullerenes, the energetically most stable isomers were chosen and studied within the PBE/3ζ quantum-chemical approximation. A phenomenological model of the dependence of the standard enthalpy of formation and entropy of the selected isomers on the number of the carbon atoms is developed. From the analysis of the constants of the phenomenological model, it follows that the C60, C70, C180, and C1500 molecules hold a prominent position among the hypothetical and/or experimentally discovered fullerenes. For the selected energy-stable isomers, the values of the singlet-triplet splitting were calculated. The ground state of the C260sbnd C3, C320sbnd D3d and C500sbnd D3d molecules were found to be of triplet multiplicity that may indicate their low kinetic stability and/or possibility of existence in the derivatized forms. In view of the lack of relevant experimental thermodynamic data on fullerenes, the obtained in this work approximation dependences, expressed in a simple analytical form, may provide useful tool for fast assessing the energetic characteristics of fullerenes, as well as for prediction of those undiscovered yet.

First-principles study of water desorption from montmorillonite surface.

PubMed

Zhang, Yao; Meng, Yingfeng; Liu, Houbin; Yang, Mingli

2016-05-01

Knowledge about water desorption is important to give a full picture of water diffusion in montmorillonites (MMT), which is a driving factor in MMT swelling. The desorption paths and energetics of water molecules from the surface of MMT with trapped Li(+), Na(+) or K(+) counterions were studied using periodic density functional theory calculations. Two paths--surface and vacuum desorption--were designed for water desorption starting from a stationary structure in which water bonds with both the counterion and the MMT surface. Surface desorption is energetically more favorable than vacuum desorption due to water-surface hydrogen bonds that help stabilize the intermediate structure of water released from the counterion. The energy barriers of water desorption are in the order of Li(+) > Na(+) > K(+), which can be attributed to the short ionic radius of Li(+), which favors strong binding with the water molecule. The temperature dependence of water adsorption and desorption rates were compared based on the computed activation energies. Our calculations reveal that the water desorption on the MMT surface has a different mechanism from water adsorption, which results from surface effects favoring stabilization of water conformers during the desorption process.

Asymmetric shape transitions of epitaxial quantum dots

PubMed Central

2016-01-01

We construct a two-dimensional continuum model to describe the energetics of shape transitions in fully faceted epitaxial quantum dots (strained islands) via minimization of elastic energy and surface energy at fixed volume. The elastic energy of the island is based on a third-order approximation, enabling us to consider shape transitions between pyramids, domes, multifaceted domes and asymmetric intermediate states. The energetics of the shape transitions are determined by numerically calculating the facet lengths that minimize the energy of a given island type of prescribed island volume. By comparing the energy of different island types with the same volume and analysing the energy surface as a function of the island shape parameters, we determine the bifurcation diagram of equilibrium solutions and their stability, as well as the lowest barrier transition pathway for the island shape as a function of increasing volume. The main result is that the shape transition from pyramid to dome to multifaceted dome occurs through sequential nucleation of facets and involves asymmetric metastable transition shapes. We also explicitly determine the effect of corner energy (facet edge energy) on shape transitions and interpret the results in terms of the relative stability of asymmetric island shapes as observed in experiment. PMID:27436989

The Efficiency of Different Salts to Screen Charge Interactions in Proteins: A Hofmeister Effect?

PubMed Central

Perez-Jimenez, Raul; Godoy-Ruiz, Raquel; Ibarra-Molero, Beatriz; Sanchez-Ruiz, Jose M.

2004-01-01

Understanding the screening by salts of charge-charge interactions in proteins is important for at least two reasons: a), screening by intracellular salt concentration may modulate the stability and interactions of proteins in vivo; and b), the in vitro experimental estimation of the contributions from charge-charge interactions to molecular processes involving proteins is generally carried out on the basis of the salt effect on process energetics, under the assumption that these interactions are screened out by moderate salt concentrations. Here, we explore experimentally the extent to which the screening efficiency depends on the nature of the salt. To this end, we have carried out an energetic characterization of the effect of NaCl (a nondenaturing salt), guanidinium chloride (a denaturing salt), and guanidinium thiocyanate (a stronger denaturant) on the stability of the wild-type form and a T14K variant of Escherichia coli thioredoxin. Our results suggest that the efficiency of different salts to screen charge-charge interactions correlates with their denaturing strength and with the position of the constituent ions in the Hofmeister rankings. This result appears consistent with the plausible relation of the Hofmeister rankings with the extent of solute accumulation/exclusion from protein surfaces. PMID:15041679

Topography of funneled landscapes determines the thermodynamics and kinetics of protein folding

PubMed Central

Wang, Jin; Oliveira, Ronaldo J.; Chu, Xiakun; Whitford, Paul C.; Chahine, Jorge; Han, Wei; Wang, Erkang; Onuchic, José N.; Leite, Vitor B.P.

2012-01-01

The energy landscape approach has played a fundamental role in advancing our understanding of protein folding. Here, we quantify protein folding energy landscapes by exploring the underlying density of states. We identify three quantities essential for characterizing landscape topography: the stabilizing energy gap between the native and nonnative ensembles δE, the energetic roughness ΔE, and the scale of landscape measured by the entropy S. We show that the dimensionless ratio between the gap, roughness, and entropy of the system accurately predicts the thermodynamics, as well as the kinetics of folding. Large Λ implies that the energy gap (or landscape slope towards the native state) is dominant, leading to more funneled landscapes. We investigate the role of topological and energetic roughness for proteins of different sizes and for proteins of the same size, but with different structural topologies. The landscape topography ratio Λ is shown to be monotonically correlated with the thermodynamic stability against trapping, as characterized by the ratio of folding temperature versus trapping temperature. Furthermore, Λ also monotonically correlates with the folding kinetic rates. These results provide the quantitative bridge between the landscape topography and experimental folding measurements. PMID:23019359

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

PubMed

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

2012-12-28

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

Analysis of inter-residue contacts reveals folding stabilizers in P-loops of potassium, sodium, and TRPV channels.

PubMed

Korkosh, V S; Zhorov, B S; Tikhonov, D B

2016-05-01

The family of P-loop channels includes potassium, sodium, calcium, cyclic nucleotide-gated and TRPV channels, as well as ionotropic glutamate receptors. Despite vastly different physiological and pharmacological properties, the channels have structurally conserved folding of the pore domain. Furthermore, crystallographic data demonstrate surprisingly similar mutual disposition of transmembrane and membrane-diving helices. To understand determinants of this conservation, here we have compared available high-resolution structures of sodium, potassium, and TRPV1 channels. We found that some residues, which are in matching positions of the sequence alignment, occur in different positions in the 3D alignment. Surprisingly, we found 3D mismatches in well-packed P-helices. Analysis of energetics of individual residues in Monte Carlo minimized structures revealed cyclic patterns of energetically favorable inter- and intra-subunit contacts of P-helices with S6 helices. The inter-subunit contacts are rather conserved in all the channels, whereas the intra-subunit contacts are specific for particular types of the channels. Our results suggest that these residue-residue contacts contribute to the folding stabilization. Analysis of such contacts is important for structural and phylogenetic studies of homologous proteins.

PKSOI Bulletin. Volume 1, Issue 2, February 2009

DTIC Science & Technology

2009-02-01

pose a threat to U.S. foreign policy, security, or eco - nomic interests. In a complementary manner, the U.S. Army defines “stability operations...plenty of advice on domestic and international priorities; making stabi- lization programs more effective may not be a front burner item, but as a

Structure-based Understanding of Binding Affinity and Mode of Estrogen Receptor α Agonists and Antagonists.

EPA Science Inventory

The flexible hydrophobic ligand binding pocket (LBP) of estrogen receptor α (ERα) allows the binding of a wide variety of endocrine disruptors. Upon ligand binding, the LBP reshapes around the contours of the ligand and stabilizes the complex by complementary hydrophobic interact...

Structure-Based Understanding of Binding Affinity and Mode of Estrogen Receptor α Agonists and Antagonists

EPA Science Inventory

The flexible hydrophobic ligand binding pocket (LBP) of estrogen receptor α (ERα) allows the binding of a wide variety of endocrine disruptors. Upon ligand binding, the LBP reshapes around the contours of the ligand and stabilizes the complex by complementary hydrophobic interact...

Nanostructure Formation by controlled dewetting on patterned substrates: A combined theoretical, modeling and experimental study.

PubMed

Lu, Liang-Xing; Wang, Ying-Min; Srinivasan, Bharathi Madurai; Asbahi, Mohamed; Yang, Joel K W; Zhang, Yong-Wei

2016-09-01

We perform systematic two-dimensional energetic analysis to study the stability of various nanostructures formed by dewetting solid films deposited on patterned substrates. Our analytical results show that by controlling system parameters such as the substrate surface pattern, film thickness and wetting angle, a variety of equilibrium nanostructures can be obtained. Phase diagrams are presented to show the complex relations between these system parameters and various nanostructure morphologies. We further carry out both phase field simulations and dewetting experiments to validate the analytically derived phase diagrams. Good agreements between the results from our energetic analyses and those from our phase field simulations and experiments verify our analysis. Hence, the phase diagrams presented here provide guidelines for using solid-state dewetting as a tool to achieve various nanostructures.

The impact of electron correlations on the energetics and stability of silicon nanoclusters

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

Matsko, N. L.; Baturin, V. S.; Lepeshkin, S. V.

2016-08-21

The first-principles prediction of stable nanocluster structure is often hampered by the existence of many isomer configurations with energies close to the ground state. This fact attaches additional importance to many-electron effects beyond density functional theory (DFT), because their contributions can change a subtle energy order of competitive structures. To analyze this problem, we consider, as an example, the energetics of silicon nanoclusters passivated by hydrogen Si{sub 10}H{sub 2n} (0 ≤ n ≤ 11), where passivation changes the structure from compact to loosely packed and branched. Our calculations performed with DFT, hybrid functionals, and Hartree-Fock methods, as well as bymore » the GW approximation, confirm a considerable sensitivity of isomer energy ordering to many-electron effects.« less

Complexation of C60 fullerene with aromatic drugs.

PubMed

Evstigneev, Maxim P; Buchelnikov, Anatoly S; Voronin, Dmitry P; Rubin, Yuriy V; Belous, Leonid F; Prylutskyy, Yuriy I; Ritter, Uwe

2013-02-25

The contributions of various physical factors to the energetics of complexation of aromatic drug molecules with C(60) fullerene are investigated in terms of the calculated magnitudes of equilibrium complexation constants and the components of the net Gibbs free energy. Models of complexation are developed taking into account the polydisperse nature of fullerene solutions in terms of the continuous or discrete (fractal) aggregation of C(60) molecules. Analysis of the energetics has shown that stabilization of the ligand-fullerene complexes in aqueous solution is mainly determined by intermolecular van der Waals interactions and, to lesser extent, by hydrophobic interactions. The results provide a physicochemical basis for a potentially new biotechnological application of fullerenes as modulators of biological activity of aromatic drugs. Copyright © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Interaction between solar energetic particles and interplanetary grains

NASA Astrophysics Data System (ADS)

Strazzulla, G.; Calcagno, L.; Foti, G.; Sheng, K. L.

Some laboratory-studied effects induced by the fluence of fast ions on frosts of astrophysical interest are summarized. The results are applied to the interaction between energetic solar ions and interplanetary dust grains assumed to be cometary debris which spends about one-million yr before being collected in the earth's atmosphere or colliding on the moon's surface. The importance of erosion by particles to the stability of ice grains is confirmed. The build up of carbonaceous material by ion fluence on hydrocarbon containing grains is discussed. It is suggested that these new materials could be the glue which cements submicron silicate particles to form a complex agglomeration whose density increases with increasing proton fluence (packing effect). The IR spectra of laboratory synthesized carbonaceous material are compared with those observed in some carbonaceous meteoritic extracts.

An ab initio molecular orbital study of the mechanism for the gas-phase water-mediated decomposition and the formation of hydrates of peroxyacetyl nitrate (PAN).

PubMed

Li, Yumin; Francisco, Joseph S

2005-08-31

There is uncertainty in the mechanism for the hydrolysis of peroxyacetyl nitrate (PAN), and experimental attempts to detect products of the direct reaction have been unsuccessful. Ab initio calculations are used to examine the energetics of water-mediated decomposition of gas-phase PAN into acetic acid and peroxynitric acid. On the basis of ab initio calculations, an alternative reaction mechanism for the decomposition of PAN is proposed. The calculations indicate that the barrier for one water addition to PAN is large. However, including additional water molecules reveals a substantially lower energy route. The calculations suggest that the formation of PAN hydrate complexes are energetically favorable and stable. Additional waters are increasingly efficient at stabilizing hydrated PAN.

Influence of ICRF heating on the stability of TAEs

NASA Astrophysics Data System (ADS)

Sears, J.; Burke, W.; Parker, R. R.; Snipes, J. A.; Wolfe, S.

2007-11-01

Unstable toroidicity-induced Alfv'en eigenmodes (TAEs) can appear spontaneously due to resonant interaction with fast particles such as fusion alphas, raising concern that TAEs may threaten ITER performance. This work investigates the progression of stable TAE damping rates toward instability during a scan of ICRF heating power up to 3.1 MW. Stable eigenmodes are identified in Alcator C-Mod by the Active MHD diagnostic. Unstable TAEs are observed to appear spontaneously in C-Mod limited L-mode plasmas at sufficient tail energies generated by >3 MW of ICRF heating. However preliminary analysis of experiments with moderate ICRF heating power show that TAE stability may not simply degrade with overall fast particle content. There are hints that the stability of some TAEs may be enhanced in the presence of fast particle distribution tails. Furthermore, the radial profile of the energetic particle distribution relative to the safety factor profile affects the ICRF power influence on TAE stability.

Thermodynamic signature of secondary nano-emulsion formation by isothermal titration calorimetry.

PubMed

Fotticchia, Iolanda; Fotticchia, Teresa; Mattia, Carlo Andrea; Netti, Paolo Antonio; Vecchione, Raffaele; Giancola, Concetta

2014-12-09

The stabilization of oil in water nano-emulsions by means of a polymer coating is extremely important; it prolongs the shelf life of the product and makes it suitable for a variety of applications ranging from nutraceutics to cosmetics and pharmaceutics. To date, an effective methodology to assess the best formulations in terms of thermodynamic stability has yet to be designed. Here, we perform a complete physicochemical characterization based on isothermal titration calorimetry (ITC) compared to conventional dynamic light scattering (DLS) to identify polymer concentration domains that are thermodynamically stable and to define the degree of stability through thermodynamic functions depending upon any relevant parameter affecting the stability itself, such as type of polymer coating, droplet distance, etc. For instance, the method was proven by measuring the energetics in the case of two different biopolymers, chitosan and poly-L-lysine, and for different concentrations of the emulsion coated with poly-L-lysine.

Energetics and Dynamics of Dissociation of Deprotonated Peptides: Fragmentation of Angiotensin Analogs

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

Laskin, Julia; Yang, Zhibo

2011-12-01

We present a first study of the energetics and dynamics of dissociation of deprotonated peptides using time- and collision-energy resolved surface-induced dissociation (SID) experiments. SID of four model peptides: RVYIHPF, HVYIHPF, DRVYIHPF, and DHVYIHPF was studied using a specially designed Fourier transform ion cyclotron resonance mass spectrometer (FT-ICR MS) configured for studying ion-surface collisions. Energy and entropy effects for the overall decomposition of the precursor ion were deduced by modeling the time- and collision energy-resolved survival curves using an RRKM based approach developed in our laboratory. The results were compared to the energetics and dynamics of dissociation of the correspondingmore » protonated species. We demonstrate that acidic peptides are less stable in the negative mode because of the low threshold associated with the kinetically hindered loss of H2O from [M-H]- ions. Comparison between the two basic peptides indicates that the lower stability of the [M-H]- ion of RVYIHPF as compared to HVYIHPF towards fragmentation is attributed to the differences in fragmentation mechanisms. Specifically, threshold energy associated with losses of NH3 and NHCNH from RVYIHPF is lower than the barrier for backbone fragmentation that dominates gas-phase decomposition of HVYIHPF. The results provide a first quantitative comparison between the energetics and dynamics of dissociation of [M+H]+ and [M-H]- ions of acidic and basic peptides.« less

Successful Stabilization of Graphene Oxide in Electrolyte Solutions: Enhancement of Bio-functionalization and Cellular Uptake

PubMed Central

Hong, Bong Jin; Compton, Owen C.; An, Zhi; Eryzazici, Ibrahim; Nguyen, SonBinh T.

2013-01-01

Aqueous dispersions of graphene oxide are inherently unstable in the presence of electrolytes, which screen the electrostatic surface charge on these nanosheets and induce irreversible aggregation. Two complementary strategies, utilizing either electrostatic or steric stabilization, have been developed to enhance the stability of graphene oxide in electrolyte solutions, allowing it to stay dispersed in cell culture media and serum. The electrostatic stabilization approach entails further oxidation of graphene oxide to low C/O ratio (~1.03) and increases ionic tolerance of these nanosheets. The steric stabilization technique employs an amphiphilic block copolymer that serves as a non-covalently bound surfactant to minimize the aggregate-induced nanosheets-nanosheet interactions. Both strategies can stabilize graphene oxide nanosheets with large dimensions (>300 nm) in biological media, allowing for an enhancement of >250% in the bioconjugation efficiency of streptavidin in comparison to untreated nanosheets. Notably, both strategies allow the stabilized nanosheets to be readily uptake by cells, demonstrating their excellent performance as potential drug delivery vehicles. PMID:22017285

Turbulent transport stabilization by ICRH minority fast ions in low rotating JET ILW L-mode plasmas

NASA Astrophysics Data System (ADS)

Bonanomi, N.; Mantica, P.; Di Siena, A.; Delabie, E.; Giroud, C.; Johnson, T.; Lerche, E.; Menmuir, S.; Tsalas, M.; Van Eester, D.; Contributors, JET

2018-05-01

The first experimental demonstration that fast ion induced stabilization of thermal turbulent transport takes place also at low values of plasma toroidal rotation has been obtained in JET ILW (ITER-like wall) L-mode plasmas with high (3He)-D ICRH (ion cyclotron resonance heating) power. A reduction of the gyro-Bohm normalized ion heat flux and higher values of the normalized ion temperature gradient have been observed at high ICRH power and low NBI (neutral beam injection) power and plasma rotation. Gyrokinetic simulations indicate that ITG (ion temperature gradient) turbulence stabilization induced by the presence of high-energetic 3He ions is the key mechanism in order to explain the experimental observations. Two main mechanisms have been identified to be responsible for the turbulence stabilization: a linear electrostatic wave-fast particle resonance mechanism and a nonlinear electromagnetic mechanism. The dependence of the stabilization on the 3He distribution function has also been studied.

Unfolding energetics and stability of banana lectin.

PubMed

Gupta, Garima; Sinha, Sharmistha; Surolia, Avadhesha

2008-08-01

The unfolding pathway of banana lectin from Musa paradisiaca was determined by isothermal denaturation induced by the chaotrope GdnCl. The unfolding was found to be a reversible process. The data obtained by isothermal denaturation provided information on conformational stability of banana lectin. The high values of DeltaG of unfolding at various temperatures indicated the strength of intersubunit interactions. It was found that banana lectin is a very stable and denatures at high chaotrope concentrations only. The basis of the stability may be attributed to strong hydrogen bonds of the order 2.5-3.1 A at the dimeric interface along with the presence of water bridges. This is perhaps very unique example in proteins where subunit association is not a consequence of the predominance of hydrophobic interactions. (c) 2008 Wiley-Liss, Inc.

Point defect stability in a semicoherent metallic interface

NASA Astrophysics Data System (ADS)

González, C.; Iglesias, R.; Demkowicz, M. J.

2015-02-01

We present a comprehensive density functional theory (DFT) -based study of different aspects of one vacancy and He impurity atom behavior at semicoherent interfaces between the low-solubility transition metals Cu and Nb. Such interfaces have not been previously modeled using DFT. A thorough analysis of the stability and mobility of the two types of defects at the interfaces and neighboring internal layers has been performed and the results have been compared to the equivalent cases in the pure metallic matrices. The different behavior of fcc and bcc metals on both sides of the interface has been specifically assessed. The modeling effort undertaken is the first attempt to study the stability and defect energetics of noncoherent Cu/Nb interfaces from first principles, in order to assess their potential use in radiation-resistant materials.

Plasma-resistivity-induced strong damping of the kinetic resistive wall mode.

PubMed

He, Yuling; Liu, Yueqiang; Liu, Yue; Hao, Guangzhou; Wang, Aike

2014-10-24

An energy-principle-based dispersion relation is derived for the resistive wall mode, which incorporates both the drift kinetic resonance between the mode and energetic particles and the resistive layer physics. The equivalence between the energy-principle approach and the resistive layer matching approach is first demonstrated for the resistive plasma resistive wall mode. As a key new result, it is found that the resistive wall mode, coupled to the favorable average curvature stabilization inside the resistive layer (as well as the toroidal plasma flow), can be substantially more stable than that predicted by drift kinetic theory with fast ion stabilization, but with the ideal fluid assumption. Since the layer stabilization becomes stronger with decreasing plasma resistivity, this regime is favorable for reactor scale, high-temperature fusion devices.

ON THE LEUKOCYTIC REACTION AND IMMUNOLOGICAL INDICES IN RABBITS SUBJECTED TO THE ACTION OF X-RAYS (in Russian)

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

Starkova, T.G.; Shuvalova, E.P.; Soldatova, V.M.

1961-12-01

The influence of x radiation (500 r) on various immunobiological reactions in rabbits (leukocyte reactions, plasma stability, serum fraction, and aglutaric, complementary, and preventive properties) was studied. The resuits show a reduced number of leukocytes accompanied by a reduced number of phagocytes in relation to dysentery and typhoid bacteria. Plasma stability is disturbed by a reduction in albumin and an increase in alpha globin. However, the blood serum in irradiated animals retained its preventtve properties with reduced titer. (R.V.J.)

Rupture of DNA aptamer: New insights from simulations

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

Mishra, Rakesh Kumar; Nath, Shesh; Kumar, Sanjay

2015-10-28

Base-pockets (non-complementary base-pairs) in a double-stranded DNA play a crucial role in biological processes. Because of thermal fluctuations, it can lower the stability of DNA, whereas, in case of DNA aptamer, small molecules, e.g., adenosinemonophosphate and adenosinetriphosphate, form additional hydrogen bonds with base-pockets termed as “binding-pockets,” which enhance the stability. Using the Langevin dynamics simulations of coarse grained model of DNA followed by atomistic simulations, we investigated the influence of base-pocket and binding-pocket on the stability of DNA aptamer. Striking differences have been reported here for the separation induced by temperature and force, which require further investigation by single moleculemore » experiments.« less

Solvent effects in acid-catalyzed dehydration of the Diels-Alder cycloadduct between 2,5-dimethylfuran and maleic anhydride

NASA Astrophysics Data System (ADS)

Salavati-fard, Taha; Caratzoulas, Stavros; Doren, Douglas J.

2017-03-01

Dehydration of the cycloadduct produced from the Diels-Alder reaction between 2,5-dimethylfuran and maleic anhydride to 3,6-dimethylphthalic anhydride exemplifies an important step in producing platform chemicals from biomass. The mechanisms of dehydration and catalytic effects of Lewis and Brønsted acids are investigated with density functional theory. The uncatalyzed reaction has a very high activation barrier (68.7 kcal/mol) in the gas phase and it is not significantly affected by solvation. With a Lewis acid catalyst, modeled as an alkali ion, the activation barriers are reduced, but intermediates are also stabilized. The net effect in vacuum is that the energetic span, or apparent activation energy of the catalytic cycle, is 77.9 kcal/mol, even higher than the barrier in the uncatalyzed case. In solution, however, the energetic span is reduced by as much as 20 kcal/mol, due to differences in the solvation energy of the transition states and intermediates. In the case of a Brønsted acid catalyst, modeled as a proton, the gas phase transition state energies are reduced even more than in the Lewis acid case, and there is no strong stabilization of the intermediates. The energetic span in vacuum is only 13.8 kcal/mol and is reduced even further in solution. Brønsted acid catalysis appears to be the preferred mechanism for dehydration of this cycloadduct. Since the Diels-Alder reaction that produced the molecule has previously been shown to be catalyzed by Brønsted acids, this suggests that a single catalyst could be used to accelerate both steps.

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

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

DOE PAGES

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

2017-10-17

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

Endohedral fullerenes contaning transition-metal clusters

NASA Astrophysics Data System (ADS)

Bhusal, Shusil; Basurto, Luis; Zope, Rajendra; Baruah, Tunna

We report detailed investigation of structural, electronic, and spectroscopic properties of VSc2N-containing fullerenes in the size range C68 - C96. First, the candidate structures of the ground state are obtained using a systematic approach in which a large number of isomers of endohedral fullerenes were screened for their energetic stability. Stability of some of the most promising isomers were further studied using density functional theory at the all-electron level using large polarized Gaussian basis sets. The effect of the V doping is examined on the structure, spin states and the magnetic properties of the endohedral fullerenes. De-SC0002168, NSF-DMR 125302, DE-SC0006818.

Computational evidence for stable inorganic fullerene-like structures of ceramic and semiconductor materials

NASA Astrophysics Data System (ADS)

Chang, Ch; Patzer, A. B. C.; Sedlmayr, E.; Steinke, T.; Sülzle, D.

2001-12-01

Theoretical electronic structure techniques have become an indispensible and powerful means for predicting molecular properties and designing new materials. Based on a density functional approach and guided by geometric considerations we provide evidence for some specific inorganic fullerene-like cage molecules of ceramic and semiconductor materials which exhibit high energetic stability and point group symmetry as well as nearly perfect spherical shape.

Energy & Energetics

DTIC Science & Technology

2012-06-22

mechanical and structural failure and decomposition in ultra-fast time regimes. Our research teams are exploring novel ways to convert mechanical ...energy to thermal energy by examining initiation mechanisms , multi-phase combustion, detonation and the mechanisms that lead to the release of energy...understanding of the mechanisms of structural stability by doping Fe in LiCoPO4 and effectiveness of HFiP in stopping further oxidation of electrolytes are

Research@ARL: Energy & Energetics

DTIC Science & Technology

2012-06-01

enabling us to probe chemical, mechanical and structural failure and decomposition in ultra-fast time regimes. Our research teams are exploring novel ways...to convert mechanical energy to thermal energy by examining initiation mechanisms , multi-phase combustion, detonation and the mechanisms that lead...storage life. The understanding of the mechanisms of structural stability by doping Fe in LiCoPO4 and effectiveness of HFiP in stopping further

Physical and Chemical Toeholds for Exoplanet Bioastronomy

NASA Technical Reports Server (NTRS)

Hoehler, Tori

2013-01-01

If a search for exoplanet life were mounted today, the likely focus would be to detect oxygen (or ozone) in the atmosphere of a water-bearing rocky planet orbiting roughly 1AU from a G-type star. This appropriately conservative and practical default is necessary in large part because biological input on the question of where and how to look for life has progressed little beyond a purely empirical reliance on the example of terrestrial biology. However, fundamental physical and chemical considerations may impose significant yet universal constraints on biological potential. The liquid water + oxygen paradigm will be considered as an example, with a focus on the question, is liquid water a prerequisite for life? . Life requires a solvent to mediate interactions among biological molecules. A key class of these interactions is molecular recognition with high specificity, which is essential for high fidelity catalysis and (especially) information processing. For example, to correctly reproduce a string consisting of 600,000 units of information (e.g., 600 kilobases, equivalent to the genome of the smallest free living terrestrial organisms) with a 90% success rate requires specificity greater than 10(exp 7):1 for the target molecule vs. incorrect alternatives. Such specificity requires (i) that the correct molecular association is energetically stabilized by at least 40 kJ/mol relative to alternatives, and (ii) that the system is able to sample among possible states (alternative molecular associations) rapidly enough to allow the system to fall under thermodynamic control and express the energetic stabilization. We argue that electrostatic interactions are required to confer the necessary energetic stabilization vs. a large library of molecular alternatives, and that a solvent with polarity and dielectric properties comparable to water is required for the system to sample among possible states and express thermodynamic control. Electrostatic associations can be made in non-polar solvents, but the resulting complexes are too stable to be "unmade" with sufficient frequency to confer thermodynamic control on the system. Such considerations suggest that water, or a solvent with properties very like water, is necessary to support high-fidelity information processing a feature that must be common to all biology and can therefore be considered a critical prerequisite for life.

DNA–DNA kissing complexes as a new tool for the assembly of DNA nanostructures

PubMed Central

Barth, Anna; Kobbe, Daniela; Focke, Manfred

2016-01-01

Kissing-loop annealing of nucleic acids occurs in nature in several viruses and in prokaryotic replication, among other circumstances. Nucleobases of two nucleic acid strands (loops) interact with each other, although the two strands cannot wrap around each other completely because of the adjacent double-stranded regions (stems). In this study, we exploited DNA kissing-loop interaction for nanotechnological application. We functionalized the vertices of DNA tetrahedrons with DNA stem-loop sequences. The complementary loop sequence design allowed the hybridization of different tetrahedrons via kissing-loop interaction, which might be further exploited for nanotechnology applications like cargo transport and logical elements. Importantly, we were able to manipulate the stability of those kissing-loop complexes based on the choice and concentration of cations, the temperature and the number of complementary loops per tetrahedron either at the same or at different vertices. Moreover, variations in loop sequences allowed the characterization of necessary sequences within the loop as well as additional stability control of the kissing complexes. Therefore, the properties of the presented nanostructures make them an important tool for DNA nanotechnology. PMID:26773051

Comparison of conductor and dielectric inks in printed organic complementary transistors

NASA Astrophysics Data System (ADS)

Ng, Tse Nga; Mei, Ping; Whiting, Gregory L.; Schwartz, David E.; Abraham, Biby; Wu, Yiliang; Veres, Janos

2014-10-01

Two types of printable conductor and a bilayer gate dielectric are evaluated for use in all-additive, inkjetprinted complementary OTFTs. The Ag nanoparticle ink based on nonpolar alkyl amine surfactant or stabilizer enables good charge injection into p-channel devices, but this ink also leaves residual stabilizer that modifies the transistor backchannel and shifts the turn-on voltage to negative values. The Ag ink based on polar solvent requires dopant modification to improve charge injection to p-channel devices, but this ink allows the OTFT turn-on voltage to be close to 0 V. The reverse trend is observed for n-channel OTFTs. For gate insulator, a bilayer dielectric is demonstrated that combines the advantages of two types of insulator materials, in which a fluoropolymer reduces dipolar disorder at the semiconductor-dielectric interface, while a high-k PVDF terpolymer dielectric facilitates high gate capacitance. The dielectric is incorporated into an inverter and a three-stage ring oscillator, and the resulting circuits were demonstrated to operate at a supply voltage as low as 2 V, with bias stress levels comparable to circuits with other types of dielectrics.

Complementary activities of TPX2 and chTOG constitute an efficient importin-regulated microtubule nucleation module.

PubMed

Roostalu, Johanna; Cade, Nicholas I; Surrey, Thomas

2015-11-01

Spindle assembly and function require precise control of microtubule nucleation and dynamics. The chromatin-driven spindle assembly pathway exerts such control locally in the vicinity of chromosomes. One of the key targets of this pathway is TPX2. The molecular mechanism of how TPX2 stimulates microtubule nucleation is not understood. Using microscopy-based dynamic in vitro reconstitution assays with purified proteins, we find that human TPX2 directly stabilizes growing microtubule ends and stimulates microtubule nucleation by stabilizing early microtubule nucleation intermediates. Human microtubule polymerase chTOG (XMAP215/Msps/Stu2p/Dis1/Alp14 homologue) only weakly promotes nucleation, but acts synergistically with TPX2. Hence, a combination of distinct and complementary activities is sufficient for efficient microtubule formation in vitro. Importins control the efficiency of the microtubule nucleation by selectively blocking the interaction of TPX2 with microtubule nucleation intermediates. This in vitro reconstitution reveals the molecular mechanism of regulated microtubule formation by a minimal nucleation module essential for chromatin-dependent microtubule nucleation in cells.

Wave Energetics of the Atmosphere of Mars

NASA Astrophysics Data System (ADS)

Battalio, Joseph Michael

A comprehensive assessment of the energetics of transient waves is presented for the atmosphere of Mars using the Mars Analysis Correction Data Assimilation (MACDA) dataset (v1.0) and the eddy kinetic energy equation. Each hemisphere is divided into four representative periods covering the summer and winter solstices, a late fall period, and an early spring period for each of the three Mars years available. Northern hemisphere fall and spring eddy energetics is similar with some inter-annual and inter-seasonal variability, but winter eddy kinetic energy and its transport are strongly reduced in intensity as a result of the winter solstitial pause in wave activity. Barotropic energy conversion acts as a sink of eddy kinetic energy throughout each year with little reduction in amplitude during the solstitial pause. Baroclinic energy conversion acts as a source in fall and spring but disappears during the winter period as a result of the stabilized vertical temperature profile around winter solstice. Traveling waves are typically triggered by geopotential flux convergence. Individual waves decay through a combination of barotropic conversion of the kinetic energy from the waves to the mean flow, geopotential flux divergence, and dissipation. The southern hemisphere energetics is similar to the northern hemisphere in timing, but wave energetics is much weaker as a result of the high and zonally asymmetric topography. The effect of dust on baroclinic instability is examined by comparing a year with a global-scale dust storm (GDS) to two years without a GDS. In the GDS year, waves develop a mixed baroclinic/barotropic growth phase before decaying barotropically. Though the total amount of eddy kinetic energy generated by baroclinic energy conversion is lower during the GDS year, the maximum eddy intensity is not diminished. Instead, the number of intense eddies is reduced by about 50%.

Structural energetics of the adenine tract from an intrinsic transcription terminator.

PubMed

Huang, Yuegao; Weng, Xiaoli; Russu, Irina M

2010-04-02

Intrinsic transcription termination sites generally contain a tract of adenines in the DNA template that yields a tract of uracils at the 3' end of the nascent RNA. To understand how this base sequence contributes to termination of transcription, we have investigated two nucleic acid structures. The first is the RNA-DNA hybrid that contains the uracil tract 5'-rUUUUUAU-3' from the tR2 intrinsic terminator of bacteriophage lambda. The second is the homologous DNA-DNA duplex that contains the adenine tract 5'-dATAAAAA-3'. This duplex is present at the tR2 site when the DNA is not transcribed. The opening and the stability of each rU-dA/dT-dA base pair in the two structures are characterized by imino proton exchange and nuclear magnetic resonance spectroscopy. The results reveal concerted opening of the central rU-dA base pairs in the RNA-DNA hybrid. Furthermore, the stability profile of the adenine tract in the RNA-DNA hybrid is very different from that of the tract in the template DNA-DNA duplex. In the RNA-DNA hybrid, the stabilities of rU-dA base pairs range from 4.3 to 6.5 kcal/mol (at 10 degrees C). The sites of lowest stability are identified at the central positions of the tract. In the template DNA-DNA duplex, the dT-dA base pairs are more stable than the corresponding rU-dA base pairs in the hybrid by 0.9 to 4.6 kcal/mol and, in contrast to the RNA-DNA hybrid, the central base pairs have the highest stability. These results suggest that the central rU-dA/dT-dA base pairs in the adenine tract make the largest energetic contributions to transcription termination by promoting both the dissociation of the RNA transcript and the closing of the transcription bubble. The results also suggest that the high stability of dT-dA base pairs in the DNA provides a signal for the pausing of RNA polymerase at the termination site. Copyright 2010 Elsevier Ltd. All rights reserved.

Chirality- and sequence-selective successive self-sorting via specific homo- and complementary-duplex formations

PubMed Central

Makiguchi, Wataru; Tanabe, Junki; Yamada, Hidekazu; Iida, Hiroki; Taura, Daisuke; Ousaka, Naoki; Yashima, Eiji

2015-01-01

Self-recognition and self-discrimination within complex mixtures are of fundamental importance in biological systems, which entirely rely on the preprogrammed monomer sequences and homochirality of biological macromolecules. Here we report artificial chirality- and sequence-selective successive self-sorting of chiral dimeric strands bearing carboxylic acid or amidine groups joined by chiral amide linkers with different sequences through homo- and complementary-duplex formations. A mixture of carboxylic acid dimers linked by racemic-1,2-cyclohexane bis-amides with different amide sequences (NHCO or CONH) self-associate to form homoduplexes in a completely sequence-selective way, the structures of which are different from each other depending on the linker amide sequences. The further addition of an enantiopure amide-linked amidine dimer to a mixture of the racemic carboxylic acid dimers resulted in the formation of a single optically pure complementary duplex with a 100% diastereoselectivity and complete sequence specificity stabilized by the amidinium–carboxylate salt bridges, leading to the perfect chirality- and sequence-selective duplex formation. PMID:26051291

Complementary p- and n-type polymer doping for ambient stable graphene inverter.

PubMed

Yun, Je Moon; Park, Seokhan; Hwang, Young Hwan; Lee, Eui-Sup; Maiti, Uday; Moon, Hanul; Kim, Bo-Hyun; Bae, Byeong-Soo; Kim, Yong-Hyun; Kim, Sang Ouk

2014-01-28

Graphene offers great promise to complement the inherent limitations of silicon electronics. To date, considerable research efforts have been devoted to complementary p- and n-type doping of graphene as a fundamental requirement for graphene-based electronics. Unfortunately, previous efforts suffer from undesired defect formation, poor controllability of doping level, and subtle environmental sensitivity. Here we present that graphene can be complementary p- and n-doped by simple polymer coating with different dipolar characteristics. Significantly, spontaneous vertical ordering of dipolar pyridine side groups of poly(4-vinylpyridine) at graphene surface can stabilize n-type doping at room-temperature ambient condition. The dipole field also enhances and balances the charge mobility by screening the impurity charge effect from the bottom substrate. We successfully demonstrate ambient stable inverters by integrating p- and n-type graphene transistors, which demonstrated clear voltage inversion with a gain of 0.17 at a 3.3 V input voltage. This straightforward polymer doping offers diverse opportunities for graphene-based electronics, including logic circuits, particularly in mechanically flexible form.

Interplay between intramolecular and intermolecular structures of 1,1,2,2-tetrachloro-1,2-difluoroethane

NASA Astrophysics Data System (ADS)

Rovira-Esteva, M.; Murugan, N. A.; Pardo, L. C.; Busch, S.; Tamarit, J. Ll.; Pothoczki, Sz.; Cuello, G. J.; Bermejo, F. J.

2011-08-01

We report on the interplay between the short-range order of molecules in the liquid phase of 1,1,2,2-tetrachloro-1,2-difluoroethane and the possible molecular conformations, trans and gauche. Two complementary approaches have been used to get a comprehensive picture: analysis of neutron-diffraction data by a Bayesian fit algorithm and a molecular dynamics simulation. The results of both show that the population of trans and gauche conformers in the liquid state can only correspond to the gauche conformer being more stable than the trans conformer. Distinct conformer geometries induce distinct molecular short-range orders around them, suggesting that a deep intra- and intermolecular interaction coupling is energetically favoring one of the conformers by reducing the total molecular free energy.

Jupiter radio bursts and particle acceleration

NASA Technical Reports Server (NTRS)

Desch, Michael D.

1994-01-01

Particle acceleration processes are important in understanding many of the Jovian radio and plasma wave emissions. However, except for the high-energy electrons that generate synchrotron emission following inward diffusion from the outer magnetosphere, acceleration processes in Jupiter's magnetosphere and between Jupiter and Io are poorly understood. We discuss very recent observations from the Ulysses spacecraft of two new Jovian radio and plamas wave emissions in which particle acceleration processes are important and have been addressed directly by complementary investigations. First, radio bursts known as quasi-periodic bursts have been observed in close association with a population of highly energetic electrons. Second, a population of much lower energy (keV range) electrons on auroral field lines can be shown to be responsible for the first observation of a Jovian plasma wave emission known as auroral hiss.

Hydrogen molecules inside fullerene C70: quantum dynamics, energetics, maximum occupancy, and comparison with C60.

PubMed

Sebastianelli, Francesco; Xu, Minzhong; Bacić, Zlatko; Lawler, Ronald; Turro, Nicholas J

2010-07-21

Recent synthesis of the endohedral complexes of C(70) and its open-cage derivative with one and two H(2) molecules has opened the path for experimental and theoretical investigations of the unique dynamic, spectroscopic, and other properties of systems with multiple hydrogen molecules confined inside a nanoscale cavity. Here we report a rigorous theoretical study of the dynamics of the coupled translational and rotational motions of H(2) molecules in C(70) and C(60), which are highly quantum mechanical. Diffusion Monte Carlo (DMC) calculations were performed for up to three para-H(2) (p-H(2)) molecules encapsulated in C(70) and for one and two p-H(2) molecules inside C(60). These calculations provide a quantitative description of the ground-state properties, energetics, and the translation-rotation (T-R) zero-point energies (ZPEs) of the nanoconfined p-H(2) molecules and of the spatial distribution of two p-H(2) molecules in the cavity of C(70). The energy of the global minimum on the intermolecular potential energy surface (PES) is negative for one and two H(2) molecules in C(70) but has a high positive value when the third H(2) is added, implying that at most two H(2) molecules can be stabilized inside C(70). By the same criterion, in the case of C(60), only the endohedral complex with one H(2) molecule is energetically stable. Our results are consistent with the fact that recently both (H(2))(n)@C(70) (n = 1, 2) and H(2)@C(60) were prepared, but not (H(2))(3)@C(70) or (H(2))(2)@C(60). The ZPE of the coupled T-R motions, from the DMC calculations, grows rapidly with the number of caged p-H(2) molecules and is a significant fraction of the well depth of the intermolecular PES, 11% in the case of p-H(2)@C(70) and 52% for (p-H(2))(2)@C(70). Consequently, the T-R ZPE represents a major component of the energetics of the encapsulated H(2) molecules. The inclusion of the ZPE nearly doubles the energy by which (p-H(2))(3)@C(70) is destabilized and increases by 66% the energetic destabilization of (p-H(2))(2)@C(60). For these reasons, the T-R ZPE has to be calculated accurately and taken into account for reliable theoretical predictions regarding the stability of the endohedral fullerene complexes with hydrogen molecules and their maximum H(2) content.

Nanostructure Formation by controlled dewetting on patterned substrates: A combined theoretical, modeling and experimental study

PubMed Central

Lu, Liang-Xing; Wang, Ying-Min; Srinivasan, Bharathi Madurai; Asbahi, Mohamed; Yang, Joel K. W.; Zhang, Yong-Wei

2016-01-01

We perform systematic two-dimensional energetic analysis to study the stability of various nanostructures formed by dewetting solid films deposited on patterned substrates. Our analytical results show that by controlling system parameters such as the substrate surface pattern, film thickness and wetting angle, a variety of equilibrium nanostructures can be obtained. Phase diagrams are presented to show the complex relations between these system parameters and various nanostructure morphologies. We further carry out both phase field simulations and dewetting experiments to validate the analytically derived phase diagrams. Good agreements between the results from our energetic analyses and those from our phase field simulations and experiments verify our analysis. Hence, the phase diagrams presented here provide guidelines for using solid-state dewetting as a tool to achieve various nanostructures. PMID:27580943

Energy and Biocides Storage Compounds: Synthesis and Characterization of Energetic Bridged Bis(triiodoazoles).

PubMed

He, Chunlin; Zhao, Gang; Hooper, Joseph P; Shreeve, Jean'ne M

2017-11-06

Energetic bridged triiodopyrazoles and triiodoimidazoles were designed and synthsized by reacting potassium triiodopyrazolate or triiodoimidazolate with corresponding dichloro compounds. All compounds were fully characterized by 1 H and 13 C NMR spectroscopy, IR spectroscopy, and elemental analyses. The structure of compound 1 was further confirmed by single-crystal X-ray diffraction. All of the compounds exhibit good thermal stability with decomposition temperatures between 199 and 270 °C and high densities ranging from 2.804 to 3.358 g/cm 3 . The detonation performances and the detonation products were calculated by CHEETAH 7. Compound 3 (D v = 4765 m s -1 ; P = 17.9 GPa) and compound 7 (D v = 4841 m s -1 ; P = 18.5 GPa) show comparable detonation pressure to TNT, and high iodine content makes them promising as energy and biocides storage compounds.

Energetics and electronic properties of Pt wires of different topologies on monolayer MoSe{sub 2}

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

Jamdagni, Pooja, E-mail: j.poojaa1228@gmail.com; Ahluwalia, P. K.; Kumar, Ashok

2016-05-23

The energetics and electronic properties of different topology of Pt wires including linear, zigzag and ladder structures on MoSe{sub 2} monolayer have been investigated in the framework of density functional theory (DFT). The predicted order of stability of Pt wire on MoSe{sub 2} monolayer is found to be: linear > ladder > zigzag. Pt wires induce states near the Fermi level of MoSe{sub 2} that results into metallic characteristics of Pt-wire/MoSe{sub 2} assembled system. Valence band charge density signifies most of the contribution from Pt atoms near the Fermi energy of assembled wire/MoSe{sub 2} system. These findings are expected tomore » be important for the fabrication of devices based on MoSe{sub 2} layers for flexible nanoelectronics.« less

Solar radio continuum storms

NASA Technical Reports Server (NTRS)

1974-01-01

Radio noise continuum emission observed in metric and decametric wave frequencies is discussed. The radio noise is associated with actively varying sunspot groups accompanied by the S-component of microwave radio emissions. It is shown that the S-component emission in microwave frequencies generally occurs several days before the emission of the noise continuum storms of lower frequencies. It is likely that energetic electrons, 10 to 100 Kev, accelerated in association with the variation of sunspot magnetic fields, are the sources of the radio emissions. A model is considered to explain the relation of burst storms on radio noise. An analysis of the role of energetic electrons on the emissions of both noise continuum and type III burst storms is presented. It is shown that instabilities associated with the electrons and their relation to their own stabilizing effects are important in interpreting both of these storms.

The influence of sequence context and length on the kinetics of DNA duplex formation from complementary hairpins possessing (CNG) repeats.

PubMed

Paiva, Anthony M; Sheardy, Richard D

2005-04-20

The formation of unusual structures during DNA replication has been invoked for gene expansion in genomes possessing triplet repeat sequences, CNG, where N = A, C, G, or T. In particular, it has been suggested that the daughter strand of the leading strand partially dissociates from the parent strand and forms a hairpin. The equilibrium between the fully duplexed parent:daugter species and the parent:hairpin species is dependent upon their relative stabilities and the rates of reannealing of the daughter strand back to the parent. These stabilities and rates are ultimately influenced by the sequence context of the DNA and its length. Previous work has demonstrated that longer strands are more stable than shorter strands and that the identity of N also influences the thermal stability [Paiva, A. M.; Sheardy, R. D. Biochemistry 2004, 43, 14218-14227]. Here, we show that the rate of duplex formation from complementary hairpins is also sequence context and length dependent. In particular, longer duplexes have higher activation energies than shorter duplexes of the same sequence context. Further, [(CCG):(GGC)] duplexes have lower activation energies than corresponding [(CAG):(GTC)] duplexes of the same length. Hence, hairpins formed from long CNG sequences are more thermodynamically stable and have slower kinetics for reannealing to their complement than shorter analogues. Gene expansion can now be explained in terms of thermodynamics and kinetics.

Simultaneous protection of organic p- and n-channels in complementary inverter from aging and bias-stress by DNA-base guanine/Al2O3 double layer.

PubMed

Lee, Junyeong; Hwang, Hyuncheol; Min, Sung-Wook; Shin, Jae Min; Kim, Jin Sung; Jeon, Pyo Jin; Lee, Hee Sung; Im, Seongil

2015-01-28

Although organic field-effect transistors (OFETs) have various advantages of lightweight, low-cost, mechanical flexibility, and nowadays even higher mobility than amorphous Si-based FET, stability issue under bias and ambient condition critically hinder its practical application. One of the most detrimental effects on organic layer comes from penetrated atmospheric species such as oxygen and water. To solve such degradation problems, several molecular engineering tactics are introduced: forming a kinetic barrier, lowering the level of molecule orbitals, and increasing the band gap. However, direct passivation of organic channels, the most promising strategy, has not been reported as often as other methods. Here, we resolved the ambient stability issues of p-type (heptazole)/or n-type (PTCDI-C13) OFETs and their bias-stability issues at once, using DNA-base small molecule guanine (C5H5N5O)/Al2O3 bilayer. The guanine protects the organic channels as buffer/and H getter layer between the channels and capping Al2O3, whereas the oxide capping resists ambient molecules. As a result, both p-type and n-type OFETs are simultaneously protected from gate-bias stress and 30 days-long ambient aging, finally demonstrating a highly stable, high-gain complementary-type logic inverter.

Complementary effects of species and genetic diversity on productivity and stability of sown grasslands.

PubMed

Prieto, Iván; Violle, Cyrille; Barre, Philippe; Durand, Jean-Louis; Ghesquiere, Marc; Litrico, Isabelle

2015-03-30

Plant species diversity regulates the productivity(1-3) and stability(2,4) of natural ecosystems, along with their resilience to disturbance(5,6). The influence of species diversity on the productivity of agronomic systems is less clear(7-10). Plant genetic diversity is also suspected to influence ecosystem function(3,11-14), although empirical evidence is scarce. Given the large range of genotypes that can be generated per species through artificial selection, genetic diversity is a potentially important leverage of productivity in cultivated systems. Here we assess the effect of species and genetic diversity on the production and sustainable supply of livestock fodder in sown grasslands, comprising single and multispecies assemblages characterized by different levels of genetic diversity, exposed to drought and non-drought conditions. Multispecies assemblages proved more productive than monocultures when subject to drought, regardless of the number of genotypes per species present. Conversely, the temporal stability of production increased only with the number of genotypes present under both drought and non-drought conditions, and was unaffected by the number of species. We conclude that taxonomic and genetic diversity can play complementary roles when it comes to optimizing livestock fodder production in managed grasslands, and suggest that both levels of diversity should be considered in plant breeding programmes designed to boost the productivity and resilience of managed grasslands in the face of increasing environmental hazards.

Stability and kinetics of G-quadruplex structures

PubMed Central

Lane, Andrew N.; Chaires, J. Brad; Gray, Robert D.; Trent, John O.

2008-01-01

In this review, we give an overview of recent literature on the structure and stability of unimolecular G-rich quadruplex structures that are relevant to drug design and for in vivo function. The unifying theme in this review is energetics. The thermodynamic stability of quadruplexes has not been studied in the same detail as DNA and RNA duplexes, and there are important differences in the balance of forces between these classes of folded oligonucleotides. We provide an overview of the principles of stability and where available the experimental data that report on these principles. Significant gaps in the literature have been identified, that should be filled by a systematic study of well-defined quadruplexes not only to provide the basic understanding of stability both for design purposes, but also as it relates to in vivo occurrence of quadruplexes. Techniques that are commonly applied to the determination of the structure, stability and folding are discussed in terms of information content and limitations. Quadruplex structures fold and unfold comparatively slowly, and DNA unwinding events associated with transcription and replication may be operating far from equilibrium. The kinetics of formation and resolution of quadruplexes, and methodologies are discussed in the context of stability and their possible biological occurrence. PMID:18718931

Coarse gaining of molecular crystals: limitations imposed by molecular flexibility

NASA Astrophysics Data System (ADS)

Picu, Catalin; Pal, Anirban

Molecular crystals include molecular electronics, energetic materials, pharmaceuticals and some food components. In many of these applications the small scale mechanical behavior of the crystal is important such as for example in energetic materials where detonation is induced by the formation of hot spots which are induced thermomechanically, and in pharmaceuticals where phase stability is critical for the biochemical activity of the drug. Accurate modeling of these processes requires resolving the atomistic scale details of the material. However, the cost of these models is very large due to the complexity of the molecules forming the crystal, and some form of coarse graning is necessary. In this study we identify the limitations imposed by the need to accurately capture molecular flexibility on the development of coarse grained models for the energetic molecular crystal RDX. We define guidelines for the definition of coarse grained models that target elastic and plastic crystal scale properties such as elastic constants, thermal expansion, compressibility, the critical stress for the motion of dislocations (Peierls stress) and the stacking fault energy This work was supported by the ARO through Grant W911NF-09-1-0330 and AFRL through Grant FA8651-16-1-0004.

Amination of nitroazoles--a comparative study of structural and energetic properties.

PubMed

Zhao, Xiuxiu; Qi, Cai; Zhang, Lubo; Wang, Yuan; Li, Shenghua; Zhao, Fengqi; Pang, Siping

2014-01-14

In this work, 3-nitro-1H-1,2,4-triazole (1) and 3,5-dinitro-1H-pyrazole (2) were C-aminated and N-aminated using different amination agents, yielding their respective C-amino and N-amino products. All compounds were fully characterized by NMR (1H, 13C, 15N), IR spectroscopy, differential scanning calorimetry (DSC). X-ray crystallographic measurements were performed and delivered insight into structural characteristics as well as inter- and intramolecular interactions of the products. Their impact sensitivities were measured by using standard BAM fallhammer techniques and their explosive performances were computed using the EXPLO 5.05 program. A comparative study on the influence of those different amino substituents on the structural and energetic properties (such as density, stability, heat of formation, detonation performance) is presented. The results showed that the incorporation of an N-amino group into a nitroazole ring can improve nitrogen content, heat of formation and impact sensitivity, while the introduction of a C-amino group can enhance density, detonation velocity and pressure. The potential of N-amino and C-amino moieties for the design of next generation energetic materials is explored.

A charging model for three-axis stabilized spacecraft

NASA Technical Reports Server (NTRS)

Massaro, M. J.; Green, T.; Ling, D.

1977-01-01

A charging model was developed for geosynchronous, three-axis stabilized spacecraft when under the influence of a geomagnetic substorm. The differential charging potentials between the thermally coated or blanketed outer surfaces and metallic structure of a spacecraft were determined when the spacecraft was immersed in a dense plasma cloud of energetic particles. The spacecraft-to-environment interaction was determined by representing the charged particle environment by equivalent current source forcing functions and by representing the spacecraft by its electrically equivalent circuit with respect to the plasma charging phenomenon. The charging model included a sun/earth/spacecraft orbit model that simulated the sum illumination conditions of the spacecraft outer surfaces throughout the orbital flight on a diurnal as well as a seasonal basis. Transient and steady-state numerical results for a three-axis stabilized spacecraft are presented.

Space Particle Hazard Measurement and Modeling

DTIC Science & Technology

2007-11-30

the spacecraft and perturbations of the environment generated by the spacecraft. Koons et al. (1999) compiled and studied all spacecraft anomalies...unrealistic for D12 than for Dα0p). However, unlike the stability problems associated with the original cross diffusion terms, they are quite manageable ...E), to mono-energetic beams of charged particles of known energies which enables one, in principle , to unfold the space environment spectrum, j(E

Ionic Liquids as Energetic Materials

DTIC Science & Technology

2007-03-01

triazolium halide that can be synthesized from the electrophilic fluorination and quaternization of the amino-substituted triazole. Metathesis with a...silver salt such as silver nitrate forms the nitrate salt. By electrophilic difluoroamination of 1 -alkyl-3-nitro- 1,2,4-triazole, 1,4-dialkyl-3-nitro...nonaromatic salts (1-7) described in Table 1. The presence of small amounts of fluorine in the substituent arm contributes to the thermal stability and has

Modeling Giant Sawtooth Modes in DIII-D using the NIMROD code

NASA Astrophysics Data System (ADS)

Kruger, Scott; Jenkins, Thomas; Held, Eric; King, Jacob; NIMROD Team

2014-10-01

Ongoing efforts to model giant sawtooth cycles in DIII-D shot 96043 using NIMROD are summarized. In this discharge, an energetic ion population induced by RF heating modifies the sawtooth stability boundary, supplanting the conventional sawtooth cycle with longer-period giant sawtooth oscillations of much larger amplitude. NIMROD has the unique capability of being able to use both continuum kinetic and particle-in-cell numerical schemes to model the RF-induced hot-particle distribution effects on the sawtooth stability. This capability is used to numerically investigate the role played by the form of the energetic particle distribution, including a possible high-energy tail drawn out by the RF, to study the sawtooth threshold and subsequent nonlinear evolution. Equilibrium reconstructions from the experimental data are used to enable these detailed validation studies. Effects of other parameters on the sawtooth behavior (such as the plasma Lundquist number and hot-particle β-fraction) are also considered. Ultimately, we hope to assess the degree to which NIMROD's extended MHD model correctly simulates the observed linear onset and nonlinear behavior of the giant sawtooth, and to establish its reliability as a predictive modeling tool for these modes. This work was initiated by the late Dr. Dalton Schnack. Equilibria were provided by Dr. A. Turnbull of General Atomics.

Generation of monoenergetic ion beams via ionization dynamics (Conference Presentation)

NASA Astrophysics Data System (ADS)

Lin, Chen; Kim, I. Jong; Yu, Jinqing; Choi, Il Woo; Ma, Wenjun; Yan, Xueqing; Nam, Chang Hee

2017-05-01

The research on ion acceleration driven by high intensity laser pulse has attracted significant interests in recent decades due to the developments of laser technology. The intensive study of energetic ion bunches is particularly stimulated by wide applications in nuclear fusion, medical treatment, warm dense matter production and high energy density physics. However, to implement such compact accelerators, challenges are still existing in terms of beam quality and stability, especially in applications that require higher energy and narrow bandwidth spectra ion beams. We report on the acceleration of quasi-mono-energetic ion beams via ionization dynamics in the interaction of an intense laser pulse with a solid target. Using ionization dynamics model in 2D particle-in-cell (PIC) simulations, we found that high charge state contamination ions can only be ionized in the central spot area where the intensity of sheath field surpasses their ionization threshold. These ions automatically form a microstructure target with a width of few micron scale, which is conducive to generate mono-energetic beams. In the experiment of ultraintense (< 10^21 W/cm^2) laser pulses irradiating ultrathin targets each attracted with a contamination layer of nm-thickness, high quality < 100 MeV mono-energetic ion bunches are generated. The peak energy of the self-generated micro-structured target ions with respect to different contamination layer thickness is also examined This is relatively newfound respect, which is confirmed by the consistence between experiment data and the simulation results.

Guanidinium-Induced Denaturation by Breaking of Salt Bridges.

PubMed

Meuzelaar, Heleen; Panman, Matthijs R; Woutersen, Sander

2015-12-07

Despite its wide use as a denaturant, the mechanism by which guanidinium (Gdm(+) ) induces protein unfolding remains largely unclear. Herein, we show evidence that Gdm(+) can induce denaturation by disrupting salt bridges that stabilize the folded conformation. We study the Gdm(+) -induced denaturation of a series of peptides containing Arg/Glu and Lys/Glu salt bridges that either stabilize or destabilize the folded conformation. The peptides containing stabilizing salt bridges are found to be denatured much more efficiently by Gdm(+) than the peptides containing destabilizing salt bridges. Complementary 2D-infrared measurements suggest a denaturation mechanism in which Gdm(+) binds to side-chain carboxylate groups involved in salt bridges. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

How well do force fields capture the strength of salt bridges in proteins?

PubMed Central

Ahmed, Mustapha Carab; Papaleo, Elena

2018-01-01

Salt bridges form between pairs of ionisable residues in close proximity and are important interactions in proteins. While salt bridges are known to be important both for protein stability, recognition and regulation, we still do not have fully accurate predictive models to assess the energetic contributions of salt bridges. Molecular dynamics simulation is one technique that may be used study the complex relationship between structure, solvation and energetics of salt bridges, but the accuracy of such simulations depends on the force field used. We have used NMR data on the B1 domain of protein G (GB1) to benchmark molecular dynamics simulations. Using enhanced sampling simulations, we calculated the free energy of forming a salt bridge for three possible lysine-carboxylate ionic interactions in GB1. The NMR experiments showed that these interactions are either not formed, or only very weakly formed, in solution. In contrast, we show that the stability of the salt bridges is overestimated, to different extents, in simulations of GB1 using seven out of eight commonly used combinations of fixed charge force fields and water models. We also find that the Amber ff15ipq force field gives rise to weaker salt bridges in good agreement with the NMR experiments. We conclude that many force fields appear to overstabilize these ionic interactions, and that further work may be needed to refine our ability to model quantitatively the stability of salt bridges through simulations. We also suggest that comparisons between NMR experiments and simulations will play a crucial role in furthering our understanding of this important interaction.

Energetics of short hydrogen bonds in photoactive yellow protein.

PubMed

Saito, Keisuke; Ishikita, Hiroshi

2012-01-03

Recent neutron diffraction studies of photoactive yellow protein (PYP) proposed that the H bond between protonated Glu46 and the chromophore [ionized p-coumaric acid (pCA)] was a low-barrier H bond (LBHB). Using the atomic coordinates of the high-resolution crystal structure, we analyzed the energetics of the short H bond by two independent methods: electrostatic pK(a) calculations and a quantum mechanical/molecular mechanical (QM/MM) approach. (i) In the QM/MM optimized geometry, we reproduced the two short H-bond distances of the crystal structure: Tyr42-pCA (2.50 Å) and Glu46-pCA (2.57 Å). However, the H atoms obviously belonged to the Tyr or Glu moieties, and were not near the midpoint of the donor and acceptor atoms. (ii) The potential-energy curves of the two H bonds resembled those of standard asymmetric double-well potentials, which differ from those of LBHB. (iii) The calculated pK(a) values for Glu46 and pCA were 8.6 and 5.4, respectively. The pK(a) difference was unlikely to satisfy the prerequisite for LBHB. (iv) The LBHB in PYP was originally proposed to stabilize the ionized pCA because deprotonated Arg52 cannot stabilize it. However, the calculated pK(a) of Arg52 and QM/MM optimized geometry suggested that Arg52 was protonated on the protein surface. The short H bond between Glu46 and ionized pCA in the PYP ground state could be simply explained by electrostatic stabilization without invoking LBHB.

Calculation of the Relative Chemical Stabilities of Proteins as a Function of Temperature and Redox Chemistry in a Hot Spring

PubMed Central

Dick, Jeffrey M.; Shock, Everett L.

2011-01-01

Uncovering the chemical and physical links between natural environments and microbial communities is becoming increasingly amenable owing to geochemical observations and metagenomic sequencing. At the hot spring known as Bison Pool in Yellowstone National Park, the cooling of the water in the outflow channel is associated with an increase in oxidation potential estimated from multiple field-based measurements. Representative groups of proteins whose sequences were derived from metagenomic data also exhibit an increase in average oxidation state of carbon in the protein molecules with distance from the hot-spring source. The energetic requirements of reactions to form selected proteins used in the model were computed using amino-acid group additivity for the standard molal thermodynamic properties of the proteins, and the relative chemical stabilities of the proteins were investigated by varying temperature, pH and oxidation state, expressed as activity of dissolved hydrogen. The relative stabilities of the proteins were found to track the locations of the sampling sites when the calculations included a function for hydrogen activity that increases with temperature and is higher, or more reducing, than values consistent with measurements of dissolved oxygen, sulfide and oxidation-reduction potential in the field. These findings imply that spatial patterns in the amino acid compositions of proteins can be linked, through energetics of overall chemical reactions representing the formation of the proteins, to the environmental conditions at this hot spring, even if microbial cells maintain considerably different internal conditions. Further applications of the thermodynamic calculations are possible for other natural microbial ecosystems. PMID:21853048

C 90 temperature effects on relative stabilities of the IPR isomers

NASA Astrophysics Data System (ADS)

Slanina, Zdeněk; Zhao, Xiang; Lee, Shyi-Long; Ōsawa, Eiji

1997-07-01

The complete set of 46 isolated-pentagon-rule (IPR) isomers of C 90 is treated by the SAMI quantum-chemical method (Semi-Ab-Initio Model 1), and their energetics is also checked by ab initio SCF computations (HF/3-21G, HF/4-31G) and the AM1 and PM3 semiempirical methods. All the methods point out a C2 species as the system state (with an exception at the HF/3-21G level). However, the energetics itself is not able to produce a good agreement with recent observations (one C2 v, three C2, and one C1, separeted into three HPLC fractions). The symmetries of the five SAM1 lowest-energy structures are: C2, C2 v, Cs, D5 h, C1. In order to respect temperature effects on relative stabilities, entropy contributions are also computed and significant changes are found. The symmetries of the five structures most populated in a high-temperature region are according to the SAM1 computations: two times C2, Cs, C2 v, C1. One of the recently reported HPLC fractions shows 70 lines in the 13C NMR spectrum, assigned to a C2 species (45 lines) and C2 v species (25 lines, 5 weaker). There is however an alternative interpretation of the spectrum: a Cs (46 lines, 2 weaker) and a C2 v species (24 lines, 3 weaker). The last two structures are indeed present in the SAM1 high-temperature stability set so that agreement between observations and calculations can be achieved.

Models of Time Use in Paid and Unpaid Work

ERIC Educational Resources Information Center

Beaujot, Roderic; Liu, Jianye

2005-01-01

Models of time use need to consider especially the reproductive and productive activities of women and men. For husband-wife families, the breadwinner, one-earner, or complementary-roles model has advantages in terms of efficiency or specialization and stability; however, it is a high-risk model for women and children. The alternate model has been…

Doppler Navigation System with a Non-Stabilized Antenna as a Sea-Surface Wind Sensor.

PubMed

Nekrasov, Alexey; Khachaturian, Alena; Veremyev, Vladimir; Bogachev, Mikhail

2017-06-09

We propose a concept of the utilization of an aircraft Doppler Navigation System (DNS) as a sea-surface wind sensor complementary to its normal functionality. The DNS with an antenna, which is non-stabilized physically to the local horizontal with x -configured beams, is considered. We consider the wind measurements by the DNS configured in the multi-beam scatterometer mode for a rectilinear flight scenario. The system feasibility and the efficiency of the proposed wind algorithm retrieval are supported by computer simulations. Finally, the associated limitations of the proposed approach are considered.

Doppler Navigation System with a Non-Stabilized Antenna as a Sea-Surface Wind Sensor

PubMed Central

Nekrasov, Alexey; Khachaturian, Alena; Veremyev, Vladimir; Bogachev, Mikhail

2017-01-01

We propose a concept of the utilization of an aircraft Doppler Navigation System (DNS) as a sea-surface wind sensor complementary to its normal functionality. The DNS with an antenna, which is non-stabilized physically to the local horizontal with x-configured beams, is considered. We consider the wind measurements by the DNS configured in the multi-beam scatterometer mode for a rectilinear flight scenario. The system feasibility and the efficiency of the proposed wind algorithm retrieval are supported by computer simulations. Finally, the associated limitations of the proposed approach are considered. PMID:28598374

Lipophilic oligonucleotides spontaneously insert into lipid membranes, bind complementary DNA strands, and sequester into lipid-disordered domains.

PubMed

Bunge, Andreas; Kurz, Anke; Windeck, Anne-Kathrin; Korte, Thomas; Flasche, Wolfgang; Liebscher, Jürgen; Herrmann, Andreas; Huster, Daniel

2007-04-10

For the development of surface functionalized bilayers, we have synthesized lipophilic oligonucleotides to combine the molecular recognition mechanism of nucleic acids and the self-assembly characteristics of lipids in planar membranes. A lipophilic oligonucleotide consisting of 21 thymidine units and two lipophilic nucleotides with an alpha-tocopherol moiety as a lipophilic anchor was synthesized using solid-phase methods with a phosphoramadite strategy. The interaction of the water soluble lipophilic oligonucleotide with vesicular lipid membranes and its capability to bind complementary DNA strands was studied using complementary methods such as NMR, EPR, DSC, fluorescence spectroscopy, and fluorescence microscopy. This oligonucleotide inserted stably into preformed membranes from the aqueous phase. Thereby, no significant perturbation of the lipid bilayer and its stability was observed. However, the non-lipidated end of the oligonucleotide is exposed to the aqueous environment, is relatively mobile, and is free to interact with complementary DNA strands. Binding of the complementary single-stranded DNA molecules is fast and accomplished by the formation of Watson-Crick base pairs, which was confirmed by 1H NMR chemical shift analysis and fluorescence resonance energy transfer. The molecular structure of the membrane bound DNA double helix is very similar to the free double-stranded DNA. Further, the membrane bound DNA double strands also undergo regular melting. Finally, in raft-like membrane mixtures, the lipophilic oligonucleotide was shown to preferentially sequester into liquid-disordered membrane domains.

Artificial photosynthetic systems: assemblies of slipped cofacial porphyrins and phthalocyanines showing strong electronic coupling.

PubMed

Satake, Akiharu; Kobuke, Yoshiaki

2007-06-07

This paper reviews selected types of structurally well defined assemblies of porphyrins and phthalocyanines with strong electronic coupling. Face-to-face, head-to-tail, slipped cofacial, and non-parallel dimeric motifs constructed by covalent and non-covalent bonds are compared in the earlier sections. Their molecular orientation, electronic overlap, and absorption and fluorescence properties are discussed with a view towards the development of artificial photosynthetic systems and molecular electronics. Complementary coordination dimers are fully satisfactory in terms of structural stability, orientation factor, pi-electronic overlap, and zero fluorescence quenching. In later sections, several polymeric and macrocyclic porphyrin assemblies constructed by a combination of covalent bonds and complementary coordination bonds are discussed from the viewpoint of light-harvesting antenna functions.

Gyrokinetic Particle Simulation of Turbulent Transport in Burning Plasmas (GPS - TTBP) Final Report

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

Chame, Jacqueline

2011-05-27

The goal of this project is the development of the Gyrokinetic Toroidal Code (GTC) Framework and its applications to problems related to the physics of turbulence and turbulent transport in tokamaks,. The project involves physics studies, code development, noise effect mitigation, supporting computer science efforts, diagnostics and advanced visualizations, verification and validation. Its main scientific themes are mesoscale dynamics and non-locality effects on transport, the physics of secondary structures such as zonal flows, and strongly coherent wave-particle interaction phenomena at magnetic precession resonances. Special emphasis is placed on the implications of these themes for rho-star and current scalings and formore » the turbulent transport of momentum. GTC-TTBP also explores applications to electron thermal transport, particle transport; ITB formation and cross-cuts such as edge-core coupling, interaction of energetic particles with turbulence and neoclassical tearing mode trigger dynamics. Code development focuses on major initiatives in the development of full-f formulations and the capacity to simulate flux-driven transport. In addition to the full-f -formulation, the project includes the development of numerical collision models and methods for coarse graining in phase space. Verification is pursued by linear stability study comparisons with the FULL and HD7 codes and by benchmarking with the GKV, GYSELA and other gyrokinetic simulation codes. Validation of gyrokinetic models of ion and electron thermal transport is pursed by systematic stressing comparisons with fluctuation and transport data from the DIII-D and NSTX tokamaks. The physics and code development research programs are supported by complementary efforts in computer sciences, high performance computing, and data management.« less

Density functional theory study of defects in unalloyed δ-Pu

DOE PAGES

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

2017-03-19

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

Influence of methyl functional groups on the stability of cubane carbon cage

NASA Astrophysics Data System (ADS)

Katin, Konstantin P.; Prudkovskiy, Vladimir S.; Maslov, Mikhail M.

2016-07-01

We present a quantum-chemical study to elucidate the structure, energetics and stability of isolated polymethylcubane molecules C8H8-q(CH3)q. The results obtained by means of originally developed nonorthogonal tight-binding approach are in good agreement with the existed experimental data for solid octamethylcubane C8(CH3)8. The isomerization mechanisms for polymethylcubane family are studied in detail and the minimum energy barriers' heights preventing the decomposition are calculated. The temperature dependence of octamethylcubane molecule lifetime to the decomposition moment was determined by direct molecular dynamics simulation. It is shown that methyl groups destabilize the cubic carbon cage, but less than nitro groups.

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

Fakhri, M.; Theisen, M.; Behrendt, A.

Top gated metal-oxide thin-film transistors (TFTs) provide two benefits compared to their conventional bottom-gate counterparts: (i) The gate dielectric may concomitantly serve as encapsulation layer for the TFT channel. (ii) Damage of the dielectric due to high-energetic particles during channel deposition can be avoided. In our work, the top-gate dielectric is prepared by ozone based atomic layer deposition at low temperatures. For ultra-low gas permeation rates, we introduce nano-laminates of Al{sub 2}O{sub 3}/ZrO{sub 2} as dielectrics. The resulting TFTs show a superior environmental stability even at elevated temperatures. Their outstanding stability vs. bias stress is benchmarked against bottom-gate devices withmore » encapsulation.« less

Density functional theory study of defects in unalloyed δ-Pu

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

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

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

Stabilization of weak ferromagnetism by strong magnetic response to epitaxial strain in multiferroic BiFeO 3

DOE PAGES

Cooper, Valentino R.; Lee, Jun Hee; Krogel, Jaron T.; ...

2015-08-06

Multiferroic BiFeO 3 exhibits excellent magnetoelectric coupling critical for magnetic information processing with minimal power consumption. Thus, the degenerate nature of the easy spin axis in the (111) plane presents roadblocks for real world applications. Here, we explore the stabilization and switchability of the weak ferromagnetic moments under applied epitaxial strain using a combination of first-principles calculations and group-theoretic analyses. We demonstrate that the antiferromagnetic moment vector can be stabilized along unique crystallographic directions ([110] and [-110]) under compressive and tensile strains. A direct coupling between the anisotropic antiferrodistortive rotations and Dzyaloshinskii-Moria interactions drives the stabilization of weak ferromagnetism. Furthermore,more » energetically competing C- and G-type magnetic orderings are observed at high compressive strains, suggesting that it may be possible to switch the weak ferromagnetism on and off under application of strain. These findings emphasize the importance of strain and antiferrodistortive rotations as routes to enhancing induced weak ferromagnetism in multiferroic oxides.« less

Molecular dynamics study of thermodynamic stability and dynamics of [Li(glyme)]+ complex in lithium-glyme solvate ionic liquids

NASA Astrophysics Data System (ADS)

Shinoda, Wataru; Hatanaka, Yuta; Hirakawa, Masashi; Okazaki, Susumu; Tsuzuki, Seiji; Ueno, Kazuhide; Watanabe, Masayoshi

2018-05-01

Equimolar mixtures of glymes and organic lithium salts are known to produce solvate ionic liquids, in which the stability of the [Li(glyme)]+ complex plays an important role in determining the ionic dynamics. Since these mixtures have attractive physicochemical properties for application as electrolytes, it is important to understand the dependence of the stability of the [Li(glyme)]+ complex on the ion dynamics. A series of microsecond molecular dynamics simulations has been conducted to investigate the dynamic properties of these solvate ionic liquids. Successful solvate ionic liquids with high stability of the [Li(glyme)]+ complex have been shown to have enhanced ion dynamics. Li-glyme pair exchange rarely occurs: its characteristic time is longer than that of ion diffusion by one or two orders of magnitude. Li-glyme pair exchange most likely occurs through cluster formation involving multiple [Li(glyme)]+ pairs. In this process, multiple exchanges likely take place in a concerted manner without the production of energetically unfavorable free glyme or free Li+ ions.

Intelligent complementary sliding-mode control for LUSMS-based X-Y-theta motion control stage.

PubMed

Lin, Faa-Jeng; Chen, Syuan-Yi; Shyu, Kuo-Kai; Liu, Yen-Hung

2010-07-01

An intelligent complementary sliding-mode control (ICSMC) system using a recurrent wavelet-based Elman neural network (RWENN) estimator is proposed in this study to control the mover position of a linear ultrasonic motors (LUSMs)-based X-Y-theta motion control stage for the tracking of various contours. By the addition of a complementary generalized error transformation, the complementary sliding-mode control (CSMC) can efficiently reduce the guaranteed ultimate bound of the tracking error by half compared with the slidingmode control (SMC) while using the saturation function. To estimate a lumped uncertainty on-line and replace the hitting control of the CSMC directly, the RWENN estimator is adopted in the proposed ICSMC system. In the RWENN, each hidden neuron employs a different wavelet function as an activation function to improve both the convergent precision and the convergent time compared with the conventional Elman neural network (ENN). The estimation laws of the RWENN are derived using the Lyapunov stability theorem to train the network parameters on-line. A robust compensator is also proposed to confront the uncertainties including approximation error, optimal parameter vectors, and higher-order terms in Taylor series. Finally, some experimental results of various contours tracking show that the tracking performance of the ICSMC system is significantly improved compared with the SMC and CSMC systems.

Sensitive detection of multiple pathogens using a single DNA probe.

PubMed

Nordin, Noordiana; Yusof, Nor Azah; Abdullah, Jaafar; Radu, Son; Hushiarian, Roozbeh

2016-12-15

A simple but promising electrochemical DNA nanosensor was designed, constructed and applied to differentiate a few food-borne pathogens. The DNA probe was initially designed to have a complementary region in Vibrio parahaemolyticus (VP) genome and to make different hybridization patterns with other selected pathogens. The sensor was based on a screen printed carbon electrode (SPCE) modified with polylactide-stabilized gold nanoparticles (PLA-AuNPs) and methylene blue (MB) was employed as the redox indicator binding better to single-stranded DNA. The immobilization and hybridization events were assessed using differential pulse voltammetry (DPV). The fabricated biosensor was able to specifically distinguish complementary, non-complementary and mismatched oligonucleotides. DNA was measured in the range of 2.0×10(-9)-2.0×10(-13)M with a detection limit of 5.3×10(-12)M. The relative standard deviation for 6 replications of DPV measurement of 0.2µM complementary DNA was 4.88%. The fabricated DNA biosensor was considered stable and portable as indicated by a recovery of more than 80% after a storage period of 6 months at 4-45°C. Cross-reactivity studies against various food-borne pathogens showed a reliably sensitive detection of VP. Copyright © 2016 Elsevier B.V. All rights reserved.

First-principles calculations of the thermal stability of Ti 3SiC 2(0001) surfaces

NASA Astrophysics Data System (ADS)

Orellana, Walter; Gutiérrez, Gonzalo

2011-12-01

The energetic, thermal stability and dynamical properties of the ternary layered ceramic Ti3SiC2(0001) surface are addressed by density-functional theory calculations and molecular dynamic (MD) simulations. The equilibrium surface energy at 0 K of all terminations is contrasted with thermal stability at high temperatures, which are investigated by ab initio MD simulations in the range of 800 to 1400 °C. We find that the toplayer (sublayer) surface configurations: Si(Ti2) and Ti2(Si) show the lowest surface energies with reconstruction features for Si(Ti2). However, at high temperatures they are unstable, forming disordered structures. On the contrary, Ti1(C) and Ti2(C) despite their higher surface energies, show a remarkable thermal stability at high temperatures preserving the crystalline structures up to 1400 °C. The less stable surfaces are those terminated in C atoms, C(Ti1) and C(Ti2), which at high temperatures show surface dissociation forming amorphous TiCx structures. Two possible atomic scale mechanisms involved in the thermal stability of Ti3SiC2(0001) are discussed.

Glycerol, trehalose and glycerol-trehalose mixture effects on thermal stabilization of OCT

NASA Astrophysics Data System (ADS)

Barreca, D.; Laganà, G.; Magazù, S.; Migliardo, F.; Bellocco, E.

2013-10-01

The stabilization effects of trehalose, glycerol and their mixtures on ornithine carbamoyltransferase catalytic activity has been studied as a function of temperature by complementary techniques. The obtained results show that the kinematic viscosities of trehalose (1.0 M) and protein mixture are higher than the one of glycerol plus protein. Changing the trehalose/glycerol ratio, we notice a decrease of the kinematic viscosity values at almost all the analyzed ratio. In particular, the solution composed of 95% trehalose-5% glycerol shows a peculiar behavior. Moreover the trehalose (1.0 M) solution shows the higher OCT thermal stabilization at 343 K, while all the other solutions show minor effects. The smallest stabilizing effect is revealed for the solution that shows the maximum kinematic viscosity. These results support Inelastic Neutron Scattering (INS) and Quasi Elastic Neutron Scattering (QENS) findings, which pointed out a slowing down of the relaxation and diffusive dynamics in some investigated samples.

Chemical denaturation as a tool in the formulation optimization of biologics

PubMed Central

Freire, Ernesto; Schön, Arne; Hutchins, Burleigh M.; Brown, Richard K.

2013-01-01

Biologics have become the fastest growing segment in the pharmaceutical industry. As is the case with all proteins, biologics are susceptible to denature or to aggregate; conditions that, if present, preclude their use as pharmaceuticals. Identifying the solvent conditions that maximize their structural stability is crucial during development. Since the structural stability of a protein is susceptible to different chemical and physical conditions, the use of several complementary techniques can be expected to provide the best answers. Stability measurements that rely on temperature or chemical [urea or guanidine hydrochloride (GuHCl)] denaturation have been the preferred ones in research laboratories and together provide a thorough evaluation of protein stability. In this review, we will discuss chemical denaturation as a tool in the optimization of formulation conditions for biologics, and how chemical denaturation complements the role of thermal denaturation for this purpose. PMID:23796912

Soluble fullerene derivatives: The effect of electronic structure on transistor performance and air stability

NASA Astrophysics Data System (ADS)

Ball, James M.; Bouwer, Ricardo K. M.; Kooistra, Floris B.; Frost, Jarvist M.; Qi, Yabing; Domingo, Ester Buchaca; Smith, Jeremy; de Leeuw, Dago M.; Hummelen, Jan C.; Nelson, Jenny; Kahn, Antoine; Stingelin, Natalie; Bradley, Donal D. C.; Anthopoulos, Thomas D.

2011-07-01

The family of soluble fullerene derivatives comprises a widely studied group of electron transporting molecules for use in organic electronic and optoelectronic devices. For electronic applications, electron transporting (n-channel) materials are required for implementation into organic complementary logic circuit architectures. To date, few soluble candidate materials have been studied that fulfill the stringent requirements of high carrier mobility and air stability. Here we present a study of three soluble fullerenes with varying electron affinity to assess the impact of electronic structure on device performance and air stability. Through theoretical and experimental analysis of the electronic structure, characterization of thin-film structure, and characterization of transistor device properties we find that the air stability of the present series of fullerenes not only depends on the absolute electron affinity of the semiconductor but also on the disorder within the thin-film.

High-pressure/high-temperature polymorphs of energetic materials by first-principles simulations

NASA Astrophysics Data System (ADS)

Le, Nam; Schweigert, Igor

2017-06-01

Energetic molecular crystals exhibit complex phase diagrams that include solid-solid phase transitions, melting, and decomposition. Sorescu and Rice have recently demonstrated that first-principles molecular dynamics (MD) simulations based on dispersion-corrected density functional theory (DFT) can capture the α to γ phase transition in hexahydro-1,3,5-trinitro-1,3,5-triazine (RDX) on time scales of several picoseconds. Motivated by their work, we are using DFT-based MD to model the relative stability of solid phases in several molecular crystals. In this presentation, we report simulations of pentaerythritol tetranitrate (PETN) and 2,4,6-trinitrotoluene (TNT) under high pressures and temperatures and compare them with experimentally observed polymorphs. This work was supported by the U.S. Naval Research Laboratory via the National Research Council and by the Office of Naval Research through the U.S. Naval Research Laboratory.

Energy level alignment of self-assembled linear chains of benzenediamine on Au(111) from first principles

DOE PAGES

Li, Guo; Rangel, Tonatiuh; Liu, Zhen -Fei; ...

2016-03-24

Using density functional theory (DFT) with van der Waals functionals, we calculate the adsorption energetics and geometry of benzenediamine (BDA) molecules on Au(111) surfaces. Our results demonstrate that the reported self-assembled linear chain structure of BDA, stabilized via hydrogen bonds between amine groups, is energetically favored over previously-studied monomeric phases. Moreover, using a model based on many-body perturbation theory within the GW approximation, we obtain approximate self-energy corrections to the DFT highest occupied molecular orbital (HOMO) energy associated with BDA adsorbate phases. As a result, we find that, independent of coverage, the HOMO energy of the linear chain phase ismore » lower relative to the Fermi energy than that of the monomer phase, and in good agreement with values measured with ultraviolet photoelectron spectroscopy and X-ray photoelectron spectroscopy.« less

The challenge of improvised explosives

DOE PAGES

Maienschein, Jon L.

2012-06-14

Energetic materials have been developed for decades, and indeed centuries, with a common set of goals in mind. Performance (as a detonating explosive, a propellant, or a pyrotechnic) has always been key, equally important have been the attributes of safety, stability, and reproducibility. Research and development with those goals has led to the set of energetic materials commonly used today. In the past few decades, the adoption and use of improvised explosives in attacks by terrorists or third-world parties has led to many questions about these materials, e.g., how they may be made, what threat they pose to the intendedmore » target, how to handle them safely, and how to detect them. The unfortunate advent of improvised explosives has opened the door for research into these materials, and there are active programs in many countries. I will discuss issues and opportunities facing research into improvised explosives.« less

Energy level alignment of self-assembled linear chains of benzenediamine on Au(111) from first principles

NASA Astrophysics Data System (ADS)

Li, Guo; Rangel, Tonatiuh; Liu, Zhen-Fei; Cooper, Valentino R.; Neaton, Jeffrey B.

2016-03-01

Using density functional theory (DFT) with a van der Waals density functional, we calculate the adsorption energetics and geometry of benzenediamine (BDA) molecules on Au(111) surfaces. Our results demonstrate that the reported self-assembled linear chain structure of BDA, stabilized via hydrogen bonds between amine groups, is energetically favored over previously studied monomeric phases. Moreover, using a model, which includes nonlocal polarization effects from the substrate and the neighboring molecules and incorporates many-body perturbation theory calculations within the GW approximation, we obtain approximate self-energy corrections to the DFT highest occupied molecular orbital (HOMO) energy associated with BDA adsorbate phases. We find that, independent of coverage, the HOMO energy of the linear chain phase is lower relative to the Fermi energy than that of the monomer phase, and in good agreement with values measured with ultraviolet photoelectron spectroscopy and x-ray photoelectron spectroscopy.

Stability of boron-doped graphene/copper interface: DFT, XPS and OSEE studies

NASA Astrophysics Data System (ADS)

Boukhvalov, D. W.; Zhidkov, I. S.; Kukharenko, A. I.; Slesarev, A. I.; Zatsepin, A. F.; Cholakh, S. O.; Kurmaev, E. Z.

2018-05-01

Two different types of boron-doped graphene/copper interfaces synthesized using two different flow rates of Ar through the bubbler containing the boron source were studied. X-ray photoelectron spectra (XPS) and optically stimulated electron emission (OSEE) measurements have demonstrated that boron-doped graphene coating provides a high corrosion resistivity of Cu-substrate with the light traces of the oxidation of carbon cover. The density functional theory calculations suggest that for the case of substitutional (graphitic) boron-defect only the oxidation near boron impurity is energetically favorable and creation of the vacancies that can induce the oxidation of copper substrate is energetically unfavorable. In the case of non-graphitic boron defects oxidation of the area, a nearby impurity is metastable that not only prevent oxidation but makes boron-doped graphene. Modeling of oxygen reduction reaction demonstrates high catalytic performance of these materials.

Energetics of a uranothorite (Th 1–xU xSiO 4) solid solution

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

Guo, Xiaofeng; Szenknect, Stephanie; Mesbah, Adel

High-temperature oxide melt solution calorimetric measurements were completed to determine the enthalpies of formation of the uranothorite, (USiO 4) x–(ThSiO 4) 1–x, solid solution. Phase-pure samples with x values of 0, 0.11, 0.21, 0.35, 0.71, and 0.84 were prepared, purified, and characterized by powder X-ray diffraction, electron probe microanalysis, thermogravimetric analysis and differential scanning calorimetry coupled with in situ mass spectrometry, and high-temperature oxide melt solution calorimetry. This work confirms the energetic metastability of coffinite, USiO 4, and U-rich intermediate silicate phases with respect to a mixture of binary oxides. Furthermore, variations in unit cell parameters and negative excess volumesmore » of mixing, coupled with strongly exothermic enthalpies of mixing in the solid solution, suggest short-range cation ordering that can stabilize intermediate compositions, especially near x = 0.5.« less

The Energetic Transient Array ETA - A network of 'space buoys' in solar orbit for observations of gamma-ray bursts

NASA Technical Reports Server (NTRS)

Ricker, George R.

1990-01-01

The Energetic Transient Array (ETA) is a concept for a dedicated interplanetary network of about 40 microsatellites ('space buoys') deployed in an about 1 AU radius solar orbit for the observation of cosmic gamma ray bursts (GRBs). Such a network is essential for the determination of highly accurate (about 0.1 arcsec) error boxes for GRBs. For each of about 100 bursts which would be detectable per year of observation by such a network, high resolution spectra could be obtained through the use of passively-cooled Ge gamma-ray detectors. Stabilization of each microsatellite would be achieved by a novel technique based on the radiation pressure exerted on 'featherable' solar paddles. It should be possible to have a fully functional array of satellites in place before the end of the decade for a total cost of about $20M, exclusive of launcher fees.

Ab initio surface properties of Ag-Sn alloys: implications for lead-free soldering.

PubMed

Saleh, Gabriele; Xu, Chen; Sanvito, Stefano

2018-02-07

Ag and Sn are the major components of solder alloys adopted to assemble printed circuit boards. The qualities that make them the alloys of choice for the modern electronic industry are related to their physical and chemical properties. For corrosion resistance and solderability, surface properties are particularly important. Yet, atomic-level information about the surfaces of these alloys is not known. Here we fill this gap by presenting an extensive ab initio investigation of composition, energetics, structure and reactivity of Ag-Sn alloy surfaces. The structure and stability of various surfaces is evaluated, and the main factors determining the energetics of surface formation are uncovered. Oxygen and sulphur chemisorptions are studied and discussed in the framework of corrosion tendency, an important issue for printed circuit boards. Adsorption energy trends are rationalized based on the analysis of structural and electronic features.

Energetics of a uranothorite (Th 1–xU xSiO 4) solid solution

DOE PAGES

Guo, Xiaofeng; Szenknect, Stephanie; Mesbah, Adel; ...

2016-10-11

High-temperature oxide melt solution calorimetric measurements were completed to determine the enthalpies of formation of the uranothorite, (USiO 4) x–(ThSiO 4) 1–x, solid solution. Phase-pure samples with x values of 0, 0.11, 0.21, 0.35, 0.71, and 0.84 were prepared, purified, and characterized by powder X-ray diffraction, electron probe microanalysis, thermogravimetric analysis and differential scanning calorimetry coupled with in situ mass spectrometry, and high-temperature oxide melt solution calorimetry. This work confirms the energetic metastability of coffinite, USiO 4, and U-rich intermediate silicate phases with respect to a mixture of binary oxides. Furthermore, variations in unit cell parameters and negative excess volumesmore » of mixing, coupled with strongly exothermic enthalpies of mixing in the solid solution, suggest short-range cation ordering that can stabilize intermediate compositions, especially near x = 0.5.« less

Dissolution Rate of Propellant Energetics from Nitrocellulose Matrices

DTIC Science & Technology

2012-09-01

propellants are generally composed of a polymer, a plasticizer , and a stabilizer. These three compo- nents provide the structure, contribute the oxygen...million lb) of nitrocel- lulose is manufactured each year in the U.S. (Richie 2012; a partial listing is given in Table A1). This wood -like compound...that single- and double-base propellants are transparent to translucent and show signs of having been extruded (Fig. 10). Figure 10. Thin section

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

Katoch, Neha, E-mail: nehakatoch2@gmail.com; Kapoor, Pooja; Sharma, Munish

We report stability and electronic properties of benzene molecule adsorbed on the Au atomic layer within the framework of density function theory (DFT). Horizontal configuration of benzene on the top site of Au monolayer prefers energetically over other studied configurations. On the adsorption of benzene, the ballistic conductance of Au monolayer is found to decrease from 4G{sub 0} to 2G{sub 0} suggesting its applications for the fabrications of organic sensor devices based on the Au atomic layers.

Global Energetics in Solar Flares and Coronal Mass Ejections

NASA Astrophysics Data System (ADS)

Aschwanden, Markus J.

2017-08-01

We present a statistical study of the energetics of coronal mass ejections (CME) and compare it with the magnetic, thermal, and nonthermal energy dissipated in flares. The physical parameters of CME speeds, mass, and kinetic energies are determined with two different independent methods, i.e., the traditional white-light scattering method using LASCO/SOHO data, and the EUV dimming method using AIA/SDO data. We analyze all 860 GOES M- and X-class flare events observed during the first 7 years (2010-2016) of the SDO mission. The new ingredients of our CME modeling includes: (1) CME geometry in terms of a self-similar adiabatic expansion, (2) DEM analysis of CME mass over entire coronal temperature range, (3) deceleration of CME due to gravity force which controls the kinetic and potentail CME energy as a function of time, (4) the critical speed that controls eruptive and confined CMEs, (5) the relationship between the center-of-mass motion during EUV dimming and the leading edge motion observed in white-light coronagraphs. Novel results are: (1) Physical parameters obtained from both the EUV dimming and white-light method can be reconciled; (2) the equi-partition of CME kinetic and thermal flare energy; (3) the Rosner-Tucker-Vaiana scaling law. We find that the two methods in EUV and white-light wavelengths are highly complementary and yield more complete models than each method alone.

Role of zero-point effects in stabilizing the ground state structure of bulk Fe2P

NASA Astrophysics Data System (ADS)

Bhat, Soumya S.; Gupta, Kapil; Bhattacharjee, Satadeep; Lee, Seung-Cheol

2018-05-01

Structural stability of Fe2P is investigated in detail using first-principles calculations based on density functional theory. While the orthorhombic C23 phase is found to be energetically more stable, the experiments suggest it to be hexagonal C22 phase. In the present study, we show that in order to obtain the correct ground state structure of Fe2P from the first-principles based methods it is utmost necessary to consider the zero-point effects such as zero-point vibrations and spin fluctuations. This study demonstrates an exceptional case where a bulk material is stabilized by quantum effects, which are usually important in low-dimensional materials. Our results also indicate the possibility of magnetic field induced structural quantum phase transition in Fe2P, which should form the basis for further theoretical and experimental efforts.

Allotropes of Phosphorus with Remarkable Stability and Intrinsic Piezoelectricity

NASA Astrophysics Data System (ADS)

Li, Zhenqing; He, Chaoyu; Ouyang, Tao; Zhang, Chunxiao; Tang, Chao; Römer, Rudolf A.; Zhong, Jianxin

2018-04-01

We construct a class of two-dimensional (2D) phosphorus allotropes by assembling a previously proposed ultrathin metastable phosphorus nanotube into planar structures in different stacking orientations. Based on first-principles methods, the structures, stabilities, and fundamental electronic properties of these allotropes are systematically investigated. Our results show that these 2D van der Waals phosphorene allotropes possess remarkable stabilities due to the strong intertube van der Waals interactions, which cause an energy release of about 30 - 70 meV /atom , depending on their stacking details. Most of them are confirmed to be energetically more favorable than the experimentally viable α -P and β -P . Three of them, showing a relatively higher probability of being synthesized in the future, are further confirmed to be dynamically stable semiconductors with strain-tunable band gaps and intrinsic piezoelectricity, which may have potential applications in nanosized sensors, piezotronics, and energy harvesting in portable electronic nanodevices.

Chlorine adsorption on the InAs (001) surface

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

Bakulin, A. V.; Eremeev, S. V.; Tereshchenko, O. E.

2011-01-15

Chlorine adsorption on the In-stabilized InAs(001) surface with {zeta}-(4 Multiplication-Sign 2) and {beta}3 Prime -(4 Multiplication-Sign 2) reconstructions and on the Ga-stabilized GaAs (001)-{zeta}-(4 Multiplication-Sign 2) surface has been studied within the electron density functional theory. The equilibrium structural parameters of these reconstructions, surface atom positions, bond lengths in dimers, and their changes upon chlorine adsorption are determined. The electronic characteristics of the clean surface and the surface with adsorbed chlorine are calculated. It is shown that the most energetically favorable positions for chlorine adsorption are top positions over dimerized indium or gallium atoms. The mechanism of chlorine binding withmore » In(Ga)-stabilized surface is explained. The interaction of chlorine atoms with dimerized surface atoms weakens surface atom bonds and controls the initial stage of surface etching.« less

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

Bony, Sandrine; Stevens, Bjorn; Coppin, David

General circulation models show that as the surface temperature increases, the convective anvil clouds shrink. By analyzing radiative–convective equilibrium simulations, our work shows that this behavior is rooted in basic energetic and thermodynamic properties of the atmosphere: As the climate warms, the clouds rise and remain at nearly the same temperature, but find themselves in a more stable atmosphere; this enhanced stability reduces the convective outflow in the upper troposphere and decreases the anvil cloud fraction. By warming the troposphere and increasing the upper-tropospheric stability, the clustering of deep convection also reduces the convective outflow and the anvil cloud fraction.more » When clouds are radiatively active, this robust coupling between temperature, high clouds, and circulation exerts a positive feedback on convective aggregation and favors the maintenance of strongly aggregated atmospheric states at high temperatures. This stability iris mechanism likely contributes to the narrowing of rainy areas as the climate warms. Whether or not it influences climate sensitivity requires further investigation.« less

Origin of the Chemical and Kinetic Stability of Graphene Oxide

PubMed Central

Zhou, Si; Bongiorno, Angelo

2013-01-01

At moderate temperatures (≤ 70°C), thermal reduction of graphene oxide is inefficient and after its synthesis the material enters in a metastable state. Here, first-principles and statistical calculations are used to investigate both the low-temperature processes leading to decomposition of graphene oxide and the role of ageing on the structure and stability of this material. Our study shows that the key factor underlying the stability of graphene oxide is the tendency of the oxygen functionalities to agglomerate and form highly oxidized domains surrounded by areas of pristine graphene. Within the agglomerates of functional groups, the primary decomposition reactions are hindered by both geometrical and energetic factors. The number of reacting sites is reduced by the occurrence of local order in the oxidized domains, and due to the close packing of the oxygen functionalities, the decomposition reactions become – on average – endothermic by more than 0.6 eV. PMID:23963517

Structure-based energetics of protein interfaces guide Foot-and-Mouth Disease virus vaccine design

PubMed Central

Scott, Katherine; Burman, Alison; Loureiro, Silvia; Ren, Jingshan; Porta, Claudine; Ginn, Helen M.; Jackson, Terry; Perez-Martin, Eva; Siebert, C. Alistair; Paul, Guntram; Huiskonen, Juha T.; Jones, Ian M.; Esnouf, Robert M.; Fry, Elizabeth E.; Maree, Francois F.; Charleston, Bryan; Stuart, David I.

2018-01-01

Summary Virus capsids are primed for disassembly yet capsid integrity is key to generating a protective immune response. Here we devise a computational method to assess relative stability of protein-protein interfaces and use it to design improved candidate vaccines for two of the least stable, but globally important, serotypes of Foot-and-Mouth Disease virus (FMDV), O and SAT2. FMDV capsids comprise identical pentameric protein subunits held together by tenuous non-covalent interactions, and are often unstable. Chemically inactivated or recombinant empty capsids, which could form the basis of future vaccines, are even less stable than live virus. We use a novel restrained molecular dynamics strategy, to rank mutations predicted to strengthen the pentamer interfaces to produce stabilized capsids. Structural analyses and stability assays confirmed the predictions, and vaccinated animals generated improved neutralising antibody responses to stabilised particles over parental viruses and wild-type capsids. PMID:26389739

Probing eudesmane cation-π interactions in catalysis by aristolochene synthase with non-canonical amino acids.

PubMed

Faraldos, Juan A; Antonczak, Alicja K; González, Verónica; Fullerton, Rebecca; Tippmann, Eric M; Allemann, Rudolf K

2011-09-07

Stabilization of the reaction intermediate eudesmane cation (3) through interaction with Trp 334 during catalysis by aristolochene synthase from Penicillium roqueforti was investigated by site-directed incorporation of proteinogenic and non-canonical aromatic amino acids. The amount of germacrene A (2) generated by the mutant enzymes served as a measure of the stabilization of 3. 2 is a neutral intermediate, from which 3 is formed during PR-AS catalysis by protonation of the C6,C7 double bond. The replacement of Trp 334 with para-substituted phenylalanines of increasing electron-withdrawing properties led to a progressive accumulation of 2 that showed a good correlation with the interaction energies of simple cations such as Na(+) with substituted benzenes. These results provide compelling evidence for the stabilizing role played by Trp 334 in aristolochene synthase catalysis for the energetically demanding transformation of 2 to 3.

Ab initio correlated study of the Al13H- anion: Isomers, their kinetic stability and vertical detachment energies

NASA Astrophysics Data System (ADS)

Moc, Jerzy

2012-01-01

We report correlated ab initio calculations for the Al13H- cluster anion isomers, their kinetic stability and vertical detachment energies (VDEs). Of the two most energetically favored anion structures involving H atom in terminal and threefold bridged sites of the icosahedral Al13-, the higher energy ‘threefold bridged' isomer is shown to be of low kinetic stability. Our results are consistent with the recent photoelectron spectroscopy (PE) study of Grubisic et al. who observed two distinct Al13H- isomers, one of them identified as ‘metastable'. The VDE energies computed at the CCSD(T)/aug-cc-pVTZ//MP2/aug-cc-pVDZ level for the ‘terminal' and ‘threefold bridged' Al13H- isomers of 3.21 and 2.32 eV are in good agreement with those determined in the PE study.

Density functional theory study of phase stability and defect thermodynamics in iron-oxyhydroxide mineral materials

NASA Astrophysics Data System (ADS)

Pinney, Nathan Douglas

Due to their high surface area and reactivity toward a variety of heavy metal and oxyanion species of environmental concern, Fe-(oxyhydr)oxide materials play an important role in the geochemical fate of natural and anthropogenic contaminants in soils, aquifers and surface water environments worldwide. In this research, ab initio simulations describe the bulk structure, magnetic properties, and relative phase stability of major Fe-(oxyhydr)oxide materials, including hematite, goethite, lepidocrocite, and ferrihydrite.These bulk models are employed in further studies of point defect and alloy/dopant thermodynamics in these materials, allowing construction of a phase stability model that better replicates the structure and composition of real materials. Li + adsorption at the predominant goethite (101) surface is simulated using ab initio methods, offering energetic and structural insight into the binding mechanisms of metal cations over a range of surface protonation conditions.

Origin of the chemical and kinetic stability of graphene oxide.

PubMed

Zhou, Si; Bongiorno, Angelo

2013-01-01

At moderate temperatures (≤ 70°C), thermal reduction of graphene oxide is inefficient and after its synthesis the material enters in a metastable state. Here, first-principles and statistical calculations are used to investigate both the low-temperature processes leading to decomposition of graphene oxide and the role of ageing on the structure and stability of this material. Our study shows that the key factor underlying the stability of graphene oxide is the tendency of the oxygen functionalities to agglomerate and form highly oxidized domains surrounded by areas of pristine graphene. Within the agglomerates of functional groups, the primary decomposition reactions are hindered by both geometrical and energetic factors. The number of reacting sites is reduced by the occurrence of local order in the oxidized domains, and due to the close packing of the oxygen functionalities, the decomposition reactions become - on average - endothermic by more than 0.6 eV.

Metabolic support for the heart: complementary therapy for heart failure?

PubMed

Heggermont, Ward A; Papageorgiou, Anna-Pia; Heymans, Stephane; van Bilsen, Marc

2016-12-01

The failing heart has an increased metabolic demand and at the same time suffers from impaired energy efficiency, which is a detrimental combination. Therefore, therapies targeting the energy-deprived failing heart and rewiring cardiac metabolism are of great potential, but are lacking in daily clinical practice. Metabolic impairment in heart failure patients has been well characterized for patients with reduced ejection fraction, and is coming of age in patients with 'preserved' ejection fraction. Targeting cardiomyocyte metabolism in heart failure could complement current heart failure treatments that do improve cardiovascular haemodynamics, but not the energetic status of the heart. In this review, we discuss the hallmarks of normal cardiac metabolism, typical metabolic disturbances in heart failure, and past and present therapeutic targets that impact on cardiac metabolism. © 2016 The Authors. European Journal of Heart Failure © 2016 European Society of Cardiology.

A series of energetic metal pentazolate hydrates.

PubMed

Xu, Yuangang; Wang, Qian; Shen, Cheng; Lin, Qiuhan; Wang, Pengcheng; Lu, Ming

2017-09-07

Singly or doubly bonded polynitrogen compounds can decompose to dinitrogen (N 2 ) with an extremely large energy release. This makes them attractive as potential explosives or propellants, but also challenging to produce in a stable form. Polynitrogen materials containing nitrogen as the only element exist in the form of high-pressure polymeric phases, but under ambient conditions even metastability is realized only in the presence of other elements that provide stabilization. An early example is the molecule phenylpentazole, with a five-membered all-nitrogen ring, which was first reported in the 1900s and characterized in the 1950s. Salts containing the azide anion (N 3 - ) or pentazenium cation (N 5 + ) are also known, with compounds containing the pentazole anion, cyclo-N 5 - , a more recent addition. Very recently, a bulk material containing this species was reported and then used to prepare the first example of a solid-state metal-N 5 complex. Here we report the synthesis and characterization of five metal pentazolate hydrate complexes [Na(H 2 O)(N 5 )]·2H 2 O, [M(H 2 O) 4 (N 5 ) 2 ]·4H 2 O (M = Mn, Fe and Co) and [Mg(H 2 O) 6 (N 5 ) 2 ]·4H 2 O that, with the exception of the Co complex, exhibit good thermal stability with onset decomposition temperatures greater than 100 °C. For this series we find that the N 5 - ion can coordinate to the metal cation through either ionic or covalent interactions, and is stabilized through hydrogen-bonding interactions with water. Given their energetic properties and stability, pentazole-metal complexes might potentially serve as a new class of high-energy density materials or enable the development of such materials containing only nitrogen. We also anticipate that the adaptability of the N 5 - ion in terms of its bonding interactions will enable the exploration of inorganic nitrogen analogues of metallocenes and other unusual polynitrogen complexes.

A series of energetic metal pentazolate hydrates

NASA Astrophysics Data System (ADS)

Xu, Yuangang; Wang, Qian; Shen, Cheng; Lin, Qiuhan; Wang, Pengcheng; Lu, Ming

2017-09-01

Singly or doubly bonded polynitrogen compounds can decompose to dinitrogen (N2) with an extremely large energy release. This makes them attractive as potential explosives or propellants, but also challenging to produce in a stable form. Polynitrogen materials containing nitrogen as the only element exist in the form of high-pressure polymeric phases, but under ambient conditions even metastability is realized only in the presence of other elements that provide stabilization. An early example is the molecule phenylpentazole, with a five-membered all-nitrogen ring, which was first reported in the 1900s and characterized in the 1950s. Salts containing the azide anion (N3-) or pentazenium cation (N5+) are also known, with compounds containing the pentazole anion, cyclo-N5-, a more recent addition. Very recently, a bulk material containing this species was reported and then used to prepare the first example of a solid-state metal-N5 complex. Here we report the synthesis and characterization of five metal pentazolate hydrate complexes [Na(H2O)(N5)]·2H2O, [M(H2O)4(N5)2]·4H2O (M = Mn, Fe and Co) and [Mg(H2O)6(N5)2]·4H2O that, with the exception of the Co complex, exhibit good thermal stability with onset decomposition temperatures greater than 100 °C. For this series we find that the N5- ion can coordinate to the metal cation through either ionic or covalent interactions, and is stabilized through hydrogen-bonding interactions with water. Given their energetic properties and stability, pentazole-metal complexes might potentially serve as a new class of high-energy density materials or enable the development of such materials containing only nitrogen. We also anticipate that the adaptability of the N5- ion in terms of its bonding interactions will enable the exploration of inorganic nitrogen analogues of metallocenes and other unusual polynitrogen complexes.

Thermostability analysis of line-tension-associated nucleation at a gas-liquid interface.

PubMed

Singha, Sanat Kumar; Das, Prasanta Kumar; Maiti, Biswajit

2017-01-01

The influence of line tension on the thermostability of a droplet nucleated from an oversaturated vapor at the interface of the vapor and another immiscible liquid is investigated. Along with the condition of mechanical equilibrium, the notion of extremization of the reversible work of formation is considered to obtain the critical parameters related to heterogeneous nucleation. From the energetic formulation, the critical reversible work of formation is found to be greater than that of homogeneous nucleation for high value of the positive line tension. On the other hand, for high value of the negative line tension, the critical reversible work of formation becomes negative. Therefore, these thermodynamic instabilities under certain substrate wettability situations necessitate a free-energetics-based stability of the nucleated droplet, because the system energy is not minimized under these conditions. This thermostability is analogous to the transition-based stability proposed by Widom [B. Widom, J. Phys. Chem. 99, 2803 (1995)]10.1021/j100009a041 in the case of partial wetting phenomena along with the positive line tension. The thermostability analysis limits the domain of the solution space of the present critical-value problem as the thermodynamic transformation in connection with homogeneous and workless nucleation is considered. Within the stability range of the geometry-based wetting parameters, three limiting modes of nucleation, i.e., total-dewetting-related homogeneous nucleation, and total-wetting-associated and total-submergence-associated workless nucleation scenarios, are identified. Either of the two related limiting wetting scenarios of workless nucleation, namely, total wetting and total submergence, is found to be favorable depending on the geometry-based wetting conditions. The line-tension-associated nucleation on a liquid surface can be differentiated from that on a rigid substrate, as in the former, the stability based on mechanical equilibrium and a typical case of workless nucleation with complete submergence are observed.

Infant Temperament: Stability by Age, Gender, Birth Order, Term Status, and SES

PubMed Central

Bornstein, Marc H.; Putnick, Diane L.; Gartstein, Maria A.; Hahn, Chun-Shin; Auestad, Nancy; O’Connor, Deborah L.

2015-01-01

Two complementary studies focused on stability of infant temperament across the first year and considered infant age, gender, birth order, term status, and socioeconomic status (SES) as moderators. Study 1 consisted of 73 mothers of firstborn term girls and boys queried at 2, 5, and 13 months of age. Study 2 consisted of 335 mothers of infants of different gender, birth order, term status, and SES queried at 6 and 12 months. Consistent positive and negative affectivity factors emerged at all time-points across both studies. Infant temperament proved stable and robust across gender, birth order, term status, and SES. Stability coefficients for temperament factors and scales were medium to large for shorter (<9 months) inter-assessment intervals and small to medium for longer (>10 months) intervals. PMID:25865034

Testing Geometrical Discrimination within an Enzyme Active Site: Constrained Hydrogen Bonding in the Ketosteroid Isomerase Oxyanion Hole

PubMed Central

Sigala, Paul A.; Kraut, Daniel A.; Caaveiro, Jose M. M.; Pybus, Brandon; Ruben, Eliza A.; Ringe, Dagmar; Petsko, Gregory A.; Herschlag, Daniel

2009-01-01

Enzymes are classically proposed to accelerate reactions by binding substrates within active site environments that are structurally preorganized to optimize binding interactions with reaction transition states rather than ground states. This is a remarkably formidable task considering the limited 0.1 – 1 Å scale of most substrate rearrangements. The flexibility of active site functional groups along the coordinate of substrate rearrangement, the distance scale on which enzymes can distinguish structural rearrangement, and the energetic significance of discrimination on that scale remain open questions that are fundamental to a basic physical understanding of enzyme active sites and catalysis. We bring together high resolution X-ray crystallography, 1H and 19F NMR spectroscopy, quantum mechanical calculations, and transition state analog binding measurements to test the distance scale on which non-covalent forces can constrain side chain and ligand relaxation or translation along a specific coordinate and the energetic consequences of such geometric constraints within the active site of bacterial ketosteroid isomerase (KSI). Our results strongly suggest that packing and binding interactions within the KSI active site can constrain local side chain reorientation and prevent hydrogen bond shortening by 0.1 Å or less. Further, this constraint has substantial energetic effects on ligand binding and stabilization of negative charge within the oxyanion hole. These results provide evidence that subtle geometric effects, indistinguishable in most X-ray crystallographic structures, can have significant energetic consequences and highlight the importance of using synergistic experimental approaches to dissect enzyme function. PMID:18808119

Nitrogen-rich salts of 5,5‧-bistetrazole-1,1‧-diolate: Syntheses, structures and properties

NASA Astrophysics Data System (ADS)

Yang, Ting; Zhang, Jian-Guo; Zhang, Zhi-Bin; Gozin, Michael

2018-03-01

A series of new nitrogen-rich energetic salts containing 1H,1‧H-[5,5‧-bitetrazole]-1,1‧-diol (BTO) anion and ethane-1,2-diaminium (1), 1-amino-1H-1,2,3-triazol-3-ium (2), 4-amino-4H-1,2,4-triazol-1-ium (3) and 4,5-diamino-4H-1,2,4-triazol-1-ium (4) cations were synthesized by direct salt formation or by metathesis strategy. The structures of energetic salts 1-4 were comprehensively characterized by elemental analysis, mass spectrometry, IR and NMR spectroscopies and by X-ray crystallography. DSC and TGA methods were used to study thermal properties of these salts. Additionally, the non-isothermal kinetic parameters and thermodynamic parameters were calculated by utilizing the Kissinger's and Ozawa-Doyle's methods. The enthalpies of formation for all target compounds in this study were calculated, and their sensitivity to mechanical impact and friction was tested according to BAM guidelines. We found these new energetic salts exhibit good thermal stability and have typical decomposition temperatures above 230 °C, except for the salt 2. All our salts have highly-positive enthalpies of formation (311.1-473.6 kJ mol-1) and are insensitive to impact and friction stimuli (>40 J, 120 N). With a high nitrogen-rich content, high enthalpy of formation, good thermostability and very low sensitivity to impact, some of these new salts may have a potential for application in the field of environmentally friendly insensitive energetic materials.

Spontaneous assembly of a self-complementary oligopeptide to form a stable macroscopic membrane

NASA Technical Reports Server (NTRS)

Zhang, S.; Holmes, T.; Lockshin, C.; Rich, A.

1993-01-01

A 16-residue peptide [(Ala-Glu-Ala-Glu-Ala-Lys-Ala-Lys)2] has a characteristic beta-sheet circular dichroism spectrum in water. Upon the addition of salt, the peptide spontaneously assembles to form a macroscopic membrane. The membrane does not dissolve in heat or in acidic or alkaline solutions, nor does it dissolve upon addition of guanidine hydrochloride, SDS/urea, or a variety of proteolytic enzymes. Scanning EM reveals a network of interwoven filaments approximately 10-20 nm in diameter. An important component of the stability is probably due to formation of complementary ionic bonds between glutamic and lysine side chains. This phenomenon may be a model for studying the insoluble peptides found in certain neurological disorders. It may also have implications for biomaterials and origin-of-life research.

Biomimetic enzyme nanocomplexes and their use as antidotes and preventive measures for alcohol intoxication

NASA Astrophysics Data System (ADS)

Liu, Yang; Du, Juanjuan; Yan, Ming; Lau, Mo Yin; Hu, Jay; Han, Hui; Yang, Otto O.; Liang, Sheng; Wei, Wei; Wang, Hui; Li, Jianmin; Zhu, Xinyuan; Shi, Linqi; Chen, Wei; Ji, Cheng; Lu, Yunfeng

2013-03-01

Organisms have sophisticated subcellular compartments containing enzymes that function in tandem. These confined compartments ensure effective chemical transformation and transport of molecules, and the elimination of toxic metabolic wastes. Creating functional enzyme complexes that are confined in a similar way remains challenging. Here we show that two or more enzymes with complementary functions can be assembled and encapsulated within a thin polymer shell to form enzyme nanocomplexes. These nanocomplexes exhibit improved catalytic efficiency and enhanced stability when compared with free enzymes. Furthermore, the co-localized enzymes display complementary functions, whereby toxic intermediates generated by one enzyme can be promptly eliminated by another enzyme. We show that nanocomplexes containing alcohol oxidase and catalase could reduce blood alcohol levels in intoxicated mice, offering an alternative antidote and prophylactic for alcohol intoxication.

Accuracy of ab initio electron correlation and electron densities in vanadium dioxide

DOE PAGES

Kylänpää, Ilkka; Balachandran, Janakiraman; Ganesh, Panchapakesan; ...

2017-11-27

Here, diffusion quantum Monte Carlo results are used as a reference to analyze properties related to phase stability and magnetism in vanadium dioxide computed with various formulations of density functional theory. We introduce metrics related to energetics, electron densities and spin densities that give us insight on both local and global variations in the antiferromagnetic M1 and R phases. Importantly, these metrics can address contributions arising from the challenging description of the 3d orbital physics in this material. We observe that the best description of energetics between the structural phases does not correspond to the best accuracy in the charge density, which is consistent with observations made recently by Medvedev et~al. in the context of isolated atoms. However, we do find evidence that an accurate spin density connects to correct energetic ordering of different magnetic states in VOmore » $$_2$$, although local, semilocal, and meta-GGA functionals tend to erroneously favor demagnetization of the vanadium sites. The recently developed SCAN functional stands out as remaining nearly balanced in terms of magnetization across the M1-R transition and correctly predicting the ground state crystal structure. In addition to ranking current density functionals, our reference energies and densities serve as important benchmarks for future functional development.« less

Aromatic Side Chain Water-to-Lipid Transfer Free Energies Show a Depth Dependence across the Membrane Normal.

PubMed

McDonald, Sarah K; Fleming, Karen G

2016-06-29

Quantitating and understanding the physical forces responsible for the interactions of biomolecules are fundamental to the biological sciences. This is especially challenging for membrane proteins because they are embedded within cellular bilayers that provide a unique medium in which hydrophobic sequences must fold. Knowledge of the energetics of protein-lipid interactions is thus vital to understand cellular processes involving membrane proteins. Here we used a host-guest mutational strategy to calculate the Gibbs free energy changes of water-to-lipid transfer for the aromatic side chains Trp, Tyr, and Phe as a function of depth in the membrane. This work reveals an energetic gradient in the transfer free energies for Trp and Tyr, where transfer was most favorable to the membrane interfacial region and comparatively less favorable into the bilayer center. The transfer energetics follows the concentration gradient of polar atoms across the bilayer normal that naturally occurs in biological membranes. Additional measurements revealed nearest-neighbor coupling in the data set are influenced by a network of aromatic side chains in the host protein. Taken together, these results show that aromatic side chains contribute significantly to membrane protein stability through either aromatic-aromatic interactions or placement at the membrane interface.

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

Solomon, Jonathan M.; Shamblin, Jacob; Lang, Maik

Fluorite-structured oxides find widespread use for applications spanning nuclear energy and waste containment, energy conversion, and sensing. In such applications the host tetravalent cation is often partially substituted by trivalent cations, with an associated formation of charge-compensating oxygen vacancies. The stability and properties of such materials are known to be influenced strongly by chemical ordering of the cations and vacancies, and the nature of such ordering and associated energetics are thus of considerable interest. Here we employ density-functional theory (DFT) calculations to study the structure and energetics of cation and oxygen-vacancy ordering in Ho 2Zr 2O 7. In a recentmore » neutron total scattering study, solid solutions in this system were reported to feature local chemical ordering based on the fluorite-derivative weberite structure. The calculations show a preferred chemical ordering qualitatively consistent with these findings, and yield values for the ordering energy of 9.5 kJ/mol-cation. Similar DFT calculations are applied to additional RE 2Th 2O 7'' fluorite compounds, spanning a range of values for the ratio of the tetravalent and trivalent (RE) cation radii. Finally, the results demonstrate that weberite-type order becomes destabilized with increasing values of this size ratio, consistent with an increasing energetic preference for the tetravalent cations to have higher oxygen coordination.« less

Phase space effects on fast ion distribution function modeling in tokamaks

NASA Astrophysics Data System (ADS)

Podestà, M.; Gorelenkova, M.; Fredrickson, E. D.; Gorelenkov, N. N.; White, R. B.

2016-05-01

Integrated simulations of tokamak discharges typically rely on classical physics to model energetic particle (EP) dynamics. However, there are numerous cases in which energetic particles can suffer additional transport that is not classical in nature. Examples include transport by applied 3D magnetic perturbations and, more notably, by plasma instabilities. Focusing on the effects of instabilities, ad-hoc models can empirically reproduce increased transport, but the choice of transport coefficients is usually somehow arbitrary. New approaches based on physics-based reduced models are being developed to address those issues in a simplified way, while retaining a more correct treatment of resonant wave-particle interactions. The kick model implemented in the tokamak transport code TRANSP is an example of such reduced models. It includes modifications of the EP distribution by instabilities in real and velocity space, retaining correlations between transport in energy and space typical of resonant EP transport. The relevance of EP phase space modifications by instabilities is first discussed in terms of predicted fast ion distribution. Results are compared with those from a simple, ad-hoc diffusive model. It is then shown that the phase-space resolved model can also provide additional insight into important issues such as internal consistency of the simulations and mode stability through the analysis of the power exchanged between energetic particles and the instabilities.

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

Podesta, M.; Gorelenkova, M.; Fredrickson, E. D.

Here, integrated simulations of tokamak discharges typically rely on classical physics to model energetic particle (EP) dynamics. However, there are numerous cases in which energetic particles can suffer additional transport that is not classical in nature. Examples include transport by applied 3D magnetic perturbations and, more notably, by plasma instabilities. Focusing on the effects of instabilities,ad-hocmodels can empirically reproduce increased transport, but the choice of transport coefficients is usually somehow arbitrary. New approaches based on physics-based reduced models are being developed to address those issues in a simplified way, while retaining a more correct treatment of resonant wave-particle interactions. Themore » kick model implemented in the tokamaktransport code TRANSP is an example of such reduced models. It includes modifications of the EP distribution by instabilities in real and velocity space, retaining correlations between transport in energy and space typical of resonant EP transport. The relevance of EP phase space modifications by instabilities is first discussed in terms of predicted fast ion distribution. Results are compared with those from a simple, ad-hoc diffusive model. It is then shown that the phase-space resolved model can also provide additional insight into important issues such as internal consistency of the simulations and mode stability through the analysis of the power exchanged between energetic particles and the instabilities.« less

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

Podestà, M., E-mail: mpodesta@pppl.gov; Gorelenkova, M.; Fredrickson, E. D.

Integrated simulations of tokamak discharges typically rely on classical physics to model energetic particle (EP) dynamics. However, there are numerous cases in which energetic particles can suffer additional transport that is not classical in nature. Examples include transport by applied 3D magnetic perturbations and, more notably, by plasma instabilities. Focusing on the effects of instabilities, ad-hoc models can empirically reproduce increased transport, but the choice of transport coefficients is usually somehow arbitrary. New approaches based on physics-based reduced models are being developed to address those issues in a simplified way, while retaining a more correct treatment of resonant wave-particle interactions.more » The kick model implemented in the tokamak transport code TRANSP is an example of such reduced models. It includes modifications of the EP distribution by instabilities in real and velocity space, retaining correlations between transport in energy and space typical of resonant EP transport. The relevance of EP phase space modifications by instabilities is first discussed in terms of predicted fast ion distribution. Results are compared with those from a simple, ad-hoc diffusive model. It is then shown that the phase-space resolved model can also provide additional insight into important issues such as internal consistency of the simulations and mode stability through the analysis of the power exchanged between energetic particles and the instabilities.« less

Structural characteristics of liquid nitromethane at the nanoscale confinement in carbon nanotubes.

PubMed

Liu, Yingzhe; Lai, Weipeng; Yu, Tao; Ge, Zhongxue; Kang, Ying

2014-10-01

The stability of energetic materials confined in the carbon nanotubes can be improved at ambient pressure and room temperature, leading to potential energy storage and controlled energy release. However, the microscopic structure of confined energetic materials and the role played by the confinement size are still fragmentary. In this study, molecular dynamics simulations have been performed to explore the structural characteristics of liquid nitromethane (NM), one of the simplest energetic materials, confined in a series of armchair single-walled carbon nanotubes (SWNTs) changing from (5,5) to (16,16) at ambient conditions. The simulation results show that the size-dependent ordered structures of NM with preferred orientations are formed inside the tubular cavities driven by the van der Waals attractions between NM and SWNT together with the dipole-dipole interactions of NM, giving rise to a higher local mass density than that of bulk NM. The NM dipoles prefer to align parallel along the SWNT axis in an end-to-end fashion inside all the nanotubes except the (7,7) SWNT where a unique staggered orientation of NM dipoles perpendicular to the SWNT axis is observed. As the SWNT radius increases, the structural arrangements and dipole orientations of NM become disordered as a result of the weakening of van der Waals interactions between NM and SWNT.

Phase space effects on fast ion distribution function modeling in tokamaks

DOE Data Explorer

White, R. B. [Princeton Plasma Physics Lab. (PPPL), Princeton, NJ (United States); Podesta, M. [Princeton Plasma Physics Lab. (PPPL), Princeton, NJ (United States); Gorelenkova, M. [Princeton Plasma Physics Lab. (PPPL), Princeton, NJ (United States); Fredrickson, E. D. [Princeton Plasma Physics Lab. (PPPL), Princeton, NJ (United States); Gorelenkov, N. N. [Princeton Plasma Physics Lab. (PPPL), Princeton, NJ (United States)

2016-06-01

Integrated simulations of tokamak discharges typically rely on classical physics to model energetic particle (EP) dynamics. However, there are numerous cases in which energetic particles can suffer additional transport that is not classical in nature. Examples include transport by applied 3D magnetic perturbations and, more notably, by plasma instabilities. Focusing on the effects of instabilities, ad-hoc models can empirically reproduce increased transport, but the choice of transport coefficients is usually somehow arbitrary. New approaches based on physics-based reduced models are being developed to address those issues in a simplified way, while retaining a more correct treatment of resonant wave-particle interactions. The kick model implemented in the tokamak transport code TRANSP is an example of such reduced models. It includes modifications of the EP distribution by instabilities in real and velocity space, retaining correlations between transport in energy and space typical of resonant EP transport. The relevance of EP phase space modifications by instabilities is first discussed in terms of predicted fast ion distribution. Results are compared with those from a simple, ad-hoc diffusive model. It is then shown that the phase-space resolved model can also provide additional insight into important issues such as internal consistency of the simulations and mode stability through the analysis of the power exchanged between energetic particles and the instabilities.

Continuous engineering of nano-cocrystals for medical and energetic applications.

PubMed

Spitzer, D; Risse, B; Schnell, F; Pichot, V; Klaumünzer, M; Schaefer, M R

2014-10-10

Cocrystals, solid mixtures of different molecules on molecular scale, are supposed to be tailor made materials with improved employability compared to their pristine individual components in domains such as medicine and explosives. In medicine, cocrystals are obtained by crystallization of active pharmaceutical ingredients with precisely chosen coformers to design medicaments that demonstrate enhanced stability, high solubility, and therefore high bioavailability and optimized drug up-take. Nanoscaling may further advance these characteristica compared to their micronsized counterparts - because of a larger surface to volume ratio of nanoparticles. In the field of energetic materials, cocrystals offer the opportunity to design smart explosives, combining high reactivity with significantly reduced sensitivity, nowadays essential for a safe manipulation and handling. Furthermore, cocrystals are used in ferroelectrics, non-linear material response and electronic organics. However, state of the art batch processes produce low volume of cocrystals of variable quality and only have produced micronsized cocrystals so far, no nano-cocrystals. Here we demonstrate the continuous preparation of pharmaceutical and energetic micro- and nano-cocrystals using the Spray Flash Evaporation process. Our laboratory scale pilot plant continuously prepared up to 8 grams per hour of Caffeine/Oxalic acid 2:1, Caffeine/Glutaric acid 1:1, TNT/CL-20 1:1 and HMX/Cl-20 1:2 nano- and submicronsized cocrystals.

Continuous engineering of nano-cocrystals for medical and energetic applications

NASA Astrophysics Data System (ADS)

Spitzer, D.; Risse, B.; Schnell, F.; Pichot, V.; Klaumünzer, M.; Schaefer, M. R.

2014-10-01

Cocrystals, solid mixtures of different molecules on molecular scale, are supposed to be tailor made materials with improved employability compared to their pristine individual components in domains such as medicine and explosives. In medicine, cocrystals are obtained by crystallization of active pharmaceutical ingredients with precisely chosen coformers to design medicaments that demonstrate enhanced stability, high solubility, and therefore high bioavailability and optimized drug up-take. Nanoscaling may further advance these characteristica compared to their micronsized counterparts - because of a larger surface to volume ratio of nanoparticles. In the field of energetic materials, cocrystals offer the opportunity to design smart explosives, combining high reactivity with significantly reduced sensitivity, nowadays essential for a safe manipulation and handling. Furthermore, cocrystals are used in ferroelectrics, non-linear material response and electronic organics. However, state of the art batch processes produce low volume of cocrystals of variable quality and only have produced micronsized cocrystals so far, no nano-cocrystals. Here we demonstrate the continuous preparation of pharmaceutical and energetic micro- and nano-cocrystals using the Spray Flash Evaporation process. Our laboratory scale pilot plant continuously prepared up to 8 grams per hour of Caffeine/Oxalic acid 2:1, Caffeine/Glutaric acid 1:1, TNT/CL-20 1:1 and HMX/Cl-20 1:2 nano- and submicronsized cocrystals.

Comparing the conformational behavior of a series of diastereomeric cyclic urea HIV-1 inhibitors using the low mode:monte carlo conformational search method.

PubMed

Parish, Carol A; Yarger, Matthew; Sinclair, Kent; Dure, Myrianne; Goldberg, Alla

2004-09-23

The conformational flexibility of a series of diastereomeric cyclic urea HIV-1 protease inhibitors has been examined using the Low Mode:Monte Carlo conformational search method. Force fields were validated by a comparison of the energetic ordering of the minimum energy structures on the AMBER/GBSA(water), OPLSAA/GBSA(water) and HF/6-311G/SCRF(water) surfaces. The energetic ordering of the minima on the OPLSAA /GBSA(water) surface was in better agreement with the quantum calculations than the ordering on the AMBER/GBSA(water) surface. An ensemble of low energy structures was generated using OPLSAA/GBSA(water) and used to compare the molecular shape and flexibility of each diastereomer to the experimentally determined binding affinities and crystal structures of closely related systems. The results indicate that diastereomeric solution-phase energetic stability, conformational rigidity and ability to adopt a chair conformation correlate strongly with experimental binding affinities. Rigid body docking suggests that all of the diastereomers adopt solution-phase conformations suitable for alignment with the HIV-1 protease; however, these results indicate that the binding affinities are dependent upon subtle differences in the P1/P1' and P2/P2' substituent orientations.

Continuous engineering of nano-cocrystals for medical and energetic applications

PubMed Central

Spitzer, D.; Risse, B.; Schnell, F.; Pichot, V.; Klaumünzer, M.; Schaefer, M. R.

2014-01-01

Cocrystals, solid mixtures of different molecules on molecular scale, are supposed to be tailor made materials with improved employability compared to their pristine individual components in domains such as medicine and explosives. In medicine, cocrystals are obtained by crystallization of active pharmaceutical ingredients with precisely chosen coformers to design medicaments that demonstrate enhanced stability, high solubility, and therefore high bioavailability and optimized drug up-take. Nanoscaling may further advance these characteristica compared to their micronsized counterparts – because of a larger surface to volume ratio of nanoparticles. In the field of energetic materials, cocrystals offer the opportunity to design smart explosives, combining high reactivity with significantly reduced sensitivity, nowadays essential for a safe manipulation and handling. Furthermore, cocrystals are used in ferroelectrics, non-linear material response and electronic organics. However, state of the art batch processes produce low volume of cocrystals of variable quality and only have produced micronsized cocrystals so far, no nano-cocrystals. Here we demonstrate the continuous preparation of pharmaceutical and energetic micro- and nano-cocrystals using the Spray Flash Evaporation process. Our laboratory scale pilot plant continuously prepared up to 8 grams per hour of Caffeine/Oxalic acid 2:1, Caffeine/Glutaric acid 1:1, TNT/CL-20 1:1 and HMX/Cl-20 1:2 nano- and submicronsized cocrystals. PMID:25300652

Accuracy of ab initio electron correlation and electron densities in vanadium dioxide

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

Kylänpää, Ilkka; Balachandran, Janakiraman; Ganesh, Panchapakesan

Here, diffusion quantum Monte Carlo results are used as a reference to analyze properties related to phase stability and magnetism in vanadium dioxide computed with various formulations of density functional theory. We introduce metrics related to energetics, electron densities and spin densities that give us insight on both local and global variations in the antiferromagnetic M1 and R phases. Importantly, these metrics can address contributions arising from the challenging description of the 3d orbital physics in this material. We observe that the best description of energetics between the structural phases does not correspond to the best accuracy in the charge density, which is consistent with observations made recently by Medvedev et~al. in the context of isolated atoms. However, we do find evidence that an accurate spin density connects to correct energetic ordering of different magnetic states in VOmore » $$_2$$, although local, semilocal, and meta-GGA functionals tend to erroneously favor demagnetization of the vanadium sites. The recently developed SCAN functional stands out as remaining nearly balanced in terms of magnetization across the M1-R transition and correctly predicting the ground state crystal structure. In addition to ranking current density functionals, our reference energies and densities serve as important benchmarks for future functional development.« less

Sensor Buoy System for Monitoring Renewable Marine Energy Resources.

PubMed

García, Emilio; Quiles, Eduardo; Correcher, Antonio; Morant, Francisco

2018-03-22

In this paper we present a multi-sensor floating system designed to monitor marine energy parameters, in order to sample wind, wave, and marine current energy resources. For this purpose, a set of dedicated sensors to measure the height and period of the waves, wind, and marine current intensity and direction have been selected and installed in the system. The floating device incorporates wind and marine current turbines for renewable energy self-consumption and to carry out complementary studies on the stability of such a system. The feasibility, safety, sensor communications, and buoy stability of the floating device have been successfully checked in real operating conditions.

A Thermodynamic Theory of Solid Viscoelasticity. Part 3: Nonlinear Glassy Viscoelasticity, Stability Constraints, Specifications

NASA Technical Reports Server (NTRS)

Freed, Alan; Leonov, Arkady I.

2002-01-01

This paper, the last in the series, continues developing the nonlinear constitutive relations for non-isothermal, compressible, solid viscoelasticity. We initially discuss a single integral approach, more suitable for the glassy state of rubber-like materials, with basic functionals involved in the thermodynamic description for this type of viscoelasticity. Then we switch our attention to analyzing stability constraints, imposed on the general formulation of the nonlinear theory of solid viscoelasticity. Finally, we discuss specific (known from the literature or new) expressions for material functions that are involved in the constitutive formulations of both the rubber-like and glassy-like, complementary parts of the theory.

Sensor Buoy System for Monitoring Renewable Marine Energy Resources

PubMed Central

García, Emilio; Morant, Francisco

2018-01-01

In this paper we present a multi-sensor floating system designed to monitor marine energy parameters, in order to sample wind, wave, and marine current energy resources. For this purpose, a set of dedicated sensors to measure the height and period of the waves, wind, and marine current intensity and direction have been selected and installed in the system. The floating device incorporates wind and marine current turbines for renewable energy self-consumption and to carry out complementary studies on the stability of such a system. The feasibility, safety, sensor communications, and buoy stability of the floating device have been successfully checked in real operating conditions. PMID:29565823

Recoverable information and emergent conservation laws in fracton stabilizer codes

NASA Astrophysics Data System (ADS)

Schmitz, A. T.; Ma, Han; Nandkishore, Rahul M.; Parameswaran, S. A.

2018-04-01

We introduce a new quantity that we term recoverable information, defined for stabilizer Hamiltonians. For such models, the recoverable information provides a measure of the topological information as well as a physical interpretation, which is complementary to topological entanglement entropy. We discuss three different ways to calculate the recoverable information and prove their equivalence. To demonstrate its utility, we compute recoverable information for fracton models using all three methods where appropriate. From the recoverable information, we deduce the existence of emergent Z2 Gauss-law-type constraints, which in turn imply emergent Z2 conservation laws for pointlike quasiparticle excitations of an underlying topologically ordered phase.

Understanding oxygen adsorption on 9.375 at. % Ga-stabilized δ-Pu (111) surface: A DFT study

DOE PAGES

Hernandez, Sarah C.; Wilkerson, Marianne P.; Huda, Muhammad N.

2015-08-30

Plutonium (Pu) metal reacts rapidly in the presence of oxygen (O), resulting in an oxide layer that will eventually have an olive green rust appearance over time. Recent experimental work suggested that the incorporation of gallium (Ga) as an alloying impurity to stabilize the highly symmetric high temperature δ-phase lattice may also provide resistance against corrosion/oxidation of plutonium. In this paper, we modeled a 9.375 at. % Ga stabilized δ-Pu (111) surface and investigated adsorption of atomic O using all-electron density functional theory. Key findings revealed that the O bonded strongly to a Pu-rich threefold hollow fcc site with amore » chemisorption energy of –5.06 eV. Migration of the O atom to a Pu-rich environment was also highly sensitive to the surface chemistry of the Pu–Ga surface; when the initial on-surface O adsorption site included a bond to a nearest neighboring Ga atom, the O atom relaxed to a Ga deficient environment, thus affirming the O preference for Pu. Only one calculated final on-surface O adsorption site included a Ga-O bond, but this chemisorption energy was energetically unfavorable. Chemisorption energies for interstitial adsorption sites that included a Pu or Pu-Ga environment suggested that over-coordination of the O atom was energetically unfavorable as well. Electronic structure properties of the on-surface sites, illustrated by the partial density of states, implied that the Ga 4p states indirectly but strongly influenced the Pu 6d states strongly to hybridize with the O 2p states, while also weakly influenced the Pu 5f states to hybridize with the O 2p states, even though Ga was not participating in bonding with O.« less

Mixed convective/dynamic roll vortices and their effects on initial wind and temperature profiles

NASA Technical Reports Server (NTRS)

Haack, Tracy; Shirer, Hampton N.

1991-01-01

The onset and development of both dynamically and convectively forced boundary layer rolls are studied with linear and nonlinear analyses of a truncated spectral model of shallow Boussinesq flow. Emphasis is given here on the energetics of the dominant roll modes, on the magnitudes of the roll-induced modifications of the initial basic state wind and temperature profiles, and on the sensitivity of the linear stability results to the use of modified profiles as basic states. It is demonstrated that the roll circulations can produce substantial changes to the cross-roll component of the initial wind profile and that significant changes in orientation angle estimates can result from use of a roll-modified profile in the stability analysis. These results demonstrate that roll contributions must be removed from observed background wind profiles before using them to investigate the mechanisms underlying actual secondary flows in the boundary layer. The model is developed quite generally to accept arbitrary basic state wind profiles as dynamic forcing. An Ekman profile is chosen here merely to provide a means for easy comparison with other theoretical boundary layer studies; the ultimate application of the model is to study observed boundary layer profiles. Results of the analytic stability analysis are validated by comparing them with results from a larger linear model. For an appropriate Ekman depth, a complete set of transition curves is given in forcing parameter space for roll modes driven both thermally and dynamically. Preferred orientation angles, horizontal wavelengths and propagation frequencies, as well as energetics and wind profile modifications, are all shown to agree rather well with results from studies on Ekman layers as well as with studies on near-neutral and convective atmospheric boundary layers.

Mechanisms of stability of armored bubbles: FY 1996 Final Report

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

Rossen, W.R.; Kam, S.I.

1996-11-01

Theoretical and experimental studies examine how a coating, or {open_quotes}armor,{close_quotes} of partially wetted solid particles can stabilize tiny bubbles against diffusion of gas into the surrounding liquid, in spite of the high capillary pressures normally associated with such bubbles. Experiments with polymethylmethacrylate (PNMA) beads and carbonated water demonstrate that armored bubbles can persist for weeks in liquid unsaturated with respect to the gas in the bubbles. This question is of concern regarding gas discharges from waste tanks at the Hanford reservation. The stresses on the solid-solid contacts between particles in such cases is large and could drive sintering of themore » particles into a rigid framework. Stability analysis suggests that a slightly shrunken bubble would not expel a solid particle from its armor to relieve stress and allow the bubble to shrink further. Expulsion of particles from more stressed bubbles at zero capillary pressure is energetically favored in some cases. It is not clear, however, whether this expulsion would proceed spontaneously from a small perturbation or require a large initial disturbance of the bubble. In some cases, it appears that a bubble would expel some particles and shrink, but the bubble would approach a final, stable size rather than disappear completely. This simplified analysis leaves out several factors. For instance, only one perturbation toward expelling a solid from the armor is considered; perhaps other perturbations would be more energetically favored than that tested. Other considerations (particle deformation, surface roughness, contact-angle hysteresis, and adhesion or physical bonding between adjacent particles) would make expelling solids more difficult than indicated by this theoretical study.« less

Probing the energetics of dissociation of carbonic anhydrase-ligand complexes in the gas phase.

PubMed Central

Gao, J; Wu, Q; Carbeck, J; Lei, Q P; Smith, R D; Whitesides, G M

1999-01-01

This paper describes the use of electrospray ionization-Fourier transform ion cyclotron mass spectrometry (ESI-FTICR-MS) to study the relative stabilities of noncovalent complexes of carbonic anhydrase II (CAII, EC 4.2.1.1) and benzenesulfonamide inhibitors in the gas phase. Sustained off-resonance irradiation collision-induced dissociation (SORI-CID) was used to determine the energetics of dissociation of these CAII-sulfonamide complexes in the gas phase. When two molecules of a benzenesulfonamide (1) were bound simultaneously to one molecule of CAII, one of them was found to exhibit significantly weaker binding (DeltaE50 = 0.4 V, where E50 is defined as the amplitude of sustained off-resonance irradiation when 50% of the protein-ligand complexes are dissociated). In solution, the benzenesulfonamide group coordinates as an anion to a Zn(II) ion bound at the active site of the enzyme. The gas phase stability of the complex with the weakly bound inhibitor was the same as that of the inhibitor complexed with apoCAII (i.e., CAII with the Zn(II) ion removed from the binding site). These results indicate that specific interactions between the sulfonamide group on the inhibitor and the Zn(II) ion on CAII were preserved in the gas phase. Experiments also showed a higher gas phase stability for the complex of para-NO2-benzenesulfonamide-CAII than that for ortho-NO2-benzenesulfonamide-CAII complex. This result further suggests that steric interactions of the inhibitors with the binding pocket of CAII parallel those in solution. Overall, these results are consistent with the hypothesis that CAII retains, at least partially, the structure of its binding pocket in the gas phase on the time scale (seconds to minutes) of the ESI-FTICR measurements. PMID:10354450

Balancing the Hydrogen Evolution Reaction, Surface Energetics, and Stability of Metallic MoS2 Nanosheets via Covalent Functionalization.

PubMed

Benson, Eric E; Zhang, Hanyu; Schuman, Samuel A; Nanayakkara, Sanjini U; Bronstein, Noah D; Ferrere, Suzanne; Blackburn, Jeffrey L; Miller, Elisa M

2018-01-10

We modify the fundamental electronic properties of metallic (1T phase) nanosheets of molybdenum disulfide (MoS 2 ) through covalent chemical functionalization, and thereby directly influence the kinetics of the hydrogen evolution reaction (HER), surface energetics, and stability. Chemically exfoliated, metallic MoS 2 nanosheets are functionalized with organic phenyl rings containing electron donating or withdrawing groups. We find that MoS 2 functionalized with the most electron donating functional group (p-(CH 3 CH 2 ) 2 NPh-MoS 2 ) is the most efficient catalyst for HER in this series, with initial activity that is slightly worse compared to the pristine metallic phase of MoS 2 . The p-(CH 3 CH 2 ) 2 NPh-MoS 2 is more stable than unfunctionalized metallic MoS 2 and outperforms unfunctionalized metallic MoS 2 for continuous H 2 evolution within 10 min under the same conditions. With regards to the entire studied series, the overpotential and Tafel slope for catalytic HER are both directly correlated with the electron donating strength of the functional group. The results are consistent with a mechanism involving ground-state electron donation or withdrawal to/from the MoS 2 nanosheets, which modifies the electron transfer kinetics and catalytic activity of the MoS 2 nanosheet. The functional groups preserve the metallic nature of the MoS 2 nanosheets, inhibiting conversion to the thermodynamically stable semiconducting state (2H) when mildly annealed in a nitrogen atmosphere. We propose that the electron density and, therefore, reactivity of the MoS 2 nanosheets are controlled by the attached functional groups. Functionalizing nanosheets of MoS 2 and other transition metal dichalcogenides provides a synthetic chemical route for controlling the electronic properties and stability within the traditionally thermally unstable metallic state.

Island shape, size and interface dependency on electronic and magnetic properties of graphene hexagonal-boron nitride (h-BN) in-plane hybrids

NASA Astrophysics Data System (ADS)

Akman, Nurten; Özdoğan, Cem

2018-04-01

We systematically investigate the energetics of ion implantation, stability, electronic, and magnetic properties of graphene/hexagonal boron nitrate (h-BN) in-plane hybrids through first principle calculations. We consider hexagonal and triangular islands in supercells of graphene and h-BN layouts. In the case of triangular islands, both phases mix with each other by either solely Csbnd N or Csbnd B bonds. We also patterned triangles with predominating Csbnd N or Csbnd B bonds at their interfaces. The energetics of island implantation is discussed in detail. Formation energies point out that the island implantation could be even exothermic for all hybrids studied in this work. Effects of size and shape of the island, and dominating bonding sort at the island-layout interfaces on the stability, band gap, and magnetic properties of hybrids are studied particularly. The hybrids become more stable with increasing island size. Regardless of the layout, hybrids with hexagonal islands are all non-magnetic and semiconducting. One can thus open a band gap in the semimetallic graphene by mixing it with the h-BN phase. In general, hybrids containing graphene triangles show metallic property and exhibit considerable amount of magnetic moments for possible localized spin utilizations. Total magnetic moment of hybrids with both graphene and h-BN layouts increases with growing triangle island as well. The spin densities of magnetic hybrids are derived from interfaces of the islands and diminish towards their center. We suggest that the increase in stability and magnetic moment depend on the number of atoms at the interfaces rather than the island size.

The 3R polymorph of CaSi{sub 2}

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

Nedumkandathil, Reji; Benson, Daryn E.; Grins, Jekabs

The Zintl phase CaSi{sub 2} commonly occurs in the 6R structure where puckered hexagon layers of Si atoms are stacked in an AA′BB′CC′ fashion. In this study we show that sintering of CaSi{sub 2} in a hydrogen atmosphere (30 bar) at temperatures between 200 and 700 °C transforms 6R-CaSi{sub 2} quantitatively into 3R-CaSi{sub 2}. In the 3R polymorph (space group R-3m (no. 166), a=3.8284(1), c=15.8966(4), Z=3) puckered hexagon layers are stacked in an ABC fashion. The volume per formula unit is about 3% larger compared to 6R-CaSi{sub 2}. First principles density functional calculations reveal that 6R and 3R-CaSi{sub 2} aremore » energetically degenerate at zero Kelvin. With increasing temperature 6R-CaSi{sub 2} stabilizes over 3R because of its higher entropy. This suggests that 3R-CaSi{sub 2} should revert to 6R at elevated temperatures, which however is not observed up to 800 °C. 3R-CaSi{sub 2} may be stabilized by small amounts of incorporated hydrogen and/or defects. - Graphical abstract: The common 6R form of CaSi{sub 2} can be transformed quantitatively into 3R-CaSi{sub 2} upon sintering in a hydrogen atmosphere. - Highlights: • Quantitative and reproducible bulk synthesis of the rare 3R polymorph of CaSi{sub 2}. • Clarification of the energetic relation between 3R and conventional 6R form. • 3R-CaSi{sub 2} is presumably stabilized by small amounts of incorporated hydrogen and/or defects.« less

Understanding oxygen adsorption on 9.375 at. % Ga-stabilized δ-Pu (111) surface: A DFT study

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

Hernandez, Sarah C.; Wilkerson, Marianne P.; Huda, Muhammad N.

Plutonium (Pu) metal reacts rapidly in the presence of oxygen (O), resulting in an oxide layer that will eventually have an olive green rust appearance over time. Recent experimental work suggested that the incorporation of gallium (Ga) as an alloying impurity to stabilize the highly symmetric high temperature δ-phase lattice may also provide resistance against corrosion/oxidation of plutonium. In this paper, we modeled a 9.375 at. % Ga stabilized δ-Pu (111) surface and investigated adsorption of atomic O using all-electron density functional theory. Key findings revealed that the O bonded strongly to a Pu-rich threefold hollow fcc site with amore » chemisorption energy of –5.06 eV. Migration of the O atom to a Pu-rich environment was also highly sensitive to the surface chemistry of the Pu–Ga surface; when the initial on-surface O adsorption site included a bond to a nearest neighboring Ga atom, the O atom relaxed to a Ga deficient environment, thus affirming the O preference for Pu. Only one calculated final on-surface O adsorption site included a Ga-O bond, but this chemisorption energy was energetically unfavorable. Chemisorption energies for interstitial adsorption sites that included a Pu or Pu-Ga environment suggested that over-coordination of the O atom was energetically unfavorable as well. Electronic structure properties of the on-surface sites, illustrated by the partial density of states, implied that the Ga 4p states indirectly but strongly influenced the Pu 6d states strongly to hybridize with the O 2p states, while also weakly influenced the Pu 5f states to hybridize with the O 2p states, even though Ga was not participating in bonding with O.« less

Energetics of side-chain partitioning of β-signal residues in unassisted folding of a transmembrane β-barrel protein

PubMed Central

Iyer, Bharat Ramasubramanian; Zadafiya, Punit; Vetal, Pallavi Vijay

2017-01-01

The free energy of water-to-interface amino acid partitioning is a major contributing factor in membrane protein folding and stability. The interface residues at the C terminus of transmembrane β-barrels form the β-signal motif required for assisted β-barrel assembly in vivo but are believed to be less important for β-barrel assembly in vitro. Here, we experimentally measured the thermodynamic contribution of all 20 amino acids at the β-signal motif to the unassisted folding of the model β-barrel protein PagP. We obtained the partitioning free energy for all 20 amino acids at the lipid-facing interface (ΔΔG0w,i(φ)) and the protein-facing interface (ΔΔG0w,i(π)) residues and found that hydrophobic amino acids are most favorably transferred to the lipid-facing interface, whereas charged and polar groups display the highest partitioning energy. Furthermore, the change in non-polar surface area correlated directly with the partitioning free energy for the lipid-facing residue and inversely with the protein-facing residue. We also demonstrate that the interface residues of the β-signal motif are vital for in vitro barrel assembly, because they exhibit a side chain–specific energetic contribution determined by the change in nonpolar accessible surface. We further establish that folding cooperativity and hydrophobic collapse are balanced at the membrane interface for optimal stability of the PagP β-barrel scaffold. We conclude that the PagP C-terminal β-signal motif influences the folding cooperativity and stability of the folded β-barrel and that the thermodynamic contributions of the lipid- and protein-facing residues in the transmembrane protein β-signal motif depend on the nature of the amino acid side chain. PMID:28592485

Probing the impact of magnetic interactions on the lattice dynamics of two-dimensional Ti2X (X = C, N) MXenes.

PubMed

Sternik, Małgorzata; Wdowik, Urszula D

2018-03-14

Dynamical properties of the two-dimensional Ti 2 C and Ti 2 N MXenes were investigated using density functional theory and discussed in connection with their structures and electronic properties. To elucidate the influence of magnetic interactions on the fundamental properties of these systems, the nonmagnetic, ferromagnetic and three distinct antiferromagnetic spin arrangements on titanium sublattice were considered. Each magnetic configuration was also studied at two directions of the spin magnetic moment with respect to the MXene layer. The zero-point energy motion, following from the phonon calculations, was taken into account while analyzing the energetic stability of the magnetic phases against the nonmagnetic solution. This contribution was found not to change a sequence of the energetic stability of the considered magnetic structures of Ti 2 X (X = C, N) MXenes. Both Ti 2 X (X = C, N) systems are shown to prefer antiferromagnetic arrangement of spins between Ti layers and the ferromagnetic order within each layer. This energetically privileged phase is semiconducting for Ti 2 C and metallic for Ti 2 N. The type of magnetic order as well as the in-plane or out-of-plane spin polarizations have a relatively small impact on the structural parameters, Ti-X bonding length, force constants and phonon spectra of both Ti 2 X systems, leading to observable differences only between the nonmagnetic and any other magnetic configurations. Nonetheless, a noticeable effect of the spin orientation on degeneracy of the Ti-3d orbitals is encountered. The magnetic interactions affect to a great extent the positions and intensities of the Raman-active modes, and hence one could exploit this effect for experimental verification of the theoretically predicted magnetic state of Ti 2 X monolayers. Theoretical phonon spectra of Ti 2 X (X = C, N) MXenes exhibit a linear dependence on energy in the long-wavelength limit, which is typical for a 2D system.

Same but not alike: Structure, flexibility and energetics of domains in multi-domain proteins are influenced by the presence of other domains

PubMed Central

Vishwanath, Sneha

2018-01-01

The majority of the proteins encoded in the genomes of eukaryotes contain more than one domain. Reasons for high prevalence of multi-domain proteins in various organisms have been attributed to higher stability and functional and folding advantages over single-domain proteins. Despite these advantages, many proteins are composed of only one domain while their homologous domains are part of multi-domain proteins. In the study presented here, differences in the properties of protein domains in single-domain and multi-domain systems and their influence on functions are discussed. We studied 20 pairs of identical protein domains, which were crystallized in two forms (a) tethered to other proteins domains and (b) tethered to fewer protein domains than (a) or not tethered to any protein domain. Results suggest that tethering of domains in multi-domain proteins influences the structural, dynamic and energetic properties of the constituent protein domains. 50% of the protein domain pairs show significant structural deviations while 90% of the protein domain pairs show differences in dynamics and 12% of the residues show differences in the energetics. To gain further insights on the influence of tethering on the function of the domains, 4 pairs of homologous protein domains, where one of them is a full-length single-domain protein and the other protein domain is a part of a multi-domain protein, were studied. Analyses showed that identical and structurally equivalent functional residues show differential dynamics in homologous protein domains; though comparable dynamics between in-silico generated chimera protein and multi-domain proteins were observed. From these observations, the differences observed in the functions of homologous proteins could be attributed to the presence of tethered domain. Overall, we conclude that tethered domains in multi-domain proteins not only provide stability or folding advantages but also influence pathways resulting in differences in function or regulatory properties. PMID:29432415

Same but not alike: Structure, flexibility and energetics of domains in multi-domain proteins are influenced by the presence of other domains.

PubMed

Vishwanath, Sneha; de Brevern, Alexandre G; Srinivasan, Narayanaswamy

2018-02-01

The majority of the proteins encoded in the genomes of eukaryotes contain more than one domain. Reasons for high prevalence of multi-domain proteins in various organisms have been attributed to higher stability and functional and folding advantages over single-domain proteins. Despite these advantages, many proteins are composed of only one domain while their homologous domains are part of multi-domain proteins. In the study presented here, differences in the properties of protein domains in single-domain and multi-domain systems and their influence on functions are discussed. We studied 20 pairs of identical protein domains, which were crystallized in two forms (a) tethered to other proteins domains and (b) tethered to fewer protein domains than (a) or not tethered to any protein domain. Results suggest that tethering of domains in multi-domain proteins influences the structural, dynamic and energetic properties of the constituent protein domains. 50% of the protein domain pairs show significant structural deviations while 90% of the protein domain pairs show differences in dynamics and 12% of the residues show differences in the energetics. To gain further insights on the influence of tethering on the function of the domains, 4 pairs of homologous protein domains, where one of them is a full-length single-domain protein and the other protein domain is a part of a multi-domain protein, were studied. Analyses showed that identical and structurally equivalent functional residues show differential dynamics in homologous protein domains; though comparable dynamics between in-silico generated chimera protein and multi-domain proteins were observed. From these observations, the differences observed in the functions of homologous proteins could be attributed to the presence of tethered domain. Overall, we conclude that tethered domains in multi-domain proteins not only provide stability or folding advantages but also influence pathways resulting in differences in function or regulatory properties.

Nitrogen doping and CO2 adsorption on graphene: A thermodynamical study

NASA Astrophysics Data System (ADS)

Re Fiorentin, Michele; Gaspari, Roberto; Quaglio, Marzia; Massaglia, Gulia; Saracco, Guido

2018-04-01

Nitrogen-doped graphene has raised considerable interest for its possible applications as carbon dioxide adsorber and catalyst. In this paper, we provide a theoretical study of graphitic, pyridiniclike and pyrroliclike nitrogen defects in a free-standing graphene layer, focusing on their formation and adsorption behavior. Using density functional theory and thermodynamics, we analyze the various defects, highlighting the great stability of graphitic nitrogen in a wide temperature and pressure range. CO2 adsorption proves to be moderately thermodynamically disfavored around standard conditions for the most stable nitrogen defects and slightly favored for the more energetic ones. The combination of the results on defect stability and CO2 adsorption may open interesting possibilities in the design of carbon-based materials with promising adsorption performances.

Ferroelectricity in high-density H 2O ice

DOE PAGES

Caracas, Razvan; Hemley, Russell J.

2015-04-01

The origin of longstanding anomalies in experimental studies of the dense solid phases of H 2O ices VII, VIII, and X is examined using a combination of first-principles theoretical methods. We find that a ferroelectric variant of ice VIII is energetically competitive with the established antiferroelectric form under pressure. The existence of domains of the ferroelectric form within anti-ferroelectric ice can explain previously observed splittings in x-ray diffraction data. The ferroelectric form is stabilized by density and is accompanied by the onset of spontaneous polarization. Here, the presence of local electric fields triggers the preferential parallel orientation of the watermore » molecules in the structure, which could be stabilized in bulk using new high-pressure techniques.« less

Vapor mediated droplet interactions - models and mechanisms (Part 2)

NASA Astrophysics Data System (ADS)

Benusiglio, Adrien; Cira, Nate; Prakash, Manu

2014-11-01

When deposited on clean glass a two-component binary mixture of propylene glycol and water is energetically inclined to spread, as both pure liquids do. Instead the mixture forms droplets stabilized by evaporation induced surface tension gradients, giving them unique properties such as negligible hysteresis. When two of these special droplets are deposited several radii apart they attract each other. The vapor from one droplet destabilizes the other, resulting in an attraction force which brings both droplets together. We present a flux-based model for droplet stabilization and a model which connects the vapor profile to net force. These simple models capture the static and dynamic experimental trends, and our fundamental understanding of these droplets and their interactions allowed us to build autonomous fluidic machines.

Energetic Limitations on Microbial Respiration of Organic Compounds using Aqueous Fe(III) Complexes

NASA Astrophysics Data System (ADS)

Naughton, H.; Fendorf, S. E.

2015-12-01

Soil organic matter constitutes up to 75% of the terrestrial carbon stock. Microorganisms mediate the breakdown of organic compounds and the return of carbon to the atmosphere, predominantly through respiration. Microbial respiration requires an electron acceptor and an electron donor such as small fatty acids, organic acids, alcohols, sugars, and other molecules that differ in oxidation state of carbon. Carbon redox state affects how much energy is required to oxidize a molecule through respiration. Therefore, different organic compounds should offer a spectrum of energies to respiring microorganisms. However, microbial respiration has traditionally focused on the availability and reduction potential of electron acceptors, ignoring the organic electron donor. We found through incubation experiments that the organic compound serving as electron donor determined how rapidly Shewanella putrefaciens CN32 respires organic substrate and the extent of reduction of the electron acceptor. We simulated a range of energetically favorable to unfavorable electron acceptors using organic chelators bound to Fe(III) with equilibrium stability constants ranging from log(K) of 11.5 to 25.0 for the 1:1 complex, where more stable complexes are less favorable for microbial respiration. Organic substrates varied in nominal oxidation state of carbon from +2 to -2. The most energetically favorable substrate, lactate, promoted up to 30x more rapid increase in percent Fe(II) compared to less favorable substrates such as formate. This increased respiration on lactate was more substantial with less stable Fe(III)-chelate complexes. Intriguingly, this pattern contradicts respiration rate predicted by nominal oxidation state of carbon. Our results suggest that organic substrates will be consumed so long as the energetic toll corresponding to the electron donor half reaction is counterbalanced by the energy available from the electron accepting half reaction. We propose using the chemical structure of organic matter, elucidated with techniques such as FT-ICR MS, to improve microbial decomposition and carbon cycling models by incorporating energetic limitations due to carbon oxidation.

Collective plasma effects associated with the continuous injection model of solar flare particle streams

NASA Technical Reports Server (NTRS)

Vlahos, L.; Papadopoulos, K.

1979-01-01

A modified continuous injection model for impulsive solar flares that includes self-consistent plasma nonlinearities based on the concept of marginal stability is presented. A quasi-stationary state is established, composed of a hot truncated electron Maxwellian distribution confined by acoustic turbulence on the top of the loop and energetic electron beams precipitating in the chromosphere. It is shown that the radiation properties of the model are in accordance with observations.

A theory of solar type 3 radio bursts

NASA Technical Reports Server (NTRS)

Goldstein, M. L.; Papadopoulos, K.; Smith, R. A.

1979-01-01

Energetic electrons propagating through the interplanetary medium are shown to excite the one dimensional oscillating two stream instability (OTSI). The OTSI is in turn stabilized by anomalous resistivity which completes the transfer of long wavelength Langmuir waves to short wavelengths, out of resonance with the electrons. The theory explains the small energy losses suffered by the electrons in propagating to 1 AU, the predominance of second harmonic radiation, and the observed correlation between radio and electron fluxes.

Effect of Defects on Mechanisms of Initiation and Energy Release in Energetic Molecular Crystals

DTIC Science & Technology

2011-02-10

dynamics of NEEMs ," Aberdeen, MD, Mar. 2010. 60. Dana Dlott (invited) American Chemical Society Annual Meeting, "Vibrational Energy in Molecules with High...hydrocarbons to ascertain their stability under extreme conditions. Also, HEs are often mixed with fuel oils as well so we sought to separately...dependence of the EOS. Ab initio calculations were performed to extract the complete equation of state for an organic molecular crystal over a

Asymmetric interjoint feedback contributes to postural control of redundant multi-link systems

NASA Astrophysics Data System (ADS)

Bunderson, Nathan E.; Ting, Lena H.; Burkholder, Thomas J.

2007-09-01

Maintaining the postural configuration of a limb such as an arm or leg is a fundamental neural control task that involves the coordination of multiple linked body segments. Biological systems are known to use a complex network of inter- and intra-joint feedback mechanisms arising from muscles, spinal reflexes and higher neuronal structures to stabilize the limbs. While previous work has shown that a small amount of asymmetric heterogenic feedback contributes to the behavior of these systems, a satisfactory functional explanation for this non-conservative feedback structure has not been put forth. We hypothesized that an asymmetric multi-joint control strategy would confer both an energetic and stability advantage in maintaining endpoint position of a kinematically redundant system. We tested this hypothesis by using optimal control models incorporating symmetric versus asymmetric feedback with the goal of maintaining the endpoint location of a kinematically redundant, planar limb. Asymmetric feedback improved endpoint control performance of the limb by 16%, reduced energetic cost by 21% and increased interjoint coordination by 40% compared to the symmetric feedback system. The overall effect of the asymmetry was that proximal joint motion resulted in greater torque generation at distal joints than vice versa. The asymmetric organization is consistent with heterogenic stretch reflex gains measured experimentally. We conclude that asymmetric feedback has a functionally relevant role in coordinating redundant degrees of freedom to maintain the position of the hand or foot.

Finite size effect on hydrogen bond cooperativity in (Ala)n polypeptides: A DFT study using numeric atom-centered orbitals

NASA Astrophysics Data System (ADS)

Blum, Volker; Ireta, Joel; Scheffler, Matthias

2007-03-01

An accurate representation of the energetic contribution Ehb of hydrogen bonds to structure formation is paramount to understand the secondary structure stability of proteins, both qualitatively and quantitatively. However, Ehb depends strongly on its environment, and even on the surrounding peptide conformation itself. For instance, a short α-helical polypeptide (Ala)4 can not be stabilized by its single hydrogen bond, whereas an infinite α-helical chain (Ala)∞ is clearly energetically stable over a fully extended conformation. We here use all-electron density functional calculations in the PBE generalized gradient approximation by a recently developed, computationally efficient numeric atom-centered orbital based code^1 to investigate this H-bond cooperativity that is intrinsic to Alanine-based polypeptides (Ala)n (n=1-20,∞). We compare finite and infinite prototypical helical conformations (α, π, 310) on equal footing, with both neutral and ionic termination for finite (Ala)n peptides. Moderately sized NAO basis sets allow to capture Ehb with meV accuracy, revealing a clear jump in Ehb (cooperativity) when two H-bonds first appear in line, followed by slower and more continuous increase of Ehb towards n->∞. ^1 V. Blum, R. Gehrke, P. Havu, V. Havu, M. Scheffler, The FHI Ab Initio Molecular Simulations (aims) Project, Fritz-Haber-Institut, Berlin (2006).

Asymmetric interjoint feedback contributes to postural control of redundant multi-link systems

PubMed Central

Bunderson, Nathan E.; Ting, Lena H.; Burkholder, Thomas J.

2008-01-01

Maintaining the postural configuration of a limb such as an arm or leg is a fundamental neural control task that involves the coordination of multiple linked body segments. Biological systems are known to use a complex network of inter- and intra-joint feedback mechanisms arising from muscles, spinal reflexes, and higher neuronal structures to stabilize the limbs. While previous work has shown that a small amount of asymmetric heterogenic feedback contributes to the behavior of these systems, a satisfactory functional explanation for this nonconservative feedback structure has not been put forth. We hypothesized that an asymmetric multi-joint control strategy would confer both an energetic and stability advantage in maintaining endpoint position of a kinematically redundant system. We tested this hypothesis by using optimal control models incorporating symmetric versus asymmetric feedback with the goal of maintaining the endpoint location of a kinematically redundant, planar limb. Asymmetric feedback improved endpoint control performance of the limb by 16%, reduced energetic cost by 21% and increased interjoint coordination by 40% compared to the symmetric feedback system. The overall effect of the asymmetry was that proximal joint motion resulted in greater torque generation at distal joints than vice versa. The asymmetric organization is consistent with heterogenic stretch reflex gains measured experimentally. We conclude that asymmetric feedback has a functionally relevant role in coordinating redundant degrees of freedom to maintain the position of the hand or foot. PMID:17873426

Non-perturbative modelling of energetic particle effects on resistive wall mode: Anisotropy and finite orbit width

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

Liu, Yueqiang, E-mail: yueqiang.liu@ccfe.ac.uk; Chapman, I. T.; Graves, J. P.

2014-05-15

A non-perturbative magnetohydrodynamic-kinetic hybrid formulation is developed and implemented into the MARS-K code [Liu et al., Phys. Plasmas 15, 112503 (2008)] that takes into account the anisotropy and asymmetry [Graves et al., Nature Commun. 3, 624 (2012)] of the equilibrium distribution of energetic particles (EPs) in particle pitch angle space, as well as first order finite orbit width (FOW) corrections for both passing and trapped EPs. Anisotropic models, which affect both the adiabatic and non-adiabatic drift kinetic energy contributions, are implemented for both neutral beam injection and ion cyclotron resonant heating induced EPs. The first order FOW correction does notmore » contribute to the precessional drift resonance of trapped particles, but generally remains finite for the bounce and transit resonance contributions, as well as for the adiabatic contributions from asymmetrically distributed passing particles. Numerical results for a 9MA steady state ITER plasma suggest that (i) both the anisotropy and FOW effects can be important for the resistive wall mode stability in ITER plasmas; and (ii) the non-perturbative approach predicts less kinetic stabilization of the mode, than the perturbative approach, in the presence of anisotropy and FOW effects for the EPs. The latter may partially be related to the modification of the eigenfunction of the mode by the drift kinetic effects.« less

Titanium Dioxide Nanoparticle-Based Interdigitated Electrodes: A Novel Current to Voltage DNA Biosensor Recognizes E. coli O157:H7.

PubMed

Nadzirah, Sh; Azizah, N; Hashim, Uda; Gopinath, Subash C B; Kashif, Mohd

2015-01-01

Nanoparticle-mediated bio-sensing promoted the development of novel sensors in the front of medical diagnosis. In the present study, we have generated and examined the potential of titanium dioxide (TiO2) crystalline nanoparticles with aluminium interdigitated electrode biosensor to specifically detect single-stranded E.coli O157:H7 DNA. The performance of this novel DNA biosensor was measured the electrical current response using a picoammeter. The sensor surface was chemically functionalized with (3-aminopropyl) triethoxysilane (APTES) to provide contact between the organic and inorganic surfaces of a single-stranded DNA probe and TiO2 nanoparticles while maintaining the sensing system's physical characteristics. The complement of the target DNA of E. coli O157:H7 to the carboxylate-probe DNA could be translated into electrical signals and confirmed by the increased conductivity in the current-to-voltage curves. The specificity experiments indicate that the biosensor can discriminate between the complementary sequences from the base-mismatched and the non-complementary sequences. After duplex formation, the complementary target sequence can be quantified over a wide range with a detection limit of 1.0 x 10(-13)M. With target DNA from the lysed E. coli O157:H7, we could attain similar sensitivity. Stability of DNA immobilized surface was calculated with the relative standard deviation (4.6%), displayed the retaining with 99% of its original response current until 6 months. This high-performance interdigitated DNA biosensor with high sensitivity, stability and non-fouling on a novel sensing platform is suitable for a wide range of biomolecular interactive analyses.

Synthesis and binding properties of new selective ligands for the nucleobase opposite the AP site.

PubMed

Abe, Yukiko; Nakagawa, Osamu; Yamaguchi, Rie; Sasaki, Shigeki

2012-06-01

DNA is continuously damaged by endogenous and exogenous factors such as oxidative stress or DNA alkylating agents. These damaged nucleobases are removed by DNA N-glycosylase and form apurinic/apyrimidinic sites (AP sites) as intermediates in the base excision repair (BER) pathway. AP sites are also representative DNA damages formed by spontaneous hydrolysis. The AP sites block DNA polymerase and a mismatch nucleobase is inserted opposite the AP sites by polymerization to cause acute toxicities and mutations. Thus, AP site specific compounds have attracted much attention for therapeutic and diagnostic purposes. In this study, we have developed nucleobase-polyamine conjugates as the AP site binding ligand by expecting that the nucleobase part would play a role in the specific recognition of the nucleobase opposite the AP site by the Watson-Crick base pair formation and that the polyamine part should contribute to the access of the ligand to the AP site by a non-specific interaction to the DNA phosphate backbone. The nucleobase conjugated with 3,3'-diaminodipropylamine (A-ligand, G-ligand, C-ligand, T-ligand and U-ligand) showed a specific stabilization of the duplex containing the AP site depending on the complementary combination with the nucleobase opposite the AP site; that is A-ligand to T, G-ligand to C, C-ligand to G, T- and U-ligand to A. The thermodynamic binding parameters clearly indicated that the specific stabilization is due to specific binding of the ligands to the complementary AP site. These results have suggested that the complementary base pairs of the Watson-Crick type are formed at the AP site. Copyright © 2012 Elsevier Ltd. All rights reserved.

Titanium Dioxide Nanoparticle-Based Interdigitated Electrodes: A Novel Current to Voltage DNA Biosensor Recognizes E. coli O157:H7

PubMed Central

Nadzirah, Sh.; Azizah, N.; Hashim, Uda; Gopinath, Subash C. B.; Kashif, Mohd

2015-01-01

Nanoparticle-mediated bio-sensing promoted the development of novel sensors in the front of medical diagnosis. In the present study, we have generated and examined the potential of titanium dioxide (TiO2) crystalline nanoparticles with aluminium interdigitated electrode biosensor to specifically detect single-stranded E.coli O157:H7 DNA. The performance of this novel DNA biosensor was measured the electrical current response using a picoammeter. The sensor surface was chemically functionalized with (3-aminopropyl) triethoxysilane (APTES) to provide contact between the organic and inorganic surfaces of a single-stranded DNA probe and TiO2 nanoparticles while maintaining the sensing system’s physical characteristics. The complement of the target DNA of E. coli O157:H7 to the carboxylate-probe DNA could be translated into electrical signals and confirmed by the increased conductivity in the current-to-voltage curves. The specificity experiments indicate that the biosensor can discriminate between the complementary sequences from the base-mismatched and the non-complementary sequences. After duplex formation, the complementary target sequence can be quantified over a wide range with a detection limit of 1.0 x 10-13M. With target DNA from the lysed E. coli O157:H7, we could attain similar sensitivity. Stability of DNA immobilized surface was calculated with the relative standard deviation (4.6%), displayed the retaining with 99% of its original response current until 6 months. This high-performance interdigitated DNA biosensor with high sensitivity, stability and non-fouling on a novel sensing platform is suitable for a wide range of biomolecular interactive analyses. PMID:26445455

Phosphorus allotropes: Stability of black versus red phosphorus re-examined by means of the van der Waals inclusive density functional method

NASA Astrophysics Data System (ADS)

Aykol, Muratahan; Doak, Jeff W.; Wolverton, C.

2017-06-01

We evaluate the energetic stabilities of white, red, and black allotropes of phosphorus using density functional theory (DFT) and hybrid functional methods, van der Waals (vdW) corrections (DFT+vdW and hybrid+vdW), vdW density functionals, and random phase approximation (RPA). We find that stability of black phosphorus over red-V (i.e., the violet form) is not ubiquitous among these methods, and the calculated enthalpies for the reaction phosphorus (red-V)→phosphorus (black) are scattered between -20 and 40 meV/atom. With local density and generalized gradient approximations, and hybrid functionals, mean absolute errors (MAEs) in densities of P allotropes relative to experiments are found to be around 10%-25%, whereas with vdW-inclusive methods, MAEs in densities drop below ˜5 %. While the inconsistency among the density functional methods could not shed light on the stability puzzle of black versus red phosphorus, comparison of their accuracy in predicting densities and the supplementary RPA results on relative stabilities indicate that opposite to the common belief, black and red phosphorus are almost degenerate, or the red-V (violet) form of phosphorus might even be the ground state.

Kinetic Monte Carlo Investigation of the Effects of Vacancy Pairing on Oxygen Diffusivity in Yttria-Stabilized Zirconia

NASA Technical Reports Server (NTRS)

Good, Brian S.

2011-01-01

Yttria-stabilized zirconia s high oxygen diffusivity and corresponding high ionic conductivity, and its structural stability over a broad range of temperatures, have made the material of interest for use in a number of applications, for example, as solid electrolytes in fuel cells. At low concentrations, the stabilizing yttria also serves to increase the oxygen diffusivity through the presence of corresponding oxygen vacancies, needed to maintain charge neutrality. At higher yttria concentration, however, diffusivity is impeded by the larger number of relatively high energy migration barriers associated with yttrium cations. In addition, there is evidence that oxygen vacancies preferentially occupy nearest-neighbor sites around either dopant or Zr cations, further affecting vacancy diffusion. We present the results of ab initio calculations that indicate that it is energetically favorable for oxygen vacancies to occupy nearest-neighbor sites adjacent to Y ions, and that the presence of vacancies near either species of cation lowers the migration barriers. Kinetic Monte Carlo results from simulations incorporating this effect are presented and compared with results from simulations in which the effect is not present.

Orthogonal Operation of Constitutional Dynamic Networks Consisting of DNA-Tweezer Machines.

PubMed

Yue, Liang; Wang, Shan; Cecconello, Alessandro; Lehn, Jean-Marie; Willner, Itamar

2017-12-26

Overexpression or down-regulation of cellular processes are often controlled by dynamic chemical networks. Bioinspired by nature, we introduce constitutional dynamic networks (CDNs) as systems that emulate the principle of the nature processes. The CDNs comprise dynamically interconvertible equilibrated constituents that respond to external triggers by adapting the composition of the dynamic mixture to the energetic stabilization of the constituents. We introduce a nucleic acid-based CDN that includes four interconvertible and mechanically triggered tweezers, AA', BB', AB' and BA', existing in closed, closed, open, and open configurations, respectively. By subjecting the CDN to auxiliary triggers, the guided stabilization of one of the network constituents dictates the dynamic reconfiguration of the structures of the tweezers constituents. The orthogonal and reversible operations of the CDN DNA tweezers are demonstrated, using T-A·T triplex or K + -stabilized G-quadruplex as structural motifs that control the stabilities of the constituents. The implications of the study rest on the possible applications of input-guided CDN assemblies for sensing, logic gate operations, and programmed activation of molecular machines.

Ultrafast and nonlinear surface-enhanced Raman spectroscopy.

PubMed

Gruenke, Natalie L; Cardinal, M Fernanda; McAnally, Michael O; Frontiera, Renee R; Schatz, George C; Van Duyne, Richard P

2016-04-21

Ultrafast surface-enhanced Raman spectroscopy (SERS) has the potential to study molecular dynamics near plasmonic surfaces to better understand plasmon-mediated chemical reactions such as plasmonically-enhanced photocatalytic or photovoltaic processes. This review discusses the combination of ultrafast Raman spectroscopic techniques with plasmonic substrates for high temporal resolution, high sensitivity, and high spatial resolution vibrational spectroscopy. First, we introduce background information relevant to ultrafast SERS: the mechanisms of surface enhancement in Raman scattering, the characterization of plasmonic materials with ultrafast techniques, and early complementary techniques to study molecule-plasmon interactions. We then discuss recent advances in surface-enhanced Raman spectroscopies with ultrafast pulses with a focus on the study of molecule-plasmon coupling and molecular dynamics with high sensitivity. We also highlight the challenges faced by this field by the potential damage caused by concentrated, highly energetic pulsed fields in plasmonic hotspots, and finally the potential for future ultrafast SERS studies.

Optimizing the specificity of nucleic acid hybridization.

PubMed

Zhang, David Yu; Chen, Sherry Xi; Yin, Peng

2012-01-22

The specific hybridization of complementary sequences is an essential property of nucleic acids, enabling diverse biological and biotechnological reactions and functions. However, the specificity of nucleic acid hybridization is compromised for long strands, except near the melting temperature. Here, we analytically derived the thermodynamic properties of a hybridization probe that would enable near-optimal single-base discrimination and perform robustly across diverse temperature, salt and concentration conditions. We rationally designed 'toehold exchange' probes that approximate these properties, and comprehensively tested them against five different DNA targets and 55 spurious analogues with energetically representative single-base changes (replacements, deletions and insertions). These probes produced discrimination factors between 3 and 100+ (median, 26). Without retuning, our probes function robustly from 10 °C to 37 °C, from 1 mM Mg(2+) to 47 mM Mg(2+), and with nucleic acid concentrations from 1 nM to 5 µM. Experiments with RNA also showed effective single-base change discrimination.

Success of Solar Dynamics Observatory (SDO) Education & Public Outreach (E/PO) in Montana

NASA Astrophysics Data System (ADS)

Freed, M. S.; Lowder, S. C.; McKenzie, D. E.

2013-03-01

The Space Public Outreach Team (SPOT) program at Montana State University (MSU) is the main component of SDO E/PO efforts in Montana. SPOT brings energetic presentations of recent science & NASA missions to students in primary & secondary schools. Presenters are university undergraduates that visit a diverse group of K-12 students from both rural & urban areas of Montana. This program is extremely cost effective, a valuable service-learning experience for undergraduates at MSU and has repeatedly received praise from both teachers and students. A complementary effort for training schoolteachers entitled NASA Education Activity Training (NEAT) is also employed. NEAT illustrates to teachers inexpensive and highly effective methods for demonstrating difficult science concepts to their students. We will highlight the successes and lessons learned from SPOT & NEAT, so that other E/PO programs can use it as a template to further science literacy in our nation's schools.

Mu2e, a coherent μ --> e conversion experiment at Fermilab

NASA Astrophysics Data System (ADS)

Brown, D. N.; Mu2e Collaboration

2012-09-01

We describe a proposed experiment to search for Charged Lepton Flavor Violation (CLFV) using stopped muons at Fermilab. A primary Proton beam will strike a gold target, producing pions which decay to muons. Low-momentum negative muons will be collected, selected, and transported by a custom arrangement of solenoidal magnets and collimators. Muons will stop in thin foil targets, creating muonic atoms with significant nuclear overlap. Mu2e will search for the coherent conversion of nuclear bound muons to electrons, with an experimental signature of a single mono-energetic electron. Conversion electrons will be detected and measured in a low-mass straw tracker and a crystal calorimeter. Mu2e will have a sensitivity four orders of magnitude better than the most sensitive published result for μ → e conversion, and will have complementary physics reach to LHC experiments and μ → eγ decay experiments such as MEG.

The Sixth Omega Laser Facility Users Group Workshop

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

Petrasso, R. D.

A capacity gathering of over 100 researchers from 25 universities and laboratories met at the Laboratory for Laser Energetics (LLE) for the Sixth Omega Laser Facility Users Group (OLUG) workshop. The purpose of the 2.5-day workshop was to facilitate communications and exchanges among individual OMEGA users, and between users and the LLE management; to present ongoing and proposed research; to encourage research opportunities and collaborations that could be undertaken at the Omega Laser Facility and in a complementary fashion at other facilities [such as the National Ignition Facility (NIF) or the Laboratoire pour l’Utilisation des Lasers Intenses (LULI)]; to providemore » an opportunity for students, postdoctoral fellows, and young researchers to present their research in an informal setting; and to provide feedback from the users to LLE management about ways to improve and keep the facility and future experimental campaigns at the cutting edge.« less

The Fifth Omega Laser Facility Users Group Workshop

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

Petrasso, R. D.

A capacity gathering of over 100 researchers from 25 universities and laboratories met at the Laboratory for Laser Energetics (LLE) for the Fifth Omega Laser Facility Users Group (OLUG) workshop. The purpose of the 2.5-day workshop was to facilitate communications and exchanges among individual Omega users and between users and the LLE management; to present ongoing and proposed research; to encourage research opportunities and collaborations that could be undertaken at the Omega Laser Facility and in a complementary fashion at other facilities [such as the National Ignition Facility (NIF) or the Laboratoire pour l’Utilisation des Lasers Intenses (LULI)]; to providemore » an opportunity for students, postdoctoral fellows, and young researchers to present their research in an informal setting; and to provide feedback to LLE management from the users about ways to improve the facility and future experimental campaigns.« less

Energetic Ionic Liquids Based on Anionic Rare Earth Nitrate Complexes (Preprint)

DTIC Science & Technology

2008-07-10

a glass transition temperature (Tg) at -46 oC. However, it is only stable in dry air, and thus must be protected from water. At 75 oC, clear weight...involved highly toxic and corrosive chemicals, N2O4 and NOCl. Ligands which coordinate via oxygen atoms to a rare earth metal ion give rise to stable...complexes. Thus higher air and thermal stabilities may be obtained by introducing rare earth metal nitrates as main components of ionic liquids. We

Nanojets: Electrification, Energetics, Dynamics, Stability and Breakup

DTIC Science & Technology

2006-12-31

OF: 17. LIMITATION OF 18 . NUMBER 19a. NAME OF RESPONSIBLE PERSON a. REPORT b. ABSTRACT c. THIS PAGE ABSTRACT OF Dr Uzi Landman PAGES SU 19b. TELEPHONE...F(Ei )dE,. = Fm,, (Ero, )F,,h (Er,,b)dEro, dEwbh. (8) 16 where F,.ot( Erot ), and Fvwb(Evib) are the normalized rotational and vibrational Maxwell...corresponding to the concentrated solution, while the jet 18 dimensions are associated with radii in the range between 2.3 and 3.29 nm, with the larger

Ultrasensitive bioluminescent determinations of adenosine triphosphate (ATP) for investigating the energetics of host-grown microbes

NASA Technical Reports Server (NTRS)

Hanks, J. H.; Dhople, A. M.

1975-01-01

Stability and optimal concentrations of reagents were studied in bioluminescence assay of ATP levels. Luciferase enzyme was prepared and purified using Sephadex G-100. Interdependencies between enzyme and luciferin concentrations in presence of optimal Mg are illustrated. Optimal ionic strength was confirmed to be 0.05 M for the four buffers tested. Adapted features of the R- and H-systems are summarized, as well as the percentages of ATP pools released from representative microbes by heat and chloroform.

On the calculation of resonances by analytic continuation of eigenvalues from the stabilization graph

NASA Astrophysics Data System (ADS)

Haritan, Idan; Moiseyev, Nimrod

2017-07-01

Resonances play a major role in a large variety of fields in physics and chemistry. Accordingly, there is a growing interest in methods designed to calculate them. Recently, Landau et al. proposed a new approach to analytically dilate a single eigenvalue from the stabilization graph into the complex plane. This approach, termed Resonances Via Padé (RVP), utilizes the Padé approximant and is based on a unique analysis of the stabilization graph. Yet, analytic continuation of eigenvalues from the stabilization graph into the complex plane is not a new idea. In 1975, Jordan suggested an analytic continuation method based on the branch point structure of the stabilization graph. The method was later modified by McCurdy and McNutt, and it is still being used today. We refer to this method as the Truncated Characteristic Polynomial (TCP) method. In this manuscript, we perform an in-depth comparison between the RVP and the TCP methods. We demonstrate that while both methods are important and complementary, the advantage of one method over the other is problem-dependent. Illustrative examples are provided in the manuscript.

Multi-Sensor Based Online Attitude Estimation and Stability Measurement of Articulated Heavy Vehicles.

PubMed

Zhu, Qingyuan; Xiao, Chunsheng; Hu, Huosheng; Liu, Yuanhui; Wu, Jinjin

2018-01-13

Articulated wheel loaders used in the construction industry are heavy vehicles and have poor stability and a high rate of accidents because of the unpredictable changes of their body posture, mass and centroid position in complex operation environments. This paper presents a novel distributed multi-sensor system for real-time attitude estimation and stability measurement of articulated wheel loaders to improve their safety and stability. Four attitude and heading reference systems (AHRS) are constructed using micro-electro-mechanical system (MEMS) sensors, and installed on the front body, rear body, rear axis and boom of an articulated wheel loader to detect its attitude. A complementary filtering algorithm is deployed for sensor data fusion in the system so that steady state margin angle (SSMA) can be measured in real time and used as the judge index of rollover stability. Experiments are conducted on a prototype wheel loader, and results show that the proposed multi-sensor system is able to detect potential unstable states of an articulated wheel loader in real-time and with high accuracy.

Multi-Sensor Based Online Attitude Estimation and Stability Measurement of Articulated Heavy Vehicles

PubMed Central

Xiao, Chunsheng; Liu, Yuanhui; Wu, Jinjin

2018-01-01

Articulated wheel loaders used in the construction industry are heavy vehicles and have poor stability and a high rate of accidents because of the unpredictable changes of their body posture, mass and centroid position in complex operation environments. This paper presents a novel distributed multi-sensor system for real-time attitude estimation and stability measurement of articulated wheel loaders to improve their safety and stability. Four attitude and heading reference systems (AHRS) are constructed using micro-electro-mechanical system (MEMS) sensors, and installed on the front body, rear body, rear axis and boom of an articulated wheel loader to detect its attitude. A complementary filtering algorithm is deployed for sensor data fusion in the system so that steady state margin angle (SSMA) can be measured in real time and used as the judge index of rollover stability. Experiments are conducted on a prototype wheel loader, and results show that the proposed multi-sensor system is able to detect potential unstable states of an articulated wheel loader in real-time and with high accuracy. PMID:29342850

Distribution of chaos and periodic spikes in a three-cell population model of cancer. Auto-organization of oscillatory phases in parameter planes

NASA Astrophysics Data System (ADS)

Gallas, Michelle R.; Gallas, Marcia R.; Gallas, Jason A. C.

2014-10-01

We study complex oscillations generated by the de Pillis-Radunskaya model of cancer growth, a model including interactions between tumor cells, healthy cells, and activated immune system cells. We report a wide-ranging systematic numerical classification of the oscillatory states and of their relative abundance. The dynamical states of the cell populations are characterized here by two independent and complementary types of stability diagrams: Lyapunov and isospike diagrams. The model is found to display stability phases organized regularly in old and new ways: Apart from the familiar spirals of stability, it displays exceptionally long zig-zag networks and intermixed cascades of two- and three-doubling flanked stability islands previously detected only in feedback systems with delay. In addition, we also characterize the interplay between continuous spike-adding and spike-doubling mechanisms responsible for the unbounded complexification of periodic wave patterns. This article is dedicated to Prof. Hans Jürgen Herrmann on the occasion of his 60th birthday.

The role of surface electrostatics on the stability, function and regulation of human cystathionine β-synthase, a complex multidomain and oligomeric protein.

PubMed

Pey, Angel L; Majtan, Tomas; Kraus, Jan P

2014-09-01

Human cystathionine β-synthase (hCBS) is a key enzyme of sulfur amino acid metabolism, controlling the commitment of homocysteine to the transsulfuration pathway and antioxidant defense. Mutations in hCBS cause inherited homocystinuria (HCU), a rare inborn error of metabolism characterized by accumulation of toxic homocysteine in blood and urine. hCBS is a complex multidomain and oligomeric protein whose activity and stability are independently regulated by the binding of S-adenosyl-methionine (SAM) to two different types of sites at its C-terminal regulatory domain. Here we study the role of surface electrostatics on the complex regulation and stability of hCBS using biophysical and biochemical procedures. We show that the kinetic stability of the catalytic and regulatory domains is significantly affected by the modulation of surface electrostatics through noticeable structural and energetic changes along their denaturation pathways. We also show that surface electrostatics strongly affect SAM binding properties to those sites responsible for either enzyme activation or kinetic stabilization. Our results provide new insight into the regulation of hCBS activity and stability in vivo with implications for understanding HCU as a conformational disease. We also lend experimental support to the role of electrostatic interactions in the recently proposed binding modes of SAM leading to hCBS activation and kinetic stabilization. Copyright © 2014 Elsevier B.V. All rights reserved.

Bipolar molecular composites: a new class of high-electron-mobility organic solids

NASA Astrophysics Data System (ADS)

Lin, Liang-Bih; Jenekhe, Samson A.; Borsenberger, Paul M.

1997-10-01

We describe high electron mobility in organic solids in the form of bipolar molecular composites of N,N'-bis(1,2-dimethylpropyl)-1,4,5,8-naphthalenetetracarboxylic diimide (NTDI) and tri-p-tolylaniine (TTA). The electron mobility in the NTDI/TTA composites is ~2 x 10 cm2/Vs, which is a factor of 4 to 6 higher than in pure NTDI and isone of the highest values reported for disordered organic solids. The field and temperature dependencies of the charge mobility can be described using the disorder formalism due to Bassler and co-workers, which provides an estimation of the energy width σ of the hopping site manifold. Analysis of the data gave σ=0.081 and 0.060 eV for the electron and hole mobilities in a NTDI/TTA composite of 0.5510.45 molar ratio. The energetic disorder for electron transport in the bipolar composites is substantially lower than for pure NTDI, which is 0.093 eV. The results suggest that the observed enhancement arises from a substantial reduction of energetic disorder in the electron transport manifold of the bipolar composites. The reduction of energetic disorder may be due to intermolecular charge transfer between NTDI and TTA. Such a charge transfer could stabilize the electron transport manifold by better charge delocalization, and consequently, less energetic disorder. Another possible reason for the observed enhanced electron mobility is the reduction of NTDI dimers that can act as carrier traps by the presence of TTA molecules in the bipolar composites. These results also suggest that bipolar composites represent a promising new class of high electron mobility organic solids.

Enhanced alkaline hydrolysis and biodegradability studies of nitrocellulose-bearing missile propellant

NASA Technical Reports Server (NTRS)

Sidhoum, Mohammed; Christodoulatos, Christos; Su, Tsan-Liang; Redis, Mercurios

1995-01-01

Large amounts of energetic materials which have been accumulated over the years in various manufacturing and military installations must be disposed of in an environmentally sound manner. Historically, the method of choice for destruction of obsolete or aging energetic materials has been open burning or open detonation (OB/OD). This destruction approach has become undesirable due to air pollution problems. Therefore, there is a need for new technologies which will effectively and economically deal with the disposal of energetic materials. Along those lines, we have investigated a chemical/biological process for the safe destruction and disposal of a double base solid rocket propellant (AHH), which was used in several 8 inch projectile systems. The solid propellant is made of nitrocellulose and nitroglycerin as energetic components, two lead salts which act as ballistic modifiers, triacetin as a plasticizer and 2-Nitrodiphenylamine (2-NDPA) as a stabilizer. A process train is being developed to convert the organic components of the propellant to biodegradable products and remove the lead from the process stream. The solid propellant is first hydrolyzed through an enhanced alkaline hydrolysis process step. Following lead removal and neutralization, the digested liquor rich in nitrates and nitrites is found to be easily biodegradable. The digestion rate of the intact ground propellant as well as the release of nitrite and nitrate groups were substantially increased when ultrasound were supplied to the alkaline reaction medium compared to the conventional alkaline hydrolysis. The effects of reaction time, temperature, sodium hydroxide concentration and other relevant parameters on the digestion efficiency and biodegradability have been studied. The present work indicates that the AHH propellant can be disposed of safely with a combination of physiochemical and biological processes.

High Throughput Differential Scanning Fluorimetry (DSF) Formulation Screening with Complementary Dyes to Assess Protein Unfolding and Aggregation in Presence of Surfactants.

PubMed

McClure, Sean M; Ahl, Patrick L; Blue, Jeffrey T

2018-03-05

The purpose was to evaluate DSF for high throughput screening of protein thermal stability (unfolding/ aggregation) across a wide range of formulations. Particular focus was exploring PROTEOSTAT® - a commercially available fluorescent rotor dye - for detection of aggregation in surfactant containing formulations. Commonly used hydrophobic dyes (e.g. SYPRO™ Orange) interact with surfactants, complicating DSF measurements. CRM197 formulations were prepared and analyzed in standard 96-well plate rT-PCR system, using SYPRO™ Orange and PROTEOSTAT® dyes. Orthogonal techniques (DLS and IPF) are employed to confirm unfolding/aggregation in selected formulations. Selected formulations are subjected to non-thermal stresses (stirring and shaking) in plate based format to characterize aggregation with PROTEOSTAT®. Agreement is observed between SYPRO™ Orange (unfolding) and PROTEOSTAT® (aggregation) DSF melt temperatures across wide range of non-surfactant formulations. PROTEOSTAT® can clearly detect temperature induced aggregation in low concentration (0.2 mg/mL) CRM197 formulations containing surfactant. PROTEOSTAT® can be used to explore aggregation due to non-thermal stresses in plate based format amenable to high throughput screening. DSF measurements with complementary extrinsic dyes (PROTEOSTAT®, SYPRO™ Orange) are suitable for high throughput screening of antigen thermal stability, across a wide range of relevant formulation conditions - including surfactants -with standard, plate based rT-PCR instrumentation.

What Hinders Electron Transfer Dissociation (ETD) of DNA Cations?

NASA Astrophysics Data System (ADS)

Hari, Yvonne; Leumann, Christian J.; Schürch, Stefan

2017-12-01

Radical activation methods, such as electron transfer dissociation (ETD), produce structural information complementary to collision-induced dissociation. Herein, electron transfer dissociation of 3-fold protonated DNA hexamers was studied to gain insight into the fragmentation mechanism. The fragmentation patterns of a large set of DNA hexamers confirm cytosine as the primary target of electron transfer. The reported data reveal backbone cleavage by internal electron transfer from the nucleobase to the phosphate linker leading either to a•/ w or d/ z• ion pairs. This reaction pathway contrasts with previous findings on the dissociation processes after electron capture by DNA cations, suggesting multiple, parallel dissociation channels. However, all these channels merely result in partial fragmentation of the precursor ion because the charge-reduced DNA radical cations are quite stable. Two hypotheses are put forward to explain the low dissociation yield of DNA radical cations: it is either attributed to non-covalent interactions between complementary fragments or to the stabilization of the unpaired electron in stacked nucleobases. MS3 experiments suggest that the charge-reduced species is the intact oligonucleotide. Moreover, introducing abasic sites significantly increases the dissociation yield of DNA cations. Consequently, the stabilization of the unpaired electron by π-π-stacking provides an appropriate rationale for the high intensity of DNA radical cations after electron transfer. [Figure not available: see fulltext.

Unifying perspective: Solitary traveling waves as discrete breathers in Hamiltonian lattices and energy criteria for their stability

NASA Astrophysics Data System (ADS)

Cuevas-Maraver, Jesús; Kevrekidis, Panayotis G.; Vainchtein, Anna; Xu, Haitao

2017-09-01

In this work, we provide two complementary perspectives for the (spectral) stability of solitary traveling waves in Hamiltonian nonlinear dynamical lattices, of which the Fermi-Pasta-Ulam and the Toda lattice are prototypical examples. One is as an eigenvalue problem for a stationary solution in a cotraveling frame, while the other is as a periodic orbit modulo shifts. We connect the eigenvalues of the former with the Floquet multipliers of the latter and using this formulation derive an energy-based spectral stability criterion. It states that a sufficient (but not necessary) condition for a change in the wave stability occurs when the functional dependence of the energy (Hamiltonian) H of the model on the wave velocity c changes its monotonicity. Moreover, near the critical velocity where the change of stability occurs, we provide an explicit leading-order computation of the unstable eigenvalues, based on the second derivative of the Hamiltonian H''(c0) evaluated at the critical velocity c0. We corroborate this conclusion with a series of analytically and numerically tractable examples and discuss its parallels with a recent energy-based criterion for the stability of discrete breathers.

Thermal stability and reduction of iron oxide nanowires at moderate temperatures.

PubMed

Paolone, Annalisa; Angelucci, Marco; Panero, Stefania; Betti, Maria Grazia; Mariani, Carlo

2014-01-01

The thermal stability of iron oxide nanowires, which were obtained with a hard template method and are promising elements of Li-ion based batteries, has been investigated by means of thermogravimetry, infrared and photoemission spectroscopy measurements. The chemical state of the nanowires is typical of the Fe2O3 phase and the stoichiometry changes towards a Fe3O4 phase by annealing above 440 K. The shape and morphology of the nanowires is not modified by moderate thermal treatment, as imaged by scanning electron microscopy. This complementary spectroscopy-microscopy study allows to assess the temperature limits of these Fe2O3 nanowires during operation, malfunctioning or abuse in advanced Li-ion based batteries.

Review of A 2B 2O 7 Pyrochlore Response to Irradiation and Pressure

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

Lang, Maik; Zhang, Fuxiang; Zhang, Jiaming

2010-10-01

This article reviews recent research on swift heavy-ion irradiations and high-pressure studies on pyrochlores of the Gd 2Zr 2-xTi xO 7 binary. Applying three complementary analytical techniques (synchrotron X-ray diffraction, Raman spectroscopy and transmission electron microscopy) allowed for the investigation of the response of pyrochlore to irradiation and/or pressure. The chemical composition of pyrochlore has a strong effect on the character and energetics of the type of structural modifications that can be obtained under pressure or irradiation: For Ti-rich pyrochlores, the crystalline-to-amorphous transition is the dominant process. When Zr is substituted for Ti, an order–disorder transformation to the defect-fluorite structuremore » becomes the increasingly dominant process. Except for Gd 2Zr 2O 7, single ion tracks in pyrochlore consist of an amorphous core, surrounded by a crystalline, but disordered, defect-fluorite shell. This shell is surrounded by a defect-rich pyrochlore region. In contrast to similar effects observed when pressure or irradiation are applied separately, the response of the pyrochlore structure is significantly different when it is exposed simultaneously to pressure and irradiation. The combination of relativistic heavy ions with high pressure results in the formation of a new metastable pyrochlore phase. TEM and quantum–mechanical calculations suggest that these novel structural modifications are caused by the formation of nanocrystals and the modified energetics of nanomaterials.« less

Review of A2B2O7 Pyrochlore Response to Irradiation and Pressure

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

Lang, M.; Zhang, F; Zhang, J

2010-01-01

This article reviews recent research on swift heavy-ion irradiations and high-pressure studies on pyrochlores of the Gd{sub 2}Zr{sub 2-x}Ti{sub x}O{sub 7} binary. Applying three complementary analytical techniques (synchrotron X-ray diffraction, Raman spectroscopy and transmission electron microscopy) allowed for the investigation of the response of pyrochlore to irradiation and/or pressure. The chemical composition of pyrochlore has a strong effect on the character and energetics of the type of structural modifications that can be obtained under pressure or irradiation: For Ti-rich pyrochlores, the crystalline-to-amorphous transition is the dominant process. When Zr is substituted for Ti, an order-disorder transformation to the defect-fluorite structuremore » becomes the increasingly dominant process. Except for Gd{sub 2}Zr{sub 2}O{sub 7}, single ion tracks in pyrochlore consist of an amorphous core, surrounded by a crystalline, but disordered, defect-fluorite shell. This shell is surrounded by a defect-rich pyrochlore region. In contrast to similar effects observed when pressure or irradiation are applied separately, the response of the pyrochlore structure is significantly different when it is exposed simultaneously to pressure and irradiation. The combination of relativistic heavy ions with high pressure results in the formation of a new metastable pyrochlore phase. TEM and quantum-mechanical calculations suggest that these novel structural modifications are caused by the formation of nanocrystals and the modified energetics of nanomaterials.« less

RAiSE III: 3C radio AGN energetics and composition

NASA Astrophysics Data System (ADS)

Turner, Ross J.; Shabala, Stanislav S.; Krause, Martin G. H.

2018-03-01

Kinetic jet power estimates based exclusively on observed monochromatic radio luminosities are highly uncertain due to confounding variables and a lack of knowledge about some aspects of the physics of active galactic nuclei (AGNs). We propose a new methodology to calculate the jet powers of the largest, most powerful radio sources based on combinations of their size, lobe luminosity, and shape of their radio spectrum; this approach avoids the uncertainties encountered by previous relationships. The outputs of our model are calibrated using hydrodynamical simulations and tested against independent X-ray inverse-Compton measurements. The jet powers and lobe magnetic field strengths of radio sources are found to be recovered using solely the lobe luminosity and spectral curvature, enabling the intrinsic properties of unresolved high-redshift sources to be inferred. By contrast, the radio source ages cannot be estimated without knowledge of the lobe volumes. The monochromatic lobe luminosity alone is incapable of accurately estimating the jet power or source age without knowledge of the lobe magnetic field strength and size, respectively. We find that, on average, the lobes of the Third Cambridge Catalogue of Radio Sources (3C) have magnetic field strengths approximately a factor three lower than the equipartition value, inconsistent with equal energy in the particles and the fields at the 5σ level. The particle content of 3C radio lobes is discussed in the context of complementary observations; we do not find evidence favouring an energetically dominant proton population.

The Cosmic Ray Energetics And Mass Project

NASA Astrophysics Data System (ADS)

Seo, Eun-Suk; Iss-Cream Collaboration

2017-01-01

The balloon-borne Cosmic Ray Energetics And Mass (CREAM) experiment was flown for 161 days in six flights over Antarctica, the longest known exposure for a single balloon project. Elemental spectra were measured for Z = 1- 26 nuclei over a wide energy range from 1010 to >1014 eV. Building on the success of those balloon flights, one of the two balloon payloads was transformed for exposure on the International Space Station (ISS) Japanese Experiment Module Exposed Facility (JEM-EF). This ISS-CREAM instrument is configured with redundant and complementary particle detectors. The four layers of its finely segmented Silicon Charge Detector provide precise charge measurements, and its ionization calorimeter provides energy measurements. In addition, scintillator-based Top and Bottom Counting Detectors and the Boronated Scintillator Detector distinguish electrons from nuclei. An order of magnitude increase in data collecting power is expected to reach the highest energies practical with direct measurements. Following completion of its qualification tests at NASA Goddard Space Flight Center, the ISS-CREAM payload was delivered to NASA Kennedy Space Center in August 2015 to await its launch to the ISS. While waiting for ISS-CREAM to launch, the other balloon payload including a Transition Radiation Detector, which is too large for the JEM-EF envelope, has been prepared for another Antarctic balloon flight in 2016. This so-called Boron And Carbon Cosmic rays in the Upper Stratosphere (BACCUS) payload will investigate cosmic ray propagation history. The overall project status and future plans will be presented.

Evolution of biofunctional semiconductor nanocrystals: a calorimetric investigation.

PubMed

Ghosh, Debasmita; Mondal, Somrita; Roy, Chandra Nath; Saha, Abhijit

2013-12-14

Semiconductor nanomaterials have found numerous applications in optoelectronic device fabrication and in platforms for drug delivery and hyperthermia cancer treatment, and in various other biomedical fields because of their high photochemical stability and size-tunable photoluminescence (PL). However, little attention has been paid to exploring the energetics of formation of these semiconductor nanoparticles. We demonstrate that formation of nanocrystals with biofunctionalization supported by widely used groups, BSA and cysteine, is an exothermic spontaneous process driven by enthalpy. The whole energetics of the reaction shows that formation of smaller particles is favored with lower synthesis temperature. Further, it is shown that the thermodynamics of nanoparticle formation is strongly influenced by the conformation of the protein matrix. We also demonstrate that protein supported formation of nanocrystals is thermodynamically more favorable compared to that involving smaller organic thiol groups. The favorable enthalpy of formation compensates unfavorable entropy, resulting in favorable Gibbs free energy. Thus, this study can open up new avenues for establishing a thermodynamic basis for the design of nanosystems with new and tunable properties.

Mass spectrometric comparison of swift heavy ion-induced and anaerobic thermal degradation of polymers

NASA Astrophysics Data System (ADS)

Lima, V.; Hossain, U. H.; Walbert, T.; Seidl, T.; Ensinger, W.

2018-03-01

The study of polymers irradiated by highly energetic ions and the resulting radiation-induced degradation is of major importance for space and particle accelerator applications. The mechanism of ion-induced molecular fragmentation of polyethylene, polyethyleneimine and polyamide was investigated by means of mass spectrometry and infrared spectroscopy. The results show that the introduction of nitrogen and oxygen into the polymer influences the stability rendering aliphatic polymers with heteroatoms less stable. A comparison to thermal decomposition data from literature reveals that ion-induced degradation is different in its bond fracture mechanism. While thermal degradation starts at the weakest bond, which is usually the carbon-heteroatom bond, energetic ion irradiation leads in the first step to scission of all types of bonds creating smaller molecular fragments. This is due to the localized extreme energy input under non-equilibrium conditions when the ions transfer kinetic energy onto electrons. These findings are of relevance for the choice of polymers for long-term application in both space and accelerator facilities.

A theoretical study of molecular structure, optical properties and bond activation of energetic compound FOX-7 under intense electric fields

NASA Astrophysics Data System (ADS)

Tao, Zhiqiang; Wang, Xin; Wei, Yuan; Lv, Li; Wu, Deyin; Yang, Mingli

2017-02-01

Molecular structure, vibrational and electronic absorption spectra, chemical reactivity of energetic compound FOX-7, one of the most widely used explosives, were studied computationally in presence of an electrostatic field of 0.01-0.05 a.u. The Csbnd N bond, which usually triggers the decomposition of FOX-7, is shortened/elongated under a parallel/antiparallel field. The Csbnd N bond activation energy varies with the external electric field, decreasing remarkably with the field strength in regardless of the field direction. This is attributed to two aspects: the bond weakening by the field parallel to the Csbnd N bond and the stabilization effect on the transition-state structure by the field antiparallel to the bond. The variations in the structure and property of FOX-7 under the electric fields were further analyzed with its distributional polarizability, which is dependent on the charge transfer characteristics through the Csbnd N bond.

Overview of Spontaneous Frequency Chirping in Confined Plasmas

NASA Astrophysics Data System (ADS)

Berk, Herbert

2012-10-01

Spontaneous rapid frequency chirping is now a commonly observed phenomenon in plasmas with an energetic particle component. These particles typically induce so called weak instabilities, where they excite background waves that the plasma can support such as shear Alfven waves. The explanation for this phenomenon attributes the frequency chirping to the formation of phase space structures in the form of holes and clumps. Normally a saturated mode, in the presence of background dissipation, would be expected decay after saturation as the background plasma absorbs the energy of the excited wave. However the phase space structures take an alternate route, and move to a regions of phase space that are lower energy states of the energetic particle distribution. Through the wave-resonant particle interaction, this movement is locked to the frequency observed by the wave. This phenomenon implies that alternate mechanisms for plasma relaxation need to be considered for plasma states new marginal stability. It is also possible that these chirping mechanisms can be used to advantage to externally control states of plasma.

Energetic metastable high-pressure phases of CO

NASA Astrophysics Data System (ADS)

Barbee, Troy W., III

1996-03-01

First-row elements present some of the best possibilities for storing chemical energy in metastable structures because of their strong bonding and light mass. Recent calculations have predicted(Mailhiot, Yang, and McMahan, Phys. Rev. B 46), 14419 (1992). that under pressure, molecular nitrogen should undergo a transition to a polymeric structure which should be metastable and energetic at ambient pressure. Because carbon monoxide is isoelectronic to N_2, the phase diagram of CO is quite similar to that of nitrogen. Observations of chemical reactions in solid CO under pressure have been made,(Katz, Schiferl, and Mills, J. Phys. Chem. 88), 3176 (1984). and the products (C_3O_2) have been recovered at ambient pressure. I will present calculations of the high-pressure stability and metastability for several candidate structures for CO at high pressure, as well as the energy stored in the metastable C_3O2 at ambient pressure. This work was performed under the auspices of the U.S. DOE by LLNL under contract No. W--7405--ENG--48.

Novel Rubidium Poly-Nitrogen Energetic Materials

NASA Astrophysics Data System (ADS)

Huff, Ashley; Steele, Brad; Oleynik, Ivan

High-nitrogen content compounds are being actively explored with the goal of discovering new high-energy density materials with performance surpassing the conventional energetic materials such as HMX or RDX. Although pure polynitrogen compounds such as cg-N are predicted to deliver 10-fold increase in detonation pressure and detonation velocity of 30 km/s, their synthesis and recovery at ambient conditions is problematic. Doping polynitrogens with other elements is a viable route to promote metastability while reducing synthesis pressure. In this work, rubidium poly-nitrides are being investigated as candidates for high energy density materials. Using first principles evolutionary structure search methods performed at varying stoichiometries and several pressures ranging from 0 to 100 GPa, several new polynitrogen compounds have been discovered. The phase diagrams containing thermodynamically stable and lowest metastable phases are calculated and the dynamical stability of the promising materials is investigated at various pressures. Raman spectra and XRD patterns are also calculated to provide experimentally relevant information useful for identification of these compounds during their synthesis.

Global variation of the para hydrogen fraction in Jupiter's atmosphere and implications for dynamics on the outer planets

NASA Technical Reports Server (NTRS)

Conrath, B. J.; Gierasch, P. J.

1984-01-01

A detailed analysis of the Voyager infrared spectrometer measurements on Jupiter's atmosphere is presented, and possible implications of para hydrogen disequilibrium for the energetics and dynamics of that atmosphere are examined. The method of data analysis is described, and results for the large scale latitude variation of the para hydrogen fraction are presented. The Jovian results show pronounced latitude variation, and are compared with other parameters including wind fields, thermal structure, and various indicators of atmospheric clouds. The problem of equilibration rate is reexamined, and it is concluded that on Jupiter the equilibration time is longer than the radiative time constant at the level of emission to space, but that this inequality reverses at greater depths. A model for the interaction of fluid motions with the ortho-para conversion process is presented, and a consistent mixing length theory for the reacting ortho-para mixture is developed. Several implications of the Jovian data for atmospheric energetics and stability on the outer planets are presented.

The site, size, spatial stability, and energetics of an X-ray flare kernel

NASA Technical Reports Server (NTRS)

Petrasso, R.; Gerassimenko, M.; Nolte, J.

1979-01-01

The site, size evolution, and energetics of an X-ray kernel that dominated a solar flare during its rise and somewhat during its peak are investigated. The position of the kernel remained stationary to within about 3 arc sec over the 30-min interval of observations, despite pulsations in the kernel X-ray brightness in excess of a factor of 10. This suggests a tightly bound, deeply rooted magnetic structure, more plausibly associated with the near chromosphere or low corona rather than with the high corona. The H-alpha flare onset coincided with the appearance of the kernel, again suggesting a close spatial and temporal coupling between the chromospheric H-alpha event and the X-ray kernel. At the first kernel brightness peak its size was no larger than about 2 arc sec, when it accounted for about 40% of the total flare flux. In the second rise phase of the kernel, a source power input of order 2 times 10 to the 24th ergs/sec is minimally required.

Ignition behavior of an aluminum-bonded explosive (ABX)

NASA Astrophysics Data System (ADS)

Hardin, D. Barrett; Zhou, Min; Horie, Yasuyuki

2017-01-01

We report the results of a study on the ignition behavior of a novel concept and design of a heterogeneous energetic material system called ABX, or aluminum-bonded explosives. The idea is to replace the polymeric binder in polymer-bonded explosives (PBX) with aluminum. The motivation of this study is that a new design may have several desirable attributes, including, among others, electrical conductivity, higher mechanical strength, enhanced integrity, higher energy content, and enhanced thermal stability at elevated temperatures. The analysis carried out concerns the replacement of the Estane binder in a HMX/Estane PBX by aluminum. The HMX volume fraction in the PBX and HMX is approximately 81%. 2D mesoscale simulations are carried out, accounting for elasticity, viscoelasticity, elasto-viscoplasticity, fracture, internal friction, and thermal conduction. Results show that, relative to the PBX, the aluminum bonded explosives (ABX) show significantly less heating and lower ignition sensitivity under the same loading conditions. The findings appear to confirm the expected promise of ABX as a next-generation heterogeneous energetic material system with more desirable attributes.

Radionuclide Incorporation and Long Term Performance of Apatite Waste Forms

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

Wang, Jianwei; Lian, Jie; Gao, Fei

2016-01-04

This project aims to combines state-of-the-art experimental and characterization techniques with atomistic simulations based on density functional theory (DFT) and molecular dynamics (MD) simulations. With an initial focus on long-lived I-129 and other radionuclides such as Cs, Sr in apatite structure, specific research objectives include the atomic scale understanding of: (1) incorporation behavior of the radionuclides and their effects on the crystal chemistry and phase stability; (2) stability and microstructure evolution of designed waste forms under coupled temperature and radiation environments; (3) incorporation and migration energetics of radionuclides and release behaviors as probed by DFT and molecular dynamics (MD) simulations;more » and (4) chemical durability as measured in dissolution experiments for long term performance evaluation and model validation.« less

First principles studies of structure stability and lithium intercalation of ZnCo2 O4

NASA Astrophysics Data System (ADS)

Zhang, Yanning; Liu, Weiwei; Beijing Computational Science Research Center Team

Among the metal oxides, which are the most widely investigated alternative anodes for use in lithium ion batteries (LIBs), binary and ternary transition metal oxides have received special attention due to their high capacity values. ZnCo2O4 is a promising candidate as anode for LIB, and one can expect a total capacity corresponding to 7.0 - 8.33 mol of recyclable Li per mole of ZnCo2O4. Here we studied the structural stability, electronic properties, lithium intercalation and diffusion barrier of ZnCo2O4 through density functional calculations. The calculated structural and energetic parameters are comparable with experiments. Our theoretical studies provide insights in understanding the mechanism of lithium ion displacement reactions in this ternary metal oxide.

First principles calculations of stability and lithium intercalation potentials of ZnCo2O4

NASA Astrophysics Data System (ADS)

Yu, L. C.; Wu, J.; Liu, H.; Zhang, Y. N.

2015-03-01

Among the metal oxides, which are the most widely investigated alternative anodes for use in lithium ion batteries (LIBs), binary and ternary tin oxides have received special attention due to their high capacity values. ZnCo2O4 is a promising candidate as the anode material for LIB, and one can expect a total capacity corresponding to 7.0 - 8.33 mol of recyclable Li per mole of ZnCo2O4. Here we studied the structural stability, electronic properties, diffusion barrier and lithium intercalation potentials of ZnCo2O4 through density functional calculations. The calculated structural and energetic parameters are comparable with experiments. Our DFT studies provide insights in understanding the mechanism of lithium ion displacement reactions in this ternary metal oxide.

Self-assembly behavior of β-cyclodextrin and imipramine. A Free energy perturbation study

NASA Astrophysics Data System (ADS)

Sun, Tingting; Shao, Xueguang; Cai, Wensheng

2010-05-01

The self-assembly behavior of β-cyclodextrin (β-CD) and imipramine (IMI), an antidepressant drug, was investigated by molecular dynamics simulations in the gas phase and in an aqueous solution. The binding free energies for 10 possible arrangements of β-CD/IMI complexes with stoichiometries of 1:1, 2:1, and 1:2 were determined using free energy perturbation calculations. The calculations suggest that the 2:1 inclusion mode is the most energetically favored in both phases, in good agreement with experiment. The environment and the neutral and charged IMI influence the stability of the aggregates. The electrostatic interactions constitute the main contribution to the stability. The results reported in this contribution shed new light on the mechanism of association of β-CD with IMI.

Rotation and kinetic modifications of the tokamak ideal-wall pressure limit.

PubMed

Menard, J E; Wang, Z; Liu, Y; Bell, R E; Kaye, S M; Park, J-K; Tritz, K

2014-12-19

The impact of toroidal rotation, energetic ions, and drift-kinetic effects on the tokamak ideal wall mode stability limit is considered theoretically and compared to experiment for the first time. It is shown that high toroidal rotation can be an important destabilizing mechanism primarily through the angular velocity shear; non-Maxwellian fast ions can also be destabilizing, and drift-kinetic damping can potentially offset these destabilization mechanisms. These results are obtained using the unique parameter regime accessible in the spherical torus NSTX of high toroidal rotation speed relative to the thermal and Alfvén speeds and high kinetic pressure relative to the magnetic pressure. Inclusion of rotation and kinetic effects significantly improves agreement between measured and predicted ideal stability characteristics and may provide new insight into tearing mode triggering.

Biomimetic DNA emulsions: specific, thermo-reversible and adjustable binding from a liquid-like DNA layer

NASA Astrophysics Data System (ADS)

Pontani, Lea-Laetitia; Feng, Lang; Dreyfus, Remi; Seeman, Nadrian; Chaikin, Paul; Brujic, Jasna

2013-03-01

We develop micron-sized emulsions coated with specific DNA sequences and complementary sticky ends. The emulsions are stabilized with phospholipids on which the DNA strands are grafted through biotin-streptavidin interactions, which allows the DNA to diffuse freely on the surface. We produce two complementary emulsions: one is functionalized with S sticky ends and dyed with red streptavidin, the other displays the complementary S' sticky ends and green streptavidin. Mixing those emulsions reveals specific adhesion between them due to the short-range S-S' hybridization. As expected this interaction is thermo-reversible: the red-green adhesive droplets dissociate upon heating and reassemble after cooling. Here the fluid phospholipids layer also leads to diffusive adhesion patches, which allows the bound droplets to rearrange throughout the packing structure. We quantify the adhesion strength between two droplets and build a theoretical framework that captures the observed trends through parameters such as the size of the droplets, the DNA surface density, the various DNA constructs or the temperature. This colloidal-scale, specific, thermo-reversible biomimetic emulsion offers a new versatile and powerful tool for the development of complex self-assembled materials.

Controllable Threshold Voltage in Organic Complementary Logic Circuits with an Electron-Trapping Polymer and Photoactive Gate Dielectric Layer.

PubMed

Dao, Toan Thanh; Sakai, Heisuke; Nguyen, Hai Thanh; Ohkubo, Kei; Fukuzumi, Shunichi; Murata, Hideyuki

2016-07-20

We present controllable and reliable complementary organic transistor circuits on a PET substrate using a photoactive dielectric layer of 6-[4'-(N,N-diphenylamino)phenyl]-3-ethoxycarbonylcoumarin (DPA-CM) doped into poly(methyl methacrylate) (PMMA) and an electron-trapping layer of poly(perfluoroalkenyl vinyl ether) (Cytop). Cu was used for a source/drain electrode in both the p-channel and n-channel transistors. The threshold voltage of the transistors and the inverting voltage of the circuits were reversibly controlled over a wide range under a program voltage of less than 10 V and under UV light irradiation. At a program voltage of -2 V, the inverting voltage of the circuits was tuned to be at nearly half of the supply voltage of the circuit. Consequently, an excellent balance between the high and low noise margins (NM) was produced (64% of NMH and 68% of NML), resulting in maximum noise immunity. Furthermore, the programmed circuits showed high stability, such as a retention time of over 10(5) s for the inverter switching voltage. Our findings bring about a flexible, simple way to obtain robust, high-performance organic circuits using a controllable complementary transistor inverter.

Online Wavelet Complementary velocity Estimator.

PubMed

Righettini, Paolo; Strada, Roberto; KhademOlama, Ehsan; Valilou, Shirin

2018-02-01

In this paper, we have proposed a new online Wavelet Complementary velocity Estimator (WCE) over position and acceleration data gathered from an electro hydraulic servo shaking table. This is a batch estimator type that is based on the wavelet filter banks which extract the high and low resolution of data. The proposed complementary estimator combines these two resolutions of velocities which acquired from numerical differentiation and integration of the position and acceleration sensors by considering a fixed moving horizon window as input to wavelet filter. Because of using wavelet filters, it can be implemented in a parallel procedure. By this method the numerical velocity is estimated without having high noise of differentiators, integration drifting bias and with less delay which is suitable for active vibration control in high precision Mechatronics systems by Direct Velocity Feedback (DVF) methods. This method allows us to make velocity sensors with less mechanically moving parts which makes it suitable for fast miniature structures. We have compared this method with Kalman and Butterworth filters over stability, delay and benchmarked them by their long time velocity integration for getting back the initial position data. Copyright © 2017 ISA. Published by Elsevier Ltd. All rights reserved.

Structures and stability of metal-doped Ge nM (n = 9, 10) clusters

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

Qin, Wei; Lu, Wen-Cai; Xia, Lin-Hua

The lowest-energy structures of neutral and cationic Ge nM (n = 9, 10; M = Si, Li, Mg, Al, Fe, Mn, Pb, Au, Ag, Yb, Pm and Dy) clusters were studied by genetic algorithm (GA) and first-principles calculations. The calculation results show that doping of the metal atoms and Si into Ge 9 and Ge 10 clusters is energetically favorable. Most of the metal-doped Ge cluster structures can be viewed as adding or substituting metal atom on the surface of the corresponding ground-state Ge n clusters. However, the neutral and cationic FeGe 9,10,MnGe 9,10 and Ge 10Al are cage-like withmore » the metal atom encapsulated inside. Such cage-like transition metal doped Ge n clusters are shown to have higher adsorption energy and thermal stability. Our calculation results suggest that Ge 9,10Fe and Ge 9Si would be used as building blocks in cluster-assembled nanomaterials because of their high stabilities.« less

Control at stability's edge minimizes energetic costs: expert stick balancing

PubMed Central

Meyer, Ryan; Zhvanetsky, Max; Ridge, Sarah; Insperger, Tamás

2016-01-01

Stick balancing on the fingertip is a complex voluntary motor task that requires the stabilization of an unstable system. For seated expert stick balancers, the time delay is 0.23 s, the shortest stick that can be balanced for 240 s is 0.32 m and there is a ° dead zone for the estimation of the vertical displacement angle in the saggital plane. These observations motivate a switching-type, pendulum–cart model for balance control which uses an internal model to compensate for the time delay by predicting the sensory consequences of the stick's movements. Numerical simulations using the semi-discretization method suggest that the feedback gains are tuned near the edge of stability. For these choices of the feedback gains, the cost function which takes into account the position of the fingertip and the corrective forces is minimized. Thus, expert stick balancers optimize control with a combination of quick manoeuvrability and minimum energy expenditures. PMID:27278361

Structures and stability of metal-doped Ge nM (n = 9, 10) clusters

DOE PAGES

Qin, Wei; Lu, Wen-Cai; Xia, Lin-Hua; ...

2015-06-26

The lowest-energy structures of neutral and cationic Ge nM (n = 9, 10; M = Si, Li, Mg, Al, Fe, Mn, Pb, Au, Ag, Yb, Pm and Dy) clusters were studied by genetic algorithm (GA) and first-principles calculations. The calculation results show that doping of the metal atoms and Si into Ge 9 and Ge 10 clusters is energetically favorable. Most of the metal-doped Ge cluster structures can be viewed as adding or substituting metal atom on the surface of the corresponding ground-state Ge n clusters. However, the neutral and cationic FeGe 9,10,MnGe 9,10 and Ge 10Al are cage-like withmore » the metal atom encapsulated inside. Such cage-like transition metal doped Ge n clusters are shown to have higher adsorption energy and thermal stability. Our calculation results suggest that Ge 9,10Fe and Ge 9Si would be used as building blocks in cluster-assembled nanomaterials because of their high stabilities.« less

Thermodynamic control of anvil cloud amount

PubMed Central

Bony, Sandrine; Stevens, Bjorn; Coppin, David; Becker, Tobias; Reed, Kevin A.; Voigt, Aiko

2016-01-01

General circulation models show that as the surface temperature increases, the convective anvil clouds shrink. By analyzing radiative–convective equilibrium simulations, we show that this behavior is rooted in basic energetic and thermodynamic properties of the atmosphere: As the climate warms, the clouds rise and remain at nearly the same temperature, but find themselves in a more stable atmosphere; this enhanced stability reduces the convective outflow in the upper troposphere and decreases the anvil cloud fraction. By warming the troposphere and increasing the upper-tropospheric stability, the clustering of deep convection also reduces the convective outflow and the anvil cloud fraction. When clouds are radiatively active, this robust coupling between temperature, high clouds, and circulation exerts a positive feedback on convective aggregation and favors the maintenance of strongly aggregated atmospheric states at high temperatures. This stability iris mechanism likely contributes to the narrowing of rainy areas as the climate warms. Whether or not it influences climate sensitivity requires further investigation. PMID:27412863

Thermodynamic control of anvil cloud amount

DOE PAGES

Bony, Sandrine; Stevens, Bjorn; Coppin, David; ...

2016-07-13

General circulation models show that as the surface temperature increases, the convective anvil clouds shrink. By analyzing radiative–convective equilibrium simulations, our work shows that this behavior is rooted in basic energetic and thermodynamic properties of the atmosphere: As the climate warms, the clouds rise and remain at nearly the same temperature, but find themselves in a more stable atmosphere; this enhanced stability reduces the convective outflow in the upper troposphere and decreases the anvil cloud fraction. By warming the troposphere and increasing the upper-tropospheric stability, the clustering of deep convection also reduces the convective outflow and the anvil cloud fraction.more » When clouds are radiatively active, this robust coupling between temperature, high clouds, and circulation exerts a positive feedback on convective aggregation and favors the maintenance of strongly aggregated atmospheric states at high temperatures. This stability iris mechanism likely contributes to the narrowing of rainy areas as the climate warms. Whether or not it influences climate sensitivity requires further investigation.« less

Structures and stability of metal-doped GenM (n = 9, 10) clusters

NASA Astrophysics Data System (ADS)

Qin, Wei; Lu, Wen-Cai; Xia, Lin-Hua; Zhao, Li-Zhen; Zang, Qing-Jun; Wang, C. Z.; Ho, K. M.

2015-06-01

The lowest-energy structures of neutral and cationic GenM (n = 9, 10; M = Si, Li, Mg, Al, Fe, Mn, Pb, Au, Ag, Yb, Pm and Dy) clusters were studied by genetic algorithm (GA) and first-principles calculations. The calculation results show that doping of the metal atoms and Si into Ge9 and Ge10 clusters is energetically favorable. Most of the metal-doped Ge cluster structures can be viewed as adding or substituting metal atom on the surface of the corresponding ground-state Gen clusters. However, the neutral and cationic FeGe9,10,MnGe9,10 and Ge10Al are cage-like with the metal atom encapsulated inside. Such cage-like transition metal doped Gen clusters are shown to have higher adsorption energy and thermal stability. Our calculation results suggest that Ge9,10Fe and Ge9Si would be used as building blocks in cluster-assembled nanomaterials because of their high stabilities.

Atomistic modeling of La3+ doping segregation effect on nanocrystalline yttria-stabilized zirconia.

PubMed

Zhang, Shenli; Sha, Haoyan; Castro, Ricardo H R; Faller, Roland

2018-05-16

The effect of La3+ doping on the structure and ionic conductivity change in nanocrystalline yttria-stabilized zirconia (YSZ) was studied using a combination of Monte Carlo and molecular dynamics simulations. The simulation revealed the segregation of La3+ at eight tilt grain boundary (GB) structures and predicted an average grain boundary (GB) energy decrease of 0.25 J m-2, which is close to the experimental values reported in the literature. Cation stabilization was found to be the main reason for the GB energy decrease, and energy fluctuations near the grain boundary are smoothed out with La3+ segregation. Both dynamic and energetic analysis on the Σ13(510)/[001] GB structure revealed La3+ doping hinders O2- diffusion in the GB region, where the diffusion coefficient monotonically decreases with increasing La3+ doping concentration. The effect was attributed to the increase in the site-dependent migration barriers for O2- hopping caused by segregated La3+, which also leads to anisotropic diffusion at the GB.

Wave energetics of the southern hemisphere of Mars

NASA Astrophysics Data System (ADS)

Battalio, Michael; Szunyogh, Istvan; Lemmon, Mark

2018-07-01

An assessment of the energetics of transient waves in the southern hemisphere of Mars is presented using the Mars Analysis Correction Data Assimilation (MACDA) dataset (v1.0) and the eddy kinetic energy equation. The dataset is divided into four representative periods covering the summer and winter solstices, a late fall period, and an early spring period for three Mars years. Spring eddies are the most intense, with eddies during the fall being less intense due to a marginally more stable mean-temperature profile and reduced recirculation of ageostrophic geopotential fluxes compared to the spring. Eddy kinetic energy during winter is reduced in intensity as a result of the winter solstitial pause in wave activity, and eddy kinetic energy during the summer is limited. Baroclinic energy conversion acts as a source in fall and spring but disappears during the winter as a result of a stabilized vertical temperature profile. Barotropic energy conversion acts as both a source and a sink of eddy kinetic energy, being most positive during the solstitial pause. Eddies take a northwest to southeast track across the southern highlands in the fall but have a more zonal track in the spring due to stronger eddy kinetic energy advection. Wave energetics is less intense in the southern compared to the northern hemisphere as a result of a shallower baroclinically unstable vertical profile.

Experimental model of a wind energy conversion system

NASA Astrophysics Data System (ADS)

Vasar, C.; Rat, C. L.; Prostean, O.

2018-01-01

The renewable energy domain represents an important issue for the sustainable development of the mankind in the actual context of increasing demand for energy along with the increasing pollution that affect the environment. A significant quota of the clean energy is represented by the wind energy. As a consequence, the developing of wind energy conversion systems (WECS) in order to achieve high energetic performances (efficiency, stability, availability, competitive cost etc) represents a topic of permanent actuality. Testing and developing of an optimized control strategy for a WECS direct implemented on a real energetic site is quite difficult and not cost efficient. Thus a more convenient solution consists in a flexible laboratory setup which requires an experimental model of a WECS. Such approach would allow the simulation of various real conditions very similar with existing energetic sites. This paper presents a grid-connected wind turbine emulator. The wind turbine is implemented through a real-time Hardware-in-the-Loop (HIL) emulator, which will be analyzed extensively in the paper. The HIL system uses software implemented in the LabVIEW programming environment to control an ABB ACS800 electric drive. ACS800 has the task of driving an induction machine coupled to a permanent magnet synchronous generator. The power obtained from the synchronous generator is rectified, filtered and sent to the main grid through a controlled inverter. The control strategy is implemented on a NI CompactRIO (cRIO) platform.

Benchmarking Inverse Statistical Approaches for Protein Structure and Design with Exactly Solvable Models.

PubMed

Jacquin, Hugo; Gilson, Amy; Shakhnovich, Eugene; Cocco, Simona; Monasson, Rémi

2016-05-01

Inverse statistical approaches to determine protein structure and function from Multiple Sequence Alignments (MSA) are emerging as powerful tools in computational biology. However the underlying assumptions of the relationship between the inferred effective Potts Hamiltonian and real protein structure and energetics remain untested so far. Here we use lattice protein model (LP) to benchmark those inverse statistical approaches. We build MSA of highly stable sequences in target LP structures, and infer the effective pairwise Potts Hamiltonians from those MSA. We find that inferred Potts Hamiltonians reproduce many important aspects of 'true' LP structures and energetics. Careful analysis reveals that effective pairwise couplings in inferred Potts Hamiltonians depend not only on the energetics of the native structure but also on competing folds; in particular, the coupling values reflect both positive design (stabilization of native conformation) and negative design (destabilization of competing folds). In addition to providing detailed structural information, the inferred Potts models used as protein Hamiltonian for design of new sequences are able to generate with high probability completely new sequences with the desired folds, which is not possible using independent-site models. Those are remarkable results as the effective LP Hamiltonians used to generate MSA are not simple pairwise models due to the competition between the folds. Our findings elucidate the reasons for the success of inverse approaches to the modelling of proteins from sequence data, and their limitations.

Adsorption structures and energetics of molecules on metal surfaces: Bridging experiment and theory

NASA Astrophysics Data System (ADS)

Maurer, Reinhard J.; Ruiz, Victor G.; Camarillo-Cisneros, Javier; Liu, Wei; Ferri, Nicola; Reuter, Karsten; Tkatchenko, Alexandre

2016-05-01

Adsorption geometry and stability of organic molecules on surfaces are key parameters that determine the observable properties and functions of hybrid inorganic/organic systems (HIOSs). Despite many recent advances in precise experimental characterization and improvements in first-principles electronic structure methods, reliable databases of structures and energetics for large adsorbed molecules are largely amiss. In this review, we present such a database for a range of molecules adsorbed on metal single-crystal surfaces. The systems we analyze include noble-gas atoms, conjugated aromatic molecules, carbon nanostructures, and heteroaromatic compounds adsorbed on five different metal surfaces. The overall objective is to establish a diverse benchmark dataset that enables an assessment of current and future electronic structure methods, and motivates further experimental studies that provide ever more reliable data. Specifically, the benchmark structures and energetics from experiment are here compared with the recently developed van der Waals (vdW) inclusive density-functional theory (DFT) method, DFT + vdWsurf. In comparison to 23 adsorption heights and 17 adsorption energies from experiment we find a mean average deviation of 0.06 Å and 0.16 eV, respectively. This confirms the DFT + vdWsurf method as an accurate and efficient approach to treat HIOSs. A detailed discussion identifies remaining challenges to be addressed in future development of electronic structure methods, for which the here presented benchmark database may serve as an important reference.

Phase space effects on fast ion distribution function modeling in tokamaks

DOE PAGES

Podesta, M.; Gorelenkova, M.; Fredrickson, E. D.; ...

2016-04-14

Here, integrated simulations of tokamak discharges typically rely on classical physics to model energetic particle (EP) dynamics. However, there are numerous cases in which energetic particles can suffer additional transport that is not classical in nature. Examples include transport by applied 3D magnetic perturbations and, more notably, by plasma instabilities. Focusing on the effects of instabilities,ad-hocmodels can empirically reproduce increased transport, but the choice of transport coefficients is usually somehow arbitrary. New approaches based on physics-based reduced models are being developed to address those issues in a simplified way, while retaining a more correct treatment of resonant wave-particle interactions. Themore » kick model implemented in the tokamaktransport code TRANSP is an example of such reduced models. It includes modifications of the EP distribution by instabilities in real and velocity space, retaining correlations between transport in energy and space typical of resonant EP transport. The relevance of EP phase space modifications by instabilities is first discussed in terms of predicted fast ion distribution. Results are compared with those from a simple, ad-hoc diffusive model. It is then shown that the phase-space resolved model can also provide additional insight into important issues such as internal consistency of the simulations and mode stability through the analysis of the power exchanged between energetic particles and the instabilities.« less

Chemical ordering in substituted fluorite oxides: a computational investigation of Ho2Zr2O7 and RE2Th2O7 (RE=Ho, Y, Gd, Nd, La).

PubMed

Solomon, Jonathan M; Shamblin, Jacob; Lang, Maik; Navrotsky, Alexandra; Asta, Mark

2016-12-12

Fluorite-structured oxides find widespread use for applications spanning nuclear energy and waste containment, energy conversion, and sensing. In such applications the host tetravalent cation is often partially substituted by trivalent cations, with an associated formation of charge-compensating oxygen vacancies. The stability and properties of such materials are known to be influenced strongly by chemical ordering of the cations and vacancies, and the nature of such ordering and associated energetics are thus of considerable interest. Here we employ density-functional theory (DFT) calculations to study the structure and energetics of cation and oxygen-vacancy ordering in Ho 2 Zr 2 O 7 . In a recent neutron total scattering study, solid solutions in this system were reported to feature local chemical ordering based on the fluorite-derivative weberite structure. The calculations show a preferred chemical ordering qualitatively consistent with these findings, and yield values for the ordering energy of 9.5 kJ/mol-cation. Similar DFT calculations are applied to additional RE 2 Th 2 O 7 fluorite compounds, spanning a range of values for the ratio of the tetravalent and trivalent (RE) cation radii. The results demonstrate that weberite-type order becomes destabilized with increasing values of this size ratio, consistent with an increasing energetic preference for the tetravalent cations to have higher oxygen coordination.

Chemical ordering in substituted fluorite oxides: a computational investigation of Ho2Zr2O7 and RE2Th2O7 (RE=Ho, Y, Gd, Nd, La)

NASA Astrophysics Data System (ADS)

Solomon, Jonathan M.; Shamblin, Jacob; Lang, Maik; Navrotsky, Alexandra; Asta, Mark

2016-12-01

Fluorite-structured oxides find widespread use for applications spanning nuclear energy and waste containment, energy conversion, and sensing. In such applications the host tetravalent cation is often partially substituted by trivalent cations, with an associated formation of charge-compensating oxygen vacancies. The stability and properties of such materials are known to be influenced strongly by chemical ordering of the cations and vacancies, and the nature of such ordering and associated energetics are thus of considerable interest. Here we employ density-functional theory (DFT) calculations to study the structure and energetics of cation and oxygen-vacancy ordering in Ho2Zr2O7. In a recent neutron total scattering study, solid solutions in this system were reported to feature local chemical ordering based on the fluorite-derivative weberite structure. The calculations show a preferred chemical ordering qualitatively consistent with these findings, and yield values for the ordering energy of 9.5 kJ/mol-cation. Similar DFT calculations are applied to additional RE2Th2O7 fluorite compounds, spanning a range of values for the ratio of the tetravalent and trivalent (RE) cation radii. The results demonstrate that weberite-type order becomes destabilized with increasing values of this size ratio, consistent with an increasing energetic preference for the tetravalent cations to have higher oxygen coordination.

Amino acid fermentation at the origin of the genetic code.

PubMed

de Vladar, Harold P

2012-02-10

There is evidence that the genetic code was established prior to the existence of proteins, when metabolism was powered by ribozymes. Also, early proto-organisms had to rely on simple anaerobic bioenergetic processes. In this work I propose that amino acid fermentation powered metabolism in the RNA world, and that this was facilitated by proto-adapters, the precursors of the tRNAs. Amino acids were used as carbon sources rather than as catalytic or structural elements. In modern bacteria, amino acid fermentation is known as the Stickland reaction. This pathway involves two amino acids: the first undergoes oxidative deamination, and the second acts as an electron acceptor through reductive deamination. This redox reaction results in two keto acids that are employed to synthesise ATP via substrate-level phosphorylation. The Stickland reaction is the basic bioenergetic pathway of some bacteria of the genus Clostridium. Two other facts support Stickland fermentation in the RNA world. First, several Stickland amino acid pairs are synthesised in abiotic amino acid synthesis. This suggests that amino acids that could be used as an energy substrate were freely available. Second, anticodons that have complementary sequences often correspond to amino acids that form Stickland pairs. The main hypothesis of this paper is that pairs of complementary proto-adapters were assigned to Stickland amino acids pairs. There are signatures of this hypothesis in the genetic code. Furthermore, it is argued that the proto-adapters formed double strands that brought amino acid pairs into proximity to facilitate their mutual redox reaction, structurally constraining the anticodon pairs that are assigned to these amino acid pairs. Significance tests which randomise the code are performed to study the extent of the variability of the energetic (ATP) yield. Random assignments can lead to a substantial yield of ATP and maintain enough variability, thus selection can act and refine the assignments into a proto-code that optimises the energetic yield. Monte Carlo simulations are performed to evaluate the establishment of these simple proto-codes, based on amino acid substitutions and codon swapping. In all cases, donor amino acids are assigned to anticodons composed of U+G, and have low redundancy (1-2 codons), whereas acceptor amino acids are assigned to the the remaining codons. These bioenergetic and structural constraints allow for a metabolic role for amino acids before their co-option as catalyst cofactors.

Cy3 and Cy5 dyes attached to oligonucleotide terminus stabilize DNA duplexes: predictive thermodynamic model.

PubMed

Moreira, Bernardo G; You, Yong; Owczarzy, Richard

2015-03-01

Cyanine dyes are important chemical modifications of oligonucleotides exhibiting intensive and stable fluorescence at visible light wavelengths. When Cy3 or Cy5 dye is attached to 5' end of a DNA duplex, the dye stacks on the terminal base pair and stabilizes the duplex. Using optical melting experiments, we have determined thermodynamic parameters that can predict the effects of the dyes on duplex stability quantitatively (ΔG°, Tm). Both Cy dyes enhance duplex formation by 1.2 kcal/mol on average, however, this Gibbs energy contribution is sequence-dependent. If the Cy5 is attached to a pyrimidine nucleotide of pyrimidine-purine base pair, the stabilization is larger compared to the attachment to a purine nucleotide. This is likely due to increased stacking interactions of the dye to the purine of the complementary strand. Dangling (unpaired) nucleotides at duplex terminus are also known to enhance duplex stability. Stabilization originated from the Cy dyes is significantly larger than the stabilization due to the presence of dangling nucleotides. If both the dangling base and Cy3 are present, their thermodynamic contributions are approximately additive. New thermodynamic parameters improve predictions of duplex folding, which will help design oligonucleotide sequences for biophysical, biological, engineering, and nanotechnology applications. Copyright © 2015. Published by Elsevier B.V.

Infant temperament: stability by age, gender, birth order, term status, and socioeconomic status.

PubMed

Bornstein, Marc H; Putnick, Diane L; Gartstein, Maria A; Hahn, Chun-Shin; Auestad, Nancy; O'Connor, Deborah L

2015-01-01

Two complementary studies focused on stability of infant temperament across the 1st year and considered infant age, gender, birth order, term status, and socioeconomic status (SES) as moderators. Study 1 consisted of 73 mothers of firstborn term girls and boys queried at 2, 5, and 13 months of age. Study 2 consisted of 335 mothers of infants of different gender, birth order, term status, and SES queried at 6 and 12 months. Consistent positive and negative affectivity factors emerged at all time points across both studies. Infant temperament proved stable and robust across gender, birth order, term status, and SES. Stability coefficients for temperament factors and scales were medium to large for shorter (< 9 months) interassessment intervals and small to medium for longer (> 10 months) intervals. Published 2015. This article is a U.S. Government work and is in the public domain in the USA.

Evaluation of physicochemical properties of root-end filling materials using conventional and Micro-CT tests.

PubMed

Torres, Fernanda Ferrari Esteves; Bosso-Martelo, Roberta; Espir, Camila Galletti; Cirelli, Joni Augusto; Guerreiro-Tanomaru, Juliane Maria; Tanomaru-Filho, Mario

2017-01-01

To evaluate solubility, dimensional stability, filling ability and volumetric change of root-end filling materials using conventional tests and new Micro-CT-based methods. 7. The results suggested correlated or complementary data between the proposed tests. At 7 days, BIO showed higher solubility and at 30 days, showed higher volumetric change in comparison with MTA (p<0.05). With regard to volumetric change, the tested materials were similar (p>0.05) at 7 days. At 30 days, they presented similar solubility. BIO and MTA showed higher dimensional stability than ZOE (p<0.05). ZOE and BIO showed higher filling ability (p<0.05). ZOE presented a higher dimensional change, and BIO had greater solubility after 7 days. BIO presented filling ability and dimensional stability, but greater volumetric change than MTA after 30 days. Micro-CT can provide important data on the physicochemical properties of materials complementing conventional tests.

Entropic contributions enhance polarity compensation for CeO2(100) surfaces

NASA Astrophysics Data System (ADS)

Capdevila-Cortada, Marçal; López, Núria

2017-03-01

Surface structure controls the physical and chemical response of materials. Surface polar terminations are appealing because of their unusual properties but they are intrinsically unstable. Several mechanisms, namely metallization, adsorption, and ordered reconstructions, can remove thermodynamic penalties rendering polar surfaces partially stable. Here, for CeO2(100), we report a complementary stabilization mechanism based on surface disorder that has been unravelled through theoretical simulations that: account for surface energies and configurational entropies; show the importance of the ion distribution degeneracy; and identify low diffusion barriers between conformations that ensure equilibration. Disordered configurations in oxides might also be further stabilized by preferential adsorption of water. The entropic stabilization term will appear for surfaces with a high number of empty sites, typically achieved when removing part of the ions in a polar termination to make the layer charge zero. Assessing the impact of surface disorder when establishing new structure-activity relationships remains a challenge.

Evolution of soil organic matter energetic and chemical composition during long-term bare fallow: implications for soil carbon vulnerability to global change

NASA Astrophysics Data System (ADS)

Barré, P.; Cécillon, L.; Plante, A. F.; Chenu, C.; Christensen, B. T.; Fernandez, J. M.; Gherardi, C. M.; Houot, S.; Kätterer, T.; van Oort, F.; Peltre, C.; Poulton, P. R.

2012-04-01

Determining the relative stability of soil organic carbon (SOC) is a critical step to better understanding its vulnerability to global change. The absence of convincing physical or chemical procedures to define, characterize or isolate relatively labile versus stable pools of SOC makes it difficult to study. Long-term bare fallow (LTBF) experiments, in which C inputs have been stopped for several decades, provide a unique opportunity to study stable SOC without the inherent artefacts induced by extraction procedures, the hypothesis being that SOC is gradually enriched in stable C with time as labile components decompose. We determined the evolution of energetic and chemical characteristics of bulk SOC in five LTBF experiments across Europe: Askov (DK), Grignon (FR), Rothamsted (UK), Ultuna (SW) and Versailles (FR), using simultaneous thermal analysis (i.e., thermogravimetry (TG), differential scanning calorimetry (DSC) and evolved CO2 gas analysis (CO2-EGA)) and diffuse reflectance Fourier transformed mid-infrared spectroscopy (DRIFT-MIRS). Results of TG analyses showed that the temperature needed to combust the first half of the SOC (i.e., TG-T50) increased with bare fallow duration at all sites. Conversely, the energy density (in mJ mg-1 C) decreased with bare fallow duration. Combined together, these results provide a means to contrast the stable, mineral-associated SOC pool from any potential pyrogenic C, which would have much greater energy density. DRIFT-MIRS results showed that the "carboxylation index" (the ratio of C=O bonds peak area over (C=C + C=O) bonds peak areas) decreased with bare fallow duration, that aromaticity (C=C bond peak area over C content) increased with bare-fallow duration, and that the "reticulation index" (CH3 peak area over CH2 peak area) decreased with increasing bare fallow duration at Rothamsted, Versailles and Ultuna. These trends were less clear or not observed at Grignon due to the presence of carbonates or at Askov due to greater variability, thus precluding unequivocal conclusions. Our results showed that in spite of the heterogeneity of the soils at the LTBF sites, generalized energetic and chemical pathways exist for SOC stabilization. The DRIFT-MIRS indices demonstrate that SOC stabilization is accompanied by a consistent evolution of its bulk chemical composition across most sites, over decades (ca. 50 years). The general decarboxylation of SOC observed in bare fallow challenges the current view of SOM decomposition, raising questions about the oxidative state of the stable C pool. The increased burning temperature and lower energy density of stable SOC suggest that decomposition of the stable C pool may be more temperature sensitive and thus vulnerable to increased temperature. Conversely, decreasing energy density suggests that priming might be the only means available for the microbial community to decompose this pool of SOC, and that SOC stability may be a function of low potential energy gain from decomposition of this material. Finally, this study illustrates the enormous value of such long-term field experiments, and a potential multi-faceted approach to quantify SOC stability as an ecosystem property.

The field effect transistor DNA biosensor based on ITO nanowires in label-free hepatitis B virus detecting compatible with CMOS technology.

PubMed

Shariati, Mohsen

2018-05-15

In this paper the field-effect transistor DNA biosensor for detecting hepatitis B virus (HBV) based on indium tin oxide nanowires (ITO NWs) in label free approach has been fabricated. Because of ITO nanowires intensive conductance and functional modified surface, the probe immobilization and target hybridization were increased strongly. The high resolution transmission electron microscopy (HRTEM) measurement showed that ITO nanowires were crystalline and less than 50nm in diameter. The single-stranded hepatitis B virus DNA (SS-DNA) was immobilized as probe on the Au-modified nanowires. The DNA targets were measured in a linear concentration range from 1fM to 10µM. The detection limit of the DNA biosensor was about 1fM. The time of the hybridization process for defined single strand was 90min. The switching ratio of the biosensor between "on" and "off" state was ~ 1.1 × 10 5 . For sensing the specificity of the biosensor, non-complementary, mismatch and complementary DNA oligonucleotide sequences were clearly discriminated. The HBV biosensor confirmed the highly satisfied specificity for differentiating complementary sequences from non-complementary and the mismatch oligonucleotides. The response time of the DNA sensor was 37s with a high reproducibility. The stability and repeatability of the DNA biosensor showed that the peak current of the biosensor retained 98% and 96% of its initial response for measurements after three and five weeks, respectively. Copyright © 2018 Elsevier B.V. All rights reserved.

Directionally Interacting Spheres and Rods Form Ordered Phases

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

Liu, Wenyan; Mahynski, Nathan A.; Gang, Oleg

The structures formed by mixtures of dissimilarly shaped nanoscale objects can significantly enhance our ability to produce nanoscale architectures. However, understanding their formation is a complex problem due to the interplay of geometric effects (entropy) and energetic interactions at the nanoscale. Spheres and rods are perhaps the most basic geometrical shapes and serve as convenient models of such dissimilar objects. The ordered phases formed by each of these individual shapes have already been explored, but, when mixed, spheres and rods have demonstrated only limited structural organization to date. We show using experiments and theory that the introduction of directional attractionsmore » between rod ends and isotropically interacting spherical nanoparticles (NPs) through DNA base pairing leads to the formation of ordered three-dimensional lattices. The spheres and rods arrange themselves in a complex alternating manner, where the spheres can form either a face-centered cubic (FCC) or hexagonal close-packed (HCP) lattice, or a disordered phase, as observed by in situ X-ray scattering. Increasing NP diameter at fixed rod length yields an initial transition from a disordered phase to the HCP crystal, energetically stabilized by rod-rod attraction across alternating crystal layers, as revealed by theory. In the limit of large NPs, the FCC structure is instead stabilized over the HCP by rod entropy. Thus, we propose that directionally specific attractions in mixtures of anisotropic and isotropic objects offer insight into unexplored self-assembly behavior of noncomplementary shaped particles.« less

Directionally Interacting Spheres and Rods Form Ordered Phases

DOE PAGES

Liu, Wenyan; Mahynski, Nathan A.; Gang, Oleg; ...

2017-05-10

The structures formed by mixtures of dissimilarly shaped nanoscale objects can significantly enhance our ability to produce nanoscale architectures. However, understanding their formation is a complex problem due to the interplay of geometric effects (entropy) and energetic interactions at the nanoscale. Spheres and rods are perhaps the most basic geometrical shapes and serve as convenient models of such dissimilar objects. The ordered phases formed by each of these individual shapes have already been explored, but, when mixed, spheres and rods have demonstrated only limited structural organization to date. We show using experiments and theory that the introduction of directional attractionsmore » between rod ends and isotropically interacting spherical nanoparticles (NPs) through DNA base pairing leads to the formation of ordered three-dimensional lattices. The spheres and rods arrange themselves in a complex alternating manner, where the spheres can form either a face-centered cubic (FCC) or hexagonal close-packed (HCP) lattice, or a disordered phase, as observed by in situ X-ray scattering. Increasing NP diameter at fixed rod length yields an initial transition from a disordered phase to the HCP crystal, energetically stabilized by rod-rod attraction across alternating crystal layers, as revealed by theory. In the limit of large NPs, the FCC structure is instead stabilized over the HCP by rod entropy. Thus, we propose that directionally specific attractions in mixtures of anisotropic and isotropic objects offer insight into unexplored self-assembly behavior of noncomplementary shaped particles.« less

Development and Application of Predictive Tools for MHD Stability Limits in Tokamaks

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

Brennan, Dylan; Miller, G. P.

This is a project to develop and apply analytic and computational tools to answer physics questions relevant to the onset of non-ideal magnetohydrodynamic (MHD) instabilities in toroidal magnetic confinement plasmas. The focused goal of the research is to develop predictive tools for these instabilities, including an inner layer solution algorithm, a resistive wall with control coils, and energetic particle effects. The production phase compares studies of instabilities in such systems using analytic techniques, PEST- III and NIMROD. Two important physics puzzles are targeted as guiding thrusts for the analyses. The first is to form an accurate description of the physicsmore » determining whether the resistive wall mode or a tearing mode will appear first as β is increased at low rotation and low error fields in DIII-D. The second is to understand the physical mechanism behind recent NIMROD results indicating strong damping and stabilization from energetic particle effects on linear resistive modes. The work seeks to develop a highly relevant predictive tool for ITER, advance the theoretical description of this physics in general, and analyze these instabilities in experiments such as ASDEX Upgrade, DIII-D, JET, JT-60U and NTSX. The awardee on this grant is the University of Tulsa. The research efforts are supervised principally by Dr. Brennan. Support is included for two graduate students, and a strong collaboration with Dr. John M. Finn of LANL. The work includes several ongoing collaborations with General Atomics, PPPL, and the NIMROD team, among others.« less

Stabilization of perturbed Boolean network attractors through compensatory interactions

PubMed Central

2014-01-01

Background Understanding and ameliorating the effects of network damage are of significant interest, due in part to the variety of applications in which network damage is relevant. For example, the effects of genetic mutations can cascade through within-cell signaling and regulatory networks and alter the behavior of cells, possibly leading to a wide variety of diseases. The typical approach to mitigating network perturbations is to consider the compensatory activation or deactivation of system components. Here, we propose a complementary approach wherein interactions are instead modified to alter key regulatory functions and prevent the network damage from triggering a deregulatory cascade. Results We implement this approach in a Boolean dynamic framework, which has been shown to effectively model the behavior of biological regulatory and signaling networks. We show that the method can stabilize any single state (e.g., fixed point attractors or time-averaged representations of multi-state attractors) to be an attractor of the repaired network. We show that the approach is minimalistic in that few modifications are required to provide stability to a chosen attractor and specific in that interventions do not have undesired effects on the attractor. We apply the approach to random Boolean networks, and further show that the method can in some cases successfully repair synchronous limit cycles. We also apply the methodology to case studies from drought-induced signaling in plants and T-LGL leukemia and find that it is successful in both stabilizing desired behavior and in eliminating undesired outcomes. Code is made freely available through the software package BooleanNet. Conclusions The methodology introduced in this report offers a complementary way to manipulating node expression levels. A comprehensive approach to evaluating network manipulation should take an "all of the above" perspective; we anticipate that theoretical studies of interaction modification, coupled with empirical advances, will ultimately provide researchers with greater flexibility in influencing system behavior. PMID:24885780

Crystal Structure and Thermodynamic Stability of Ba/Ti-Substituted Pollucites for Radioactive Cs/Ba Immobilization

DOE PAGES

Xu, Hongwu; Chavez, Manuel E.; Mitchell, Jeremy N.; ...

2015-04-23

An analogue of the mineral pollucite (CsAlSi 2O 6), CsTiSi 2O 6.5 has a potential host phase for radioactive Cs. However, as 137Cs and 135Cs transmute to 137Ba and 135Ba, respectively, through the beta decay, it is essential to study the structure and stability of this phase upon Cs → Ba substitution. In this work, two series of Ba/Ti-substituted samples, Cs xBa (1-x)/2TiSi 2O 6.5 and Cs xBa 1-xTiSi 2O 7-0.5x, (x = 0.9 and 0.7), were synthesized by high-temperature crystallization from their respective precursors. Synchrotron X-ray diffraction and Rietveld analysis reveal that while Cs xBa (1-x)/2TiSi 2O 6.5 samplesmore » are phase-pure, Cs xBa 1-xTiSi 2O 7-0.5x samples contain Cs3x/(2+x)Ba (1-x)/(2+x)TiSi 2O 6.5 pollucites (i.e., also two-Cs-to-one-Ba substitution) and a secondary phase, fresnoite (Ba2TiSi2O8). Thus, the Cs xBa 1-xTiSi 2O 7-0.5x series is energetically less favorable than Cs xBa (1-x)/2TiSi 2O 6.5. To study the stability systematics of Cs xBa (1-x)/2TiSi 2O 6.5 pollucites, high-temperature calorimetric experiments were performed at 973 K with or without the lead borate solvent. Enthalpies of formation from the constituent oxides (and elements) have thus been derived. Our results show that with increasing Ba/(Cs + Ba) ratio, the thermodynamic stability of these phases decreases with respect to their component oxides. Hence, from the energetic viewpoint, continued Cs → Ba transmutation tends to destabilize the parent silicotitanate pollucite structure. However, the Ba-substituted pollucite co-forms with fresnoite (which incorporates the excess Ba), thereby providing viable ceramic waste forms for all the Ba decay products.« less

Investigating homology between proteins using energetic profiles.

PubMed

Wrabl, James O; Hilser, Vincent J

2010-03-26

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

Studies of Mineral-Water Surfaces

NASA Astrophysics Data System (ADS)

Ross, Nancy L.; Spencer, Elinor C.; Levchenko, Andrey A.; Kolesnikov, Alexander I.; Wesolowski, David J.; Cole, David R.; Mamontov, Eugene; Vlcek, Lukas

In this chapter we discuss the application of inelastic and quasielastic neutron scattering to the elucidation of the structure, energetics, and dynamics of water confined on the surfaces of mineral oxide nanoparticles. We begin by highlighting recent advancements in this active field of research before providing a brief review of the theory underpinning inelastic neutron scattering (INS) and quasielastic neutron scattering (QENS) techniques. We then discuss examples illustrating the use of neutron scattering methods for studying hydration layers that are an integral part of the nanoparticle structure. The first investigation of this kind, namely the INS analysis of hydrated ZrO2 nanoparticles, is described, as well as a later, complementary QENS study that allowed for the dynamics of diffusion of the water molecules within the hydration layer to be examined in detail. The diverse range of information available from INS experiments is illustrated by a recent study combining INS with calorimetric experiments that elucidated the thermodynamic properties of adsorbed water on anatase (TiO2) nanoparticles. To emphasize the importance of molecular dynamics (MD) simulations for deconvoluting complex QENS spectra, we describe both the MD and the QENS analysis of rutile (TiO2) and cassiterite (SnO2) nanoparticle systems and show that, when combined, data obtained by these two complementary methods can provide a complete description of the motion of the water molecules on the nanoparticle surface. We close with a glimpse into the future for this thriving field of research.

Stability-maneuverability trade-offs during lateral steps.

PubMed

Acasio, Julian; Wu, Mengnan/Mary; Fey, Nicholas P; Gordon, Keith E

2017-02-01

Selecting a specific foot placement strategy to perform walking maneuvers requires the management of several competing factors, including: maintaining stability, positioning oneself to actively generate impulses, and minimizing mechanical energy requirements. These requirements are unlikely to be independent. Our purpose was to determine the impact of lateral foot placement on stability, maneuverability, and energetics during walking maneuvers. Ten able-bodied adults performed laterally-directed walking maneuvers. Mediolateral placement of the "Push-off" foot during the maneuvers was varied, ranging from a cross-over step to a side-step. We hypothesized that as mediolateral foot placement became wider, passive stability in the direction of the maneuver, the lateral impulse generated to create the maneuver, and mechanical energy cost would all increase. We also hypothesized that subjects would prefer an intermediate step width reflective of trade-offs between stability vs. both maneuverability and energy. In support of our first hypothesis, we found that as Push-off step width increased, lateral margin of stability, peak lateral impulse, and total joint work all increased. In support of our second hypothesis, we found that when subjects had no restrictions on their mediolateral foot placement, they chose a foot placement between the two extreme positions. We found a significant relationship (p<0.05) between lateral margin of stability and peak lateral impulse (r=0.773), indicating a trade-off between passive stability and the force input required to maneuver. These findings suggest that during anticipated maneuvers people select foot placement strategies that balance competing costs to maintain stability, actively generate impulses, and minimize mechanical energy costs. Published by Elsevier B.V.

Stope Stability Assessment and Effect of Horizontal to Vertical Stress Ratio on the Yielding and Relaxation Zones Around Underground Open Stopes Using Empirical and Finite Element Methods

NASA Astrophysics Data System (ADS)

Sepehri, Mohammadali; Apel, Derek; Liu, Wei

2017-09-01

Predicting the stability of open stopes can be a challenging task for underground mine engineers. For decades, the stability graph method has been used as the first step of open stope design around the world. However, there are some shortcomings with this method. For instance, the stability graph method does not account for the relaxation zones around the stopes. Another limitation of the stability graph is that this method cannot to be used to evaluate the stability of the stopes with high walls made of backfill materials. However, there are several analytical and numerical methods that can be used to overcome these limitations. In this study, both empirical and numerical methods have been used to assess the stability of an open stope located between mine levels N9225 and N9250 at Diavik diamond underground mine. It was shown that the numerical methods can be used as complementary methods along with other analytical and empirical methods to assess the stability of open stopes. A three dimensional elastoplastic finite element model was constructed using Abaqus software. In this paper a sensitivity analysis was performed to investigate the impact of the stress ratio "k" on the extent of the yielding and relaxation zones around the hangingwall and footwall of the understudy stope.

Calorimetric Determination of Thermodynamic Stability of MAX and MXene Phases

DOE PAGES

Sharma, Geetu; Naguib, Michael; Feng, Dawei; ...

2016-11-19

MXenes are layered two dimensional materials with exciting properties useful to a wide range of energy applications. They are derived from ceramics (MAX phases) by leaching and their properties reflect their resulting complex compositions which include intercalating cations and anions and water. Their thermodynamic stability is likely linked to these functional groups but has not yet been addressed by quantitative experimental measurements. We report enthalpies of formation from the elements at 25 °C measured using high temperature oxide melt solution calorimetry for a layered Ti-Al-C MAX phase, and the corresponding Ti-C based MXene. The thermodynamic stability of the Ti 3Cmore » 2T x MXene (Tx stands for anionic surface moieties, and intercalated cations) was assessed by calculating the enthalpy of reaction of the MAX phase (ideal composition Ti 3AlC 2) to form MXene, The very exothermic enthalpy of reaction confirms the stability of MXene in an aqueous environment. The surface terminations (O, OH and F) and cations (Li) chemisorbed on the surface and intercalated in the interlayers play a major role in the thermodynamic stabilization of MXene. These findings help to understand and potentially improve properties and performance by characterizing the energetics of species binding to MXene surfaces during synthesis and in energy storage, water desalination and other applications.« less

Zwitterionic versus canonical amino acids over the various defects in zeolites: A two-layer ONIOM calculation

PubMed Central

Yang, Gang; Zhou, Lijun

2014-01-01

Defects are often considered as the active sites for chemical reactions. Here a variety of defects in zeolites are used to stabilize zwitterionic glycine that is not self-stable in gas phase; in addition, effects of acidic strengths and zeolite channels on zwitterionic stabilization are demonstrated. Glycine zwitterions can be stabilized by all these defects and energetically prefer to canonical structures over Al and Ga Lewis acidic sites rather than Ti Lewis acidic site, silanol and titanol hydroxyls. For titanol (Ti-OH), glycine interacts with framework Ti and hydroxyl sites competitively, and the former with Lewis acidity predominates. The transformations from canonical to zwitterionic glycine are obviously more facile over Al and Ga Lewis acidic sites than over Ti Lewis acidic site, titanol and silanol hydroxyls. Charge transfers that generally increase with adsorption energies are found to largely decide the zwitterionic stabilization effects. Zeolite channels play a significant role during the stabilization process. In absence of zeolite channels, canonical structures predominate for all defects; glycine zwitterions remain stable over Al and Ga Lewis acidic sites and only with synergy of H-bonding interactions can exist over Ti Lewis acidic site, while automatically transform to canonical structures over silanol and titanol hydroxyls. PMID:25307449

Development of an Electrochemical DNA Biosensor to Detect a Foodborne Pathogen.

PubMed

Nordin, Noordiana; Yusof, Nor Azah; Radu, Son; Hushiarian, Roozbeh

2018-06-03

Vibrio parahaemolyticus (V. parahaemolyticus) is a common foodborne pathogen that contributes to a large proportion of public health problems globally, significantly affecting the rate of human mortality and morbidity. Conventional methods for the detection of V. parahaemolyticus such as culture-based methods, immunological assays, and molecular-based methods require complicated sample handling and are time-consuming, tedious, and costly. Recently, biosensors have proven to be a promising and comprehensive detection method with the advantages of fast detection, cost-effectiveness, and practicality. This research focuses on developing a rapid method of detecting V. parahaemolyticus with high selectivity and sensitivity using the principles of DNA hybridization. In the work, characterization of synthesized polylactic acid-stabilized gold nanoparticles (PLA-AuNPs) was achieved using X-ray Diffraction (XRD), Ultraviolet-visible Spectroscopy (UV-Vis), Transmission Electron Microscopy (TEM), Field-emission Scanning Electron Microscopy (FESEM), and Cyclic Voltammetry (CV). We also carried out further testing of stability, sensitivity, and reproducibility of the PLA-AuNPs. We found that the PLA-AuNPs formed a sound structure of stabilized nanoparticles in aqueous solution. We also observed that the sensitivity improved as a result of the smaller charge transfer resistance (Rct) value and an increase of active surface area (0.41 cm 2 ). The development of our DNA biosensor was based on modification of a screen-printed carbon electrode (SPCE) with PLA-AuNPs and using methylene blue (MB) as the redox indicator. We assessed the immobilization and hybridization events by differential pulse voltammetry (DPV). We found that complementary, non-complementary, and mismatched oligonucleotides were specifically distinguished by the fabricated biosensor. It also showed reliably sensitive detection in cross-reactivity studies against various food-borne pathogens and in the identification of V. parahaemolyticus in fresh cockles.

Effect of metal ion intercalation on the structure of MXene and water dynamics on its internal surfaces

DOE PAGES

Osti, Naresh C.; Naguib, Michael; Ostadhossein, Alireza; ...

2016-03-24

MXenes are a recently discovered class of 2D materials with an excellent potential for energy storage applications. Because MXene surfaces are hydrophilic and attractive interaction forces between the layers are relatively weak, water molecules can spontaneously intercalate at ambient humidity and significantly influence the key properties of this 2D material. Using complementary X-ray and neutron scattering techniques, we demonstrate that intercalation with potassium cations significantly improves structural homogeneity and water stability in MXenes. Furthermore, in agreement with molecular dynamics simulations, intercalated potassium ions reduce the water self-diffusion coefficient by 2 orders of magnitude, suggesting greater stability of hydrated MXene againstmore » changing environmental conditions.« less

Influence of N-Oxide Introduction on the Stability of Nitrogen-Rich Heteroaromatic Rings: A Quantum Chemical Study.

PubMed

Yuan, Jia; Long, Xinping; Zhang, Chaoyang

2016-12-01

N-Oxidization is an important strategy for enhancing the density and energy of energetic materials. Nevertheless, the influence of N + -O - introduction on molecular stability remains relatively unknown. Thus, the present work comprehensively studied 102 basic N-rich ring structures, including azoles, furazans, and azines, as well as their N-oxides by quantum chemical calculations. The introduction of N + -O - weakens molecular stability in most cases because the process elongates chemical bonds, decreases ring aromaticity, narrows the gaps between the highest occupied and lowest unoccupied molecular orbitals, and increases the photochemical reactivity. Besides, the easy H transfer to the neighboring O atom, which forms a N-OH isomer in azoles, renders the stabilization by N-oxide introduction ineffective. However, N-oxide introduction can enhance the molecular stability of 1,2,3,4-tetrazine-1,3-dioxide and tetrazino-tetrazine 1,3,6,8-tetraoxide by promoting σ-π separation and relieving lone-pair repulsion. Moreover, the alternate arrangement of positive and negative charges is another factor stabilizing the 1,2,3,4-tetrazine ring by 1,3-dioxidation. Finally, we assess the accessibility of N-oxidized azoles and azines by regarding N 2 O and H 2 O 2 as oxidizers. We find that all the oxidations were exothermic, thermodynamically spontaneous, and kinetically feasible. After an overall evaluation, we propose 19 N-oxides as basic structures for high-energy materials with considerable stability.

Vision-based flight control in the hawkmoth Hyles lineata

PubMed Central

Windsor, Shane P.; Bomphrey, Richard J.; Taylor, Graham K.

2014-01-01

Vision is a key sensory modality for flying insects, playing an important role in guidance, navigation and control. Here, we use a virtual-reality flight simulator to measure the optomotor responses of the hawkmoth Hyles lineata, and use a published linear-time invariant model of the flight dynamics to interpret the function of the measured responses in flight stabilization and control. We recorded the forces and moments produced during oscillation of the visual field in roll, pitch and yaw, varying the temporal frequency, amplitude or spatial frequency of the stimulus. The moths’ responses were strongly dependent upon contrast frequency, as expected if the optomotor system uses correlation-type motion detectors to sense self-motion. The flight dynamics model predicts that roll angle feedback is needed to stabilize the lateral dynamics, and that a combination of pitch angle and pitch rate feedback is most effective in stabilizing the longitudinal dynamics. The moths’ responses to roll and pitch stimuli coincided qualitatively with these functional predictions. The moths produced coupled roll and yaw moments in response to yaw stimuli, which could help to reduce the energetic cost of correcting heading. Our results emphasize the close relationship between physics and physiology in the stabilization of insect flight. PMID:24335557

Vision-based flight control in the hawkmoth Hyles lineata.

PubMed

Windsor, Shane P; Bomphrey, Richard J; Taylor, Graham K

2014-02-06

Vision is a key sensory modality for flying insects, playing an important role in guidance, navigation and control. Here, we use a virtual-reality flight simulator to measure the optomotor responses of the hawkmoth Hyles lineata, and use a published linear-time invariant model of the flight dynamics to interpret the function of the measured responses in flight stabilization and control. We recorded the forces and moments produced during oscillation of the visual field in roll, pitch and yaw, varying the temporal frequency, amplitude or spatial frequency of the stimulus. The moths' responses were strongly dependent upon contrast frequency, as expected if the optomotor system uses correlation-type motion detectors to sense self-motion. The flight dynamics model predicts that roll angle feedback is needed to stabilize the lateral dynamics, and that a combination of pitch angle and pitch rate feedback is most effective in stabilizing the longitudinal dynamics. The moths' responses to roll and pitch stimuli coincided qualitatively with these functional predictions. The moths produced coupled roll and yaw moments in response to yaw stimuli, which could help to reduce the energetic cost of correcting heading. Our results emphasize the close relationship between physics and physiology in the stabilization of insect flight.

The effect of low velocity impact in the strength characteristics of composite materials laminates

NASA Technical Reports Server (NTRS)

Liebowitz, H.

1983-01-01

The nonlinear vibration response of a double cantilevered beam subjected to pulse loading over a central sector is studied. The initial response is generated in detail to ascertain the energetics of the response. The total energy is used as a gauge of the stability and accuracy of the solution. It is shown that to obtain accurate and stable initial solutions an extremely high spatial and time resolution is required. This requirement was only evident through an examination of the energy of the system. It is proposed, therefore, to use the total energy of the system as a necessary stability and accuracy criterion for the nonlinear response of conservative systems. The results also demonstrate that even for moderate nonlinearities, the effects of membrane forces have a significant influence on the system.

Theoretical prediction of a novel inorganic fullerene-like family of silicon-carbon materials

NASA Astrophysics Data System (ADS)

Wang, Ruoxi; Zhang, Dongju; Liu, Chengbu

2005-08-01

In an effort to search for new inorganic fullerene-like structures, we designed a series of novel silicon-carbon cages, (SiC) n ( n = 6-36), based on the uniformly hybrid Si-C four- and six-membered-rings, and researched their geometrical and electronic structures, as well as their relative stabilities using the density function theory. Among these cages, the structures for n = 12, 16, and 36 were found to been energetically more favorable. The calculated disproportionation energy and binding energy per SiC unit show that the (SiC) 12 cage is the most stable one among these designed structures. The present calculations not only indicate that silicon-carbon fullerenes are promised to be synthesized in future, but also provide a new way for stabilizing silicon cages by uniformly doping carbon atoms into silicon structures.

Exploring the Structure of Nitrogen-Rich Ionic Liquids and Their Binding to the Surface of Oxide-Free Boron Nanoparticles

DTIC Science & Technology

2013-01-29

Shreeve et al . synthesized a number of highly energetic ionic liquids with multiple nitrogen atoms in their structures,18−23 in the hope of increasing...results have to be interpreted with caution. Lovelock et al .61 have shown that clean surfaces can be obtained by sputtering for the [CnC1Im][Tf2N] IL...flat on the gold surface while a long chain ether functional group is directed away from the surface, providing steric stabilization.74 Zhang et al

Materials for Photovoltaic Applications

NASA Astrophysics Data System (ADS)

Dimova-Malinovska, Doriana

Energy priorities are changing nowadays. As mankind will probably have to face energy crisis, factors such as energy independence, energy security, stability of energy supply and the variety of energy sources become much more vital these days. Photovoltaics is exceptional compared to other renewable sources of energy due to its wide opportunity to gain energetic and environmental benefits. An overview of the present state of knowledge of the materials aspects of photovoltaic cells will be given, and new semiconductor materials, including nanomaterials, with potential for application in photovoltaic devices will be identified.

Fullerene-like CS x: A first-principles study of synthetic growth

NASA Astrophysics Data System (ADS)

Goyenola, C.; Gueorguiev, G. K.; Stafström, S.; Hultman, L.

2011-04-01

Fullerene-Like (FL) Sulpho-Carbide (CSx) compounds have been addressed by first principles calculations. Geometry optimization and cohesive energy results are presented for the relative stability of precursor species such as C2S, CS2, and C2S2 in isolated form. The energy cost for structural defects, arising from the substitution of C by S is also reported. Similar to previously synthesized FL-CNx and FL-CPx compounds, the pentagon, the double pentagon defects as well as the Stone-Wales defects are confirmed as energetically feasible in CSx compounds.

Olefin Epoxidation by Methyltrioxorhenium: A Density Functional Study on Energetics and Mechanisms.

PubMed

Gisdakis, Philip; Antonczak, Serge; Köstlmeier, Sibylle; Herrmann, Wolfgang A; Rösch, Notker

1998-09-04

A spiro attack on a peroxo group is calculated to be the preferred reaction pathway for olefin epoxidation with the catalytic system CH 3 ReO 3 /H 2 O 2 (see picture). This finding is supported by density functional calculations on more than ten transition states for the most probable mechanisms. Hydration has significant effects on various reaction species: it stabilizes the intermediates and destabilizes, with one exception, the transition states. © 1998 WILEY-VCH Verlag GmbH, Weinheim, Fed. Rep. of Germany.

Surface regulated arsenenes as Dirac materials: From density functional calculations

NASA Astrophysics Data System (ADS)

Yuan, Junhui; Xie, Qingxing; Yu, Niannian; Wang, Jiafu

2017-02-01

Using first principle calculations based on density functional theory (DFT), we have systematically investigated the structure stability and electronic properties of chemically decorated arsenenes, AsX (X = CN, NC, NCO, NCS and NCSe). Phonon dispersion and formation energy analysis reveal that all the five chemically decorated buckled arsenenes are energetically favorable and could be synthesized. Our study shows that wide-bandgap arsenene would turn into Dirac materials when functionalized by -X (X = CN, NC, NCO, NCS and NCSe) groups, rendering new promises in next generation high-performance electronic devices.

A simple photoionization scheme for characterizing electron and ion spectrometers

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

Wituschek, A.; Vangerow, J. von; Grzesiak, J.

We present a simple diode laser-based photoionization scheme for generating electrons and ions with well-defined spatial and energetic (≲2 eV) structures. This scheme can easily be implemented in ion or electron imaging spectrometers for the purpose of off-line characterization and calibration. The low laser power ∼1 mW needed from a passively stabilized diode laser and the low flux of potassium atoms in an effusive beam make our scheme a versatile source of ions and electrons for applications in research and education.

Demographic stability metrics for conservation prioritization of isolated populations.

PubMed

Finn, Debra S; Bogan, Michael T; Lytle, David A

2009-10-01

Systems of geographically isolated habitat patches house species that occur naturally as small, disjunct populations. Many of these species are of conservation concern, particularly under the interacting influences of isolation and rapid global change. One potential conservation strategy is to prioritize the populations most likely to persist through change and act as sources for future recolonization of less stable localities. We propose an approach to classify long-term population stability (and, presumably, future persistence potential) with composite demographic metrics derived from standard population-genetic data. Stability metrics can be related to simple habitat measures for a straightforward method of classifying localities to inform conservation management. We tested these ideas in a system of isolated desert headwater streams with mitochondrial sequence data from 16 populations of a flightless aquatic insect. Populations exhibited a wide range of stability scores, which were significantly predicted by dry-season aquatic habitat size. This preliminary test suggests strong potential for our proposed method of classifying isolated populations according to persistence potential. The approach is complementary to existing methods for prioritizing local habitats according to diversity patterns and should be tested further in other systems and with additional loci to inform composite demographic stability scores.

Field Tests of a Tractor Rollover Detection and Emergency Notification System.

PubMed

Liu, B; Koc, A B

2015-04-01

The objective of this research was to assess the feasibility of a rollover detection and emergency notification system for farm tractors using field tests. The emergency notification system was developed based on a tractor stability model and implemented on a mobile electronic device with the iOS operating system. A complementary filter was implemented to combine the data from the accelerometer and gyroscope sensors to improve their accuracies in calculating the roll and pitch angles and the roll and pitch rates. The system estimates a stability index value during tractor operation, displays feedback messages when the stability index is lower than a preset threshold value, and transmits emergency notification messages when an overturn happens. Ten tractor rollover tests were conducted on a field track. The developed system successfully monitored the stability of the tractor during all of the tests. The iOS application was able to detect rollover accidents and transmit emergency notifications in the form of a phone call and email when an accident was detected. The system can be a useful tool for training and education in safe tractor operation. The system also has potential for stability monitoring and emergency notification of other on-road and off-road motorized vehicles.

Balancing the Hydrogen Evolution Reaction, Surface Energetics, and Stability of Metallic MoS 2 Nanosheets via Covalent Functionalization

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

Benson, Eric E.; Zhang, Hanyu; Schuman, Samuel A.

We modify the fundamental electronic properties of metallic (1T phase) nanosheets of molybdenum disulfide (MoS 2) through covalent chemical functionalization, and thereby directly influence the kinetics of the hydrogen evolution reaction (HER), surface energetics, and stability. Chemically exfoliated, metallic MoS 2 nanosheets are functionalized with organic phenyl rings containing electron donating or withdrawing groups. We find that MoS 2 functionalized with the most electron donating functional group (p-(CH 3CH 2) 2NPh-MoS 2) is the most efficient catalyst for HER in this series, with initial activity that is slightly worse compared to the pristine metallic phase of MoS 2. The p-(CHmore » 3CH 2) 2NPh-MoS 2 is more stable than unfunctionalized metallic MoS 2 and outperforms unfunctionalized metallic MoS 2 for continuous H 2 evolution within 10 min under the same conditions. With regards to the entire studied series, the overpotential and Tafel slope for catalytic HER are both directly correlated with the electron donating strength of the functional group. The results are consistent with a mechanism involving ground-state electron donation or withdrawal to/from the MoS 2 nanosheets, which modifies the electron transfer kinetics and catalytic activity of the MoS 2 nanosheet. The functional groups preserve the metallic nature of the MoS 2 nanosheets, inhibiting conversion to the thermodynamically stable semiconducting state (2H) when mildly annealed in a nitrogen atmosphere. We propose that the electron density and, therefore, reactivity of the MoS 2 nanosheets are controlled by the attached functional groups. Functionalizing nanosheets of MoS 2 and other transition metal dichalcogenides provides a synthetic chemical route for controlling the electronic properties and stability within the traditionally thermally unstable metallic state.« less

Dancing through Life: Molecular Dynamics Simulations and Network-Centric Modeling of Allosteric Mechanisms in Hsp70 and Hsp110 Chaperone Proteins.

PubMed

Stetz, Gabrielle; Verkhivker, Gennady M

2015-01-01

Hsp70 and Hsp110 chaperones play an important role in regulating cellular processes that involve protein folding and stabilization, which are essential for the integrity of signaling networks. Although many aspects of allosteric regulatory mechanisms in Hsp70 and Hsp110 chaperones have been extensively studied and significantly advanced in recent experimental studies, the atomistic picture of signal propagation and energetics of dynamics-based communication still remain unresolved. In this work, we have combined molecular dynamics simulations and protein stability analysis of the chaperone structures with the network modeling of residue interaction networks to characterize molecular determinants of allosteric mechanisms. We have shown that allosteric mechanisms of Hsp70 and Hsp110 chaperones may be primarily determined by nucleotide-induced redistribution of local conformational ensembles in the inter-domain regions and the substrate binding domain. Conformational dynamics and energetics of the peptide substrate binding with the Hsp70 structures has been analyzed using free energy calculations, revealing allosteric hotspots that control negative cooperativity between regulatory sites. The results have indicated that cooperative interactions may promote a population-shift mechanism in Hsp70, in which functional residues are organized in a broad and robust allosteric network that can link the nucleotide-binding site and the substrate-binding regions. A smaller allosteric network in Hsp110 structures may elicit an entropy-driven allostery that occurs in the absence of global structural changes. We have found that global mediating residues with high network centrality may be organized in stable local communities that are indispensable for structural stability and efficient allosteric communications. The network-centric analysis of allosteric interactions has also established that centrality of functional residues could correlate with their sensitivity to mutations across diverse chaperone functions. This study reconciles a wide spectrum of structural and functional experiments by demonstrating how integration of molecular simulations and network-centric modeling may explain thermodynamic and mechanistic aspects of allosteric regulation in chaperones.

Balancing the Hydrogen Evolution Reaction, Surface Energetics, and Stability of Metallic MoS 2 Nanosheets via Covalent Functionalization

DOE PAGES

Benson, Eric E.; Zhang, Hanyu; Schuman, Samuel A.; ...

2017-12-27

We modify the fundamental electronic properties of metallic (1T phase) nanosheets of molybdenum disulfide (MoS 2) through covalent chemical functionalization, and thereby directly influence the kinetics of the hydrogen evolution reaction (HER), surface energetics, and stability. Chemically exfoliated, metallic MoS 2 nanosheets are functionalized with organic phenyl rings containing electron donating or withdrawing groups. We find that MoS 2 functionalized with the most electron donating functional group (p-(CH 3CH 2) 2NPh-MoS 2) is the most efficient catalyst for HER in this series, with initial activity that is slightly worse compared to the pristine metallic phase of MoS 2. The p-(CHmore » 3CH 2) 2NPh-MoS 2 is more stable than unfunctionalized metallic MoS 2 and outperforms unfunctionalized metallic MoS 2 for continuous H 2 evolution within 10 min under the same conditions. With regards to the entire studied series, the overpotential and Tafel slope for catalytic HER are both directly correlated with the electron donating strength of the functional group. The results are consistent with a mechanism involving ground-state electron donation or withdrawal to/from the MoS 2 nanosheets, which modifies the electron transfer kinetics and catalytic activity of the MoS 2 nanosheet. The functional groups preserve the metallic nature of the MoS 2 nanosheets, inhibiting conversion to the thermodynamically stable semiconducting state (2H) when mildly annealed in a nitrogen atmosphere. We propose that the electron density and, therefore, reactivity of the MoS 2 nanosheets are controlled by the attached functional groups. Functionalizing nanosheets of MoS 2 and other transition metal dichalcogenides provides a synthetic chemical route for controlling the electronic properties and stability within the traditionally thermally unstable metallic state.« less

Dancing through Life: Molecular Dynamics Simulations and Network-Centric Modeling of Allosteric Mechanisms in Hsp70 and Hsp110 Chaperone Proteins

PubMed Central

Stetz, Gabrielle; Verkhivker, Gennady M.

2015-01-01

Hsp70 and Hsp110 chaperones play an important role in regulating cellular processes that involve protein folding and stabilization, which are essential for the integrity of signaling networks. Although many aspects of allosteric regulatory mechanisms in Hsp70 and Hsp110 chaperones have been extensively studied and significantly advanced in recent experimental studies, the atomistic picture of signal propagation and energetics of dynamics-based communication still remain unresolved. In this work, we have combined molecular dynamics simulations and protein stability analysis of the chaperone structures with the network modeling of residue interaction networks to characterize molecular determinants of allosteric mechanisms. We have shown that allosteric mechanisms of Hsp70 and Hsp110 chaperones may be primarily determined by nucleotide-induced redistribution of local conformational ensembles in the inter-domain regions and the substrate binding domain. Conformational dynamics and energetics of the peptide substrate binding with the Hsp70 structures has been analyzed using free energy calculations, revealing allosteric hotspots that control negative cooperativity between regulatory sites. The results have indicated that cooperative interactions may promote a population-shift mechanism in Hsp70, in which functional residues are organized in a broad and robust allosteric network that can link the nucleotide-binding site and the substrate-binding regions. A smaller allosteric network in Hsp110 structures may elicit an entropy-driven allostery that occurs in the absence of global structural changes. We have found that global mediating residues with high network centrality may be organized in stable local communities that are indispensable for structural stability and efficient allosteric communications. The network-centric analysis of allosteric interactions has also established that centrality of functional residues could correlate with their sensitivity to mutations across diverse chaperone functions. This study reconciles a wide spectrum of structural and functional experiments by demonstrating how integration of molecular simulations and network-centric modeling may explain thermodynamic and mechanistic aspects of allosteric regulation in chaperones. PMID:26619280

Predicting oligonucleotide affinity to nucleic acid targets.

PubMed Central

Mathews, D H; Burkard, M E; Freier, S M; Wyatt, J R; Turner, D H

1999-01-01

A computer program, OligoWalk, is reported that predicts the equilibrium affinity of complementary DNA or RNA oligonucleotides to an RNA target. This program considers the predicted stability of the oligonucleotide-target helix and the competition with predicted secondary structure of both the target and the oligonucleotide. Both unimolecular and bimolecular oligonucleotide self structure are considered with a user-defined concentration. The application of OligoWalk is illustrated with three comparisons to experimental results drawn from the literature. PMID:10580474

Special section containing papers presented at the 13th IAEA Technical Meeting on Energetic Particles in Magnetic Confinement Systems (Beijing, China, 17-20 September 2013) Special section containing papers presented at the 13th IAEA Technical Meeting on Energetic Particles in Magnetic Confinement Systems (Beijing, China, 17-20 September 2013)

NASA Astrophysics Data System (ADS)

Lin, Z.

2014-10-01

In magnetic fusion plasmas, a significant fraction of the kinetic pressure is contributed by superthermal charged particles produced by auxiliary heating (fast ions and electrons) and fusion reactions (a-particles). Since these energetic particles are often far away from thermal equilibrium due to their non-Maxwellian distribution and steep pressure gradients, the free energy can excite electromagnetic instabilities to intensity levels well above the thermal fluctuations. The resultant electromagnetic turbulence could induce large transport of energetic particles, which could reduce heating efficiency, degrade overall plasma confinement, and damage fusion devices. Therefore, understanding and predicting energetic particle confinement properties are critical to the success of burning plasma experiments such as ITER since the ignition relies on plasma self-heating by a-particles. To promote international exchanges and collaborations on energetic particle physics, the biannual conference series under the auspices of the International Atomic Energy Agency (IAEA) were help in Kyiv (1989), Aspenas (1991), Trieste (1993), Princeton (1995), JET/Abingdon (1997), Naka (1999), Gothenburg (2001), San Diego (2003), Takayama (2005), Kloster Seeon (2007), Kyiv (2009), and Austin (2011). The papers in this special section were presented at the most recent meeting, the 13th IAEA Technical Meeting on Energetic Particles in Magnetic Confinement Systems, which was hosted by the Fusion Simulation Center, Peking University, Beijing, China (17-20 September 2013). The program of the meeting consisted of 71 presentations, including 13 invited talks, 26 oral contributed talks, 30 posters, and 2 summary talks, which were selected by the International Advisory Committee (IAC). The IAC members include H. Berk, L.G. Eriksson, A. Fasoli, W. Heidbrink, Ya. Kolesnichenko, Ph. Lauber, Z. Lin, R. Nazikian, S. Pinches, S. Sharapov, K. Shinohara, K. Toi, G. Vlad, and X.T. Ding. The conference program, abstracts of all papers, and slides of oral presentations are available at the conference website:www.phy.pku.edu.cn/fsc/w18419.jsp As a measure of the breadth in current research activities, a wide range of topics in energetic particle physics were covered in the meeting program, including dynamics of various Alfvén eigenmodes and energetic particle modes, energetic particle transport, energetic particle effects on magnetohydrodynamic (MHD) modes, runaway electrons, and diagnostics of energetic particles and neutrons. Energetic particle experiments were reported on tokamaks, stellarators, spherical tori, reversed field pinches, and linear devices. Most of the papers have direct comparisons between experimental data and simulation results, a very healthy trend in the research of energetic particle physics. As an indication for the depth in current research activities and possible future directions in energetic particle physics, some exciting progress reported at the meeting is highlighted here. The 3D fields of resonant magnetic perturbations (RMP) for controlling edge localized modes (ELM) are found to drive significant ripple loss of fast ions in DIII-D and ASDEX-U experiments. Similar loss is predicted for ITER RMP fields in the vacuum approximation. Fortunately, plasma response to RMP fields is found by the simulation to reduce the loss of fast ions and α-particles to a benign level. These results call for more accurate measurements and more reliable modeling of the plasma response to RMP fields in existing tokamak experiments and in future ITER experiments. Interesting progress on energetic particle transport by Alfvén eigenmodes was made in reduced 1D models based on the critical gradients model, in which energetic particle pressure gradients are relaxed to the local threshold of Alfvén eigenmode stability. Some experimental support for the critical gradient model was reported in DIII-D off-axis neutral beam injection (NBI) experiments, in which the fast-ion density relaxes to similar profiles for all injection angles. Further verification and validation of these reduced models by existing tokamak experiments and nonlinear simulations are needed. Impressive progress in first-principles simulations of Alfvén eigenmodes and energetic particle transport was prominently featured at the meeting. Rigorous verification and validation have been successfully carried out for global gyrokinetic simulations of Alfvén eigenmodes with kinetic effects of thermal plasmas and non-perturbative contributions by energetic particles. The gyrokinetic turbulence simulation provides an indispensable new capability for studying the nonlinear physics of energetic particles and Alfvén eigenmodes by incorporating important physics of radial variations and toroidal mode coupling. For example, gyrokinetic simulations have found nonlinear oscillations of Alfvén eigenmode amplitude and frequency consistent with experimental observations. With better understanding of linear and nonlinear properties of Alfvén eigenmodes, a fruitful future direction is the self-consistent simulation of energetic particle transport, which requires long time simulations of nonlinear interactions between multiple Alfvén eigenmodes. A significant step in this direction has been taken by MHD-gyrokinetic hybrid simulations, which have demonstrated that fast ion profile is flattened by enhanced transport due to resonance overlaps in multiple interacting Alfvén eigenmodes with realistic amplitudes. A very interesting physics here is that the re-distribution of the energetic particle profile by an initially dominant Alfvén eigenmode leads to the excitation of other Alfvén eigenmodes. The broaden phase space volume for the extraction of free energy can then drive large fluctuation amplitudes and enhanced energetic particle transport. Some experimental evidences of such indirect interaction of multiple modes through energetic particles were observed in JT-60U and ASDEX-U experiments. Thirteen papers presented at the meeting were reviewed to the usual high standard of Nuclear Fusion and published in this special section. On behalf of the IAC, I would like to thank all participants for their contributions to this conference and to thank Nuclear Fusion for publishing this special section. The next meeting of this series will be organized by Simon Pinches and will be held at the IAEA headquarters in Vienna, in the fall of 2015.

Vehicle-to-grid power implementation: From stabilizing the grid to supporting large-scale renewable energy

NASA Astrophysics Data System (ADS)

Kempton, Willett; Tomić, Jasna

Vehicle-to-grid power (V2G) uses electric-drive vehicles (battery, fuel cell, or hybrid) to provide power for specific electric markets. This article examines the systems and processes needed to tap energy in vehicles and implement V2G. It quantitatively compares today's light vehicle fleet with the electric power system. The vehicle fleet has 20 times the power capacity, less than one-tenth the utilization, and one-tenth the capital cost per prime mover kW. Conversely, utility generators have 10-50 times longer operating life and lower operating costs per kWh. To tap V2G is to synergistically use these complementary strengths and to reconcile the complementary needs of the driver and grid manager. This article suggests strategies and business models for doing so, and the steps necessary for the implementation of V2G. After the initial high-value, V2G markets saturate and production costs drop, V2G can provide storage for renewable energy generation. Our calculations suggest that V2G could stabilize large-scale (one-half of US electricity) wind power with 3% of the fleet dedicated to regulation for wind, plus 8-38% of the fleet providing operating reserves or storage for wind. Jurisdictions more likely to take the lead in adopting V2G are identified.

Methods for reducing interference in the Complementary Learning Systems model: oscillating inhibition and autonomous memory rehearsal.

PubMed

Norman, Kenneth A; Newman, Ehren L; Perotte, Adler J

2005-11-01

The stability-plasticity problem (i.e. how the brain incorporates new information into its model of the world, while at the same time preserving existing knowledge) has been at the forefront of computational memory research for several decades. In this paper, we critically evaluate how well the Complementary Learning Systems theory of hippocampo-cortical interactions addresses the stability-plasticity problem. We identify two major challenges for the model: Finding a learning algorithm for cortex and hippocampus that enacts selective strengthening of weak memories, and selective punishment of competing memories; and preventing catastrophic forgetting in the case of non-stationary environments (i.e. when items are temporarily removed from the training set). We then discuss potential solutions to these problems: First, we describe a recently developed learning algorithm that leverages neural oscillations to find weak parts of memories (so they can be strengthened) and strong competitors (so they can be punished), and we show how this algorithm outperforms other learning algorithms (CPCA Hebbian learning and Leabra at memorizing overlapping patterns. Second, we describe how autonomous re-activation of memories (separately in cortex and hippocampus) during REM sleep, coupled with the oscillating learning algorithm, can reduce the rate of forgetting of input patterns that are no longer present in the environment. We then present a simple demonstration of how this process can prevent catastrophic interference in an AB-AC learning paradigm.

Thiophene antibacterials that allosterically stabilize DNA-cleavage complexes with DNA gyrase.

PubMed

Chan, Pan F; Germe, Thomas; Bax, Benjamin D; Huang, Jianzhong; Thalji, Reema K; Bacqué, Eric; Checchia, Anna; Chen, Dongzhao; Cui, Haifeng; Ding, Xiao; Ingraham, Karen; McCloskey, Lynn; Raha, Kaushik; Srikannathasan, Velupillai; Maxwell, Anthony; Stavenger, Robert A

2017-05-30

A paucity of novel acting antibacterials is in development to treat the rising threat of antimicrobial resistance, particularly in Gram-negative hospital pathogens, which has led to renewed efforts in antibiotic drug discovery. Fluoroquinolones are broad-spectrum antibacterials that target DNA gyrase by stabilizing DNA-cleavage complexes, but their clinical utility has been compromised by resistance. We have identified a class of antibacterial thiophenes that target DNA gyrase with a unique mechanism of action and have activity against a range of bacterial pathogens, including strains resistant to fluoroquinolones. Although fluoroquinolones stabilize double-stranded DNA breaks, the antibacterial thiophenes stabilize gyrase-mediated DNA-cleavage complexes in either one DNA strand or both DNA strands. X-ray crystallography of DNA gyrase-DNA complexes shows the compounds binding to a protein pocket between the winged helix domain and topoisomerase-primase domain, remote from the DNA. Mutations of conserved residues around this pocket affect activity of the thiophene inhibitors, consistent with allosteric inhibition of DNA gyrase. This druggable pocket provides potentially complementary opportunities for targeting bacterial topoisomerases for antibiotic development.

DNA cytoskeleton for stabilizing artificial cells.

PubMed

Kurokawa, Chikako; Fujiwara, Kei; Morita, Masamune; Kawamata, Ibuki; Kawagishi, Yui; Sakai, Atsushi; Murayama, Yoshihiro; Nomura, Shin-Ichiro M; Murata, Satoshi; Takinoue, Masahiro; Yanagisawa, Miho

2017-07-11

Cell-sized liposomes and droplets coated with lipid layers have been used as platforms for understanding live cells, constructing artificial cells, and implementing functional biomedical tools such as biosensing platforms and drug delivery systems. However, these systems are very fragile, which results from the absence of cytoskeletons in these systems. Here, we construct an artificial cytoskeleton using DNA nanostructures. The designed DNA oligomers form a Y-shaped nanostructure and connect to each other with their complementary sticky ends to form networks. To undercoat lipid membranes with this DNA network, we used cationic lipids that attract negatively charged DNA. By encapsulating the DNA into the droplets, we successfully created a DNA shell underneath the membrane. The DNA shells increased interfacial tension, elastic modulus, and shear modulus of the droplet surface, consequently stabilizing the lipid droplets. Such drastic changes in stability were detected only when the DNA shell was in the gel phase. Furthermore, we demonstrate that liposomes with the DNA gel shell are substantially tolerant against outer osmotic shock. These results clearly show the DNA gel shell is a stabilizer of the lipid membrane akin to the cytoskeleton in live cells.

Bipolar disorder and complementary medicine: current evidence, safety issues, and clinical considerations.

PubMed

Sarris, Jerome; Lake, James; Hoenders, Rogier

2011-10-01

Bipolar disorder (BD) is a debilitating syndrome that is often undiagnosed and undertreated. Population surveys show that persons with BD often self-medicate with complementary and alternative medicine (CAM) or integrative therapies in spite of limited research evidence supporting their use. To date, no review has focused specifically on nonconventional treatments of BD. The study objectives were to present a review of nonconventional (complementary and integrative) interventions examined in clinical trials on BD, and to offer provisional guidelines for the judicious integrative use of CAM in the management of BD. PubMed, CINAHL,(®) Web of Science, and Cochrane Library databases were searched for human clinical trials in English during mid-2010 using Bipolar Disorder and CAM therapy and CAM medicine search terms. Effect sizes (Cohen's d) were also calculated where data were available. Several positive high-quality studies on nutrients in combination with conventional mood stabilizers and antipsychotic medications in BD depression were identified, while branched-chain amino acids and magnesium were effective (small studies) in attenuating mania in BD. In the treatment of bipolar depression, evidence was mixed regarding omega-3, while isolated studies provide provisional support for a multinutrient formula, n-acetylcysteine, and l-tryptophan. In one study, acupuncture was found to have favorable but nonsignificant effects on mania and depression outcomes. Current evidence supports the integrative treatment of BD using combinations of mood stabilizers and select nutrients. Other CAM or integrative modalities used to treat BD have not been adequately explored to date; however, some early findings are promising. Select CAM and integrative interventions add to established conventional treatment of BD and may be considered when formulating a treatment plan. It is hoped that the safety issues and clinical considerations addressed in this article may encourage the practice of safety-conscious and evidence-based integrative management of BD.

Solution structure of a highly stable DNA duplex conjugated to a minor groove binder.

PubMed Central

Kumar, S; Reed, M W; Gamper, H B; Gorn, V V; Lukhtanov, E A; Foti, M; West, J; Meyer, R B; Schweitzer, B I

1998-01-01

The tripeptide 1,2-dihydro-(3 H )-pyrrolo[3,2- e ]indole-7-carboxylate (CDPI3) binds to the minor groove of DNA with high affinity. When this minor groove binder is conjugated to the 5'-end of short oligonucleotides the conjugates form unusually stable hybrids with complementary DNA and thus may have useful diagnostic and/or therapeutic applications. In order to gain an understanding of the structural interactions between the CDPI3minor groove binding moiety and the DNA, we have determined and compared the solution structure of a duplex consisting of oligodeoxyribonucleotide 5'-TGATTATCTG-3' conjugated at the 5'-end to CDPI3 and its complementary strand to an unmodified control duplex of the same sequence using nuclear magnetic resonance techniques. Thermal denaturation studies indicated that the hybrid of this conjugate with its complementary strand had a melting temperature that was 30 degrees C higher compared with the unmodified control duplex. Following restrained molecular dynamics and relaxation matrix refinement, the solution structure of the CDPI3-conjugated DNA duplex demonstrated that the overall shape of the duplex was that of a straight B-type helix and that the CDPI3moiety was bound snugly in the minor groove, where it was stabilized by extensive van der Waal's interactions. PMID:9443977

Solution structure of a highly stable DNA duplex conjugated to a minor groove binder.

PubMed

Kumar, S; Reed, M W; Gamper, H B; Gorn, V V; Lukhtanov, E A; Foti, M; West, J; Meyer, R B; Schweitzer, B I

1998-02-01

The tripeptide 1,2-dihydro-(3 H )-pyrrolo[3,2- e ]indole-7-carboxylate (CDPI3) binds to the minor groove of DNA with high affinity. When this minor groove binder is conjugated to the 5'-end of short oligonucleotides the conjugates form unusually stable hybrids with complementary DNA and thus may have useful diagnostic and/or therapeutic applications. In order to gain an understanding of the structural interactions between the CDPI3minor groove binding moiety and the DNA, we have determined and compared the solution structure of a duplex consisting of oligodeoxyribonucleotide 5'-TGATTATCTG-3' conjugated at the 5'-end to CDPI3 and its complementary strand to an unmodified control duplex of the same sequence using nuclear magnetic resonance techniques. Thermal denaturation studies indicated that the hybrid of this conjugate with its complementary strand had a melting temperature that was 30 degrees C higher compared with the unmodified control duplex. Following restrained molecular dynamics and relaxation matrix refinement, the solution structure of the CDPI3-conjugated DNA duplex demonstrated that the overall shape of the duplex was that of a straight B-type helix and that the CDPI3moiety was bound snugly in the minor groove, where it was stabilized by extensive van der Waal's interactions.

Effect of amino acid mutations on intra-dimer tubulin-tubulin binding strength of microtubules.

PubMed

Liu, Ning; Pidaparti, Ramana; Wang, Xianqiao

2017-12-11

Energetic interactions inside αβ-tubulin dimers of a microtubule (MT) with atomic resolutions are of importance in determining the mechanical properties and structural stability of the MT as well as designing self-assembled functional structures from it. Here, we carry out several comprehensive atomistic simulations to investigate the interaction properties within αβ-tubulin dimers and effect of residue mutations on the intra-dimer tubulin-tubulin (IDTT) binding strength. Results indicate that the force-displacement responses of the dimer could be roughly divided into three stages involving increasing, decreasing, and fluctuating forces. Energetic analysis shows that electrostatic interactions dominate the IDTT binding strength. Further per-residue energetic analysis shows that the major part of the interface interaction energy (approximately 72% for α-tubulin and 62% for β-tubulin) comes from amino acid residues with net charges, namely arginine (ARG), lysine (LYS), glutamic acid (GLU), aspartic acid (ASP). Residue mutations are completed for ARG105 on α-tubulin and ASP251 on β-tubulin to study the effect of mutations on the IDTT binding strength. Results indicate that stiffness, rupture force, and interface interaction energy of αβ-tubulin dimer can be improved by up to 28%, 13% and 28%, respectively. Overall, our results provide a thorough atomistic understanding of the IDTT binding strength within αβ-tubulin heterodimers and help pave the way for eventually designing and controlling the self-assembled functional structures from MTs.

Chemical ordering in substituted fluorite oxides: a computational investigation of Ho 2Zr 2O 7 and RE 2Th 2O 7 (RE=Ho, Y, Gd, Nd, La)

DOE PAGES

Solomon, Jonathan M.; Shamblin, Jacob; Lang, Maik; ...

2016-12-12

Fluorite-structured oxides find widespread use for applications spanning nuclear energy and waste containment, energy conversion, and sensing. In such applications the host tetravalent cation is often partially substituted by trivalent cations, with an associated formation of charge-compensating oxygen vacancies. The stability and properties of such materials are known to be influenced strongly by chemical ordering of the cations and vacancies, and the nature of such ordering and associated energetics are thus of considerable interest. Here we employ density-functional theory (DFT) calculations to study the structure and energetics of cation and oxygen-vacancy ordering in Ho 2Zr 2O 7. In a recentmore » neutron total scattering study, solid solutions in this system were reported to feature local chemical ordering based on the fluorite-derivative weberite structure. The calculations show a preferred chemical ordering qualitatively consistent with these findings, and yield values for the ordering energy of 9.5 kJ/mol-cation. Similar DFT calculations are applied to additional RE 2Th 2O 7'' fluorite compounds, spanning a range of values for the ratio of the tetravalent and trivalent (RE) cation radii. Finally, the results demonstrate that weberite-type order becomes destabilized with increasing values of this size ratio, consistent with an increasing energetic preference for the tetravalent cations to have higher oxygen coordination.« less

In situ TEM of radiation effects in complex ceramics.

PubMed

Lian, Jie; Wang, L M; Sun, Kai; Ewing, Rodney C

2009-03-01

In situ transmission electron microscopy (TEM) has been extensively applied to study radiation effects in a wide variety of materials, such as metals, ceramics and semiconductors and is an indispensable tool in obtaining a fundamental understanding of energetic beam-matter interactions, damage events, and materials' behavior under intense radiation environments. In this article, in situ TEM observations of radiation effects in complex ceramics (e.g., oxides, silicates, and phosphates) subjected to energetic ion and electron irradiations have been summarized with a focus on irradiation-induced microstructural evolution, changes in microchemistry, and the formation of nanostructures. New results for in situ TEM observation of radiation effects in pyrochlore, A(2)B(2)O(7), and zircon, ZrSiO(4), subjected to multiple beam irradiations are presented, and the effects of simultaneous irradiations of alpha-decay and beta-decay on the microstructural evolution of potential nuclear waste forms are discussed. Furthermore, in situ TEM results of radiation effects in a sodium borosilicate glass subjected to electron-beam exposure are introduced to highlight the important applications of advanced analytical TEM techniques, including Z-contrast imaging, energy filtered TEM (EFTEM), and electron energy loss spectroscopy (EELS), in studying radiation effects in materials microstructural evolution and microchemical changes. By combining ex situ TEM and advanced analytical TEM techniques with in situ TEM observations under energetic beam irradiations, one can obtain invaluable information on the phase stability and response behaviors of materials under a wide range of irradiation conditions. (c) 2009 Wiley-Liss, Inc.

Synthesis and energetics of gold nanoclusters tailored by interfacial bonding structure

NASA Astrophysics Data System (ADS)

Tang, Zhenghua

In addition to the well known quantum confinement effects resulted from size and shape, interfacial bond structure is another factor, affecting the properties of the nanomaterial that is rarely studied. Inspired by the "Au-S-Au" staple motif discovered from the crystal structure of monothiol protected Au102 nanocluster (Science, 2007, 318, 430), dithiol molecules (e.g. 1, 2-dithiol, 1, 4-dithiol, etc.) with molecular structural constraint have been employed to create dithiolate protected clusters or mixed monothiolate and dithiolate protected clusters. The structure and properties of the Au clusters are expected to change due to two effects: The entropy gain of dithiol over monothiol protection and the constraint to the formation of the thiol bridging motif. DMPS (1, 2-dithiol molecule) stabilized clusters with characteristic absorption bands have been obtained, and characterized by multiple techniques. Monolayer reaction on gold core surface between the monothiol tiopronin and dithiol DMPS has been performed, and the mechanism has been probed. Mixed phenylethanethiolate and durene-dithiolate (1, 4-dithiol molecule) protected Au130 clusters with rich electrochemical features have been created, and the optical and electrochemical energetics have been successfully correlated based on core and core-ligand energy states. Furthermore, the impact of 1, 4-dithiolate-Au bonding on the near infrared luminescence has been studied. INDEX WORDS: Au MPCs, Staple motif, DMPS, Au DTCs, Au4, Tiopronin, Monolayer reaction, Durene-DT, Au MTCs, Au130, Optical energetic, Electrochemistry, Near infrared luminescence, 1, 4-Dithiolate-Au bonding.

The dynamics, structure, and conformational free energy of proline-containing antifreeze glycoprotein.

PubMed Central

Nguyen, Dat H; Colvin, Michael E; Yeh, Yin; Feeney, Robert E; Fink, William H

2002-01-01

Recent NMR studies of the solution structure of the 14-amino acid antifreeze glycoprotein AFGP-8 have concluded that the molecule lacks long-range order. The implication that an apparently unstructured molecule can still have a very precise function as a freezing inhibitor seems startling at first consideration. To gain insight into the nature of conformations and motions in AFGP-8, we have undertaken molecular dynamics simulations augmented with free energy calculations using a continuum solvation model. Starting from 10 different NMR structures, 20 ns of dynamics of AFGP were explored. The dynamics show that AFGP structure is composed of four segments, joined by very flexible pivots positioned at alanine 5, 8, and 11. The dynamics also show that the presence of prolines in this small AFGP structure facilitates the adoption of the poly-proline II structure as its overall conformation, although AFGP does adopt other conformations during the course of dynamics as well. The free energies calculated using a continuum solvation model show that the lowest free energy conformations, while being energetically equal, are drastically different in conformations. In other words, this AFGP molecule has many structurally distinct and energetically equal minima in its energy landscape. In addition, conformational, energetic, and hydrogen bond analyses suggest that the intramolecular hydrogen bonds between the N-acetyl group and the protein backbone are an important integral part of the overall stability of the AFGP molecule. The relevance of these findings to the mechanism of freezing inhibition is discussed. PMID:12023212

The dynamics, structure, and conformational free energy of proline-containing antifreeze glycoprotein.

PubMed

Nguyen, Dat H; Colvin, Michael E; Yeh, Yin; Feeney, Robert E; Fink, William H

2002-06-01

Recent NMR studies of the solution structure of the 14-amino acid antifreeze glycoprotein AFGP-8 have concluded that the molecule lacks long-range order. The implication that an apparently unstructured molecule can still have a very precise function as a freezing inhibitor seems startling at first consideration. To gain insight into the nature of conformations and motions in AFGP-8, we have undertaken molecular dynamics simulations augmented with free energy calculations using a continuum solvation model. Starting from 10 different NMR structures, 20 ns of dynamics of AFGP were explored. The dynamics show that AFGP structure is composed of four segments, joined by very flexible pivots positioned at alanine 5, 8, and 11. The dynamics also show that the presence of prolines in this small AFGP structure facilitates the adoption of the poly-proline II structure as its overall conformation, although AFGP does adopt other conformations during the course of dynamics as well. The free energies calculated using a continuum solvation model show that the lowest free energy conformations, while being energetically equal, are drastically different in conformations. In other words, this AFGP molecule has many structurally distinct and energetically equal minima in its energy landscape. In addition, conformational, energetic, and hydrogen bond analyses suggest that the intramolecular hydrogen bonds between the N-acetyl group and the protein backbone are an important integral part of the overall stability of the AFGP molecule. The relevance of these findings to the mechanism of freezing inhibition is discussed.

Chemical ordering in substituted fluorite oxides: a computational investigation of Ho2Zr2O7 and RE2Th2O7 (RE=Ho, Y, Gd, Nd, La)

PubMed Central

Solomon, Jonathan M.; Shamblin, Jacob; Lang, Maik; Navrotsky, Alexandra; Asta, Mark

2016-01-01

Fluorite-structured oxides find widespread use for applications spanning nuclear energy and waste containment, energy conversion, and sensing. In such applications the host tetravalent cation is often partially substituted by trivalent cations, with an associated formation of charge-compensating oxygen vacancies. The stability and properties of such materials are known to be influenced strongly by chemical ordering of the cations and vacancies, and the nature of such ordering and associated energetics are thus of considerable interest. Here we employ density-functional theory (DFT) calculations to study the structure and energetics of cation and oxygen-vacancy ordering in Ho2Zr2O7. In a recent neutron total scattering study, solid solutions in this system were reported to feature local chemical ordering based on the fluorite-derivative weberite structure. The calculations show a preferred chemical ordering qualitatively consistent with these findings, and yield values for the ordering energy of 9.5 kJ/mol-cation. Similar DFT calculations are applied to additional RE2Th2O7 fluorite compounds, spanning a range of values for the ratio of the tetravalent and trivalent (RE) cation radii. The results demonstrate that weberite-type order becomes destabilized with increasing values of this size ratio, consistent with an increasing energetic preference for the tetravalent cations to have higher oxygen coordination. PMID:27941870

Energy flow and functional compensation in Great Basin small mammals under natural and anthropogenic environmental change

PubMed Central

Terry, Rebecca C.; Rowe, Rebecca J.

2015-01-01

Research on the ecological impacts of environmental change has primarily focused at the species level, leaving the responses of ecosystem-level properties like energy flow poorly understood. This is especially so over millennial timescales inaccessible to direct observation. Here we examine how energy flow within a Great Basin small mammal community responded to climate-driven environmental change during the past 12,800 y, and use this baseline to evaluate responses observed during the past century. Our analyses reveal marked stability in energy flow during rapid climatic warming at the terminal Pleistocene despite dramatic turnover in the distribution of mammalian body sizes and habitat-associated functional groups. Functional group turnover was strongly correlated with climate-driven changes in regional vegetation, with climate and vegetation change preceding energetic shifts in the small mammal community. In contrast, the past century has witnessed a substantial reduction in energy flow caused by an increase in energetic dominance of small-bodied species with an affinity for closed grass habitats. This suggests that modern changes in land cover caused by anthropogenic activities—particularly the spread of nonnative annual grasslands—has led to a breakdown in the compensatory dynamics of energy flow. Human activities are thus modifying the small mammal community in ways that differ from climate-driven expectations, resulting in an energetically novel ecosystem. Our study illustrates the need to integrate across ecological and temporal scales to provide robust insights for long-term conservation and management. PMID:26170294

Energetics, kinetics, and pathway of SNARE folding and assembly revealed by optical tweezers.

PubMed

Zhang, Yongli

2017-07-01

Soluble N-ethylmaleimide-sensitive factor attachment protein receptors (SNAREs) are universal molecular engines that drive membrane fusion. Particularly, synaptic SNAREs mediate fast calcium-triggered fusion of neurotransmitter-containing vesicles with plasma membranes for synaptic transmission, the basis of all thought and action. During membrane fusion, complementary SNAREs located on two apposed membranes (often called t- and v-SNAREs) join together to assemble into a parallel four-helix bundle, releasing the energy to overcome the energy barrier for fusion. A long-standing hypothesis suggests that SNAREs act like a zipper to draw the two membranes into proximity and thereby force them to fuse. However, a quantitative test of this SNARE zippering hypothesis was hindered by difficulties to determine the energetics and kinetics of SNARE assembly and to identify the relevant folding intermediates. Here, we first review different approaches that have been applied to study SNARE assembly and then focus on high-resolution optical tweezers. We summarize the folding energies, kinetics, and pathways of both wild-type and mutant SNARE complexes derived from this new approach. These results show that synaptic SNAREs assemble in four distinct stages with different functions: slow N-terminal domain association initiates SNARE assembly; a middle domain suspends and controls SNARE assembly; and rapid sequential zippering of the C-terminal domain and the linker domain directly drive membrane fusion. In addition, the kinetics and pathway of the stagewise assembly are shared by other SNARE complexes. These measurements prove the SNARE zippering hypothesis and suggest new mechanisms for SNARE assembly regulated by other proteins. © 2017 The Protein Society.

Interplay of short-range correlations and nuclear symmetry energy in hard-photon production from heavy-ion reactions at Fermi energies

NASA Astrophysics Data System (ADS)

Yong, Gao-Chan; Li, Bao-An

2017-12-01

Within an isospin- and momentum-dependent transport model for nuclear reactions at intermediate energies, we investigate the interplay of the nucleon-nucleon short-range correlations (SRCs) and nuclear symmetry energy Esym(ρ ) on hard-photon spectra in collisions of several Ca isotopes on 112Sn and 124Sn targets at a beam energy of 45 MeV/nucleon. It is found that over the whole spectra of hard photons studied, effects of the SRCs overwhelm those owing to the Esym(ρ ) . The energetic photons come mostly from the high-momentum tails (HMTs) of single-nucleon momentum distributions in the target and projectile. Within the neutron-proton dominance model of SRCs based on the consideration that the tensor force acts mostly in the isosinglet and spin-triplet nucleon-nucleon interaction channel, there are equal numbers of neutrons and protons, thus a zero isospin asymmetry in the HMTs. Therefore, experimental measurements of the energetic photons from heavy-ion collisions at Fermi energies have the great potential to help us better understand the nature of SRCs without any appreciable influence by the uncertain Esym(ρ ) . These measurements will be complementary to but also have some advantages over the ongoing and planned experiments using hadronic messengers from reactions induced by high-energy electrons or protons. Because the underlying physics of SRCs and Esym(ρ ) are closely correlated, a better understanding of the SRCs will, in turn, help constrain the nuclear symmetry energy more precisely in a broad density range.

Finite element approximation of the fields of bulk and interfacial line defects

NASA Astrophysics Data System (ADS)

Zhang, Chiqun; Acharya, Amit; Puri, Saurabh

2018-05-01

A generalized disclination (g.disclination) theory (Acharya and Fressengeas, 2015) has been recently introduced that goes beyond treating standard translational and rotational Volterra defects in a continuously distributed defects approach; it is capable of treating the kinematics and dynamics of terminating lines of elastic strain and rotation discontinuities. In this work, a numerical method is developed to solve for the stress and distortion fields of g.disclination systems. Problems of small and finite deformation theory are considered. The fields of a single disclination, a single dislocation treated as a disclination dipole, a tilt grain boundary, a misfitting grain boundary with disconnections, a through twin boundary, a terminating twin boundary, a through grain boundary, a star disclination/penta-twin, a disclination loop (with twist and wedge segments), and a plate, a lenticular, and a needle inclusion are approximated. It is demonstrated that while the far-field topological identity of a dislocation of appropriate strength and a disclination-dipole plus a slip dislocation comprising a disconnection are the same, the latter microstructure is energetically favorable. This underscores the complementary importance of all of topology, geometry, and energetics in understanding defect mechanics. It is established that finite element approximations of fields of interfacial and bulk line defects can be achieved in a systematic and routine manner, thus contributing to the study of intricate defect microstructures in the scientific understanding and predictive design of materials. Our work also represents one systematic way of studying the interaction of (g.)disclinations and dislocations as topological defects, a subject of considerable subtlety and conceptual importance (Aharoni et al., 2017; Mermin, 1979).

New Magnetospheric Substorm Injection Monitor: Image Electron Spectrometer On Board a Chinese Navigation IGSO Satellite

NASA Astrophysics Data System (ADS)

Zong, Qiugang; Wang, Yongfu; Zou, Hong; Wang, Linghua; Rankin, Robert; Zhang, Xiaoxin

2018-02-01

Substorm injections are one of the most dynamic processes in Earth's magnetosphere and have global consequences and broad implications for space weather modeling. They can be monitored using energetic electron detectors on geosynchronous satellites. The Imaging Electron Spectrometer (IES) on board a Chinese navigation satellite, launched on 16 October 2015 into an inclined geosynchronous satellite orbit (IGSO), provides the first energetic electron measurement in IGSO orbit to the best of our knowledge. The IES was developed by Peking University and is named hereafter as BD-IES. Using a pin-hole technique, the BD-IES instrument measures 50-600 keV incident electrons in eight energy channels from nine directions covering a range of 180° in polar angle. Data collection by the BD-IES instrument have recently passed the 1 year mark, which reflects a successful milestone for the mission. The innermost and outermost signatures of substorm injection at L 6 and 12 have been observed by the BD-IES with a high L shell spatial coverage, complementary to the existing missions such as the Van Allen Probes that covers the range below L 6. There are another two BD-IES instruments to be installed in the coming Chinese Sun-synchronous and geosynchronous satellites, respectively. Such a configuration will provide a unique opportunity to investigate inward and outward radial propagation of the substorm injection region simultaneously at high and low L shells. It will further elucidate potential mechanisms for the particle energization and transport, two of the most important topics in magnetospheric dynamics.

Integrative mental health care: from theory to practice, Part 2.

PubMed

Lake, James

2008-01-01

Integrative approaches will lead to more accurate and different understandings of mental illness. Beneficial responses to complementary and alternative therapies provide important clues about the phenomenal nature of the human body in space-time and disparate biological, informational, and energetic factors associated with normal and abnormal psychological functioning. The conceptual framework of contemporary Western psychiatry includes multiple theoretical viewpoints, and there is no single best explanatory model of mental illness. Future theories of mental illness causation will not depend exclusively on empirical verification of strictly biological processes but will take into account both classically described biological processes and non-classical models, including complexity theory, resulting in more complete explanations of the characteristics and causes of symptoms and mechanisms of action that result in beneficial responses to treatments. Part 1 of this article examined the limitations of the theory and contemporary clinical methods employed in Western psychiatry and discussed implications of emerging paradigms in physics and the biological sciences for the future of psychiatry. In part 2, a practical methodology, for planning integrative assessment and treatment strategies in mental health care is proposed. Using this methodology the integrative management of moderate and severe psychiatric symptoms is reviewed in detail. As the conceptual framework of Western medicine evolves toward an increasingly integrative perspective, novel understanding of complex relationships between biological, informational, and energetic processes associated with normal psychological functioning and mental illness will lead to more effective integrative assessment and treatment strategies addressing the causes or meanings of symptoms at multiple hierarchic levels of body-brain-mind.

Integrative mental health care: from theory to practice, part 1.

PubMed

Lake, James

2007-01-01

Integrative approaches will lead to more accurate and different understandings of mental illness. Beneficial responses to complementary and alternative therapies provide important clues about the phenomenal nature of the human body in space-time and disparate biological, informational, and energetic factors associated with normal and abnormal psychological functioning. The conceptual framework of contemporary Western psychiatry includes multiple theoretical viewpoints, and there is no single best explanatory model of mental illness. Future theories of mental illness causation will not depend exclusively on empirical verification of strictly biological processes but will take into account both classically described biological processes and non-classical models, including complexity theory, resulting in more complete explanations of the characteristics and causes of symptoms and mechanisms of action that result in beneficial responses to treatments. Part 1 of this article examines the limitations of the theory and contemporary clinical methods employed in Western psychiatry and discusses implications of emerging paradigms in physics and the biological sciences for the future of psychiatry. In part 2, a practical methodology for planning integrative assessment and treatment strategies in mental health care is proposed. Using this methodology the integrative management of moderate and severe psychiatric symptoms is reviewed in detail. As the conceptual framework of Western medicine evolves toward an increasingly integrative perspective, novel understandings of complex relationships between biological, informational, and energetic processes associated with normal psychological functioning and mental illness will lead to more effective integrative assessment and treatment strategies addressing the causes or meanings of symptoms at multiple hierarchic levels of body-brain-mind.

Synthesis and Investigation of Advanced Energetic Materials Based on Bispyrazolylmethanes.

PubMed

Fischer, Dennis; Gottfried, Jennifer L; Klapötke, Thomas M; Karaghiosoff, Konstantin; Stierstorfer, Jörg; Witkowski, Tomasz G

2016-12-23

Herein we present the preparation and characterization of three new bispyrazolyl-based energetic compounds with great potential as explosive materials. The reaction of sodium 4-amino-3,5-dinitropyrazolate (5) with dimethyl iodide yielded bis(4-amino-3,5-dinitropyrazolyl)methane (6), which is a secondary explosive with high heat resistance (T dec =310 °C). The oxidation of this compound afforded bis(3,4,5-trinitropyrazolyl)methane (7), which is a combined nitrogen- and oxygen-rich secondary explosive with very high theoretical and estimated experimental detonation performance (V det (theor)=9304 m s -1 versus V det (exp)=9910 m s -1 ) in the range of that of CL-20. Also, the thermal stability (T dec =205 °C) and sensitivities of 7 are auspicious. The reaction of 6 with in situ generated nitrous acid yielded the primary explosive bis(4-diazo-5-nitro-3-oxopyrazolyl)methane (8), which showed superior properties to those of currently used diazodinitrophenol (DDNP). © 2016 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

U(v) in metal uranates: A combined experimental and theoretical study of MgUO 4, CrUO 4, and FeUO 4

DOE PAGES

Guo, Xiaofeng; Tiferet, Eitan; Qi, Liang; ...

2016-01-01

Although pentavalent uranium can exist in aqueous solution, its presence in the solid state is uncommon. Metal monouranates, MgUO 4, CrUO 4 and FeUO 4 were synthesized for detailed structural and energetic investigations. Structural characteristics of these uranates used powder X-ray diffraction, synchrotron X-ray absorption spectroscopy, X-ray photoelectron spectroscopy, and 57Fe-Mossbauer spectroscopy. Enthalpies of formation were measured by high temperature oxide melt solution calorimetry. Density functional theory (DFT) calculations provided both structural and energetic information. The measured structural and thermodynamic properties show good consistency with those predicted from DFT. The presence of U 5+ has been solidly confirmed in CrUOmore » 4 and FeUO 4, which are thermodynamically stable compounds, and the origin and stability of U 5+ in the system was elaborated by DFT. Lastly, the structural and thermodynamic behaviour of U 5+ elucidated in this work is relevant to fundamental actinide redox chemistry and to applications in the nuclear industry and radioactive waste disposal.« less

Tunable ferroelectric polarization and its interplay with spin-orbit coupling in tin iodide perovskites

NASA Astrophysics Data System (ADS)

Stroppa, Alessandro; di Sante, Domenico; Barone, Paolo; Bokdam, Menno; Kresse, Georg; Franchini, Cesare; Whangbo, Myung-Hwan; Picozzi, Silvia

2014-12-01

Ferroelectricity is a potentially crucial issue in halide perovskites, breakthrough materials in photovoltaic research. Using density functional theory simulations and symmetry analysis, we show that the lead-free perovskite iodide (FA)SnI3, containing the planar formamidinium cation FA, (NH2CHNH2)+, is ferroelectric. In fact, the perpendicular arrangement of FA planes, leading to a ‘weak’ polarization, is energetically more stable than parallel arrangements of FA planes, being either antiferroelectric or ‘strong’ ferroelectric. Moreover, we show that the ‘weak’ and ‘strong’ ferroelectric states with the polar axis along different crystallographic directions are energetically competing. Therefore, at least at low temperatures, an electric field could stabilize different states with the polarization rotated by π/4, resulting in a highly tunable ferroelectricity appealing for multistate logic. Intriguingly, the relatively strong spin-orbit coupling in noncentrosymmetric (FA)SnI3 gives rise to a co-existence of Rashba and Dresselhaus effects and to a spin texture that can be induced, tuned and switched by an electric field controlling the ferroelectric state.

The accurate particle tracer code

NASA Astrophysics Data System (ADS)

Wang, Yulei; Liu, Jian; Qin, Hong; Yu, Zhi; Yao, Yicun

2017-11-01

The Accurate Particle Tracer (APT) code is designed for systematic large-scale applications of geometric algorithms for particle dynamical simulations. Based on a large variety of advanced geometric algorithms, APT possesses long-term numerical accuracy and stability, which are critical for solving multi-scale and nonlinear problems. To provide a flexible and convenient I/O interface, the libraries of Lua and Hdf5 are used. Following a three-step procedure, users can efficiently extend the libraries of electromagnetic configurations, external non-electromagnetic forces, particle pushers, and initialization approaches by use of the extendible module. APT has been used in simulations of key physical problems, such as runaway electrons in tokamaks and energetic particles in Van Allen belt. As an important realization, the APT-SW version has been successfully distributed on the world's fastest computer, the Sunway TaihuLight supercomputer, by supporting master-slave architecture of Sunway many-core processors. Based on large-scale simulations of a runaway beam under parameters of the ITER tokamak, it is revealed that the magnetic ripple field can disperse the pitch-angle distribution significantly and improve the confinement of energetic runaway beam on the same time.

Electronic structure and optical properties of Ta-doped and (Ta, N)-codoped SrTiO3 from hybrid functional calculations

NASA Astrophysics Data System (ADS)

Liu, Yanyu; Zhou, Wei; Wu, Ping

2017-02-01

A systematic study has been carried out to research the effect of Ta monodoping and (Ta, N)-codoping on the electronic structure and optical properties of SrTiO3. The results indicate that the incorporation of N into the SrTiO3 lattice is in favor of the substitution of Ta at a Ti site, which is the most favorable structure with respect to both the energetic stability and high photocatalytic activity. Furthermore, the carrier recombination centers induced by Ta monodoping are passivated in the (Ta, N)-codoped SrTiO3 system with Ta at a Ti site. Simultaneous incorporation of N and Ta results in a band gap decreasing about 0.7 eV due to the appearance of the new states hybridized by N-p states with the O-p states above the valence band. The band alignment verifies that the (Ta, N)-codoped SrTiO3 simultaneously meets the criteria of band-edge energetic positions and band gap for the overall water splitting under visible light.