Computational study of RNA folding kinetics and thermodynamics

NASA Astrophysics Data System (ADS)

Morgan, Steven Robert

RNA in its many forms is involved in the processes of protein manufacture, gene splicing, catalysis and gene regulation. It is also the store of genetic information in some viruses. The function of the RNA is determined by its structure, and it is the purpose of this thesis to investigate kinetic and thermodynamic properties of RNA secondary structures in order to obtain a better understanding of their formation and function. Our main tenet is that kinetic formation of RNA structure is necessary to explain features found in natural RNA structures, as well as aspects of the biological function of RNA. Firstly we show that examination of the energies of fragments of RNA secondary structure provides evidence for kinetic formation of structure. Local regions of RNA of length less than about 100 nucleotides adopt a conformation with energy near or equal to the minimum possible for those regions, whilst the energies of larger domains are much further from the their respective minima. This is consistent with the patterns that would be expected if RNA structure is folded Idneticatic during transcription. A Monte-Carlo algorithm is then used to model the kinetic folding of RNA during transcriptional growth. The algorithm is capable of finding the correct structure of a natural RNA for which the minimum free energy approach is unsuccessful. In the viral phage MS2 Idneticatic formed RNA structure plays an important role in the regulation of gene expression. The folding algorithm can accurately model this by IdneticaUy controlling access to the gene initiation region. The algorithm is also successfully used to model the control of replication in the ColEl plasmid. Taking a different approach, we then use a simplified model of RNA secondary structure to investigate the size of energy barriers between degenerate minimum energy structures. This model has much in common with physical systems such as spin glasses, and in fact shows similar behaviour to these systems in that energy barriers between structures grow quickly with the length of the RNA sequence. These barriers will serve to trap RNA in non-optimal structures. Together these studies demonstrate the necessity of studying RNA secondary structure from a kinetic point of view, and provide clear directions in which further work may be taken. Kinetic models of RNA secondary structure should continue to prove useful in modelling the structure and function of RNA.

Efficiently explore the energy landscape of proteins in molecular dynamics simulations by amplifying collective motions

NASA Astrophysics Data System (ADS)

He, Jianbin; Zhang, Zhiyong; Shi, Yunyu; Liu, Haiyan

2003-08-01

We describe a method for efficient sampling of the energy landscape of a protein in atomic molecular dynamics simulations. A simulation is divided into alternatively occurring relaxation phases and excitation phases. In the relaxation phase (conventional simulation), we use a frequently updated reference structure and deviations from this reference structure to mark whether the system has been trapped in a local minimum. In that case, the simulation enters the excitation phase, during which a few slow collective modes of the system are coupled to a higher temperature bath. After the system has escaped from the minimum (also judged by deviations from the reference structure) the simulation reenters the relaxation phase. The collective modes are obtained from a coarse-grained Gaussian elastic network model. The scheme, which we call ACM-AME (amplified collective motion-assisted minimum escaping), is compared with conventional simulations as well as an alternative scheme that elevates the temperature of all degrees of freedom during the excitation phase (amplified overall motion-assisted minimum escaping, or AOM-AME). Comparison is made using simulations on four peptides starting from non-native extended or all helical structures. In terms of sampling low energy conformations and continuously sampling new conformations throughout a simulation, the ACM-AME scheme demonstrates very good performance while the AOM-AME scheme shows little improvement upon conventional simulations. Limited success is achieved in producing structures close to the native structures of the peptides: for an S-peptide analog, the ACM-AME approach is able to reproduce its native helical structure, and starting from an all-helical structure of the villin headpiece subdomain (HP-36) in implicit solvent, two out of three 150 ns ACM-AME runs are able to sample structures with 3-4 Å backbone root-mean-square deviations from the nuclear magnetic resonance structure of the protein.

The fcc - bcc structural transition: I. A band theoretical study for Li, K, Rb, Ca, Sr, and the transition metals Ti and V

NASA Astrophysics Data System (ADS)

Sliwko, V. L.; Mohn, P.; Schwarz, K.; Blaha, P.

1996-02-01

Employing a high-precision band structure method (FP LAPW - full potential linearized augmented plane wave) we calculate the total energy variation along the tetragonal distortion path connecting the body centred cubic (bcc) and the face centred cubic (fcc) structures. The total energy along this Bain transformation is calculated, varying c/a and volume, providing a first-principles energy surface which has two minima as a function of c/a. These are shallow and occur for the sp metals at the two cubic structures, while Ti (V) has a minimum at fcc (bcc) but a saddle point (i.e. a minimum in volume and a maximum with respect to c/a) at the other cubic structure. These features can be analysed in terms of an interplay between the Madelung contribution and the band energies. Our total energy results allow us to calculate the elastic constants 0953-8984/8/7/006/img1 and 0953-8984/8/7/006/img2 and to study the influence of pressure on the phase stability. These energy surfaces will be used in part II of this paper to investigate finite-temperature effects by mapping them to a Landau - Ginzburg expansion.

Automatic procedure for stable tetragonal or hexagonal structures: application to tetragonal Y and Cd

NASA Astrophysics Data System (ADS)

Marcus, P. M.; Jona, F.

2005-05-01

A simple effective procedure (MNP) for finding equilibrium tetragonal and hexagonal states under pressure is described and applied. The MNP procedure finds a path to minima of the Gibbs free energy G at T=0 K (G=E+pV, E=energy per atom, p=pressure, V=volume per atom) for tetragonal and hexagonal structures by using the approximate expansion of G in linear and quadratic strains at an arbitrary initial structure to find a change in the strains which moves toward a minimum of G. Iteration automatically proceeds to a minimum within preset convergence criteria on the calculation of the minimum. Comparison is made with experimental results for the ground states of seven metallic elements in hexagonal close-packed (hcp), face- and body-centered cubic structures, and with a previous procedure for finding minima based on tracing G along the epitaxial Bain path (EBP) to a minimum; the MNP is more easily generalized than the EBP procedure to lower symmetry and more atoms in the unit cell. Comparison is also made with a molecular-dynamics program for crystal equilibrium structures under pressure and with CRYSTAL, a program for crystal equilibrium structures at zero pressure. Application of MNP to the elements Y and Cd, which have hcp ground states at zero pressure, finds minima of E at face-centered cubic (fcc) structure for both Y and Cd. Evaluation of all the elastic constants shows that fcc Y is stable, hence a metastable phase, but fcc Cd is unstable.

Nearly metastable rhombohedral phases of bcc metals

NASA Astrophysics Data System (ADS)

Mehl, Michael J.; Finkenstadt, Daniel

2008-02-01

The energy E(c/a) for a bcc element stretched along its [001] axis (the Bain path) has a minimum at c/a=1 , a maximum at c/a=2 , and an elastically unstable local minimum at c/a>2 . An alternative path connecting the bcc and fcc structures is the rhombohedral lattice. The primitive lattice has R3¯m symmetry, with the angle α changing from 109.4° (bcc), to 90° (simple cubic), to 60 ° (fcc). We study this path for the non-magnetic bcc transition metals (V, Nb, Mo, Ta, and W) using both all-electron linearized augmented plane wave and projector augmented wave VASP codes. Except for Ta, the energy E(α) has a local maximum at α=60° , with local minima near 55° and 70° , the latter having lower energy, suggesting the possibility of a metastable rhombohedral state for these materials. We first examine the elastic stability of the 70° minimum structure, and determine that only W is elastically stable in this structure, with the smallest eigenvalue of the elastic tensor at 4GPa . We then consider the possibility that tungsten is actually metastable in this structure by looking at its vibrational and third-order elastic stability.

Equilibrium structure and atomic vibrations of Nin clusters

NASA Astrophysics Data System (ADS)

Borisova, Svetlana D.; Rusina, Galina G.

2017-12-01

The equilibrium bond lengths and binding energy, second differences in energy and vibrational frequencies of free clusters Nin (2 ≤ n ≤ 20) were calculated with the use of the interaction potential obtained in the tight-binding approximation (TBA). The results show that the minimum vibration frequency plays a significant role in the evaluation of the dynamic stability of the clusters. A nonmonotonic dependence of the minimum vibration frequency of clusters on their size and the extreme values for the number of atoms in a cluster n = 4, 6, 13, and 19 are demonstrated. This result agrees with the theoretical and experimental data on stable structures of small metallic clusters.

The origin of unequal bond lengths in the C 1B 2 state of SO 2: Signatures of high-lying potential energy surface crossings in the low-lying vibrational structure

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

Park, G. Barratt; Jiang, Jun; Field, Robert W.

Here the C 1B 2 state of SO 2 has a double-minimum potential in the antisymmetric stretch coordinate, such that the minimum energy geometry has nonequivalent SO bond lengths. The asymmetry in the potential energy surface is expressed as a staggering in the energy levels of the v' 3 progression. We have recently made the first observation of low-lying levels with odd quanta of v' 3, which allows us--in the current work--to characterize the origins of the level staggering. Our work demonstrates the usefulness of low-lying vibrational level structure, where the character of the wavefunctions can be relatively easily understood,more » to extract information about dynamically important potential energy surface crossings that occur at much higher energy. The measured staggering pattern is consistent with a vibronic coupling model for the double-minimum, which involves direct coupling to the bound 2 1A 1 state and indirect coupling with the repulsive 3 1A 1 state. The degree of staggering in the v' 3 levels increases with quanta of bending excitation, which is consistent with the approach along the C state potential energy surface to a conical intersection with the 2 1A 1 surface at a bond angle of ~145°.« less

The origin of unequal bond lengths in the C 1B 2 state of SO 2: Signatures of high-lying potential energy surface crossings in the low-lying vibrational structure

DOE PAGES

Park, G. Barratt; Jiang, Jun; Field, Robert W.

2016-04-14

Here the C 1B 2 state of SO 2 has a double-minimum potential in the antisymmetric stretch coordinate, such that the minimum energy geometry has nonequivalent SO bond lengths. The asymmetry in the potential energy surface is expressed as a staggering in the energy levels of the v' 3 progression. We have recently made the first observation of low-lying levels with odd quanta of v' 3, which allows us--in the current work--to characterize the origins of the level staggering. Our work demonstrates the usefulness of low-lying vibrational level structure, where the character of the wavefunctions can be relatively easily understood,more » to extract information about dynamically important potential energy surface crossings that occur at much higher energy. The measured staggering pattern is consistent with a vibronic coupling model for the double-minimum, which involves direct coupling to the bound 2 1A 1 state and indirect coupling with the repulsive 3 1A 1 state. The degree of staggering in the v' 3 levels increases with quanta of bending excitation, which is consistent with the approach along the C state potential energy surface to a conical intersection with the 2 1A 1 surface at a bond angle of ~145°.« less

Stacking fault effects in Mg-doped GaN

NASA Astrophysics Data System (ADS)

Schmidt, T. M.; Miwa, R. H.; Orellana, W.; Chacham, H.

2002-01-01

First-principles total energy calculations are performed to investigate the interaction of a stacking fault with a p-type impurity in both zinc-blende and wurtzite GaN. For both structures we find that, in the presence of a stacking fault, the impurity level is a more localized state in the band gap. In zinc-blende GaN, the minimum energy position of the substitutional Mg atom is at the plane of the stacking fault. In contrast, in wurtzite GaN the substitutional Mg atom at the plane of the stacking fault is a local minimum and the global minimum is the substitutional Mg far from the fault. This behavior can be understood as a packing effect which induces a distinct strain relief process, since the local structure of the stacking fault in zinc-blende GaN is similar to fault-free wurtzite GaN and vice-versa.

The transition from the open minimum to the ring minimum on the ground state and on the lowest excited state of like symmetry in ozone: A configuration interaction study

DOE PAGES

Theis, Daniel; Ivanic, Joseph; Windus, Theresa L.; ...

2016-03-10

The metastable ring structure of the ozone 1 1A 1 ground state, which theoretical calculations have shown to exist, has so far eluded experimental detection. An accurate prediction for the energy difference between this isomer and the lower open structure is therefore of interest, as is a prediction for the isomerization barrier between them, which results from interactions between the lowest two 1A 1 states. In the present work, valence correlated energies of the 1 1A 1 state and the 2 1A 1 state were calculated at the 1 1A 1 open minimum, the 1 1A 1 ring minimum, themore » transition state between these two minima, the minimum of the 2 1A 1 state, and the conical intersection between the two states. The geometries were determined at the full-valence multi-configuration self-consistent-field level. Configuration interaction (CI) expansions up to quadruple excitations were calculated with triple-zeta atomic basis sets. The CI expansions based on eight different reference configuration spaces were explored. To obtain some of the quadruple excitation energies, the method of CorrelationEnergy Extrapolation by Intrinsic Scaling was generalized to the simultaneous extrapolation for two states. This extrapolation method was shown to be very accurate. On the other hand, none of the CI expansions were found to have converged to millihartree (mh) accuracy at the quadruple excitation level. The data suggest that convergence to mh accuracy is probably attained at the sextuple excitation level. On the 11A1 state, the present calculations yield the estimates of (ring minimum—open minimum) ~45–50 mh and (transition state—open minimum) ~85–90 mh. For the (2 1A 1– 1A 1) excitation energy, the estimate of ~130–170 mh is found at the open minimum and 270–310 mh at the ring minimum. At the transition state, the difference (2 1A 1– 1A 1) is found to be between 1 and 10 mh. The geometry of the transition state on the 11A1 surface and that of the minimum on the 2 1A 1 surface nearly coincide. More accurate predictions of the energydifferences also require CI expansions to at least sextuple excitations with respect to the valence space. Furthermore, for every wave function considered, the omission of the correlations of the 2s oxygen orbitals, which is a widely used approximation, was found to cause errors of about ±10 mh with respect to the energy differences.« less

The transition from the open minimum to the ring minimum on the ground state and on the lowest excited state of like symmetry in ozone: A configuration interaction study

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

Theis, Daniel; Ivanic, Joseph; Windus, Theresa L.

The metastable ring structure of the ozone 1 1A 1 ground state, which theoretical calculations have shown to exist, has so far eluded experimental detection. An accurate prediction for the energy difference between this isomer and the lower open structure is therefore of interest, as is a prediction for the isomerization barrier between them, which results from interactions between the lowest two 1A 1 states. In the present work, valence correlated energies of the 1 1A 1 state and the 2 1A 1 state were calculated at the 1 1A 1 open minimum, the 1 1A 1 ring minimum, themore » transition state between these two minima, the minimum of the 2 1A 1 state, and the conical intersection between the two states. The geometries were determined at the full-valence multi-configuration self-consistent-field level. Configuration interaction (CI) expansions up to quadruple excitations were calculated with triple-zeta atomic basis sets. The CI expansions based on eight different reference configuration spaces were explored. To obtain some of the quadruple excitation energies, the method of CorrelationEnergy Extrapolation by Intrinsic Scaling was generalized to the simultaneous extrapolation for two states. This extrapolation method was shown to be very accurate. On the other hand, none of the CI expansions were found to have converged to millihartree (mh) accuracy at the quadruple excitation level. The data suggest that convergence to mh accuracy is probably attained at the sextuple excitation level. On the 11A1 state, the present calculations yield the estimates of (ring minimum—open minimum) ~45–50 mh and (transition state—open minimum) ~85–90 mh. For the (2 1A 1– 1A 1) excitation energy, the estimate of ~130–170 mh is found at the open minimum and 270–310 mh at the ring minimum. At the transition state, the difference (2 1A 1– 1A 1) is found to be between 1 and 10 mh. The geometry of the transition state on the 11A1 surface and that of the minimum on the 2 1A 1 surface nearly coincide. More accurate predictions of the energydifferences also require CI expansions to at least sextuple excitations with respect to the valence space. Furthermore, for every wave function considered, the omission of the correlations of the 2s oxygen orbitals, which is a widely used approximation, was found to cause errors of about ±10 mh with respect to the energy differences.« less

The transition from the open minimum to the ring minimum on the ground state and on the lowest excited state of like symmetry in ozone: A configuration interaction study

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

Theis, Daniel; Windus, Theresa L.; Ruedenberg, Klaus

The metastable ring structure of the ozone 1{sup 1}A{sub 1} ground state, which theoretical calculations have shown to exist, has so far eluded experimental detection. An accurate prediction for the energy difference between this isomer and the lower open structure is therefore of interest, as is a prediction for the isomerization barrier between them, which results from interactions between the lowest two {sup 1}A{sub 1} states. In the present work, valence correlated energies of the 1{sup 1}A{sub 1} state and the 2{sup 1}A{sub 1} state were calculated at the 1{sup 1}A{sub 1} open minimum, the 1{sup 1}A{sub 1} ring minimum,more » the transition state between these two minima, the minimum of the 2{sup 1}A{sub 1} state, and the conical intersection between the two states. The geometries were determined at the full-valence multi-configuration self-consistent-field level. Configuration interaction (CI) expansions up to quadruple excitations were calculated with triple-zeta atomic basis sets. The CI expansions based on eight different reference configuration spaces were explored. To obtain some of the quadruple excitation energies, the method of Correlation Energy Extrapolation by Intrinsic Scaling was generalized to the simultaneous extrapolation for two states. This extrapolation method was shown to be very accurate. On the other hand, none of the CI expansions were found to have converged to millihartree (mh) accuracy at the quadruple excitation level. The data suggest that convergence to mh accuracy is probably attained at the sextuple excitation level. On the 1{sup 1}A{sub 1} state, the present calculations yield the estimates of (ring minimum—open minimum) ∼45–50 mh and (transition state—open minimum) ∼85–90 mh. For the (2{sup 1}A{sub 1}–{sup 1}A{sub 1}) excitation energy, the estimate of ∼130–170 mh is found at the open minimum and 270–310 mh at the ring minimum. At the transition state, the difference (2{sup 1}A{sub 1}–{sup 1}A{sub 1}) is found to be between 1 and 10 mh. The geometry of the transition state on the 1{sup 1}A{sub 1} surface and that of the minimum on the 2{sup 1}A{sub 1} surface nearly coincide. More accurate predictions of the energy differences also require CI expansions to at least sextuple excitations with respect to the valence space. For every wave function considered, the omission of the correlations of the 2s oxygen orbitals, which is a widely used approximation, was found to cause errors of about ±10 mh with respect to the energy differences.« less

Ground and excited states of vanadium hydroxide isomers and their cations, VOH0,+ and HVO0,+

NASA Astrophysics Data System (ADS)

Miliordos, Evangelos; Harrison, James F.; Hunt, Katharine L. C.

2013-03-01

Employing correlation consistent basis sets of quadruple-zeta quality and applying both multireference configuration interaction and single-reference coupled cluster methodologies, we studied the electronic and geometrical structure of the [V,O,H]0,+ species. The electronic structure of HVO0,+ is explained by considering a hydrogen atom approaching VO0,+, while VOH0,+ molecules are viewed in terms of the interaction of V+,2+ with OH-. The potential energy curves for H-VO0,+ and V0,+-OH have been constructed as functions of the distance between the interacting subunits, and the potential energy curves have also been determined as functions of the H-V-O angle. For the stationary points that we have located, we report energies, geometries, harmonic frequencies, and dipole moments. We find that the most stable bent HVO0,+ structure is lower in energy than any of the linear HVO0,+ structures. Similarly, the most stable state of bent VOH is lower in energy than the linear structures, but linear VOH+ is lower in energy than bent VOH+. The global minimum on the potential energy surface for the neutral species is the tilde{X}^3A″ state of bent HVO, although the tilde{X}^5A″ state of bent VOH is less than 5 kcal/mol higher in energy. The global minimum on the potential surface for the cation is the tilde{X}^4Σ ^- state of linear VOH+, with bent VOH+ and bent HVO+ both more than 10 kcal/mol higher in energy. For the neutral species, the bent geometries exhibit significantly higher dipole moments than the linear structures.

The Multiple-Minima Problem in Protein Folding

NASA Astrophysics Data System (ADS)

Scheraga, Harold A.

1991-10-01

The conformational energy surface of a polypeptide or protein has many local minima, and conventional energy minimization procedures reach only a local minimum (near the starting point of the optimization algorithm) instead of the global minimum (the multiple-minima problem). Several procedures have been developed to surmount this problem, the most promising of which are: (a) build up procedure, (b) optimization of electrostatics, (c) Monte Carlo-plus-energy minimization, (d) electrostatically-driven Monte Carlo, (e) inclusion of distance restraints, (f) adaptive importance-sampling Monte Carlo, (g) relaxation of dimensionality, (h) pattern-recognition, and (i) diffusion equation method. These procedures have been applied to a variety of polypeptide structural problems, and the results of such computations are presented. These include the computation of the structures of open-chain and cyclic peptides, fibrous proteins and globular proteins. Present efforts are being devoted to scaling up these procedures from small polypeptides to proteins, to try to compute the three-dimensional structure of a protein from its amino sequence.

Methanol clusters (CH3OH)n: putative global minimum-energy structures from model potentials and dispersion-corrected density functional theory.

PubMed

Kazachenko, Sergey; Bulusu, Satya; Thakkar, Ajit J

2013-06-14

Putative global minima are reported for methanol clusters (CH3OH)n with n ≤ 15. The predictions are based on global optimization of three intermolecular potential energy models followed by local optimization and single-point energy calculations using two variants of dispersion-corrected density functional theory. Recurring structural motifs include folded and/or twisted rings, folded rings with a short branch, and stacked rings. Many of the larger structures are stabilized by weak C-H···O bonds.

N(2)O in small para-hydrogen clusters: Structures and energetics.

PubMed

Zhu, Hua; Xie, Daiqian

2009-04-30

We present the minimum-energy structures and energetics of clusters of the linear N(2)O molecule with small numbers of para-hydrogen molecules with pairwise additive potentials. Interaction energies of (p-H(2))-N(2)O and (p-H(2))-(p-H(2)) complexes were calculated by averaging the corresponding full-dimensional potentials over the H(2) angular coordinates. The averaged (p-H(2))-N(2)O potential has three minima corresponding to the T-shaped and the linear (p-H(2))-ONN and (p-H(2))-NNO structures. Optimization of the minimum-energy structures was performed using a Genetic Algorithm. It was found that p-H(2) molecules fill three solvation rings around the N(2)O axis, each of them containing up to five p-H(2) molecules, followed by accumulation of two p-H(2) molecules at the oxygen and nitrogen ends. The first solvation shell is completed at N = 17. The calculated chemical potential oscillates with cluster size up to the completed first solvation shell. These results are consistent with the available experimental measurements. (c) 2009 Wiley Periodicals, Inc.

Transformation Paths from Cubic to Low-Symmetry Structures in Heusler Ni2MnGa Compound.

PubMed

Zelený, Martin; Straka, Ladislav; Sozinov, Alexei; Heczko, Oleg

2018-05-08

In order to explain the formation of low-temperature phases in stoichiometric Ni 2 MnGa magnetic shape memory alloy, we investigate the phase transformation paths from cubic austenite with Heusler structure to low-symmetry martensitic structures. We used ab initio calculations combined with the generalized solid state nudged elastic band method to determine the minimum energy path and corresponding changes in crystal lattice. The four-, five-, and seven-layered modulated phases of martensite (4O, 10M, and 14M) are built as the relaxed nanotwinned non-modulated (NM) phase. Despite having a total energy larger than the other martensitic phases, the 10M phase will spontaneously form at 0 K, because there is no energy barrier on the path and the energy decreases with a large negative slope. Moreover, a similar negative slope in the beginning of path is found also for the transformation to the 6M premartensite, which appears as a local minimum on the path leading further to 10M martensite. Transformation paths to other structures exhibit more or less significant barriers in the beginning hindering such a transformation from austenite. These findings correspond to experiment and demonstrates that the kinetics of the transformation is decisive for the selection of the particular low-symmetry structure.

Surface-enhanced Raman spectroscopy of hexabenzobenzene, C24H12, an analogue of a graphene nanostructure

NASA Astrophysics Data System (ADS)

Owens, Frank J.

2018-05-01

While large scale fabrication of graphene nanoribbons remains a challenge, there exist materials which can be fabricated in quantities such as hexabenzobenzene,HBZB, (C24H12) and which have a two-dimensional (2D) carbon structure similar to graphene nanostructures. Using a 632 nm laser, no Raman spectra could be obtained from the solid material because of a strong luminescence produced by the laser. However, surface-enhanced Raman spectroscopy enabled the measurement of some of the Raman active modes. The G and D modes, which are characteristic fingerprints of a 2D graphene structure, were observed at 1331 and 1600 cm-1, respectively. Density functional theory at the B3LYP/6-31G* level was used to calculate the minimum energy structure and the Raman active vibrational frequencies of HBZB. The calculated minimum energy structure was 2D having D6h symmetry in agreement with the experimental structure in the liquid phase. The calculated frequencies were in good agreement with the measured values.

Dehydrogenation of benzene on Pt(111) surface

NASA Astrophysics Data System (ADS)

Gao, W.; Zheng, W. T.; Jiang, Q.

2008-10-01

The dehydrogenation of benzene on Pt(111) surface is studied by ab initio density functional theory. The minimum energy pathways for benzene dehydrogenation are found with the nudge elastic band method including several factors of the associated barriers, reactive energies, intermediates, and transient states. The results show that there are two possible parallel minimum energy pathways on the Pt(111) surface. Moreover, the tilting angle of the H atom in benzene can be taken as an index for the actual barrier of dehydrogenation. In addition, the properties of dehydrogenation radicals on the Pt(111) surface are explored through their adsorption energy, adsorption geometry, and electronic structure on the surface. The vibrational frequencies of the dehydrogenation radicals derived from the calculations are in agreement with literature data.

Dehydrogenation of benzene on Pt(111) surface.

PubMed

Gao, W; Zheng, W T; Jiang, Q

2008-10-28

The dehydrogenation of benzene on Pt(111) surface is studied by ab initio density functional theory. The minimum energy pathways for benzene dehydrogenation are found with the nudge elastic band method including several factors of the associated barriers, reactive energies, intermediates, and transient states. The results show that there are two possible parallel minimum energy pathways on the Pt(111) surface. Moreover, the tilting angle of the H atom in benzene can be taken as an index for the actual barrier of dehydrogenation. In addition, the properties of dehydrogenation radicals on the Pt(111) surface are explored through their adsorption energy, adsorption geometry, and electronic structure on the surface. The vibrational frequencies of the dehydrogenation radicals derived from the calculations are in agreement with literature data.

Low energy dislocation structures in epitaxy

NASA Technical Reports Server (NTRS)

Van Der Merwe, Jan H.; Woltersdorf, J.; Jesser, W. A.

1986-01-01

The principle of minimum energy was applied to epitaxial interfaces to show the interrelationship beteen misfit, overgrowth thickness and misfit dislocation spacing. The low energy dislocation configurations were presented for selected interfacial geometries. A review of the interfacial energy calculations was made and a critical assessment of the agreement between theory and experiment was presented. Modes of misfit accommodation were presented with emphasis on the distinction between kinetic effects and equilibrium conditions. Two-dimensional and three-dimensional overgrowths were treated together with interdiffusion-modified interfaces, and several models of interfacial structure were treated including the classical and the current models. The paper is concluded by indicating areas of needed investigation into interfacial structure.

Spherical harmonics based descriptor for neural network potentials: Structure and dynamics of Au147 nanocluster.

PubMed

Jindal, Shweta; Chiriki, Siva; Bulusu, Satya S

2017-05-28

We propose a highly efficient method for fitting the potential energy surface of a nanocluster using a spherical harmonics based descriptor integrated with an artificial neural network. Our method achieves the accuracy of quantum mechanics and speed of empirical potentials. For large sized gold clusters (Au 147 ), the computational time for accurate calculation of energy and forces is about 1.7 s, which is faster by several orders of magnitude compared to density functional theory (DFT). This method is used to perform the global minimum optimizations and molecular dynamics simulations for Au 147 , and it is found that its global minimum is not an icosahedron. The isomer that can be regarded as the global minimum is found to be 4 eV lower in energy than the icosahedron and is confirmed from DFT. The geometry of the obtained global minimum contains 105 atoms on the surface and 42 atoms in the core. A brief study on the fluxionality in Au 147 is performed, and it is concluded that Au 147 has a dynamic surface, thus opening a new window for studying its reaction dynamics.

Spherical harmonics based descriptor for neural network potentials: Structure and dynamics of Au147 nanocluster

NASA Astrophysics Data System (ADS)

Jindal, Shweta; Chiriki, Siva; Bulusu, Satya S.

2017-05-01

We propose a highly efficient method for fitting the potential energy surface of a nanocluster using a spherical harmonics based descriptor integrated with an artificial neural network. Our method achieves the accuracy of quantum mechanics and speed of empirical potentials. For large sized gold clusters (Au147), the computational time for accurate calculation of energy and forces is about 1.7 s, which is faster by several orders of magnitude compared to density functional theory (DFT). This method is used to perform the global minimum optimizations and molecular dynamics simulations for Au147, and it is found that its global minimum is not an icosahedron. The isomer that can be regarded as the global minimum is found to be 4 eV lower in energy than the icosahedron and is confirmed from DFT. The geometry of the obtained global minimum contains 105 atoms on the surface and 42 atoms in the core. A brief study on the fluxionality in Au147 is performed, and it is concluded that Au147 has a dynamic surface, thus opening a new window for studying its reaction dynamics.

Kinetics of pattern formation in symmetric diblock copolymer melts

NASA Astrophysics Data System (ADS)

Ren, Yongzhi; Müller, Marcus

2018-05-01

In equilibrium, copolymers self-assemble into spatially modulated phases with long-range order. When the system is quenched far below the order-disorder transition temperature, however, such an idealized, defect-free structure is difficult to obtain in experiments and simulations, instead a fingerprint-like structure forms. The relaxation toward long-range order is very protracted because it involves numerous thermally activated processes, and the rugged free-energy landscape has been likened to that of glass-forming systems. Using large-scale particle-based simulations of high-aspect-ratio, quasi-two-dimensional systems with periodic boundary condition, we study the kinetics of structure formation in symmetric, lamella-forming diblock copolymers after a quench from the disordered state. We characterize the ordering process by the correlation length of the lamellar structure and its Euler characteristic and observe that the growth of the correlation length and the rate of change of the Euler characteristic significantly slow down in the range of incompatibilities, 15 ≤ χN ≤ 20, studied. The increase of the time scale of ordering is, however, gradual. The density fields of snapshots of the particle-based simulations are used as starting values for self-consistent field theory (SCFT) calculations. The latter converge to the local, metastable minimum of the free-energy basin. This combination of particle-based simulations and SCFT calculations allows us to relate an instantaneous configuration of the particle-based model to a corresponding metastable free-energy minimum of SCFT—the inherent morphology—and we typically observe that a change of a free-energy basin is associated with a change of the Euler characteristic of the particle-based morphology, i.e., changes of free-energy basins are correlated to changes of the domain topology. Subsequently, we employ the string method in conjunction with SCFT to study the minimum free-energy paths (MFEPs) of changes of the domain topology. Since the time scales of relaxing toward the inherent morphology within a free-energy basin and jumps between free-energy basins are not well separated, the MFEP may overestimate the barriers encountered in the course of ordering.

Lowest-energy structures of (C60)nX (X=Li+,Na+,K+,Cl-) and (C60)nYCl (Y=Li,Na,K) clusters for n

PubMed

Hernández-Rojas, J; Bretón, J; Gomez Llorente, J M; Wales, D J

2004-12-22

Basin-hopping global optimization is used to find likely candidates for the lowest minima on the potential energy surface of (C(60))(n)X (X=Li(+),Na(+),K(+),Cl(-)) and (C(60))(n)YCl (Y=Li,Na,K) clusters with n

Tuning exciton energy and fine-structure splitting in single InAs quantum dots by applying uniaxial stress

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

Su, Dan; Dou, Xiuming; Wu, Xuefei

2016-04-15

Exciton and biexciton emission energies as well as excitonic fine-structure splitting (FSS) in single InAs/GaAs quantum dots (QDs) have been continuously tuned in situ in an optical cryostat using a developed uniaxial stress device. With increasing tensile stress, the red shift of excitonic emission is up to 5 nm; FSS decreases firstly and then increases monotonically, reaching a minimum value of approximately 10 μeV; biexciton binding energy decreases from 460 to 106 μeV. This technique provides a simple and convenient means to tune QD structural symmetry, exciton energy and biexciton binding energy and can be used for generating entangled andmore » indistinguishable photons.« less

NASA advanced design program: Analysis, design, and construction of a solar powered aircraft. B.S. Thesis

NASA Technical Reports Server (NTRS)

Chan, Agnes; Conley, Kristin; Javorski, Christian T.; Cheung, Kwok-Hung; Crivelli, Paul M.; Torrey, Nancy P.; Traver, Michael L.

1992-01-01

Increase in energy demands coupled with rapid depletion of natural energy resources have deemed solar energy as the most logical alternative source of power. The major objective of this project was to build a solar powered remotely controlled aircraft to demonstrate the feasibility of solar energy as an effective, alternate source of power. The final design was optimized for minimum weight and maximum strength of the structure. These design constraints necessitated a carbon fiber composite structure. Surya is a lightweight, durable aircraft capable of achieving level flight powered entirely by solar cells.

Competition between quasi-planar and cage-like structures in the B29- cluster: photoelectron spectroscopy and ab initio calculations.

PubMed

Li, Hai-Ru; Jian, Tian; Li, Wei-Li; Miao, Chang-Qing; Wang, Ying-Jin; Chen, Qiang; Luo, Xue-Mei; Wang, Kang; Zhai, Hua-Jin; Li, Si-Dian; Wang, Lai-Sheng

2016-10-26

Size-selected boron clusters have been found to be predominantly planar or quasi-planar (2D) in the small size regime with the appearance of three-dimensional (3D) borospherene cages of larger sizes. A seashell-like B 28 - cluster was previously shown to be the smallest borospherene, which competes with a quasi-planar isomer for the global minimum. Here we report a study on the structures and bonding of the B 29 - and B 29 clusters using photoelectron spectroscopy (PES) and first-principles calculations and demonstrate the continued competition between the 2D and borospherene structures. The PES spectrum of B 29 - displays a complex pattern with evidence of low-lying isomers. Global-minimum searches and extensive theoretical calculations revealed a complicated potential energy surface for B 29 - with five low-lying isomers, among which the lowest three were shown to contribute to the experimental spectrum. A 3D seashell-like C s (2, 1 A') isomer, featuring two heptagons on the waist and one octagon at the bottom, is the global minimum for B 29 - , followed by a 2D C 1 (3, 1 A) isomer with a hexagonal hole and a stingray-shaped 2D C s (1, 1 A') isomer with a pentagonal hole. However, by taking into account the entropic effects, the stingray-shaped isomer 1 was shown to be the lowest in energy at room temperature and was found to dominate the PES spectrum. Isomers 2 and 3, which have lower electron binding energies, were also found to be present in the experiment. Chemical bonding analyses showed that isomer 1 is an all-boron analogue of benzo[ghi]fluoranthene (C 18 H 10 ), whereas the borospherene isomer 2 possesses 18π electrons, conforming to the 2(N + 1) 2 electron counting rule for spherical aromaticity. For the B 29 neutral cluster, the seashell-like borospherene isomer is the global minimum, significantly lower in energy than the stingray-shaped quasi-planar structure.

SASS: A symmetry adapted stochastic search algorithm exploiting site symmetry

NASA Astrophysics Data System (ADS)

Wheeler, Steven E.; Schleyer, Paul v. R.; Schaefer, Henry F.

2007-03-01

A simple symmetry adapted search algorithm (SASS) exploiting point group symmetry increases the efficiency of systematic explorations of complex quantum mechanical potential energy surfaces. In contrast to previously described stochastic approaches, which do not employ symmetry, candidate structures are generated within simple point groups, such as C2, Cs, and C2v. This facilitates efficient sampling of the 3N-6 Pople's dimensional configuration space and increases the speed and effectiveness of quantum chemical geometry optimizations. Pople's concept of framework groups [J. Am. Chem. Soc. 102, 4615 (1980)] is used to partition the configuration space into structures spanning all possible distributions of sets of symmetry equivalent atoms. This provides an efficient means of computing all structures of a given symmetry with minimum redundancy. This approach also is advantageous for generating initial structures for global optimizations via genetic algorithm and other stochastic global search techniques. Application of the SASS method is illustrated by locating 14 low-lying stationary points on the cc-pwCVDZ ROCCSD(T) potential energy surface of Li5H2. The global minimum structure is identified, along with many unique, nonintuitive, energetically favorable isomers.

Electronic structure and molecular dynamics of Na2Li

NASA Astrophysics Data System (ADS)

Malcolm, Nathaniel O. J.; McDouall, Joseph J. W.

Following the first report (Mile, B., Sillman, P. D., Yacob, A. R. and Howard, J. A., 1996, J. chem. Soc. Dalton Trans , 653) of the EPR spectrum of the mixed alkali-metal trimer Na2Li a detailed study has been made of the electronic structure and structural dynamics of this species. Two isomeric forms have been found: one of the type, Na-Li-Na, of C , symmetry and another, Li-Na-Na, of C symmetry. Also, there are two linear saddle points which correspond to 'inversion' transition structures, and a saddle point of C symmetry which connects the two minima. A molecular dynamics investigation of these species shows that, at the temperature of the reported experiments (170 K), the C minimum is not 'static', but undergoes quite rapid inversion. At higher temperatures the C minimum converts to the C form, but by a mechanism very different from that suggested by minimum energy path considerations. 2 2v s s 2v 2v s

Preferential flow, connectivity and the principle of "minimum time to equilibrium": a new perspective on environmental water flow

NASA Astrophysics Data System (ADS)

Zehe, E.; Blume, T.; Bloeschl, G.

2008-12-01

Preferential/rapid flow and transport is known as one key process in soil hydrology for more than 20 years. It seems to be rather the rule, than the exception. It occurs in soils, in surface rills and river networks. If connective preferential are present at any scale, they crucially control water flow and solute transport. Why? Is there an underlying principle? If energy is conserved a system follows Fermat's principle of minimum action i.e. it follows the trajectory that minimise the integral of the total energy/ La Grangian over time. Hydrological systems are, however, non-conservative as surface and subsurface water flows dissipate energy. From thermodynamics it is well known that natural processes minimize the free energy of the system. For hydrological systems we suggest, therefore, that flow in a catchment arranges in such a way that time to a minimum of free energy becomes minimal for a given rainfall input (disturbance) and under given constraints. Free energy in a soil is determined by potential energy and capillary energy. The pore size distribution of the soil, soil structures, depth to groundwater and most important vegetation make up the constraints. The pore size distribution determines whether potential energy or capillarity dominates the free energy of the soil system. The first term is minimal when the pore space is completely de-saturated the latter becomes minimal at soil saturation. Hence, the soil determines a) the amount of excess (gravity) water that has to be exported from the soil to reach a minimum state of free energy and b) whether redistribution or groundwater recharge is more efficient to reach that equilibrium. On the other hand, the pore size distribution of the soil and the connectivity of preferential pathways (root channels, worm holes and cracks) determine flow velocities and the redistribution of water within the pore space. As water flow and ground water recharge are fast in sandy soils and capillary energy is of minor importance, connective preferential pathways do not mean any advantage for an efficient transition to an equilibrium in these systems. In fine grained soils Darcy velocities and therefore redistribution of water is 2-4 orders of magnitude slower. As capillary energy dominates in these soils an effective redistribution of water within the pore space is crucial for a fast transition of system to an equilibrium state. Connective preferential pathways ore even cracks allow a faster redistribution of water and seem therefore necessary for a fast transition into a state of minimum free energy. The suggested principle "of minimum time to equilibrium" may explain the "advantage" of preferential flow as a much more efficient dissipation of energy in fine grained soils and therefore why connective preferential pathways control environmental flow. From a fundamental, long term perspective the principle may help us to understand whether and why soil structures and even cracks evolve in different landscapes and climates and b) to link soil hydrology and (landscape) ecology. Along the lines the proposed study will present model results to test the stated hypothesis.

Dark gap solitons in exciton-polariton condensates in a periodic potential.

PubMed

Cheng, Szu-Cheng; Chen, Ting-Wei

2018-03-01

We show that dark spatial gap solitons can occur inside the band gap of an exciton-polariton condensate (EPC) in a one-dimensional periodic potential. The energy dispersions of an EPC loaded into a periodic potential show a band-gap structure. Using the effective-mass model of the complex Gross-Pitaevskii equation with pump and dissipation in an EPC in a periodic potential, dark gap solitons are demonstrated near the minimum energy points of the band center and band edge of the first and second bands, respectively. The excitation energies of dark gap solitons are below these minimum points and fall into the band gap. The spatial width of a dark gap soliton becomes smaller as the pump power is increased.

Dark gap solitons in exciton-polariton condensates in a periodic potential

NASA Astrophysics Data System (ADS)

Cheng, Szu-Cheng; Chen, Ting-Wei

2018-03-01

We show that dark spatial gap solitons can occur inside the band gap of an exciton-polariton condensate (EPC) in a one-dimensional periodic potential. The energy dispersions of an EPC loaded into a periodic potential show a band-gap structure. Using the effective-mass model of the complex Gross-Pitaevskii equation with pump and dissipation in an EPC in a periodic potential, dark gap solitons are demonstrated near the minimum energy points of the band center and band edge of the first and second bands, respectively. The excitation energies of dark gap solitons are below these minimum points and fall into the band gap. The spatial width of a dark gap soliton becomes smaller as the pump power is increased.

Tidal evolution in close binary systems.

NASA Technical Reports Server (NTRS)

Kopal, Z.

1972-01-01

Mathematical outline of the theory of tidal evolution in close binary systems of secularly constant total momentum. Following a general outline of the problem the basic expressions for the energy and momenta of close binaries consisting of components of arbitrary internal structure are established, and the maximum and minimum values of the energy (kinetic and potential) which such systems can attain for a given amount of total momentum are investigated. These results are compared with the actual facts encountered in binaries with components whose internal structure (and, therefore, rotational momenta) are known from evidence furnished by the observed rates of apsidal advance. The results show that all such systems whether of detached or semidetached type - disclose that more than 99% of their total momenta are stored in the orbital momentum. The sum of the rotational momenta of the constituent components amounts to less than 1% of the total -a situation characteristic of a state close to the minimum energy for given total momentum.

Evolutionary-inspired probabilistic search for enhancing sampling of local minima in the protein energy surface

PubMed Central

2012-01-01

Background Despite computational challenges, elucidating conformations that a protein system assumes under physiologic conditions for the purpose of biological activity is a central problem in computational structural biology. While these conformations are associated with low energies in the energy surface that underlies the protein conformational space, few existing conformational search algorithms focus on explicitly sampling low-energy local minima in the protein energy surface. Methods This work proposes a novel probabilistic search framework, PLOW, that explicitly samples low-energy local minima in the protein energy surface. The framework combines algorithmic ingredients from evolutionary computation and computational structural biology to effectively explore the subspace of local minima. A greedy local search maps a conformation sampled in conformational space to a nearby local minimum. A perturbation move jumps out of a local minimum to obtain a new starting conformation for the greedy local search. The process repeats in an iterative fashion, resulting in a trajectory-based exploration of the subspace of local minima. Results and conclusions The analysis of PLOW's performance shows that, by navigating only the subspace of local minima, PLOW is able to sample conformations near a protein's native structure, either more effectively or as well as state-of-the-art methods that focus on reproducing the native structure for a protein system. Analysis of the actual subspace of local minima shows that PLOW samples this subspace more effectively that a naive sampling approach. Additional theoretical analysis reveals that the perturbation function employed by PLOW is key to its ability to sample a diverse set of low-energy conformations. This analysis also suggests directions for further research and novel applications for the proposed framework. PMID:22759582

Unusual structures of MgF5- superhalogen anion

NASA Astrophysics Data System (ADS)

Anusiewicz, Iwona; Skurski, Piotr

2007-05-01

The vertical electron detachment energies (VDE) of three MgF5- anions were calculated at the outer valence Green function level with the 6-311 + G(3df) basis sets. This species was found to form unusual geometrical structures each of which corresponds to an anionic state exhibiting superhalogen nature. The global minimum structure was described as a system in which two central magnesium atoms are linked via symmetrical triangle formed by three fluorine atoms. Extremely large electron binding energies of these anions (exceeding 8.5 eV in all cases) were predicted and discussed.

SGO: A fast engine for ab initio atomic structure global optimization by differential evolution

NASA Astrophysics Data System (ADS)

Chen, Zhanghui; Jia, Weile; Jiang, Xiangwei; Li, Shu-Shen; Wang, Lin-Wang

2017-10-01

As the high throughout calculations and material genome approaches become more and more popular in material science, the search for optimal ways to predict atomic global minimum structure is a high research priority. This paper presents a fast method for global search of atomic structures at ab initio level. The structures global optimization (SGO) engine consists of a high-efficiency differential evolution algorithm, accelerated local relaxation methods and a plane-wave density functional theory code running on GPU machines. The purpose is to show what can be achieved by combining the superior algorithms at the different levels of the searching scheme. SGO can search the global-minimum configurations of crystals, two-dimensional materials and quantum clusters without prior symmetry restriction in a relatively short time (half or several hours for systems with less than 25 atoms), thus making such a task a routine calculation. Comparisons with other existing methods such as minima hopping and genetic algorithm are provided. One motivation of our study is to investigate the properties of magnetic systems in different phases. The SGO engine is capable of surveying the local minima surrounding the global minimum, which provides the information for the overall energy landscape of a given system. Using this capability we have found several new configurations for testing systems, explored their energy landscape, and demonstrated that the magnetic moment of metal clusters fluctuates strongly in different local minima.

SU-E-T-489: Quantum versus Classical Trajectory Monte Carlo Simulations of Low Energy Electron Transport.

PubMed

Thomson, R; Kawrakow, I

2012-06-01

Widely-used classical trajectory Monte Carlo simulations of low energy electron transport neglect the quantum nature of electrons; however, at sub-1 keV energies quantum effects have the potential to become significant. This work compares quantum and classical simulations within a simplified model of electron transport in water. Electron transport is modeled in water droplets using quantum mechanical (QM) and classical trajectory Monte Carlo (MC) methods. Water droplets are modeled as collections of point scatterers representing water molecules from which electrons may be isotropically scattered. The role of inelastic scattering is investigated by introducing absorption. QM calculations involve numerically solving a system of coupled equations for the electron wavefield incident on each scatterer. A minimum distance between scatterers is introduced to approximate structured water. The average QM water droplet incoherent cross section is compared with the MC cross section; a relative error (RE) on the MC results is computed. RE varies with electron energy, average and minimum distances between scatterers, and scattering amplitude. The mean free path is generally the relevant length scale for estimating RE. The introduction of a minimum distance between scatterers increases RE substantially (factors of 5 to 10), suggesting that the structure of water must be modeled for accurate simulations. Inelastic scattering does not improve agreement between QM and MC simulations: for the same magnitude of elastic scattering, the introduction of inelastic scattering increases RE. Droplet cross sections are sensitive to droplet size and shape; considerable variations in RE are observed with changing droplet size and shape. At sub-1 keV energies, quantum effects may become non-negligible for electron transport in condensed media. Electron transport is strongly affected by the structure of the medium. Inelastic scatter does not improve agreement between QM and MC simulations of low energy electron transport in condensed media. © 2012 American Association of Physicists in Medicine.

A phase transition in energy-filtered RNA secondary structures.

PubMed

Han, Hillary S W; Reidys, Christian M

2012-10-01

In this article we study the effect of energy parameters on minimum free energy (mfe) RNA secondary structures. Employing a simplified combinatorial energy model that is only dependent on the diagram representation and is not sequence-specific, we prove the following dichotomy result. Mfe structures derived via the Turner energy parameters contain only finitely many complex irreducible substructures, and just minor parameter changes produce a class of mfe structures that contain a large number of small irreducibles. We localize the exact point at which the distribution of irreducibles experiences this phase transition from a discrete limit to a central limit distribution and, subsequently, put our result into the context of quantifying the effect of sparsification of the folding of these respective mfe structures. We show that the sparsification of realistic mfe structures leads to a constant time and space reduction, and that the sparsification of the folding of structures with modified parameters leads to a linear time and space reduction. We, furthermore, identify the limit distribution at the phase transition as a Rayleigh distribution.

Refractive effects and Airy structure in inelastic 16O+12C rainbow scattering

NASA Astrophysics Data System (ADS)

Ohkubo, S.; Hirabayashi, Y.; Ogloblin, A. A.; Gloukhov, Yu. A.; Dem'yanova, A. S.; Trzaska, W. H.

2014-12-01

Inelastic 16O+12C rainbow scattering to the 2+ (4.44 MeV) state of 12C was measured at the incident energies, EL = 170, 181, 200, 260, and 281 MeV. A systematic analysis of the experimental angular distributions was performed using the coupled-channels method with an extended double folding potential derived from realistic wave functions for 12C and 16O calculated with a microscopic α cluster model and a finite-range density-dependent nucleon-nucleon force. The coupled-channels analysis of the measured inelastic-scattering data shows consistently some Airy-like structure in the inelastic-scattering cross sections for the first 2+ state of 12C, which is somewhat obscured and still not clearly visible in the measured data. The Airy minimum was identified from the analysis and the systematic energy evolution of the Airy structure was studied. The Airy minimum in inelastic scattering is found to be shifted backward compared with that in elastic scattering.

Manufacturing Energy Intensity and Opportunity Analysis for Fiber-Reinforced Polymer Composites and Other Lightweight Materials

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

Liddell, Heather; Brueske, Sabine; Carpenter, Alberta

With their high strength-to-weight ratios, fiber-reinforced polymer (FRP) composites are important materials for lightweighting in structural applications; however, manufacturing challenges such as low process throughput and poor quality control can lead to high costs and variable performance, limiting their use in commercial applications. One of the most significant challenges for advanced composite materials is their high manufacturing energy intensity. This study explored the energy intensities of two lightweight FRP composite materials (glass- and carbon-fiber-reinforced polymers), with three lightweight metals (aluminum, magnesium, and titanium) and structural steel (as a reference material) included for comparison. Energy consumption for current typical and state-of-the-artmore » manufacturing processes were estimated for each material, deconstructing manufacturing process energy use by sub-process and manufacturing pathway in order to better understand the most energy intensive steps. Energy saving opportunities were identified and quantified for each production step based on a review of applied R&D technologies currently under development in order to estimate the practical minimum energy intensity. Results demonstrate that while carbon fiber reinforced polymer (CFRP) composites have the highest current manufacturing energy intensity of all materials considered, the large differences between current typical and state-of-the-art energy intensity levels (the 'current opportunity') and between state-of-the-art and practical minimum energy intensity levels (the 'R&D opportunity') suggest that large-scale energy savings are within reach.« less

Design and Analysis of Optimal Ascent Trajectories for Stratospheric Airships

NASA Astrophysics Data System (ADS)

Mueller, Joseph Bernard

Stratospheric airships are lighter-than-air vehicles that have the potential to provide a long-duration airborne presence at altitudes of 18-22 km. Designed to operate on solar power in the calm portion of the lower stratosphere and above all regulated air traffic and cloud cover, these vehicles represent an emerging platform that resides between conventional aircraft and satellites. A particular challenge for airship operation is the planning of ascent trajectories, as the slow moving vehicle must traverse the high wind region of the jet stream. Due to large changes in wind speed and direction across altitude and the susceptibility of airship motion to wind, the trajectory must be carefully planned, preferably optimized, in order to ensure that the desired station be reached within acceptable performance bounds of flight time and energy consumption. This thesis develops optimal ascent trajectories for stratospheric airships, examines the structure and sensitivity of these solutions, and presents a strategy for onboard guidance. Optimal ascent trajectories are developed that utilize wind energy to achieve minimum-time and minimum-energy flights. The airship is represented by a three-dimensional point mass model, and the equations of motion include aerodynamic lift and drag, vectored thrust, added mass effects, and accelerations due to mass flow rate, wind rates, and Earth rotation. A representative wind profile is developed based on historical meteorological data and measurements. Trajectory optimization is performed by first defining an optimal control problem with both terminal and path constraints, then using direct transcription to develop an approximate nonlinear parameter optimization problem of finite dimension. Optimal ascent trajectories are determined using SNOPT for a variety of upwind, downwind, and crosswind launch locations. Results of extensive optimization solutions illustrate definitive patterns in the ascent path for minimum time flights across varying launch locations, and show that significant energy savings can be realized with minimum-energy flights, compared to minimum-time time flights, given small increases in flight time. The performance of the optimal trajectories are then studied with respect to solar energy production during ascent, as well as sensitivity of the solutions to small changes in drag coefficient and wind model parameters. Results of solar power model simulations indicate that solar energy is sufficient to power ascent flights, but that significant energy loss can occur for certain types of trajectories. Sensitivity to the drag and wind model is approximated through numerical simulations, showing that optimal solutions change gradually with respect to changing wind and drag parameters and providing deeper insight into the characteristics of optimal airship flights. Finally, alternative methods are developed to generate near-optimal ascent trajectories in a manner suitable for onboard implementation. The structures and characteristics of previously developed minimum-time and minimum-energy ascent trajectories are used to construct simplified trajectory models, which are efficiently solved in a smaller numerical optimization problem. Comparison of these alternative solutions to the original SNOPT solutions show excellent agreement, suggesting the alternate formulations are an effective means to develop near-optimal solutions in an onboard setting.

Dynamics Sampling in Transition Pathway Space.

PubMed

Zhou, Hongyu; Tao, Peng

2018-01-09

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

DFT study of gases adsorption on sharp tip nano-catalysts surface for green fertilizer synthesis

NASA Astrophysics Data System (ADS)

Yahya, Noorhana; Irfan, Muhammad; Shafie, Afza; Soleimani, Hassan; Alqasem, Bilal; Rehman, Zia Ur; Qureshi, Saima

2016-11-01

The energy minimization and spin modifications of sorbates with sorbents in magnetic induction method (MIM) play a vital role in yield of fertilizer. Hence, in this article the focus of study is the interaction of sorbates/reactants (H2, N2 and CO2) in term of average total adsorption energies, average isosteric heats of adsorption energies, magnetic moments, band gaps energies and spin modifications over identical cone tips nanocatalyst (sorbents) of Fe2O3, Fe3O4 (magnetic), CuO and Al2O3 (non-magnetic) for green nano-fertilizer synthesis. Study of adsorption energy, band structures and density of states of reactants with sorbents are purely classical and quantum mechanical based concepts that are vividly illustrated and supported by ADSORPTION LOCATOR and Cambridge Seriel Total Energy Package (CASTEP) modules following classical and first principle DFT simulation study respectively. Maximum values of total average energies, total average adsorption energies and average adsorption energies of H2, N2 and CO2 molecules are reported as -14.688 kcal/mol, -13.444 kcal/mol, -3.130 kcal/mol, - kcal/mol and -6.348 kcal/mol over Al2O3 cone tips respectively and minimum over magnetic cone tips. Whereas, the maximum and average minimum values of average isosteric heats of adsorption energies of H2, N2 and CO2 molecules are figured out to be 3.081 kcal/mol, 4.842 kcal/mol and 6.848 kcal/mol, 0.988 kcal/mol, 1.554 kcal/mol and 2.236 kcal/mol over aluminum oxide and Fe3O4 cone tips respectively. In addition to the adsorption of reactants over identical cone sorbents the maximum and minimum values of net spin, electrons and number of bands for magnetite and aluminum oxide cone structures are attributed to 82 and zero, 260 and 196, 206 and 118 for Fe3O4 and Al2O3 cones respectively. Maximum and least observed values of band gap energies are figured out to be 0.188 eV and 0.018 eV with Al2O3 and Fe3O4 cone structures respectively. Ultimately, with the adsorption of reactants an identical increment of 14 electrons each in up and down spins is resulted.

Use of density functional theory method to calculate structures of neutral carbon clusters C{sub n} (3 ≤ n ≤ 24) and study their variability of structural forms

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

Yen, T. W.; Lai, S. K., E-mail: sklai@coll.phy.ncu.edu.tw

2015-02-28

In this work, we present modifications to the well-known basin hopping (BH) optimization algorithm [D. J. Wales and J. P. Doye, J. Phys. Chem. A 101, 5111 (1997)] by incorporating in it the unique and specific nature of interactions among valence electrons and ions in carbon atoms through calculating the cluster’s total energy by the density functional tight-binding (DFTB) theory, using it to find the lowest energy structures of carbon clusters and, from these optimized atomic and electronic structures, studying their varied forms of topological transitions, which include a linear chain, a monocyclic to a polycyclic ring, and a fullerene/cage-likemore » geometry. In this modified BH (MBH) algorithm, we define a spatial volume within which the cluster’s lowest energy structure is to be searched, and introduce in addition a cut-and-splice genetic operator to increase the searching performance of the energy minimum than the original BH technique. The present MBH/DFTB algorithm is, therefore, characteristically distinguishable from the original BH technique commonly applied to nonmetallic and metallic clusters, technically more thorough and natural in describing the intricate couplings between valence electrons and ions in a carbon cluster, and thus theoretically sound in putting these two charged components on an equal footing. The proposed modified minimization algorithm should be more appropriate, accurate, and precise in the description of a carbon cluster. We evaluate the present algorithm, its energy-minimum searching in particular, by its optimization robustness. Specifically, we first check the MBH/DFTB technique for two representative carbon clusters of larger size, i.e., C{sub 60} and C{sub 72} against the popular cut-and-splice approach [D. M. Deaven and K. M. Ho, Phys. Rev. Lett. 75, 288 (1995)] that normally is combined with the genetic algorithm method for finding the cluster’s energy minimum, before employing it to investigate carbon clusters in the size range C{sub 3}-C{sub 24} studying their topological transitions. An effort was also made to compare our MBH/DFTB and its re-optimized results carried out by full density functional theory (DFT) calculations with some early DFT-based studies.« less

A hybrid optimization algorithm to explore atomic configurations of TiO 2 nanoparticles

DOE PAGES

Inclan, Eric J.; Geohegan, David B.; Yoon, Mina

2017-10-17

Here in this paper we present a hybrid algorithm comprised of differential evolution, coupled with the Broyden–Fletcher–Goldfarb–Shanno quasi-Newton optimization algorithm, for the purpose of identifying a broad range of (meta)stable Ti nO 2n nanoparticles, as an example system, described by Buckingham interatomic potential. The potential and its gradient are modified to be piece-wise continuous to enable use of these continuous-domain, unconstrained algorithms, thereby improving compatibility. To measure computational effectiveness a regression on known structures is used. This approach defines effectiveness as the ability of an algorithm to produce a set of structures whose energy distribution follows the regression as themore » number of Ti nO 2n increases such that the shape of the distribution is consistent with the algorithm’s stated goals. Our calculation demonstrates that the hybrid algorithm finds global minimum configurations more effectively than the differential evolution algorithms, widely employed in the field of materials science. Specifically, the hybrid algorithm is shown to reproduce the global minimum energy structures reported in the literature up to n = 5, and retains good agreement with the regression up to n = 25. For 25 < n < 100, where literature structures are unavailable, the hybrid effectively obtains structures that are in lower energies per TiO 2 unit as the system size increases.« less

Investigating the Sensitivity of Model Intraseasonal Variability to Minimum Entrainment

NASA Astrophysics Data System (ADS)

Hannah, W. M.; Maloney, E. D.

2008-12-01

Previous studies have shown that using a Relaxed Arakawa-Schubert (RAS) convective parameterization with appropriate convective triggers and assumptions about rain re-evaporation produces realistic intraseasonal variability. RAS represents convection with an ensemble of clouds detraining at different heights, each with different entrainment rate, the highest clouds having the lowest entrainment rates. If tropospheric temperature gradients are weak and boundary layer moist static energy is relatively constant, then by limiting the minimum entrainment rate deep convection is suppressed in the presence of dry tropospheric air. This allows moist static energy to accumulate and be discharged during strong intraseasonal convective events, which is consistent with the discharge/recharge paradigm. This study will examine the sensitivity of intra-seasonal variability to changes in minimum entrainment rate in the NCAR-CAM3 with the RAS scheme. Simulations using several minimum entrainment rate thresholds will be investigated. A frequency-wavenumber analysis will show the improvement of the MJO signal as minimum entrainment rate is increased. The spatial and vertical structure of MJO-like disturbances will be examined, including an analysis of the time evolution of vertical humidity distribution for each simulation. Simulated results will be compared to observed MJO events in NCEP-1 reanalysis and CMAP precipitation.

Absence of metastable states in strained monoatomic cubic crystals.

NASA Astrophysics Data System (ADS)

Aguayo, Aarón; Mehl, Michael L.; de Coss, Romeo

2005-03-01

The Bain path distortion of a metal with an fcc (bcc) ground state toward the bcc (fcc) structure initially requires an increase in energy, but at some point along the Bain path the energy will again decrease until a local minimum is reached. We have studied the tetragonal distortion (Bain path) of monoatomic cubic crystals, using a combination of parametrized tight-binding and first-principles linearized augmented plane wave calculations. We show that this local minimum is unstable with respect to an elastic distortion, except in the rare case that the minimum is at the bcc (fcc) point on the Bain path. This shows that body-centered-tetragonal phases of these materials, which have been seen in epitaxially grown thin films, must be stabilized by the substrate and cannot be freestanding films. This work was partially supported by Consejo Nacional de Ciencia y Tecnolog'ia (CONACYT, M'exico) under Grant No. 43830-F.

Minimum free-energy paths for the self-organization of polymer brushes.

PubMed

Gleria, Ignacio; Mocskos, Esteban; Tagliazucchi, Mario

2017-03-22

A methodology to calculate minimum free-energy paths based on the combination of a molecular theory and the improved string method is introduced and applied to study the self-organization of polymer brushes under poor solvent conditions. Polymer brushes in a poor solvent cannot undergo macroscopic phase separation due to the physical constraint imposed by the grafting points; therefore, they microphase separate forming aggregates. Under some conditions, the theory predicts that the homogeneous brush and the aggregates can exist as two different minima of the free energy. The theoretical methodology introduced in this work allows us to predict the minimum free-energy path connecting these two minima as well as the morphology of the system along the path. It is shown that the transition between the homogeneous brush and the aggregates may involve a free-energy barrier or be barrierless depending on the relative stability of the two morphologies and the chain length and grafting density of the polymer. In the case where a free-energy barrier exists, one of the morphologies is a metastable structure and, therefore, the properties of the brush as the quality of the solvent is cycled are expected to display hysteresis. The theory is also applied to study the adhesion/deadhesion transition between two opposing surfaces modified by identical polymer brushes and it is shown that this process may also require surpassing a free-energy barrier.

Expedite random structure searching using objects from Wyckoff positions

NASA Astrophysics Data System (ADS)

Wang, Shu-Wei; Hsing, Cheng-Rong; Wei, Ching-Ming

2018-02-01

Random structure searching has been proved to be a powerful approach to search and find the global minimum and the metastable structures. A true random sampling is in principle needed yet it would be highly time-consuming and/or practically impossible to find the global minimum for the complicated systems in their high-dimensional configuration space. Thus the implementations of reasonable constraints, such as adopting system symmetries to reduce the independent dimension in structural space and/or imposing chemical information to reach and relax into low-energy regions, are the most essential issues in the approach. In this paper, we propose the concept of "object" which is either an atom or composed of a set of atoms (such as molecules or carbonates) carrying a symmetry defined by one of the Wyckoff positions of space group and through this process it allows the searching of global minimum for a complicated system to be confined in a greatly reduced structural space and becomes accessible in practice. We examined several representative materials, including Cd3As2 crystal, solid methanol, high-pressure carbonates (FeCO3), and Si(111)-7 × 7 reconstructed surface, to demonstrate the power and the advantages of using "object" concept in random structure searching.

Airy structure in 16O+14C nuclear rainbow scattering

NASA Astrophysics Data System (ADS)

Ohkubo, S.; Hirabayashi, Y.

2015-08-01

The Airy structure in 16 O +14 C rainbow scattering is studied with an extended double-folding (EDF) model that describes all the diagonal and off-diagonal coupling potentials derived from the microscopic realistic wave functions for 16 O by using a density-dependent nucleon-nucleon force. The experimental angular distributions at EL=132 , 281, and 382.2 MeV are well reproduced by the calculations. By studying the energy evolution of the Airy structure, the Airy minimum around θ =76∘ in the angular distribution at EL=132 MeV is assigned as the second-order Airy minimum A 2 in contrast to the recent literature which assigns it as the third order A 3 . The Airy minima in the 90∘ excitation function is investigated in comparison with well-known 16 O +16 O and 12 C +12 C systems. Evolution of the Airy structure into the molecular resonances with the 16 O +14 C cluster structure in the low-energy region around Ec .m .=30 MeV is discussed. It is predicted theoretically for the first time for a non-4 N 16O +14 C system that Airy elephants in the 90∘ excitation function are present.

Experimental and theoretical investigation of three-dimensional nitrogen-doped aluminum clusters AI 8N - and AI 8N

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

Wang, Leiming; Huang, Wei; Wang, Lai S.

The structure and electronic properties of the Al 8N - and Al 8N clusters were investigated by combined photoelectron spectroscopy and ab initio studies. Congested photoelectron spectra were observed and experimental evidence was obtained for the presence of multiple isomers for Al 8N - Global minimum searches revealed several structures for Al 8N - with close energies. The calculated vertical detachment energies of the two lowest-lying isomers, which are of C 2v and C s symmetry, respectively, were shown to agree well with the experimental data. Unlike the three-dimensional structures of Al 6N - and Al 7N -, in whichmore » the dopant N atom has a high coordination number of 6,the dopant N atom in the two low-lying isomers of Al 8N - has a lower coordination number of 4 and 5, respectively. The competition between the Al–Al and Al–N interactions are shown to determine the global minimum structures of the doped aluminum clusters and results in the structural diversity for both Al 8N - and Al8N. © 2009 American Institute of Physics« less

Protein homology model refinement by large-scale energy optimization.

PubMed

Park, Hahnbeom; Ovchinnikov, Sergey; Kim, David E; DiMaio, Frank; Baker, David

2018-03-20

Proteins fold to their lowest free-energy structures, and hence the most straightforward way to increase the accuracy of a partially incorrect protein structure model is to search for the lowest-energy nearby structure. This direct approach has met with little success for two reasons: first, energy function inaccuracies can lead to false energy minima, resulting in model degradation rather than improvement; and second, even with an accurate energy function, the search problem is formidable because the energy only drops considerably in the immediate vicinity of the global minimum, and there are a very large number of degrees of freedom. Here we describe a large-scale energy optimization-based refinement method that incorporates advances in both search and energy function accuracy that can substantially improve the accuracy of low-resolution homology models. The method refined low-resolution homology models into correct folds for 50 of 84 diverse protein families and generated improved models in recent blind structure prediction experiments. Analyses of the basis for these improvements reveal contributions from both the improvements in conformational sampling techniques and the energy function.

The conformational preferences of γ-lactam and its role in constraining peptide structure

NASA Astrophysics Data System (ADS)

Paul, P. K. C.; Burney, P. A.; Campbell, M. M.; Osguthorpe, D. J.

1990-09-01

The conformational constraints imposed by γ-lactams in peptides have been studied using valence force field energy calculations and flexible geometry maps. It has been found that while cyclisation restrains the Ψ of the lactam, non-bonded interactions contribute to the constraints on ϕ of the lactam. The γ-lactam also affects the (ϕ,Ψ) of the residue after it in a peptide sequence. For an l-lactam, the ring geometry restricts Ψ to about-120°, and ϕ has two minima, the lowest energy around-140° and a higher minimum (5 kcal/mol higher) at 60°, making an l-γ-lactam more favourably accommodated in a near extended conformation than in position 2 of a type II' β-turn. The energy of the ϕ˜+60° minimum can be lowered substantially until it is more favoured than the-140° minimum by progressive substitution of bulkier groups on the amide N of the l-γ-lactam. The (ϕ,Ψ) maps of the residue succeeding a γ-lactam show subtle differences from those of standard N-methylated residues. The dependence of the constraints on the chirality of γ-lactams and N-substituted γ-lactams, in terms of the formation of secondary structures like β-turns is discussed and the comparison of the theoretical conformations with experimental results is highlighted.

Turbulence, selective decay, and merging in the SSX plasma wind tunnel

NASA Astrophysics Data System (ADS)

Gray, Tim; Brown, Michael; Flanagan, Ken; Werth, Alexandra; Lukin, V.

2012-10-01

A helical, relaxed plasma state has been observed in a long cylindrical volume. The cylinder has dimensions L = 1 m and R = 0.08 m. The cylinder is long enough so that the predicted minimum energy state is a close approximation to the infinite cylinder solution. The plasma is injected at v >=50 km/s by a coaxial magnetized plasma gun located at one end of the cylindrical volume. Typical plasma parameters are Ti= 25 eV, ne>=10^15 cm-3, and B = 0.25 T. The relaxed state is rapidly attained in 1--2 axial Alfv'en times after initiation of the plasma. Magnetic data is favorably compared with an analytical model. Magnetic data exhibits broadband fluctuations of the measured axial modes during the formation period. The broadband activity rapidly decays as the energy condenses into the lowest energy mode, which is in agreement to the minimum energy eigenstate of ∇xB = λB. While the global structure roughly corresponds to the minimum energy eigenstate for the wind tunnel geometry, the plasma is high beta (β= 0.5) and does not have a flat λ profile. Merging of two plasmoids in this configuration results in noticeably more dynamic activity compared to a single plasmoid. These episodes of activity exhibit s

A genetic code Boolean structure. II. The genetic information system as a Boolean information system.

PubMed

Sanchez, Robersy; Grau, Ricardo

2005-09-01

A Boolean structure of the genetic code where Boolean deductions have biological and physicochemical meanings was discussed in a previous paper. Now, from these Boolean deductions we propose to define the value of amino acid information in order to consider the genetic information system as a communication system and to introduce the semantic content of information ignored by the conventional information theory. In this proposal, the value of amino acid information is proportional to the molecular weight of amino acids with a proportional constant of about 1.96 x 10(25) bits per kg. In addition to this, for the experimental estimations of the minimum energy dissipation in genetic logic operations, we present two postulates: (1) the energy Ei (i=1,2,...,20) of amino acids in the messages conveyed by proteins is proportional to the value of information, and (2) amino acids are distributed according to their energy Ei so the amino acid population in proteins follows a Boltzmann distribution. Specifically, in the genetic message carried by the DNA from the genomes of living organisms, we found that the minimum energy dissipation in genetic logic operations was close to kTLn(2) joules per bit.

10 CFR 440.16 - Minimum program requirements.

Code of Federal Regulations, 2014 CFR

2014-01-01

... 10 Energy 3 2014-01-01 2014-01-01 false Minimum program requirements. 440.16 Section 440.16 Energy DEPARTMENT OF ENERGY ENERGY CONSERVATION WEATHERIZATION ASSISTANCE FOR LOW-INCOME PERSONS § 440.16 Minimum...) Families with children; (4) High residential energy users; and (5) Households with a high energy burden. (c...

10 CFR 440.16 - Minimum program requirements.

Code of Federal Regulations, 2012 CFR

2012-01-01

... 10 Energy 3 2012-01-01 2012-01-01 false Minimum program requirements. 440.16 Section 440.16 Energy DEPARTMENT OF ENERGY ENERGY CONSERVATION WEATHERIZATION ASSISTANCE FOR LOW-INCOME PERSONS § 440.16 Minimum...) Families with children; (4) High residential energy users; and (5) Households with a high energy burden. (c...

10 CFR 440.16 - Minimum program requirements.

Code of Federal Regulations, 2013 CFR

2013-01-01

... 10 Energy 3 2013-01-01 2013-01-01 false Minimum program requirements. 440.16 Section 440.16 Energy DEPARTMENT OF ENERGY ENERGY CONSERVATION WEATHERIZATION ASSISTANCE FOR LOW-INCOME PERSONS § 440.16 Minimum...) Families with children; (4) High residential energy users; and (5) Households with a high energy burden. (c...

Exchange-Hole Dipole Dispersion Model for Accurate Energy Ranking in Molecular Crystal Structure Prediction II: Nonplanar Molecules.

PubMed

Whittleton, Sarah R; Otero-de-la-Roza, A; Johnson, Erin R

2017-11-14

The crystal structure prediction (CSP) of a given compound from its molecular diagram is a fundamental challenge in computational chemistry with implications in relevant technological fields. A key component of CSP is the method to calculate the lattice energy of a crystal, which allows the ranking of candidate structures. This work is the second part of our investigation to assess the potential of the exchange-hole dipole moment (XDM) dispersion model for crystal structure prediction. In this article, we study the relatively large, nonplanar, mostly flexible molecules in the first five blind tests held by the Cambridge Crystallographic Data Centre. Four of the seven experimental structures are predicted as the energy minimum, and thermal effects are demonstrated to have a large impact on the ranking of at least another compound. As in the first part of this series, delocalization error affects the results for a single crystal (compound X), in this case by detrimentally overstabilizing the π-conjugated conformation of the monomer. Overall, B86bPBE-XDM correctly predicts 16 of the 21 compounds in the five blind tests, a result similar to the one obtained using the best CSP method available to date (dispersion-corrected PW91 by Neumann et al.). Perhaps more importantly, the systems for which B86bPBE-XDM fails to predict the experimental structure as the energy minimum are mostly the same as with Neumann's method, which suggests that similar difficulties (absence of vibrational free energy corrections, delocalization error,...) are not limited to B86bPBE-XDM but affect GGA-based DFT-methods in general. Our work confirms B86bPBE-XDM as an excellent option for crystal energy ranking in CSP and offers a guide to identify crystals (organic salts, conjugated flexible systems) where difficulties may appear.

Epistemic uncertainty propagation in energy flows between structural vibrating systems

NASA Astrophysics Data System (ADS)

Xu, Menghui; Du, Xiaoping; Qiu, Zhiping; Wang, Chong

2016-03-01

A dimension-wise method for predicting fuzzy energy flows between structural vibrating systems coupled by joints with epistemic uncertainties is established. Based on its Legendre polynomial approximation at α=0, both the minimum and maximum point vectors of the energy flow of interest are calculated dimension by dimension within the space spanned by the interval parameters determined by fuzzy those at α=0 and the resulted interval bounds are used to assemble the concerned fuzzy energy flows. Besides the proposed method, vertex method as well as two current methods is also applied. Comparisons among results by different methods are accomplished by two numerical examples and the accuracy of all methods is simultaneously verified by Monte Carlo simulation.

Probing the global potential energy minimum of (CH2O)2: THz absorption spectrum of (CH2O)2 in solid neon and para-hydrogen.

PubMed

Andersen, J; Voute, A; Mihrin, D; Heimdal, J; Berg, R W; Torsson, M; Wugt Larsen, R

2017-06-28

The true global potential energy minimum configuration of the formaldehyde dimer (CH 2 O) 2 , including the presence of a single or a double weak intermolecular CH⋯O hydrogen bond motif, has been a long-standing subject among both experimentalists and theoreticians as two different energy minima conformations of C s and C 2h symmetry have almost identical energies. The present work demonstrates how the class of large-amplitude hydrogen bond vibrational motion probed in the THz region provides excellent direct spectroscopic observables for these weak intermolecular CH⋯O hydrogen bond motifs. The combination of concentration dependency measurements, observed isotopic spectral shifts associated with H/D substitutions and dedicated annealing procedures, enables the unambiguous assignment of three large-amplitude infrared active hydrogen bond vibrational modes for the non-planar C s configuration of (CH 2 O) 2 embedded in cryogenic neon and enriched para-hydrogen matrices. A (semi)-empirical value for the change of vibrational zero-point energy of 5.5 ± 0.3 kJ mol -1 is proposed for the dimerization process. These THz spectroscopic observations are complemented by CCSD(T)-F12/aug-cc-pV5Z (electronic energies) and MP2/aug-cc-pVQZ (force fields) electronic structure calculations yielding a (semi)-empirical value of 13.7 ± 0.3 kJ mol -1 for the dissociation energy D 0 of this global potential energy minimum.

Probing the global potential energy minimum of (CH2O)2: THz absorption spectrum of (CH2O)2 in solid neon and para-hydrogen

NASA Astrophysics Data System (ADS)

Andersen, J.; Voute, A.; Mihrin, D.; Heimdal, J.; Berg, R. W.; Torsson, M.; Wugt Larsen, R.

2017-06-01

The true global potential energy minimum configuration of the formaldehyde dimer (CH2O)2, including the presence of a single or a double weak intermolecular CH⋯O hydrogen bond motif, has been a long-standing subject among both experimentalists and theoreticians as two different energy minima conformations of Cs and C2h symmetry have almost identical energies. The present work demonstrates how the class of large-amplitude hydrogen bond vibrational motion probed in the THz region provides excellent direct spectroscopic observables for these weak intermolecular CH⋯O hydrogen bond motifs. The combination of concentration dependency measurements, observed isotopic spectral shifts associated with H/D substitutions and dedicated annealing procedures, enables the unambiguous assignment of three large-amplitude infrared active hydrogen bond vibrational modes for the non-planar Cs configuration of (CH2O)2 embedded in cryogenic neon and enriched para-hydrogen matrices. A (semi)-empirical value for the change of vibrational zero-point energy of 5.5 ± 0.3 kJ mol-1 is proposed for the dimerization process. These THz spectroscopic observations are complemented by CCSD(T)-F12/aug-cc-pV5Z (electronic energies) and MP2/aug-cc-pVQZ (force fields) electronic structure calculations yielding a (semi)-empirical value of 13.7 ± 0.3 kJ mol-1 for the dissociation energy D0 of this global potential energy minimum.

Table of superdeformed nuclear bands and fission isomers

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

Firestone, R.B.; Singh, B.

A minimum in the second potential well of deformed nuclei was predicted and the associated shell gaps are illustrated in the harmonic oscillator potential shell energy surface calculations shown in this report. A strong superdeformed minimum in {sup 152}Dy was predicted for {beta}{sub 2}-0.65. Subsequently, a discrete set of {gamma}-ray transitions in {sup 152}DY was observed and, assigned to the predicted superdeformed band. Extensive research at several laboratories has since focused on searching for other mass regions of large deformation. A new generation of {gamma}-ray detector arrays is already producing a wealth of information about the mechanisms for feeding andmore » deexciting superdeformed bands. These bands have been found in three distinct regions near A=l30, 150, and 190. This research extends upon previous work in the actinide region near A=240 where fission isomers were identified and also associated with the second potential well. Quadrupole moment measurements for selected cases in each mass region are consistent with assigning the bands to excitations in the second local minimum. As part of our committment to maintain nuclear structure data as current as possible in the Evaluated Nuclear Structure Reference File (ENSDF) and the Table of Isotopes, we have updated the information on superdeformed nuclear bands. As of April 1994, we have complied data from 86 superdeformed bands and 46 fission isomers identified in 73 nuclides for this report. For each nuclide there is a complete level table listing both normal and superdeformed band assignments; level energy, spin, parity, half-life, magneto moments, decay branchings; and the energies, final levels, relative intensities, multipolarities, and mixing ratios for transitions deexciting each level. Mass excess, decay energies, and proton and neutron separation energies are also provided from the evaluation of Audi and Wapstra.« less

RNAiFold: a web server for RNA inverse folding and molecular design.

PubMed

Garcia-Martin, Juan Antonio; Clote, Peter; Dotu, Ivan

2013-07-01

Synthetic biology and nanotechnology are poised to make revolutionary contributions to the 21st century. In this article, we describe a new web server to support in silico RNA molecular design. Given an input target RNA secondary structure, together with optional constraints, such as requiring GC-content to lie within a certain range, requiring the number of strong (GC), weak (AU) and wobble (GU) base pairs to lie in a certain range, the RNAiFold web server determines one or more RNA sequences, whose minimum free-energy secondary structure is the target structure. RNAiFold provides access to two servers: RNA-CPdesign, which applies constraint programming, and RNA-LNSdesign, which applies the large neighborhood search heuristic; hence, it is suitable for larger input structures. Both servers can also solve the RNA inverse hybridization problem, i.e. given a representation of the desired hybridization structure, RNAiFold returns two sequences, whose minimum free-energy hybridization is the input target structure. The web server is publicly accessible at http://bioinformatics.bc.edu/clotelab/RNAiFold, which provides access to two specialized servers: RNA-CPdesign and RNA-LNSdesign. Source code for the underlying algorithms, implemented in COMET and supported on linux, can be downloaded at the server website.

Energy-efficiency increase of reinforced concrete columns with recessed working fittings

NASA Astrophysics Data System (ADS)

Muradyan, Viktor; Mailyan, Dmitry; Lyapin, Alexander; Chubarov, Valery

2017-10-01

One of the most important ways of increasing the energy-efficiency of the construction industry is the reduction of the material capacity of structures and labour intensity of their manufacturing. Since manufacturing of reinforced concrete structures requires considerable financial and energy expenses, then reduction of technological cycle operations is sure to be the urgent task today. It is well known, that in the recessed reinforced concrete elements the transverse reinforcement is fixed for the purpose of ensuring the longitudinal rods fixity. Besides, the thickness of the protective layer, as a rule, is taken the minimum. The authors proposed to increase the protective layer, and that will reduce the amount of transverse reinforcement rods significantly and will make the technological process of structures manufacturing easier.

Global minimum-energy structure and spectroscopic properties of I2(*-) x n H2O clusters: a Monte Carlo simulated annealing study.

PubMed

Pathak, Arup Kumar; Mukherjee, Tulsi; Maity, Dilip Kumar

2010-01-18

The vibrational (IR and Raman) and photoelectron spectral properties of hydrated iodine-dimer radical-anion clusters, I(2)(*-) x n H(2)O (n=1-10), are presented. Several initial guess structures are considered for each size of cluster to locate the global minimum-energy structure by applying a Monte Carlo simulated annealing procedure including spin-orbit interaction. In the Raman spectrum, hydration reduces the intensity of the I-I stretching band but enhances the intensity of the O-H stretching band of water. Raman spectra of more highly hydrated clusters appear to be simpler than the corresponding IR spectra. Vibrational bands due to simultaneous stretching vibrations of O-H bonds in a cyclic water network are observed for I(2)(*-) x n H(2)O clusters with n > or = 3. The vertical detachment energy (VDE) profile shows stepwise saturation that indicates closing of the geometrical shell in the hydrated clusters on addition of every four water molecules. The calculated VDE of finite-size small hydrated clusters is extrapolated to evaluate the bulk VDE value of I(2)(*-) in aqueous solution as 7.6 eV at the CCSD(T) level of theory. Structure and spectroscopic properties of these hydrated clusters are compared with those of hydrated clusters of Cl(2)(*-) and Br(2)(*-).

Is nuclear matter a quantum crystal?

NASA Technical Reports Server (NTRS)

Canuto, V.; Chitre, S. M.

1973-01-01

A possible alternative to the ordinary gas-like computation for nuclear matter is investigated under the assumption that the nucleons are arranged in a lattice. BCC, FCC and HCP structures are investigated. Only HCP shows a minimum in the energy vs. density curve with a modest binding energy of -1.5 MeV. The very low density limit is investigated and sensible results are obtained only if the tensor force decreases with the density. A study of the elastic properties indicates that the previous structures are mechanically unstable against shearing stresses.

The structure of the NO(X (2)Pi)-N(2) complex: A joint experimental-theoretical study.

PubMed

Wen, B; Meyer, H; Kłos, J

2010-04-21

We report the first measurement of the spectrum of the NO-N(2) complex in the region of the first vibrational NO overtone transition. The origin band of the complex is blueshifted by 0.30 cm(-1) from the corresponding NO monomer frequency. The observed spectrum consists of three bands assigned to the origin band, the excitation of one quantum of z-axis rotation and one associated hot band. The spacing of the bands and the rotational structure indicate a T-shaped vibrationally averaged structure with the NO molecule forming the top of the T. These findings are confirmed by high level ab initio calculations of the potential energy surfaces in planar symmetry. The deepest minimum is found for a T-shaped geometry on the A(")-surface. As a result the sum potential also has the global minimum for this structure. The different potential surfaces show several additional local minima at slightly higher energies indicating that the complex most likely will perform large amplitude motion even in its ground vibrational state. Nevertheless, as suggested by the measured spectra, the complex must, on average, spend a substantial amount of time near the T-shaped configuration.

Chemistry of Aviation Fuels

NASA Technical Reports Server (NTRS)

Knepper, Bryan; Hwang, Soon Muk; DeWitt, Kenneth J.

2004-01-01

Minimum ignition energies of various methanol/air mixtures were measured in a temperature controlled constant volume combustion vessel using a spark ignition method with a spark gap distance of 2 mm. The minimum ignition energies decrease rapidly as the mixture composition (equivalence ratio, Phi) changes from lean to stoichiometric, reach a minimum value, and then increase rather slowly with Phi. The minimum of the minimum ignition energy (MIE) and the corresponding mixture composition were determined to be 0.137 mJ and Phi = 1.16, a slightly rich mixture. The variation of minimum ignition energy with respect to the mixture composition is explained in terms of changes in reaction chemistry.

Minimum energy control and optimal-satisfactory control of Boolean control network

NASA Astrophysics Data System (ADS)

Li, Fangfei; Lu, Xiwen

2013-12-01

In the literatures, to transfer the Boolean control network from the initial state to the desired state, the expenditure of energy has been rarely considered. Motivated by this, this Letter investigates the minimum energy control and optimal-satisfactory control of Boolean control network. Based on the semi-tensor product of matrices and Floyd's algorithm, minimum energy, constrained minimum energy and optimal-satisfactory control design for Boolean control network are given respectively. A numerical example is presented to illustrate the efficiency of the obtained results.

Doping Induced Structural Stability and Electronic Properties of GaN Nanotubes

PubMed Central

Khan, Mohammad Irfan; Tyagi, Neha; Swaroop Khare, Purnima

2014-01-01

The present paper discusses the effect of manganese doping on the structural stability and electronic band gap of chiral (2, 1), armchair (3, 3), and zigzag ((6, 0) and (10, 0)) single walled GaN nanotube by using density functional theory based Atomistix Toolkit (ATK) Virtual NanoLab (VNL). The structural stability has been analyzed in terms of minimum ground state total energy, binding, and formation energy. As an effect of Mn doping (1–4 atoms), all the GaN nanotubes taken into consideration show semiconducting to metallic transition first and after certain level of Mn doping changes its trend. PMID:24707225

A new method for finding the minimum free energy pathway of ions and small molecule transportation through protein based on 3D-RISM theory and the string method

NASA Astrophysics Data System (ADS)

Yoshida, Norio

2018-05-01

A new method for finding the minimum free energy pathway (MFEP) of ions and small molecule transportation through a protein based on the three-dimensional reference interaction site model (3D-RISM) theory combined with the string method has been proposed. The 3D-RISM theory produces the distribution function, or the potential of mean force (PMF), for transporting substances around the given protein structures. By applying the string method to the PMF surface, one can readily determine the MFEP on the PMF surface. The method has been applied to consider the Na+ conduction pathway of channelrhodopsin as an example.

Combined gradient projection/single component artificial force induced reaction (GP/SC-AFIR) method for an efficient search of minimum energy conical intersection (MECI) geometries

NASA Astrophysics Data System (ADS)

Harabuchi, Yu; Taketsugu, Tetsuya; Maeda, Satoshi

2017-04-01

We report a new approach to search for structures of minimum energy conical intersection (MECIs) automatically. Gradient projection (GP) method and single component artificial force induced reaction (SC-AFIR) method were combined in the present approach. As case studies, MECIs of benzene and naphthalene between their ground and first excited singlet electronic states (S0/S1-MECIs) were explored. All S0/S1-MECIs reported previously were obtained automatically. Furthermore, the number of force calculations was reduced compared to the one required in the previous search. Improved convergence in a step in which various geometrical displacements are induced by SC-AFIR would contribute to the cost reduction.

Final State of Ecosystem Containing Grass, Sheep and Wolves with Aging

NASA Astrophysics Data System (ADS)

He, Mingfeng; Pan, Qiu-Hui; Wang, Shuang

This paper describes a cellular automata model containing movable wolves, sheep and reproducible grass. Each wolf or sheep is characterized by Penna bitstrings. In addition, we introduce the energy rule and the predator-prey mechanism for wolf and sheep. With considering age-structured, genetic strings, minimum reproduction age, cycle of the reproduction, number of offspring, we get three possible states of a predator-prey system: the coexisting one with predators and prey, the absorbing one with prey only, and the empty one where no animal survived. In this paper, we mainly discuss the effect of the number of poor genes, the energy supply (food), the minimum reproduction age, the reproductive cycle and the birth rate on the above three possible final states.

10 CFR 862.6 - Voluntary minimum altitude.

Code of Federal Regulations, 2011 CFR

2011-01-01

... 10 Energy 4 2011-01-01 2011-01-01 false Voluntary minimum altitude. 862.6 Section 862.6 Energy DEPARTMENT OF ENERGY RESTRICTIONS ON AIRCRAFT LANDING AND AIR DELIVERY AT DEPARTMENT OF ENERGY NUCLEAR SITES... designated site. Applicable FAA prohibitions or restrictions take precedence over this voluntary minimum...

Structural and mechanical properties of glassy water in nanoscale confinement.

PubMed

Lombardo, Thomas G; Giovambattista, Nicolás; Debenedetti, Pablo G

2009-01-01

We investigate the structure and mechanical properties of glassy water confined between silica-based surfaces with continuously tunable hydrophobicity and hydrophilicity by computing and analyzing minimum energy, mechanically stable configurations (inherent structures). The structured silica substrate imposes long-range order on the first layer of water molecules under hydrophobic confinement at high density (p > or = 1.0 g cm(-3)). This proximal layer is also structured in hydrophilic confinement at very low density (p approximately 0.4 g cm(-3)). The ordering of water next to the hydrophobic surface greatly enhances the mechanical strength of thin films (0.8 nm). This leads to a substantial stress anisotropy; the transverse strength of the film exceeds the normal strength by 500 MPa. The large transverse strength results in a minimum in the equation of state of the energy landscape that does not correspond to a mechanical instability, but represents disruption of the ordered layer of water next to the wall. In addition, we find that the mode of mechanical failure is dependent on the type of confinement. Under large lateral strain, water confined by hydrophilic surfaces preferentially forms voids in the middle of the film and fails cohesively. In contrast, water under hydrophobic confinement tends to form voids near the walls and fails by loss of adhesion.

Global optimization of small bimetallic Pd-Co binary nanoalloy clusters: a genetic algorithm approach at the DFT level.

PubMed

Aslan, Mikail; Davis, Jack B A; Johnston, Roy L

2016-03-07

The global optimisation of small bimetallic PdCo binary nanoalloys are systematically investigated using the Birmingham Cluster Genetic Algorithm (BCGA). The effect of size and composition on the structures, stability, magnetic and electronic properties including the binding energies, second finite difference energies and mixing energies of Pd-Co binary nanoalloys are discussed. A detailed analysis of Pd-Co structural motifs and segregation effects is also presented. The maximal mixing energy corresponds to Pd atom compositions for which the number of mixed Pd-Co bonds is maximised. Global minimum clusters are distinguished from transition states by vibrational frequency analysis. HOMO-LUMO gap, electric dipole moment and vibrational frequency analyses are made to enable correlation with future experiments.

The inverted free energy landscape of an intrinsically disordered peptide by simulations and experiments.

PubMed

Granata, Daniele; Baftizadeh, Fahimeh; Habchi, Johnny; Galvagnion, Celine; De Simone, Alfonso; Camilloni, Carlo; Laio, Alessandro; Vendruscolo, Michele

2015-10-26

The free energy landscape theory has been very successful in rationalizing the folding behaviour of globular proteins, as this representation provides intuitive information on the number of states involved in the folding process, their populations and pathways of interconversion. We extend here this formalism to the case of the Aβ40 peptide, a 40-residue intrinsically disordered protein fragment associated with Alzheimer's disease. By using an advanced sampling technique that enables free energy calculations to reach convergence also in the case of highly disordered states of proteins, we provide a precise structural characterization of the free energy landscape of this peptide. We find that such landscape has inverted features with respect to those typical of folded proteins. While the global free energy minimum consists of highly disordered structures, higher free energy regions correspond to a large variety of transiently structured conformations with secondary structure elements arranged in several different manners, and are not separated from each other by sizeable free energy barriers. From this peculiar structure of the free energy landscape we predict that this peptide should become more structured and not only more compact, with increasing temperatures, and we show that this is the case through a series of biophysical measurements.

The inverted free energy landscape of an intrinsically disordered peptide by simulations and experiments

PubMed Central

Granata, Daniele; Baftizadeh, Fahimeh; Habchi, Johnny; Galvagnion, Celine; De Simone, Alfonso; Camilloni, Carlo; Laio, Alessandro; Vendruscolo, Michele

2015-01-01

The free energy landscape theory has been very successful in rationalizing the folding behaviour of globular proteins, as this representation provides intuitive information on the number of states involved in the folding process, their populations and pathways of interconversion. We extend here this formalism to the case of the Aβ40 peptide, a 40-residue intrinsically disordered protein fragment associated with Alzheimer’s disease. By using an advanced sampling technique that enables free energy calculations to reach convergence also in the case of highly disordered states of proteins, we provide a precise structural characterization of the free energy landscape of this peptide. We find that such landscape has inverted features with respect to those typical of folded proteins. While the global free energy minimum consists of highly disordered structures, higher free energy regions correspond to a large variety of transiently structured conformations with secondary structure elements arranged in several different manners, and are not separated from each other by sizeable free energy barriers. From this peculiar structure of the free energy landscape we predict that this peptide should become more structured and not only more compact, with increasing temperatures, and we show that this is the case through a series of biophysical measurements. PMID:26498066

Transient low-barrier hydrogen bond in the photoactive state of green fluorescent protein.

PubMed

Nadal-Ferret, Marc; Gelabert, Ricard; Moreno, Miquel; Lluch, José M

2015-12-14

In this paper, we have analyzed the feasibility of spontaneous proton transfer in GFP at the Franck-Condon region directly after photoexcitation. Computation of a sizeable portion of the potential energy surface at the Franck-Condon region of A the structure shows the process of proton transfer to be unfavorable by 3 kcal mol(-1) in S1 if no further structural relaxation is permitted. The ground vibrational state is found to lie above the potential energy barrier of the proton transfer in both S0 and S1. Expectation values of the geometry reveal that the proton shared between the chromophore and W22, and the proton shared between Ser205 and Glu222 are very close to the center of the respective hydrogen bonds, giving support to the claim that the first transient intermediate detected after photoexcitation (I0*) has characteristics similar to those of a low-barrier hydrogen bond [Di Donato et al., Phys. Chem. Chem. Phys., 2012, 13, 16295]. A quantum dynamical calculation of the evolution in the excited state shows an even larger probability of finding those two protons close to the center compared to in the ground state, but no formation of the proton-transferred product is observed. A QM/MM photoactive state geometry optimization, initiated using a configuration obtained by taking the A minimum and moving the protons to the product side, yields a minimum energy structure with the protons transferred and in which the His148 residue is substantially closer to the now anionic chromophore. These results indicate that: (1) proton transfer is not possible if structural relaxation of the surroundings of the chromophore is prevented; (2) protons H1 and H3 especially are found very close to the point halfway between the donor and acceptor after photoexcitation when the zero-point energy is considered; (3) a geometrical parameter exists (the His148-Cro distance) under which the structure with the protons transferred is not a minimum, and that, if included, should lead to the fluorescing I* structure. The existence of an oscillating stationary state between the reactants and products of the triple proton transfer reaction can explain the dual emission reported for the I0* intermediate of wtGFP.

10 CFR 862.6 - Voluntary minimum altitude.

Code of Federal Regulations, 2010 CFR

2010-01-01

... 10 Energy 4 2010-01-01 2010-01-01 false Voluntary minimum altitude. 862.6 Section 862.6 Energy DEPARTMENT OF ENERGY RESTRICTIONS ON AIRCRAFT LANDING AND AIR DELIVERY AT DEPARTMENT OF ENERGY NUCLEAR SITES § 862.6 Voluntary minimum altitude. In addition to complying with all applicable FAA prohibitions or...

An O(n(5)) algorithm for MFE prediction of kissing hairpins and 4-chains in nucleic acids.

PubMed

Chen, Ho-Lin; Condon, Anne; Jabbari, Hosna

2009-06-01

Efficient methods for prediction of minimum free energy (MFE) nucleic secondary structures are widely used, both to better understand structure and function of biological RNAs and to design novel nano-structures. Here, we present a new algorithm for MFE secondary structure prediction, which significantly expands the class of structures that can be handled in O(n(5)) time. Our algorithm can handle H-type pseudoknotted structures, kissing hairpins, and chains of four overlapping stems, as well as nested substructures of these types.

Effect of alcohol on the structure of cytochrome C: FCS and molecular dynamics simulations

NASA Astrophysics Data System (ADS)

Amin, Md. Asif; Halder, Ritaban; Ghosh, Catherine; Jana, Biman; Bhattacharyya, Kankan

2016-12-01

Effect of ethanol on the size and structure of a protein cytochrome C (Cyt C) is investigated using fluorescence correlation spectroscopy (FCS) and molecular dynamics (MD) simulations. For FCS studies, Cyt C is covalently labeled with a fluorescent probe, alexa 488. FCS studies indicate that on addition of ethanol, the size of the protein varies non-monotonically. The size of Cyt C increases (i.e., the protein unfolds) on addition of alcohol (ethanol) up to a mole fraction of 0.2 (44.75% v/v) and decreases at higher alcohol concentration. In order to provide a molecular origin of this structural transition, we explore the conformational free energy landscape of Cyt C as a function of radius of gyration (Rg) at different compositions of water-ethanol binary mixture using MD simulations. Cyt C exhibits a minimum at Rg ˜ 13 Å in bulk water (0% alcohol). Upon increasing ethanol concentration, a second minimum appears in the free energy surface with gradually larger Rg up to χEtOH ˜ 0.2 (44.75% v/v). This suggests gradual unfolding of the protein. At a higher concentration of alcohol (χEtOH > 0.2), the minimum at large Rg vanishes, indicating compaction. Analysis of the contact map and the solvent organization around protein indicates a preferential solvation of the hydrophobic residues by ethanol up to χEtOH = 0.2 (44.75% v/v) and this causes the gradual unfolding of the protein. At high concentration (χEtOH = 0.3 (58% v/v)), due to structural organization in bulk water-ethanol binary mixture, the extent of preferential solvation by ethanol decreases. This causes a structural transition of Cyt C towards a more compact state.

Commercial-Off-The-Shelf (COTS) Indirect Energy Conversion Isotope (IDEC) Design Structure and Power Management

DTIC Science & Technology

2014-12-01

RETURN YOUR FORM TO THE ABOVE ADDRESS. 1. REPORT DATE (DD-MM-YYYY) December 2014 2. REPORT TYPE Final 3. DATES COVERED (From - To) 4. TITLE AND...must last the lifetime of the sensor. Unlike chemical batteries, the higher energy densities of radioisotopes allow the sensors to operate for...because they are self-contained energy sources using radioisotope decay. The minimum power needed to fully accomplish a wide range of duties would be

Energy and IAQ Implications of Alternative Minimum Ventilation Rates in California Retail and School Buildings

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

Dutton, Spencer M.; Fisk, William J.

For a stand-alone retail building, a primary school, and a secondary school in each of the 16 California climate zones, the EnergyPlus building energy simulation model was used to estimate how minimum mechanical ventilation rates (VRs) affect energy use and indoor air concentrations of an indoor-generated contaminant. The modeling indicates large changes in heating energy use, but only moderate changes in total building energy use, as minimum VRs in the retail building are changed. For example, predicted state-wide heating energy consumption in the retail building decreases by more than 50% and total building energy consumption decreases by approximately 10% asmore » the minimum VR decreases from the Title 24 requirement to no mechanical ventilation. The primary and secondary schools have notably higher internal heat gains than in the retail building models, resulting in significantly reduced demand for heating. The school heating energy use was correspondingly less sensitive to changes in the minimum VR. The modeling indicates that minimum VRs influence HVAC energy and total energy use in schools by only a few percent. For both the retail building and the school buildings, minimum VRs substantially affected the predicted annual-average indoor concentrations of an indoor generated contaminant, with larger effects in schools. The shape of the curves relating contaminant concentrations with VRs illustrate the importance of avoiding particularly low VRs.« less

Multistate metadynamics for automatic exploration of conical intersections

NASA Astrophysics Data System (ADS)

Lindner, Joachim O.; Röhr, Merle I. S.; Mitrić, Roland

2018-05-01

We introduce multistate metadynamics for automatic exploration of conical intersection seams between adiabatic Born-Oppenheimer potential energy surfaces in molecular systems. By choosing the energy gap between the electronic states as a collective variable the metadynamics drives the system from an arbitrary ground-state configuration toward the intersection seam. Upon reaching the seam, the multistate electronic Hamiltonian is extended by introducing biasing potentials into the off-diagonal elements, and the molecular dynamics is continued on a modified potential energy surface obtained by diagonalization of the latter. The off-diagonal bias serves to locally open the energy gap and push the system to the next intersection point. In this way, the conical intersection energy landscape can be explored, identifying minimum energy crossing points and the barriers separating them. We illustrate the method on the example of furan, a prototype organic molecule exhibiting rich photophysics. The multistate metadynamics reveals plateaus on the conical intersection energy landscape from which the minimum energy crossing points with characteristic geometries can be extracted. The method can be combined with the broad spectrum of electronic structure methods and represents a generally applicable tool for the exploration of photophysics and photochemistry in complex molecules and materials.

Semi-Metallic Be5C2 Monolayer Global Minimum with Quasi-Planar Pentacoordinate Carbons and Negative Poissons Ratio (Open Access Publisher’s Version)

DTIC Science & Technology

2016-05-03

ARTICLE Received 25 Nov 2015 | Accepted 1 Apr 2016 | Published 3 May 2016 Semi-metallic Be5C2 monolayer global minimum with quasi -planar...forming a quasi -planar pentacoordinate carbon moiety. Be5C2 monolayer appears to have good stability as revealed by its moderate cohesive energy...some promise to be realized experimentally . Be5C2 monolayer is a gapless semiconductor with a Dirac-like point in the band structure and also has an

Investigating energy-based pool structure selection in the structure ensemble modeling with experimental distance constraints: The example from a multidomain protein Pub1.

PubMed

Zhu, Guanhua; Liu, Wei; Bao, Chenglong; Tong, Dudu; Ji, Hui; Shen, Zuowei; Yang, Daiwen; Lu, Lanyuan

2018-05-01

The structural variations of multidomain proteins with flexible parts mediate many biological processes, and a structure ensemble can be determined by selecting a weighted combination of representative structures from a simulated structure pool, producing the best fit to experimental constraints such as interatomic distance. In this study, a hybrid structure-based and physics-based atomistic force field with an efficient sampling strategy is adopted to simulate a model di-domain protein against experimental paramagnetic relaxation enhancement (PRE) data that correspond to distance constraints. The molecular dynamics simulations produce a wide range of conformations depicted on a protein energy landscape. Subsequently, a conformational ensemble recovered with low-energy structures and the minimum-size restraint is identified in good agreement with experimental PRE rates, and the result is also supported by chemical shift perturbations and small-angle X-ray scattering data. It is illustrated that the regularizations of energy and ensemble-size prevent an arbitrary interpretation of protein conformations. Moreover, energy is found to serve as a critical control to refine the structure pool and prevent data overfitting, because the absence of energy regularization exposes ensemble construction to the noise from high-energy structures and causes a more ambiguous representation of protein conformations. Finally, we perform structure-ensemble optimizations with a topology-based structure pool, to enhance the understanding on the ensemble results from different sources of pool candidates. © 2018 Wiley Periodicals, Inc.

Protein structure prediction with local adjust tabu search algorithm

PubMed Central

2014-01-01

Background Protein folding structure prediction is one of the most challenging problems in the bioinformatics domain. Because of the complexity of the realistic protein structure, the simplified structure model and the computational method should be adopted in the research. The AB off-lattice model is one of the simplification models, which only considers two classes of amino acids, hydrophobic (A) residues and hydrophilic (B) residues. Results The main work of this paper is to discuss how to optimize the lowest energy configurations in 2D off-lattice model and 3D off-lattice model by using Fibonacci sequences and real protein sequences. In order to avoid falling into local minimum and faster convergence to the global minimum, we introduce a novel method (SATS) to the protein structure problem, which combines simulated annealing algorithm and tabu search algorithm. Various strategies, such as the new encoding strategy, the adaptive neighborhood generation strategy and the local adjustment strategy, are adopted successfully for high-speed searching the optimal conformation corresponds to the lowest energy of the protein sequences. Experimental results show that some of the results obtained by the improved SATS are better than those reported in previous literatures, and we can sure that the lowest energy folding state for short Fibonacci sequences have been found. Conclusions Although the off-lattice models is not very realistic, they can reflect some important characteristics of the realistic protein. It can be found that 3D off-lattice model is more like native folding structure of the realistic protein than 2D off-lattice model. In addition, compared with some previous researches, the proposed hybrid algorithm can more effectively and more quickly search the spatial folding structure of a protein chain. PMID:25474708

Helicity and singular structures in fluid dynamics

PubMed Central

Moffatt, H. Keith

2014-01-01

Helicity is, like energy, a quadratic invariant of the Euler equations of ideal fluid flow, although, unlike energy, it is not sign definite. In physical terms, it represents the degree of linkage of the vortex lines of a flow, conserved when conditions are such that these vortex lines are frozen in the fluid. Some basic properties of helicity are reviewed, with particular reference to (i) its crucial role in the dynamo excitation of magnetic fields in cosmic systems; (ii) its bearing on the existence of Euler flows of arbitrarily complex streamline topology; (iii) the constraining role of the analogous magnetic helicity in the determination of stable knotted minimum-energy magnetostatic structures; and (iv) its role in depleting nonlinearity in the Navier-Stokes equations, with implications for the coherent structures and energy cascade of turbulence. In a final section, some singular phenomena in low Reynolds number flows are briefly described. PMID:24520175

On-the-Fly Machine Learning of Atomic Potential in Density Functional Theory Structure Optimization

NASA Astrophysics Data System (ADS)

Jacobsen, T. L.; Jørgensen, M. S.; Hammer, B.

2018-01-01

Machine learning (ML) is used to derive local stability information for density functional theory calculations of systems in relation to the recently discovered SnO2 (110 )-(4 ×1 ) reconstruction. The ML model is trained on (structure, total energy) relations collected during global minimum energy search runs with an evolutionary algorithm (EA). While being built, the ML model is used to guide the EA, thereby speeding up the overall rate by which the EA succeeds. Inspection of the local atomic potentials emerging from the model further shows chemically intuitive patterns.

On the structure of critical energy levels for the cubic focusing NLS on star graphs

NASA Astrophysics Data System (ADS)

Adami, Riccardo; Cacciapuoti, Claudio; Finco, Domenico; Noja, Diego

2012-05-01

We provide information on a non-trivial structure of phase space of the cubic nonlinear Schrödinger (NLS) on a three-edge star graph. We prove that, in contrast to the case of the standard NLS on the line, the energy associated with the cubic focusing Schrödinger equation on the three-edge star graph with a free (Kirchhoff) vertex does not attain a minimum value on any sphere of constant L2-norm. We moreover show that the only stationary state with prescribed L2-norm is indeed a saddle point.

An optimized surface plasmon photovoltaic structure using energy transfer between discrete nano-particles.

PubMed

Lin, Albert; Fu, Sze-Ming; Chung, Yen-Kai; Lai, Shih-Yun; Tseng, Chi-Wei

2013-01-14

Surface plasmon enhancement has been proposed as a way to achieve higher absorption for thin-film photovoltaics, where surface plasmon polariton(SPP) and localized surface plasmon (LSP) are shown to provide dense near field and far field light scattering. Here it is shown that controlled far-field light scattering can be achieved using successive coupling between surface plasmonic (SP) nano-particles. Through genetic algorithm (GA) optimization, energy transfer between discrete nano-particles (ETDNP) is identified, which enhances solar cell efficiency. The optimized energy transfer structure acts like lumped-element transmission line and can properly alter the direction of photon flow. Increased in-plane component of wavevector is thus achieved and photon path length is extended. In addition, Wood-Rayleigh anomaly, at which transmission minimum occurs, is avoided through GA optimization. Optimized energy transfer structure provides 46.95% improvement over baseline planar cell. It achieves larger angular scattering capability compared to conventional surface plasmon polariton back reflector structure and index-guided structure due to SP energy transfer through mode coupling. Via SP mediated energy transfer, an alternative way to control the light flow inside thin-film is proposed, which can be more efficient than conventional index-guided mode using total internal reflection (TIR).

Ab Initio and Analytic Intermolecular Potentials for Ar–CH3OH

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

Tasic, Uros; Alexeev, Yuri; Vayner, Grigoriy

2006-09-20

Ab initio calculations at the CCSD(T)/aug-cc-pVTZ level of theory were used to characterize the Ar–CH₃y6tOH intermolecular potential energy surface (PES). Potential energy curves were calculated for four different Ar + CH₃OH orientations and used to derive an analytic function for the intermolecular PES. A sum of Ar–C, Ar–O, Ar–H(C), and Ar–H(O) two-body potentials gives an excellent fit to these potential energy curves up to 100 kcal mol¯¹, and adding an additional r¯¹n term to the Buckingham two-body potential results in only a minor improvement in the fit. Three Ar–CH₃OH van der Waals minima were found from the CCSD(T)/aug-cc-pVTZ//MP2/aug-cc-pVTZ calculations. Themore » structure of the global minimum is in overall good agreement with experiment (X.-C. Tan, L. Sun and R. L. Kuczkowski, J. Mol. Spectrosc., 1995, 171, 248). It is T-shaped with the hydroxyl H-atom syn with respect to Ar. Extrapolated to the complete basis set (CBS) limit, the global minimum has a well depth of 0.72 kcal mol¯¹ with basis set superposition error (BSSE) correction. The aug-cc-pVTZ basis set gives a well depth only 0.10 kcal mol¯¹ smaller than this value. The well depths of the other two minima are within 0.16 kcal mol¯¹ of the global minimum. The analytic Ar–CH₃OH intermolecular potential also identifies these three minima as the only van der Waals minima and the structures predicted by the analytic potential are similar to the ab initio structures. The analytic potential identifies the same global minimum and the predicted well depths for the minima are within 0.05 kcal mol¯1 of the ab initio values. Combining this Ar–CH₃OH intermolecular potential with a potential for a OH-terminated alkylthiolate self-assembled monolayer surface (i.e., HO-SAM) provides a potential to model Ar + HO-SAM collisions.« less

Conformational Analysis of Free and Bound Retinoic Acid

PubMed Central

Fu, Zheng; Li, Xue; Merz, Kenneth M.

2012-01-01

The conformational profiles of unbound all-trans and 9-cis retinoic acid (RA) have been determined using classical and quantum mechanical calculations. Sixty-six all-trans-RA (ATRA) and forty-eight 9-cis-RA energy minimum conformers were identified via HF/6-31G* geometry optimizations in vacuo. Their relative conformational energies were estimated utilizing the M06, M06-2x and MP2 methods combined with the 6-311+G(d,p), aug-cc-pVDZ and aug-cc-pVTZ basis sets, as well as complete basis set MP2 extrapolations using the latter two basis sets. Single-point energy calculations performed with the M06-2x density functional were found to yield similar results to MP2/CBS for the low-energy retinoic acid conformations. Not unexpectedly, the conformational propensities of retinoic acid were governed by the orientation and arrangement of the torsion angles associated with the polyene tail. We also used previously reported QM/MM X-ray refinement results on four ATRA-protein crystal structures plus one newly refined 9-cis-RA complex (PDB ID 1XDK) in order to investigate the conformational preferences of bound retinoic acid. In the re-refined RA conformers the conjugated double bonds are nearly coplanar, which is consistent with the global minimum identified by the Omega/QM method rather than the corresponding crystallographically determined conformations given in the PDB. Consequently, a 91.3% average reduction of the local strain energy in the gas phase, as well as 92.1% in PCM solvent, was observed using the QM/MM refined structures versus the PDB deposited RA conformations. These results thus demonstrate that our QM/MM X-ray refinement approach can significantly enhance the quality of X-ray crystal structures refined by conventional refinement protocols, thereby providing reliable drug-target structural information for use in structure-based drug discovery applications. PMID:22844234

Neural-network-enhanced evolutionary algorithm applied to supported metal nanoparticles

NASA Astrophysics Data System (ADS)

Kolsbjerg, E. L.; Peterson, A. A.; Hammer, B.

2018-05-01

We show that approximate structural relaxation with a neural network enables orders of magnitude faster global optimization with an evolutionary algorithm in a density functional theory framework. The increased speed facilitates reliable identification of global minimum energy structures, as exemplified by our finding of a hollow Pt13 nanoparticle on an MgO support. We highlight the importance of knowing the correct structure when studying the catalytic reactivity of the different particle shapes. The computational speedup further enables screening of hundreds of different pathways in the search for optimum kinetic transitions between low-energy conformers and hence pushes the limits of the insight into thermal ensembles that can be obtained from theory.

Appropriate Technology and Journal Writing: Structured Dialogues that Enhance Learning

ERIC Educational Resources Information Center

Longhurst, James; Sandage, Scott A.

2004-01-01

Of the many available options, instructors should choose "appropriate technology" that meets pedagogical goals with minimum disruption. Student journal assignments follow many teaching "best practices" but consume time and energy; we recommend e-mail as the most appropriate choice for journal assignments. E-mail encourages fast and personalized…

Glass Forming Ability in Systems with Competing Orderings

NASA Astrophysics Data System (ADS)

Russo, John; Romano, Flavio; Tanaka, Hajime

2018-04-01

Some liquids, if cooled rapidly enough to avoid crystallization, can be frozen into a nonergodic glassy state. The tendency for a material to form a glass when quenched is called "glass-forming ability," and it is of key significance both fundamentally and for materials science applications. Here, we consider liquids with competing orderings, where an increase in the glass-forming ability is signaled by a depression of the melting temperature towards its minimum at triple or eutectic points. With simulations of two model systems where glass-forming ability can be tuned by an external parameter, we are able to interpolate between crystal-forming and glass-forming behavior. We find that the enhancement of the glass-forming ability is caused by an increase in the structural difference between liquid and crystal: stronger competition in orderings towards the melting point minimum makes a liquid structure more disordered (more complex). This increase in the liquid-crystal structure difference can be described by a single adimensional parameter, i.e., the interface energy cost scaled by the thermal energy, which we call the "thermodynamic interface penalty." Our finding may provide a general physical principle for not only controlling the glass-forming ability but also the emergence of glassy behavior of various systems with competing orderings, including orderings of structural, magnetic, electronic, charge, and dipolar origin.

Competitive annealing of multiple DNA origami: formation of chimeric origami

NASA Astrophysics Data System (ADS)

Majikes, Jacob M.; Nash, Jessica A.; LaBean, Thomas H.

2016-11-01

Scaffolded DNA origami are a robust tool for building discrete nanoscale objects at high yield. This strategy ensures, in the design process, that the desired nanostructure is the minimum free energy state for the designed set of DNA sequences. Despite aiming for the minimum free energy structure, the folding process which leads to that conformation is difficult to characterize, although it has been the subject of much research. In order to shed light on the molecular folding pathways, this study intentionally frustrates the folding process of these systems by simultaneously annealing the staple pools for multiple target or parent origami structures, forcing competition. A surprising result of these competitive, simultaneous anneals is the formation of chimeric DNA origami which inherit structural regions from both parent origami. By comparing the regions inherited from the parent origami, relative stability of substructures were compared. This allowed examination of the folding process with typical characterization techniques and materials. Anneal curves were then used as a means to rapidly generate a phase diagram of anticipated behavior as a function of staple excess and parent staple ratio. This initial study shows that competitive anneals provide an exciting way to create diverse new nanostructures and may be used to examine the relative stability of various structural motifs.

Low-energy tautomers and conformers of neutral and protonated arginine.

PubMed

Rak, J; Skurski, P; Simons, J; Gutowski, M

2001-11-28

The relative stabilities of zwitterionic and canonical forms of neutral arginine and of its protonated derivative were studied by using ab initio electronic structure methods. Trial structures were first identified at the PM3 level of theory with use of a genetic algorithm to systematically vary geometrical parameters. Further geometry optimizations of these structures were performed at the MP2 and B3LYP levels of theory with basis sets of the 6-31++G** quality. The final energies were determined at the CCSD/6-31++G** level and corrected for thermal effects determined at the B3LYP level. Two new nonzwitterionic structures of the neutral were identified, and one of them is the lowest energy structure found so far. The five lowest energy structures of neutral arginine are all nonzwitterionic in nature and are clustered within a narrow energy range of 2.3 kcal/mol. The lowest energy zwitterion structure is less stable than the lowest nonzwitterion structure by 4.0 kcal/mol. For no level of theory is a zwitterion structure suggested to be the global minimum. The calculated proton affinity of 256.3 kcal/mol and gas-phase basicity of 247.8 kcal/mol of arginine are in reasonable agreement with the measured values of 251.2 and 240.6 kcal/mol, respectively. The calculated vibrational characteristics of the low-energy structures of neutral arginine provide an alternative interpretation of the IR-CRLAS spectrum (Chapo et al. J. Am. Chem. Soc. 1998, 120, 12956-12957).

Guiding Conformation Space Search with an All-Atom Energy Potential

PubMed Central

Brunette, TJ; Brock, Oliver

2009-01-01

The most significant impediment for protein structure prediction is the inadequacy of conformation space search. Conformation space is too large and the energy landscape too rugged for existing search methods to consistently find near-optimal minima. To alleviate this problem, we present model-based search, a novel conformation space search method. Model-based search uses highly accurate information obtained during search to build an approximate, partial model of the energy landscape. Model-based search aggregates information in the model as it progresses, and in turn uses this information to guide exploration towards regions most likely to contain a near-optimal minimum. We validate our method by predicting the structure of 32 proteins, ranging in length from 49 to 213 amino acids. Our results demonstrate that model-based search is more effective at finding low-energy conformations in high-dimensional conformation spaces than existing search methods. The reduction in energy translates into structure predictions of increased accuracy. PMID:18536015

Temperature dependent energy levels of methylammonium lead iodide perovskite

NASA Astrophysics Data System (ADS)

Foley, Benjamin J.; Marlowe, Daniel L.; Sun, Keye; Saidi, Wissam A.; Scudiero, Louis; Gupta, Mool C.; Choi, Joshua J.

2015-06-01

Temperature dependent energy levels of methylammonium lead iodide are investigated using a combination of ultraviolet photoemission spectroscopy and optical spectroscopy. Our results show that the valence band maximum and conduction band minimum shift down in energy by 110 meV and 77 meV as temperature increases from 28 °C to 85 °C. Density functional theory calculations using slab structures show that the decreased orbital splitting due to thermal expansion is a major contribution to the experimentally observed shift in energy levels. Our results have implications for solar cell performance under operating conditions with continued sunlight exposure and increased temperature.

New analytical model for the ozone electronic ground state potential surface and accurate ab initio vibrational predictions at high energy range.

PubMed

Tyuterev, Vladimir G; Kochanov, Roman V; Tashkun, Sergey A; Holka, Filip; Szalay, Péter G

2013-10-07

An accurate description of the complicated shape of the potential energy surface (PES) and that of the highly excited vibration states is of crucial importance for various unsolved issues in the spectroscopy and dynamics of ozone and remains a challenge for the theory. In this work a new analytical representation is proposed for the PES of the ground electronic state of the ozone molecule in the range covering the main potential well and the transition state towards the dissociation. This model accounts for particular features specific to the ozone PES for large variations of nuclear displacements along the minimum energy path. The impact of the shape of the PES near the transition state (existence of the "reef structure") on vibration energy levels was studied for the first time. The major purpose of this work was to provide accurate theoretical predictions for ozone vibrational band centres at the energy range near the dissociation threshold, which would be helpful for understanding the very complicated high-resolution spectra and its analyses currently in progress. Extended ab initio electronic structure calculations were carried out enabling the determination of the parameters of a minimum energy path PES model resulting in a new set of theoretical vibrational levels of ozone. A comparison with recent high-resolution spectroscopic data on the vibrational levels gives the root-mean-square deviations below 1 cm(-1) for ozone band centres up to 90% of the dissociation energy. New ab initio vibrational predictions represent a significant improvement with respect to all previously available calculations.

Lumbar load attenuation for rotorcraft occupants using a design methodology for the seat impact energy-absorbing system

NASA Astrophysics Data System (ADS)

Moradi, Rasoul; Beheshti, Hamid K.; Lankarani, Hamid M.

2012-12-01

Aircraft occupant crash-safety considerations require a minimum cushion thickness to limit the relative vertical motion of the seat-pelvis during high vertical impact loadings in crash landings or accidents. In military aircraft and helicopter seat design, due to the potential for high vertical accelerations in crash scenarios, the seat system must be provided with an energy absorber to attenuate the acceleration level sustained by the occupants. Because of the limited stroke available for the seat structure, the design of the energy absorber becomes a trade-off problem between minimizing the stroke and maximizing the energy absorption. The available stroke must be used to prevent bottoming out of the seat as well as to absorb maximum impact energy to protect the occupant. In this study, the energy-absorbing system in a rotorcraft seat design is investigated using a mathematical model of the occupant/seat system. Impact theories between interconnected bodies in multibody mechanical systems are utilized to study the impact between the seat pan and the occupant. Experimental responses of the seat system and the occupant are utilized to validate the results from this study for civil and military helicopters according to FAR 23 and 25 and MIL-S-58095 requirements. A model for the load limiter is proposed to minimize the lumbar load for the occupant by minimizing the relative velocity between the seat pan and the occupant's pelvis. The modified energy absorber/load limiter is then implemented for the seat structure so that it absorbs the energy of impact in an effective manner and below the tolerable limit for the occupant in a minimum stroke. Results show that for a designed stroke, the level of occupant lumbar spine injury would be significantly attenuated using this modified energy-absorber system.

Evolutionary Strategies for Protein Folding

NASA Astrophysics Data System (ADS)

Murthy Gopal, Srinivasa; Wenzel, Wolfgang

2006-03-01

The free energy approach for predicting the protein tertiary structure describes the native state of a protein as the global minimum of an appropriate free-energy forcefield. The low-energy region of the free-energy landscape of a protein is extremely rugged. Efficient optimization methods must therefore speed up the search for the global optimum by avoiding high energy transition states, adapt large scale moves or accept unphysical intermediates. Here we investigate an evolutionary strategies(ES) for optimizing a protein conformation in our all-atom free-energy force field([1],[2]). A set of random conformations is evolved using an ES to get a diverse population containing low energy structure. The ES is shown to balance energy improvement and yet maintain diversity in structures. The ES is implemented as a master-client model for distributed computing. Starting from random structures and by using this optimization technique, we were able to fold a 20 amino-acid helical protein and 16 amino-acid beta hairpin[3]. We compare ES to basin hopping method. [1]T. Herges and W. Wenzel,Biophys.J. 87,3100(2004) [2] A. Verma and W. Wenzel Stabilization and folding of beta-sheet and alpha-helical proteins in an all-atom free energy model(submitted)(2005) [3] S. M. Gopal and W. Wenzel Evolutionary Strategies for Protein Folding (in preparation)

Autonomous Sensor Motes Employing Liquid-Bearing Rotary Stages

DTIC Science & Technology

2014-03-06

breaks off (Fig. 27d) as shown in the sudden change in force, indicating rotor pull off. The minimum of each curve indicates the maximum tensile load...configuration, with marks on the curves at the minimum energy positions are shown in Fig. 39. The minimum energy positions from Fig. 39are plotted as...rates between 5 and 17 Hz rotation rate plotted vs. rotor eccentricity. The minimum energy positions are indicated on each curve . 3.3 Discussion

Orientations of dendritic growth during solidification

NASA Astrophysics Data System (ADS)

Lee, Dong Nyung

2017-03-01

Dendrites are crystalline forms which grow far from the limit of stability of the plane front and adopt an orientation which is as close as possible to the heat flux direction. Dendritic growth orientations for cubic metals, bct Sn, and hcp Zn, can be controlled by thermal conductivity, Young's modulus, and surface energy. The control factors have been elaborated. Since the dendrite is a single crystal, its properties such as thermal conductivity that influences the heat flux direction, the minimum Young's modulus direction that influences the strain energy minimization, and the minimum surface energy plane that influences the crystal/liquid interface energy minimization have been proved to control the dendritic growth direction. The dendritic growth directions of cubic metals are determined by the minimum Young's modulus direction and/or axis direction of symmetry of the minimum crystal surface energy plane. The dendritic growth direction of bct Sn is determined by its maximum thermal conductivity direction and the minimum surface energy plane normal direction. The primary dendritic growth direction of hcp Zn is determined by its maximum thermal conductivity direction and the minimum surface energy plane normal direction and the secondary dendrite arm direction of hcp Zn is normal to the primary dendritic growth direction.

Refined energetic ordering for sulphate-water (n = 3-6) clusters using high-level electronic structure calculations

NASA Astrophysics Data System (ADS)

Lambrecht, Daniel S.; McCaslin, Laura; Xantheas, Sotiris S.; Epifanovsky, Evgeny; Head-Gordon, Martin

2012-10-01

This work reports refinements of the energetic ordering of the known low-energy structures of sulphate-water clusters ? (n = 3-6) using high-level electronic structure methods. Coupled cluster singles and doubles with perturbative triples (CCSD(T)) is used in combination with an estimate of basis set effects up to the complete basis set limit using second-order Møller-Plesset theory. Harmonic zero-point energy (ZPE), included at the B3LYP/6-311 + + G(3df,3pd) level, was found to have a significant effect on the energetic ordering. In fact, we show that the energetic ordering is a result of a delicate balance between the electronic and vibrational energies. Limitations of the ZPE calculations, both due to electronic structure errors, and use of the harmonic approximation, probably constitute the largest remaining errors. Due to the often small energy differences between cluster isomers, and the significant role of ZPE, deuteration can alter the relative energies of low-lying structures, and, when it is applied in conjunction with calculated harmonic ZPEs, even alters the global minimum for n = 5. Experiments on deuterated clusters, as well as more sophisticated vibrational calculations, may therefore be quite interesting.

Infrared, Raman and density functional characterization and structural study of 2-Nitro-2-phenyl-propane-1,3-diol

NASA Astrophysics Data System (ADS)

Kaya, Mehmet Fatih; Bağlayan, Özge; Kaya, Esma Güneş; Alver, Özgür

2017-12-01

Nitro compound and nitro derivatives are industrially important to produce rubber and agricultural chemicals. In this study, one of the promising derivatives of nitro compound 2-Nitro-2-phenyl-propane-1,3-diol (2NPP) is examined in detail. FT-Infrared and dispersive Raman spectra of 2NPP (C9H11NO4) were respectively recorded in 4000-10 cm-1 and 4000-100 cm-1. The bond distances and angles, conformational distributions, vibrational frequencies and the assignment of each mode, some thermodynamic parameters and reactivity descriptors: total energy, hardness, chemical potential, electrophilicity index, electronegativity, frontier orbitals energy gap of 2NPP were investigated by using DFT/B3LYP method with 6-31++G (d,p) basis set. In order to locate the global minimum on the potential energy surface of 2NPP, a beforehand conformational examinations were carried out using Spartan 10 along with semi-emprical PM6 method. The results of conformational analyses showed that there are five possible conformations having energies under 2 kcal/mol. Comparison of the theoretical and experimental results clearly indicates that density functional hybrid B3LYP/6-31++G (d,p) level of theory can be used to predict vibrational frequencies and structural parameters of 2NPP. Further, C1 geometry is considered to be the global minimum conformation of 2NPP.

Inherent structures of crystalline pentacene

NASA Astrophysics Data System (ADS)

Della Valle, Raffaele Guido; Venuti, Elisabetta; Brillante, Aldo; Girlando, Alberto

2003-01-01

Using a quasi-Monte Carlo scheme, we search the potential energy surface of crystalline pentacene to sample its local minima, which represent the "inherent" structures, i.e., the possible configurations of mechanical equilibrium. The system is described in terms of rigid molecules interacting through a standard atom-atom potential model. Several hundreds of distinct minima are encountered, with a surprising variety of structural arrangements. We find that deep minima are easily accessible because they exhibit a favorable energy distribution and their attraction basins tend to be wide. Thanks to these features of the potential surface, the localization the global minimum becomes entirely feasible, allowing reliable a priori predictions of the crystallographic structures. The results for pentacene are very satisfactory. In fact, the two deepest minima correspond to the structures of the two known experimental polymorphs, which are described correctly. Further polymorphs are also likely to exist.

Energy consumption program: A computer model simulating energy loads in buildings

NASA Technical Reports Server (NTRS)

Stoller, F. W.; Lansing, F. L.; Chai, V. W.; Higgins, S.

1978-01-01

The JPL energy consumption computer program developed as a useful tool in the on-going building modification studies in the DSN energy conservation project is described. The program simulates building heating and cooling loads and computes thermal and electric energy consumption and cost. The accuracy of computations are not sacrificed, however, since the results lie within + or - 10 percent margin compared to those read from energy meters. The program is carefully structured to reduce both user's time and running cost by asking minimum information from the user and reducing many internal time-consuming computational loops. Many unique features were added to handle two-level electronics control rooms not found in any other program.

The molecular matching problem

NASA Technical Reports Server (NTRS)

Kincaid, Rex K.

1993-01-01

Molecular chemistry contains many difficult optimization problems that have begun to attract the attention of optimizers in the Operations Research community. Problems including protein folding, molecular conformation, molecular similarity, and molecular matching have been addressed. Minimum energy conformations for simple molecular structures such as water clusters, Lennard-Jones microclusters, and short polypeptides have dominated the literature to date. However, a variety of interesting problems exist and we focus here on a molecular structure matching (MSM) problem.

The fabrication of a programmable via using phase-change material in CMOS-compatible technology.

PubMed

Chen, Kuan-Neng; Krusin-Elbaum, Lia

2010-04-02

We demonstrate an energy-efficient programmable via concept using indirectly heated phase-change material. This via structure has maximum phase-change volume to achieve a minimum on resistance for high performance logic applications. Process development and material investigations for this device structure are reported. The device concept is successfully demonstrated in a standard CMOS-compatible technology capable of multiple cycles between on/off states for reconfigurable applications.

Thermodynamics of RNA structures by Wang–Landau sampling

PubMed Central

Lou, Feng; Clote, Peter

2010-01-01

Motivation: Thermodynamics-based dynamic programming RNA secondary structure algorithms have been of immense importance in molecular biology, where applications range from the detection of novel selenoproteins using expressed sequence tag (EST) data, to the determination of microRNA genes and their targets. Dynamic programming algorithms have been developed to compute the minimum free energy secondary structure and partition function of a given RNA sequence, the minimum free-energy and partition function for the hybridization of two RNA molecules, etc. However, the applicability of dynamic programming methods depends on disallowing certain types of interactions (pseudoknots, zig-zags, etc.), as their inclusion renders structure prediction an nondeterministic polynomial time (NP)-complete problem. Nevertheless, such interactions have been observed in X-ray structures. Results: A non-Boltzmannian Monte Carlo algorithm was designed by Wang and Landau to estimate the density of states for complex systems, such as the Ising model, that exhibit a phase transition. In this article, we apply the Wang-Landau (WL) method to compute the density of states for secondary structures of a given RNA sequence, and for hybridizations of two RNA sequences. Our method is shown to be much faster than existent software, such as RNAsubopt. From density of states, we compute the partition function over all secondary structures and over all pseudoknot-free hybridizations. The advantage of the WL method is that by adding a function to evaluate the free energy of arbitary pseudoknotted structures and of arbitrary hybridizations, we can estimate thermodynamic parameters for situations known to be NP-complete. This extension to pseudoknots will be made in the sequel to this article; in contrast, the current article describes the WL algorithm applied to pseudoknot-free secondary structures and hybridizations. Availability: The WL RNA hybridization web server is under construction at http://bioinformatics.bc.edu/clotelab/. Contact: clote@bc.edu PMID:20529917

Structure, Stabilities, Thermodynamic Properties, and IR Spectra of Acetylene Clusters (C2H2)n=2-5.

PubMed

Karthikeyan, S; Lee, Han Myoung; Kim, Kwang S

2010-10-12

There are no clear conclusions over the structures of the acetylene clusters. In this regard, we have carried out high-level calculations for acetylene clusters (C2H2)2-5 using dispersion-corrected density functional theory (DFT-D), Møller-Plesset second-order perturbation theory (MP2); and coupled-cluster theory with single, double, and perturbative triple excitations [CCSD(T)] at the complete basis set limit. The lowest energy structure of the acetylene dimer has a T-shaped structure of C2v symmetry, but it is nearly isoenergetic to the displaced stacked structure of C2h symmetry. We find that the structure shows the quantum statistical distribution for configurations between the T-shaped and displaced stacked structures for which the average angle (|θ̃|) between two acetylene molecules would be 53-78°, close to the T-shaped structure. The trimer has a triangular structure of C3h symmetry. The tetramer has two lowest energy isomers of S4 and C2h symmetry in zero-point energy (ZPE)-uncorrected energy (ΔEe), but one lowest energy isomer of C2v symmetry in ZPE-corrected energy (ΔE0). For the pentamer, the global minimum structure is C1 symmetry with eight sets of T-type π-H interactions and a set of π-π interactions. Our high-level ab initio calculations are consistent with available experimental data.

Wang-Landau density of states based study of the folding-unfolding transition in the mini-protein Trp-cage (TC5b)

NASA Astrophysics Data System (ADS)

Singh, Priya; Sarkar, Subir K.; Bandyopadhyay, Pradipta

2014-07-01

We present the results of a high-statistics equilibrium study of the folding/unfolding transition for the 20-residue mini-protein Trp-cage (TC5b) in water. The ECEPP/3 force field is used and the interaction with water is treated by a solvent-accessible surface area method. A Wang-Landau type simulation is used to calculate the density of states and the conditional probabilities for the various values of the radius of gyration and the number of native contacts at fixed values of energy—along with a systematic check on their convergence. All thermodynamic quantities of interest are calculated from this information. The folding-unfolding transition corresponds to a peak in the temperature dependence of the computed specific heat. This is corroborated further by the structural signatures of folding in the distributions for radius of gyration and the number of native contacts as a function of temperature. The potentials of mean force are also calculated for these variables, both separately and jointly. A local free energy minimum, in addition to the global minimum, is found in a temperature range substantially below the folding temperature. The free energy at this second minimum is approximately 5 kBT higher than the value at the global minimum.

Continuum Theory of Retroviral Capsids

NASA Astrophysics Data System (ADS)

Nguyen, T. T.; Bruinsma, R. F.; Gelbart, W. M.

2006-02-01

We present a self-assembly phase diagram for the shape of retroviral capsids, based on continuum elasticity theory. The spontaneous curvature of the capsid proteins drives a weakly first-order transition from spherical to spherocylindrical shapes. The conical capsid shape which characterizes the HIV-1 retrovirus is never stable under unconstrained energy minimization. Only under conditions of fixed volume and/or fixed spanning length can the conical shape be a minimum energy structure. Our results indicate that, unlike the capsids of small viruses, retrovirus capsids are not uniquely determined by the molecular structure of the constituent proteins but depend in an essential way on physical constraints present during assembly.

Theoretical study of Ag doping-induced vacancies defects in armchair graphene

NASA Astrophysics Data System (ADS)

Benchallal, L.; Haffad, S.; Lamiri, L.; Boubenider, F.; Zitoune, H.; Kahouadji, B.; Samah, M.

2018-06-01

We have performed a density functional theory (DFT) study of the absorption of silver atoms (Ag,Ag2 and Ag3) in graphene using SIESTA code, in the generalized gradient approximation (GGA). The absorption energy, geometry, magnetic moments and charge transfer of Ag clusters-graphene system are calculated. The minimum energy configuration demonstrates that all structures remain planar and silver atoms fit into this plane. The charge transfer between the silver clusters and carbon atoms constituting the graphene surface is an indicative of a strong bond. The structure doped with a single silver atom has a magnetic moment and the two other are nonmagnetic.

Phenomena of nonlinear oscillation and special resonance of a dielectric elastomer minimum energy structure rotary joint

NASA Astrophysics Data System (ADS)

Zhao, Jianwen; Niu, Junyang; McCoul, David; Ren, Zhi; Pei, Qibing

2015-03-01

The dielectric elastomer minimum energy structure can realize large angular deformations by a small voltage-induced strain of the dielectric elastomer, so it is a suitable candidate to make a rotary joint for a soft robot. Driven with an alternating electric field, the joint deformation vibrational frequency follows the input voltage frequency. However, the authors find that if the rotational inertia increases such that the inertial torque makes the frame deform over a negative angle, then the joint motion will become complicated and the vibrational mode will alter with the change of voltage frequency. The vibration with the largest amplitude does not occur while the voltage frequency is equal to natural response frequency of the joint. Rather, the vibrational amplitude will be quite large over a range of other frequencies at which the vibrational frequency is half of the voltage frequency. This phenomenon was analyzed by a comparison of the timing sequences between voltage and joint vibration. This vibrational mode with the largest amplitude can be applied to the generation lift in a flapping wing actuated by dielectric elastomers.

The effect of tidal forces on the minimum energy configurations of the full three-body problem

NASA Astrophysics Data System (ADS)

Levine, Edward

We investigate the evolution of minimum energy configurations for the Full Three Body Problem (3BP). A stable ternary asteroid system will gradually become unstable due to the Yarkovsky-O'Keefe-Radzievskii-Paddack (YORP) effect and an unpredictable trajectory will ensue. Through the interaction of tidal torques, energy in the system will dissipate in the form of heat until a stable minimum energy configuration is reached. We present a simulation that describes the dynamical evolution of three bodies under the mutual effects of gravity and tidal torques. Simulations show that bodies do not get stuck in local minima and transition to the predicted minimum energy configuration.

Collectivity and manifestations of minimum-bias jets in high-energy nuclear collisions

NASA Astrophysics Data System (ADS)

Trainor, Thomas A.

2018-01-01

Collectivity, as interpreted to mean flow of a dense medium in high-energy A-A collisions described by hydrodynamics, has been attributed to smaller collision systems - p-A and even p-p collisions - based on recent analysis of LHC data. However, alternative methods reveal that some data features attributed to flows are actually manifestations of minimum-bias (MB) jets. In this presentation I review the differential structure of single-particle pt spectra from SPS to LHC energies in the context of a two-component (soft + hard) model (TCM) of hadron production. I relate the spectrum hard component to measured properties of isolated jets. I use the spectrum TCM to predict accurately the systematics of ensemble-mean p̅t in p-p, p-A and A-A collision systems over a large energy interval. Detailed comparisons of the TCM with spectrum and correlation data suggest that MB jets play a dominant role in hadron production near midrapidity. Claimed flow phenomena are better explained as jet manifestations agreeing quantitatively with measured jet properties.

Towards black-box calculations of tunneling splittings obtained from vibrational structure methods based on normal coordinates.

PubMed

Neff, Michael; Rauhut, Guntram

2014-02-05

Multidimensional potential energy surfaces obtained from explicitly correlated coupled-cluster calculations and further corrections for high-order correlation contributions, scalar relativistic effects and core-correlation energy contributions were generated in a fully automated fashion for the double-minimum benchmark systems OH3(+) and NH3. The black-box generation of the potentials is based on normal coordinates, which were used in the underlying multimode expansions of the potentials and the μ-tensor within the Watson operator. Normal coordinates are not the optimal choice for describing double-minimum potentials and the question remains if they can be used for accurate calculations at all. However, their unique definition is an appealing feature, which removes remaining errors in truncated potential expansions arising from different choices of curvilinear coordinate systems. Fully automated calculations are presented, which demonstrate, that the proposed scheme allows for the determination of energy levels and tunneling splittings as a routine application. Copyright © 2013 Elsevier B.V. All rights reserved.

Monopolar vortices as relative equilibria and their dissipative decay

NASA Astrophysics Data System (ADS)

Vandefliert, B. W.; Vangroesen, E. W. C.

1991-11-01

Families of confined rotating monopolar vortices are characterized using a variational formulation with the angular momentum as the driving force for confinement. The characterization for positive monopolar vortices given, can be extended to negative vortices or to vortices within a rotating frame of reference. Besides the uniform Kirchhoff paths, new branches of vorticity solutions are found restricting the dynamics to levelsets of both the angular momentum and the quadratic anisotropy. The rotation rate of the smooth vorticity structures depends on the vorticity profile. This is made perceptible by considering both minimum energy vortices and minimizing vortices, rotating counterclockwise and clockwise respectively. An approximation for the decay of the vortices due to dissipation is given in terms of the dissipation of the integrals in the inviscid system. This description enables us to consider dissipation of vortices without loss of confinement. The elliptical Kirchhoff patches are found to symmetrize into circular patches. The minimum energy vortices gradually diminish while expending their support, while the maximum energy vortices are unstable for the dissipative evolution.

Electric Vehicles Mileage Extender Kinetic Energy Storage

NASA Astrophysics Data System (ADS)

Jivkov, Venelin; Draganov, Vutko; Stoyanova, Yana

2015-03-01

The proposed paper considers small urban vehicles with electric hybrid propulsion systems. Energy demands are examined on the basis of European drive cycle (NEUDC) and on an energy recuperation coefficient and are formulated for description of cycle energy transfers. Numerical simulation results show real possibilities for increasing in achievable vehicle mileage at the same energy levels of a main energy source - the electric battery. Kinetic energy storage (KES), as proposed to be used as an energy buffer and different structural schemes of the hybrid propulsion system are commented. Minimum energy levels for primary (the electric battery) and secondary (KES) sources are evaluated. A strategy for reduced power flows control is examined, and its impact on achievable vehicle mileage is investigated. Results show an additional increase in simulated mileage at the same initial energy levels.

Electronic effects on melting: Comparison of aluminum cluster anions and cations

NASA Astrophysics Data System (ADS)

Starace, Anne K.; Neal, Colleen M.; Cao, Baopeng; Jarrold, Martin F.; Aguado, Andrés; López, José M.

2009-07-01

Heat capacities have been measured as a function of temperature for aluminum cluster anions with 35-70 atoms. Melting temperatures and latent heats are determined from peaks in the heat capacities; cohesive energies are obtained for solid clusters from the latent heats and dissociation energies determined for liquid clusters. The melting temperatures, latent heats, and cohesive energies for the aluminum cluster anions are compared to previous measurements for the corresponding cations. Density functional theory calculations have been performed to identify the global minimum energy geometries for the cluster anions. The lowest energy geometries fall into four main families: distorted decahedral fragments, fcc fragments, fcc fragments with stacking faults, and "disordered" roughly spherical structures. The comparison of the cohesive energies for the lowest energy geometries with the measured values allows us to interpret the size variation in the latent heats. Both geometric and electronic shell closings contribute to the variations in the cohesive energies (and latent heats), but structural changes appear to be mainly responsible for the large variations in the melting temperatures with cluster size. The significant charge dependence of the latent heats found for some cluster sizes indicates that the electronic structure can change substantially when the cluster melts.

A Simple ab initio Model for the Hydrated Electron that Matches Experiment

PubMed Central

Kumar, Anil; Walker, Jonathan A.; Bartels, David M.; Sevilla, Michael D.

2015-01-01

Since its discovery over 50 years ago, the “structure” and properties of the hydrated electron has been a subject for wonderment and also fierce debate. In the present work we seriously explore a minimal model for the aqueous electron, consisting of a small water anion cluster embedded in a polarized continuum, using several levels of ab initio calculation and basis set. The minimum energy zero “Kelvin” structure found for any 4-water (or larger) anion cluster, at any post-Hartree-Fock theory level, is very similar to a recently reported embedded-DFT-in-classical-water-MD simulation (UMJ: Uhlig, Marsalek, and Jungwirth, Journal of Physical Chemistry Letters 2012, 3, 3071-5), with four OH bonds oriented toward the maximum charge density in a small central “void”. The minimum calculation with just four water molecules does a remarkably good job of reproducing the resonance Raman properties, the radius of gyration derived from the optical spectrum, the vertical detachment energy, and the hydration free energy. For the first time we also successfully calculate the EPR g-factor and (low temperature ice) hyperfine couplings. The simple tetrahedral anion cluster model conforms very well to experiment, suggesting it does in fact represent the dominant structural motif of the hydrated electron. PMID:26275103

Temporal change in the electromechanical properties of dielectric elastomer minimum energy structures

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

Buchberger, G., E-mail: erda.buchberger@jku.at; Hauser, B.; Jakoby, B.

Dielectric elastomer minimum energy structures (DEMES) are soft electronic transducers and energy harvesters with potential for consumer goods. The temporal change in their electromechanical properties is of major importance for engineering tasks. Therefore, we study acrylic DEMES by impedance spectroscopy and by optical methods for a total time period of approx. 4.5 months. We apply either compliant electrodes from carbon black particles only or fluid electrodes from a mixture of carbon black particles and silicone oil. From the measurement data, the equivalent series capacitances and resistances as well as the bending angles of the transducers are obtained. We find thatmore » the equivalent series capacitances change in average between −12 %/1000 h and −4.0 %/1000 h, while the bending angles decrease linearly with slopes ranging from −15 %/1000 h to −7 %/1000 h. Transducers with high initial bending angles and electrodes from carbon black particles show the smallest changes of the electromechanical characteristics. The capacitances decrease faster for DEMES with fluid electrodes. Some DEMES of this type reveal huge and unpredictable fluctuations of the resistances over time due to the ageing of the contacts. Design guidelines for DEMES follow directly from the observed transient changes of their electromechanical performance.« less

Theoretical study of the interaction of N/sub 2/ with water molecules. (H/sub 2/O)/sub n/:N/sub 2/, n = 1--8

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

Curtiss, L.A.; Eisgruber, C.L.

1984-03-01

Ab initio molecular orbital calculations including correlation energy have been carried out on the interaction of a single H/sub 2/O molecule with N/sub 2/. The potential energy surface for H/sub 2/O:N/sub 2/ is found to have a minimum corresponding to a HOH xxx N/sub 2/ structure with a weak (<2 kcal mol/sup -1/) hydrogen bond. A second, less stable, configuration corresponding to a H/sub 2/O xxx N/sub 2/ structure with N/sub 2/ bonded side on to the oxygen of H/sub 2/O was found to be either a minimum or a saddle point in the potential energy surface depending on themore » level of calculation. The minimal STO-3G basis set was used to investigate the interaction of up to eight H/sub 2/O molecules with N/sub 2/. Two types of clusters, one containing only HOH xxx N/sub 2/ interactions and the other containing both HOH xxxN/sub 2/ and H/sub 2/O xxx N/sub 2/ interactions, were investigated for (N/sub 2/:(H/sub 2/O)/sub n/, n = 2--8).« less

Isomers and energy landscapes of micro-hydrated sulfite and chlorate clusters

NASA Astrophysics Data System (ADS)

Hey, John C.; Doyle, Emily J.; Chen, Yuting; Johnston, Roy L.

2018-03-01

We present putative global minima for the micro-hydrated sulfite SO32-(H2O)N and chlorate ClO32(H2O)N systems in the range 3≤N≤15 found using basin-hopping global structure optimization with an empirical potential. We present a structural analysis of the hydration of a large number of minimized structures for hydrated sulfite and chlorate clusters in the range 3≤N≤50. We show that sulfite is a significantly stronger net acceptor of hydrogen bonding within water clusters than chlorate, completely suppressing the appearance of hydroxyl groups pointing out from the cluster surface (dangling OH bonds), in low-energy clusters. We also present a qualitative analysis of a highly explored energy landscape in the region of the global minimum of the eight water hydrated sulfite and chlorate systems. This article is part of the theme issue `Modern theoretical chemistry'.

Isomers and energy landscapes of micro-hydrated sulfite and chlorate clusters.

PubMed

Hey, John C; Doyle, Emily J; Chen, Yuting; Johnston, Roy L

2018-03-13

We present putative global minima for the micro-hydrated sulfite SO 3 2- (H 2 O) N and chlorate ClO 3 - (H 2 O) N systems in the range 3≤ N ≤15 found using basin-hopping global structure optimization with an empirical potential. We present a structural analysis of the hydration of a large number of minimized structures for hydrated sulfite and chlorate clusters in the range 3≤ N ≤50. We show that sulfite is a significantly stronger net acceptor of hydrogen bonding within water clusters than chlorate, completely suppressing the appearance of hydroxyl groups pointing out from the cluster surface (dangling OH bonds), in low-energy clusters. We also present a qualitative analysis of a highly explored energy landscape in the region of the global minimum of the eight water hydrated sulfite and chlorate systems.This article is part of the theme issue 'Modern theoretical chemistry'. © 2018 The Authors.

Mechanics of tunable helices and geometric frustration in biomimetic seashells

NASA Astrophysics Data System (ADS)

Guo, Qiaohang; Chen, Zi; Li, Wei; Dai, Pinqiang; Ren, Kun; Lin, Junjie; Taber, Larry A.; Chen, Wenzhe

2014-03-01

Helical structures are ubiquitous in nature and engineering, ranging from DNA molecules to plant tendrils, from sea snail shells to nanoribbons. While the helical shapes in natural and engineered systems often exhibit nearly uniform radius and pitch, helical shell structures with changing radius and pitch, such as seashells and some plant tendrils, add to the variety of this family of aesthetic beauty. Here we develop a comprehensive theoretical framework for tunable helical morphologies, and report the first biomimetic seashell-like structure resulting from mechanics of geometric frustration. In previous studies, the total potential energy is everywhere minimized when the system achieves equilibrium. In this work, however, the local energy minimization cannot be realized because of the geometric incompatibility, and hence the whole system deforms into a shape with a global energy minimum whereby the energy in each segment may not necessarily be locally optimized. This novel approach can be applied to develop materials and devices of tunable geometries with a range of applications in nano/biotechnology.

Investigation of the electronic, magnetic and optical properties of newest carbon allotrope

NASA Astrophysics Data System (ADS)

Kazemi, Samira; Moradian, Rostam

2018-05-01

We investigate triple properties of monolayer pentagon graphene that include electronic, magnetic and optical properties based on density functional theory (DFT). Our results show that in the electronic and magnetic properties this structure with a direct energy gap of about 2.2 eV along Γ - Γ direction and total magnetic moment of 0.0013 μB per unit cell is almost a non-magnetic semiconductor. Also, its optical properties show that if this allotrope used in solar cell technology, its efficiency in the low energy will be better, because, in the range of energy, its loss energy function and reflectivity will be minimum.

From molecule to solid: The prediction of organic crystal structures

NASA Astrophysics Data System (ADS)

Dzyabchenko, A. V.

2008-10-01

A method for predicting the structure of a molecular crystal based on the systematic search for a global potential energy minimum is considered. The method takes into account unequal occurrences of the structural classes of organic crystals and symmetry of the multidimensional configuration space. The programs of global minimization PMC, comparison of crystal structures CRYCOM, and approximation to the distributions of the electrostatic potentials of molecules FitMEP are presented as tools for numerically solving the problem. Examples of predicted structures substantiated experimentally and the experience of author’s participation in international tests of crystal structure prediction organized by the Cambridge Crystallographic Data Center (Cambridge, UK) are considered.

Electronic structures and geometries of the XF{sub 3} (X = Cl, Br, I, At) fluorides

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

Sergentu, Dumitru-Claudiu; CEISAM, UMR CNRS 6230, Université de Nantes, 2 Rue de la Houssinière, BP 92208, 44322 Nantes Cedex 3; Amaouch, Mohamed

The potential energy surfaces of the group 17 XF{sub 3} (X = Cl, Br, I, At) fluorides have been investigated for the first time with multiconfigurational wave function theory approaches. In agreement with experiment, bent T-shaped C{sub 2v} structures are computed for ClF{sub 3}, BrF{sub 3}, and IF{sub 3}, while we predict that an average D{sub 3h} structure would be experimentally observed for AtF{sub 3}. Electron correlation and scalar relativistic effects strongly reduce the energy difference between the D{sub 3h} geometry and the C{sub 2v} one, along the XF{sub 3} series, and in the X = At case, spin-orbit couplingmore » also slightly reduces this energy difference. AtF{sub 3} is a borderline system where the D{sub 3h} structure becomes a minimum, i.e., the pseudo-Jahn-Teller effect is inhibited since electron correlation and scalar-relativistic effects create small energy barriers leading to the global C{sub 2v} minima, although both types of effects interfere.« less

Physical nature of ethidium and proflavine interactions with nucleic acid bases in the intercalation plane.

PubMed

Langner, Karol M; Kedzierski, Pawel; Sokalski, W Andrzej; Leszczynski, Jerzy

2006-05-18

On the basis of the crystallographic structures of three nucleic acid intercalation complexes involving ethidium and proflavine, we have analyzed the interaction energies between intercalator chromophores and their four nearest bases, using a hybrid variation-perturbation method at the second-order Møller-Plesset theory level (MP2) with a 6-31G(d,p) basis set. A total MP2 interaction energy minimum precisely reproduces the crystallographic position of the ethidium chromophore in the intercalation plane between UA/AU bases. The electrostatic component constitutes the same fraction of the total energy for all three studied structures. The multipole electrostatic interaction energy, calculated from cumulative atomic multipole moments (CAMMs), was found to converge only after including components above the fifth order. CAMM interaction surfaces, calculated on grids in the intercalation planes of these structures, reasonably reproduce the alignment of intercalators in crystal structures; they exhibit additional minima in the direction of the DNA grooves, however, which also need to be examined at higher theory levels if no crystallographic data are given.

High speed reaction wheels for satellite attitude control and energy storage

NASA Technical Reports Server (NTRS)

Studer, P.; Rodriguez, E.

1985-01-01

The combination of spacecraft attitude control and energy storage (ACES) functions in common hardware, to synergistically maintain three-axis attitude control while supplying electrical power during earth orbital eclipses, allows the generation of control torques by high rotating speed wheels that react against the spacecraft structure via a high efficiency bidirectional energy conversion motor/generator. An ACES system encompasses a minimum of four wheels, controlling power and the three torque vectors. Attention is given to the realization of such a system with composite flywheel rotors that yield high energy density, magnetic suspension technology yielding low losses at high rotational speeds, and an ironless armature permanent magnet motor/generator yielding high energy conversion efficiency.

Oxygen enhanced switching to combustion of lower rank fuels

DOEpatents

Kobayashi, Hisashi; Bool, III, Lawrence E.; Wu, Kuang Tsai

2004-03-02

A furnace that combusts fuel, such as coal, of a given minimum energy content to obtain a stated minimum amount of energy per unit of time is enabled to combust fuel having a lower energy content, while still obtaining at least the stated minimum energy generation rate, by replacing a small amount of the combustion air fed to the furnace by oxygen. The replacement of oxygen for combustion air also provides reduction in the generation of NOx.

Vibrational spectroscopic and structural investigations on fullerene: A DFT approach

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

Christy, P. Anto; Premkumar, S.; Asath, R. Mohamed

2016-05-06

The molecular structure of fullerene (C{sub 60}) molecule was optimized by the DFT/B3LYP method with 6-31G and 6-31G(d,p) basis sets using Gaussian 09 program. The vibrational frequencies were calculated for the optimized molecular structure of the molecule. The calculated vibrational frequencies confirm that the molecular structure of the molecule was located at the minimum energy potential energy surface. The calculated vibrational frequencies were assigned on the basis of functional group analysis and also confirmed using the GaussView 05 software. The frontier molecular orbitals analysis was carried out. The FMOs related molecular properties were predicted. The higher ionization potential, higher electronmore » affinity, higher softness, lower band gap energy and lower hardness values were obtained, which confirm that the fullerene molecule has a higher molecular reactivity. The Mulliken atomic charge distribution of the molecule was also calculated. Hence, these results play an important role due to its potential applications as drug delivery devices.« less

Machine learning prediction for classification of outcomes in local minimisation

NASA Astrophysics Data System (ADS)

Das, Ritankar; Wales, David J.

2017-01-01

Machine learning schemes are employed to predict which local minimum will result from local energy minimisation of random starting configurations for a triatomic cluster. The input data consists of structural information at one or more of the configurations in optimisation sequences that converge to one of four distinct local minima. The ability to make reliable predictions, in terms of the energy or other properties of interest, could save significant computational resources in sampling procedures that involve systematic geometry optimisation. Results are compared for two energy minimisation schemes, and for neural network and quadratic functions of the inputs.

RNAdualPF: software to compute the dual partition function with sample applications in molecular evolution theory.

PubMed

Garcia-Martin, Juan Antonio; Bayegan, Amir H; Dotu, Ivan; Clote, Peter

2016-10-19

RNA inverse folding is the problem of finding one or more sequences that fold into a user-specified target structure s 0 , i.e. whose minimum free energy secondary structure is identical to the target s 0 . Here we consider the ensemble of all RNA sequences that have low free energy with respect to a given target s 0 . We introduce the program RNAdualPF, which computes the dual partition function Z ∗ , defined as the sum of Boltzmann factors exp(-E(a,s 0 )/RT) of all RNA nucleotide sequences a compatible with target structure s 0 . Using RNAdualPF, we efficiently sample RNA sequences that approximately fold into s 0 , where additionally the user can specify IUPAC sequence constraints at certain positions, and whether to include dangles (energy terms for stacked, single-stranded nucleotides). Moreover, since we also compute the dual partition function Z ∗ (k) over all sequences having GC-content k, the user can require that all sampled sequences have a precise, specified GC-content. Using Z ∗ , we compute the dual expected energy 〈E ∗ 〉, and use it to show that natural RNAs from the Rfam 12.0 database have higher minimum free energy than expected, thus suggesting that functional RNAs are under evolutionary pressure to be only marginally thermodynamically stable. We show that C. elegans precursor microRNA (pre-miRNA) is significantly non-robust with respect to mutations, by comparing the robustness of each wild type pre-miRNA sequence with 2000 [resp. 500] sequences of the same GC-content generated by RNAdualPF, which approximately [resp. exactly] fold into the wild type target structure. We confirm and strengthen earlier findings that precursor microRNAs and bacterial small noncoding RNAs display plasticity, a measure of structural diversity. We describe RNAdualPF, which rapidly computes the dual partition function Z ∗ and samples sequences having low energy with respect to a target structure, allowing sequence constraints and specified GC-content. Using different inverse folding software, another group had earlier shown that pre-miRNA is mutationally robust, even controlling for compositional bias. Our opposite conclusion suggests a cautionary note that computationally based insights into molecular evolution may heavily depend on the software used. C/C++-software for RNAdualPF is available at http://bioinformatics.bc.edu/clotelab/RNAdualPF .

Extended Plate and Beam Wall System

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

Gunderson, Patti

Home Innovation Research Labs studied the extended plate and beam wall (EP&B) system during a two-year period from mid-2015 to mid-2017 to determine the wall’s structural performance, moisture durability, constructability, and costeffectiveness for use as a high-R enclosure system for energy code minimum and above-code performance in climate zones 4–8.

Parameterized study of the ionospheric modification associated with sun-aligned polar cap arcs

NASA Technical Reports Server (NTRS)

Crain, D. J.; Sojka, J. J.; Schunk, R. W.; Zhu, L.

1993-01-01

The local ionospheric modification that is due to a generalized steady state solar aligned (SA) arc structure is addressed. For a representative set of SA arc parameters which includes both convection and precipitation, emphasis is placed on the modification by SA polar cap arcs upon the F region electron density and the height integrated conductivity. At low fluxes and low characteristic energies, SA polar cap arcs have the most pronounced relative effect at F region altitudes in darkness for winter solar minimum conditions. The absolute enhancement in summer solar minimum and winter solar maximum is equivalent to that of winter solar minimum, but the higher ambient densities make the relative enhancement less. The TEC enhancement associated with an SA arc may be used to indicate the degree of plasma cross flow across the arc.

Deformation bands, the LEDS theory, and their importance in texture development: Part II. Theoretical conclusions

NASA Astrophysics Data System (ADS)

Kuhlmann-Wilsdorf, D.

1999-09-01

The facts regarding “regular” deformation bands (DBs) outlined in Part I of this series of articles are related to the low-energy dislocation structure (LEDS) theory of dislocation-based plasticity. They prompt an expansion of the theory by including the stresses due to strain gradients on account of changing selections of slip systems to the previously known dislocation driving forces. This last and until now neglected driving force is much smaller than the components considered hitherto, principally due to the applied stress and to mutual stress-screening among neighbor dislocations. As a result, it permits a near-proof of the LEDS hypothesis, to wit that among all structures which, in principle, are accessible to the dislocations, that one is realized which has the lowest free energy. Specifically, the temperature rises that would result from annihilating the largest DBs amount to only several millidegrees Centigrade, meaning that they, and by implication the entire dislocation structures, are close to thermodynamical equilibrium. This is in stark contrast to the assumption of the presently widespread self-organizing dislocation structures (SODS) modeling that plastic deformation occurs far from equilibrium and is subject to Prigogine’s thermodynamics of energy-flow-through systems. It also holds out promise for future rapid advances in the construction of constitutive equations, since the LEDS hypothesis is the principal basis of the LEDS theory of plastic deformation and follows directly from the second law of thermodynamics in conjunction with Newton’s third law. By contrast, all other known models of metal plasticity are in conflict with the LEDS hypothesis. In regard to texture modeling, the present analysis shows that Taylor’s criterion of minimum plastic work is incorrect and should be replaced by the criterion of minimum free energy in the stressed state. Last, the LEDS hypothesis is but a special case of the more general low-energy structure (LES) hypothesis, applying to plastic deformation independent of the deformation mechanism. It is thus seen that plastic deformation is one of nature’s means to generate order, as a byproduct of the entropy generation when mechanical work is largely converted into heat.

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

PubMed

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

2013-07-01

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

Metastable phases of silver and gold in hexagonal structure

NASA Astrophysics Data System (ADS)

Jona, F.; Marcus, P. M.

2004-07-01

Metastable phases of silver and gold in hexagonal close-packed structures are investigated by means of first-principles total-energy calculations. Two different methods are employed to find the equilibrium states: determination of the minima along the hexagonal epitaxial Bain path, and direct determination of minima of the total energy by a new minimum-path procedure. Both metals have two equilibrium states at different values of the hexagonal axial ratio c/a. For both metals, the elastic constants show that the high-c/a states are stable, hence, since the ground states are face-centred cubic, these states represent hexagonal close-packed metastable phases. The elastic constants of the low-c/a states show that they are unstable.

Genetic-evolution-based optimization methods for engineering design

NASA Technical Reports Server (NTRS)

Rao, S. S.; Pan, T. S.; Dhingra, A. K.; Venkayya, V. B.; Kumar, V.

1990-01-01

This paper presents the applicability of a biological model, based on genetic evolution, for engineering design optimization. Algorithms embodying the ideas of reproduction, crossover, and mutation are developed and applied to solve different types of structural optimization problems. Both continuous and discrete variable optimization problems are solved. A two-bay truss for maximum fundamental frequency is considered to demonstrate the continuous variable case. The selection of locations of actuators in an actively controlled structure, for minimum energy dissipation, is considered to illustrate the discrete variable case.

Quantifying Hydrogen Bond Cooperativity in Water: VRT Spectroscopy of the Water Tetramer

NASA Astrophysics Data System (ADS)

Cruzan, J. D.; Braly, L. B.; Liu, Kun; Brown, M. G.; Loeser, J. G.; Saykally, R. J.

1996-01-01

Measurement of the far-infrared vibration-rotation tunneling spectrum of the perdeuterated water tetramer is described. Precisely determined rotational constants and relative intensity measurements indicate a cyclic quasi-planar minimum energy structure, which is in agreement with recent ab initio calculations. The O-O separation deduced from the data indicates a rapid exponential convergence to the ordered bulk value with increasing cluster size. Observed quantum tunneling splittings are interpreted in terms of hydrogen bond rearrangements connecting two degenerate structures.

Applications of molecular modeling in coal research

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

Carlson, G.A.; Faulon, J.L.

Over the past several years, molecular modeling has been applied to study various characteristics of coal molecular structures. Powerful workstations coupled with molecular force-field-based software packages have been used to study coal and coal-related molecules. Early work involved determination of the minimum-energy three-dimensional conformations of various published coal structures (Given, Wiser, Solomon and Shinn), and the dominant role of van der Waals and hydrogen bonding forces in defining the energy-minimized structures. These studies have been extended to explore various physical properties of coal structures, including density, microporosity, surface area, and fractal dimension. Other studies have related structural characteristics to cross-linkmore » density and have explored small molecule interactions with coal. Finally, recent studies using a structural elucidation (molecular builder) technique have constructed statistically diverse coal structures based on quantitative and qualitative data on coal and its decomposition products. This technique is also being applied to study coalification processes based on postulated coalification chemistry.« less

Experimental investigations of the minimum ignition energy and the minimum ignition temperature of inert and combustible dust cloud mixtures.

PubMed

Addai, Emmanuel Kwasi; Gabel, Dieter; Krause, Ulrich

2016-04-15

The risks associated with dust explosions still exist in industries that either process or handle combustible dust. This explosion risk could be prevented or mitigated by applying the principle of inherent safety (moderation). This is achieved by adding an inert material to a highly combustible material in order to decrease the ignition sensitivity of the combustible dust. The presented paper deals with the experimental investigation of the influence of adding an inert dust on the minimum ignition energy and the minimum ignition temperature of the combustible/inert dust mixtures. The experimental investigation was done in two laboratory scale equipment: the Hartmann apparatus and the Godbert-Greenwald furnace for the minimum ignition energy and the minimum ignition temperature test respectively. This was achieved by mixing various amounts of three inert materials (magnesium oxide, ammonium sulphate and sand) and six combustible dusts (brown coal, lycopodium, toner, niacin, corn starch and high density polyethylene). Generally, increasing the inert materials concentration increases the minimum ignition energy as well as the minimum ignition temperatures until a threshold is reached where no ignition was obtained. The permissible range for the inert mixture to minimize the ignition risk lies between 60 to 80%. Copyright © 2016 Elsevier B.V. All rights reserved.

Pseudo paths towards minimum energy states in network dynamics

NASA Astrophysics Data System (ADS)

Hedayatifar, L.; Hassanibesheli, F.; Shirazi, A. H.; Vasheghani Farahani, S.; Jafari, G. R.

2017-10-01

The dynamics of networks forming on Heider balance theory moves towards lower tension states. The condition derived from this theory enforces agents to reevaluate and modify their interactions to achieve equilibrium. These possible changes in network's topology can be considered as various paths that guide systems to minimum energy states. Based on this theory the final destination of a system could reside on a local minimum energy, ;jammed state;, or the global minimum energy, balanced states. The question we would like to address is whether jammed states just appear by chance? Or there exist some pseudo paths that bound a system towards a jammed state. We introduce an indicator to suspect the location of a jammed state based on the Inverse Participation Ratio method (IPR). We provide a margin before a local minimum where the number of possible paths dramatically drastically decreases. This is a condition that proves adequate for ending up on a jammed states.

Minimum airflow reset of single-duct VAV terminal boxes

NASA Astrophysics Data System (ADS)

Cho, Young-Hum

Single duct Variable Air Volume (VAV) systems are currently the most widely used type of HVAC system in the United States. When installing such a system, it is critical to determine the minimum airflow set point of the terminal box, as an optimally selected set point will improve the level of thermal comfort and indoor air quality (IAQ) while at the same time lower overall energy costs. In principle, this minimum rate should be calculated according to the minimum ventilation requirement based on ASHRAE standard 62.1 and maximum heating load of the zone. Several factors must be carefully considered when calculating this minimum rate. Terminal boxes with conventional control sequences may result in occupant discomfort and energy waste. If the minimum rate of airflow is set too high, the AHUs will consume excess fan power, and the terminal boxes may cause significant simultaneous room heating and cooling. At the same time, a rate that is too low will result in poor air circulation and indoor air quality in the air-conditioned space. Currently, many scholars are investigating how to change the algorithm of the advanced VAV terminal box controller without retrofitting. Some of these controllers have been found to effectively improve thermal comfort, indoor air quality, and energy efficiency. However, minimum airflow set points have not yet been identified, nor has controller performance been verified in confirmed studies. In this study, control algorithms were developed that automatically identify and reset terminal box minimum airflow set points, thereby improving indoor air quality and thermal comfort levels, and reducing the overall rate of energy consumption. A theoretical analysis of the optimal minimum airflow and discharge air temperature was performed to identify the potential energy benefits of resetting the terminal box minimum airflow set points. Applicable control algorithms for calculating the ideal values for the minimum airflow reset were developed and applied to actual systems for performance validation. The results of the theoretical analysis, numeric simulations, and experiments show that the optimal control algorithms can automatically identify the minimum rate of heating airflow under actual working conditions. Improved control helps to stabilize room air temperatures. The vertical difference in the room air temperature was lower than the comfort value. Measurements of room CO2 levels indicate that when the minimum airflow set point was reduced it did not adversely affect the indoor air quality. According to the measured energy results, optimal control algorithms give a lower rate of reheating energy consumption than conventional controls.

A general intermolecular force field based on tight-binding quantum chemical calculations

NASA Astrophysics Data System (ADS)

Grimme, Stefan; Bannwarth, Christoph; Caldeweyher, Eike; Pisarek, Jana; Hansen, Andreas

2017-10-01

A black-box type procedure is presented for the generation of a molecule-specific, intermolecular potential energy function. The method uses quantum chemical (QC) information from our recently published extended tight-binding semi-empirical scheme (GFN-xTB) and can treat non-covalently bound complexes and aggregates with almost arbitrary chemical structure. The necessary QC information consists of the equilibrium structure, Mulliken atomic charges, charge centers of localized molecular orbitals, and also of frontier orbitals and orbital energies. The molecular pair potential includes model density dependent Pauli repulsion, penetration, as well as point charge electrostatics, the newly developed D4 dispersion energy model, Drude oscillators for polarization, and a charge-transfer term. Only one element-specific and about 20 global empirical parameters are needed to cover systems with nuclear charges up to radon (Z = 86). The method is tested for standard small molecule interaction energy benchmark sets where it provides accurate intermolecular energies and equilibrium distances. Examples for structures with a few hundred atoms including charged systems demonstrate the versatility of the approach. The method is implemented in a stand-alone computer code which enables rigid-body, global minimum energy searches for molecular aggregation or alignment.

Dynamical Bifurcation in Gas-Phase XH- + CH3 Y SN 2 Reactions: The Role of Energy Flow and Redistribution in Avoiding the Minimum Energy Path.

PubMed

Proenza, Yaicel G; de Souza, Miguel A F; Longo, Ricardo L

2016-11-02

The gas-phase reactions of XH - (X=O, S) + CH 3 Y (Y=F, Cl, Br) span nearly the whole range of S N 2 pathways, and show an intrinsic reaction coordinate (IRC) (minimum energy path) with a deep well owing to the CH 3 XH⋅⋅⋅Y - (or CH 3 S - ⋅⋅⋅HF) hydrogen-bonded postreaction complex. MP2 quasiclassical-type direct dynamics starting at the [HX⋅⋅⋅CH 3 ⋅⋅⋅Y] - transition-state (TS) structure reveal distinct mechanistic behaviors. Trajectories that yield the separated CH 3 XH+Y - (or CH 3 S - +HF) products directly are non-IRC, whereas those that sample the CH 3 XH⋅⋅⋅Y - (or CH 3 S - ⋅⋅⋅HF) complex are IRC. The IRCIRC/non-IRC ratios of 90:10, 40:60, 25:75, 2:98, 0:100, and 0:100 are obtained for (X, Y)=(S, F), (O, F), (S, Cl), (S, Br), (O, Cl), and (O, Br), respectively. The properties of the energy profiles after the TS cannot provide a rationalization of these results. Analysis of the energy flow in dynamics shows that the trajectories cross a dynamical bifurcation, and that the inability to follow the minimum energy path arises from long vibration periods of the X-C⋅⋅⋅Y bending mode. The partition of the available energy to the products into vibrational, rotational, and translational energies reveals that if the vibrational contribution is more than 80 %, non-IRC behavior dominates, unless the relative fraction of the rotational and translational components is similar, in which case a richer dynamical mechanism is shown, with an IRC/non-IRC ratio that correlates to this relative fraction. © 2016 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Insights into geometries, stabilities, electronic structures, reactivity descriptors, and magnetic properties of bimetallic Nim Cun-m (m = 1, 2; n = 3-13) clusters: Comparison with pure copper clusters.

PubMed

Singh, Raman K; Iwasa, Takeshi; Taketsugu, Tetsuya

2018-05-25

A long-range corrected density functional theory (LC-DFT) was applied to study the geometric structures, relative stabilities, electronic structures, reactivity descriptors and magnetic properties of the bimetallic NiCu n -1 and Ni 2 Cu n -2 (n = 3-13) clusters, obtained by doping one or two Ni atoms to the lowest energy structures of Cu n , followed by geometry optimizations. The optimized geometries revealed that the lowest energy structures of the NiCu n -1 and Ni 2 Cu n -2 clusters favor the Ni atom(s) situated at the most highly coordinated position of the host copper clusters. The averaged binding energy, the fragmentation energies and the second-order energy differences signified that the Ni doped clusters can continue to gain an energy during the growth process. The electronic structures revealed that the highest occupied molecular orbital and the lowest unoccupied molecular orbital energies of the LC-DFT are reliable and can be used to predict the vertical ionization potential and the vertical electron affinity of the systems. The reactivity descriptors such as the chemical potential, chemical hardness and electrophilic power, and the reactivity principle such as the minimum polarizability principle are operative for characterizing and rationalizing the electronic structures of these clusters. Moreover, doping of Ni atoms into the copper clusters carry most of the total spin magnetic moment. © 2018 Wiley Periodicals, Inc. © 2018 Wiley Periodicals, Inc.

The cost of energy from utility-owned solar electric systems. A required revenue methodology for ERDA/EPRI evaluations

NASA Technical Reports Server (NTRS)

1976-01-01

This methodology calculates the electric energy busbar cost from a utility-owned solar electric system. This approach is applicable to both publicly- and privately-owned utilities. Busbar cost represents the minimum price per unit of energy consistent with producing system-resultant revenues equal to the sum of system-resultant costs. This equality is expressed in present value terms, where the discount rate used reflects the rate of return required on invested capital. Major input variables describe the output capabilities and capital cost of the energy system, the cash flows required for system operation amd maintenance, and the financial structure and tax environment of the utility.

Excited state conformational dynamics in carotenoids: dark intermediates and excitation energy transfer.

PubMed

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

2015-04-15

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

Demonstration of a Wingless Electromagnetic Air Vehicle

DTIC Science & Technology

2011-12-20

moving parts and assures near instantaneous response time. For the first time, the aircraft structure, propulsion, energy production and storage, and...of an electromagnetically driven wingless aircraft * with no moving component that will be able to self- lift, hover and fly reliably especially...8217&)?$@&;! First successful lift-off using plasma propulsion. Main Achievement Aerogel actuators are thus far the lightest plasma actuators with minimum

Free energy decomposition of protein-protein interactions.

PubMed

Noskov, S Y; Lim, C

2001-08-01

A free energy decomposition scheme has been developed and tested on antibody-antigen and protease-inhibitor binding for which accurate experimental structures were available for both free and bound proteins. Using the x-ray coordinates of the free and bound proteins, the absolute binding free energy was computed assuming additivity of three well-defined, physical processes: desolvation of the x-ray structures, isomerization of the x-ray conformation to a nearby local minimum in the gas-phase, and subsequent noncovalent complex formation in the gas phase. This free energy scheme, together with the Generalized Born model for computing the electrostatic solvation free energy, yielded binding free energies in remarkable agreement with experimental data. Two assumptions commonly used in theoretical treatments; viz., the rigid-binding approximation (which assumes no conformational change upon complexation) and the neglect of vdW interactions, were found to yield large errors in the binding free energy. Protein-protein vdW and electrostatic interactions between complementary surfaces over a relatively large area (1400--1700 A(2)) were found to drive antibody-antigen and protease-inhibitor binding.

ARGO-YBJ OBSERVATION OF THE LARGE-SCALE COSMIC RAY ANISOTROPY DURING THE SOLAR MINIMUM BETWEEN CYCLES 23 AND 24

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

Bartoli, B.; Catalanotti, S.; Piazzoli, B. D’Ettorre

2015-08-10

This paper reports on the measurement of the large-scale anisotropy in the distribution of cosmic-ray arrival directions using the data collected by the air shower detector ARGO-YBJ from 2008 January to 2009 December, during the minimum of solar activity between cycles 23 and 24. In this period, more than 2 × 10{sup 11} showers were recorded with energies between ∼1 and 30 TeV. The observed two-dimensional distribution of cosmic rays is characterized by two wide regions of excess and deficit, respectively, both of relative intensity ∼10{sup −3} with respect to a uniform flux, superimposed on smaller size structures. The harmonicmore » analysis shows that the large-scale cosmic-ray relative intensity as a function of R.A. can be described by the first and second terms of a Fouries series. The high event statistics allow the study of the energy dependence of the anistropy, showing that the amplitude increases with energy, with a maximum intensity at ∼10 TeV, and then decreases while the phase slowly shifts toward lower values of R.A. with increasing energy. The ARGO-YBJ data provide accurate observations over more than a decade of energy around this feature of the anisotropy spectrum.« less

Recent developments in the theory of protein folding: searching for the global energy minimum.

PubMed

Scheraga, H A

1996-04-16

Statistical mechanical theories and computer simulation are being used to gain an understanding of the fundamental features of protein folding. A major obstacle in the computation of protein structures is the multiple-minima problem arising from the existence of many local minima in the multidimensional energy landscape of the protein. This problem has been surmounted for small open-chain and cyclic peptides, and for regular-repeating sequences of models of fibrous proteins. Progress is being made in resolving this problem for globular proteins.

Impact of Rate Design Alternatives on Residential Solar Customer Bills. Increased Fixed Charges, Minimum Bills and Demand-based Rates

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

Bird, Lori; Davidson, Carolyn; McLaren, Joyce

With rapid growth in energy efficiency and distributed generation, electric utilities are anticipating stagnant or decreasing electricity sales, particularly in the residential sector. Utilities are increasingly considering alternative rates structures that are designed to recover fixed costs from residential solar photovoltaic (PV) customers with low net electricity consumption. Proposed structures have included fixed charge increases, minimum bills, and increasingly, demand rates - for net metered customers and all customers. This study examines the electricity bill implications of various residential rate alternatives for multiple locations within the United States. For the locations analyzed, the results suggest that residential PV customers offset,more » on average, between 60% and 99% of their annual load. However, roughly 65% of a typical customer's electricity demand is non-coincidental with PV generation, so the typical PV customer is generally highly reliant on the grid for pooling services.« less

Detailed study of the water trimer potential energy surface

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

Fowler, J.E.; Schaefer, H.F. III

The potential energy surface of the water trimer has been studied through the use of ab initio quantum mechanical methods. Five stationary points were located, including one minimum and two transition states. All geometries were optimized at levels up to the double-[Zeta] plus polarization plus diffuse (DZP + diff) single and double excitation coupled cluster (CCSD) level of theory. CCSD single energy points were obtained for the minimum, two transition states, and the water monomer using the triple-[Zeta] plus double polarization plus diffuse (TZ2P + diff) basis at the geometries predicted by the DZP + diff CCSD method. Reported aremore » the following: geometrical parameters, total and relative energies, harmonic vibrational frequencies and infrared intensities for the minimum, and zero point vibrational energies for the minimum, two transition states, and three separated water molecules. 27 refs., 5 figs., 10 tabs.« less

Energy band structure and electrical properties of Ga-oxide/GaN interface formed by remote oxygen plasma

NASA Astrophysics Data System (ADS)

Yamamoto, Taishi; Taoka, Noriyuki; Ohta, Akio; Truyen, Nguyen Xuan; Yamada, Hisashi; Takahashi, Tokio; Ikeda, Mitsuhisa; Makihara, Katsunori; Nakatsuka, Osamu; Shimizu, Mitsuaki; Miyazaki, Seiichi

2018-06-01

The energy band structure of a Ga-oxide/GaN structure formed by remote oxygen plasma exposure and the electrical interface properties of the GaN metal–oxide–semiconductor (MOS) capacitors with the SiO2/Ga-oxide/GaN structures with postdeposition annealing (PDA) at various temperatures have been investigated. Reflection high-energy electron diffraction and X-ray photoelectron spectroscopy clarified that the formed Ga-oxide layer is neither a single nor polycrystalline phase with high crystallinity. We found that the energy band offsets at the conduction band minimum and at the valence band maximum between the Ga-oxide layer and the GaN surface were 0.4 and 1.2 ± 0.2 eV, respectively. Furthermore, capacitance–voltage (C–V) characteristics revealed that the interface trap density (D it) is lower than the evaluation limit of Terman method without depending on the PDA temperatures, and that the SiO2/Ga-oxide stack can work as a protection layer to maintain the low D it, avoiding the significant decomposition of GaN at the high PDA temperature of 800 °C.

Calculation of the structure of carbon clusters based on fullerene-like C24 and C48 molecules

NASA Astrophysics Data System (ADS)

Krylova, K. A.; Baimova, Yu. A.; Dmitriev, S. V.; Mulyukov, R. R.

2016-02-01

Equilibrium structures obtained by linking with valence bonds the carbon carcasses of two fullerene-like molecules have been studied by molecular dynamics simulation. In free fullerene, carbon atoms form sp 2 hybridized bonds, but at places of links between fullerenes, sp 3 hybridized bonds are formed, which determines the changes in the properties of such structures. In the literature, the topology of diamond-like phases is described, but equilibrium clusters based on fullerene-like molecules are underexplored. The right angles between the C-C bonds are energetically unfavorable, and the reduction in the energy of clusters in the process of relaxation is connected with the optimization of valence angles, which leads to a reduction in the symmetry of clusters and, in a number of cases, even to disruption of some valence bonds. It is shown that different fashions of linking two fullerenes result in the formation of clusters with different structures and energies. Different initial conditions can lead to different configurations of clusters with the same topology. Among the analyzed clusters, a structure with the minimum potential energy per atom was found. The results of this work contribute to the study of the real structure of carbon clusters.

Can two H2 molecules be inserted into C60 - an accurate first-principles exploration of structural, energetic and vibrational properties of the 2H2@C60 complex

NASA Astrophysics Data System (ADS)

Dolgonos, Grygoriy A.; Peslherbe, Gilles H.

2016-10-01

The 2H2@C60 minimum structure of C2 symmetry has been fully characterized at the density-fitting local second-order Møller-Plesset (DF-LMP2) level of theory. Its uncorrected and zero-point energy (ZPE) corrected complexation energies equal 1.9 and 6.2 kcal/mol, respectively, confirming the instability of the complex. This structure exhibits the largest intermolecular host-guest and guest-guest separations among all the complexes studied in this work. The calculated infrared spectrum of 2H2@C60 does not show any frequency shifts for the modes associated with radial or tangential displacements in C60 (except for one mode), but shows a weak red Hsbnd H vibrational frequency shift.

Studying the varied shapes of gold clusters by an elegant optimization algorithm that hybridizes the density functional tight-binding theory and the density functional theory

NASA Astrophysics Data System (ADS)

Yen, Tsung-Wen; Lim, Thong-Leng; Yoon, Tiem-Leong; Lai, S. K.

2017-11-01

We combined a new parametrized density functional tight-binding (DFTB) theory (Fihey et al. 2015) with an unbiased modified basin hopping (MBH) optimization algorithm (Yen and Lai 2015) and applied it to calculate the lowest energy structures of Au clusters. From the calculated topologies and their conformational changes, we find that this DFTB/MBH method is a necessary procedure for a systematic study of the structural development of Au clusters but is somewhat insufficient for a quantitative study. As a result, we propose an extended hybridized algorithm. This improved algorithm proceeds in two steps. In the first step, the DFTB theory is employed to calculate the total energy of the cluster and this step (through running DFTB/MBH optimization for given Monte-Carlo steps) is meant to efficiently bring the Au cluster near to the region of the lowest energy minimum since the cluster as a whole has explicitly considered the interactions of valence electrons with ions, albeit semi-quantitatively. Then, in the second succeeding step, the energy-minimum searching process will continue with a skilledly replacement of the energy function calculated by the DFTB theory in the first step by one calculated in the full density functional theory (DFT). In these subsequent calculations, we couple the DFT energy also with the MBH strategy and proceed with the DFT/MBH optimization until the lowest energy value is found. We checked that this extended hybridized algorithm successfully predicts the twisted pyramidal structure for the Au40 cluster and correctly confirms also the linear shape of C8 which our previous DFTB/MBH method failed to do so. Perhaps more remarkable is the topological growth of Aun: it changes from a planar (n =3-11) → an oblate-like cage (n =12-15) → a hollow-shape cage (n =16-18) and finally a pyramidal-like cage (n =19, 20). These varied forms of the cluster's shapes are consistent with those reported in the literature.

Swellix: a computational tool to explore RNA conformational space.

PubMed

Sloat, Nathan; Liu, Jui-Wen; Schroeder, Susan J

2017-11-21

The sequence of nucleotides in an RNA determines the possible base pairs for an RNA fold and thus also determines the overall shape and function of an RNA. The Swellix program presented here combines a helix abstraction with a combinatorial approach to the RNA folding problem in order to compute all possible non-pseudoknotted RNA structures for RNA sequences. The Swellix program builds on the Crumple program and can include experimental constraints on global RNA structures such as the minimum number and lengths of helices from crystallography, cryoelectron microscopy, or in vivo crosslinking and chemical probing methods. The conceptual advance in Swellix is to count helices and generate all possible combinations of helices rather than counting and combining base pairs. Swellix bundles similar helices and includes improvements in memory use and efficient parallelization. Biological applications of Swellix are demonstrated by computing the reduction in conformational space and entropy due to naturally modified nucleotides in tRNA sequences and by motif searches in Human Endogenous Retroviral (HERV) RNA sequences. The Swellix motif search reveals occurrences of protein and drug binding motifs in the HERV RNA ensemble that do not occur in minimum free energy or centroid predicted structures. Swellix presents significant improvements over Crumple in terms of efficiency and memory use. The efficient parallelization of Swellix enables the computation of sequences as long as 418 nucleotides with sufficient experimental constraints. Thus, Swellix provides a practical alternative to free energy minimization tools when multiple structures, kinetically determined structures, or complex RNA-RNA and RNA-protein interactions are present in an RNA folding problem.

Electron Heat Flux in Pressure Balance Structures at Ulysses

NASA Technical Reports Server (NTRS)

Yamauchi, Yohei; Suess, Steven T.; Sakurai, Takashi; Whitaker, Ann F. (Technical Monitor)

2001-01-01

Pressure balance structures (PBSs) are a common feature in the high-latitude solar wind near solar minimum. Rom previous studies, PBSs are believed to be remnants of coronal plumes and be related to network activity such as magnetic reconnection in the photosphere. We investigated the magnetic structures of the PBSs, applying a minimum variance analysis to Ulysses/Magnetometer data. At 2001 AGU Spring meeting, we reported that PBSs have structures like current sheets or plasmoids, and suggested that they are associated with network activity at the base of polar plumes. In this paper, we have analyzed high-energy electron data at Ulysses/SWOOPS to see whether bi-directional electron flow exists and confirm the conclusions more precisely. As a result, although most events show a typical flux directed away from the Sun, we have obtained evidence that some PBSs show bi-directional electron flux and others show an isotropic distribution of electron pitch angles. The evidence shows that plasmoids are flowing away from the Sun, changing their flow direction dynamically in a way not caused by Alfven waves. From this, we have concluded that PBSs are generated due to network activity at the base of polar plumes and their magnetic structures axe current sheets or plasmoids.

RandSpg: An open-source program for generating atomistic crystal structures with specific spacegroups

NASA Astrophysics Data System (ADS)

Avery, Patrick; Zurek, Eva

2017-04-01

A new algorithm, RANDSPG, that can be used to generate trial crystal structures with specific space groups and compositions is described. The program has been designed for systems where the atoms are independent of one another, and it is therefore primarily suited towards inorganic systems. The structures that are generated adhere to user-defined constraints such as: the lattice shape and size, stoichiometry, set of space groups to be generated, and factors that influence the minimum interatomic separations. In addition, the user can optionally specify if the most general Wyckoff position is to be occupied or constrain select atoms to specific Wyckoff positions. Extensive testing indicates that the algorithm is efficient and reliable. The library is lightweight, portable, dependency-free and is published under a license recognized by the Open Source Initiative. A web interface for the algorithm is publicly accessible at http://xtalopt.openmolecules.net/randSpg/randSpg.html. RANDSPG has also been interfaced with the XTALOPT evolutionary algorithm for crystal structure prediction, and it is illustrated that the use of symmetric lattices in the first generation of randomly created individuals decreases the number of structures that need to be optimized to find the global energy minimum.

On the physical basis of succussion.

PubMed

Torres, J L

2002-10-01

It is argued that succussion drives the homeopathic tincture undergoing potentisation to a turbulent regime, where vortices continually form and disappear, ranging in size from the linear extent of the container to a minimum scale determined by viscosity and the rate of energy dissipation. Input mechanical energy cascades down this population of eddies and becomes available at the microscopic level to perform work (chemical, electrical, etc). A structure generated in the tincture would be rupted by vortices smaller than it, and this sets definite limits on the strength of succussion, so the power input leads to larger vortices than the structures one is trying to create and preserve through potentisation. An experimental procedure to test this proposal is suggested, based on Rayleigh scattering.

Theoretical investigations on diamondoids (CnHm, n = 10-41): Nomenclature, structural stabilities, and gap distributions

NASA Astrophysics Data System (ADS)

Wang, Ya-Ting; Zhao, Yu-Jun; Liao, Ji-Hai; Yang, Xiao-Bao

2018-01-01

Combining the congruence check and the first-principles calculations, we have systematically investigated the structural stabilities and gap distributions of possible diamondoids (CnHm) with the carbon numbers (n) from 10 to 41. A simple method for the nomenclature is proposed, which can be used to distinguish and screen the candidates with high efficiency. Different from previous theoretical studies, the possible diamondoids can be enumerated according to our nomenclature, without any pre-determination from experiments. The structural stabilities and electronic properties have been studied by density functional based tight binding and first-principles methods, where a nearly linear correlation is found between the energy gaps obtained by these two methods. According to the formation energy of structures, we have determined the stable configurations as a function of chemical potential. The maximum and minimum energy gaps are found to be dominated by the shape of diamondoids for clusters with a given number of carbon atoms, while the gap decreases in general as the size increases due to the quantum confinement.

The surface energy of water: functional implications of hexagonal/cuboidal transformations in the surface arrays.

PubMed

Widdas, W F

2006-10-30

Hyde's scientific book The Language of Shape has emphasized the importance of minimum surfaces in the structure of biological membranes. Minimum surfaces can be visualized as the property which brings many droplets of liquids to spherical bubbles, since a sphere has the minimum surface to volume ratio. Thus, a sphere with a surface of 4pir2 and volume of 4/3pir3 has a surface to volume ratio of 3/r, that is, the ratio is dependent upon the reciprocal of the radius. The chemistry of water as dihydrides of the electronegative element oxygen is fundamentally dependent upon its polar properties and particularly the delta positive charges on the hydrogen atoms and the double delta negative charge on the larger oxygen atom, which from its mass (16 Da) is regarded as the centre of the water molecules. The cohesion of water as a liquid or as semi-crystal like structures in the surface depends upon electrostatic forces that are comparable in strength to covalent bonds. This review discusses the functional implications of some unexpected properties which have been evinced by model building and illustrated as a Poster in the 4th World Congress of Cellular and Molecular Biology.

Molecular mechanisms of hydrogen loaded B-hydroquinone clathrate

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

Daschbach, John L.; Chang, Tsun-Mei; Corrales, Louis R.

2006-09-07

Molecular dynamics simulations are used to investigate the molecular interactions of hydrogen loaded beta-hydroquinone clathrate. It is found that at lower temperatures, higher loadings are more stable, whereas, at higher temperatures, lower loadings are more stable. This trend can be understood based on the interactions in the system. For loadings greater than one, the repulsive forces between the guest molecules shove each other towards the attractive forces between the guest and host molecules leading to a stabilized minimum energy configuration at low temperatures. At higher temperatures greater displacements take the system away from the shallow energy minimum and the trendmore » reverses. The asymmetries of the clathrate cage structure are due to the presence of the attractive forces at loadings greater than one that lead to confined states. The nature of the cavity structure is nearly spherical for a loading of one, leads to preferential occupation near the hydroxyl ring crowns of the cavity with a loading of two, and at higher loadings, leads to occupation of the interstitial sites (the hydroxyl rings) between cages by a single H2 molecule with the remaining molecules occupying the equatorial plane of the cavity. At higher temperatures, the cavity is more uniformly occupied for all loadings, where the occupation of the interstitial positions of the cavities leads to facile diffusion. ACKNOWLEDGEMENT This work was partially supported by NIDO (Japan), LDRD (PNNL), EERE U.S. Department of Energy, and by OBES, U.S. DOE. The Pacific Northwest National Laboratory is operated by Battelle for the U.S. Department of Energy« less

A parallel implementation of the Wuchty algorithm with additional experimental filters to more thoroughly explore RNA conformational space.

PubMed

Stone, Jonathan W; Bleckley, Samuel; Lavelle, Sean; Schroeder, Susan J

2015-01-01

We present new modifications to the Wuchty algorithm in order to better define and explore possible conformations for an RNA sequence. The new features, including parallelization, energy-independent lonely pair constraints, context-dependent chemical probing constraints, helix filters, and optional multibranch loops, provide useful tools for exploring the landscape of RNA folding. Chemical probing alone may not necessarily define a single unique structure. The helix filters and optional multibranch loops are global constraints on RNA structure that are an especially useful tool for generating models of encapsidated viral RNA for which cryoelectron microscopy or crystallography data may be available. The computations generate a combinatorially complete set of structures near a free energy minimum and thus provide data on the density and diversity of structures near the bottom of a folding funnel for an RNA sequence. The conformational landscapes for some RNA sequences may resemble a low, wide basin rather than a steep funnel that converges to a single structure.

Ascent trajectory optimization for stratospheric airship with thermal effects

NASA Astrophysics Data System (ADS)

Guo, Xiao; Zhu, Ming

2013-09-01

Ascent trajectory optimization with thermal effects is addressed for a stratospheric airship. Basic thermal characteristics of the stratospheric airship are introduced. Besides, the airship’s equations of motion are constructed by including the factors about aerodynamic force, added mass and wind profiles which are developed based on horizontal-wind model. For both minimum-time and minimum-energy flights during ascent, the trajectory optimization problem is described with the path and terminal constraints in different scenarios and then, is converted into a parameter optimization problem by a direct collocation method. Sparse Nonlinear OPTimizer(SNOPT) is employed as a nonlinear programming solver and two scenarios are adopted. The solutions obtained illustrate that the trajectories are greatly affected by the thermal behaviors which prolong the daytime minimum-time flights of about 20.8% compared with that of nighttime in scenario 1 and of about 10.5% in scenario 2. And there is the same trend for minimum-energy flights. For the energy consumption of minimum-time flights, 6% decrease is abstained in scenario 1 and 5% decrease in scenario 2. However, a few energy consumption reduction is achieved for minimum-energy flights. Solar radiation is the principal component and the natural wind also affects the thermal behaviors of stratospheric airship during ascent. The relationship between take-off time and performance of airship during ascent is discussed. it is found that the take-off time at dusk is best choice for stratospheric airship. And in addition, for saving energy, airship prefers to fly downwind.

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

Do, Hainam, E-mail: h.do@nottingham.ac.uk, E-mail: richard.wheatley@nottingham.ac.uk; Wheatley, Richard J., E-mail: h.do@nottingham.ac.uk, E-mail: richard.wheatley@nottingham.ac.uk

A robust and model free Monte Carlo simulation method is proposed to address the challenge in computing the classical density of states and partition function of solids. Starting from the minimum configurational energy, the algorithm partitions the entire energy range in the increasing energy direction (“upward”) into subdivisions whose integrated density of states is known. When combined with the density of states computed from the “downward” energy partitioning approach [H. Do, J. D. Hirst, and R. J. Wheatley, J. Chem. Phys. 135, 174105 (2011)], the equilibrium thermodynamic properties can be evaluated at any temperature and in any phase. The methodmore » is illustrated in the context of the Lennard-Jones system and can readily be extended to other molecular systems and clusters for which the structures are known.« less

Holmium Doped Solid State Laser Resonantly Pumped and Q-Switched by Novel GaSb-Based Photonic Devices

DTIC Science & Technology

2011-08-31

dominant role of inter valence band absorption [7]. Details of the conduction band structure of the particular 0 20 40 60 80 100 0 10 20 30 CW 30s...here the n-cladding composition resulted into material with three valleys in conduction band to have almost the same energy minimum so no inter...emitting GaSb -based diode lasers was improved by utilization of the waveguide structure with asymmetric claddings. The AlGaAsSb p-cladding contained

Energies of the X- and L-valleys in In{sub 0.53}Ga{sub 0.47}As from electronic structure calculations

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

Greene-Diniz, Gabriel; Greer, J. C.; Fischetti, M. V.

2016-02-07

Several theoretical electronic structure methods are applied to study the relative energies of the minima of the X- and L-conduction-band satellite valleys of In{sub x}Ga{sub 1−x}As with x = 0.53. This III-V semiconductor is a contender as a replacement for silicon in high-performance n-type metal-oxide-semiconductor transistors. The energy of the low-lying valleys relative to the conduction-band edge governs the population of channel carriers as the transistor is brought into inversion, hence determining current drive and switching properties at gate voltages above threshold. The calculations indicate that the position of the L- and X-valley minima are ∼1 eV and ∼1.2 eV, respectively, higher in energymore » with respect to the conduction-band minimum at the Γ-point.« less

Inner reorganization limiting electron transfer controlled hydrogen bonding: intra- vs. intermolecular effects.

PubMed

Martínez-González, Eduardo; Frontana, Carlos

2014-05-07

In this work, experimental evidence of the influence of the electron transfer kinetics during electron transfer controlled hydrogen bonding between anion radicals of metronidazole and ornidazole, derivatives of 5-nitro-imidazole, and 1,3-diethylurea as the hydrogen bond donor, is presented. Analysis of the variations of voltammetric EpIcvs. log KB[DH], where KB is the binding constant, allowed us to determine the values of the binding constant and also the electron transfer rate k, confirmed by experiments obtained at different scan rates. Electronic structure calculations at the BHandHLYP/6-311++G(2d,2p) level for metronidazole, including the solvent effect by the Cramer/Truhlar model, suggested that the minimum energy conformer is stabilized by intramolecular hydrogen bonding. In this structure, the inner reorganization energy, λi,j, contributes significantly (0.5 eV) to the total reorganization energy of electron transfer, thus leading to a diminishment of the experimental k.

Ion nose spectral structures observed by the Van Allen Probes

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

Ferradas, C. P.; Zhang, J. -C.; Spence, H. E.

Here, we present a statistical study of nose-like structures observed in energetic hydrogen, helium, and oxygen ions near the inner edge of the plasma sheet. Nose structures are spectral features named after the characteristic shapes of energy bands or gaps in the energy-time spectrograms of in situ measured ion fluxes. Using 22 months of observations from the Helium Oxygen Proton Electron (HOPE) instrument onboard Van Allen Probe A, we determine the number of noses observed, and the minimum L-shell reached and energy of each nose on each pass through the inner magnetosphere. We find that multiple noses occur more frequentlymore » in heavy ions than in H +, and are most often observed during quiet times. The heavy-ion noses penetrate to lower L shells than H + noses and there is an energy-magnetic local time (MLT) dependence in the nose locations and energies that is similar for all species. The observations are interpreted using a steady-state model of ion drift in the inner magnetosphere. The model is able to explain the energy and MLT dependence of the different types of nose structures. Different ion charge exchange lifetimes are the main cause for the deeper penetration of heavy-ion noses. The species dependence and preferred geomagnetic conditions of multiple-nose events indicate that they must be on long drift paths, leading to strong charge-exchange effects. The results provide important insight into the spatial distribution, species dependence, and geomagnetic conditions under which nose structures occur.« less

Ion nose spectral structures observed by the Van Allen Probes

DOE PAGES

Ferradas, C. P.; Zhang, J. -C.; Spence, H. E.; ...

2016-11-22

Here, we present a statistical study of nose-like structures observed in energetic hydrogen, helium, and oxygen ions near the inner edge of the plasma sheet. Nose structures are spectral features named after the characteristic shapes of energy bands or gaps in the energy-time spectrograms of in situ measured ion fluxes. Using 22 months of observations from the Helium Oxygen Proton Electron (HOPE) instrument onboard Van Allen Probe A, we determine the number of noses observed, and the minimum L-shell reached and energy of each nose on each pass through the inner magnetosphere. We find that multiple noses occur more frequentlymore » in heavy ions than in H +, and are most often observed during quiet times. The heavy-ion noses penetrate to lower L shells than H + noses and there is an energy-magnetic local time (MLT) dependence in the nose locations and energies that is similar for all species. The observations are interpreted using a steady-state model of ion drift in the inner magnetosphere. The model is able to explain the energy and MLT dependence of the different types of nose structures. Different ion charge exchange lifetimes are the main cause for the deeper penetration of heavy-ion noses. The species dependence and preferred geomagnetic conditions of multiple-nose events indicate that they must be on long drift paths, leading to strong charge-exchange effects. The results provide important insight into the spatial distribution, species dependence, and geomagnetic conditions under which nose structures occur.« less

Ion nose spectral structures observed by the Van Allen Probes

NASA Astrophysics Data System (ADS)

Ferradas, C. P.; Zhang, J.-C.; Spence, H. E.; Kistler, L. M.; Larsen, B. A.; Reeves, G.; Skoug, R.; Funsten, H.

2016-12-01

We present a statistical study of nose-like structures observed in energetic hydrogen, helium, and oxygen ions near the inner edge of the plasma sheet. Nose structures are spectral features named after the characteristic shapes of energy bands or gaps in the energy-time spectrograms of in situ measured ion fluxes. Using 22 months of observations from the Helium Oxygen Proton Electron instrument onboard Van Allen Probe A, we determine the number of noses observed, and the minimum L shell reached and energy of each nose on each pass through the inner magnetosphere. We find that multiple noses occur more frequently in heavy ions than in H+ and are most often observed during quiet times. The heavy-ion noses penetrate to lower L shells than H+ noses, and there is an energy-magnetic local time (MLT) dependence in the nose locations and energies that is similar for all species. The observations are interpreted by using a steady state model of ion drift in the inner magnetosphere. The model is able to explain the energy and MLT dependence of the different types of nose structures. Different ion charge-exchange lifetimes are the main cause for the deeper penetration of heavy-ion noses. The species dependence and preferred geomagnetic conditions of multiple-nose events indicate that they must be on long drift paths, leading to strong charge-exchange effects. The results provide important insight into the spatial distribution, species dependence, and geomagnetic conditions under which nose structures occur.

Leanergy(TM): how lean manufacturing can improve energy efficiency.

PubMed

Riche, Jean-Pierre

2013-01-01

Energy efficiency has become a competitive issue for industrial companies. The evolution of energy prices and regulation will make this issue even more important in the future. For several years, the energy-intensive chemical industry has been implementing corrective actions. Helped by the absorption of base load energy consumption by larger production volumes, specific energy consumption (KWh per production unit) has been significantly reduced in recent years. However, most plants have reached the end of their first action plan based on improving the utilities performance. The Leanergy(TM) method developed by the consultancy company Okavango-energy, is a structured approach based on lean manufacturing which widens the scope of saving sources to process and operations. Starting from the analysis of actual production requirements, Okavango is able to adjust consumption to minimum requirements and so remove any energy consumption that does not contribute to the added value creation.

Structure and screening in molecular and metallic hydrogen at high pressure

NASA Technical Reports Server (NTRS)

Wood, D. M.; Ashcroft, N. W.

1981-01-01

A variational wavefunction is used to express the (spin restricted) Hartree-Fock energy as reciprocal lattice sums for static lattice FCC monatomic hydrogen and diatomic Pa3 molecular hydrogen. In the monatomic phase the hydrogenic orbital range closely parallels the inverse Thomas-Fermi wavevector; the corresponding energy E has a minimum of -0.929 Ryd/electron at r sub s = 1.67. For the diatomic phase E(r sub s) is similar, but the constituent energies, screening, and bond length reflect a qualitative change in the nature of the solid at r sub s = 2.8. This change is interpreted in terms of a transition from protons as structural units (at high density) to weakly interacting models (at low density). Insensitivity of the total energy to a rapid fall in the bond length suggests association with the rotational transition where the rapid molecular orientations characteristic of high pressures disappear and the molecules rotate freely at low pressure.

Heteroaromatic π-Stacking Energy Landscapes

PubMed Central

2014-01-01

In this study we investigate π-stacking interactions of a variety of aromatic heterocycles with benzene using dispersion corrected density functional theory. We calculate extensive potential energy surfaces for parallel-displaced interaction geometries. We find that dispersion contributes significantly to the interaction energy and is complemented by a varying degree of electrostatic interactions. We identify geometric preferences and minimum interaction energies for a set of 13 5- and 6-membered aromatic heterocycles frequently encountered in small drug-like molecules. We demonstrate that the electrostatic properties of these systems are a key determinant for their orientational preferences. The results of this study can be applied in lead optimization for the improvement of stacking interactions, as it provides detailed energy landscapes for a wide range of coplanar heteroaromatic geometries. These energy landscapes can serve as a guide for ring replacement in structure-based drug design. PMID:24773380

Molecular structure and vibrational assignments of 2,4-dichlorophenoxyacetic acid herbicide

NASA Astrophysics Data System (ADS)

Badawi, Hassan M.

2010-09-01

The structural stability of 2,4-dichlorophenoxyacetic acid was investigated by the DFT-B3LYP and the ab initio MP2 calculations with the 6-311G** basis set. From the calculations at both levels of theory the Cgcpp structure was predicted to be the lowest energy minimum for the acid. The DFT and the MP2 levels disagreed about the nature of the second stable structure of 2,4-dichlorophenoxyacetic acid. At the DFT-B3LYP level of calculation the planar Tttp ( transoid O dbnd C sbnd O sbnd H) and the non-planar Tgcpp ( cisoid O dbnd C sbnd O sbnd H) forms were predicted to be 0.7 and 1.5 kcal/mol, respectively higher in energy than the Cgcpp conformation. At the MP2 level the two high energy Tttp and Tgcpp forms were predicted to be 2.7 and 1.4 kcal/mol, respectively higher in energy than the ground state Cgcpp structure. The Tgcpp form was adopted as the second possible structure of 2,4-dichlorophenoxyacetic acid on the basis of the fact that the Møller-Plesset calculations account better than the DFT ones for the non-bonding O⋯H interactions. The vibrational frequencies of the lowest energy Cgcpp conformer were computed at the B3LYP level of theory and tentative vibrational assignments were provided on the basis of normal coordinate analysis and experimental infrared and Raman data.

Electronic and magnetic properties of small rhodium clusters

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

Soon, Yee Yeen; Yoon, Tiem Leong; Lim, Thong Leng

2015-04-24

We report a theoretical study of the electronic and magnetic properties of rhodium-atomic clusters. The lowest energy structures at the semi-empirical level of rhodium clusters are first obtained from a novel global-minimum search algorithm, known as PTMBHGA, where Gupta potential is used to describe the atomic interaction among the rhodium atoms. The structures are then re-optimized at the density functional theory (DFT) level with exchange-correlation energy approximated by Perdew-Burke-Ernzerhof generalized gradient approximation. For the purpose of calculating the magnetic moment of a given cluster, we calculate the optimized structure as a function of the spin multiplicity within the DFT framework.more » The resultant magnetic moments with the lowest energies so obtained allow us to work out the magnetic moment as a function of cluster size. Rhodium atomic clusters are found to display a unique variation in the magnetic moment as the cluster size varies. However, Rh{sub 4} and Rh{sub 6} are found to be nonmagnetic. Electronic structures of the magnetic ground-state structures are also investigated within the DFT framework. The results are compared against those based on different theoretical approaches available in the literature.« less

Ferromagnetic core valve gives rapid action on minimum energy

NASA Technical Reports Server (NTRS)

Larson, A. V.; Tinkham, J. P.

1967-01-01

Miniature solenoid valve controls propellant flow during tests on a coaxial plasma accelerator. It uses an advanced ferromagnetic core design which meets all the rapid-acting requirements with a minimum of input energy.

Reactive Resonances in N+N2 Exchange Reaction

NASA Technical Reports Server (NTRS)

Wang, Dunyou; Huo, Winifred M.; Dateo, Christopher E.; Schwenke, David W.; Stallcop, James R.

2003-01-01

Rich reactive resonances are found in a 3D quantum dynamics study of the N + N2 exchange reaction using a recently developed ab initio potential energy surface. This surface is characterized by a feature in the interaction region called Lake Eyring , that is, two symmetric transition states with a shallow minimum between them. An L2 analysis of the quasibound states associated with the shallow minimum confirms that the quasibound states associated with oscillations in all three degrees of freedom in Lake Eyring are responsible for the reactive resonances in the state-to-state reaction probabilities. The quasibound states, mostly the bending motions, give rise to strong reasonance peaks, whereas other motions contribute to the bumps and shoulders in the resonance structure. The initial state reaction probability further proves that the bending motions are the dominating factors of the reaction probability and have longer life times than the stretching motions. This is the first observation of reactive resonances from a "Lake Eyring" feature in a potential energy surface.

SphinX Measurements of the 2009 Solar Minimum X-Ray Emission

NASA Astrophysics Data System (ADS)

Sylwester, J.; Kowalinski, M.; Gburek, S.; Siarkowski, M.; Kuzin, S.; Farnik, F.; Reale, F.; Phillips, K. J. H.; Bakała, J.; Gryciuk, M.; Podgorski, P.; Sylwester, B.

2012-06-01

The SphinX X-ray spectrophotometer on the CORONAS-PHOTON spacecraft measured soft X-ray emission in the 1-15 keV energy range during the deep solar minimum of 2009 with a sensitivity much greater than GOES. Several intervals are identified when the X-ray flux was exceptionally low, and the flux and solar X-ray luminosity are estimated. Spectral fits to the emission at these times give temperatures of 1.7-1.9 MK and emission measures between 4 × 1047 cm-3 and 1.1 × 1048 cm-3. Comparing SphinX emission with that from the Hinode X-ray Telescope, we deduce that most of the emission is from general coronal structures rather than confined features like bright points. For one of 27 intervals of exceptionally low activity identified in the SphinX data, the Sun's X-ray luminosity in an energy range roughly extrapolated to that of ROSAT (0.1-2.4 keV) was less than most nearby K and M dwarfs.

The Minimum Binding Energy and Size of Doubly Muonic D3 Molecule

NASA Astrophysics Data System (ADS)

Eskandari, M. R.; Faghihi, F.; Mahdavi, M.

The minimum energy and size of doubly muonic D3 molecule, which two of the electrons are replaced by the much heavier muons, are calculated by the well-known variational method. The calculations show that the system possesses two minimum positions, one at typically muonic distance and the second at the atomic distance. It is shown that at the muonic distance, the effective charge, zeff is 2.9. We assumed a symmetric planar vibrational model between two minima and an oscillation potential energy is approximated in this region.

Determining the size dependence of structural properties of clusters

NASA Astrophysics Data System (ADS)

Dong, Yi; Springborg, Michael

2012-12-01

Problems related to the determination of the structure of the global total-energy minimum for clusters are discussed through three examples. For isolated gold clusters it is shown that low-symmetry structures result due to covalent bonding. Subsequently, SiNGeN and (HAlO)N clusters are treated for which the occurrence of so called homotops leads to additional computational complexity. For the former it is found that the structures are not directly related to those of the pure monatomic clusters, and for the latter the results are shown to be in agreement with available experimental information on nanostructured HAlO. In order to illustrate and analyze the results, various descriptors are introduced and applied.

Computational modeling of carbohydrate recognition in protein complex

NASA Astrophysics Data System (ADS)

Ishida, Toyokazu

2017-11-01

To understand the mechanistic principle of carbohydrate recognition in proteins, we propose a systematic computational modeling strategy to identify complex carbohydrate chain onto the reduced 2D free energy surface (2D-FES), determined by MD sampling combined with QM/MM energy corrections. In this article, we first report a detailed atomistic simulation study of the norovirus capsid proteins with carbohydrate antigens based on ab initio QM/MM combined with MD-FEP simulations. The present result clearly shows that the binding geometries of complex carbohydrate antigen are determined not by one single, rigid carbohydrate structure, but rather by the sum of averaged conformations mapped onto the minimum free energy region of QM/MM 2D-FES.

Structural-functional integrated concrete with macro-encapsulated inorganic PCM

NASA Astrophysics Data System (ADS)

Mohseni, Ehsan; Tang, Waiching; Wang, Zhiyu

2017-09-01

Over the last few years the application of thermal energy storage system incorporating phase change materials (PCMs) to foster productivity and efficiency of buildings energy has grown rapidly. In this study, a structural-functional integrated concrete was developed using macro-encapsulated PCM-lightweight aggregate (LWA) as partial replacement (25 and 50% by volume) of coarse aggregate in control concrete. The PCM-LWA was prepared by incorporation of an inorganic PCM into porous LWAs through vacuum impregnation. The mechanical and thermal performance of PCM-LWA concrete were studied. The test results revealed that though the compressive strength of concrete with PCM-LWA was lower than the control concrete, but ranged from 22.02 MPa to 42.88 MPa which above the minimum strength requirement for structural application. The thermal performance test indicated that macro-encapsulated PCM-LWA has underwent the phase change transition reducing the indoor temperature.

Electronic structure and vibrational analysis of AHA⋯HX complexes

NASA Astrophysics Data System (ADS)

Joshi, Kaustubh A.; Gejji, Shridhar P.

2005-10-01

Electronic structures of the binary complexes of acetohydroxamic acid (AHA) and hydrogen halides, HX (X = F, Cl, Br) have been investigated using the second order perturbation theory. In the lowest energy structure of AHA⋯HF complex, hydrogen fluoride acts as a proton-donor with carbonyl oxygen and simultaneously as a proton-acceptor with the hydroxyl group. For chloro- and bromo-substituted derivatives, however, the lowest minimum possesses hydrogen-bonded interactions with the carbonyl oxygen in addition to those from the methyl proton of AHA. Frequency shifts of NH and CN stretching vibrations enable one to distinguish different conformers of AHA⋯HX complexes.

Rock climbing: A local-global algorithm to compute minimum energy and minimum free energy pathways.

PubMed

Templeton, Clark; Chen, Szu-Hua; Fathizadeh, Arman; Elber, Ron

2017-10-21

The calculation of minimum energy or minimum free energy paths is an important step in the quantitative and qualitative studies of chemical and physical processes. The computations of these coordinates present a significant challenge and have attracted considerable theoretical and computational interest. Here we present a new local-global approach to study reaction coordinates, based on a gradual optimization of an action. Like other global algorithms, it provides a path between known reactants and products, but it uses a local algorithm to extend the current path in small steps. The local-global approach does not require an initial guess to the path, a major challenge for global pathway finders. Finally, it provides an exact answer (the steepest descent path) at the end of the calculations. Numerical examples are provided for the Mueller potential and for a conformational transition in a solvated ring system.

Resonance of relativistic electrons with electromagnetic ion cyclotron waves

DOE PAGES

Denton, R. E.; Jordanova, V. K.; Bortnik, J.

2015-06-29

Relativistic electrons have been thought to more easily resonate with electromagnetic ion cyclotron EMIC waves if the total density is large. We show that, for a particular EMIC mode, this dependence is weak due to the dependence of the wave frequency and wave vector on the density. A significant increase in relativistic electron minimum resonant energy might occur for the H band EMIC mode only for small density, but no changes in parameters significantly decrease the minimum resonant energy from a nominal value. The minimum resonant energy depends most strongly on the thermal velocity associated with the field line motionmore » of the hot ring current protons that drive the instability. High density due to a plasmasphere or plasmaspheric plume could possibly lead to lower minimum resonance energy by causing the He band EMIC mode to be dominant. We demonstrate these points using parameters from a ring current simulation.« less

Consistent free energy landscapes and thermodynamic properties of small proteins based on a single all-atom force field employing an implicit solvation.

PubMed

Kim, Eunae; Jang, Soonmin; Pak, Youngshang

2007-10-14

We have attempted to improve the PARAM99 force field in conjunction with the generalized Born (GB) solvation model with a surface area correction for more consistent protein folding simulations. For this purpose, using an extended alphabeta training set of five well-studied molecules with various folds (alpha, beta, and betabetaalpha), a previously modified version of PARAM99/GBSA is further refined, such that all native states of the five training species correspond to their lowest free energy minimum states. The resulting modified force field (PARAM99MOD5/GBSA) clearly produces reasonably acceptable conformational free energy surfaces of the training set with correct identifications of their native states in the free energy minimum states. Moreover, due to its well-balanced nature, this new force field is expected to describe secondary structure propensities of diverse folds in a more consistent manner. Remarkably, temperature dependent behaviors simulated with the current force field are in good agreement with the experiment. This agreement is a significant improvement over the existing standard all-atom force fields. In addition, fundamentally important thermodynamic quantities, such as folding enthalpy (DeltaH) and entropy (DeltaS), agree reasonably well with the experimental data.

Elementary Mechanisms of Shear-Coupled Grain Boundary Migration

NASA Astrophysics Data System (ADS)

Rajabzadeh, A.; Mompiou, F.; Legros, M.; Combe, N.

2013-06-01

A detailed theoretical study of the elementary mechanisms occurring during the shear-coupled grain boundary (GB) migration at low temperature is performed focusing on both the energetic and structural characteristics. The migration of a Σ13(320) GB in a copper bicrystal in response to external shear displacements is simulated using a semiempirical potential. The minimum energy path of the shear-coupled GB migration is computed using the nudge elastic band method. The GB migration occurs through the nucleation and motion of GB steps identified as disconnections. Energy barriers for the GB and disconnection migrations are evaluated.

Cooled window for X-rays or charged particles

DOEpatents

Logan, Clinton M.

1996-01-01

A window that provides good structural integrity and a very high capacity for removal of the heat deposited by x-rays, electrons, or ions, with minimum attenuation of the desired beam. The window is cooled by providing microchannels therein through which a coolant is pumped. For example, the window may be made of silicon with etched microchannels therein and covered by a silicon member. A window made of silicon with a total thickness of 520 .mu.m transmits 96% of the x-rays at an energy of 60 keV, and the transmission is higher than 90% for higher energy photons.

Electron attachment to the guanine-cytosine nucleic acid base pair and the effects of monohydration and proton transfer.

PubMed

Gupta, Ashutosh; Jaeger, Heather M; Compaan, Katherine R; Schaefer, Henry F

2012-05-17

The guanine-cytosine (GC) radical anion and its interaction with a single water molecule is studied using ab initio and density functional methods. Z-averaged second-order perturbation theory (ZAPT2) was applied to GC radical anion for the first time. Predicted spin densities show that the radical character is localized on cytosine. The Watson-Crick monohydrated GC anion is compared to neutral GC·H2O, as well as to the proton-transferred analogue on the basis of structural and energetic properties. In all three systems, local minima are identified that correspond to water positioned in the major and minor grooves of macromolecular DNA. On the anionic surface, two novel structures have water positioned above or below the GC plane. On the neutral and anionic surfaces, the global minimum can be described as water interacting with the minor groove. These structures are predicted to have hydration energies of 9.7 and 11.8 kcal mol(-1), respectively. Upon interbase proton-transfer (PT), the anionic global minimum has water positioned in the major groove, and the hydration energy increases to 13.4 kcal mol(-1). PT GC·H2O(•-) has distonic character; the radical character resides on cytosine, while the negative charge is localized on guanine. The effects of proton transfer are further investigated through the computed adiabatic electron affinities (AEA) of GC and monohydrated GC, and the vertical detachment energies (VDE) of the corresponding anions. Monohydration increases the AEAs and VDEs by only 0.1 eV, while proton-transfer increases the VDEs substantially (0.8 eV). The molecular charge distribution of monohydrated guanine-cytosine radical anion depends heavily on interbase proton transfer.

Quadratic String Method for Locating Instantons in Tunneling Splitting Calculations.

PubMed

Cvitaš, Marko T

2018-03-13

The ring-polymer instanton (RPI) method is an efficient technique for calculating approximate tunneling splittings in high-dimensional molecular systems. In the RPI method, tunneling splitting is evaluated from the properties of the minimum action path (MAP) connecting the symmetric wells, whereby the extensive sampling of the full potential energy surface of the exact quantum-dynamics methods is avoided. Nevertheless, the search for the MAP is usually the most time-consuming step in the standard numerical procedures. Recently, nudged elastic band (NEB) and string methods, originaly developed for locating minimum energy paths (MEPs), were adapted for the purpose of MAP finding with great efficiency gains [ J. Chem. Theory Comput. 2016 , 12 , 787 ]. In this work, we develop a new quadratic string method for locating instantons. The Euclidean action is minimized by propagating the initial guess (a path connecting two wells) over the quadratic potential energy surface approximated by means of updated Hessians. This allows the algorithm to take many minimization steps between the potential/gradient calls with further reductions in the computational effort, exploiting the smoothness of potential energy surface. The approach is general, as it uses Cartesian coordinates, and widely applicable, with computational effort of finding the instanton usually lower than that of determining the MEP. It can be combined with expensive potential energy surfaces or on-the-fly electronic-structure methods to explore a wide variety of molecular systems.

Determinants of residential electricity consumption: Using smart meter data to examine the effect of climate, building characteristics, appliance stock, and occupants' behavior

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

Kavousian, A; Rajagopal, R; Fischer, M

2013-06-15

We propose a method to examine structural and behavioral determinants of residential electricity consumption, by developing separate models for daily maximum (peak) and minimum (idle) consumption. We apply our method on a data set of 1628 households' electricity consumption. The results show that weather, location and floor area are among the most important determinants of residential electricity consumption. In addition to these variables, number of refrigerators and entertainment devices (e.g., VCRs) are among the most important determinants of daily minimum consumption, while number of occupants and high-consumption appliances such as electric water heaters are the most significant determinants of dailymore » maximum consumption. Installing double-pane windows and energy-efficient lights helped to reduce consumption, as did the energy-conscious use of electric heater. Acknowledging climate change as a motivation to save energy showed correlation with lower electricity consumption. Households with individuals over 55 or between 19 and 35 years old recorded lower electricity consumption, while pet owners showed higher consumption. Contrary to some previous studies, we observed no significant correlation between electricity consumption and income level, home ownership, or building age. Some otherwise energy-efficient features such as energy-efficient appliances, programmable thermostats, and insulation were correlated with slight increase in electricity consumption. (C) 2013 Elsevier Ltd. All rights reserved.« less

Rectenna System Design. [energy conversion solar power satellites

NASA Technical Reports Server (NTRS)

Woodcock, G. R.; Andryczyk, R. W.

1980-01-01

The fundamental processes involved in the operation of the rectenna system designed for the solar power satellite system are described. The basic design choices are presented based on the desired microwave rf field concentration prior to rectification and based on the ground clearance requirements for the rectenna structure. A nonconcentrating inclined planar panel with a 2 meter minimum clearance configuration is selected as a representative of the typical rectenna.

Low-Lying Energy Isomers and Global Minima of Aqueous Nanoclusters: Structures and Spectroscopic Features of the Pentagonal Dodecahedron (H2O)20 and (H3O)+(H2O)20

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

Xantheas, Sotiris S.

We rely on a hierarchy of methods to identify the low-lying isomers for the pentagonal dodecahedron (H2O)20 and the H3O+(H2O)20 clusters. Initial screening of isomers was performed with classical potentials [TIP4P, TTM2-F, TTM2.1-F for (H2O)20 and ASP for H3O+(H2O)20] and the networks obtained with those potentials were subsequently reoptimized at the DFT (B3LYP) and MP2 levels of theory. For the pentagonal dodecahedron (H2O)20 it was found that DFT (B3LYP) and MP2 produced the same global minimum. However, this was not the case for the H3O+(H2O)20 cluster, for which MP2 produced a different network for the global minimum when compared tomore » DFT (B3LYP). All low-lying minima of H3O+(H2O)20 correspond to hydrogen bonding networks having 9 ''free'' OH bonds and the hydronium ion on the surface of the cluster. The fact that DFT (B3LYP) and MP2 produce different results and issues related to the use of a smaller basis set, explains the discrepancy between the current results and the structure previously suggested [Science 304, 1137 (2004)] for the global minimum of the H3O+(H2O)20 cluster. Additionally, the IR spectra of the MP2 global minimum are closer to the experimentally measured ones than the spectra of the previously suggested DFT global minimum. The latter exhibit additional bands in the most red-shifted region of the OH stretching vibrations (corresponding to the ''fingerprint'' of the underlying hydrogen bonding network), which are absent from both the experimental as well as the spectra of the new structure suggested for the global minimum of this cluster.« less

On the critical flame radius and minimum ignition energy for spherical flame initiation

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

Chen, Zheng; Burke, M. P.; Ju, Yiguang

2011-01-01

Spherical flame initiation from an ignition kernel is studied theoretically and numerically using different fuel/oxygen/helium/argon mixtures (fuel: hydrogen, methane, and propane). The emphasis is placed on investigating the critical flame radius controlling spherical flame initiation and its correlation with the minimum ignition energy. It is found that the critical flame radius is different from the flame thickness and the flame ball radius and that their relationship depends strongly on the Lewis number. Three different flame regimes in terms of the Lewis number are observed and a new criterion for the critical flame radius is introduced. For mixtures with Lewis numbermore » larger than a critical Lewis number above unity, the critical flame radius is smaller than the flame ball radius but larger than the flame thickness. As a result, the minimum ignition energy can be substantially over-predicted (under-predicted) based on the flame ball radius (the flame thickness). The results also show that the minimum ignition energy for successful spherical flame initiation is proportional to the cube of the critical flame radius. Furthermore, preferential diffusion of heat and mass (i.e. the Lewis number effect) is found to play an important role in both spherical flame initiation and flame kernel evolution after ignition. It is shown that the critical flame radius and the minimum ignition energy increase significantly with the Lewis number. Therefore, for transportation fuels with large Lewis numbers, blending of small molecule fuels or thermal and catalytic cracking will significantly reduce the minimum ignition energy.« less

Electronic Structure of Two-Dimensional Hydrocarbon Networks of sp2 and sp3 C Atoms

NASA Astrophysics Data System (ADS)

Fujii, Yasumaru; Maruyama, Mina; Wakabayashi, Katsunori; Nakada, Kyoko; Okada, Susumu

2018-03-01

Based on density functional theory with the generalized gradient approximation, we have investigated the geometric and electronic structures of two-dimensional hexagonal covalent networks consisting of oligoacenes and fourfold coordinated hydrocarbon atoms, which are alternately arranged in a hexagonal manner. All networks were semiconductors with a finite energy gap at the Γ point, which monotonically decreased with the increase of the oligoacene length. As a result of a Kagome network of oligoacene connected through sp3 C atoms, the networks possess peculiar electron states in their valence and conduction bands, which consist of a flat dispersion band and a Dirac cone. The total energy of the networks depends on the oligoacene length and has a minimum for the network comprising naphthalene.

A Novel Intrinsic Interface State Controlled by Atomic Stacking Sequence at Interfaces of SiC/SiO2.

PubMed

Matsushita, Yu-Ichiro; Oshiyama, Atsushi

2017-10-11

On the basis of ab initio total-energy electronic-structure calculations, we find that electron states localized at the SiC/SiO 2 interface emerge in the energy region between 0.3 eV below and 1.2 eV above the bulk conduction-band minimum (CBM) of SiC, being sensitive to the sequence of atomic bilayers in SiC near the interface. These new interface states unrecognized in the past are due to the peculiar characteristics of the CBM states that are distributed along the crystallographic channels. We also find that the electron doping modifies the energetics among the different stacking structures. Implication for performance of electron devices fabricated on different SiC surfaces is discussed.

Protein folding: Over half a century lasting quest. Comment on "There and back again: Two views on the protein folding puzzle" by Alexei V. Finkelstein et al.

NASA Astrophysics Data System (ADS)

Krokhotin, Andrey; Dokholyan, Nikolay V.

2017-07-01

Most proteins fold into unique three-dimensional (3D) structures that determine their biological functions, such as catalytic activity or macromolecular binding. Misfolded proteins can pose a threat through aberrant interactions with other proteins leading to a number of diseases including Alzheimer's disease, Parkinson's disease, and amyotrophic lateral sclerosis [1,2]. What does determine 3D structure of proteins? The first clue to this question came more than fifty years ago when Anfinsen demonstrated that unfolded proteins can spontaneously fold to their native 3D structures [3,4]. Anfinsen's experiments lead to the conclusion that proteins fold to unique native structure corresponding to the stable and kinetically accessible free energy minimum, and protein native structure is solely determined by its amino acid sequence. The question of how exactly proteins find their free energy minimum proved to be a difficult problem. One of the puzzles, initially pointed out by Levinthal, was an inconsistency between observed protein folding times and theoretical estimates. A self-avoiding polymer model of a globular protein of 100-residues length on a cubic lattice can sample at least 1047 states. Based on the assumption that conformational sampling occurs at the highest vibrational mode of proteins (∼picoseconds), predicted folding time by searching among all the possible conformations leads to ∼1027 years (much larger than the age of the universe) [5]. In contrast, observed protein folding time range from microseconds to minutes. Due to tremendous theoretical progress in protein folding field that has been achieved in past decades, the source of this inconsistency is currently understood that is thoroughly described in the review by Finkelstein et al. [6].

Development of Advanced Methods of Structural and Trajectory Analysis for Transport Aircraft

NASA Technical Reports Server (NTRS)

Ardema, Mark D.; Windhorst, Robert; Phillips, James

1998-01-01

This paper develops a near-optimal guidance law for generating minimum fuel, time, or cost fixed-range trajectories for supersonic transport aircraft. The approach uses a choice of new state variables along with singular perturbation techniques to time-scale decouple the dynamic equations into multiple equations of single order (second order for the fast dynamics). Application of the maximum principle to each of the decoupled equations, as opposed to application to the original coupled equations, avoids the two point boundary value problem and transforms the problem from one of a functional optimization to one of multiple function optimizations. It is shown that such an approach produces well known aircraft performance results such as minimizing the Brequet factor for minimum fuel consumption and the energy climb path. Furthermore, the new state variables produce a consistent calculation of flight path angle along the trajectory, eliminating one of the deficiencies in the traditional energy state approximation. In addition, jumps in the energy climb path are smoothed out by integration of the original dynamic equations at constant load factor. Numerical results performed for a supersonic transport design show that a pushover dive followed by a pullout at nominal load factors are sufficient maneuvers to smooth the jump.

Cavity Born-Oppenheimer Approximation for Correlated Electron-Nuclear-Photon Systems.

PubMed

Flick, Johannes; Appel, Heiko; Ruggenthaler, Michael; Rubio, Angel

2017-04-11

In this work, we illustrate the recently introduced concept of the cavity Born-Oppenheimer approximation [ Flick et al. PNAS 2017 , 10.1073/pnas.1615509114 ] for correlated electron-nuclear-photon problems in detail. We demonstrate how an expansion in terms of conditional electronic and photon-nuclear wave functions accurately describes eigenstates of strongly correlated light-matter systems. For a GaAs quantum ring model in resonance with a photon mode we highlight how the ground-state electronic potential-energy surface changes the usual harmonic potential of the free photon mode to a dressed mode with a double-well structure. This change is accompanied by a splitting of the electronic ground-state density. For a model where the photon mode is in resonance with a vibrational transition, we observe in the excited-state electronic potential-energy surface a splitting from a single minimum to a double minimum. Furthermore, for a time-dependent setup, we show how the dynamics in correlated light-matter systems can be understood in terms of population transfer between potential energy surfaces. This work at the interface of quantum chemistry and quantum optics paves the way for the full ab initio description of matter-photon systems.

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

Bazante, Alexandre P., E-mail: abazante@chem.ufl.edu; Bartlett, Rodney J.; Davidson, E. R.

The benzene radical anion is studied with ab initio coupled-cluster theory in large basis sets. Unlike the usual assumption, we find that, at the level of theory investigated, the minimum energy geometry is non-planar with tetrahedral distortion at two opposite carbon atoms. The anion is well known for its instability to auto-ionization which poses computational challenges to determine its properties. Despite the importance of the benzene radical anion, the considerable attention it has received in the literature so far has failed to address the details of its structure and shape-resonance character at a high level of theory. Here, we examinemore » the dynamic Jahn-Teller effect and its impact on the anion potential energy surface. We find that a minimum energy geometry of C{sub 2} symmetry is located below one D{sub 2h} stationary point on a C{sub 2h} pseudo-rotation surface. The applicability of standard wave function methods to an unbound anion is assessed with the stabilization method. The isotropic hyperfine splitting constants (A{sub iso}) are computed and compared to data obtained from experimental electron spin resonance experiments. Satisfactory agreement with experiment is obtained with coupled-cluster theory and large basis sets such as cc-pCVQZ.« less

Energy management of three-dimensional minimum-time intercept. [for aircraft flight optimization

NASA Technical Reports Server (NTRS)

Kelley, H. J.; Cliff, E. M.; Visser, H. G.

1985-01-01

A real-time computer algorithm to control and optimize aircraft flight profiles is described and applied to a three-dimensional minimum-time intercept mission. The proposed scheme has roots in two well known techniques: singular perturbations and neighboring-optimal guidance. Use of singular-perturbation ideas is made in terms of the assumed trajectory-family structure. A heading/energy family of prestored point-mass-model state-Euler solutions is used as the baseline in this scheme. The next step is to generate a near-optimal guidance law that will transfer the aircraft to the vicinity of this reference family. The control commands fed to the autopilot (bank angle and load factor) consist of the reference controls plus correction terms which are linear combinations of the altitude and path-angle deviations from reference values, weighted by a set of precalculated gains. In this respect the proposed scheme resembles neighboring-optimal guidance. However, in contrast to the neighboring-optimal guidance scheme, the reference control and state variables as well as the feedback gains are stored as functions of energy and heading in the present approach. Some numerical results comparing open-loop optimal and approximate feedback solutions are presented.

Ratio of shear viscosity to entropy density in multifragmentation of Au + Au

NASA Astrophysics Data System (ADS)

Zhou, C. L.; Ma, Y. G.; Fang, D. Q.; Li, S. X.; Zhang, G. Q.

2012-06-01

The ratio of the shear viscosity (η) to entropy density (s) for the intermediate energy heavy-ion collisions has been calculated by using the Green-Kubo method in the framework of the quantum molecular dynamics model. The theoretical curve of η/s as a function of the incident energy for the head-on Au + Au collisions displays that a minimum region of η/s has been approached at higher incident energies, where the minimum η/s value is about 7 times Kovtun-Son-Starinets (KSS) bound (1/4π). We argue that the onset of minimum η/s region at higher incident energies corresponds to the nuclear liquid gas phase transition in nuclear multifragmentation.

Structure, dynamics, and thermodynamics of a family of potentials with tunable softness

NASA Astrophysics Data System (ADS)

Shi, Zane; Debenedetti, Pablo G.; Stillinger, Frank H.; Ginart, Paul

2011-08-01

We investigate numerically the structure, thermodynamics, and relaxation behavior of a family of (n, 6) Lennard-Jones-like glass-forming binary mixtures interacting via pair potentials with variable softness, fixed well depth, and fixed well depth location. These constraints give rise to progressively more negative attractive tails upon softening, for separations greater than the potential energy minimum. Over the range of conditions examined, we find only modest dependence of structure on softness. In contrast, decreasing the repulsive exponent from n = 12 to n = 7 causes the diffusivity to increase by as much as two orders of magnitude at fixed temperature and density, and produces mechanically stable packings (inherent structures) with cohesive energies that are, on average, ˜1.7 well depths per particle larger than for the corresponding Lennard-Jones (n = 12) case. The softer liquids have markedly higher entropies and lower Kauzmann temperatures than their Lennard-Jones (n = 12) counterparts, and they remain diffusive down to appreciably lower temperatures. We find that softening leads to a modest increase in fragility.

Revealing the structure of isolated peptides: IR-IR predissociation spectroscopy of protonated triglycine isomers

NASA Astrophysics Data System (ADS)

Voss, Jonathan M.; Fischer, Kaitlyn C.; Garand, Etienne

2018-05-01

We report an isomer specific IR-IR double resonance study of the mass-selected protonated triglycine peptide. Comparison of experimental spectra with calculations reveals the presence of two isomers, with protonation occurring at either the terminal amine site or one of the amide oxygen sites. The amine protonated isomer identified in our experiment contains an atypical cis amide configuration as well as a more typical trans amide. The amide protonated peptide, on the other hand, contains two trans amide moieties. Both isomers are found to be the lowest energy structures for their respective protonation site, but it is unclear, from experiments and calculations, which one is the global minimum. The presence of both in our experiments likely points to kinetic trapping of a higher energy structure. Finally, the observed frequencies of the Nsbnd H and Osbnd H stretch vibrations are used to estimate the hydrogen-bond strengths present in each isomer, accounting for the relative stabilities of these structures.

Revealing the structure of isolated peptides: IR-IR predissociation spectroscopy of protonated triglycine isomers

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

Voss, Jonathan M.; Fischer, Kaitlyn C.; Garand, Etienne

Here, we report an isomer specific IR-IR double resonance study of the mass-selected protonated triglycine peptide. Comparison of experimental spectra with calculations reveals the presence of two isomers, with protonation occurring at either the terminal amine site or one of the amide oxygen sites. The amine protonated isomer identified in our experiment contains an atypical cis amide configuration as well as a more typical trans amide. The amide protonated peptide, on the other hand, contains two trans amide moieties. Both isomers are found to be the lowest energy structures for their respective protonation site, but it is unclear, from experimentsmore » and calculations, which one is the global minimum. The presence of both in our experiments likely points to kinetic trapping of a higher energy structure. Lastly, the observed frequencies of the NH and OH stretch vibrations are used to estimate the hydrogen-bond strengths present in each isomer, accounting for the relative stabilities of these structures.« less

Revealing the structure of isolated peptides: IR-IR predissociation spectroscopy of protonated triglycine isomers

DOE PAGES

Voss, Jonathan M.; Fischer, Kaitlyn C.; Garand, Etienne

2018-03-08

Here, we report an isomer specific IR-IR double resonance study of the mass-selected protonated triglycine peptide. Comparison of experimental spectra with calculations reveals the presence of two isomers, with protonation occurring at either the terminal amine site or one of the amide oxygen sites. The amine protonated isomer identified in our experiment contains an atypical cis amide configuration as well as a more typical trans amide. The amide protonated peptide, on the other hand, contains two trans amide moieties. Both isomers are found to be the lowest energy structures for their respective protonation site, but it is unclear, from experimentsmore » and calculations, which one is the global minimum. The presence of both in our experiments likely points to kinetic trapping of a higher energy structure. Lastly, the observed frequencies of the NH and OH stretch vibrations are used to estimate the hydrogen-bond strengths present in each isomer, accounting for the relative stabilities of these structures.« less

Minimum weight structural sandwich

Treesearch

Edward W. Kuenzi

1965-01-01

This note presents theoretical analyses for determination of dimensions of structural sandwich of minimum weight that will have certain stiffness and load-carrying capabilities. Included is a brief discussion of the resultant minimum weight configurations.

Hierarchical structure of the energy landscape of proteins revisited by time series analysis. I. Mimicking protein dynamics in different time scales

NASA Astrophysics Data System (ADS)

Alakent, Burak; Camurdan, Mehmet C.; Doruker, Pemra

2005-10-01

Time series models, which are constructed from the projections of the molecular-dynamics (MD) runs on principal components (modes), are used to mimic the dynamics of two proteins: tendamistat and immunity protein of colicin E7 (ImmE7). Four independent MD runs of tendamistat and three independent runs of ImmE7 protein in vacuum are used to investigate the energy landscapes of these proteins. It is found that mean-square displacements of residues along the modes in different time scales can be mimicked by time series models, which are utilized in dividing protein dynamics into different regimes with respect to the dominating motion type. The first two regimes constitute the dominance of intraminimum motions during the first 5ps and the random walk motion in a hierarchically higher-level energy minimum, which comprise the initial time period of the trajectories up to 20-40ps for tendamistat and 80-120ps for ImmE7. These are also the time ranges within which the linear nonstationary time series are completely satisfactory in explaining protein dynamics. Encountering energy barriers enclosing higher-level energy minima constrains the random walk motion of the proteins, and pseudorelaxation processes at different levels of minima are detected in tendamistat, depending on the sampling window size. Correlation (relaxation) times of 30-40ps and 150-200ps are detected for two energy envelopes of successive levels for tendamistat, which gives an overall idea about the hierarchical structure of the energy landscape. However, it should be stressed that correlation times of the modes are highly variable with respect to conformational subspaces and sampling window sizes, indicating the absence of an actual relaxation. The random-walk step sizes and the time length of the second regime are used to illuminate an important difference between the dynamics of the two proteins, which cannot be clarified by the investigation of relaxation times alone: ImmE7 has lower-energy barriers enclosing the higher-level energy minimum, preventing the protein to relax and letting it move in a random-walk fashion for a longer period of time.

Sphalerons in composite and nonstandard Higgs models

NASA Astrophysics Data System (ADS)

Spannowsky, Michael; Tamarit, Carlos

2017-01-01

After the discovery of the Higgs boson and the rather precise measurement of all electroweak boson's masses the local structure of the electroweak symmetry breaking potential is already quite well established. However, despite being a key ingredient to a fundamental understanding of the underlying mechanism of electroweak symmetry breaking, the global structure of the electroweak potential remains entirely unknown. The existence of sphalerons, unstable solutions of the classical action of motion that are interpolating between topologically distinct vacua, is a direct consequence of the Standard Model's SU (2 )L gauge group. Nevertheless, the sphaleron energy depends on the shape of the Higgs potential away from the minimum and can therefore be a litmus test for its global structure. Focusing on two scenarios, the minimal composite Higgs model SO (5 )/SO (4 ) or an elementary Higgs with a deformed electroweak potential, we calculate the change of the sphaleron energy compared to the Standard Model prediction. We find that the sphaleron energy would have to be measured to O (10 )% accuracy to exclude sizeable global deviations from the Standard Model Higgs potential. We further find that because of the periodicity of the scalar potential in composite Higgs models a second sphaleron branch with larger energy arises.

First-Principles Investigation of Radiation Induced Defects in SiC and Si.

NASA Astrophysics Data System (ADS)

Windl, Wolfgang; Lenosky, Thomas J.; Kress, Joel D.; Voter, Arthur F.

1997-03-01

SiC shows promise as a structural material for fusion reactors, partly because of its low activation under neutron irradiation. This radiation, however, can cause damage to its crystal structure, thereby degrading its properties. The focus of this work is the understanding of this neutron-induced radiation damage to SiC. Neutrons interact with matter primarily by scattering off nuclei, an event which suddenly imparts energy and momentum to an atom. If enough energy is transferred, this scattering event creates structural damage, such as displacement of the impacted atom from its original position to an interstitial site. We performed quantum molecular dynamics simulations to determine the displacement energy threshold, i.e., the minimum energy transfer required to create damage. To do this, we used the self-consistent Demkov-Ortega-Grumbach-Sankey (DOGS) extension(A. A. Demkov et al.), Phys. Rev. B 52, 1618 (1995). of the Harris-functional local orbital LDA method of Sankey et al. In order to benchmark the quality of our methodology for studying radiation damage, we compare our results to those of calculations employing classical interatomic potentials; furthermore, we performed similar simulations for Si, where experimental data exist.

DETERMINING MINIMUM IGNITION ENERGIES AND QUENCHING DISTANCES OF DIFFICULT-TO-IGNITE COMPOUNDS

EPA Science Inventory

Minimum spark energies and corresponding flat-plate electrode quenching distances required to initiate propagation of a combustion wave have been experimentally measured for four flammable hydrofluorocarbon (HFC) refrigerants and propane using ASTM (American Society for Testing a...

Conformational study and structure of N-(2,5-methylphenyl)salicylaldimine

NASA Astrophysics Data System (ADS)

Elmali, A.; Elerman, Y.; Zeyrek, C. T.

1998-02-01

N-(2,5-methylphenyl)salicylaldimine (C 15H 15NO) has been investigated by X-ray analysis and AM1 semi-empirical quantum mechanical method. The crystal is in the orthorhombic space group P2 12 12 1 with a = 6.839(1), b = 7.720(4), c = 23.183(3) Å, V = 1224.1(2) Å3, Z = 4, Dc = 1.222 g cm -3 and μ(Mo K α) = 0.076 mm -1. The title structure was solved by direct methods and refined to R = 0.0364 for 1489 reflections [ I > 2 σ( I)] by full-matrix anisotropic least-squares methods. The title compound is photochromic and the molecule is not planar. There is a strong intramolecular hydrogen bond of distance 2.604(2) Å between the hydroxyl oxygen atom and imine nitrogen atom, the hydrogen atom essentially being bonded to the oxygen atom. Minimum energy conformations from AM1 were calculated as a function of three torsion angles, θ1 (C8N1C7C6), θ2 (C9C8N1C7) and θ3 (N1C7C6C5), varied every 10°. The optimized geometry of the crystal structure corresponding to non-planar conformation is the most stable conformation in all calculations. The results strongly indicate that the minimum energy conformation is primarily determined by non-bonded hydrogen-hydrogen repulsions.

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

Mishra, P.; Purdue University, West Lafayette, Indiana 47907; Verma, K.

Borazine is isoelectronic with benzene and is popularly referred to as inorganic benzene. The study of non-covalent interactions with borazine and comparison with its organic counterpart promises to show interesting similarities and differences. The motivation of the present study of the borazine-water interaction, for the first time, stems from such interesting possibilities. Hydrogen-bonded complexes of borazine and water were studied using matrix isolation infrared spectroscopy and quantum chemical calculations. Computations were performed at M06-2X and MP2 levels of theory using 6-311++G(d,p) and aug-cc-pVDZ basis sets. At both the levels of theory, the complex involving an N–H⋯O interaction, where the N–Hmore » of borazine serves as the proton donor to the oxygen of water was found to be the global minimum, in contrast to the benzene-water system, which showed an H–π interaction. The experimentally observed infrared spectra of the complexes corroborated well with our computations for the complex corresponding to the global minimum. In addition to the global minimum, our computations also located two local minima on the borazine-water potential energy surface. Of the two local minima, one corresponded to a structure where the water was the proton donor to the nitrogen of borazine, approaching the borazine ring from above the plane of the ring; a structure that resembled the global minimum in the benzene-water H–π complex. The second local minimum corresponded to an interaction of the oxygen of water with the boron of borazine, which can be termed as the boron bond. Clearly the borazine-water system presents a richer landscape than the benzene-water system.« less

Comparing solvophobic and multivalent induced collapse in polyelectrolyte brushes

DOE PAGES

Jackson, Nicholas E.; Brettmann, Blair K.; Vishwanath, Venkatram; ...

2017-02-03

Here, coarse-grained molecular dynamics enhanced by free-energy sampling methods is used to examine the roles of solvophobicity and multivalent salts on polyelectrolyte brush collapse. Specifically, we demonstrate that while ostensibly similar, solvophobic collapsed brushes and multivalent-ion collapsed brushes exhibit distinct mechanistic and structural features. Notably, multivalent-induced heterogeneous brush collapse is observed under good solvent polymer backbone conditions, demonstrating that the mechanism of multivalent collapse is not contingent upon a solvophobic backbone. Umbrella sampling of the potential of mean-force (PMF) between two individual brush strands confirms this analysis, revealing starkly different PMFs under solvophobic and multivalent conditions, suggesting the role ofmore » multivalent “bridging” as the discriminating feature in trivalent collapse. Structurally, multivalent ions show a propensity for nucleating order within collapsed brushes, whereas poor-solvent collapsed brushes are more disordered; this difference is traced to the existence of a metastable PMF minimum for poor solvent conditions, and a global PMF minimum for trivalent systems, under experimentally relevant conditions.« less

Comparing solvophobic and multivalent induced collapse in polyelectrolyte brushes

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

Jackson, Nicholas E.; Brettmann, Blair K.; Vishwanath, Venkatram

Here, coarse-grained molecular dynamics enhanced by free-energy sampling methods is used to examine the roles of solvophobicity and multivalent salts on polyelectrolyte brush collapse. Specifically, we demonstrate that while ostensibly similar, solvophobic collapsed brushes and multivalent-ion collapsed brushes exhibit distinct mechanistic and structural features. Notably, multivalent-induced heterogeneous brush collapse is observed under good solvent polymer backbone conditions, demonstrating that the mechanism of multivalent collapse is not contingent upon a solvophobic backbone. Umbrella sampling of the potential of mean-force (PMF) between two individual brush strands confirms this analysis, revealing starkly different PMFs under solvophobic and multivalent conditions, suggesting the role ofmore » multivalent “bridging” as the discriminating feature in trivalent collapse. Structurally, multivalent ions show a propensity for nucleating order within collapsed brushes, whereas poor-solvent collapsed brushes are more disordered; this difference is traced to the existence of a metastable PMF minimum for poor solvent conditions, and a global PMF minimum for trivalent systems, under experimentally relevant conditions.« less

Gaussian process regression to accelerate geometry optimizations relying on numerical differentiation

NASA Astrophysics Data System (ADS)

Schmitz, Gunnar; Christiansen, Ove

2018-06-01

We study how with means of Gaussian Process Regression (GPR) geometry optimizations, which rely on numerical gradients, can be accelerated. The GPR interpolates a local potential energy surface on which the structure is optimized. It is found to be efficient to combine results on a low computational level (HF or MP2) with the GPR-calculated gradient of the difference between the low level method and the target method, which is a variant of explicitly correlated Coupled Cluster Singles and Doubles with perturbative Triples correction CCSD(F12*)(T) in this study. Overall convergence is achieved if both the potential and the geometry are converged. Compared to numerical gradient-based algorithms, the number of required single point calculations is reduced. Although introducing an error due to the interpolation, the optimized structures are sufficiently close to the minimum of the target level of theory meaning that the reference and predicted minimum only vary energetically in the μEh regime.

Theoretical study of mixed LiLnX4 (Ln = La, Dy; X = F, Cl, Br, I) rare earth/alkali halide complexes.

PubMed

Groen, C P; Oskam, A; Kovács, A

2000-12-25

The structure, bonding and vibrational properties of the mixed LiLnX4 (Ln = La, Dy; X = F, Cl, Br, I) rare earth/alkali halide complexes were studied using various quantum chemical methods (HF, MP2 and the Becke3-Lee-Yang-Parr exchange-correlation density functional) in conjunction with polarized triple-zeta valence basis sets and quasi-relativistic effective core potentials for the heavy atoms. Our comparative study indicated the superiority of MP2 theory while the HF and B3-LYP methods as well as less sophisticated basis sets failed for the correct energetic relations. In particular, f polarization functions on Li and X proved to be important for the Li...X interaction in the complexes. From the three characteristic structures of such complexes, possessing 1-(C3v), 2-(C2v), or 3-fold coordination (C3v) between the alkali metal and the bridging halide atoms, the bi- and tridentate forms are located considerably lower on the potential energy surface then the monodentate isomer. Therefore only the bi- and tridentate isomers have chemical relevance. The monodentate isomer is only a high-lying local minimum in the case of X = F. For X = Cl, Br, and I this structure is found to be a second-order saddle point. The bidentate structure was found to be the global minimum for the systems with X = F, Cl, and Br. However, the relative stability with respect to the tridentate structure is very small (1-5 kJ/mol) for the heavier halide derivatives and the relative order is reversed in the case of the iodides. The energy difference between the three structures and the dissociation energy decrease in the row F to I. The ionic bonding in the complexes was characterized by natural charges and a topological analysis of the electron density distribution according to Bader's theorem. Variation of the geometrical and bonding characteristics between the lanthanum and dysprosium complexes reflects the effect of "lanthanide contraction". The calculated vibrational data indicate that infrared spectroscopy may be an effective tool for experimental investigation and characterization of LiLnX4 molecules.

Relaxation mode analysis and Markov state relaxation mode analysis for chignolin in aqueous solution near a transition temperature

NASA Astrophysics Data System (ADS)

Mitsutake, Ayori; Takano, Hiroshi

2015-09-01

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

Analysis of the Free-Energy Surface of Proteins from Reversible Folding Simulations

PubMed Central

Allen, Lucy R.; Krivov, Sergei V.; Paci, Emanuele

2009-01-01

Computer generated trajectories can, in principle, reveal the folding pathways of a protein at atomic resolution and possibly suggest general and simple rules for predicting the folded structure of a given sequence. While such reversible folding trajectories can only be determined ab initio using all-atom transferable force-fields for a few small proteins, they can be determined for a large number of proteins using coarse-grained and structure-based force-fields, in which a known folded structure is by construction the absolute energy and free-energy minimum. Here we use a model of the fast folding helical λ-repressor protein to generate trajectories in which native and non-native states are in equilibrium and transitions are accurately sampled. Yet, representation of the free-energy surface, which underlies the thermodynamic and dynamic properties of the protein model, from such a trajectory remains a challenge. Projections over one or a small number of arbitrarily chosen progress variables often hide the most important features of such surfaces. The results unequivocally show that an unprojected representation of the free-energy surface provides important and unbiased information and allows a simple and meaningful description of many-dimensional, heterogeneous trajectories, providing new insight into the possible mechanisms of fast-folding proteins. PMID:19593364

Analysis of the free-energy surface of proteins from reversible folding simulations.

PubMed

Allen, Lucy R; Krivov, Sergei V; Paci, Emanuele

2009-07-01

Computer generated trajectories can, in principle, reveal the folding pathways of a protein at atomic resolution and possibly suggest general and simple rules for predicting the folded structure of a given sequence. While such reversible folding trajectories can only be determined ab initio using all-atom transferable force-fields for a few small proteins, they can be determined for a large number of proteins using coarse-grained and structure-based force-fields, in which a known folded structure is by construction the absolute energy and free-energy minimum. Here we use a model of the fast folding helical lambda-repressor protein to generate trajectories in which native and non-native states are in equilibrium and transitions are accurately sampled. Yet, representation of the free-energy surface, which underlies the thermodynamic and dynamic properties of the protein model, from such a trajectory remains a challenge. Projections over one or a small number of arbitrarily chosen progress variables often hide the most important features of such surfaces. The results unequivocally show that an unprojected representation of the free-energy surface provides important and unbiased information and allows a simple and meaningful description of many-dimensional, heterogeneous trajectories, providing new insight into the possible mechanisms of fast-folding proteins.

Simulation studies for surfaces and materials strength

NASA Technical Reports Server (NTRS)

Halicioglu, T.

1986-01-01

During this reporting period three investigations were carried out. The first area of research concerned the analysis of the structure-energy relationship in small clusters. This study is very closely related to the improvement of the potential energy functions which are suitable and simple enough to be used in atomistic simulation studies. Parameters obtained from ab initio calculations for dimers and trimers of Al were used to estimate energetics and global minimum energy structures of clusters continuing up to 15 Al atoms. The second research topic addressed modeling of the collision process for atoms impinging on surfaces. In this simulation study qualitative aspects of the O atom collision with a graphite surface were analyzed. Four different O/graphite systems were considered and the aftermath of the impact was analyzed. The final area of investigation was related to the simulation of thin amorphous Si films on crystalline Si substrates. Parameters obtained in an earlier study were used to model an exposed amorphous Si surface and an a-Si/c-Si interface. Structural details for various film thicknesses were investigated at an atomistic level.

The structure, energetics, and nature of the chemical bonding of phenylthiol adsorbed on the Au(111) surface: implications for density-functional calculations of molecular-electronic conduction.

PubMed

Bilić, Ante; Reimers, Jeffrey R; Hush, Noel S

2005-03-01

The adsorption of phenylthiol on the Au(111) surface is modeled using Perdew and Wang density-functional calculations. Both direct molecular physisorption and dissociative chemisorption via S-H bond cleavage are considered as well as dimerization to form disulfides. For the major observed product, the chemisorbed thiol, an extensive potential-energy surface is produced as a function of both the azimuthal orientation of the adsorbate and the linear translation of the adsorbate through the key fcc, hcp, bridge, and top binding sites. Key structures are characterized, the lowest-energy one being a broad minimum of tilted orientation ranging from the bridge structure halfway towards the fcc one. The vertically oriented threefold binding sites, often assumed to dominate molecular electronics measurements, are identified as transition states at low coverage but become favored in dense monolayers. A similar surface is also produced for chemisorption of phenylthiol on Ag(111); this displays significant qualitative differences, consistent with the qualitatively different observed structures for thiol chemisorption on Ag and Au. Full contours of the minimum potential energy as a function of sulfur translation over the crystal face are described, from which the barrier to diffusion is deduced to be 5.8 kcal mol(-1), indicating that the potential-energy surface has low corrugation. The calculated bond lengths, adsorbate charge and spin density, and the density of electronic states all indicate that, at all sulfur locations, the adsorbate can be regarded as a thiyl species that forms a net single covalent bond to the surface of strength 31 kcal mol(-1). No detectable thiolate character is predicted, however, contrary to experimental results for alkyl thiols that indicate up to 20%-30% thiolate involvement. This effect is attributed to the asymptotic-potential error of all modern density functionals that becomes manifest through a 3-4 eV error in the lineup of the adsorbate and substrate bands. Significant implications are described for density-functional calculations of through-molecule electron transport in molecular electronics.

Energy-efficient algorithm for broadcasting in ad hoc wireless sensor networks.

PubMed

Xiong, Naixue; Huang, Xingbo; Cheng, Hongju; Wan, Zheng

2013-04-12

Broadcasting is a common and basic operation used to support various network protocols in wireless networks. To achieve energy-efficient broadcasting is especially important for ad hoc wireless sensor networks because sensors are generally powered by batteries with limited lifetimes. Energy consumption for broadcast operations can be reduced by minimizing the number of relay nodes based on the observation that data transmission processes consume more energy than data reception processes in the sensor nodes, and how to improve the network lifetime is always an interesting issue in sensor network research. The minimum-energy broadcast problem is then equivalent to the problem of finding the minimum Connected Dominating Set (CDS) for a connected graph that is proved NP-complete. In this paper, we introduce an Efficient Minimum CDS algorithm (EMCDS) with help of a proposed ordered sequence list. EMCDS does not concern itself with node energy and broadcast operations might fail if relay nodes are out of energy. Next we have proposed a Minimum Energy-consumption Broadcast Scheme (MEBS) with a modified version of EMCDS, and aimed at providing an efficient scheduling scheme with maximized network lifetime. The simulation results show that the proposed EMCDS algorithm can find smaller CDS compared with related works, and the MEBS can help to increase the network lifetime by efficiently balancing energy among nodes in the networks.

Minimum energy control for in vitro neurons.

PubMed

Nabi, Ali; Stigen, Tyler; Moehlis, Jeff; Netoff, Theoden

2013-06-01

To demonstrate the applicability of optimal control theory for designing minimum energy charge-balanced input waveforms for single periodically-firing in vitro neurons from brain slices of Long-Evans rats. The method of control uses the phase model of a neuron and does not require prior knowledge of the neuron's biological details. The phase model of a neuron is a one-dimensional model that is characterized by the neuron's phase response curve (PRC), a sensitivity measure of the neuron to a stimulus applied at different points in its firing cycle. The PRC for each neuron is experimentally obtained by measuring the shift in phase due to a short-duration pulse injected into the periodically-firing neuron at various phase values. Based on the measured PRC, continuous-time, charge-balanced, minimum energy control waveforms have been designed to regulate the next firing time of the neuron upon application at the onset of an action potential. The designed waveforms can achieve the inter-spike-interval regulation for in vitro neurons with energy levels that are lower than those of conventional monophasic pulsatile inputs of past studies by at least an order of magnitude. They also provide the advantage of being charge-balanced. The energy efficiency of these waveforms is also shown by performing several supporting simulations that compare the performance of the designed waveforms against that of phase shuffled surrogate inputs, variants of the minimum energy waveforms obtained from suboptimal PRCs, as well as pulsatile stimuli that are applied at the point of maximum PRC. It was found that the minimum energy waveforms perform better than all other stimuli both in terms of control and in the amount of energy used. Specifically, it was seen that these charge-balanced waveforms use at least an order of magnitude less energy than conventional monophasic pulsatile stimuli. The significance of this work is that it uses concepts from the theory of optimal control and introduces a novel approach in designing minimum energy charge-balanced input waveforms for neurons that are robust to noise and implementable in electrophysiological experiments.

Minimum energy control for in vitro neurons

NASA Astrophysics Data System (ADS)

Nabi, Ali; Stigen, Tyler; Moehlis, Jeff; Netoff, Theoden

2013-06-01

Objective. To demonstrate the applicability of optimal control theory for designing minimum energy charge-balanced input waveforms for single periodically-firing in vitro neurons from brain slices of Long-Evans rats. Approach. The method of control uses the phase model of a neuron and does not require prior knowledge of the neuron’s biological details. The phase model of a neuron is a one-dimensional model that is characterized by the neuron’s phase response curve (PRC), a sensitivity measure of the neuron to a stimulus applied at different points in its firing cycle. The PRC for each neuron is experimentally obtained by measuring the shift in phase due to a short-duration pulse injected into the periodically-firing neuron at various phase values. Based on the measured PRC, continuous-time, charge-balanced, minimum energy control waveforms have been designed to regulate the next firing time of the neuron upon application at the onset of an action potential. Main result. The designed waveforms can achieve the inter-spike-interval regulation for in vitro neurons with energy levels that are lower than those of conventional monophasic pulsatile inputs of past studies by at least an order of magnitude. They also provide the advantage of being charge-balanced. The energy efficiency of these waveforms is also shown by performing several supporting simulations that compare the performance of the designed waveforms against that of phase shuffled surrogate inputs, variants of the minimum energy waveforms obtained from suboptimal PRCs, as well as pulsatile stimuli that are applied at the point of maximum PRC. It was found that the minimum energy waveforms perform better than all other stimuli both in terms of control and in the amount of energy used. Specifically, it was seen that these charge-balanced waveforms use at least an order of magnitude less energy than conventional monophasic pulsatile stimuli. Significance. The significance of this work is that it uses concepts from the theory of optimal control and introduces a novel approach in designing minimum energy charge-balanced input waveforms for neurons that are robust to noise and implementable in electrophysiological experiments.

Energy Minimization of Discrete Protein Titration State Models Using Graph Theory.

PubMed

Purvine, Emilie; Monson, Kyle; Jurrus, Elizabeth; Star, Keith; Baker, Nathan A

2016-08-25

There are several applications in computational biophysics that require the optimization of discrete interacting states, for example, amino acid titration states, ligand oxidation states, or discrete rotamer angles. Such optimization can be very time-consuming as it scales exponentially in the number of sites to be optimized. In this paper, we describe a new polynomial time algorithm for optimization of discrete states in macromolecular systems. This algorithm was adapted from image processing and uses techniques from discrete mathematics and graph theory to restate the optimization problem in terms of "maximum flow-minimum cut" graph analysis. The interaction energy graph, a graph in which vertices (amino acids) and edges (interactions) are weighted with their respective energies, is transformed into a flow network in which the value of the minimum cut in the network equals the minimum free energy of the protein and the cut itself encodes the state that achieves the minimum free energy. Because of its deterministic nature and polynomial time performance, this algorithm has the potential to allow for the ionization state of larger proteins to be discovered.

Energy Minimization of Discrete Protein Titration State Models Using Graph Theory

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

Purvine, Emilie AH; Monson, Kyle E.; Jurrus, Elizabeth R.

There are several applications in computational biophysics which require the optimization of discrete interacting states; e.g., amino acid titration states, ligand oxidation states, or discrete rotamer angles. Such optimization can be very time-consuming as it scales exponentially in the number of sites to be optimized. In this paper, we describe a new polynomial-time algorithm for optimization of discrete states in macromolecular systems. This algorithm was adapted from image processing and uses techniques from discrete mathematics and graph theory to restate the optimization problem in terms of maximum flow-minimum cut graph analysis. The interaction energy graph, a graph in which verticesmore » (amino acids) and edges (interactions) are weighted with their respective energies, is transformed into a flow network in which the value of the minimum cut in the network equals the minimum free energy of the protein, and the cut itself encodes the state that achieves the minimum free energy. Because of its deterministic nature and polynomial-time performance, this algorithm has the potential to allow for the ionization state of larger proteins to be discovered.« less

Energy Minimization of Discrete Protein Titration State Models Using Graph Theory

PubMed Central

Purvine, Emilie; Monson, Kyle; Jurrus, Elizabeth; Star, Keith; Baker, Nathan A.

2016-01-01

There are several applications in computational biophysics which require the optimization of discrete interacting states; e.g., amino acid titration states, ligand oxidation states, or discrete rotamer angles. Such optimization can be very time-consuming as it scales exponentially in the number of sites to be optimized. In this paper, we describe a new polynomial-time algorithm for optimization of discrete states in macromolecular systems. This algorithm was adapted from image processing and uses techniques from discrete mathematics and graph theory to restate the optimization problem in terms of “maximum flow-minimum cut” graph analysis. The interaction energy graph, a graph in which vertices (amino acids) and edges (interactions) are weighted with their respective energies, is transformed into a flow network in which the value of the minimum cut in the network equals the minimum free energy of the protein, and the cut itself encodes the state that achieves the minimum free energy. Because of its deterministic nature and polynomial-time performance, this algorithm has the potential to allow for the ionization state of larger proteins to be discovered. PMID:27089174

Kinematical synthesis of an inversion of the double linked fourbar for morphing wing applications

NASA Astrophysics Data System (ADS)

Aguirrebeitia, J.; Avilés, R.; Fernández, I.; Abasolo, M.

2013-03-01

This paper presents the kinematical features of an inversion of the double linked fourbar for morphing wing purposes. The structure of the mechanism is obtained using structural synthesis concepts, from an initial conceptual schematic. Then, kinematic characteristics as instant center of rotation, lock positions, dead point positions and uncertainty positions are derived for this mechanism in order to face the last step, the dimensional synthesis; in this sense, two kinds of dimensional synthesis are arranged to guide the wing along two positions, and to fulfill with the second one some aerodynamic and minimum actuation energy related issues.

Abstract shapes of RNA.

PubMed

Giegerich, Robert; Voss, Björn; Rehmsmeier, Marc

2004-01-01

The function of a non-protein-coding RNA is often determined by its structure. Since experimental determination of RNA structure is time-consuming and expensive, its computational prediction is of great interest, and efficient solutions based on thermodynamic parameters are known. Frequently, however, the predicted minimum free energy structures are not the native ones, leading to the necessity of generating suboptimal solutions. While this can be accomplished by a number of programs, the user is often confronted with large outputs of similar structures, although he or she is interested in structures with more fundamental differences, or, in other words, with different abstract shapes. Here, we formalize the concept of abstract shapes and introduce their efficient computation. Each shape of an RNA molecule comprises a class of similar structures and has a representative structure of minimal free energy within the class. Shape analysis is implemented in the program RNAshapes. We applied RNAshapes to the prediction of optimal and suboptimal abstract shapes of several RNAs. For a given energy range, the number of shapes is considerably smaller than the number of structures, and in all cases, the native structures were among the top shape representatives. This demonstrates that the researcher can quickly focus on the structures of interest, without processing up to thousands of near-optimal solutions. We complement this study with a large-scale analysis of the growth behaviour of structure and shape spaces. RNAshapes is available for download and as an online version on the Bielefeld Bioinformatics Server.

Equilibrium Droplets on Deformable Substrates: Equilibrium Conditions.

PubMed

Koursari, Nektaria; Ahmed, Gulraiz; Starov, Victor M

2018-05-15

Equilibrium conditions of droplets on deformable substrates are investigated, and it is proven using Jacobi's sufficient condition that the obtained solutions really provide equilibrium profiles of both the droplet and the deformed support. At the equilibrium, the excess free energy of the system should have a minimum value, which means that both necessary and sufficient conditions of the minimum should be fulfilled. Only in this case, the obtained profiles provide the minimum of the excess free energy. The necessary condition of the equilibrium means that the first variation of the excess free energy should vanish, and the second variation should be positive. Unfortunately, the mentioned two conditions are not the proof that the obtained profiles correspond to the minimum of the excess free energy and they could not be. It is necessary to check whether the sufficient condition of the equilibrium (Jacobi's condition) is satisfied. To the best of our knowledge Jacobi's condition has never been verified for any already published equilibrium profiles of both the droplet and the deformable substrate. A simple model of the equilibrium droplet on the deformable substrate is considered, and it is shown that the deduced profiles of the equilibrium droplet and deformable substrate satisfy the Jacobi's condition, that is, really provide the minimum to the excess free energy of the system. To simplify calculations, a simplified linear disjoining/conjoining pressure isotherm is adopted for the calculations. It is shown that both necessary and sufficient conditions for equilibrium are satisfied. For the first time, validity of the Jacobi's condition is verified. The latter proves that the developed model really provides (i) the minimum of the excess free energy of the system droplet/deformable substrate and (ii) equilibrium profiles of both the droplet and the deformable substrate.

Minimum energy dissipation required for a logically irreversible operation

NASA Astrophysics Data System (ADS)

Takeuchi, Naoki; Yoshikawa, Nobuyuki

2018-01-01

According to Landauer's principle, the minimum heat emission required for computing is linked to logical entropy, or logical reversibility. The validity of Landauer's principle has been investigated for several decades and was finally demonstrated in recent experiments by showing that the minimum heat emission is associated with the reduction in logical entropy during a logically irreversible operation. Although the relationship between minimum heat emission and logical reversibility is being revealed, it is not clear how much free energy is required to be dissipated for a logically irreversible operation. In the present study, in order to reveal the connection between logical reversibility and free energy dissipation, we numerically demonstrated logically irreversible protocols using adiabatic superconductor logic. The calculation results of work during the protocol showed that, while the minimum heat emission conforms to Landauer's principle, the free energy dissipation can be arbitrarily reduced by performing the protocol quasistatically. The above results show that logical reversibility is not associated with thermodynamic reversibility, and that heat is not only emitted from logic devices but also absorbed by logic devices. We also formulated the heat emission from adiabatic superconductor logic during a logically irreversible operation at a finite operation speed.

Low energy isomers of (H{sub 2}O){sub 25} from a hierarchical method based on Monte Carlo temperature basin paving and molecular tailoring approaches benchmarked by MP2 calculations

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

Sahu, Nityananda; Gadre, Shridhar R., E-mail: gadre@iitk.ac.in, E-mail: sotiris.xantheas@pnnl.gov; Rakshit, Avijit

2014-10-28

We report new global minimum candidate structures for the (H{sub 2}O){sub 25} cluster that are lower in energy than the ones reported previously and correspond to hydrogen bonded networks with 42 hydrogen bonds and an interior, fully coordinated water molecule. These were obtained as a result of a hierarchical approach based on initial Monte Carlo Temperature Basin Paving sampling of the cluster's Potential Energy Surface with the Effective Fragment Potential, subsequent geometry optimization using the Molecular Tailoring Approach with the fragments treated at the second order Møller-Plesset (MP2) perturbation (MTA-MP2) and final refinement of the entire cluster at the MP2more » level of theory. The MTA-MP2 optimized cluster geometries, constructed from the fragments, were found to be within <0.5 kcal/mol from the minimum geometries obtained from the MP2 optimization of the entire (H{sub 2}O){sub 25} cluster. In addition, the grafting of the MTA-MP2 energies yields electronic energies that are within <0.3 kcal/mol from the MP2 energies of the entire cluster while preserving their energy rank order. Finally, the MTA-MP2 approach was found to reproduce the MP2 harmonic vibrational frequencies, constructed from the fragments, quite accurately when compared to the MP2 ones of the entire cluster in both the HOH bending and the OH stretching regions of the spectra.« less

The free energy landscape of pseudorotation in 3'-5' and 2'-5' linked nucleic acids.

PubMed

Li, Li; Szostak, Jack W

2014-02-19

The five-membered furanose ring is a central component of the chemical structure of biological nucleic acids. The conformations of the furanose ring can be analytically described using the concept of pseudorotation, and for RNA and DNA they are dominated by the C2'-endo and C3'-endo conformers. While the free energy difference between these two conformers can be inferred from NMR measurements, a free energy landscape of the complete pseudorotation cycle of nucleic acids in solution has remained elusive. Here, we describe a new free energy calculation method for molecular dynamics (MD) simulations using the two pseudorotation parameters directly as the collective variables. To validate our approach, we calculated the free energy surface of ribose pseudorotation in guanosine and 2'-deoxyguanosine. The calculated free energy landscape reveals not only the relative stability of the different pseudorotation conformers, but also the main transition path between the stable conformations. Applying this method to a standard A-form RNA duplex uncovered the expected minimum at the C3'-endo state. However, at a 2'-5' linkage, the minimum shifts to the C2'-endo conformation. The free energy of the C3'-endo conformation is 3 kcal/mol higher due to a weaker hydrogen bond and a reduced base stacking interaction. Unrestrained MD simulations suggest that the conversion from C3'-endo to C2'-endo and vice versa is on the nanosecond and microsecond time scale, respectively. These calculations suggest that 2'-5' linkages may enable folded RNAs to sample a wider spectrum of their pseudorotation conformations.

Can Structural Optimization Explain Slow Dynamics of Rocks?

NASA Astrophysics Data System (ADS)

Kim, H.; Vistisen, O.; Tencate, J. A.

2009-12-01

Slow dynamics is a recovery process that describes the return to an equilibrium state after some external energy input is applied and then removed. Experimental studies on many rocks have shown that a modest acoustic energy input results in slow dynamics. The recovery process of the stiffness has consistently been found to be linear to log(time) for a wide range of geomaterials and the time constants appear to be unique to the material [TenCate JA, Shankland TJ (1996), Geophys Res Lett 23, 3019-3022]. Measurements of this nonequilibrium effect in rocks (e.g. sandstones and limestones) have been linked directly to the cement holding the individual grains together [Darling TW, TenCate JA, Brown DW, Clausen B, Vogel SC (2004), Geophys Res Lett 31, L16604], also suggesting a potential link to porosity and permeability. Noting that slow dynamics consistently returns the overall stiffness of rocks to its maximum (original) state, it is hypothesized that the original state represents the global minimum strain energy state. Consequently the slow dynamics process represents the global minimization or optimization process. Structural optimization, which has been developed for engineering design, minimises the total strain energy by rearranging the material distribution [Kim H, Querin OM, Steven GP, Xie YM (2002), Struct Multidiscip Optim 24, 441-448]. The optimization process effectively rearranges the way the material is cemented. One of the established global optimization methods is simulated annealing (SA). Derived from cooling of metal to a thermal equilibrium, SA finds an optimum solution by iteratively moving the system towards the minimum energy state with a probability of 'uphill' moves. It has been established that the global optimum can be guaranteed by applying a log(time) linear cooling schedule [Hajek B (1988, Math Ops Res, 15, 311-329]. This work presents the original study of applying SA to the maximum stiffness optimization problem. Preliminary results indicate that the maximum stiffness solutions are achieved when using log(time) linear cooling schedule. The optimization history reveals that the overall stiffness of the structure is increased linearly to log(time). The results closely resemble the slow dynamics stiffness recovery of geomaterials and support the hypothesis that the slow dynamics is an optimization process for strain energy. [Work supported by the Department of Energy through the LANL/LDRD Program].

Concentrated energy addition for active drag reduction in hypersonic flow regime

NASA Astrophysics Data System (ADS)

Ashwin Ganesh, M.; John, Bibin

2018-01-01

Numerical optimization of hypersonic drag reduction technique based on concentrated energy addition is presented in this study. A reduction in wave drag is realized through concentrated energy addition in the hypersonic flowfield upstream of the blunt body. For the exhaustive optimization presented in this study, an in-house high precision inviscid flow solver has been developed. Studies focused on the identification of "optimum energy addition location" have revealed the existence of multiple minimum drag points. The wave drag coefficient is observed to drop from 0.85 to 0.45 when 50 Watts of energy is added to an energy bubble of 1 mm radius located at 74.7 mm upstream of the stagnation point. A direct proportionality has been identified between energy bubble size and wave drag coefficient. Dependence of drag coefficient on the upstream added energy magnitude is also revealed. Of the observed multiple minimum drag points, the energy deposition point (EDP) that offers minimum wave drag just after a sharp drop in drag is proposed as the most optimum energy addition location.

Computer-aided molecular modeling techniques for predicting the stability of drug cyclodextrin inclusion complexes in aqueous solutions

NASA Astrophysics Data System (ADS)

Faucci, Maria Teresa; Melani, Fabrizio; Mura, Paola

2002-06-01

Molecular modeling was used to investigate factors influencing complex formation between cyclodextrins and guest molecules and predict their stability through a theoretical model based on the search for a correlation between experimental stability constants ( Ks) and some theoretical parameters describing complexation (docking energy, host-guest contact surfaces, intermolecular interaction fields) calculated from complex structures at a minimum conformational energy, obtained through stochastic methods based on molecular dynamic simulations. Naproxen, ibuprofen, ketoprofen and ibuproxam were used as model drug molecules. Multiple Regression Analysis allowed identification of the significant factors for the complex stability. A mathematical model ( r=0.897) related log Ks with complex docking energy and lipophilic molecular fields of cyclodextrin and drug.

DFT approach to (benzylthio)acetic acid: Conformational search, molecular (monomer and dimer) structure, vibrational spectroscopy and some electronic properties

NASA Astrophysics Data System (ADS)

Sienkiewicz-Gromiuk, Justyna

2018-01-01

The DFT studies were carried out with the B3LYP method utilizing the 6-31G and 6-311++G(d,p) basis sets depending on whether the aim of calculations was to gain the geometry at equilibrium, or to calculate the optimized molecular structure of (benzylthio)acetic acid (Hbta) in the forms of monomer and dimer. The minimum conformational energy search was followed by the potential energy surface (PES) scan of all rotary bonds existing in the acid molecule. The optimized geometrical monomeric and dimeric structures of the title compound were compared with the experimental structural data in the solid state. The detailed vibrational interpretation of experimental infrared and Raman bands was performed on the basis of theoretically simulated ESFF-scaled wavenumbers calculated for the monomer and dimer structures of Hbta. The electronic characteristics of Hbta is also presented in terms of Mulliken atomic charges, frontier molecular orbitals and global reactivity descriptors. Additionally, the MEP and ESP surfaces were computed to predict coordination sites for potential metal complex formation.

Molecular Dynamic Simulation and Inhibitor Prediction of Cysteine Synthase Structured Model as a Potential Drug Target for Trichomoniasis

PubMed Central

Singh, Satendra; Singh, Atul Kumar; Gautam, Budhayash

2013-01-01

In our presented research, we made an attempt to predict the 3D model for cysteine synthase (A2GMG5_TRIVA) using homology-modeling approaches. To investigate deeper into the predicted structure, we further performed a molecular dynamics simulation for 10 ns and calculated several supporting analysis for structural properties such as RMSF, radius of gyration, and the total energy calculation to support the predicted structured model of cysteine synthase. The present findings led us to conclude that the proposed model is stereochemically stable. The overall PROCHECK G factor for the homology-modeled structure was −0.04. On the basis of the virtual screening for cysteine synthase against the NCI subset II molecule, we present the molecule 1-N, 4-N-bis [3-(1H-benzimidazol-2-yl) phenyl] benzene-1,4-dicarboxamide (ZINC01690699) having the minimum energy score (−13.0 Kcal/Mol) and a log P value of 6 as a potential inhibitory molecule used to inhibit the growth of T. vaginalis infection. PMID:24073401

Potential energy function for CH3+CH3 ⇆ C2H6: Attributes of the minimum energy path

NASA Astrophysics Data System (ADS)

Robertson, S. H.; Wardlaw, D. M.; Hirst, D. M.

1993-11-01

The region of the potential energy surface for the title reaction in the vicinity of its minimum energy path has been predicted from the analysis of ab initio electronic energy calculations. The ab initio procedure employs a 6-31G** basis set and a configuration interaction calculation which uses the orbitals obtained in a generalized valence bond calculation. Calculated equilibrium properties of ethane and of isolated methyl radical are compared to existing theoretical and experimental results. The reaction coordinate is represented by the carbon-carbon interatomic distance. The following attributes are reported as a function of this distance and fit to functional forms which smoothly interpolate between reactant and product values of each attribute: the minimum energy path potential, the minimum energy path geometry, normal mode frequencies for vibrational motion orthogonal to the reaction coordinate, a torsional potential, and a fundamental anharmonic frequency for local mode, out-of-plane CH3 bending (umbrella motion). The best representation is provided by a three-parameter modified Morse function for the minimum energy path potential and a two-parameter hyperbolic tangent switching function for all other attributes. A poorer but simpler representation, which may be satisfactory for selected applications, is provided by a standard Morse function and a one-parameter exponential switching function. Previous applications of the exponential switching function to estimate the reaction coordinate dependence of the frequencies and geometry of this system have assumed the same value of the range parameter α for each property and have taken α to be less than or equal to the ``standard'' value of 1.0 Å-1. Based on the present analysis this is incorrect: The α values depend on the property and range from ˜1.2 to ˜1.8 Å-1.

Information dynamics in living systems: prokaryotes, eukaryotes, and cancer.

PubMed

Frieden, B Roy; Gatenby, Robert A

2011-01-01

Living systems use information and energy to maintain stable entropy while far from thermodynamic equilibrium. The underlying first principles have not been established. We propose that stable entropy in living systems, in the absence of thermodynamic equilibrium, requires an information extremum (maximum or minimum), which is invariant to first order perturbations. Proliferation and death represent key feedback mechanisms that promote stability even in a non-equilibrium state. A system moves to low or high information depending on its energy status, as the benefit of information in maintaining and increasing order is balanced against its energy cost. Prokaryotes, which lack specialized energy-producing organelles (mitochondria), are energy-limited and constrained to an information minimum. Acquisition of mitochondria is viewed as a critical evolutionary step that, by allowing eukaryotes to achieve a sufficiently high energy state, permitted a phase transition to an information maximum. This state, in contrast to the prokaryote minima, allowed evolution of complex, multicellular organisms. A special case is a malignant cell, which is modeled as a phase transition from a maximum to minimum information state. The minimum leads to a predicted power-law governing the in situ growth that is confirmed by studies measuring growth of small breast cancers. We find living systems achieve a stable entropic state by maintaining an extreme level of information. The evolutionary divergence of prokaryotes and eukaryotes resulted from acquisition of specialized energy organelles that allowed transition from information minima to maxima, respectively. Carcinogenesis represents a reverse transition: of an information maximum to minimum. The progressive information loss is evident in accumulating mutations, disordered morphology, and functional decline characteristics of human cancers. The findings suggest energy restriction is a critical first step that triggers the genetic mutations that drive somatic evolution of the malignant phenotype.

Au11Re: A hollow or endohedral binary cluster?

NASA Astrophysics Data System (ADS)

MacLeod Carey, Desmond; Muñoz-Castro, Alvaro

2018-06-01

In this letter, we discussed the plausible formation of [Au11Re] as a superatom with an electronic structure accounted by the 1S21P61D10 shell order, denoting similar stability to [W@Au12]. The possible hollow or endohedral structures show a variable HOMO-LUMO gap according to the given structure (from 0.33 to 1.30 eV, at the PBE/ZORA level). Our results show that the energy minimum is an endohedral arrangement, where Re is encapsulated in a D3h-Au11 cage, retaining a higher gold-dopant stoichiometric ratio. This approach is useful for further rationalization and design of novel superatoms expanding the libraries of endohedral clusters.

30 CFR 250.908 - What are the minimum structural fatigue design requirements?

Code of Federal Regulations, 2010 CFR

2010-07-01

... 30 Mineral Resources 2 2010-07-01 2010-07-01 false What are the minimum structural fatigue design... Platform Approval Program § 250.908 What are the minimum structural fatigue design requirements? (a) API RP... (incorporated by reference as specified in 30 CFR 250.198), requires that the design fatigue life of each joint...

Probing the structural evolution of ruthenium doped germanium clusters: Photoelectron spectroscopy and density functional theory calculations

PubMed Central

Jin, Yuanyuan; Lu, Shengjie; Hermann, Andreas; Kuang, Xiaoyu; Zhang, Chuanzhao; Lu, Cheng; Xu, Hongguang; Zheng, Weijun

2016-01-01

We present a combined experimental and theoretical study of ruthenium doped germanium clusters, RuGen− (n = 3–12), and their corresponding neutral species. Photoelectron spectra of RuGen− clusters are measured at 266 nm. The vertical detachment energies (VDEs) and adiabatic detachment energies (ADEs) are obtained. Unbiased CALYPSO structure searches confirm the low-lying structures of anionic and neutral ruthenium doped germanium clusters in the size range of 3 ≤ n ≤ 12. Subsequent geometry optimizations using density functional theory (DFT) at PW91/LANL2DZ level are carried out to determine the relative stability and electronic properties of ruthenium doped germanium clusters. It is found that most of the anionic and neutral clusters have very similar global features. Although the global minimum structures of the anionic and neutral clusters are different, their respective geometries are observed as the low-lying isomers in either case. In addition, for n > 8, the Ru atom in RuGen−/0 clusters is absorbed endohedrally in the Ge cage. The theoretically predicted vertical and adiabatic detachment energies are in good agreement with the experimental measurements. The excellent agreement between DFT calculations and experiment enables a comprehensive evaluation of the geometrical and electronic structures of ruthenium doped germanium clusters. PMID:27439955

[Analysis of grey correlation between energy consumption and economic growth in Liaoning Province, China.

PubMed

Wang, Li; Xi, Feng Ming; Wang, Jiao Yue

2016-03-01

The contradiction between energy consumption and economic growth is increasingly prominent in China. Liaoning Province as one of Chinese heavy industrial bases, consumes a large amount of energy. Its economic development has a strong dependence on energy consumption, but the energy in short supply become more apparent. In order to further understand the relationship between energy consumption and economic growth and put forward scientific suggestions on low carbon development, we used the grey correlation analysis method to separately examine the relevance of economic growth with energy consumption industries and energy consumption varieties through analy sis of energy consumption and economic growth data in Liaoning Province from 2000 to 2012. The results showed that the wholesale and retail sector and hotel and restaurant sector were in the minimum energy consumption in all kinds of sectors, but they presented the closest connection with the economic growth. Although industry energy consumption was the maximum, the degree of connection between industry energy consumption and economic growth was weak. In all types of energy consumption, oil and hydro-power consumption had a significant connection with economic growth. However, the degree of connection of coal consumption with economic growth was not significant, which meant that coal utilization efficiency was low. In order to achieve low carbon and sustainable development, Liaoning Province should transform the economic growth mode, adjust industry structure, optimize energy structure, and improve energy utilization efficiency, especially promote producer services and develop clean and renewable energy.

RNAmutants: a web server to explore the mutational landscape of RNA secondary structures

PubMed Central

Waldispühl, Jerome; Devadas, Srinivas; Berger, Bonnie; Clote, Peter

2009-01-01

The history and mechanism of molecular evolution in DNA have been greatly elucidated by contributions from genetics, probability theory and bioinformatics—indeed, mathematical developments such as Kimura's neutral theory, Kingman's coalescent theory and efficient software such as BLAST, ClustalW, Phylip, etc., provide the foundation for modern population genetics. In contrast to DNA, the function of most noncoding RNA depends on tertiary structure, experimentally known to be largely determined by secondary structure, for which dynamic programming can efficiently compute the minimum free energy secondary structure. For this reason, understanding the effect of pointwise mutations in RNA secondary structure could reveal fundamental properties of structural RNA molecules and improve our understanding of molecular evolution of RNA. The web server RNAmutants provides several efficient tools to compute the ensemble of low-energy secondary structures for all k-mutants of a given RNA sequence, where k is bounded by a user-specified upper bound. As we have previously shown, these tools can be used to predict putative deleterious mutations and to analyze regulatory sequences from the hepatitis C and human immunodeficiency genomes. Web server is available at http://bioinformatics.bc.edu/clotelab/RNAmutants/, and downloadable binaries at http://rnamutants.csail.mit.edu/. PMID:19531740

c-T phase diagram and Landau free energies of (AgAu)55 nanoalloy via neural-network molecular dynamic simulations.

PubMed

Chiriki, Siva; Jindal, Shweta; Bulusu, Satya S

2017-10-21

For understanding the structure, dynamics, and thermal stability of (AgAu) 55 nanoalloys, knowledge of the composition-temperature (c-T) phase diagram is essential due to the explicit dependence of properties on composition and temperature. Experimentally, generating the phase diagrams is very challenging, and therefore theoretical insight is necessary. We use an artificial neural network potential for (AgAu) 55 nanoalloys. Predicted global minimum structures for pure gold and gold rich compositions are lower in energy compared to previous reports by density functional theory. The present work based on c-T phase diagram, surface area, surface charge, probability of isomers, and Landau free energies supports the enhancement of catalytic property of Ag-Au nanoalloys by incorporation of Ag up to 24% by composition in Au nanoparticles as found experimentally. The phase diagram shows that there is a coexistence temperature range of 70 K for Ag 28 Au 27 compared to all other compositions. We propose the power spectrum coefficients derived from spherical harmonics as an order parameter to calculate Landau free energies.

Computing the Partition Function for Kinetically Trapped RNA Secondary Structures

PubMed Central

Lorenz, William A.; Clote, Peter

2011-01-01

An RNA secondary structure is locally optimal if there is no lower energy structure that can be obtained by the addition or removal of a single base pair, where energy is defined according to the widely accepted Turner nearest neighbor model. Locally optimal structures form kinetic traps, since any evolution away from a locally optimal structure must involve energetically unfavorable folding steps. Here, we present a novel, efficient algorithm to compute the partition function over all locally optimal secondary structures of a given RNA sequence. Our software, RNAlocopt runs in time and space. Additionally, RNAlocopt samples a user-specified number of structures from the Boltzmann subensemble of all locally optimal structures. We apply RNAlocopt to show that (1) the number of locally optimal structures is far fewer than the total number of structures – indeed, the number of locally optimal structures approximately equal to the square root of the number of all structures, (2) the structural diversity of this subensemble may be either similar to or quite different from the structural diversity of the entire Boltzmann ensemble, a situation that depends on the type of input RNA, (3) the (modified) maximum expected accuracy structure, computed by taking into account base pairing frequencies of locally optimal structures, is a more accurate prediction of the native structure than other current thermodynamics-based methods. The software RNAlocopt constitutes a technical breakthrough in our study of the folding landscape for RNA secondary structures. For the first time, locally optimal structures (kinetic traps in the Turner energy model) can be rapidly generated for long RNA sequences, previously impossible with methods that involved exhaustive enumeration. Use of locally optimal structure leads to state-of-the-art secondary structure prediction, as benchmarked against methods involving the computation of minimum free energy and of maximum expected accuracy. Web server and source code available at http://bioinformatics.bc.edu/clotelab/RNAlocopt/. PMID:21297972

Ab initio study of the CO-N2 complex: a new highly accurate intermolecular potential energy surface and rovibrational spectrum.

PubMed

Cybulski, Hubert; Henriksen, Christian; Dawes, Richard; Wang, Xiao-Gang; Bora, Neha; Avila, Gustavo; Carrington, Tucker; Fernández, Berta

2018-05-09

A new, highly accurate ab initio ground-state intermolecular potential-energy surface (IPES) for the CO-N2 complex is presented. Thousands of interaction energies calculated with the CCSD(T) method and Dunning's aug-cc-pVQZ basis set extended with midbond functions were fitted to an analytical function. The global minimum of the potential is characterized by an almost T-shaped structure and has an energy of -118.2 cm-1. The symmetry-adapted Lanczos algorithm was used to compute rovibrational energies (up to J = 20) on the new IPES. The RMSE with respect to experiment was found to be on the order of 0.038 cm-1 which confirms the very high accuracy of the potential. This level of agreement is among the best reported in the literature for weakly bound systems and considerably improves on those of previously published potentials.

Industrial femtosecond lasers for machining of heat-sensitive polymers (Conference Presentation)

NASA Astrophysics Data System (ADS)

Hendricks, Frank; Bernard, Benjamin; Matylitsky, Victor V.

2017-03-01

Heat-sensitive materials, such as polymers, are used increasingly in various industrial sectors such as medical device manufacturing and organic electronics. Medical applications include implantable devices like stents, catheters and wires, which need to be structured and cut with minimum heat damage. Also the flat panel display market moves from LCD displays to organic LED (OLED) solutions, which utilize heat-sensitive polymer substrates. In both areas, the substrates often consist of multilayer stacks with different types of materials, such as metals, dielectric layers and polymers with different physical characteristic. The different thermal behavior and laser absorption properties of the materials used makes these stacks difficult to machine using conventional laser sources. Femtosecond lasers are an enabling technology for micromachining of these materials since it is possible to machine ultrafine structures with minimum thermal impact and very precise control over material removed. An industrial femtosecond Spirit HE laser system from Spectra-Physics with pulse duration <400 fs, pulse energies of >120 μJ and average output powers of >16 W is an ideal tool for industrial micromachining of a wide range of materials with highest quality and efficiency. The laser offers process flexibility with programmable pulse energy, repetition rate, and pulse width. In this paper, we provide an overview of machining heat-sensitive materials using Spirit HE laser. In particular, we show how the laser parameters (e.g. laser wavelength, pulse duration, applied energy and repetition rate) and the processing strategy (gas assisted single pass cut vs. multi-scan process) influence the efficiency and quality of laser processing.

Molecular structure and conformation of N-2-[3'-(methoxysalicylideneimino)benzyl]-3″-methoxysalicylideneimine

NASA Astrophysics Data System (ADS)

Dey, D. K.; Dey, S. P.; Elmali, A.; Elerman, Y.

2001-05-01

The Schiff base, N-2-[3'-(methoxysalicylideneimino)benzyl]-3″-methoxysalicylidene-imine, 1,2-C 6H 4[NCHC 6H 3(OMe-3')OH-2']CH 2NCHC 6H 3(OMe-3″)OH-2″, has been prepared by the reaction of 2-amino-1-benzylamine and 3-methoxysalicylaldehyde ( o-vanillin) in ethanol. The molecular structure has been confirmed by single crystal X-ray crystallography. The crystal is in the monoclinic space group P2 1/ n with a=16.179(5), b=6.715(5), c=18.780(6) Å, β=100.56(3)°, Dcalc=1.293 mg cm -3, V=2006(2) Å 3 and R=0.0357 for 3929 independent reflections. The 1H and 13C NMR spectra in CDCl 3 solution indicate the retention of solid state structure in solution. The title compound is not planar. Intramolecular hydrogen bonds occur between O(1) and N(1) [2.614(2) Å] and between O(2) and N(2) [2.585(2) Å] atoms, the hydrogen atom essentially being bonded to the oxygen atom. Minimum energy conformations from AM1 were calculated as a function of five torsion angles θ1 (C6-C7-N1-C8), θ2 (C14-N2-C15-C16), θ3 (C9-C8-N1-C7), θ4 (C13-C14-N2-C15) and θ5 (C10-C9-C8-N1), varied every 5°. The optimized geometry of the crystal structure corresponding to the non-planar conformation is the most stable conformation in all calculations. The results strongly indicate that the minimum energy conformation is primarily determined by non-bonded hydrogen-hydrogen repulsions.

The drift-diffusion interpretation of the electron current within the organic semiconductor characterized by the bulk single energy trap level

NASA Astrophysics Data System (ADS)

Cvikl, B.

2010-01-01

The closed solution for the internal electric field and the total charge density derived in the drift-diffusion approximation for the model of a single layer organic semiconductor structure characterized by the bulk shallow single trap-charge energy level is presented. The solutions for two examples of electric field boundary conditions are tested on room temperature current density-voltage data of the electron conducting aluminum/tris(8-hydroxyquinoline aluminum/calcium structure [W. Brütting et al., Synth. Met. 122, 99 (2001)] for which jexp∝Va3.4, within the interval of bias 0.4 V≤Va≤7. In each case investigated the apparent electron mobility determined at given bias is distributed within a given, finite interval of values. The bias dependence of the logarithm of their lower limit, i.e., their minimum values, is found to be in each case, to a good approximation, proportional to the square root of the applied electric field. On account of the bias dependence as incorporated in the minimum value of the apparent electron mobility the spatial distribution of the organic bulk electric field as well as the total charge density turn out to be bias independent. The first case investigated is based on the boundary condition of zero electric field at the electron injection interface. It is shown that for minimum valued apparent mobilities, the strong but finite accumulation of electrons close to the anode is obtained, which characterize the inverted space charge limited current (SCLC) effect. The second example refers to the internal electric field allowing for self-adjustment of its boundary values. The total electron charge density is than found typically to be of U shape, which may, depending on the parameters, peak at both or at either Alq3 boundary. It is this example in which the proper SCLC effect is consequently predicted. In each of the above two cases, the calculations predict the minimum values of the electron apparent mobility, which substantially exceed the corresponding published measurements. For this reason the effect of the drift term alone is additionally investigated. On the basis of the published empirical electron mobilities and the diffusion term revoked, it is shown that the steady state electron current density within the Al/Alq3 (97 nm)/Ca single layer organic structure may well be pictured within the drift-only interpretation of the charge carriers within the Alq3 organic characterized by the single (shallow) trap energy level. In order to arrive at this result, it is necessary that the nonzero electric field, calculated to exist at the electron injecting Alq3/Ca boundary, is to be appropriately accounted for in the computation.

Free Energy Calculations of Crystalline Hard Sphere Complexes Using Density Functional Theory

DOE PAGES

Gunawardana, K. G.S.H.; Song, Xueyu

2014-12-22

Recently developed fundamental measure density functional theory (FMT) is used to study binary hard sphere (HS) complexes in crystalline phases. By comparing the excess free energy, pressure and phase diagram, we show that the fundamental measure functional yields good agreements to the available simulation results of AB, AB 2 and AB 13 crystals. Additionally, we use this functional to study the HS models of five binary crystals, Cu 5Zr(C15 b), Cu 51Zr 14(β), Cu 10Zr 7(φ), CuZr(B2) and CuZr 2 (C11 b), which are observed in the Cu-Zr system. The FMT functional gives well behaved minimum for most of themore » hard sphere crystal complexes in the two dimensional Gaussian space, namely a crystalline phase. However, the current version of FMT functional (white Bear) fails to give a stable minimum for the structure Cu 10Zr 7(φ). We argue that the observed solid phases for the HS models of the Cu-Zr system are true thermodynamic stable phases and can be used as a reference system in perturbation calculations.« less

Free energy and hidden barriers of the β-sheet structure of prion protein.

PubMed

Paz, S Alexis; Abrams, Cameron F

2015-10-13

On-the-fly free-energy parametrization is a new collective variable biasing approach akin to metadynamics with one important distinction: rather than acquiring an accelerated distribution via a history-dependent bias potential, sampling on this distribution is achieved from the beginning of the simulation using temperature-accelerated molecular dynamics. In the present work, we compare the performance of both approaches to compute the free-energy profile along a scalar collective variable measuring the H-bond registry of the β-sheet structure of the mouse Prion protein. Both methods agree on the location of the free-energy minimum, but free-energy profiles from well-tempered metadynamics are subject to a much higher degree of statistical noise due to hidden barriers. The sensitivity of metadynamics to hidden barriers is shown to be a consequence of the history dependence of the bias potential, and we detail the nature of these barriers for the prion β-sheet. In contrast, on-the-fly parametrization is much less sensitive to these barriers and thus displays improved convergence behavior relative to that of metadynamics. While hidden barriers are a frequent and central issue in free-energy methods, on-the-fly free-energy parametrization appears to be a robust and preferable method to confront this issue.

Principle of Minimum Energy in Magnetic Reconnection in a Self-organized Critical Model for Solar Flares

NASA Astrophysics Data System (ADS)

Farhang, Nastaran; Safari, Hossein; Wheatland, Michael S.

2018-05-01

Solar flares are an abrupt release of magnetic energy in the Sun’s atmosphere due to reconnection of the coronal magnetic field. This occurs in response to turbulent flows at the photosphere that twist the coronal field. Similar to earthquakes, solar flares represent the behavior of a complex system, and expectedly their energy distribution follows a power law. We present a statistical model based on the principle of minimum energy in a coronal loop undergoing magnetic reconnection, which is described as an avalanche process. We show that the distribution of peaks for the flaring events in this self-organized critical system is scale-free. The obtained power-law index of 1.84 ± 0.02 for the peaks is in good agreement with satellite observations of soft X-ray flares. The principle of minimum energy can be applied for general avalanche models to describe many other phenomena.

Theoretical investigation on the potential energy surface for the reactions of B, Al and Ga with NO

NASA Astrophysics Data System (ADS)

Zhang, Luning; Zhou, Mingfei

2000-06-01

The structures, binding energies and vibrational frequencies of various MNO structural isomers (M=B, Al and Ga) in their ground triplet states have been determined using the density functional (B3LYP, BP86 and B3PW91) and MP2 methods. The potential energy surfaces of the M+NO reactions have been developed at the B3LYP/6-311+G(d) level of theory, and transition states on the isomerization potential energy surfaces have been characterized. Our calculation results show that four BNO isomers, namely, nitrosyl BNO, isonitrosyl BON, side-bonded B- η2-NO and the inserted NBO molecules are stationary points, while for Al and Ga, only the MNO (nitrosyl), MON (isonitrosyl) and the OMN (insertion) molecules are local minimum. The B+NO reaction products are more strongly bonded compared to the Al and Ga+NO systems due to strong covalent bonding. The interactions of B, Al and Ga atoms with NO to generate nitrosyl and isonitrosyl addition molecules are barrierless, but subsequent isomerization reactions to form the side-bonded molecules and the inserted products require activation energy.

Energy Harvesting from Fluid Flow in Water Pipelines for Smart Metering Applications

NASA Astrophysics Data System (ADS)

Hoffmann, D.; Willmann, A.; Göpfert, R.; Becker, P.; Folkmer, B.; Manoli, Y.

2013-12-01

In this paper a rotational, radial-flux energy harvester incorporating a three-phase generation principle is presented for converting energy from water flow in domestic water pipelines. The energy harvester together with a power management circuit and energy storage is used to power a smart metering system installed underground making it independent from external power supplies or depleting batteries. The design of the radial-flux energy harvester is adapted to the housing of a conventional mechanical water flow meter enabling the use of standard components such as housing and impeller. The energy harvester is able to generate up to 720 mW when using a flow rate of 20 l/min (fully opened water tab). A minimum flow rate of 3 l/min is required to get the harvester started. In this case a power output of 2 mW is achievable. By further design optimization of the mechanical structure including the impeller and magnetic circuit the threshold flow rate can be further reduced.

Homogeneous and heterogeneous noncovalent dimers of formaldehyde and thioformaldehyde: structures, energetics, and vibrational frequencies.

PubMed

Van Dornshuld, Eric; Holy, Christina M; Tschumper, Gregory S

2014-05-08

This work provides the first characterization of five stationary points of the homogeneous thioformaldehyde dimer, (CH2S)2, and seven stationary points of the heterogeneous formaldehyde/thioformaldehyde dimer, CH2O/CH2S, with correlated ab initio electronic structure methods. Full geometry optimizations and corresponding harmonic vibrational frequencies were computed with second-order Møller-Plesset perturbation theory (MP2) and 13 different density functionals in conjunction with triple-ζ basis sets augmented with diffuse and multiple sets of polarization functions. The MP2 results indicate that the three stationary points of (CH2S)2 and four of CH2O/CH2S are minima, in contrast to two stationary points of the formaldehyde dimer, (CH2O)2. Single-point energies were also computed using the explicitly correlated MP2-F12 and CCSD(T)-F12 methods and basis sets as large as heavy-aug-cc-pVTZ. The (CH2O)2 and CH2O/CH2S MP2 and MP2-F12 binding energies deviated from the CCSD(T)-F12 binding energies by no more than 0.2 and 0.4 kcal mol(-1), respectively. The (CH2O)2 and CH2O/CH2S global minimum is the same at every level of theory. However, the MP2 methods overbind (CH2S)2 by as much as 1.1 kcal mol(-1), effectively altering the energetic ordering of the thioformaldehyde dimer minima relative to the CCSD(T)-F12 energies. The CCSD(T)-F12 binding energies of the (CH2O)2 and CH2O/CH2S stationary points are quite similar, with the former ranging from around -2.4 to -4.6 kcal mol(-1) and the latter from about -1.1 to -4.4 kcal mol(-1). Corresponding (CH2S)2 stationary points have appreciably smaller CCSD(T)-F12 binding energies ranging from ca. -1.1 to -3.4 kcal mol(-1). The vibrational frequency shifts upon dimerization are also reported for each minimum on the MP2 potential energy surfaces.

Exploring load, velocity, and surface disorder dependence of friction with one-dimensional and two-dimensional models.

PubMed

Dagdeviren, Omur E

2018-08-03

The effect of surface disorder, load, and velocity on friction between a single asperity contact and a model surface is explored with one-dimensional and two-dimensional Prandtl-Tomlinson (PT) models. We show that there are fundamental physical differences between the predictions of one-dimensional and two-dimensional models. The one-dimensional model estimates a monotonic increase in friction and energy dissipation with load, velocity, and surface disorder. However, a two-dimensional PT model, which is expected to approximate a tip-sample system more realistically, reveals a non-monotonic trend, i.e. friction is inert to surface disorder and roughness in wearless friction regime. The two-dimensional model discloses that the surface disorder starts to dominate the friction and energy dissipation when the tip and the sample interact predominantly deep into the repulsive regime. Our numerical calculations address that tracking the minimum energy path and the slip-stick motion are two competing effects that determine the load, velocity, and surface disorder dependence of friction. In the two-dimensional model, the single asperity can follow the minimum energy path in wearless regime; however, with increasing load and sliding velocity, the slip-stick movement dominates the dynamic motion and results in an increase in friction by impeding tracing the minimum energy path. Contrary to the two-dimensional model, when the one-dimensional PT model is employed, the single asperity cannot escape to the minimum energy minimum due to constraint motion and reveals only a trivial dependence of friction on load, velocity, and surface disorder. Our computational analyses clarify the physical differences between the predictions of the one-dimensional and two-dimensional models and open new avenues for disordered surfaces for low energy dissipation applications in wearless friction regime.

A Multi-Level Decision Fusion Strategy for Condition Based Maintenance of Composite Structures

PubMed Central

Sharif Khodaei, Zahra; Aliabadi, M.H.

2016-01-01

In this work, a multi-level decision fusion strategy is proposed which weighs the Value of Information (VoI) against the intended functions of a Structural Health Monitoring (SHM) system. This paper presents a multi-level approach for three different maintenance strategies in which the performance of the SHM systems is evaluated against its intended functions. Level 1 diagnosis results in damage existence with minimum sensors covering a large area by finding the maximum energy difference for the guided waves propagating in pristine structure and the post-impact state; Level 2 diagnosis provides damage detection and approximate localization using an approach based on Electro-Mechanical Impedance (EMI) measures, while Level 3 characterizes damage (exact location and size) in addition to its detection by utilising a Weighted Energy Arrival Method (WEAM). The proposed multi-level strategy is verified and validated experimentally by detection of Barely Visible Impact Damage (BVID) on a curved composite fuselage panel. PMID:28773910

Analysis of Protein Thermostability Enhancing Factors in Industrially Important Thermus Bacteria Species

PubMed Central

Kumwenda, Benjamin; Litthauer, Derek; Bishop, Özlem Tastan; Reva, Oleg

2013-01-01

Elucidation of evolutionary factors that enhance protein thermostability is a critical problem and was the focus of this work on Thermus species. Pairs of orthologous sequences of T. scotoductus SA-01 and T. thermophilus HB27, with the largest negative minimum folding energy (MFE) as predicted by the UNAFold algorithm, were statistically analyzed. Favored substitutions of amino acids residues and their properties were determined. Substitutions were analyzed in modeled protein structures to determine their locations and contribution to energy differences using PyMOL and FoldX programs respectively. Dominant trends in amino acid substitutions consistent with differences in thermostability between orthologous sequences were observed. T. thermophilus thermophilic proteins showed an increase in non-polar, tiny, and charged amino acids. An abundance of alanine substituted by serine and threonine, as well as arginine substituted by glutamine and lysine was observed in T. thermophilus HB27. Structural comparison showed that stabilizing mutations occurred on surfaces and loops in protein structures. PMID:24023508

Preferential flow in connected soil structures and the principle of "maximum energy dissipation": A thermodynamic perspective

NASA Astrophysics Data System (ADS)

Zehe, E.; Blume, T.; Bloeschl, G.

2009-04-01

"There is preferential flow at all scales"? This was a key message in a talk on ?Idle thoughts on a unifying theory of catchment hydrology? given by Bloeschl (2006). In this context ?preferential flow? was used to address rapid water flow along spatially connected flow paths of minimum flow resistance. Preferential flow seems in fact rather the rule than the exception. It occurs locally in non capillary macropores, at the hillslope scale in surface rills or through subsurface pipes. Rapid flow in connected biopores or sometimes shrinkage cracks is today accepted to play a key role for transport of agrochemicals in cohesive soils. The spatial distribution of worm burrows in the landscape may, furthermore, exert crucial control on rainfall runoff response and sediment yields at the hillslope and catchment scales. However, even if the population of connected biopores/macropores is known in soil we struggle in predicting onset, timing and strength of preferential flow events. Preferential flow is an intermittent, threshold phenomenon. Onset and intensity seems to be determined by the strength of the rainfall forcing and the wetness state of the soil. Furthermore, burrows of deep digging aenecic earthworms can ? even when being abandoned ? persist over decades as suggested by accumulation of clay particles or even radio nuclides. Thus, these structures ?survive? severe rainfall and subsurface flow events and still remain functional in the hydrological system. Why is it sometimes ?favourable? to take flow paths of minimum flow resistance and sometimes not? Why do these flow paths/ structures persist such a long time? Following Kleidon and Schimansky (2008) we suggest that a thermodynamic perspective ? looking at soil water flow as dissipative process in an open, non equilibrium thermodynamic system ? may help unrevealing these questions. However, we suggest a complementary perspective on soil water flow focusing rather on entropy production but on dissipation of Helmholtz free energy. Thermodynamic equilibrium is a state of minimum free energy. The latter is determined by potential energy and capillary energy in soil, which in turn strongly depends on soil moisture, pore size distribution and depth to groundwater. The objective of this study is threefold. First, we will introduce the necessary theoretical background. Second we suggest ? based on simulations with a physically based hydrological model ? that water flow in connected preferential pathways assures a faster relaxation towards thermodynamic equilibrium through a faster drainage of ?excess water? and a faster redistribution of ?capillary water? within the soil. The latter process is of prime importance in case of cohesive soils where the pore size distribution is dominated by medium and small pores. Third, an application of a physically based hydrological model to predict water flow and runoff response from a pristine catchment in the Chilenean Andes underpins this hypothesis. Behavioral model structures that allow a good match of the observed hydrographs turned out to be most efficient in dissipating free energy by means of preferential flow. It seems that a population of connected preferential pathways is favourable both for resilience and stability of these soils during extreme events and to retain water resources for the ecosystem at the same time. We suggest that this principle of ?maximum energy dissipation? may on the long term help us to better understand why soil structures remain stable, threshold nature of preferential as well as offer a means to further reduce model structural uncertainty. Bloeschl, G. 2006. Idle thoughts on a unifying theory of catchment Hydrology. Geophysical Research Abstracts, Vol. 8, 10677, 2006 SRef-ID: 1607-7962/gra/EGU06-A-10677 European Geosciences Union 2006 Kleidon, A., and S. Schymanski (2008), Thermodynamics and optimality of the water budget on land: A review, Geophys. Res. Lett., 35, L20404, doi:10.1029/ 2008GL035393.

Predictions of thermal buckling strengths of hypersonic aircraft sandwich panels using minimum potential energy and finite element methods

NASA Technical Reports Server (NTRS)

Ko, William L.

1995-01-01

Thermal buckling characteristics of hypersonic aircraft sandwich panels of various aspect ratios were investigated. The panel is fastened at its four edges to the substructures under four different edge conditions and is subjected to uniform temperature loading. Minimum potential energy theory and finite element methods were used to calculate the panel buckling temperatures. The two methods gave fairly close buckling temperatures. However, the finite element method gave slightly lower buckling temperatures than those given by the minimum potential energy theory. The reasons for this slight discrepancy in eigensolutions are discussed in detail. In addition, the effect of eigenshifting on the eigenvalue convergence rate is discussed.

Effects of Energy Dissipation in the Sphere-Restricted Full Three-Body Problem

NASA Astrophysics Data System (ADS)

Gabriel, T. S. J.

Recently, the classical N-Body Problem has been adjusted to account for celestial bodies made of constituents of finite density. By imposing a minima on the achievable distance between particles, minimum energy resting states are allowed by the problem. The Full N-Body Problem allows for the dissipation of mechanical energy through surface-surface interactions via impacts or by way of tidal deformation. Barring exogeneous forces and allowing for the dissipation of energy, these systems have discrete, and sometimes multiple, minimum energy states for a given angular momentum. Building the dynamical framework of such finite density systems is a necessary process in outlining the evolution of rubble pile asteroids and other gravitational-granular systems such as protoplanetary discs, and potentially planetary rings, from a theoretical point of view. In all cases, resting states are expected to occur as a necessary step in the ongoing processes of solar system formation and evolution. Previous studies of this problem have been performed in the N=3 case where the bodies are indistinguishable spheres, with all possible relative equilibria and their stability having been identified as a function of the angular momentum of the system. These studies uncovered that at certain levels of angular momentum there exists two minimum energy states, a global and local minimum. Thus a question of interest is in which of these states a dissipative system would preferentially settle and the sensitivity of results to changes in dissipation parameters. Assuming equal-sized, perfectly-rigid bodies, this study investigates the dynamical evolution of three spheres under the influence of mutual gravity and impact mechanics as a function of dissipation parameters. A purpose-written, C-based, Hard Sphere Discrete Element Method code has been developed to integrate trajectories and resolve contact mechanics as grains evolve into minimum energy configurations. By testing many randomized initial conditions, statistics are measured regarding minimum energy states for a given angular momentum range. A trend in the Sphere-Restricted Full Three-Body Problem producing an end state of one configuration over another is found as a function of angular momentum and restitution.

Potential Energy Surface-Based Automatic Deduction of Conformational Transition Networks and Its Application on Quantum Mechanical Landscapes of d-Glucose Conformers.

PubMed

Satoh, Hiroko; Oda, Tomohiro; Nakakoji, Kumiyo; Uno, Takeaki; Tanaka, Hiroaki; Iwata, Satoru; Ohno, Koichi

2016-11-08

This paper describes our approach that is built upon the potential energy surface (PES)-based conformational analysis. This approach automatically deduces a conformational transition network, called a conformational reaction route map (r-map), by using the Scaled Hypersphere Search of the Anharmonic Downward Distortion Following method (SHS-ADDF). The PES-based conformational search has been achieved by using large ADDF, which makes it possible to trace only low transition state (TS) barriers while restraining bond lengths and structures with high free energy. It automatically performs sampling the minima and TS structures by simply taking into account the mathematical feature of PES without requiring any a priori specification of variable internal coordinates. An obtained r-map is composed of equilibrium (EQ) conformers connected by reaction routes via TS conformers, where all of the reaction routes are already confirmed during the process of the deduction using the intrinsic reaction coordinate (IRC) method. The postcalculation analysis of the deduced r-map is interactively carried out using the RMapViewer software we have developed. This paper presents computational details of the PES-based conformational analysis and its application to d-glucose. The calculations have been performed for an isolated glucose molecule in the gas phase at the RHF/6-31G level. The obtained conformational r-map for α-d-glucose is composed of 201 EQ and 435 TS conformers and that for β-d-glucose is composed of 202 EQ and 371 TS conformers. For the postcalculation analysis of the conformational r-maps by using the RMapViewer software program we have found multiple minimum energy paths (MEPs) between global minima of 1 C 4 and 4 C 1 chair conformations. The analysis using RMapViewer allows us to confirm the thermodynamic and kinetic predominance of 4 C 1 conformations; that is, the potential energy of the global minimum of 4 C 1 is lower than that of 1 C 4 (thermodynamic predominance) and that the highest energy of those of all the TS structures along a route from 4 C 1 to 1 C 4 is lower than that of 1 C 4 to 4 C 1 (kinetic predominance).

Dynamic Energy Landscapes of Riboswitches Help Interpret Conformational Rearrangements and Function

PubMed Central

Quarta, Giulio; Sin, Ken; Schlick, Tamar

2012-01-01

Riboswitches are RNAs that modulate gene expression by ligand-induced conformational changes. However, the way in which sequence dictates alternative folding pathways of gene regulation remains unclear. In this study, we compute energy landscapes, which describe the accessible secondary structures for a range of sequence lengths, to analyze the transcriptional process as a given sequence elongates to full length. In line with experimental evidence, we find that most riboswitch landscapes can be characterized by three broad classes as a function of sequence length in terms of the distribution and barrier type of the conformational clusters: low-barrier landscape with an ensemble of different conformations in equilibrium before encountering a substrate; barrier-free landscape in which a direct, dominant “downhill” pathway to the minimum free energy structure is apparent; and a barrier-dominated landscape with two isolated conformational states, each associated with a different biological function. Sharing concepts with the “new view” of protein folding energy landscapes, we term the three sequence ranges above as the sensing, downhill folding, and functional windows, respectively. We find that these energy landscape patterns are conserved in various riboswitch classes, though the order of the windows may vary. In fact, the order of the three windows suggests either kinetic or thermodynamic control of ligand binding. These findings help understand riboswitch structure/function relationships and open new avenues to riboswitch design. PMID:22359488

Analysis and sizing of Mars aerobrake structure

NASA Technical Reports Server (NTRS)

Raju, I. S.; Craft, W. J.

1993-01-01

A cone-sphere aeroshell structure for aerobraking into Martian atmosphere is studied. Using this structural configuration, a space frame load-bearing structure is proposed. To generate this structure efficiently and to perform a variety of studies of several configurations, a mesh generator that utilizes only a few configurational parameters is developed. A finite element analysis program that analyzes space frame structures was developed. A sizing algorithm that arrives at a minimum mass configuration was developed and integrated into the finite element analysis program. A typical 135-ft-diam aerobrake configuration was analyzed and sized. The minimum mass obtained in this study using high modulus graphite/epoxy composite material members is compared with the masses obtained from two other aerobrake structures using lightweight erectable tetrahedral truss and part-spherical truss configurations. Excellent agreement for the minimum mass was obtained with the three different aerobrake structures. Also, the minimum mass using the present structure was obtained when the supports were not at the base but at about 75 percent of the base diameter.

Cytotoxic and antibacterial dihydrochalcones from Piper aduncum.

PubMed

Orjala, J; Wright, A D; Behrends, H; Folkers, G; Sticher, O; Rüegger, H; Rali, T

1994-01-01

Bioactivity-guided fractionation of a CH2Cl2 extract from the leaves of Piper aduncum afforded three new dihydrochalcones, piperaduncins A [3], B [4], and C [5], as well as two known dihydrochalcones, 2',6'-dihydroxy-4'-methoxydihydrochalcone [1] and 2',6',4-trihydroxy-4'-methoxydihydrochalcone [2] (asebogenin), together with sakuranetin, anodendroic acid methyl ester, and the carotenoid lutein. The structures of the isolates were elucidated by spectroscopic methods, mainly 1D- and 2D nmr spectroscopy. The proposed stereochemistry for compound 4 was deduced by NOESY spectroscopy and the corresponding energy minimum was established by molecular modelling calculations and translated into a 3D structure.

Sparse RNA folding revisited: space-efficient minimum free energy structure prediction.

PubMed

Will, Sebastian; Jabbari, Hosna

2016-01-01

RNA secondary structure prediction by energy minimization is the central computational tool for the analysis of structural non-coding RNAs and their interactions. Sparsification has been successfully applied to improve the time efficiency of various structure prediction algorithms while guaranteeing the same result; however, for many such folding problems, space efficiency is of even greater concern, particularly for long RNA sequences. So far, space-efficient sparsified RNA folding with fold reconstruction was solved only for simple base-pair-based pseudo-energy models. Here, we revisit the problem of space-efficient free energy minimization. Whereas the space-efficient minimization of the free energy has been sketched before, the reconstruction of the optimum structure has not even been discussed. We show that this reconstruction is not possible in trivial extension of the method for simple energy models. Then, we present the time- and space-efficient sparsified free energy minimization algorithm SparseMFEFold that guarantees MFE structure prediction. In particular, this novel algorithm provides efficient fold reconstruction based on dynamically garbage-collected trace arrows. The complexity of our algorithm depends on two parameters, the number of candidates Z and the number of trace arrows T; both are bounded by [Formula: see text], but are typically much smaller. The time complexity of RNA folding is reduced from [Formula: see text] to [Formula: see text]; the space complexity, from [Formula: see text] to [Formula: see text]. Our empirical results show more than 80 % space savings over RNAfold [Vienna RNA package] on the long RNAs from the RNA STRAND database (≥2500 bases). The presented technique is intentionally generalizable to complex prediction algorithms; due to their high space demands, algorithms like pseudoknot prediction and RNA-RNA-interaction prediction are expected to profit even stronger than "standard" MFE folding. SparseMFEFold is free software, available at http://www.bioinf.uni-leipzig.de/~will/Software/SparseMFEFold.

Bookending the Opportunity to Lower Wind’s LCOE by Reducing the Uncertainty Surrounding Annual Energy Production

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

Bolinger, Mark

Reducing the performance risk surrounding a wind project can potentially lead to a lower weighted-average cost of capital (WACC), and hence a lower levelized cost of energy (LCOE), through an advantageous shift in capital structure, and possibly also a reduction in the cost of capital. Specifically, a reduction in performance risk will move the 1-year P99 annual energy production (AEP) estimate closer to the P50 AEP estimate, which in turn reduces the minimum debt service coverage ratio (DSCR) required by lenders, thereby allowing the project to be financed with a greater proportion of low-cost debt. In addition, a reduction inmore » performance risk might also reduce the cost of one or more of the three sources of capital that are commonly used to finance wind projects: sponsor or cash equity, tax equity, and/or debt. Preliminary internal LBNL analysis of the maximum possible LCOE reduction attainable from reducing the performance risk of a wind project found a potentially significant opportunity for LCOE reduction of ~$10/MWh, by reducing the P50 DSCR to its theoretical minimum value of 1.0 (Bolinger 2015b, 2014) and by reducing the cost of sponsor equity and debt by one-third to one-half each (Bolinger 2015a, 2015b). However, with FY17 funding from the U.S. Department of Energy’s Atmosphere to Electrons (A2e) Performance Risk, Uncertainty, and Finance (PRUF) initiative, LBNL has been revisiting this “bookending” exercise in more depth, and now believes that its earlier preliminary assessment of the LCOE reduction opportunity was overstated. This reassessment is based on two new-found understandings: (1) Due to ever-present and largely irreducible inter-annual variability (IAV) in the wind resource, the minimum required DSCR cannot possibly fall to 1.0 (on a P50 basis), and (2) A reduction in AEP uncertainty will not necessarily lead to a reduction in the cost of capital, meaning that a shift in capital structure is perhaps the best that can be expected (perhaps along with a modest decline in the cost of cash equity as new investors enter the market).« less

A search for anisotropy in the arrival directions of ultra high energy cosmic rays recorded at the Pierre Auger Observatory

NASA Astrophysics Data System (ADS)

Pierre Auger Collaboration; Abreu, P.; Aglietta, M.; Ahlers, M.; Ahn, E. J.; Albuquerque, I. F. M.; Allard, D.; Allekotte, I.; Allen, J.; Allison, P.; Almela, A.; Alvarez Castillo, J.; Alvarez-Muñiz, J.; Ambrosio, M.; Aminaei, A.; Anchordoqui, L.; Andringa, S.; Antici'c, T.; Aramo, C.; Arganda, E.; Arqueros, F.; Asorey, H.; Assis, P.; Aublin, J.; Ave, M.; Avenier, M.; Avila, G.; Bäcker, T.; Badescu, A. M.; Balzer, M.; Barber, K. B.; Barbosa, A. F.; Bardenet, R.; Barroso, S. L. C.; Baughman, B.; Bäuml, J.; Beatty, J. J.; Becker, B. R.; Becker, K. H.; Bellétoile, A.; Bellido, J. A.; BenZvi, S.; Berat, C.; Bertou, X.; Biermann, P. L.; Billoir, P.; Blanco, F.; Blanco, M.; Bleve, C.; Blümer, H.; Bohácová, M.; Boncioli, D.; Bonifazi, C.; Bonino, R.; Borodai, N.; Brack, J.; Brancus, I.; Brogueira, P.; Brown, W. C.; Bruijn, R.; Buchholz, P.; Bueno, A.; Burton, R. E.; Caballero-Mora, K. S.; Caccianiga, B.; Caramete, L.; Caruso, R.; Castellina, A.; Catalano, O.; Cataldi, G.; Cazon, L.; Cester, R.; Chauvin, J.; Cheng, S. H.; Chiavassa, A.; Chinellato, J. A.; Chirinos Diaz, J.; Chudoba, J.; Cilmo, M.; Clay, R. W.; Coluccia, M. R.; Conceição, R.; Contreras, F.; Cook, H.; Cooper, M. J.; Coppens, J.; Cordier, A.; Coutu, S.; Covault, C. E.; Creusot, A.; Criss, A.; Cronin, J.; Curutiu, A.; Dagoret-Campagne, S.; Dallier, R.; Dasso, S.; Daumiller, K.; Dawson, B. R.; de Almeida, R. M.; De Domenico, M.; De Donato, C.; de Jong, S. J.; De La Vega, G.; de Mello Junior, W. J. M.; de Mello Neto, J. R. T.; De Mitri, I.; de Souza, V.; de Vries, K. D.; del Peral, L.; del Río, M.; Deligny, O.; Dembinski, H.; Dhital, N.; Di Giulio, C.; Díaz Castro, M. L.; Diep, P. N.; Diogo, F.; Dobrigkeit, C.; Docters, W.; D'Olivo, J. C.; Dong, P. N.; Dorofeev, A.; dos Anjos, J. C.; Dova, M. T.; D'Urso, D.; Dutan, I.; Ebr, J.; Engel, R.; Erdmann, M.; Escobar, C. O.; Espadanal, J.; Etchegoyen, A.; Facal San Luis, P.; Fajardo Tapia, I.; Falcke, H.; Farrar, G.; Fauth, A. C.; Fazzini, N.; Ferguson, A. P.; Fick, B.; Filevich, A.; Filipcic, A.; Fliescher, S.; Fracchiolla, C. E.; Fraenkel, E. D.; Fratu, O.; Fröhlich, U.; Fuchs, B.; Gaior, R.; Gamarra, R. F.; Gambetta, S.; García, B.; Garcia Roca, S. T.; Garcia-Gamez, D.; Garcia-Pinto, D.; Gascon, A.; Gemmeke, H.; Ghia, P. L.; Giaccari, U.; Giller, M.; Glass, H.; Gold, M. S.; Golup, G.; Gomez Albarracin, F.; Gómez Berisso, M.; Gómez Vitale, P. F.; Gonçalves, P.; Gonzalez, D.; Gonzalez, J. G.; Gookin, B.; Gorgi, A.; Gouffon, P.; Grashorn, E.; Grebe, S.; Griffith, N.; Grigat, M.; Grillo, A. F.; Guardincerri, Y.; Guarino, F.; Guedes, G. P.; Guzman, A.; Hague, J. D.; Hansen, P.; Harari, D.; Harmsma, S.; Harrison, T. A.; Harton, J. L.; Haungs, A.; Hebbeker, T.; Heck, D.; Herve, A. E.; Hojvat, C.; Hollon, N.; Holmes, V. C.; Homola, P.; Hörandel, J. R.; Horneffer, A.; Horvath, P.; Hrabovský, M.; Huege, T.; Insolia, A.; Ionita, F.; Italiano, A.; Jarne, C.; Jiraskova, S.; Josebachuili, M.; Kadija, K.; Kampert, K. H.; Karhan, P.; Kasper, P.; Kégl, B.; Keilhauer, B.; Keivani, A.; Kelley, J. L.; Kemp, E.; Kieckhafer, R. M.; Klages, H. O.; Kleifges, M.; Kleinfeller, J.; Knapp, J.; Koang, D.-H.; Kotera, K.; Krohm, N.; Krömer, O.; Kruppke-Hansen, D.; Kuehn, F.; Kuempel, D.; Kulbartz, J. K.; Kunka, N.; La Rosa, G.; Lachaud, C.; Lauer, R.; Lautridou, P.; Le Coz, S.; Leão, M. S. A. B.; Lebrun, D.; Lebrun, P.; Leigui de Oliveira, M. A.; Letessier-Selvon, A.; Lhenry-Yvon, I.; Link, K.; López, R.; Lopez Agüera, A.; Louedec, K.; Lozano Bahilo, J.; Lu, L.; Lucero, A.; Ludwig, M.; Lyberis, H.; Macolino, C.; Maldera, S.; Mandat, D.; Mantsch, P.; Mariazzi, A. G.; Marin, J.; Marin, V.; Maris, I. C.; Marquez Falcon, H. R.; Marsella, G.; Martello, D.; Martin, L.; Martinez, H.; Martínez Bravo, O.; Mathes, H. J.; Matthews, J.; Matthews, J. A. J.; Matthiae, G.; Maurel, D.; Maurizio, D.; Mazur, P. O.; Medina-Tanco, G.; Melissas, M.; Melo, D.; Menichetti, E.; Menshikov, A.; Mertsch, P.; Meurer, C.; Mi'canovi'c, S.; Micheletti, M. I.; Minaya, I. A.; Miramonti, L.; Molina-Bueno, L.; Mollerach, S.; Monasor, M.; Monnier Ragaigne, D.; Montanet, F.; Morales, B.; Morello, C.; Moreno, E.; Moreno, J. C.; Mostafá, M.; Moura, C. A.; Muller, M. A.; Müller, G.; Münchmeyer, M.; Mussa, R.; Navarra, G.; Navarro, J. L.; Navas, S.; Necesal, P.; Nellen, L.; Nelles, A.; Neuser, J.; Nhung, P. T.; Niechciol, M.; Niemietz, L.; Nierstenhoefer, N.; Nitz, D.; Nosek, D.; Nožka, L.; Nyklicek, M.; Oehlschläger, J.; Olinto, A.; Ortiz, M.; Pacheco, N.; Pakk Selmi-Dei, D.; Palatka, M.; Pallotta, J.; Palmieri, N.; Parente, G.; Parizot, E.; Parra, A.; Pastor, S.; Paul, T.; Pech, M.; Pekala, J.; Pelayo, R.; Pepe, I. M.; Perrone, L.; Pesce, R.; Petermann, E.; Petrera, S.; Petrinca, P.; Petrolini, A.; Petrov, Y.; Petrovic, J.; Pfendner, C.; Piegaia, R.; Pierog, T.; Pieroni, P.; Pimenta, M.; Pirronello, V.; Platino, M.; Ponce, V. H.; Pontz, M.; Porcelli, A.; Privitera, P.; Prouza, M.; Quel, E. J.; Querchfeld, S.; Rautenberg, J.; Ravel, O.; Ravignani, D.; Revenu, B.; Ridky, J.; Riggi, S.; Risse, M.; Ristori, P.; Rivera, H.; Rizi, V.; Roberts, J.; Rodrigues de Carvalho, W.; Rodriguez, G.; Rodriguez Martino, J.; Rodriguez Rojo, J.; Rodriguez-Cabo, I.; Rodríguez-Frías, M. D.; Ros, G.; Rosado, J.; Rossler, T.; Roth, M.; Rouillé-d'Orfeuil, B.; Roulet, E.; Rovero, A. C.; Rühle, C.; Saftoiu, A.; Salamida, F.; Salazar, H.; Salesa Greus, F.; Salina, G.; Sánchez, F.; Santo, C. E.; Santos, E.; Santos, E. M.; Sarazin, F.; Sarkar, B.; Sarkar, S.; Sato, R.; Scharf, N.; Scherini, V.; Schieler, H.; Schiffer, P.; Schmidt, A.; Scholten, O.; Schoorlemmer, H.; Schovancova, J.; Schovánek, P.; Schröder, F.; Schulte, S.; Schuster, D.; Sciutto, S. J.; Scuderi, M.; Segreto, A.; Settimo, M.; Shadkam, A.; Shellard, R. C.; Sidelnik, I.; Sigl, G.; Silva Lopez, H. H.; Sima, O.; 'Smiałkowski, A.; Šmída, R.; Snow, G. R.; Sommers, P.; Sorokin, J.; Spinka, H.; Squartini, R.; Srivastava, Y. N.; Stanic, S.; Stapleton, J.; Stasielak, J.; Stephan, M.; Stutz, A.; Suarez, F.; Suomijärvi, T.; Supanitsky, A. D.; Šuša, T.; Sutherland, M. S.; Swain, J.; Szadkowski, Z.; Szuba, M.; Tapia, A.; Tartare, M.; Taşcău, O.; Tavera Ruiz, C. G.; Tcaciuc, R.; Tegolo, D.; Thao, N. T.; Thomas, D.; Tiffenberg, J.; Timmermans, C.; Tkaczyk, W.; Todero Peixoto, C. J.; Toma, G.; Tomé, B.; Tonachini, A.; Travnicek, P.; Tridapalli, D. B.; Tristram, G.; Trovato, E.; Tueros, M.; Ulrich, R.; Unger, M.; Urban, M.; Valdés Galicia, J. F.; Valiño, I.; Valore, L.; van den Berg, A. M.; Varela, E.; Vargas Cárdenas, B.; Vázquez, J. R.; Vázquez, R. A.; Veberic, D.; Verzi, V.; Vicha, J.; Videla, M.; Villaseñor, L.; Wahlberg, H.; Wahrlich, P.; Wainberg, O.; Walz, D.; Watson, A. A.; Weber, M.; Weidenhaupt, K.; Weindl, A.; Werner, F.; Westerhoff, S.; Whelan, B. J.; Widom, A.; Wieczorek, G.; Wiencke, L.; Wilczyńska, B.; Wilczyński, H.; Will, M.; Williams, C.; Winchen, T.; Wommer, M.; Wundheiler, B.; Yamamoto, T.; Yapici, T.; Younk, P.; Yuan, G.; Yushkov, A.; Zamorano, B.; Zas, E.; Zavrtanik, D.; Zavrtanik, M.; Zaw, I.; Zepeda, A.; Zhu, Y.; Zimbres Silva, M.; Ziolkowski, M.

2012-04-01

Observations of cosmic ray arrival directions made with the Pierre Auger Observatory have previously provided evidence of anisotropy at the 99% CL using the correlation of ultra high energy cosmic rays (UHECRs) with objects drawn from the Véron-Cetty Véron catalog. In this paper we report on the use of three catalog independent methods to search for anisotropy. The 2pt-L, 2pt+ and 3pt methods, each giving a different measure of self-clustering in arrival directions, were tested on mock cosmic ray data sets to study the impacts of sample size and magnetic smearing on their results, accounting for both angular and energy resolutions. If the sources of UHECRs follow the same large scale structure as ordinary galaxies in the local Universe and if UHECRs are deflected no more than a few degrees, a study of mock maps suggests that these three methods can efficiently respond to the resulting anisotropy with a P-value = 1.0% or smaller with data sets as few as 100 events. Using data taken from January 1, 2004 to July 31, 2010 we examined the 20,30,...,110 highest energy events with a corresponding minimum energy threshold of about 49.3 EeV. The minimum P-values found were 13.5% using the 2pt-L method, 1.0% using the 2pt+ method and 1.1% using the 3pt method for the highest 100 energy events. In view of the multiple (correlated) scans performed on the data set, these catalog-independent methods do not yield strong evidence of anisotropy in the highest energy cosmic rays.

The Free Energy Landscape of Pseudorotation in 3′–5′ and 2′–5′ Linked Nucleic Acids

PubMed Central

2014-01-01

The five-membered furanose ring is a central component of the chemical structure of biological nucleic acids. The conformations of the furanose ring can be analytically described using the concept of pseudorotation, and for RNA and DNA they are dominated by the C2′-endo and C3′-endo conformers. While the free energy difference between these two conformers can be inferred from NMR measurements, a free energy landscape of the complete pseudorotation cycle of nucleic acids in solution has remained elusive. Here, we describe a new free energy calculation method for molecular dynamics (MD) simulations using the two pseudorotation parameters directly as the collective variables. To validate our approach, we calculated the free energy surface of ribose pseudorotation in guanosine and 2′-deoxyguanosine. The calculated free energy landscape reveals not only the relative stability of the different pseudorotation conformers, but also the main transition path between the stable conformations. Applying this method to a standard A-form RNA duplex uncovered the expected minimum at the C3′-endo state. However, at a 2′–5′ linkage, the minimum shifts to the C2′-endo conformation. The free energy of the C3′-endo conformation is 3 kcal/mol higher due to a weaker hydrogen bond and a reduced base stacking interaction. Unrestrained MD simulations suggest that the conversion from C3′-endo to C2′-endo and vice versa is on the nanosecond and microsecond time scale, respectively. These calculations suggest that 2′–5′ linkages may enable folded RNAs to sample a wider spectrum of their pseudorotation conformations. PMID:24499340

Independent saturation of three TrpRS subsites generates a partially assembled state similar to those observed in molecular simulations

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

Laowanapiban, Poramaet; Kapustina, Maryna; Vonrhein, Clemens

2009-03-05

Two new crystal structures of Bacillus stearothermophilus tryptophanyl-tRNA synthetase (TrpRS) afford evidence that a closed interdomain hinge angle requires a covalent bond between AMP and an occupant of either pyrophosphate or tryptophan subsite. They also are within experimental error of a cluster of structures observed in a nonequilibrium molecular dynamics simulation showing partial active-site assembly. Further, the highest energy structure in a minimum action pathway computed by using elastic network models for Open and Pretransition state (PreTS) conformations for the fully liganded TrpRS monomer is intermediate between that simulated structure and a partially disassembled structure from a nonequilibrium molecular dynamicsmore » trajectory for the unliganded PreTS. These mutual consistencies provide unexpected validation of inferences drawn from molecular simulations.« less

On the combinatorics of sparsification.

PubMed

Huang, Fenix Wd; Reidys, Christian M

2012-10-22

We study the sparsification of dynamic programming based on folding algorithms of RNA structures. Sparsification is a method that improves significantly the computation of minimum free energy (mfe) RNA structures. We provide a quantitative analysis of the sparsification of a particular decomposition rule, Λ∗. This rule splits an interval of RNA secondary and pseudoknot structures of fixed topological genus. Key for quantifying sparsifications is the size of the so called candidate sets. Here we assume mfe-structures to be specifically distributed (see Assumption 1) within arbitrary and irreducible RNA secondary and pseudoknot structures of fixed topological genus. We then present a combinatorial framework which allows by means of probabilities of irreducible sub-structures to obtain the expectation of the Λ∗-candidate set w.r.t. a uniformly random input sequence. We compute these expectations for arc-based energy models via energy-filtered generating functions (GF) in case of RNA secondary structures as well as RNA pseudoknot structures. Furthermore, for RNA secondary structures we also analyze a simplified loop-based energy model. Our combinatorial analysis is then compared to the expected number of Λ∗-candidates obtained from the folding mfe-structures. In case of the mfe-folding of RNA secondary structures with a simplified loop-based energy model our results imply that sparsification provides a significant, constant improvement of 91% (theory) to be compared to an 96% (experimental, simplified arc-based model) reduction. However, we do not observe a linear factor improvement. Finally, in case of the "full" loop-energy model we can report a reduction of 98% (experiment). Sparsification was initially attributed a linear factor improvement. This conclusion was based on the so called polymer-zeta property, which stems from interpreting polymer chains as self-avoiding walks. Subsequent findings however reveal that the O(n) improvement is not correct. The combinatorial analysis presented here shows that, assuming a specific distribution (see Assumption 1), of mfe-structures within irreducible and arbitrary structures, the expected number of Λ∗-candidates is Θ(n2). However, the constant reduction is quite significant, being in the range of 96%. We furthermore show an analogous result for the sparsification of the Λ∗-decomposition rule for RNA pseudoknotted structures of genus one. Finally we observe that the effect of sparsification is sensitive to the employed energy model.

FlexStem: improving predictions of RNA secondary structures with pseudoknots by reducing the search space.

PubMed

Chen, Xiang; He, Si-Min; Bu, Dongbo; Zhang, Fa; Wang, Zhiyong; Chen, Runsheng; Gao, Wen

2008-09-15

RNA secondary structures with pseudoknots are often predicted by minimizing free energy, which is proved to be NP-hard. Due to kinetic reasons the real RNA secondary structure often has local instead of global minimum free energy. This implies that we may improve the performance of RNA secondary structure prediction by taking kinetics into account and minimize free energy in a local area. we propose a novel algorithm named FlexStem to predict RNA secondary structures with pseudoknots. Still based on MFE criterion, FlexStem adopts comprehensive energy models that allow complex pseudoknots. Unlike classical thermodynamic methods, our approach aims to simulate the RNA folding process by successive addition of maximal stems, reducing the search space while maintaining or even improving the prediction accuracy. This reduced space is constructed by our maximal stem strategy and stem-adding rule induced from elaborate statistical experiments on real RNA secondary structures. The strategy and the rule also reflect the folding characteristic of RNA from a new angle and help compensate for the deficiency of merely relying on MFE in RNA structure prediction. We validate FlexStem by applying it to tRNAs, 5SrRNAs and a large number of pseudoknotted structures and compare it with the well-known algorithms such as RNAfold, PKNOTS, PknotsRG, HotKnots and ILM according to their overall sensitivities and specificities, as well as positive and negative controls on pseudoknots. The results show that FlexStem significantly increases the prediction accuracy through its local search strategy. Software is available at http://pfind.ict.ac.cn/FlexStem/. Supplementary data are available at Bioinformatics online.

Energy Efficiency Building Code for Commercial Buildings in Sri Lanka

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

Busch, John; Greenberg, Steve; Rubinstein, Francis

2000-09-30

1.1.1 To encourage energy efficient design or retrofit of commercial buildings so that they may be constructed, operated, and maintained in a manner that reduces the use of energy without constraining the building function, the comfort, health, or the productivity of the occupants and with appropriate regard for economic considerations. 1.1.2 To provide criterion and minimum standards for energy efficiency in the design or retrofit of commercial buildings and provide methods for determining compliance with them. 1.1.3 To encourage energy efficient designs that exceed these criterion and minimum standards.

The effect of weight and drag on the sinking speed and lift/drag ratio of gliders

NASA Technical Reports Server (NTRS)

Kosin, R

1934-01-01

The most important factors in evaluating performance of gliders are minimum sinking speed and minimum gliding angle. To assure their optimum value the energy necessary for flight, that is, the energy of lift and friction must be kept very low, or in other words, weight and total drag which have a decisive effect on the sinking speed and on the gliding angle, must be kept to a minimum. How great the effect of a reduction of these two quantities will be shown in the following.

An explanation for the tiny value of the cosmological constant and the low vacuum energy density

NASA Astrophysics Data System (ADS)

Nassif, Cláudio

2015-09-01

The paper aims to provide an explanation for the tiny value of the cosmological constant and the low vacuum energy density to represent the dark energy. To accomplish this, we will search for a fundamental principle of symmetry in space-time by means of the elimination of the classical idea of rest, by including an invariant minimum limit of speed in the subatomic world. Such a minimum speed, unattainable by particles, represents a preferred reference frame associated with a background field that breaks down the Lorentz symmetry. The metric of the flat space-time shall include the presence of a uniform vacuum energy density, which leads to a negative pressure at cosmological length scales. Thus, the equation of state for the cosmological constant [ p(pressure) (energy density)] naturally emerges from such a space-time with an energy barrier of a minimum speed. The tiny values of the cosmological constant and the vacuum energy density will be successfully obtained, being in agreement with the observational results of Perlmutter, Schmidt and Riess.

Analysis of vibrational, structural, and electronic properties of rivastigmine by density functional theory

NASA Astrophysics Data System (ADS)

Prasad, O.; Sinha, L.; Misra, N.; Narayan, V.; Kumar, N.; Kumar, A.

2010-09-01

The present work deals with the structural, electronic, and vibrational analysis of rivastigmine. Rivastigmine, an antidementia medicament, is credited with significant therapeutic effects on the cognitive, functional, and behavioural problems that are commonly associated with Alzheimer’s dementia. For rivastigmine, a number of minimum energy conformations are possible. The geometry of twelve possible conformers has been analyzed and the most stable conformer was further optimized at a higher basis set. The electronic properties and vibrational frequencies were then calculated using a density functional theory at the B3LYP level with the 6-311+G(d, p) basis set. The different molecular surfaces have also been drawn to understand the activity of the molecule. A narrower frontier orbital energy gap in rivastigmine makes it softer and more reactive than water and dimethylfuran. The calculated value of the dipole moment is 2.58 debye.

Ligand Shaping in Induced Fit Docking of MraY Inhibitors. Polynomial Discriminant and Laplacian Operator as Biological Activity Descriptors.

PubMed

Lungu, Claudiu N; Diudea, Mircea V; Putz, Mihai V

2017-06-27

Docking-i.e., interaction of a small molecule (ligand) with a proteic structure (receptor)-represents the ground of drug action mechanism of the vast majority of bioactive chemicals. Ligand and receptor accommodate their geometry and energy, within this interaction, in the benefit of receptor-ligand complex. In an induced fit docking, the structure of ligand is most susceptible to changes in topology and energy, comparative to the receptor. These changes can be described by manifold hypersurfaces, in terms of polynomial discriminant and Laplacian operator. Such topological surfaces were represented for each MraY (phospho-MurNAc-pentapeptide translocase) inhibitor, studied before and after docking with MraY. Binding affinities of all ligands were calculated by this procedure. For each ligand, Laplacian and polynomial discriminant were correlated with the ligand minimum inhibitory concentration (MIC) retrieved from literature. It was observed that MIC is correlated with Laplacian and polynomial discriminant.

A dynamic measure of controllability and observability for the placement of actuators and sensors on large space structures

NASA Technical Reports Server (NTRS)

Vandervelde, W. E.; Carignan, C. R.

1982-01-01

The degree of controllability of a large space structure is found by a four step procedure: (1) finding the minimum control energy for driving the system from a given initial state to the origin in the prescribed time; (2) finding the region of initial state which can be driven to the origin with constrained control energy and time using optimal control strategy; (3) scaling the axes so that a unit displacement in every direction is equally important to control; and (4) finding the linear measurement of the weighted "volume" of the ellipsoid in the equicontrol space. For observability, the error covariance must be reduced toward zero using measurements optimally, and the criterion must be standardized by the magnitude of tolerable errors. The results obtained using these methods are applied to the vibration modes of a free-free beam.

Effect of control surface mass unbalance on the stability of a closed-loop active control system

NASA Technical Reports Server (NTRS)

Nissim, E.

1989-01-01

The effects on stability of inertial forces arising from closed-loop activation of mass-unbalanced control surfaces are studied analytically using inertial energy approach, similar to the aerodynamic energy approach used for flutter suppression. The limitations of a single control surface like a leading-edge (LE) control or a trailing-edge (TE) control are demonstrated and compared to the superior combined LE-TE mass unbalanced system. It is shown that a spanwise section for sensor location can be determined which ensures minimum sensitivity to the mode shapes of the aircraft. It is shown that an LE control exhibits compatibility between inertial stabilization and aerodynamic stabilization, and that a TE control lacks such compatibility. The results of the present work should prove valuable, both for the purpose of flutter suppression using mass unbalanced control surfaces, or for the stabilization of structural modes of large space structures by means of inertial forces.

Scattered electrons in microscopy and microanalysis

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

Ottensmeyer, F.P.

The use of scattered electrons alone for direct imaging of biological specimens makes it possible to obtain structural information at atomic and near-atomic spatial resolutions of 0.3 to 0.5 nanometer. While this is not as good as the resolution possible with x-ray crystallography, such an approach provides structural information rapidly on individual macromolecules that have not been, and possibly cannot be, crystallized. Analysis of the spectrum of energies of scattered electrons and imaging of the latter with characteristic energy bands within the spectrum produces a powerful new technique of atomic microanalysis. This technique, which has a spatial resolution of aboutmore » 0.5 nanometer and a minimum detection sensitivity of about 50 atoms of phosphorus, is especially useful for light atom analysis and appears to have applications in molecular biology, cell biology, histology, pathology, botany, and many other fields.« less

Scattered electrons in microscopy and microanalysis

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

Ottensmeyer, F.P.

The use of scattered electrons alone for direct imaging of biological specimens makes it possible to obtain structural information at atomic and near-atomic spatial resolutions of 0.3 to 0.5 nanometer. While this is not as good as the resolution possible with x-ray crystallography, such an approach provides structural information rapidly on individual macromolecules that have not been, and possibly cannot be, crystallized. Analysis of the spectrum of energies of scattered electrons and imaging of the latter with characteristic energy bands within the spectrum produce a powerful new technique of atomic microanalysis. This technique, which has a spatial resolution of aboutmore » 0.5 nanometer and a minimum detection sensitivity of about 50 atoms of phosphorus, is especially useful for light atom analysis and appears to have applications in molecular biology, cell biology, histology, pathology, botany, and many other fields.« less

Electronic structure and reactivity of cobalt oxide dimers and their hexacarbonyl complexes: a density functional study.

PubMed

Uzunova, Ellie L; Mikosch, Hans

2012-03-29

The dimers of cobalt oxide (CoO)(2) with cyclic and open bent structure are studied with the B1LYP density functional; the ordering of states is validated by the CCSD(T) method. The D(2h)-symmetry rhombic dioxide Co(2)O(2) with antiferromagnetically ordered electrons on cobalt centers is the global minimum. The cyclic peroxide Co(2)(O(2)) with side-on-bonded dioxygen in (7)B(2) ground state is separated from the global minimum by an energy gap of 3.15 eV. The dioxide is highly reactive as indicated by the high value of proton affinity and chemical reactivity indices. The four-member ring structures are more stable than those with three-member ring or chain configuration. The thermodynamic stability toward dissociation to CoO increases upon carbonylation, whereas proton affinity and reactivity with release of molecular oxygen also increase. The global minimum of Co(2)O(2)(CO)(6) corresponds to a triplet state (3)A" with oxygen atoms shifted above the molecular plane of the rhombic dioxide Co(2)O(2). The SOMO-LUMO gap in the ground-state carbonylated dioxide is wider, compared to the same gap in the bare dicobalt dioxide. The peroxo-isomer Co(2)(O(2))(CO)(6) retains the planar Co(2)(O(2)) ring and is only stable in a high-spin state (7)A". The carbonylated clusters have increased reactivity in both redox and nucleophilic reactions, as a result of the increased electron density in the Co(2)O(2)-ring area.

Observation of Anomalous Potential Electric Energy in Distilled Water Under Solar Heating

NASA Astrophysics Data System (ADS)

Smarandache, Florentin; Christianto, V.

2011-04-01

In this paper, we describe a very simple experiment with distilled water which could exhibit anomalous potential electrical energy with very minimum preparation energy. While this observed excess energy here is less impressive than J-P. Beberian's and M. Porringa's, and the material used is also far less exotic than common LENR-CANR experiments, from the viewpoint of minimum preparation requirement --and therefore less barrier for rapid implementation--, it seems that further experiments could be recommended in order to verify and also to explore various implications of this new proposition.

Electron affinities and ionization energies of Cu and Ag delafossite compounds: A hybrid functional study

NASA Astrophysics Data System (ADS)

Miao, Mao-Sheng; Yarbro, Sam; Barton, Phillip T.; Seshadri, Ram

2014-01-01

Using density functional theory with a hybrid functional, we calculate the ionization energies and electron affinities of a series of delafossite compounds (AMO2: A =Cu, Ag; M =B, Al, Ga, In, Sc). The alignments of the valence band maximum and the conduction band minimum, which directly relate to the ionization energies and electron affinities, were obtained by calculations of supercell slab models constructed in a nonpolar orientation. Our calculations reveal that the ionization energy decreases with an increasing atomic number of group-III elements, and thus suggest an improved p-type doping propensity for heavier compounds. For keeping both a low ionization energy and a band gap of sufficient size, CuScO2 is superior to the Cu-based group-III delafossites. By analyzing the electronic structures, we demonstrate that the compositional trend of the ionization energies and electron affinities is the result of a combined effect of d-band broadening due to Cu(Ag)-Cu(Ag) coupling and a repositioning of the d-band center.

Topology-energy relationships and lowest energy configurations for pentagonal dodecahedral (H2O)20X clusters, X=empty, H2O, NH3, H3O+: The importance of O-topology

NASA Astrophysics Data System (ADS)

Anick, David J.

2010-04-01

For (H2O)20X water clusters consisting of X enclosed by the 512 dodecahedral cage, X=empty, H2O, NH3, and H3O+, databases are made consisting of 55-82 isomers optimized via B3LYP/6-311++G∗∗. Correlations are explored between ground state electronic energy (Ee) or electronic energy plus zero point energy (Ee+ZPE) and the clusters' topology, defined as the set of directed H-bonds. Linear regression is done to identify topological features that correlate with cluster energy. For each X, variables are found that account for 99% of the variance in Ee and predict it with a rms error under 0.2 kcal/mol. The method of analysis emphasizes the importance of an intermediate level of structure, the "O-topology," consisting of O-types and a list of O pairs that are bonded but omitting H-bond directions, as a device to organize the databases and reduce the number of structures one needs to consider. Relevant variables include three parameters, which count the number of H-bonds having particular donor and acceptor types; |M|2, where M is the cluster's vector dipole moment; and the projection of M onto the symmetry axis of X. Scatter diagrams for Ee or Ee+ZPE versus |M| show that clusters fall naturally into "families" defined by the values of certain discrete parameters, the "major parameters," for each X. Combining "family" analysis and O-topologies, a small group of clusters is identified for each X that are candidates to be the global minimum, and the minimum is determined. For X=H3O+, one cluster with central hydronium lies just 2.08 kcal/mol above the lowest isomer with surface hydronium. Implications of the methodology for dodecahedral (H2O)20(NH4+) and (H2O)20(NH4+)(OH-) are discussed, and new lower energy isomers are found. For MP2/TZVP, the lowest-energy (H2O)20(NH4+) isomer features a trifurcated H-bond. The results suggest a much more efficient and comprehensive way of seeking low-energy water cluster geometries that may have wide applicability.

Topology-energy relationships and lowest energy configurations for pentagonal dodecahedral (H2O)20X clusters, X = empty, H2O, NH3, H3O+: the importance of O-topology.

PubMed

Anick, David J

2010-04-28

For (H(2)O)(20)X water clusters consisting of X enclosed by the 5(12) dodecahedral cage, X = empty, H(2)O, NH(3), and H(3)O(+), databases are made consisting of 55-82 isomers optimized via B3LYP/6-311++G(**). Correlations are explored between ground state electronic energy (Ee) or electronic energy plus zero point energy (Ee+ZPE) and the clusters' topology, defined as the set of directed H-bonds. Linear regression is done to identify topological features that correlate with cluster energy. For each X, variables are found that account for 99% of the variance in Ee and predict it with a rms error under 0.2 kcal/mol. The method of analysis emphasizes the importance of an intermediate level of structure, the "O-topology," consisting of O-types and a list of O pairs that are bonded but omitting H-bond directions, as a device to organize the databases and reduce the number of structures one needs to consider. Relevant variables include three parameters, which count the number of H-bonds having particular donor and acceptor types; absolute value(M)(2), where M is the cluster's vector dipole moment; and the projection of M onto the symmetry axis of X. Scatter diagrams for Ee or Ee+ZPE versus absolute value(M) show that clusters fall naturally into "families" defined by the values of certain discrete parameters, the "major parameters," for each X. Combining "family" analysis and O-topologies, a small group of clusters is identified for each X that are candidates to be the global minimum, and the minimum is determined. For X = H(3)O(+), one cluster with central hydronium lies just 2.08 kcal/mol above the lowest isomer with surface hydronium. Implications of the methodology for dodecahedral (H(2)O)(20)(NH(4)(+)) and (H(2)O)(20)(NH(4)(+))(OH(-)) are discussed, and new lower energy isomers are found. For MP2/TZVP, the lowest-energy (H(2)O)(20)(NH(4)(+)) isomer features a trifurcated H-bond. The results suggest a much more efficient and comprehensive way of seeking low-energy water cluster geometries that may have wide applicability.

New insights from cluster analysis methods for RNA secondary structure prediction

PubMed Central

Rogers, Emily; Heitsch, Christine

2016-01-01

A widening gap exists between the best practices for RNA secondary structure prediction developed by computational researchers and the methods used in practice by experimentalists. Minimum free energy (MFE) predictions, although broadly used, are outperformed by methods which sample from the Boltzmann distribution and data mine the results. In particular, moving beyond the single structure prediction paradigm yields substantial gains in accuracy. Furthermore, the largest improvements in accuracy and precision come from viewing secondary structures not at the base pair level but at lower granularity/higher abstraction. This suggests that random errors affecting precision and systematic ones affecting accuracy are both reduced by this “fuzzier” view of secondary structures. Thus experimentalists who are willing to adopt a more rigorous, multilayered approach to secondary structure prediction by iterating through these levels of granularity will be much better able to capture fundamental aspects of RNA base pairing. PMID:26971529

Origins of Fermi-level pinning on GaN and InN polar and nonpolar surfaces

NASA Astrophysics Data System (ADS)

Segev, D.; Van de Walle, C. G.

2006-10-01

Using band structure and total energy methods, we study the atomic and electronic structures of the polar (+c and - c plane) and nonpolar (a and m plane) surfaces of GaN and InN. We identify two distinct microscopic origins for Fermi-level pinning on GaN and InN, depending on surface stoichiometry and surface polarity. At moderate Ga/N ratios unoccupied gallium dangling bonds pin the Fermi level on n-type GaN at 0.5 0.7 eV below the conduction-band minimum. Under highly Ga-rich conditions metallic Ga adlayers lead to Fermi-level pinning at 1.8 eV above the valence-band maximum. We also explain the source of the intrinsic electron accumulation that has been universally observed on polar InN surfaces. It is caused by In-In bonds leading to occupied surface states above the conduction-band minimum. We predict that such a charge accumulation will be absent on the nonpolar surfaces of InN, when prepared under specific conditions.

On the Improvement of Convergence Performance for Integrated Design of Wind Turbine Blade Using a Vector Dominating Multi-objective Evolution Algorithm

NASA Astrophysics Data System (ADS)

Wang, L.; Wang, T. G.; Wu, J. H.; Cheng, G. P.

2016-09-01

A novel multi-objective optimization algorithm incorporating evolution strategies and vector mechanisms, referred as VD-MOEA, is proposed and applied in aerodynamic- structural integrated design of wind turbine blade. In the algorithm, a set of uniformly distributed vectors is constructed to guide population in moving forward to the Pareto front rapidly and maintain population diversity with high efficiency. For example, two- and three- objective designs of 1.5MW wind turbine blade are subsequently carried out for the optimization objectives of maximum annual energy production, minimum blade mass, and minimum extreme root thrust. The results show that the Pareto optimal solutions can be obtained in one single simulation run and uniformly distributed in the objective space, maximally maintaining the population diversity. In comparison to conventional evolution algorithms, VD-MOEA displays dramatic improvement of algorithm performance in both convergence and diversity preservation for handling complex problems of multi-variables, multi-objectives and multi-constraints. This provides a reliable high-performance optimization approach for the aerodynamic-structural integrated design of wind turbine blade.

Band gap tuning of amorphous Al oxides by Zr alloying

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

Canulescu, S., E-mail: stec@fotonik.dtu.dk; Schou, J.; Jones, N. C.

2016-08-29

The optical band gap and electronic structure of amorphous Al-Zr mixed oxides with Zr content ranging from 4.8 to 21.9% were determined using vacuum ultraviolet and X-ray absorption spectroscopy. The light scattering by the nano-porous structure of alumina at low wavelengths was estimated based on the Mie scattering theory. The dependence of the optical band gap of the Al-Zr mixed oxides on the Zr content deviates from linearity and decreases from 7.3 eV for pure anodized Al{sub 2}O{sub 3} to 6.45 eV for Al-Zr mixed oxides with a Zr content of 21.9%. With increasing Zr content, the conduction band minimum changes non-linearlymore » as well. Fitting of the energy band gap values resulted in a bowing parameter of ∼2 eV. The band gap bowing of the mixed oxides is assigned to the presence of the Zr d-electron states localized below the conduction band minimum of anodized Al{sub 2}O{sub 3}.« less

Formation, optical properties, and electronic structure of thin Yb silicide films on Si(111)

NASA Astrophysics Data System (ADS)

Galkin, N. G.; Maslov, A. M.; Polyarnyi, V. O.

2005-06-01

Continuous very thin (2.5-3.0 nm) and thin (16-18 nm) ytterbium suicide films with some pinhole density (3×107- 1×108 cm-2) have been formed on Si(111) by solid phase epitaxy (SPE) and reactive deposition epitaxy (RDE) growth methods on templates. The stoichiometric ytterbium suicide (YbSi2) formation has shown in SPE grown films by AES and EELS data. Very thin Yb suicide films grown by RDE method had the silicon enrichment in YbSi2 suicide composition. The analysis of LEED data and AFM imaging has shown that ytterbium suicide films had non-oriented blocks with the polycrystalline structure. The analysis of scanning region length dependencies of the root mean square roughness deviation (σR(L)) for grown suicide films has shown that the formation of ytterbium suicide in SPE and RDE growth methods is determined by the surface diffusion of Yb atoms during the three-dimensional growth process. Optical functions (n, k, α, ɛ1, ɛ2, Im ɛ1-1, neff, ɛeff) of ytterbium silicide films grown on Si(1 1 1) have been calculated from transmittance and reflectance spectra in the energy range of 0.1-6.2 eV. Two nearly discrete absorption bands have been observed in the electronic structure of Yb silicide films with different composition, which connected with interband transitions on divalent and trivalent Yb states. It was established that the reflection coefficient minimum in R-spectra at energies higher 4.2 eV corresponds to the state density minimum in Yb suicide between divalent and trivalent Yb states. It was shown from optical data that Yb silicide films have the semi-metallic properties with low state densities at energies less 0.4 eV and high state densities at 0.5-2.5 eV.

String method for calculation of minimum free-energy paths in Cartesian space in freely-tumbling systems.

PubMed

Branduardi, Davide; Faraldo-Gómez, José D

2013-09-10

The string method is a molecular-simulation technique that aims to calculate the minimum free-energy path of a chemical reaction or conformational transition, in the space of a pre-defined set of reaction coordinates that is typically highly dimensional. Any descriptor may be used as a reaction coordinate, but arguably the Cartesian coordinates of the atoms involved are the most unprejudiced and intuitive choice. Cartesian coordinates, however, present a non-trivial problem, in that they are not invariant to rigid-body molecular rotations and translations, which ideally ought to be unrestricted in the simulations. To overcome this difficulty, we reformulate the framework of the string method to integrate an on-the-fly structural-alignment algorithm. This approach, referred to as SOMA (String method with Optimal Molecular Alignment), enables the use of Cartesian reaction coordinates in freely tumbling molecular systems. In addition, this scheme permits the dissection of the free-energy change along the most probable path into individual atomic contributions, thus revealing the dominant mechanism of the simulated process. This detailed analysis also provides a physically-meaningful criterion to coarse-grain the representation of the path. To demonstrate the accuracy of the method we analyze the isomerization of the alanine dipeptide in vacuum and the chair-to-inverted-chair transition of β -D mannose in explicit water. Notwithstanding the simplicity of these systems, the SOMA approach reveals novel insights into the atomic mechanism of these isomerizations. In both cases, we find that the dynamics and the energetics of these processes are controlled by interactions involving only a handful of atoms in each molecule. Consistent with this result, we show that a coarse-grained SOMA calculation defined in terms of these subsets of atoms yields nearidentical minimum free-energy paths and committor distributions to those obtained via a highly-dimensional string.

String method for calculation of minimum free-energy paths in Cartesian space in freely-tumbling systems

PubMed Central

Branduardi, Davide; Faraldo-Gómez, José D.

2014-01-01

The string method is a molecular-simulation technique that aims to calculate the minimum free-energy path of a chemical reaction or conformational transition, in the space of a pre-defined set of reaction coordinates that is typically highly dimensional. Any descriptor may be used as a reaction coordinate, but arguably the Cartesian coordinates of the atoms involved are the most unprejudiced and intuitive choice. Cartesian coordinates, however, present a non-trivial problem, in that they are not invariant to rigid-body molecular rotations and translations, which ideally ought to be unrestricted in the simulations. To overcome this difficulty, we reformulate the framework of the string method to integrate an on-the-fly structural-alignment algorithm. This approach, referred to as SOMA (String method with Optimal Molecular Alignment), enables the use of Cartesian reaction coordinates in freely tumbling molecular systems. In addition, this scheme permits the dissection of the free-energy change along the most probable path into individual atomic contributions, thus revealing the dominant mechanism of the simulated process. This detailed analysis also provides a physically-meaningful criterion to coarse-grain the representation of the path. To demonstrate the accuracy of the method we analyze the isomerization of the alanine dipeptide in vacuum and the chair-to-inverted-chair transition of β-D mannose in explicit water. Notwithstanding the simplicity of these systems, the SOMA approach reveals novel insights into the atomic mechanism of these isomerizations. In both cases, we find that the dynamics and the energetics of these processes are controlled by interactions involving only a handful of atoms in each molecule. Consistent with this result, we show that a coarse-grained SOMA calculation defined in terms of these subsets of atoms yields nearidentical minimum free-energy paths and committor distributions to those obtained via a highly-dimensional string. PMID:24729762

Theoretical Study of Tautomerization Reactions for the Ground and First Excited Electronic States of Adenine

NASA Technical Reports Server (NTRS)

Salter, Latasha M.; Chaban, Galina M.; Kwak, Dochan (Technical Monitor)

2002-01-01

Geometrical structures and energetic properties for different tautomers of adenine are calculated in this study, using multi-configurational wave functions. Both the ground and the lowest singlet excited state potential energy surfaces are studied. Four tautomeric forms are considered, and their energetic order is found to be different on the ground and the excited state potential energy surfaces. Minimum energy reaction paths are obtained for hydrogen atom transfer (tautomerization) reactions in the ground and the lowest excited electronic states. It is found that the barrier heights and the shapes of the reaction paths are different for the ground and the excited electronic states, suggesting that the probability of such tautomerization reaction is higher on the excited state potential energy surface. This tautomerization process should become possible in the presence of water or other polar solvent molecules and should play an important role in the photochemistry of adenine.

A generalized force-modified potential energy surface (G-FMPES) for mechanochemical simulations

DOE PAGES

Subramanian, Gopinath; Mathew, Nithin; Leiding, Jeffery A.

2015-10-05

We describe the modifications that a spatially varying external load produces on a Born-Oppenheimer potential energy surface (PES) by calculating static quantities of interest. The effects of the external loads are exemplified using electronic structure calculations (at the HF/6-31G** level) of two different molecules: ethane and hexahydro-1,3,5-trinitro-s-triazine (RDX). The calculated transition states and The Hessian matrices of stationary points show that spatially varying external loads shift the stationary points and modify the curvature of the PES, thereby affecting the harmonic transition rates by altering both the energy barrier as well as the prefactor. The harmonic spectra of both molecules aremore » blue-shifted with increasing compressive “pressure.” Some stationary points on the RDX-PES disappear under application of the external load, indicating the merging of an energy minimum with a saddle point.« less

Optimization of Stability Constrained Geometrically Nonlinear Shallow Trusses Using an Arc Length Sparse Method with a Strain Energy Density Approach

NASA Technical Reports Server (NTRS)

Hrinda, Glenn A.; Nguyen, Duc T.

2008-01-01

A technique for the optimization of stability constrained geometrically nonlinear shallow trusses with snap through behavior is demonstrated using the arc length method and a strain energy density approach within a discrete finite element formulation. The optimization method uses an iterative scheme that evaluates the design variables' performance and then updates them according to a recursive formula controlled by the arc length method. A minimum weight design is achieved when a uniform nonlinear strain energy density is found in all members. This minimal condition places the design load just below the critical limit load causing snap through of the structure. The optimization scheme is programmed into a nonlinear finite element algorithm to find the large strain energy at critical limit loads. Examples of highly nonlinear trusses found in literature are presented to verify the method.

Band gap narrowing in n-type and p-type 3C-, 2H-, 4H-, 6H-SiC, and Si

NASA Astrophysics Data System (ADS)

Persson, C.; Lindefelt, U.; Sernelius, B. E.

1999-10-01

Doping-induced energy shifts of the conduction band minimum and the valence band maximum have been calculated for n-type and p-type 3C-, 2H-, 4H-, 6H-SiC, and Si. The narrowing of the fundamental band gap and of the optical band gap are presented as functions of ionized impurity concentration. The calculations go beyond the common parabolic treatments of the ground state energy dispersion by using energy dispersion and overlap integrals from band structure calculations. The nonparabolic valence band curvatures influence strongly the energy shifts especially in p-type materials. The utilized method is based on a zero-temperature Green's function formalism within the random phase approximation with local field correction according to Hubbard. We have parametrized the shifts of the conduction and the valence bands and made comparisons with recently published results from a semi-empirical model.

A multi-populations multi-strategies differential evolution algorithm for structural optimization of metal nanoclusters

NASA Astrophysics Data System (ADS)

Fan, Tian-E.; Shao, Gui-Fang; Ji, Qing-Shuang; Zheng, Ji-Wen; Liu, Tun-dong; Wen, Yu-Hua

2016-11-01

Theoretically, the determination of the structure of a cluster is to search the global minimum on its potential energy surface. The global minimization problem is often nondeterministic-polynomial-time (NP) hard and the number of local minima grows exponentially with the cluster size. In this article, a multi-populations multi-strategies differential evolution algorithm has been proposed to search the globally stable structure of Fe and Cr nanoclusters. The algorithm combines a multi-populations differential evolution with an elite pool scheme to keep the diversity of the solutions and avoid prematurely trapping into local optima. Moreover, multi-strategies such as growing method in initialization and three differential strategies in mutation are introduced to improve the convergence speed and lower the computational cost. The accuracy and effectiveness of our algorithm have been verified by comparing the results of Fe clusters with Cambridge Cluster Database. Meanwhile, the performance of our algorithm has been analyzed by comparing the convergence rate and energy evaluations with the classical DE algorithm. The multi-populations, multi-strategies mutation and growing method in initialization in our algorithm have been considered respectively. Furthermore, the structural growth pattern of Cr clusters has been predicted by this algorithm. The results show that the lowest-energy structure of Cr clusters contains many icosahedra, and the number of the icosahedral rings rises with increasing size.

Performance evaluation of the inverse dynamics method for optimal spacecraft reorientation

NASA Astrophysics Data System (ADS)

Ventura, Jacopo; Romano, Marcello; Walter, Ulrich

2015-05-01

This paper investigates the application of the inverse dynamics in the virtual domain method to Euler angles, quaternions, and modified Rodrigues parameters for rapid optimal attitude trajectory generation for spacecraft reorientation maneuvers. The impact of the virtual domain and attitude representation is numerically investigated for both minimum time and minimum energy problems. Owing to the nature of the inverse dynamics method, it yields sub-optimal solutions for minimum time problems. Furthermore, the virtual domain improves the optimality of the solution, but at the cost of more computational time. The attitude representation also affects solution quality and computational speed. For minimum energy problems, the optimal solution can be obtained without the virtual domain with any considered attitude representation.

α Centauri A in the far infrared. First measurement of the temperature minimum of a star other than the Sun

NASA Astrophysics Data System (ADS)

Liseau, R.; Montesinos, B.; Olofsson, G.; Bryden, G.; Marshall, J. P.; Ardila, D.; Bayo Aran, A.; Danchi, W. C.; del Burgo, C.; Eiroa, C.; Ertel, S.; Fridlund, M. C. W.; Krivov, A. V.; Pilbratt, G. L.; Roberge, A.; Thébault, P.; Wiegert, J.; White, G. J.

2013-01-01

Context. Chromospheres and coronae are common phenomena on solar-type stars. Understanding the energy transfer to these heated atmospheric layers requires direct access to the relevant empirical data. Study of these structures has, by and large, been limited to the Sun thus far. Aims: The region of the temperature reversal can be directly observed only in the far infrared and submillimetre spectral regime. We aim at determining the characteristics of the atmosphere in the region of the temperature minimum of the solar sister star α Cen A. As a bonus this will also provide a detailed mapping of the spectral energy distribution, i.e. knowledge that is crucial when searching for faint, Kuiper belt-like dust emission around other stars. Methods: For the nearby binary system α Cen, stellar parameters are known with high accuracy from measurements. For the basic model parameters Teff, log g and [Fe/H], we interpolate stellar model atmospheres in the grid of Gaia/PHOENIX and compute the corresponding model for the G2 V star α Cen A. Comparison with photometric measurements shows excellent agreement between observed photospheric data in the optical and infrared. For longer wavelengths, the modelled spectral energy distribution is compared to Spitzer-MIPS, Herschel-PACS, Herschel-SPIRE, and APEX-LABOCA photometry. A specifically tailored Uppsala model based on the MARCS code and extending further in wavelength is used to gauge the emission characteristics of α Cen A in the far infared. Results: Similar to the Sun, the far infrared (FIR) emission of α Cen A originates in the minimum temperature region above the stellar photosphere in the visible. However, in comparison with the solar case, the FIR photosphere of α Cen A appears marginally cooler, Tmin ~ T160 μm = 3920 ± 375 K. Beyond the minimum near 160 μm, the brightness temperatures increase, and this radiation very likely originates in warmer regions of the chromosphere of α Cen A. Conclusions: To the best of our knowledge, this is the first time a temperature minimum has been directly measured on a main-sequence star other than the Sun. Based on observations with Herschel, which is an ESA space observatory with science instruments provided by the European-led Principal Investigator consortia and with important participation from NASA.

Molecules for materials: germanium hydride neutrals and anions. Molecular structures, electron affinities, and thermochemistry of GeHn/GeHn- (n = 0-4) and Ge2Hn/Ge2Hn(-) (n = 0-6).

PubMed

Li, Qian-Shu; Lü, Rui-Hua; Xie, Yaoming; Schaefer, Henry F

2002-12-01

The GeH(n) (n = 0-4) and Ge(2)H(n) (n = 0-6) systems have been studied systematically by five different density functional methods. The basis sets employed are of double-zeta plus polarization quality with additional s- and p-type diffuse functions, labeled DZP++. For each compound plausible energetically low-lying structures were optimized. The methods used have been calibrated against a comprehensive tabulation of experimental electron affinities (Chemical Reviews 102, 231, 2002). The geometries predicted in this work include yet unknown anionic species, such as Ge(2)H(-), Ge(2)H(2)(-), Ge(2)H(3)(-), Ge(2)H(4)(-), and Ge(2)H(5)(-). In general, the BHLYP method predicts the geometries closest to the few available experimental structures. A number of structures rather different from the analogous well-characterized hydrocarbon radicals and anions are predicted. For example, a vinylidene-like GeGeH(2) (-) structure is the global minimum of Ge(2)H(2) (-). For neutral Ge(2)H(4), a methylcarbene-like HGë-GeH(3) is neally degenerate with the trans-bent H(2)Ge=GeH(2) structure. For the Ge(2)H(4) (-) anion, the methylcarbene-like system is the global minimum. The three different neutral-anion energy differences reported in this research are: the adiabatic electron affinity (EA(ad)), the vertical electron affinity (EA(vert)), and the vertical detachment energy (VDE). For this family of molecules the B3LYP method appears to predict the most reliable electron affinities. The adiabatic electron affinities after the ZPVE correction are predicted to be 2.02 (Ge(2)), 2.05 (Ge(2)H), 1.25 (Ge(2)H(2)), 2.09 (Ge(2)H(3)), 1.71 (Ge(2)H(4)), 2.17 (Ge(2)H(5)), and -0.02 (Ge(2)H(6)) eV. We also reported the dissociation energies for the GeH(n) (n = 1-4) and Ge(2)H(n) (n = 1-6) systems, as well as those for their anionic counterparts. Our theoretical predictions provide strong motivation for the further experimental study of these important germanium hydrides. Copyright 2002 Wiley Periodicals, Inc.

Direct dynamics simulation of dioxetane formation and decomposition via the singlet .O-O-CH2-CH2. biradical: Non-RRKM dynamics

NASA Astrophysics Data System (ADS)

Sun, Rui; Park, Kyoyeon; de Jong, Wibe A.; Lischka, Hans; Windus, Theresa L.; Hase, William L.

2012-07-01

Electronic structure calculations and direct chemical dynamics simulations are used to study the formation and decomposition of dioxetane on its ground state singlet potential energy surface. The stationary points for 1O2 + C2H4, the singlet .O-O-CH2-CH2. biradical, the transition state (TS) connecting this biradical with dioxetane, and the two transition states and gauche .O-CH2-CH2-O. biradical connecting dioxetane with the formaldehyde product molecules are investigated at different levels of electronic structure theory including UB3LYP, UMP2, MRMP2, and CASSCF and a range of basis sets. The UB3LYP/6-31G* method was found to give representative energies for the reactive system and was used as a model for the simulations. UB3LYP/6-31G* direct dynamics trajectories were initiated at the TS connecting the .O-O-CH2-CH2. biradical and dioxetane by sampling the TS's vibrational energy levels, and rotational and reaction coordinate energies, with Boltzmann distributions at 300, 1000, and 1500 K. This corresponds to the transition state theory model for trajectories that pass the TS. The trajectories were directed randomly towards both the biradical and dioxetane. A small fraction of the trajectories directed towards the biradical recrossed the TS and formed dioxetane. The remainder formed 1O2 + C2H4 and of these ˜ 40% went directly from the TS to 1O2 + C2H4 without getting trapped and forming an intermediate in the .O-O-CH2-CH2. biradical potential energy minimum, a non-statistical result. The dioxetane molecules which are formed dissociate to two formaldehyde molecules with a rate constant two orders of magnitude smaller than that predicted by Rice-Ramsperger-Kassel-Marcus theory. The reaction dynamics from dioxetane to the formaldehyde molecules do not follow the intrinsic reaction coordinate or involve trapping in the gauche .O-CH2-CH2-O. biradical potential energy minimum. Important non-statistical dynamics are exhibited for this reactive system.

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

Ngo, Van; Wang, Yibo; Haas, Stephan

Crystal structures of several bacterial Na v channels have been recently published and molecular dynamics simulations of ion permeation through these channels are consistent with many electrophysiological properties of eukaryotic channels. Bacterial Na v channels have been characterized as functionally asymmetric, and the mechanism of this asymmetry has not been clearly understood. To address this question, we combined non-equilibrium simulation data with two-dimensional equilibrium unperturbed landscapes generated by umbrella sampling and Weighted Histogram Analysis Methods for multiple ions traversing the selectivity filter of bacterial Na vAb channel. This approach provided new insight into the mechanism of selective ion permeation inmore » bacterial Nav channels. The non-equilibrium simulations indicate that two or three extracellular K + ions can block the entrance to the selectivity filter of Na vAb in the presence of applied forces in the inward direction, but not in the outward direction. The block state occurs in an unstable local minimum of the equilibrium unperturbed free-energy landscape of two K+ ions that can be ‘locked’ in place bymodest applied forces. In contrast to K +, three Na + ions move favorably through the selectivity filter together as a unit in a loose “knock-on” mechanism of permeation in both inward and outward directions, and there is no similar local minimum in the two-dimensional free-energy landscape of two Na + ions for a block state. The useful work predicted by the non-equilibrium simulations that is required to break the K + block is equivalent to large applied potentials experimentally measured for two bacterial Na v channels to induce inward currents of K + ions. Here, these results illustrate how inclusion of non-equilibrium factors in the simulations can provide detailed information about mechanisms of ion selectivity that is missing from mechanisms derived from either crystal structures or equilibrium unperturbed free-energy landscapes.« less

On the ultraviolet photodissociation of H2Te

NASA Astrophysics Data System (ADS)

Alekseyev, Aleksey B.; Liebermann, Heinz-Peter; Wittig, Curt

2004-11-01

The photodissociation of H2Te through excitation in the first absorption band is investigated by means of multireference spin-orbit configuration interaction (CI) calculations. Bending potentials for low-lying electronic states of H2Te are obtained in C2v symmetry for Te-H distances fixed at the ground state equilibrium value of 3.14a0, as well as for the minimum energy path constrained to R1=R2. Asymmetric cuts of potential energy surfaces for excited states (at R1=3.14a0 and θ=90.3°) are obtained for the first time. It is shown that vibrational structure in the 380-400 nm region of the long wavelength absorption tail is due to transitions to 3A', which has a shallow minimum at large HTe-H separations. Transitions to this state are polarized in the molecular plane, and this state converges to the excited TeH(2Π1/2)+H(2S) limit. These theoretical data are in accord with the selectivity toward TeH(2Π1/2) relative to TeH(2Π3/2) that has been found experimentally for 355 nm H2Te photodissociation. The calculated 3A'←X˜A' transition dipole moment increases rapidly with HTe-H distance; this explains the observation of 3A' vibrational structure for low vibrational levels, despite unfavorable Franck-Condon factors. According to the calculated vertical energies and transition moment data, the maximum in the first absorption band at ≈245 nm is caused by excitation to 4A″, which has predominantly 21A″ (1B1 in C2v symmetry) character.

Minimum Free Energy Path of Ligand-Induced Transition in Adenylate Kinase

PubMed Central

Matsunaga, Yasuhiro; Fujisaki, Hiroshi; Terada, Tohru; Furuta, Tadaomi; Moritsugu, Kei; Kidera, Akinori

2012-01-01

Large-scale conformational changes in proteins involve barrier-crossing transitions on the complex free energy surfaces of high-dimensional space. Such rare events cannot be efficiently captured by conventional molecular dynamics simulations. Here we show that, by combining the on-the-fly string method and the multi-state Bennett acceptance ratio (MBAR) method, the free energy profile of a conformational transition pathway in Escherichia coli adenylate kinase can be characterized in a high-dimensional space. The minimum free energy paths of the conformational transitions in adenylate kinase were explored by the on-the-fly string method in 20-dimensional space spanned by the 20 largest-amplitude principal modes, and the free energy and various kinds of average physical quantities along the pathways were successfully evaluated by the MBAR method. The influence of ligand binding on the pathways was characterized in terms of rigid-body motions of the lid-shaped ATP-binding domain (LID) and the AMP-binding (AMPbd) domains. It was found that the LID domain was able to partially close without the ligand, while the closure of the AMPbd domain required the ligand binding. The transition state ensemble of the ligand bound form was identified as those structures characterized by highly specific binding of the ligand to the AMPbd domain, and was validated by unrestrained MD simulations. It was also found that complete closure of the LID domain required the dehydration of solvents around the P-loop. These findings suggest that the interplay of the two different types of domain motion is an essential feature in the conformational transition of the enzyme. PMID:22685395

A stochastic algorithm for global optimization and for best populations: A test case of side chains in proteins

PubMed Central

Glick, Meir; Rayan, Anwar; Goldblum, Amiram

2002-01-01

The problem of global optimization is pivotal in a variety of scientific fields. Here, we present a robust stochastic search method that is able to find the global minimum for a given cost function, as well as, in most cases, any number of best solutions for very large combinatorial “explosive” systems. The algorithm iteratively eliminates variable values that contribute consistently to the highest end of a cost function's spectrum of values for the full system. Values that have not been eliminated are retained for a full, exhaustive search, allowing the creation of an ordered population of best solutions, which includes the global minimum. We demonstrate the ability of the algorithm to explore the conformational space of side chains in eight proteins, with 54 to 263 residues, to reproduce a population of their low energy conformations. The 1,000 lowest energy solutions are identical in the stochastic (with two different seed numbers) and full, exhaustive searches for six of eight proteins. The others retain the lowest 141 and 213 (of 1,000) conformations, depending on the seed number, and the maximal difference between stochastic and exhaustive is only about 0.15 Kcal/mol. The energy gap between the lowest and highest of the 1,000 low-energy conformers in eight proteins is between 0.55 and 3.64 Kcal/mol. This algorithm offers real opportunities for solving problems of high complexity in structural biology and in other fields of science and technology. PMID:11792838

Helical coil buckling mechanism for a stiff nanowire on an elastomeric substrate

NASA Astrophysics Data System (ADS)

Chen, Youlong; Liu, Yilun; Yan, Yuan; Zhu, Yong; Chen, Xi

2016-10-01

When a stiff nanowire is deposited on a compliant soft substrate, it may buckle into a helical coil form when the system is compressed. Using theoretical and finite element method (FEM) analyses, the detailed three-dimensional coil buckling mechanism for a silicon nanowire (SiNW) on a polydimethylsiloxane (PDMS) substrate is studied. A continuum mechanics approach based on the minimization of the strain energy in the SiNW and elastomeric substrate is developed. Due to the helical buckling, the bending strain in SiNW is significantly reduced and the maximum local strain is almost uniformly distributed along SiNW. Based on the theoretical model, the energy landscape for different buckling modes of SiNW on PDMS substrate is given, which shows that both the in-plane and out-of-plane buckling modes have the local minimum potential energy, whereas the helical buckling model has the global minimum potential energy. Furthermore, the helical buckling spacing and amplitudes are deduced, taking into account the influences of the elastic properties and dimensions of SiNWs. These features are verified by systematic FEM simulations and parallel experiments. As the effective compressive strain in elastomeric substrate increases, the buckling profile evolves from a vertical ellipse to a lateral ellipse, and then approaches to a circle when the effective compressive strain is larger than 30%. The study may shed useful insights on the design and optimization of high-performance stretchable electronics and 3D complex nano-structures.

Auger electron and characteristic energy loss spectra for electro-deposited americium-241

NASA Astrophysics Data System (ADS)

Varma, Matesh N.; Baum, John W.

1983-07-01

Auger electron energy spectra for electro-deposited americium-241 on platinum substrate were obtained using a cylindrical mirror analyzer. Characteristic energy loss spectra for this sample were also obtained at primary electron beam energies of 990 and 390 eV. From these measurements PI, PII, and PIII energy levels for americium-241 are determined. Auger electron energies are compared with theoretically calculated values. Minimum detectability under the present condition of sample preparation and equipment was estimated at approximately 1.2×10-8 g/cm2 or 3.9×10-8 Ci/cm2. Minimum detectability for plutonium-239 under similar conditions was estimated at about 7.2×10-10 Ci/cm2.

Simultaneous Wireless Power Transfer and Secure Multicasting in Cooperative Decode-and-Forward Relay Networks.

PubMed

Lee, Jong-Ho; Sohn, Illsoo; Kim, Yong-Hwa

2017-05-16

In this paper, we investigate simultaneous wireless power transfer and secure multicasting via cooperative decode-and-forward (DF) relays in the presence of multiple energy receivers and eavesdroppers. Two scenarios are considered under a total power budget: maximizing the minimum harvested energy among the energy receivers under a multicast secrecy rate constraint; and maximizing the multicast secrecy rate under a minimum harvested energy constraint. For both scenarios, we solve the transmit power allocation and relay beamformer design problems by using semidefinite relaxation and bisection technique. We present numerical results to analyze the energy harvesting and secure multicasting performances in cooperative DF relay networks.

Simultaneous Wireless Power Transfer and Secure Multicasting in Cooperative Decode-and-Forward Relay Networks

PubMed Central

Lee, Jong-Ho; Sohn, Illsoo; Kim, Yong-Hwa

2017-01-01

In this paper, we investigate simultaneous wireless power transfer and secure multicasting via cooperative decode-and-forward (DF) relays in the presence of multiple energy receivers and eavesdroppers. Two scenarios are considered under a total power budget: maximizing the minimum harvested energy among the energy receivers under a multicast secrecy rate constraint; and maximizing the multicast secrecy rate under a minimum harvested energy constraint. For both scenarios, we solve the transmit power allocation and relay beamformer design problems by using semidefinite relaxation and bisection technique. We present numerical results to analyze the energy harvesting and secure multicasting performances in cooperative DF relay networks. PMID:28509841

Tantalum-based semiconductors for solar water splitting.

PubMed

Zhang, Peng; Zhang, Jijie; Gong, Jinlong

2014-07-07

Solar energy utilization is one of the most promising solutions for the energy crises. Among all the possible means to make use of solar energy, solar water splitting is remarkable since it can accomplish the conversion of solar energy into chemical energy. The produced hydrogen is clean and sustainable which could be used in various areas. For the past decades, numerous efforts have been put into this research area with many important achievements. Improving the overall efficiency and stability of semiconductor photocatalysts are the research focuses for the solar water splitting. Tantalum-based semiconductors, including tantalum oxide, tantalate and tantalum (oxy)nitride, are among the most important photocatalysts. Tantalum oxide has the band gap energy that is suitable for the overall solar water splitting. The more negative conduction band minimum of tantalum oxide provides photogenerated electrons with higher potential for the hydrogen generation reaction. Tantalates, with tunable compositions, show high activities owning to their layered perovskite structure. (Oxy)nitrides, especially TaON and Ta3N5, have small band gaps to respond to visible-light, whereas they can still realize overall solar water splitting with the proper positions of conduction band minimum and valence band maximum. This review describes recent progress regarding the improvement of photocatalytic activities of tantalum-based semiconductors. Basic concepts and principles of solar water splitting will be discussed in the introduction section, followed by the three main categories regarding to the different types of tantalum-based semiconductors. In each category, synthetic methodologies, influencing factors on the photocatalytic activities, strategies to enhance the efficiencies of photocatalysts and morphology control of tantalum-based materials will be discussed in detail. Future directions to further explore the research area of tantalum-based semiconductors for solar water splitting are also discussed.

A search for anisotropy in the arrival directions of ultra high energy cosmic rays recorded at the Pierre Auger Observatory

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

Abreu, P.

2012-01-01

Observations of cosmic ray arrival directions made with the Pierre Auger Observatory have previously provided evidence of anisotropy at the 99% CL using the correlation of ultra high energy cosmic rays (UHECRs) with objects drawn from the Veron-Cetty Veron catalog. In this paper we report on the use of three catalog independent methods to search for anisotropy. The 2pt-L, 2pt+ and 3pt methods, each giving a different measure of self-clustering in arrival directions, were tested on mock cosmic ray data sets to study the impacts of sample size and magnetic smearing on their results, accounting for both angular and energymore » resolutions. If the sources of UHECRs follow the same large scale structure as ordinary galaxies in the local Universe and if UHECRs are deflected no more than a few degrees, a study of mock maps suggests that these three methods can efficiently respond to the resulting anisotropy with a P-value = 1.0% or smaller with data sets as few as 100 events. Using data taken from January 1, 2004 to July 31, 2010 we examined the 20, 30, ..., 110 highest energy events with a corresponding minimum energy threshold of about 51 EeV. The minimum P-values found were 13.5% using the 2pt-L method, 1.0% using the 2pt+ method and 1.1% using the 3pt method for the highest 100 energy events. In view of the multiple (correlated) scans performed on the data set, these catalog-independent methods do not yield strong evidence of anisotropy in the highest energy cosmic rays.« less

Feasibility of utilizing small diameter southern pine for biomass in the Virginia Coastal Plain

Treesearch

Nathan C. Hanzelka; M. Chad Bolding; Scott M. Barrett; Jay Sullivan

2016-01-01

New or retrofitted wood-fired energy plants have increased demand for woody biomass in the stateof Virginia. Loblolly pine (Pinus taeda) commonly serves as a feedstock for these energy plants. Pulpwood conventionally requires a minimum diameter of 4 inches diameter at breast height (DBH) for merchantability, whereas a minimum merchantable diameter...

An estimate of equatorial wave energy flux at 9- to 90-day periods in the Central Pacific

NASA Technical Reports Server (NTRS)

Eriksen, Charles C.; Richman, James G.

1988-01-01

Deep fluctuations in current along the equator in the Central Pacific are dominated by coherent structures which correspond closely to narrow-band propagating equatorial waves. Currents were measured roughly at 1500 and 3000 m depths at five moorings between 144 and 148 deg W from January 1981 to March 1983, as part of the Pacific Equatorial Ocean Dynamics program. In each frequency band resolved, a single complex empirical orthogonal function accounts for half to three quarters of the observed variance in either zonal or meridional current. Dispersion for equatorial first meridional Rossby and Rossby gravity waves is consistent with the observed vertical-zonal coherence structure. The observations indicate that energy flux is westward and downward in long first meridional mode Rossby waves at periods 45 days and longer, and eastward and downward in short first meridional mode Rossby waves and Rossby-gravity waves at periods 30 days and shorter. A local minimum in energy flux occurs at periods corresponding to a maximum in upper-ocean meridional current energy contributed by tropical instability waves. Total vertical flux across the 9- to 90-day period range is 2.5 kW/m.

Energy design for protein-protein interactions

PubMed Central

Ravikant, D. V. S.; Elber, Ron

2011-01-01

Proteins bind to other proteins efficiently and specifically to carry on many cell functions such as signaling, activation, transport, enzymatic reactions, and more. To determine the geometry and strength of binding of a protein pair, an energy function is required. An algorithm to design an optimal energy function, based on empirical data of protein complexes, is proposed and applied. Emphasis is made on negative design in which incorrect geometries are presented to the algorithm that learns to avoid them. For the docking problem the search for plausible geometries can be performed exhaustively. The possible geometries of the complex are generated on a grid with the help of a fast Fourier transform algorithm. A novel formulation of negative design makes it possible to investigate iteratively hundreds of millions of negative examples while monotonically improving the quality of the potential. Experimental structures for 640 protein complexes are used to generate positive and negative examples for learning parameters. The algorithm designed in this work finds the correct binding structure as the lowest energy minimum in 318 cases of the 640 examples. Further benchmarks on independent sets confirm the significant capacity of the scoring function to recognize correct modes of interactions. PMID:21842951

Evidence of Cholesterol Accumulated in High Curvature Regions: Implication ot the Curvature Elastic Energy for Lipid Mixtures

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

Wang,W.; Yang, L.; Huang, H.

2007-01-01

Recent experiments suggested that cholesterol and other lipid components of high negative spontaneous curvature facilitate membrane fusion. This is taken as evidence supporting the stalk-pore model of membrane fusion in which the lipid bilayers go through intermediate structures of high curvature. How do the high-curvature lipid components lower the free energy of the curved structure? Do the high-curvature lipid components modify the average spontaneous curvature of the relevant monolayer, thereby facilitate its bending, or do the lipid components redistribute in the curved structure so as to lower the free energy? This question is fundamental to the curvature elastic energy formore » lipid mixtures. Here we investigate the lipid distribution in a monolayer of a binary lipid mixture before and after bending, or more precisely in the lamellar, hexagonal, and distorted hexagonal phases. The lipid mixture is composed of 2:1 ratio of brominated di18:0PC and cholesterol. Using a newly developed procedure for the multiwavelength anomalous diffraction method, we are able to isolate the bromine distribution and reconstruct the electron density distribution of the lipid mixture in the three phases. We found that the lipid distribution is homogenous and uniform in the lamellar and hexagonal phases. But in the distorted hexagonal phase, the lipid monolayer has nonuniform curvature, and cholesterol almost entirely concentrates in the high curvature region. This finding demonstrates that the association energies between lipid molecules vary with the curvature of membrane. Thus, lipid components in a mixture may redistribute under conditions of nonuniform curvature, such as in the stalk structure. In such cases, the spontaneous curvature depends on the local lipid composition and the free energy minimum is determined by lipid distribution as well as curvature.« less

A population-based evolutionary search approach to the multiple minima problem in de novo protein structure prediction

PubMed Central

2013-01-01

Background Elucidating the native structure of a protein molecule from its sequence of amino acids, a problem known as de novo structure prediction, is a long standing challenge in computational structural biology. Difficulties in silico arise due to the high dimensionality of the protein conformational space and the ruggedness of the associated energy surface. The issue of multiple minima is a particularly troublesome hallmark of energy surfaces probed with current energy functions. In contrast to the true energy surface, these surfaces are weakly-funneled and rich in comparably deep minima populated by non-native structures. For this reason, many algorithms seek to be inclusive and obtain a broad view of the low-energy regions through an ensemble of low-energy (decoy) conformations. Conformational diversity in this ensemble is key to increasing the likelihood that the native structure has been captured. Methods We propose an evolutionary search approach to address the multiple-minima problem in decoy sampling for de novo structure prediction. Two population-based evolutionary search algorithms are presented that follow the basic approach of treating conformations as individuals in an evolving population. Coarse graining and molecular fragment replacement are used to efficiently obtain protein-like child conformations from parents. Potential energy is used both to bias parent selection and determine which subset of parents and children will be retained in the evolving population. The effect on the decoy ensemble of sampling minima directly is measured by additionally mapping a conformation to its nearest local minimum before considering it for retainment. The resulting memetic algorithm thus evolves not just a population of conformations but a population of local minima. Results and conclusions Results show that both algorithms are effective in terms of sampling conformations in proximity of the known native structure. The additional minimization is shown to be key to enhancing sampling capability and obtaining a diverse ensemble of decoy conformations, circumventing premature convergence to sub-optimal regions in the conformational space, and approaching the native structure with proximity that is comparable to state-of-the-art decoy sampling methods. The results are shown to be robust and valid when using two representative state-of-the-art coarse-grained energy functions. PMID:24565020

A density functional study of silicon fullerene endohedral X@Si20F20 and exohedral X-Si20F20 (X=O2-, S2-, Se2-) complexes

NASA Astrophysics Data System (ADS)

Behzadi, Hadi; Esrafili, Mehdi D.; Manzetti, Sergio; Roonasi, Payman

2014-02-01

This study reports the structure and electronic properties of three stable endohedral X@Si20F20 and exohedral X-Si20F20 (X=O2-, S2-, Se2-) complexes. The study revealed that the endohedral complexes with S2- and Se2- result as energy minimum structures, with the guest anion located in the cage center. In the case of endohedral O2--complexes, the pattern is quite different whereas the O2- complexes dramatically deviated from the architecture of S2- and Se2-, by having O2- located toward one of silicon atoms in the cage. With respect to the exohedral form, the energy minimized structure is obtained by positioning the anion between two silicon atoms and forming two Si-X bonds. For both cases, the strength of the interactions is calculated to increase accordingly to the pattern: Se2-@Si20F20 (Se2--Si20F20)

Tungsten Ditelluride: a layered semimetal.

PubMed

Lee, Chia-Hui; Silva, Eduardo Cruz; Calderin, Lazaro; Nguyen, Minh An T; Hollander, Matthew J; Bersch, Brian; Mallouk, Thomas E; Robinson, Joshua A

2015-06-12

Tungsten ditelluride (WTe2) is a transition metal dichalcogenide (TMD) with physical and electronic properties that make it attractive for a variety of electronic applications. Although WTe2 has been studied for decades, its structure and electronic properties have only recently been correctly described. We experimentally and theoretically investigate the structure, dynamics and electronic properties of WTe2, and verify that WTe2 has its minimum energy configuration in a distorted 1T structure (Td structure), which results in metallic-like transport. Our findings unambiguously confirm the metallic nature of WTe2, introduce new information about the Raman modes of Td-WTe2, and demonstrate that Td-WTe2 is readily oxidized via environmental exposure. Finally, these findings confirm that, in its thermodynamically favored Td form, the utilization of WTe2 in electronic device architectures such as field effect transistors may need to be reevaluated.

The Rainbow Spectrum of RNA Secondary Structures.

PubMed

Li, Thomas J X; Reidys, Christian M

2018-06-01

In this paper, we analyze the length spectrum of rainbows in RNA secondary structures. A rainbow in a secondary structure is a maximal arc with respect to the partial order induced by nesting. We show that there is a significant gap in this length spectrum. We shall prove that there asymptotically almost surely exists a unique longest rainbow of length at least [Formula: see text] and that with high probability any other rainbow has finite length. We show that the distribution of the length of the longest rainbow converges to a discrete limit law and that, for finite k, the distribution of rainbows of length k becomes for large n a negative binomial distribution. We then put the results of this paper into context, comparing the analytical results with those observed in RNA minimum free energy structures, biological RNA structures and relate our findings to the sparsification of folding algorithms.

Theoretical analysis of the time-resolved binary (e, 2e) binding energy spectra on three-body photodissociation of acetone at 195 nm

NASA Astrophysics Data System (ADS)

Yamazaki, M.; Nakayama, S.; Zhu, C. Y.; Takahashi, M.

2017-11-01

We report on theoretical progress in time-resolved (e, 2e) electron momentum spectroscopy of photodissociation dynamics of the deuterated acetone molecule at 195 nm. We have examined the predicted minimum energy reaction path to investigate whether associated (e, 2e) calculations meet the experimental results. A noticeable difference between the experiment and calculations has been found at around binding energy of 10 eV, suggesting that the observed difference may originate, at least partly, in ever-unconsidered non-minimum energy paths.

Minimum energy efficiency standards for appliances: Old and new economic rationales

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

Houde, Sebastien; Spurlock, C. Anna

In this study, we revisit Hausman and Joskow (1982)'s economic rationales for appliance minimum energy efficiency standards. In addition to the four market failures they argued could justify appliance standards--energy prices below marginal social cost, consumers underestimating energy prices, consumer discount rates above social discount rates, or principal agent problems--we discuss two additional market failures that are relevant and potentially economically important in this context: market power and innovation market failures. We highlight puzzles uncovered by recent empirical results, and suggest directions future research should take to better understand the normative implications of appliance standards.

Minimum energy efficiency standards for appliances: Old and new economic rationales

DOE PAGES

Houde, Sebastien; Spurlock, C. Anna

2016-09-01

In this study, we revisit Hausman and Joskow (1982)'s economic rationales for appliance minimum energy efficiency standards. In addition to the four market failures they argued could justify appliance standards--energy prices below marginal social cost, consumers underestimating energy prices, consumer discount rates above social discount rates, or principal agent problems--we discuss two additional market failures that are relevant and potentially economically important in this context: market power and innovation market failures. We highlight puzzles uncovered by recent empirical results, and suggest directions future research should take to better understand the normative implications of appliance standards.

Molecular mechanism of direct proflavine-DNA intercalation: evidence for drug-induced minimum base-stacking penalty pathway.

PubMed

Sasikala, Wilbee D; Mukherjee, Arnab

2012-10-11

DNA intercalation, a biophysical process of enormous clinical significance, has surprisingly eluded molecular understanding for several decades. With appropriate configurational restraint (to prevent dissociation) in all-atom metadynamics simulations, we capture the free energy surface of direct intercalation from minor groove-bound state for the first time using an anticancer agent proflavine. Mechanism along the minimum free energy path reveals that intercalation happens through a minimum base stacking penalty pathway where nonstacking parameters (Twist→Slide/Shift) change first, followed by base stacking parameters (Buckle/Roll→Rise). This mechanism defies the natural fluctuation hypothesis and provides molecular evidence for the drug-induced cavity formation hypothesis. The thermodynamic origin of the barrier is found to be a combination of entropy and desolvation energy.

Changes in the structure of nuclei between the magic neutron numbers 50 and 82 as indicated by a rotating-cluster analysis of the energy values of the first 2+ excited states of isotopes of cadmium, tin, and tellurium

PubMed Central

Pauling, Linus

1981-01-01

Values of R, the radius of rotation of the rotating cluster, are calculated from the observed values of the energy of the lowest 2+ states of the even isotopes of 48Cd, 50Sn, and 52Te with the assumption that the cluster is α, p2, and α, respectively. R shows a maximum at ≈N = 58, a minimum at ≈N = 62, and a second maximum at ≈N = 70. The increase to the first maximum is interpreted as resulting from the overcrowding of spherons (alphas and tritons) in the mantle (outer layer) of the nuclei, causing the cluster to change from rotating in the mantle to skimming over its surface; the decrease to the minimum results from the addition of three dineutrons to the core, expanding the mantle and permitting the rotating cluster to begin to drop back into it; and the increase to the second maximum results from the overcrowding of the larger mantle surrounding the core containing the semi-magic number 14 of neutrons rather than the magic number 8 for N = 50. The decrease after the second maximum results from the further increase in the number of core neutrons to 20, corresponding to the magic number 82. Some additional evidence for the change to an intermediate structure between N = 50 and N = 82 is also discussed. PMID:16593084

The effect of Mn/Ni on thermodynamic properties of critical nucleus in Fe-Cu-Mn (Ni) ternary alloys

DOE PAGES

Li, Boyan; Zhang, Lei; Li, Chengliang; ...

2018-04-18

The aging- or radiation-induced hardening of Cu/Mn/Ni precipitates in Fe alloys is one of property degradation mechanisms in structural materials in nuclear reactors. Experiments show that aging or radiation leads the formation of Cu-rich precipitates, and the addition of Mn or Ni elements enhances the precipitation kinetics. In this study, the phase-field model coupled with the constrained string method have been applied to investigate the thermodynamic properties of critical nuclei such as the minimum energy path of Cu/Mn/Ni precipitation in Fe-Cu-Mn and Fe-Cu-Ni ternary alloys. The chemical free energies used in the model are taken from CALPHAD. The simulation resultsmore » show that the formation of Cu/Mn/Ni clusters needs to overcome an energy barrier, and the precipitate has a Core-Shell structure. The thermodynamic properties of the critical nucleus are influenced by temperature and Cu/Mn/Ni overall concentrations, which are in accordance with the simulation results as well as the experimental observations.« less

The effect of Mn/Ni on thermodynamic properties of critical nucleus in Fe-Cu-Mn (Ni) ternary alloys

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

Li, Boyan; Zhang, Lei; Li, Chengliang

The aging- or radiation-induced hardening of Cu/Mn/Ni precipitates in Fe alloys is one of property degradation mechanisms in structural materials in nuclear reactors. Experiments show that aging or radiation leads the formation of Cu-rich precipitates, and the addition of Mn or Ni elements enhances the precipitation kinetics. In this study, the phase-field model coupled with the constrained string method have been applied to investigate the thermodynamic properties of critical nuclei such as the minimum energy path of Cu/Mn/Ni precipitation in Fe-Cu-Mn and Fe-Cu-Ni ternary alloys. The chemical free energies used in the model are taken from CALPHAD. The simulation resultsmore » show that the formation of Cu/Mn/Ni clusters needs to overcome an energy barrier, and the precipitate has a Core-Shell structure. The thermodynamic properties of the critical nucleus are influenced by temperature and Cu/Mn/Ni overall concentrations, which are in accordance with the simulation results as well as the experimental observations.« less

Properties of model atomic free-standing thin films.

PubMed

Shi, Zane; Debenedetti, Pablo G; Stillinger, Frank H

2011-03-21

We present a computational study of the thermodynamic, dynamic, and structural properties of free-standing thin films, investigated via molecular dynamics simulation of a glass-forming binary Lennard-Jones mixture. An energy landscape analysis is also performed to study glassy states. At equilibrium, species segregation occurs, with the smaller minority component preferentially excluded from the surface. The film's interior density and interface width depend solely on temperature and not the initialization density. The atoms at the surface of the film have a higher lateral diffusivity when compared to the interior. The average difference between the equilibrium and inherent structure energies assigned to individual particles, as a function of the distance from the center of the film, increases near the surface. A minimum of this difference occurs in the region just under the liquid-vapor interface. This suggests that the surface atoms are able to sample the underlying energy landscape more effectively than those in the interior, and we suggest a possible relationship of this observation to the recently reported formation of stable glasses by vapor phase deposition.

Energy consumption analysis and simulation of waste heat recovery technology of ceramic rotary kiln

NASA Astrophysics Data System (ADS)

Chen, Zhiguang; Zhou, Yu; Qin, Chaokui; Zhang, Xuemei

2018-03-01

Ceramsite is widely used in the construction industry, insulation works and oil industry in China, and the manufacture equipment is mainly industrial kiln. In this paper, energy consumption analysis had been carried out through experimental test of a Ceramsite kiln in Henan province. Results showed that the discharge temperature of Ceramsite was about 1393K, and the waste heat accounted for 22.1% of the total energy consumption. A structure of cyclone preheater which recovered waste heat of the high temperature Ceramsite by blast cooling was designed. Then, using Fluent software, performance of the unit was simulated. The minimum temperature that Ceramsite could reach, heat dissipating capacity of Ceramsite, temperature at air outlet, wall temperature of the unit and pressure loss were analyzed. Performance of the designed unit under different inlet velocity was analyzed as well.

Equilibrium intermediate-state patterns in a type-I superconducting slab in an arbitrarily oriented applied magnetic field

DOE PAGES

Clem, John; Prozorov, Ruslan; Wijngaarden, Rinke J.

2013-09-04

The equilibrium topology of superconducting and normal domains in flat type-I superconductors is investigated. Important improvements with respect to previous work are that (1) the energy of the external magnetic field, as deformed by the presence of superconducting domains, is calculated in the same way for three different topologies and (2) calculations are made for arbitrary orientation of the applied field. A phase diagram is presented for the minimum-energy topology as a function of applied field magnitude and angle. For small (large) applied fields, normal (superconducting) tubes are found, while for intermediate fields, parallel domains have a lower energy. Themore » range of field magnitudes for which the superconducting-tubes structure is favored shrinks when the field is more in-plane oriented.« less

Photodissociation Dynamics of Phenol: Multistate Trajectory Simulations including Tunneling

DOE PAGES

Xu, Xuefei; Zheng, Jingjing; Yang, Ke R.; ...

2014-10-27

We report multistate trajectory simulations, including coherence, decoherence, and multidimensional tunneling, of phenol photodissociation dynamics. The calculations are based on full-dimensional anchor-points reactive potential surfaces and state couplings fit to electronic structure calculations including dynamical correlation with an augmented correlation-consistent polarized valence double-ζ basis set. The calculations successfully reproduce the experimentally observed bimodal character of the total kinetic energy release spectra and confirm the interpretation of the most recent experiments that the photodissociation process is dominated by tunneling. Analysis of the trajectories uncovers an unexpected dissociation pathway for one quantum excitation of the O–H stretching mode of the S 1more » state, namely, tunneling in a coherent mixture of states starting in a smaller R OH (~0.9–1.0 Å) region than has previously been invoked. The simulations also show that most trajectories do not pass close to the S 1–S 2 conical intersection (they have a minimum gap greater than 0.6 eV), they provide statistics on the out-of-plane angles at the locations of the minimum energy adiabatic gap, and they reveal information about which vibrational modes are most highly activated in the products.« less

Basin Hopping Graph: a computational framework to characterize RNA folding landscapes

PubMed Central

Kucharík, Marcel; Hofacker, Ivo L.; Stadler, Peter F.; Qin, Jing

2014-01-01

Motivation: RNA folding is a complicated kinetic process. The minimum free energy structure provides only a static view of the most stable conformational state of the system. It is insufficient to give detailed insights into the dynamic behavior of RNAs. A sufficiently sophisticated analysis of the folding free energy landscape, however, can provide the relevant information. Results: We introduce the Basin Hopping Graph (BHG) as a novel coarse-grained model of folding landscapes. Each vertex of the BHG is a local minimum, which represents the corresponding basin in the landscape. Its edges connect basins when the direct transitions between them are ‘energetically favorable’. Edge weights endcode the corresponding saddle heights and thus measure the difficulties of these favorable transitions. BHGs can be approximated accurately and efficiently for RNA molecules well beyond the length range accessible to enumerative algorithms. Availability and implementation: The algorithms described here are implemented in C++ as standalone programs. Its source code and supplemental material can be freely downloaded from http://www.tbi.univie.ac.at/bhg.html. Contact: qin@bioinf.uni-leipzig.de Supplementary information: Supplementary data are available at Bioinformatics online. PMID:24648041

The ViennaRNA web services.

PubMed

Gruber, Andreas R; Bernhart, Stephan H; Lorenz, Ronny

2015-01-01

The ViennaRNA package is a widely used collection of programs for thermodynamic RNA secondary structure prediction. Over the years, many additional tools have been developed building on the core programs of the package to also address issues related to noncoding RNA detection, RNA folding kinetics, or efficient sequence design considering RNA-RNA hybridizations. The ViennaRNA web services provide easy and user-friendly web access to these tools. This chapter describes how to use this online platform to perform tasks such as prediction of minimum free energy structures, prediction of RNA-RNA hybrids, or noncoding RNA detection. The ViennaRNA web services can be used free of charge and can be accessed via http://rna.tbi.univie.ac.at.

Topology Trivialization and Large Deviations for the Minimum in the Simplest Random Optimization

NASA Astrophysics Data System (ADS)

Fyodorov, Yan V.; Le Doussal, Pierre

2014-01-01

Finding the global minimum of a cost function given by the sum of a quadratic and a linear form in N real variables over (N-1)-dimensional sphere is one of the simplest, yet paradigmatic problems in Optimization Theory known as the "trust region subproblem" or "constraint least square problem". When both terms in the cost function are random this amounts to studying the ground state energy of the simplest spherical spin glass in a random magnetic field. We first identify and study two distinct large-N scaling regimes in which the linear term (magnetic field) leads to a gradual topology trivialization, i.e. reduction in the total number {N}_{tot} of critical (stationary) points in the cost function landscape. In the first regime {N}_{tot} remains of the order N and the cost function (energy) has generically two almost degenerate minima with the Tracy-Widom (TW) statistics. In the second regime the number of critical points is of the order of unity with a finite probability for a single minimum. In that case the mean total number of extrema (minima and maxima) of the cost function is given by the Laplace transform of the TW density, and the distribution of the global minimum energy is expected to take a universal scaling form generalizing the TW law. Though the full form of that distribution is not yet known to us, one of its far tails can be inferred from the large deviation theory for the global minimum. In the rest of the paper we show how to use the replica method to obtain the probability density of the minimum energy in the large-deviation approximation by finding both the rate function and the leading pre-exponential factor.

Multidisciplinary tailoring of hot composite structures

NASA Technical Reports Server (NTRS)

Singhal, Surendra N.; Chamis, Christos C.

1993-01-01

A computational simulation procedure is described for multidisciplinary analysis and tailoring of layered multi-material hot composite engine structural components subjected to simultaneous multiple discipline-specific thermal, structural, vibration, and acoustic loads. The effect of aggressive environments is also simulated. The simulation is based on a three-dimensional finite element analysis technique in conjunction with structural mechanics codes, thermal/acoustic analysis methods, and tailoring procedures. The integrated multidisciplinary simulation procedure is general-purpose including the coupled effects of nonlinearities in structure geometry, material, loading, and environmental complexities. The composite material behavior is assessed at all composite scales, i.e., laminate/ply/constituents (fiber/matrix), via a nonlinear material characterization hygro-thermo-mechanical model. Sample tailoring cases exhibiting nonlinear material/loading/environmental behavior of aircraft engine fan blades, are presented. The various multidisciplinary loads lead to different tailored designs, even those competing with each other, as in the case of minimum material cost versus minimum structure weight and in the case of minimum vibration frequency versus minimum acoustic noise.

Physical effects of mechanical design parameters on photon sensitivity and spatial resolution performance of a breast-dedicated PET system.

PubMed

Spanoudaki, V C; Lau, F W Y; Vandenbroucke, A; Levin, C S

2010-11-01

This study aims to address design considerations of a high resolution, high sensitivity positron emission tomography scanner dedicated to breast imaging. The methodology uses a detailed Monte Carlo model of the system structures to obtain a quantitative evaluation of several performance parameters. Special focus was given to the effect of dense mechanical structures designed to provide mechanical robustness and thermal regulation to the minuscule and temperature sensitive detectors. For the energies of interest around the photopeak (450-700 keV energy window), the simulation results predict a 6.5% reduction in the single photon detection efficiency and a 12.5% reduction in the coincidence photon detection efficiency in the case that the mechanical structures are interspersed between the detectors. However for lower energies, a substantial increase in the number of detected events (approximately 14% and 7% for singles at a 100-200 keV energy window and coincidences at a lower energy threshold of 100 keV, respectively) was observed with the presence of these structures due to backscatter. The number of photon events that involve multiple interactions in various crystal elements is also affected by the presence of the structures. For photon events involving multiple interactions among various crystal elements, the coincidence photon sensitivity is reduced by as much as 20% for a point source at the center of the field of view. There is no observable effect on the intrinsic and the reconstructed spatial resolution and spatial resolution uniformity. Mechanical structures can have a considerable effect on system sensitivity, especially for systems processing multi-interaction photon events. This effect, however, does not impact the spatial resolution. Various mechanical structure designs are currently under evaluation in order to achieve optimum trade-off between temperature stability, accurate detector positioning, and minimum influence on system performance.

Physical effects of mechanical design parameters on photon sensitivity and spatial resolution performance of a breast-dedicated PET system

PubMed Central

Spanoudaki, V. C.; Lau, F. W. Y.; Vandenbroucke, A.; Levin, C. S.

2010-01-01

Purpose: This study aims to address design considerations of a high resolution, high sensitivity positron emission tomography scanner dedicated to breast imaging. Methods: The methodology uses a detailed Monte Carlo model of the system structures to obtain a quantitative evaluation of several performance parameters. Special focus was given to the effect of dense mechanical structures designed to provide mechanical robustness and thermal regulation to the minuscule and temperature sensitive detectors. Results: For the energies of interest around the photopeak (450–700 keV energy window), the simulation results predict a 6.5% reduction in the single photon detection efficiency and a 12.5% reduction in the coincidence photon detection efficiency in the case that the mechanical structures are interspersed between the detectors. However for lower energies, a substantial increase in the number of detected events (approximately 14% and 7% for singles at a 100–200 keV energy window and coincidences at a lower energy threshold of 100 keV, respectively) was observed with the presence of these structures due to backscatter. The number of photon events that involve multiple interactions in various crystal elements is also affected by the presence of the structures. For photon events involving multiple interactions among various crystal elements, the coincidence photon sensitivity is reduced by as much as 20% for a point source at the center of the field of view. There is no observable effect on the intrinsic and the reconstructed spatial resolution and spatial resolution uniformity. Conclusions: Mechanical structures can have a considerable effect on system sensitivity, especially for systems processing multi-interaction photon events. This effect, however, does not impact the spatial resolution. Various mechanical structure designs are currently under evaluation in order to achieve optimum trade-off between temperature stability, accurate detector positioning, and minimum influence on system performance. PMID:21158296

Design for minimum energy in interstellar communication

NASA Astrophysics Data System (ADS)

Messerschmitt, David G.

2015-02-01

Microwave digital communication at interstellar distances is the foundation of extraterrestrial civilization (SETI and METI) communication of information-bearing signals. Large distances demand large transmitted power and/or large antennas, while the propagation is transparent over a wide bandwidth. Recognizing a fundamental tradeoff, reduced energy delivered to the receiver at the expense of wide bandwidth (the opposite of terrestrial objectives) is advantageous. Wide bandwidth also results in simpler design and implementation, allowing circumvention of dispersion and scattering arising in the interstellar medium and motion effects and obviating any related processing. The minimum energy delivered to the receiver per bit of information is determined by cosmic microwave background alone. By mapping a single bit onto a carrier burst, the Morse code invented for the telegraph in 1836 comes closer to this minimum energy than approaches used in modern terrestrial radio. Rather than the terrestrial approach of adding phases and amplitudes increases information capacity while minimizing bandwidth, adding multiple time-frequency locations for carrier bursts increases capacity while minimizing energy per information bit. The resulting location code is simple and yet can approach the minimum energy as bandwidth is expanded. It is consistent with easy discovery, since carrier bursts are energetic and straightforward modifications to post-detection pattern recognition can identify burst patterns. Time and frequency coherence constraints leading to simple signal discovery are addressed, and observations of the interstellar medium by transmitter and receiver constrain the burst parameters and limit the search scope.

Riemannian geometric approach to human arm dynamics, movement optimization, and invariance

NASA Astrophysics Data System (ADS)

Biess, Armin; Flash, Tamar; Liebermann, Dario G.

2011-03-01

We present a generally covariant formulation of human arm dynamics and optimization principles in Riemannian configuration space. We extend the one-parameter family of mean-squared-derivative (MSD) cost functionals from Euclidean to Riemannian space, and we show that they are mathematically identical to the corresponding dynamic costs when formulated in a Riemannian space equipped with the kinetic energy metric. In particular, we derive the equivalence of the minimum-jerk and minimum-torque change models in this metric space. Solutions of the one-parameter family of MSD variational problems in Riemannian space are given by (reparametrized) geodesic paths, which correspond to movements with least muscular effort. Finally, movement invariants are derived from symmetries of the Riemannian manifold. We argue that the geometrical structure imposed on the arm’s configuration space may provide insights into the emerging properties of the movements generated by the motor system.

Boltzmann transport properties of ultra thin-layer of h-CX monolayers

NASA Astrophysics Data System (ADS)

Kansara, Shivam; Gupta, Sanjeev K.; Sonvane, Yogesh

2018-04-01

Structural, electronic and thermoelectric properties of monolayer h-CX (X= Al, As, B, Bi, Ga, In, P, N, Sb and Tl) have been computed using density functional theory (DFT). The structural, electronic band structure, phonon dispersion curves and thermoelectric properties have been investigated. h-CGa and h-CTl show the periodically lattice vibrations and h-CB and h-CIn show small imaginary ZA frequencies. Thermoelectric properties are obtained using BoltzTrap code with the constant relaxation time (τ) approximation such as electronic, thermal and electrical conductivity calculated for various temperatures. The results indicate that h-CGa, h-CIn, h-CTl and h-CAl have direct band gaps with minimum electronic thermal and electrical conductivity while h-CB and h-CN show the high electronic thermal and electrical conductivity with highest cohesive energy.

Mechanics and geometry in the seashell-like (Turritella) surface

NASA Astrophysics Data System (ADS)

Guo, Qiaohang; Chen, Zi; Li, Wei; Ren, Kun; Lin, Junjie; Taber, Larry A.; Chen, Wenzhe

2013-03-01

Helical structures are ubiquitous in nature and engineering, ranging from DNA molecules to plant tendrils, from sea snail shells to nanoribbons. While the helical shapes in natural and engineered systems often exhibit nearly uniform radius and pitch, helical shell structures with changing radius and pitch, such as seashells and some plant tendrils, adds to the variety of this family of aesthetic beauty. Here we report the first biomimetic seashell-like structure resulting from mechanics of geometric frustration. In previous studies, the total potential energy is everywhere minimized when the system achieves an equilibrium. In this study, however, the local energy minimization cannot be realized because of the geometric incompatibility, and hence the whole system deforms into a shape with a global energy minimum whereby the energy in each segment may not necessary be locally optimized. This novel approach can be applied to develop materials and systems with desirable geometries by exploiting mechanics of geometric frustration. The authors would like to thank Yushan Huang, Zhen Liu, Si Chen for their assistance in the experimental demonstration. This work has been in part supported by NSFC (Grant No.11102040 and No.11201001044), the Sigma Xi Grants-in-Aid of Research (GIAR) program, American Academy of Mechanics Founder's Award from the Robert M. and Mary Haythornthwaite Foundation, and Society in Science, The Branco Weiss Fellowship, administered by ETH Zurich. Qiaohang Guo and Zi Chen contributed equally to this work.

Theoretical studies on the possible sensitizers of DSSC: Nanocomposites of graphene quantum dot hybrid phthalocyanine/tetrabenzoporphyrin/tetrabenzotriazaporphyrins/cis-tetrabenzodiazaporphyrins/tetrabenzomonoazaporphyrins and their Cu-metallated macrocycles

NASA Astrophysics Data System (ADS)

Gao, Feng; Yang, Chuan-Lu; Wang, Mei-Shan; Ma, Xiao-Guang; Liu, Wen-Wang

2018-04-01

The feasibility of nanocomposites of cir-coronene graphene quantum dot (GQD) with phthalocyanine, tetrabenzoporphyrin, tetrabenzotriazaporphyrins, cis-tetrabenzodiazaporphyrins, tetrabenzomonoazaporphyrins and their Cu-metallated macrocycles as a sensitizer of dye-sensitized solar cells (DSSC) are investigated. Based on the first principles density functional theory (DFT), the geometrical structures of the separate GQD and 10 macrocycles, and their hybridized nanocomposites are fully optimized. The energy stabilities of the obtained structures are confirmed by harmonic frequency analysis. The optical absorptions of the optimized structures are calculated with time-dependent DFT. The feasibility of the nanocomposites as the sensitizer of DSSC is examined by the charge spatial separation, the electron transfer, the molecular orbital energy levels of the nanocomposites and the electrolyte, and the conduction band minimum of TiO2 electrode. The results demonstrate that all the nanocomposites have enhanced absorptions in the visible light range, and their molecular orbital energies satisfy the requirement of sensitizers. However, only two of the ten considered nanocomposites demonstrate significantly charge spatial separation. The GQD-Cu-TBP is identified as the most favorable candidate sensitizer of DSSC by the most enhanced in optical absorption, obvious charge spatial separation, suitable LUMO energy levels and driving force for electron transfer, and low recombination rate of electron and hole.

Plate with decentralised velocity feedback loops: Power absorption and kinetic energy considerations

NASA Astrophysics Data System (ADS)

Gardonio, P.; Miani, S.; Blanchini, F.; Casagrande, D.; Elliott, S. J.

2012-04-01

This paper is focused on the vibration effects produced by an array of decentralised velocity feedback loops that are evenly distributed over a rectangular thin plate to minimise its flexural response. The velocity feedback loops are formed by collocated ideal velocity sensor and point force actuator pairs, which are unconditionally stable and produce 'sky-hook' damping on the plate. The study compares how the overall flexural vibration of the plate and the local absorption of vibration power by the feedback loops vary with the control gains. The analysis is carried out both considering a typical frequency-domain formulation based on kinetic energy and structural power physical quantities, which is normally used to study vibration and noise problems, and a time-domain formulation also based on kinetic energy and structural power, which is usually implemented to investigate control problems. The time-domain formulation shows to be much more computationally efficient and robust with reference to truncation errors. Thus it has been used to perform a parametric study to assess if, and under which conditions, the minimum of the kinetic energy and the maximum of the absorbed power cost functions match with reference to: (a) the number of feedback control loops, (b) the structural damping in the plate, (c) the mutual distance of a pair of control loops and (d) the mutual gains implemented in a pair of feedback loops.

Accurate representation of B-DNA double helical structure with implicit solvent and counterions.

PubMed Central

Wang, Lihua; Hingerty, Brian E; Srinivasan, A R; Olson, Wilma K; Broyde, Suse

2002-01-01

High-resolution nuclear magnetic resonance (NMR) and crystallographic data have been taken to refine the force field used in the torsion angle space nucleic acids molecular mechanics program DUPLEX. The population balance deduced from NMR studies of two carcinogen-modified DNA conformers in equilibrium was used to fine tune a sigmoidal, distance-dependent dielectric function so that reasonable relative energies could be obtained. In addition, the base-pair and backbone geometry from high-resolution crystal structures of the Dickerson-Drew dodecamer was used to re-evaluate the deoxyribose pseudorotation profile and the Lennard-Jones nonbonded energy terms. With a modified dielectric function that assumes a very steep distance-dependent form, a deoxyribose pseudorotation profile with reduced energy barriers between C2'- and C3'-endo minima, and a shift of the Lennard-Jones potential energy minimum to a distance approximately 0.4 A greater than the sum of the van der Waals' radii, the sequence-dependent conformational features of the Dickerson-Drew dodecamer in both the solid state and the aqueous liquid crystalline phase are well reproduced. The robust performance of the revised force field, in conjunction with its efficiency through implicit treatment of solvent and counterions, provides a valuable tool for elucidating conformations and structure-function relationships of DNA, including those of molecules modified by carcinogens and other ligands. PMID:12080128

A canonical stability-elasticity relationship verified for one million face-centred-cubic structures.

PubMed

Maisel, Sascha B; Höfler, Michaela; Müller, Stefan

2012-11-29

Any thermodynamically stable or metastable phase corresponds to a local minimum of a potentially very complicated energy landscape. But however complex the crystal might be, this energy landscape is of parabolic shape near its minima. Roughly speaking, the depth of this energy well with respect to some reference level determines the thermodynamic stability of the system, and the steepness of the parabola near its minimum determines the system's elastic properties. Although changing alloying elements and their concentrations in a given material to enhance certain properties dates back to the Bronze Age, the systematic search for desirable properties in metastable atomic configurations at a fixed stoichiometry is a very recent tool in materials design. Here we demonstrate, using first-principles studies of four binary alloy systems, that the elastic properties of face-centred-cubic intermetallic compounds obey certain rules. We reach two conclusions based on calculations on a huge subset of the face-centred-cubic configuration space. First, the stiffness and the heat of formation are negatively correlated with a nearly constant Spearman correlation for all concentrations. Second, the averaged stiffness of metastable configurations at a fixed concentration decays linearly with their distance to the ground-state line (the phase diagram of an alloy at zero Kelvin). We hope that our methods will help to simplify the quest for new materials with optimal properties from the vast configuration space available.

Solar-Cycle Variability of Magnetosheath Fluctuations at Earth and Venus

NASA Astrophysics Data System (ADS)

Dwivedi, N. K.; Narita, Y.; Kovacs, P.

2014-12-01

The magnetosheath is a region between the bow-shock and magnetopause and the magnetosheath plasma is mostly in the turbulent state. In the present investigation we put an effort to closely examine the magnetosheath fluctuations dependency on the solar-cycles (solar-maximum and solar minimum) at the magnetized planetary body (Earth) and their comparison with the un-magnetized planetary body (Venus) for the solar minimum. We use the CLUSTER FGM data for the solar-maximum (2001-2002), solar-minimum (2006-2008) and Venus fluxgate magnetometer data for the solar-minimum (2006-2008) to perform a comparative statistical study on the energy spectra and probability density function (PDF) and asses the spectral features of the magnetic fluctuations of the both planetary bodies. In the comparison we study the relation between the inertial ranges of the spectra and the temporal scales of non-Gaussian magnetic fluctuations derived from PDF analyses. The first can refer to turbulent cascade dynamics, while the latter may indicate intermittency. We first transformed the magnetic field data into mean field aligned coordinate system with respect to the large-scale magnetic field direction and then after we compute the power spectral density with the help of Welch algorithm. The computed energy spectra of Earth's magnetosheath show a moderate variability with the solar-cycles and have a broader inertial range. However the estimated energy spectra for the solar-minimum at Venus give the clear evidence of the existence of the break point in the vicinity of the ion gyroradius. After the break-point the energy spectra become steeper and show a distinctive spectral scales which is interpreted as the realization of the begging of the energy cascade. We also briefly address the influence of turbulence on the plasma transport and wave dynamics responsible for the spectral break and predict spectral features of the energy spectra for the solar-maximum at Venus based on the results obtained for the solar-minimum. The research leading to these results has received funding from the European Community's Seventh Framework Programme ([FP7/2007-2013]) under grant agreement number 313038/STORM.

Thermal Analysis of a Structural Solution for Sustainable, Modular and Prefabricated Buildings

NASA Astrophysics Data System (ADS)

Isopescu, D. N.; Maxineasa, S. G.; Neculai, O.

2017-06-01

In the construction field, the design principles for an efficient and operational use of buildings and a minimal impact on the environment are essential aspects of sustainable development. In this regard, several aspects must be taken into consideration, such as: durability, easy maintenance, flexibility in interior design, and reduced energy consumption. Decreasing energy consumption in buildings during the service life (heating / cooling / drinking water / electricity) can mean lower costs, but also a lower impact on the environment. The paper presents the thermal analysis for a GF+1F height structure, consisting of several identical, adjacent and / or overlapped metallic cubic modules. The spaces inside this cubes ensemble solve the functionality of a family home building. The good carrying capacity, the rapidity of execution, the superior degree of thermal insulation and the minimum losses of material in execution were the main advantages provided by this structural solution. Regarding the thermal comfort for the users of this constructive system, the thermal analysis showed that the internal temperatures are constant and uniform, without cold surfaces or temperature fluctuations. In addition, humidity is controlled and there is no risk of condensation.

Conformations of n-butyl imidazole: matrix isolation infrared and DFT studies.

PubMed

Ramanathan, N; Sundararajan, K; Sankaran, K

2015-03-15

Conformations of n-butyl imidazole (B-IMID) were studied using matrix isolation infrared spectroscopy by trapping in argon, xenon and nitrogen matrixes using an effusive nozzle source. The experimental studies were supported by DFT computations performed at the B3LYP/6-311++G(d,p) level. Computations identified nine unique minima for B-IMID, corresponding to conformers with tg(±)tt, tg(±)g(∓)t, tg(±)g(±)t, tg(±)tg(±), tg(±)tg(∓), tg(±)g(∓)g(∓), tg(±)g(±)g(±), tg(±)g(∓)g(±) and tg(±)g(±)g(∓) structures, given in order of increasing energy. Computations of the transition state structures connecting the higher energy conformers to the global minimum, tg(±)tt structure were carried out. The barriers for the conformer inter-conversion were found to be ∼2 kcal/mol. Natural Bond Orbital (NBO) analysis was performed to understand the reasons for conformational preferences in B-IMID. Copyright © 2014 Elsevier B.V. All rights reserved.

On Prolonging Network Lifetime through Load-Similar Node Deployment in Wireless Sensor Networks

PubMed Central

Li, Qiao-Qin; Gong, Haigang; Liu, Ming; Yang, Mei; Zheng, Jun

2011-01-01

This paper is focused on the study of the energy hole problem in the Progressive Multi-hop Rotational Clustered (PMRC)-structure, a highly scalable wireless sensor network (WSN) architecture. Based on an analysis on the traffic load distribution in PMRC-based WSNs, we propose a novel load-similar node distribution strategy combined with the Minimum Overlapping Layers (MOL) scheme to address the energy hole problem in PMRC-based WSNs. In this strategy, sensor nodes are deployed in the network area according to the load distribution. That is, more nodes shall be deployed in the range where the average load is higher, and then the loads among different areas in the sensor network tend to be balanced. Simulation results demonstrate that the load-similar node distribution strategy prolongs network lifetime and reduces the average packet latency in comparison with existing nonuniform node distribution and uniform node distribution strategies. Note that, besides the PMRC structure, the analysis model and the proposed load-similar node distribution strategy are also applicable to other multi-hop WSN structures. PMID:22163809

Multiregion apodized photon sieve with enhanced efficiency and enlarged pinhole sizes.

PubMed

Liu, Tao; Zhang, Xin; Wang, Lingjie; Wu, Yanxiong; Zhang, Jizhen; Qu, Hemeng

2015-08-20

A novel multiregion structure apodized photon sieve is proposed. The number of regions, the apodization window values, and pinhole sizes of each pinhole ring are all optimized to enhance the energy efficiency and enlarge the pinhole sizes. The design theory and principle are thoroughly proposed and discussed. Two numerically designed apodized photon sieves with the same diameter are given as examples. Comparisons have shown that the multiregion apodized photon sieve has a 25.5% higher energy efficiency and the minimum pinhole size is enlarged by 27.5%. Meanwhile, the two apodized photon sieves have the same form of normalized intensity distribution at the focal plane. This method could improve the flexibility of the design and the fabrication the apodized photon sieve.

Materials for Better Li-based Storage Systems for a "Green Energy Society"

ScienceCinema

Jean-Marie Tarascon

2017-12-09

Li-ion batteries are strongly considered for powering the upcoming generations of HEVs and PHEVs, but there are still the issues of safety and costs in terms of materials resources and abundances, synthesis, and recycling processes. Notions of materials having minimum footprint in nature, made via eco-efficient processes, must be integrated in our new research towards the next generation of sustainable and "greener" Li-ion batteries. In this July 13, 2009 talk sponsored by Berkeley Lab's Environental Energy Technologies Division, Jean-Marie Tarascon, a professor at the University of Picardie (Amiens), discuss Eco-efficient synthesis via hydrothermal/solvothermal processes using latent bases as well as structure directing templates or other bio-related approaches of LiFePO4 nanopowders.

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

Liu Kun; Zhao Hongmei; Wang Caixia

Bromoiodomethane photodissociation in the low-lying excited states has been characterized using unrestricted Hartree-Fock, configuration-interaction-singles, and complete active space self-consistent field calculations with the SDB-aug-cc-pVTZ, aug-cc-pVTZ, and 3-21g** basis sets. According to the results of the vertical excited energies and oscillator strengths of these low-lying excited states, bond selectivity is predicted. Subsequently, the minimum energy paths of the first excited singlet state and the third excited state for the dissociation reactions were calculated using the complete active space self-consistent field method with 3-21g** basis set. Good agreement is found between the calculations and experimental data. The relationships of excitations, the electronicmore » structures at Franck-Condon points, and bond selectivity are discussed.« less

Neutron detection with a NaI spectrometer using high-energy photons

NASA Astrophysics Data System (ADS)

Holm, Philip; Peräjärvi, Kari; Sihvonen, Ari-Pekka; Siiskonen, Teemu; Toivonen, Harri

2013-01-01

Neutrons can be indirectly detected by high-energy photons. The performance of a 4″×4″×16″ NaI portal monitor was compared to a 3He-based portal monitor with a comparable cross-section of the active volume. Measurements were performed with bare and shielded 252Cf and AmBe sources. With an optimum converter and moderator structure for the NaI detector, the detection efficiencies and minimum detectable activities of the portal monitors were similar. The NaI portal monitor preserved its detection efficiency much better with shielded sources, making the method very interesting for security applications. For heavily shielded sources, the NaI detector was 2-3 times more sensitive than the 3He-based detector.

The tert-butyl cation on zeolite Y: A theoretical and experimental study

NASA Astrophysics Data System (ADS)

Rosenbach, Nilton, Jr.; dos Santos, Alex P. A.; Franco, Marcelo; Mota, Claudio J. A.

2010-01-01

The structure and energy of the tert-butyl cation on zeolite Y were calculated at ONIOM(MP2(FULL)/6-31G( d, p):MNDO) level. The results indicated that the tert-butyl cation is a minimum and lies between 40 and 51 kJ mol -1 above in energy to the tert-butoxide, depending on the level of calculation. Both species are stabilized through hydrogen bonding interactions with the framework oxygen atoms. Experimental data of nucleophilic substitution of tert-butylchloride and bromide over NaY impregnated with NaCl or NaBr give additional support for the formation of the tert-butyl cation as a discrete intermediate on zeolite Y, in agreement with the calculations.

Cyclo-biphenalenyl Biradicaloid Molecular Materials: Conformation, Tautomerization, Magnetism, and Thermochromism

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

Huang, Jingsong; Meunier, Vincent; Tian, Yong-Hui

2010-01-01

Phenalenyl and its derivatives have recently attracted a great deal of interest as a result of a two-electron multicenter (2e/mc) - bonding between two -stacked phenalenyl units. The 2e/mc bonded -dimers are close in energy to the -dimers of phenalenyl and therefore fickle properties may emerge from bond fluctuation, yielding smart -functional materials. Here, we examine the valence tautomerization of two cyclo-biphenalenyl biradicaloid molecular materials with chair and boat conformations by spin-restricted (R) and unrestricted (U) DFT using the M06 and B3LYP functionals. We found that the chair conformation involves a 2e/4c - bonded structure, whereas the boat conformation involvesmore » a 2e/12c - bonded structure on their potential energy surfaces. The global minimum for the chair conformation is the -bonded structure, whereas it is the - bonded structure for the boat conformation. The chair conformation exhibits a stepwise [3,3]-sigmatropic rearrangement, and calculations predict a negligible paramagnetic susceptibility near room temperature. In comparison, the paramagnetism of the boat conformation should be observable by SQUID and ESR. According to the energy differences of the respective - and -dimers of the two conformations and the UV-vis calculations, the color of the chair conformation is expected to become darker, whereas that of the boat conformation should become lighter with increasing temperature.« less

Competing Intramolecular vs. Intermolecular Hydrogen Bonds in Solution

PubMed Central

Nagy, Peter I.

2014-01-01

A hydrogen bond for a local-minimum-energy structure can be identified according to the definition of the International Union of Pure and Applied Chemistry (IUPAC recommendation 2011) or by finding a special bond critical point on the density map of the structure in the framework of the atoms-in-molecules theory. Nonetheless, a given structural conformation may be simply favored by electrostatic interactions. The present review surveys the in-solution competition of the conformations with intramolecular vs. intermolecular hydrogen bonds for different types of small organic molecules. In their most stable gas-phase structure, an intramolecular hydrogen bond is possible. In a protic solution, the intramolecular hydrogen bond may disrupt in favor of two solute-solvent intermolecular hydrogen bonds. The balance of the increased internal energy and the stabilizing effect of the solute-solvent interactions regulates the new conformer composition in the liquid phase. The review additionally considers the solvent effects on the stability of simple dimeric systems as revealed from molecular dynamics simulations or on the basis of the calculated potential of mean force curves. Finally, studies of the solvent effects on the type of the intermolecular hydrogen bond (neutral or ionic) in acid-base complexes have been surveyed. PMID:25353178

Evaluation of Structural Robustness against Column Loss: Methodology and Application to RC Frame Buildings.

PubMed

Bao, Yihai; Main, Joseph A; Noh, Sam-Young

2017-08-01

A computational methodology is presented for evaluating structural robustness against column loss. The methodology is illustrated through application to reinforced concrete (RC) frame buildings, using a reduced-order modeling approach for three-dimensional RC framing systems that includes the floor slabs. Comparisons with high-fidelity finite-element model results are presented to verify the approach. Pushdown analyses of prototype buildings under column loss scenarios are performed using the reduced-order modeling approach, and an energy-based procedure is employed to account for the dynamic effects associated with sudden column loss. Results obtained using the energy-based approach are found to be in good agreement with results from direct dynamic analysis of sudden column loss. A metric for structural robustness is proposed, calculated by normalizing the ultimate capacities of the structural system under sudden column loss by the applicable service-level gravity loading and by evaluating the minimum value of this normalized ultimate capacity over all column removal scenarios. The procedure is applied to two prototype 10-story RC buildings, one employing intermediate moment frames (IMFs) and the other employing special moment frames (SMFs). The SMF building, with its more stringent seismic design and detailing, is found to have greater robustness.

Minimum energy information fusion in sensor networks

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

Chapline, G

1999-05-11

In this paper we consider how to organize the sharing of information in a distributed network of sensors and data processors so as to provide explanations for sensor readings with minimal expenditure of energy. We point out that the Minimum Description Length principle provides an approach to information fusion that is more naturally suited to energy minimization than traditional Bayesian approaches. In addition we show that for networks consisting of a large number of identical sensors Kohonen self-organization provides an exact solution to the problem of combing the sensor outputs into minimal description length explanations.

Fully invariant wavelet enhanced minimum average correlation energy filter for object recognition in cluttered and occluded environments

NASA Astrophysics Data System (ADS)

Tehsin, Sara; Rehman, Saad; Riaz, Farhan; Saeed, Omer; Hassan, Ali; Khan, Muazzam; Alam, Muhammad S.

2017-05-01

A fully invariant system helps in resolving difficulties in object detection when camera or object orientation and position are unknown. In this paper, the proposed correlation filter based mechanism provides the capability to suppress noise, clutter and occlusion. Minimum Average Correlation Energy (MACE) filter yields sharp correlation peaks while considering the controlled correlation peak value. Difference of Gaussian (DOG) Wavelet has been added at the preprocessing stage in proposed filter design that facilitates target detection in orientation variant cluttered environment. Logarithmic transformation is combined with a DOG composite minimum average correlation energy filter (WMACE), capable of producing sharp correlation peaks despite any kind of geometric distortion of target object. The proposed filter has shown improved performance over some of the other variant correlation filters which are discussed in the result section.

A cavitation transition in the energy landscape of simple cohesive liquids and glasses

NASA Astrophysics Data System (ADS)

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

2016-12-01

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

Effect of local minima on adiabatic quantum optimization.

PubMed

Amin, M H S

2008-04-04

We present a perturbative method to estimate the spectral gap for adiabatic quantum optimization, based on the structure of the energy levels in the problem Hamiltonian. We show that, for problems that have an exponentially large number of local minima close to the global minimum, the gap becomes exponentially small making the computation time exponentially long. The quantum advantage of adiabatic quantum computation may then be accessed only via the local adiabatic evolution, which requires phase coherence throughout the evolution and knowledge of the spectrum. Such problems, therefore, are not suitable for adiabatic quantum computation.

Relaxation and collective excitations of cluster nano-plasmas

NASA Astrophysics Data System (ADS)

Reinholz, Heidi; Röpke, Gerd; Broda, Ingrid; Morozov, Igor; Bystryi, Roman; Lavrinenko, Yaroslav

2018-01-01

Nano-plasmas produced, for example, in clusters after short-pulse laser irradiation, can show collective excitations, as derived from the time evolution of fluctuations in thermodynamic equilibrium. Molecular dynamical simulations are performed for various cluster sizes. New data are obtained for the minimum value of the stationary cluster charge. The bi-local autocorrelation function gives the spatial structure of the eigenmodes, for which energy eigenvalues are obtained. By varying the cluster size, starting from a few-particle cluster, the emergence of macroscopic properties such as collective excitations is shown.

Magnetic energy dissipation in force-free jets

NASA Technical Reports Server (NTRS)

Choudhuri, Arnab Rai; Konigl, Arieh

1986-01-01

It is shown that a magnetic pressure-dominated, supersonic jet which expands or contracts in response to variations in the confining external pressure can dissipate magnetic energy through field-line reconnection as it relaxes to a minimum-energy configuration. In order for a continuous dissipation to occur, the effective reconnection time must be a fraction of the expansion time. The dissipation rate for the axisymmetric minimum-energy field configuration is analytically derived. The results indicate that the field relaxation process could be a viable mechanism for powering the synchrotron emission in extragalactic jets if the reconnection time is substantially shorter than the nominal resistive tearing time in the jet.

New Ways of Treating Data for Diatomic Molecule 'shelf' and Double-Minimum States

NASA Astrophysics Data System (ADS)

Le Roy, Robert J.; Tao, Jason; Khanna, Shirin; Pashov, Asen; Tellinghuisen, Joel

2017-06-01

Electronic states whose potential energy functions have 'shelf' or double-minimum shapes have always presented special challenges because, as functions of vibrational quantum number, the vibrational energies/spacings and inertial rotational constants either have an abrupt change of character with discontinuous slope, or past a given point, become completely chaotic. The present work shows that a `traditional' methodology developed for deep `regular' single-well potentials can also provide accurate `parameter-fit' descriptions of the v-dependence of the vibrational energies and rotational constants of shelf-state potentials that allow a conventional RKR calculation of their Potential energy functions. It is also shown that a merging of Pashov's uniquely flexible 'spline point-wise' potential function representation with Le Roy's `Morse/Long-Range' (MLR) analytic functional form which automatically incorporates the correct theoretically known long-range form, yields an analytic function that incorporates most of the advantages of both approaches. An illustrative application of this method to data to a double-minimum state of Na_2 will be described.

Biologically important conformational features of DNA as interpreted by quantum mechanics and molecular mechanics computations of its simple fragments.

PubMed

Poltev, V; Anisimov, V M; Dominguez, V; Gonzalez, E; Deriabina, A; Garcia, D; Rivas, F; Polteva, N A

2018-02-01

Deciphering the mechanism of functioning of DNA as the carrier of genetic information requires identifying inherent factors determining its structure and function. Following this path, our previous DFT studies attributed the origin of unique conformational characteristics of right-handed Watson-Crick duplexes (WCDs) to the conformational profile of deoxydinucleoside monophosphates (dDMPs) serving as the minimal repeating units of DNA strand. According to those findings, the directionality of the sugar-phosphate chain and the characteristic ranges of dihedral angles of energy minima combined with the geometric differences between purines and pyrimidines determine the dependence on base sequence of the three-dimensional (3D) structure of WCDs. This work extends our computational study to complementary deoxydinucleotide-monophosphates (cdDMPs) of non-standard conformation, including those of Z-family, Hoogsteen duplexes, parallel-stranded structures, and duplexes with mispaired bases. For most of these systems, except Z-conformation, computations closely reproduce experimental data within the tolerance of characteristic limits of dihedral parameters for each conformation family. Computation of cdDMPs with Z-conformation reveals that their experimental structures do not correspond to the internal energy minimum. This finding establishes the leading role of external factors in formation of the Z-conformation. Energy minima of cdDMPs of non-Watson-Crick duplexes demonstrate different sequence-dependence features than those known for WCDs. The obtained results provide evidence that the biologically important regularities of 3D structure distinguish WCDs from duplexes having non-Watson-Crick nucleotide pairing.

Resolving the 180-degree ambiguity in vector magnetic field measurements: The 'minimum' energy solution

NASA Technical Reports Server (NTRS)

Metcalf, Thomas R.

1994-01-01

I present a robust algorithm that resolves the 180-deg ambiguity in measurements of the solar vector magnetic field. The technique simultaneously minimizes both the divergence of the magnetic field and the electric current density using a simulated annealing algorithm. This results in the field orientation with approximately minimum free energy. The technique is well-founded physically and is simple to implement.

Numerical simulation and experimental validation of the large deformation bending and folding behavior of magneto-active elastomer composites

NASA Astrophysics Data System (ADS)

Sheridan, Robert; Roche, Juan; Lofland, Samuel E.; vonLockette, Paris R.

2014-09-01

This work seeks to provide a framework for the numerical simulation of magneto-active elastomer (MAE) composite structures for use in origami engineering applications. The emerging field of origami engineering employs folding techniques, an array of crease patterns traditionally on a single flat sheet of paper, to produce structures and devices that perform useful engineering operations. Effective means of numerical simulation offer an efficient way to optimize the crease patterns while coupling to the performance and behavior of the active material. The MAE materials used herein are comprised of nominally 30% v/v, 325 mesh barium hexafarrite particles embedded in Dow HS II silicone elastomer compound. These particulate composites are cured in a magnetic field to produce magneto-elastic solids with anisotropic magnetization, e.g. they have a preferred magnetic axis parallel to the curing axis. The deformed shape and/or blocked force characteristics of these MAEs are examined in three geometries: a monolithic cantilever as well as two- and four-segment composite accordion structures. In the accordion structures, patches of MAE material are bonded to a Gelest OE41 unfilled silicone elastomer substrate. Two methods of simulation, one using the Maxwell stress tensor applied as a traction boundary condition and another employing a minimum energy kinematic (MEK) model, are investigated. Both methods capture actuation due to magnetic torque mechanisms that dominate MAE behavior. Comparison with experimental data show good agreement with only a single adjustable parameter, either an effective constant magnetization of the MAE material in the finite element models (at small and moderate deformations) or an effective modulus in the minimum energy model. The four-segment finite element model was prone to numerical locking at large deformation. The effective magnetization and modulus values required are a fraction of the actual experimentally measured values which suggests a reduction in the amount of magnetic torque transferred from the particles to the matrix.

Stellar fibril magnetic systems. I - Reduced energy state

NASA Technical Reports Server (NTRS)

Parker, E. N.

1984-01-01

The remarkable fibril structure of the magnetic fields at the surface of the sun (with fibrils compressed to 1,000-2,000 gauss) lies outside existing statistical theories of magnetohydrodynamic turbulence. The total energy of the fibril field is enhanced by a factor of more than 100 above the energy for the mean field in a continuum state. The magnetic energy density within a fibril is of the order of 100 times the local kinetic energy density, so that no simple application of equipartition principles is possible. It is pointed out that the total energy of the atmosphere (thermal + gravitational + magnetic) is reduced by the fibril state of the field by avoiding the magnetic inhibition of the convective overturning, suggesting that the formation of the observed intense fibril state may be in response to the associated energy reduction. Calculation of the minimum total energy of a polytropic atmosphere permeated by magnetic fibrils yields theoretical fibril fields of the order of 1-5 kilogauss when characteristics appropriate to the solar convective zone are introduced, in rough agreement with the actual fields of 1-2 kilogauss. The polytrope model, although crude, establishes that a large reduction in total energy is made possible by the fibril state.

Elemental GCR Observations during the 2009-2010 Solar Minimum Period

NASA Technical Reports Server (NTRS)

Lave, K. A.; Israel, M. H.; Binns, W. R.; Christian, E. R.; Cummings, A. C.; Davis, A. J.; deNolfo, G. A.; Leske, R. A.; Mewaldt, R. A.; Stone, E. C.;

Tungsten Ditelluride: a layered semimetal

PubMed Central

Lee, Chia-Hui; Silva, Eduardo Cruz; Calderin, Lazaro; Nguyen, Minh An T.; Hollander, Matthew J.; Bersch, Brian; Mallouk, Thomas E.; Robinson, Joshua A.

2015-01-01

Tungsten ditelluride (WTe2) is a transition metal dichalcogenide (TMD) with physical and electronic properties that make it attractive for a variety of electronic applications. Although WTe2 has been studied for decades, its structure and electronic properties have only recently been correctly described. We experimentally and theoretically investigate the structure, dynamics and electronic properties of WTe2, and verify that WTe2 has its minimum energy configuration in a distorted 1T structure (Td structure), which results in metallic-like transport. Our findings unambiguously confirm the metallic nature of WTe2, introduce new information about the Raman modes of Td-WTe2, and demonstrate that Td-WTe2 is readily oxidized via environmental exposure. Finally, these findings confirm that, in its thermodynamically favored Td form, the utilization of WTe2 in electronic device architectures such as field effect transistors may need to be reevaluated. PMID:26066766

Novel Approach to Analyzing MFE of Noncoding RNA Sequences

PubMed Central

George, Tina P.; Thomas, Tessamma

2016-01-01

Genomic studies have become noncoding RNA (ncRNA) centric after the study of different genomes provided enormous information on ncRNA over the past decades. The function of ncRNA is decided by its secondary structure, and across organisms, the secondary structure is more conserved than the sequence itself. In this study, the optimal secondary structure or the minimum free energy (MFE) structure of ncRNA was found based on the thermodynamic nearest neighbor model. MFE of over 2600 ncRNA sequences was analyzed in view of its signal properties. Mathematical models linking MFE to the signal properties were found for each of the four classes of ncRNA analyzed. MFE values computed with the proposed models were in concordance with those obtained with the standard web servers. A total of 95% of the sequences analyzed had deviation of MFE values within ±15% relative to those obtained from standard web servers. PMID:27695341

Novel Approach to Analyzing MFE of Noncoding RNA Sequences.

PubMed

George, Tina P; Thomas, Tessamma

2016-01-01

Genomic studies have become noncoding RNA (ncRNA) centric after the study of different genomes provided enormous information on ncRNA over the past decades. The function of ncRNA is decided by its secondary structure, and across organisms, the secondary structure is more conserved than the sequence itself. In this study, the optimal secondary structure or the minimum free energy (MFE) structure of ncRNA was found based on the thermodynamic nearest neighbor model. MFE of over 2600 ncRNA sequences was analyzed in view of its signal properties. Mathematical models linking MFE to the signal properties were found for each of the four classes of ncRNA analyzed. MFE values computed with the proposed models were in concordance with those obtained with the standard web servers. A total of 95% of the sequences analyzed had deviation of MFE values within ±15% relative to those obtained from standard web servers.

10 CFR 905.16 - What are the requirements for the minimum investment report alternative?

Code of Federal Regulations, 2013 CFR

2013-01-01

... report alternative? 905.16 Section 905.16 Energy DEPARTMENT OF ENERGY ENERGY PLANNING AND MANAGEMENT...; renewable energy; efficiency and alternative energy-related research and development; low-income energy... collected for and spent on DSM, renewable energy, efficiency or alternative energy-related research and...

10 CFR 905.16 - What are the requirements for the minimum investment report alternative?

Code of Federal Regulations, 2014 CFR

2014-01-01

... report alternative? 905.16 Section 905.16 Energy DEPARTMENT OF ENERGY ENERGY PLANNING AND MANAGEMENT...; renewable energy; efficiency and alternative energy-related research and development; low-income energy... collected for and spent on DSM, renewable energy, efficiency or alternative energy-related research and...

10 CFR 905.16 - What are the requirements for the minimum investment report alternative?

Code of Federal Regulations, 2011 CFR

2011-01-01

... report alternative? 905.16 Section 905.16 Energy DEPARTMENT OF ENERGY ENERGY PLANNING AND MANAGEMENT...; renewable energy; efficiency and alternative energy-related research and development; low-income energy... collected for and spent on DSM, renewable energy, efficiency or alternative energy-related research and...

10 CFR 905.16 - What are the requirements for the minimum investment report alternative?

Code of Federal Regulations, 2012 CFR

2012-01-01

... report alternative? 905.16 Section 905.16 Energy DEPARTMENT OF ENERGY ENERGY PLANNING AND MANAGEMENT...; renewable energy; efficiency and alternative energy-related research and development; low-income energy... collected for and spent on DSM, renewable energy, efficiency or alternative energy-related research and...

Theoretical study of the structural and electronic properties of novel stanene-based buckled nanotubes and their adsorption behaviors

NASA Astrophysics Data System (ADS)

Abbasi, Amirali; Sardroodi, Jaber Jahanbin; Ebrahimzadeh, Alireza Rastkar; Yaghoobi, Mina

2018-03-01

Density functional theory calculations were performed to investigate the geometrical, electronic and adsorption properties of stanene based nanotubes in order to fully exploit the gas sensing capability of these nanotubes. The strain energy, structural parameters and electronic properties of stanene-based nanotubes with armchair and zigzag chirality with various diameters were examined in detail. The results show that, these nanotubes have a buckled structure, in which the tin atoms were arranged in chair-like honeycomb configuration. Calculated strain energy for considered nanotubes are relatively small compared to some other nanotubes pointed to flexibility of stanene mono layer. It was found that the strain energies for (4, 0), (5, 0) and (6, 0) nanotubes have negative values, indicating their stability with respect to stanene nanosheet. The band structure calculations reveal that the armchair nanotubes are semiconductors with two maximums with nearly same energies in valence band. However, the zigzag ones show both conductor and semiconductor behaviors by direct band gap in ᴦ point. Also the spatial distribution of molecular orbitals in valence band maximums and conduction band minimums were presented and discussed. Moreover, the adsorption behaviors of (6, 6) and (8, 8) nanotubes as chemical O3 detection device were investigated in detail. We found that O3 molecule dissociates into O2 over the considered nanotubes, being an effective strategy to help in the reduction of the concentration of these harmful pollutants in the environment. The results also suggest that O3 dissociation over the (6, 6) nanotube is more favorable in energy than that on the (8, 8) nanotube. The results present a great potential of stanene based nanotube for application as a highly sensitive ozone gas sensor.

Global optimization algorithms to compute thermodynamic equilibria in large complex systems with performance considerations

DOE PAGES

Piro, M. H. A.; Simunovic, S.

2016-03-17

Several global optimization methods are reviewed that attempt to ensure that the integral Gibbs energy of a closed isothermal isobaric system is a global minimum to satisfy the necessary and sufficient conditions for thermodynamic equilibrium. In particular, the integral Gibbs energy function of a multicomponent system containing non-ideal phases may be highly non-linear and non-convex, which makes finding a global minimum a challenge. Consequently, a poor numerical approach may lead one to the false belief of equilibrium. Furthermore, confirming that one reaches a global minimum and that this is achieved with satisfactory computational performance becomes increasingly more challenging in systemsmore » containing many chemical elements and a correspondingly large number of species and phases. Several numerical methods that have been used for this specific purpose are reviewed with a benchmark study of three of the more promising methods using five case studies of varying complexity. A modification of the conventional Branch and Bound method is presented that is well suited to a wide array of thermodynamic applications, including complex phases with many constituents and sublattices, and ionic phases that must adhere to charge neutrality constraints. Also, a novel method is presented that efficiently solves the system of linear equations that exploits the unique structure of the Hessian matrix, which reduces the calculation from a O(N 3) operation to a O(N) operation. As a result, this combined approach demonstrates efficiency, reliability and capabilities that are favorable for integration of thermodynamic computations into multi-physics codes with inherent performance considerations.« less

Global optimization algorithms to compute thermodynamic equilibria in large complex systems with performance considerations

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

Piro, M. H. A.; Simunovic, S.

Several global optimization methods are reviewed that attempt to ensure that the integral Gibbs energy of a closed isothermal isobaric system is a global minimum to satisfy the necessary and sufficient conditions for thermodynamic equilibrium. In particular, the integral Gibbs energy function of a multicomponent system containing non-ideal phases may be highly non-linear and non-convex, which makes finding a global minimum a challenge. Consequently, a poor numerical approach may lead one to the false belief of equilibrium. Furthermore, confirming that one reaches a global minimum and that this is achieved with satisfactory computational performance becomes increasingly more challenging in systemsmore » containing many chemical elements and a correspondingly large number of species and phases. Several numerical methods that have been used for this specific purpose are reviewed with a benchmark study of three of the more promising methods using five case studies of varying complexity. A modification of the conventional Branch and Bound method is presented that is well suited to a wide array of thermodynamic applications, including complex phases with many constituents and sublattices, and ionic phases that must adhere to charge neutrality constraints. Also, a novel method is presented that efficiently solves the system of linear equations that exploits the unique structure of the Hessian matrix, which reduces the calculation from a O(N 3) operation to a O(N) operation. As a result, this combined approach demonstrates efficiency, reliability and capabilities that are favorable for integration of thermodynamic computations into multi-physics codes with inherent performance considerations.« less

A systematic study of posterior cervical lymph node irradiation with electrons: Conventional versus customized planning.

PubMed

Jankowska, Petra J; Kong, Christine; Burke, Kevin; Harrington, Kevin J; Nutting, Christopher

2007-10-01

High dose irradiation of the posterior cervical lymph nodes usually employs applied electron fields to treat the target volume and maintain the spinal cord dose within tolerance. In the light of recent advances in elective lymph node localisation we investigated optimization of field shape and electron energy to treat this target volume. In this study, three sequential hypotheses were tested. Firstly, that customization of the electron fields based on the nodal PTV outlined gives better PTV coverage than conventional field delineation. Using the consensus guidelines, customization of the electron field shape was compared to conventional fields based on bony landmarks. Secondly, that selection of electron energy using DVHs for spinal cord and PTV improves the minimum dose to PTV. Electron dose-volume histograms (DVHs) for the PTV, spinal cord and para-vertebral muscles, were generated using the Monte Carlo electron algorithm. These DVHs were used to compare standard vs optimized electron energy calculations. Finally, that combination of field customization and electron energy optimization improves both the minimum and mean doses to PTV compared with current standard practice. Customized electron beam shaping based on the consensus guidelines led to fewer geographical misses than standard field shaping. Customized electron energy calculation led to higher minimum doses to the PTV. Overall, the customization of field shape and energy resulted in an improved mean dose to the PTV (92% vs 83% p=0.02) and a 27% improvement in the minimum dose delivered to the PTV (45% vs 18% p=0.0009). Optimization of electron field shape and beam energy based on current consensus guidelines led to significant improvement in PTV coverage and may reduce recurrence rates.

Antibacterial activity, thermal stability and ab initio study of copolymer containing sulfobetaine and carboxybetaine groups

NASA Astrophysics Data System (ADS)

Tarannum, Nazia; Singh, Meenakshi; Yadav, Anil K.

2017-10-01

Here, we have explored the antibacterial activity, thermal stability and theoretical study of two copolymers that contain sulfobetaine and carboetaine moiety. Copolymers were synthesized based on Schiff base chemistry with generation of zwitterionic centres by nucleophilic addition of sultone/lactone. To predict and confirm the molecular structure of zwitterionic polyelectrolyte molecule, the theoretical study of structural features and other thermodynamic characteristics of copolymer constituents was obtained by ab initio calculations. Various parameters such as geometry optimization, energy calculations, frequency calculations and intrinsic reaction coefficient (IRC) are simulated using Hartree Fock (HF) method. The geometry optimizations are analyzed at HF/3-21 G default level of theory. The vibrational frequency is calculated via density functional theory (DFT)/B3LYP 6-31G*(d) level whose values are in accord with the experimental observed frequency. Both copolymers have been successfully assessed for antibacterial activity against Staphylococcus aureus and Pseudomonas aeuroginosa bacterial strains by disc diffusion method. The antibacterial study helped in evaluating zone of inhibition, minimum inhibitory concentration and minimum bactericidal concentration. Sulfobetaine copolymer is found to be more effective in curtailing the infection caused by bacteria as compared to carbobetaine.

A multi-period optimization model for energy planning with CO(2) emission consideration.

PubMed

Mirzaesmaeeli, H; Elkamel, A; Douglas, P L; Croiset, E; Gupta, M

2010-05-01

A novel deterministic multi-period mixed-integer linear programming (MILP) model for the power generation planning of electric systems is described and evaluated in this paper. The model is developed with the objective of determining the optimal mix of energy supply sources and pollutant mitigation options that meet a specified electricity demand and CO(2) emission targets at minimum cost. Several time-dependent parameters are included in the model formulation; they include forecasted energy demand, fuel price variability, construction lead time, conservation initiatives, and increase in fixed operational and maintenance costs over time. The developed model is applied to two case studies. The objective of the case studies is to examine the economical, structural, and environmental effects that would result if the electricity sector was required to reduce its CO(2) emissions to a specified limit. Copyright 2009 Elsevier Ltd. All rights reserved.

Doping-stabilized two-dimensional black phosphorus.

PubMed

Xuan, Xiaoyu; Zhang, Zhuhua; Guo, Wanlin

2018-05-03

Two-dimensional (2D) black phosphorus (BP) has attracted broad interests but remains to be synthesized. One of the issues lies in its large number of 2D allotropes with highly degenerate energies, especially 2D blue phosphorus. Here, we show that both nitrogen and hole-carrier doping can lift the energy degeneracy and locate 2D BP in a deep global energy minimum, while arsenic doping favours the formation of 2D blue phosphorus, attributed to a delicate interplay between s-p overlapping and repulsion of lone pairs. Chemically inert substrates, e.g. graphene and hexagonal boron nitride, can be synergic with carrier doping to stabilize the BP further over other 2D allotropes, while frequently used metal substrates severely reduce the stability of 2D BP. These results not only offer new insight into the structural stability of 2D phosphorus but also suggest a promising pathway towards the chemical synthesis of 2D BP.

Design of control laws for flutter suppression based on the aerodynamic energy concept and comparisons with other design methods

NASA Technical Reports Server (NTRS)

Nissim, Eli

1990-01-01

The aerodynamic energy method is used to synthesize control laws for NASA's drone for aerodynamic and structural testing-aerodynamic research wing 1 (DAST-ARW1) mathematical model. The performance of these control laws in terms of closed-loop flutter dynamic pressure, control surface activity, and robustness is compared with other control laws that relate to the same model. A control law synthesis technique that makes use of the return difference singular values is developed. It is based on the aerodynamic energy approach and is shown to yield results that are superior to those results given in the literature and are based on optimal control theory. Nyquist plots are presented, together with a short discussion regarding the relative merits of the minimum singular value as a measure of robustness as compared with the more traditional measure involving phase and gain margins.

Design of control laws for flutter suppression based on the aerodynamic energy concept and comparisons with other design methods

NASA Technical Reports Server (NTRS)

Nissim, E.

1989-01-01

The aerodynamic energy method is used in this paper to synthesize control laws for NASA's Drone for Aerodynamic and Structural Testing-Aerodynamic Research Wing 1 (DAST-ARW1) mathematical model. The performance of these control laws in terms of closed-loop flutter dynamic pressure, control surface activity, and robustness is compared against other control laws that appear in the literature and relate to the same model. A control law synthesis technique that makes use of the return difference singular values is developed in this paper. it is based on the aerodynamic energy approach and is shown to yield results superior to those given in the literature and based on optimal control theory. Nyquist plots are presented together with a short discussion regarding the relative merits of the minimum singular value as a measure of robustness, compared with the more traditional measure of robustness involving phase and gain margins.

Structure determination in 55-atom Li-Na and Na-K nanoalloys.

PubMed

Aguado, Andrés; López, José M

2010-09-07

The structure of 55-atom Li-Na and Na-K nanoalloys is determined through combined empirical potential (EP) and density functional theory (DFT) calculations. The potential energy surface generated by the EP model is extensively sampled by using the basin hopping technique, and a wide diversity of structural motifs is reoptimized at the DFT level. A composition comparison technique is applied at the DFT level in order to make a final refinement of the global minimum structures. For dilute concentrations of one of the alkali atoms, the structure of the pure metal cluster, namely, a perfect Mackay icosahedron, remains stable, with the minority component atoms entering the host cluster as substitutional impurities. At intermediate concentrations, the nanoalloys adopt instead a core-shell polyicosahedral (p-Ih) packing, where the element with smaller atomic size and larger cohesive energy segregates to the cluster core. The p-Ih structures show a marked prolate deformation, in agreement with the predictions of jelliumlike models. The electronic preference for a prolate cluster shape, which is frustrated in the 55-atom pure clusters due to the icosahedral geometrical shell closing, is therefore realized only in the 55-atom nanoalloys. An analysis of the electronic densities of states suggests that photoelectron spectroscopy would be a sufficiently sensitive technique to assess the structures of nanoalloys with fixed size and varying compositions.

Crystal structure and theoretical studies of derivative of imidazo-1,2,4-triazine

NASA Astrophysics Data System (ADS)

Dybała, Izabela; Sztanke, Krzysztof

2016-09-01

In this study, we present the result of X-ray structure analysis of methyl [8-(3-chlorophenyl)-4-oxo-2,3,4,6,7,8-heksahydroimidazo[2,1-c][1,2,4]triazin-3-yl]acetate (1). The molecule conformation is flat, with a chlorophenyl substituent and the ester moiety lying in the plain of the heterobicyclic scaffold. Its conformation is stabilized by an intramolecular Nsbnd H…O hydrogen bond. Within the crystalline structure of 1, molecules associate with one another by weak Csbnd H…O, Csbnd H…Cl and Csbnd H…π bonds. The molecular and crystal structure of 1 was compared with the previously described structurally similar compound possessing the same bicyclic rigid core and similar chemical nature of the functional ester moiety. Very interesting differences in molecules geometry and association were observed. Non-covalent bonds within the crystals are additionally visualized by determination of Hirshfeld surfaces. Moreover, the quantum chemical calculation for 1 in the gas phase were carried out. The DFT calculation methods was used to optimize of molecule geometry and obtain molecular energy profiles with respect to selected torsion angles. The quantum chemical conformational analysis that was carried out for compound 1 in the gas phase suggests that in the solid state the molecules adopt the minimum energy conformation.

Interactions of Oxygen and Hydrogen on Pd(111) surface

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

Demchenko, D.O.; Sacha, G.M.; Salmeron, M.

2008-06-25

The coadsorption and interactions of oxygen and hydrogen on Pd(1 1 1) was studied by scanning tunneling microscopy and density functional theory calculations. In the absence of hydrogen oxygen forms a (2 x 2) ordered structure. Coadsorption of hydrogen leads to a structural transformation from (2 x 2) to a ({radical}3 x {radical}3)R30 degree structure. In addition to this transformation, hydrogen enhances the mobility of oxygen. To explain these observations, the interaction of oxygen and hydrogen on Pd(1 1 1) was studied within the density functional theory. In agreement with the experiment the calculations find a total energy minimum formore » the oxygen (2 x 2) structure. The interaction between H and O atoms was found to be repulsive and short ranged, leading to a compression of the O islands from (2 x 2) to ({radical}3 x {radical}3)R30 degree ordered structure at high H coverage. The computed energy barriers for the oxygen diffusion were found to be reduced due to the coadsorption of hydrogen, in agreement with the experimentally observed enhancement of oxygen mobility. The calculations also support the finding that at low temperatures the water formation reaction does not occur on Pd(1 1 1).« less

30 CFR 250.908 - What are the minimum structural fatigue design requirements?

Code of Federal Regulations, 2011 CFR

2011-07-01

... 30 Mineral Resources 2 2011-07-01 2011-07-01 false What are the minimum structural fatigue design... fatigue design requirements? (a) API RP 2A-WSD, Recommended Practice for Planning, Designing and... the design fatigue life of each joint and member be twice the intended service life of the structure...

Semi-metallic Be5C2 monolayer global minimum with quasi-planar pentacoordinate carbons and negative Poisson's ratio.

PubMed

Wang, Yu; Li, Feng; Li, Yafei; Chen, Zhongfang

2016-05-03

Designing new materials with novel topological properties and reduced dimensionality is always desirable for material innovation. Here we report the design of a two-dimensional material, namely Be5C2 monolayer on the basis of density functional theory computations. In Be5C2 monolayer, each carbon atom binds with five beryllium atoms in almost the same plane, forming a quasi-planar pentacoordinate carbon moiety. Be5C2 monolayer appears to have good stability as revealed by its moderate cohesive energy, positive phonon modes and high melting point. It is the lowest-energy structure with the Be5C2 stoichiometry in two-dimensional space and therefore holds some promise to be realized experimentally. Be5C2 monolayer is a gapless semiconductor with a Dirac-like point in the band structure and also has an unusual negative Poisson's ratio. If synthesized, Be5C2 monolayer may find applications in electronics and mechanics.

First-principles study of structural, electronic, linear and nonlinear optical properties of Ga{2}PSb ternary chalcopyrite

NASA Astrophysics Data System (ADS)

Ouahrani, T.; Reshak, A. H.; de La Roza, A. Otero; Mebrouki, M.; Luaña, V.; Khenata, R.; Amrani, B.

2009-12-01

We report results from first-principles density functional calculations using the full-potential linear augmented plane wave (FP-LAPW) method. The generalized gradient approximation (GGA) and the Engel-Vosko-generalized gradient approximation (EV-GGA) were used for the exchange-correlation energy of the structural, electronic, linear and nonlinear optical properties of the chalcopyrite Ga2PSb compound. The valence band maximum (VBM) is located at the Γv point, and the conduction band minimum (CBM) is located at the Γc point, resulting in a direct band gap of about 0.365 eV for GGA and 0.83 eV for EV-GGA. In comparison with the experimental one (1.2 eV) we found that EV-GGA calculation gives energy gap in reasonable agreement with the experiment. The spin orbit coupling has marginal influence on the optical properties. The ground state quantities such as lattice parameters (a, c and u), bulk modules B and its pressure derivative B^primeare evaluated.

MHD Modeling of the Solar Wind with Turbulence Transport and Heating

NASA Technical Reports Server (NTRS)

Goldstein, M. L.; Usmanov, A. V.; Matthaeus, W. H.; Breech, B.

2009-01-01

We have developed a magnetohydrodynamic model that describes the global axisymmetric steady-state structure of the solar wind near solar minimum with account for transport of small-scale turbulence associated heating. The Reynolds-averaged mass, momentum, induction, and energy equations for the large-scale solar wind flow are solved simultaneously with the turbulence transport equations in the region from 0.3 to 100 AU. The large-scale equations include subgrid-scale terms due to turbulence and the turbulence (small-scale) equations describe the effects of transport and (phenomenologically) dissipation of the MHD turbulence based on a few statistical parameters (turbulence energy, normalized cross-helicity, and correlation scale). The coupled set of equations is integrated numerically for a source dipole field on the Sun by a time-relaxation method in the corotating frame of reference. We present results on the plasma, magnetic field, and turbulence distributions throughout the heliosphere and on the role of the turbulence in the large-scale structure and temperature distribution in the solar wind.

Aspects of structural landscape of human islet amyloid polypeptide

NASA Astrophysics Data System (ADS)

He, Jianfeng; Dai, Jin; Li, Jing; Peng, Xubiao; Niemi, Antti J.

2015-01-01

The human islet amyloid polypeptide (hIAPP) co-operates with insulin to maintain glycemic balance. It also constitutes the amyloid plaques that aggregate in the pancreas of type-II diabetic patients. We have performed extensive in silico investigations to analyse the structural landscape of monomeric hIAPP, which is presumed to be intrinsically disordered. For this, we construct from first principles a highly predictive energy function that describes a monomeric hIAPP observed in a nuclear magnetic resonance experiment, as a local energy minimum. We subject our theoretical model of hIAPP to repeated heating and cooling simulations, back and forth between a high temperature regime where the conformation resembles a random walker and a low temperature limit where no thermal motions prevail. We find that the final low temperature conformations display a high level of degeneracy, in a manner which is fully in line with the presumed intrinsically disordered character of hIAPP. In particular, we identify an isolated family of α-helical conformations that might cause the transition to amyloidosis, by nucleation.

Ligand Shaping in Induced Fit Docking of MraY Inhibitors. Polynomial Discriminant and Laplacian Operator as Biological Activity Descriptors

PubMed Central

Diudea, Mircea V.; Putz, Mihai V.

2017-01-01

Docking—i.e., interaction of a small molecule (ligand) with a proteic structure (receptor)—represents the ground of drug action mechanism of the vast majority of bioactive chemicals. Ligand and receptor accommodate their geometry and energy, within this interaction, in the benefit of receptor–ligand complex. In an induced fit docking, the structure of ligand is most susceptible to changes in topology and energy, comparative to the receptor. These changes can be described by manifold hypersurfaces, in terms of polynomial discriminant and Laplacian operator. Such topological surfaces were represented for each MraY (phospho-MurNAc-pentapeptide translocase) inhibitor, studied before and after docking with MraY. Binding affinities of all ligands were calculated by this procedure. For each ligand, Laplacian and polynomial discriminant were correlated with the ligand minimum inhibitory concentration (MIC) retrieved from literature. It was observed that MIC is correlated with Laplacian and polynomial discriminant. PMID:28653980

Detecting Molecular Rotational Dynamics Complementing the Low-Frequency Terahertz Vibrations in a Zirconium-Based Metal-Organic Framework

NASA Astrophysics Data System (ADS)

Ryder, Matthew R.; Van de Voorde, Ben; Civalleri, Bartolomeo; Bennett, Thomas D.; Mukhopadhyay, Sanghamitra; Cinque, Gianfelice; Fernandez-Alonso, Felix; De Vos, Dirk; Rudić, Svemir; Tan, Jin-Chong

2017-06-01

We show clear experimental evidence of cooperative terahertz (THz) dynamics observed below 3 THz (˜100 cm-1 ), for a low-symmetry Zr-based metal-organic framework structure, termed MIL-140A [ZrO (O2C-C 6H4-CO2) ]. Utilizing a combination of high-resolution inelastic neutron scattering and synchrotron radiation far-infrared spectroscopy, we measured low-energy vibrations originating from the hindered rotations of organic linkers, whose energy barriers and detailed dynamics have been elucidated via ab initio density functional theory calculations. The complex pore architecture caused by the THz rotations has been characterized. We discovered an array of soft modes with trampolinelike motions, which could potentially be the source of anomalous mechanical phenomena such as negative thermal expansion. Our results demonstrate coordinated shear dynamics (2.47 THz), a mechanism which we have shown to destabilize the framework structure, in the exact crystallographic direction of the minimum shear modulus (Gmin ).

Energetic constraints on life in deep marine sediments

NASA Astrophysics Data System (ADS)

Amend, J.; LaRowe, D.

2013-12-01

Microorganisms are abundant in deep-sea sediments, but what percentage of cells is active, how fast do they grow, and what factors control their diversity and population size? Geochemical modelling of redox reaction energetics can help in answering these questions. Calculations of Gibbs energies reveal which reactions are thermodynamically possible, but they also highlight which geochemical variables (e.g., temperature, pressure, pH, composition) may control microbial activity and how the amount and type of biomass are affected by energy limitations. We will discuss recent results from sediment cores collected at the Peru Margin (active continental shelf with high primary productivity and significant organic matter accumulation), the South Pacific Gyre (ultra-slow sedimentation rate and low organic carbon content), and the Juan de Fuca Ridge flank (high rate of sedimentation influenced by hydrothermal circulation). However, this approach to evaluating bioenergetic potential and predicting microbial activity can be applied to any environment where the geochemistry is well characterized, even if microbiology data have not been collected. When Gibbs energies are calculated on a basis of per mole of electrons transferred (as is commonly done), aerobic oxidation of hydrogen and organic matter in South Pacific Gyre sediments is the most exergonic. Based on this, one might posit that the fastest catabolic rates and the largest biomass would be found there. However, cell counts at Juan de Fuca and the Peru Margin are several orders of magnitude higher. When recast as energy densities (in J per cm3 of sediment), we observe far more energy available in sediments at Juan de Fuca and the Peru Margin than at those in the South Pacific Gyre. We also note that the identity of the most exergonic reaction changes with depth, suggesting corresponding changes in the microbial community structure. The thermodynamic approach used here for energy supply can also be used for energy demand, including the often-considered minimum or threshold energy, also referred to as the biological energy quantum. Based on this energetic minimum theory, many reactions cannot support microbial communities because their energy yield is apparently too low. However, we show that when evaluated as energy densities, some energetically ';impossible' catabolisms become ';possible' and vice versa.

Adaptability of Protein Structures to Enable Functional Interactions and Evolutionary Implications

PubMed Central

Haliloglu, Turkan; Bahar, Ivet

2015-01-01

Several studies in recent years have drawn attention to the ability of proteins to adapt to intermolecular interactions by conformational changes along structure-encoded collective modes of motions. These so-called soft modes, primarily driven by entropic effects, facilitate, if not enable, functional interactions. They represent excursions on the conformational space along principal low-ascent directions/paths away from the original free energy minimum, and they are accessible to the protein even prior to protein-protein/ligand interactions. An emerging concept from these studies is the evolution of structures or modular domains to favor such modes of motion that will be recruited or integrated for enabling functional interactions. Structural dynamics, including the allosteric switches in conformation that are often stabilized upon formation of complexes and multimeric assemblies, emerge as key properties that are evolutionarily maintained to accomplish biological activities, consistent with the paradigm sequence → structure → dynamics → function where ‘dynamics’ bridges structure and function. PMID:26254902

Photonic microstructures for energy-generating clear glass and net-zero energy buildings

NASA Astrophysics Data System (ADS)

Vasiliev, Mikhail; Alghamedi, Ramzy; Nur-E-Alam, Mohammad; Alameh, Kamal

2016-08-01

Transparent energy-harvesting windows are emerging as practical building-integrated photovoltaics (BIPV), capable of generating electricity while simultaneously reducing heating and cooling demands. By incorporating spectrally-selective diffraction gratings as light deflecting structures of high visible transparency into lamination interlayers and using improved spectrally-selective thin-film coatings, most of the visible solar radiation can be transmitted through the glass windows with minimum attenuation. At the same time, the ultraviolet (UV) and a part of incident solar infrared (IR) radiation energy are converted and/or deflected geometrically towards the panel edge for collection by CuInSe2 solar cells. Experimental results show power conversion efficiencies in excess of 3.04% in 10 cm × 10 cm vertically-placed clear glass panels facing direct sunlight, and up to 2.08% in 50 cm × 50 cm installation-ready framed window systems. These results confirm the emergence of a new class of solar window system ready for industrial application.

Photonic microstructures for energy-generating clear glass and net-zero energy buildings.

PubMed

Vasiliev, Mikhail; Alghamedi, Ramzy; Nur-E-Alam, Mohammad; Alameh, Kamal

2016-08-23

Transparent energy-harvesting windows are emerging as practical building-integrated photovoltaics (BIPV), capable of generating electricity while simultaneously reducing heating and cooling demands. By incorporating spectrally-selective diffraction gratings as light deflecting structures of high visible transparency into lamination interlayers and using improved spectrally-selective thin-film coatings, most of the visible solar radiation can be transmitted through the glass windows with minimum attenuation. At the same time, the ultraviolet (UV) and a part of incident solar infrared (IR) radiation energy are converted and/or deflected geometrically towards the panel edge for collection by CuInSe2 solar cells. Experimental results show power conversion efficiencies in excess of 3.04% in 10 cm × 10 cm vertically-placed clear glass panels facing direct sunlight, and up to 2.08% in 50 cm × 50 cm installation-ready framed window systems. These results confirm the emergence of a new class of solar window system ready for industrial application.

Energy efficient engine component development and integration program

NASA Technical Reports Server (NTRS)

1982-01-01

The objective of the Energy Efficient Engine Component Development and Integration program is to develop, evaluate, and demonstrate the technology for achieving lower installed fuel consumption and lower operating costs in future commercial turbofan engines. Minimum goals have been set for a 12 percent reduction in thrust specific fuel consumption (TSFC), 5 percent reduction in direct operating cost (DOC), and 50 percent reduction in performance degradation for the Energy Efficient Engine (flight propulsion system) relative to the JT9D-7A reference engine. The Energy Efficienct Engine features a twin spool, direct drive, mixed flow exhaust configuration, utilizing an integrated engine nacelle structure. A short, stiff, high rotor and a single stage high pressure turbine are among the major enhancements in providing for both performance retention and major reductions in maintenance and direct operating costs. Improved clearance control in the high pressure compressor and turbines, and advanced single crystal materials in turbine blades and vanes are among the major features providing performance improvement. Highlights of work accomplished and programs modifications and deletions are presented.

Photonic microstructures for energy-generating clear glass and net-zero energy buildings

PubMed Central

Vasiliev, Mikhail; Alghamedi, Ramzy; Nur-E-Alam, Mohammad; Alameh, Kamal

2016-01-01

Transparent energy-harvesting windows are emerging as practical building-integrated photovoltaics (BIPV), capable of generating electricity while simultaneously reducing heating and cooling demands. By incorporating spectrally-selective diffraction gratings as light deflecting structures of high visible transparency into lamination interlayers and using improved spectrally-selective thin-film coatings, most of the visible solar radiation can be transmitted through the glass windows with minimum attenuation. At the same time, the ultraviolet (UV) and a part of incident solar infrared (IR) radiation energy are converted and/or deflected geometrically towards the panel edge for collection by CuInSe2 solar cells. Experimental results show power conversion efficiencies in excess of 3.04% in 10 cm × 10 cm vertically-placed clear glass panels facing direct sunlight, and up to 2.08% in 50 cm × 50 cm installation-ready framed window systems. These results confirm the emergence of a new class of solar window system ready for industrial application. PMID:27550827

Collective degrees of freedom involved in absorption and desorption of surfactant molecules in spherical non-ionic micelles

NASA Astrophysics Data System (ADS)

Ahn, Yong Nam; Mohan, Gunjan; Kopelevich, Dmitry I.

2012-10-01

Dynamics of absorption and desorption of a surfactant monomer into and out of a spherical non-ionic micelle is investigated by coarse-grained molecular dynamics (MD) simulations. It is shown that these processes involve a complex interplay between the micellar structure and the monomer configuration. A quantitative model for collective dynamics of these degrees of freedom is developed. This is accomplished by reconstructing a multi-dimensional free energy landscape of the surfactant-micelle system using constrained MD simulations in which the distance between the micellar and monomer centers of mass is held constant. Results of this analysis are verified by direct (unconstrained) MD simulations of surfactant absorption in the micelle. It is demonstrated that the system dynamics is likely to deviate from the minimum energy path on the energy landscape. These deviations create an energy barrier for the monomer absorption and increase an existing barrier for the monomer desorption. A reduced Fokker-Planck equation is proposed to model these effects.

Theoretical study of the C-H/O-H stretching vibrations in malonaldehyde

NASA Astrophysics Data System (ADS)

Pitsevich, G. A.; Malevich, A. E.; Kozlovskaya, E. N.; Doroshenko, I. Yu.; Pogorelov, V. E.; Sablinskas, V.; Balevicius, V.

2015-06-01

IR and Raman spectra of the malonaldehyde molecule and its deuterated analogues were calculated in the B3LYP/cc-pVQZ approximation. Anharmonicity effects were taken into account both in the context of a standard model of the second order perturbation theory and by constructing the potential energy surfaces (PES) with a limited number of dimensions using the Cartesian coordinates of the hydroxyl hydrogen atom and the stretching coordinates of С-Н, C-D, O-H, and O-D bonds. It was shown that in each of the two equivalent forms of the molecule, besides the global minimum, an additional local minimum at the PES is formed with the energy more than 3000 cm-1 higher than the energy in the global minimum. Calculations carried out by constructing the 2D and 3D PESs indicate a high anharmonicity level and multiple manifestations of the stretching О-Н vibrations, despite the fact that the model used does not take into account the splitting of the ground-state and excited vibrational energy levels. In particular, the vibration with the frequency 3258 cm-1 may be associated with proton transfer to the region of a local minimum of energy. Comparing the results obtained with the experimental data presented in the literature allowed us to propose a new variant of bands assignments in IR and Raman spectra of the molecule in the spectral region 2500-3500 cm-1.

Creosote bush (Larrea tridentata) resin increases water demands and reduces energy availability in desert woodrats (Neotoma lepida).

PubMed

Mangione, Antonio M; Dearing, M Denise; Karasov, William H

2004-07-01

Although many plant secondary compounds are known to have serious consequences for herbivores, the costs of processing them are generally unknown. Two potential costs of ingestion and detoxification of secondary compounds are elevation of the minimum drinking water requirement and excretion of energetically expensive metabolites (i.e., glucuronides) in the urine. To address these impacts, we studied the costs of ingestion of resin from creosote bush (Larrea tridentata) on desert woodrats (Neotoma lepida). The following hypotheses were tested: ingestion of creosote resin by woodrats (1) increases minimum water requirement and (2) reduces energy available by increasing fecal and urinary energy losses. We tested the first hypothesis, by measuring the minimum water requirement of woodrats fed a control diet with and without creosote resin. Drinking water was given in decreasing amounts until woodrats could no longer maintain constant body mass. In two separate experiments, the minimum drinking water requirement of woodrats fed resin was higher than that of controls by 18-30% (about 1-1.7 ml/d). We tested several potential mechanisms of increased water loss associated with the increase in water requirement. The rate of fecal water loss was higher in woodrats consuming resin. Neither urinary water nor evaporative water loss was affected by ingestion of resin. Hypothesis 2 was tested by measuring energy fluxes of woodrats consuming control vs. resin-treated diets. Woodrats on a resin diet had higher urinary energy losses and, thus, metabolized a lower proportion of the dietary energy than did woodrats on control diet. Fecal energy excretion was not affected by resin. The excretion of glucuronic acid represented almost half of the energy lost as a consequence of resin ingestion. The increased water requirement and energy losses of woodrats consuming a diet with resin could have notable ecological consequences.

Development of Low-Carbon, Copper-Strengthened HSLA Steel Plate for Naval Ship Construction

DTIC Science & Technology

1990-06-01

steel plate microstructures, 2% nital etch . ...................................................... 13 2. Charpy V-notch impact energy transition for...met a minimum yield strength requirement of 80 ksi yield strength through 3/4 inch gage, had high Charpy V-notch impact energy at low tempera- tures...tempered HSLA line-pipe steels, which typically could not meet the minimum Charpy V-notch impact toughness requirement of 35 ft-lb at -1 200 F. In 1984

Dynamical correlation effects on photoisomerization: Ab initio multiple spawning dynamics with MS-CASPT2 for a model trans-protonated Schiff base

DOE PAGES

Liu, Lihong; Liu, Jian; Martinez, Todd J.

2015-12-17

Here, we investigate the photoisomerization of a model retinal protonated Schiff base (trans-PSB3) using ab initio multiple spawning (AIMS) based on multi-state second order perturbation theory (MSPT2). Discrepancies between the photodynamical mechanism computed with three-root state-averaged complete active space self-consistent field (SA-3-CASSCF, which does not include dynamic electron correlation effects) and MSPT2 show that dynamic correlation is critical in this photoisomerization reaction. Furthermore, we show that the photodynamics of trans-PSB3 is not well described by predictions based on minimum energy conical intersections (MECIs) or minimum energy conical intersection (CI) seam paths. Instead, most of the CIs involved in the photoisomerizationmore » are far from MECIs and minimum energy CI seam paths. Thus, both dynamical nuclear effects and dynamic electron correlation are critical to understanding the photochemical mechanism.« less

Synthesis of correlation filters: a generalized space-domain approach for improved filter characteristics

NASA Astrophysics Data System (ADS)

Sudharsanan, Subramania I.; Mahalanobis, Abhijit; Sundareshan, Malur K.

1990-12-01

Discrete frequency domain design of Minimum Average Correlation Energy filters for optical pattern recognition introduces an implementational limitation of circular correlation. An alternative methodology which uses space domain computations to overcome this problem is presented. The technique is generalized to construct an improved synthetic discriminant function which satisfies the conflicting requirements of reduced noise variance and sharp correlation peaks to facilitate ease of detection. A quantitative evaluation of the performance characteristics of the new filter is conducted and is shown to compare favorably with the well known Minimum Variance Synthetic Discriminant Function and the space domain Minimum Average Correlation Energy filter, which are special cases of the present design.

Thermal decomposition of ammonium hexachloroosmate.

PubMed

Asanova, T I; Kantor, I; Asanov, I P; Korenev, S V; Yusenko, K V

2016-12-07

Structural changes of (NH 4 ) 2 [OsCl 6 ] occurring during thermal decomposition in a reduction atmosphere have been studied in situ using combined energy-dispersive X-ray absorption spectroscopy (ED-XAFS) and powder X-ray diffraction (PXRD). According to PXRD, (NH 4 ) 2 [OsCl 6 ] transforms directly to metallic Os without the formation of any crystalline intermediates but through a plateau where no reactions occur. XANES and EXAFS data by means of Multivariate Curve Resolution (MCR) analysis show that thermal decomposition occurs with the formation of an amorphous intermediate {OsCl 4 } x with a possible polymeric structure. Being revealed for the first time the intermediate was subjected to determine the local atomic structure around osmium. The thermal decomposition of hexachloroosmate is much more complex and occurs within a minimum two-step process, which has never been observed before.

Theoretical/best practice energy use in metalcasting operations

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

Schifo, J. F.; Radia, J. T.

2004-05-01

This study determined the theoretical minimum energy requirements for melting processes for all ferrous and noferrous engenieering alloys. Also the report details the Best Practice energy consumption for the industry.

Sulci segmentation using geometric active contours

NASA Astrophysics Data System (ADS)

Torkaman, Mahsa; Zhu, Liangjia; Karasev, Peter; Tannenbaum, Allen

2017-02-01

Sulci are groove-like regions lying in the depth of the cerebral cortex between gyri, which together, form a folded appearance in human and mammalian brains. Sulci play an important role in the structural analysis of the brain, morphometry (i.e., the measurement of brain structures), anatomical labeling and landmark-based registration.1 Moreover, sulcal morphological changes are related to cortical thickness, whose measurement may provide useful information for studying variety of psychiatric disorders. Manually extracting sulci requires complying with complex protocols, which make the procedure both tedious and error prone.2 In this paper, we describe an automatic procedure, employing geometric active contours, which extract the sulci. Sulcal boundaries are obtained by minimizing a certain energy functional whose minimum is attained at the boundary of the given sulci.

Influence of the chemical surface structure on the nanoscale friction in plasma nitrided and post-oxidized ferrous alloy

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

Freislebem, Márcia; Menezes, Caren M.; Cemin, Felipe

2014-09-15

Friction is a ubiquitous phenomenon in everyday activities spanning from vehicles where efficient brakes are mandatory up to mechanical devices where its minimum effects are pursued for energy efficiency issues. Recently, theoretical models succeed correlating the friction behavior with energy transference via phonons between sliding surfaces. Therefore, considering that the energy losses by friction are prompted through phonons, the chemical surface structure between sliding surfaces is very important to determine the friction phenomenon. In this work, we address the issue of friction between a conical diamond tip sliding on different functionalized flat steel surfaces by focusing the influence of themore » chemical bonds in the outermost layers on the sliding resistance. This geometry allows probing the coupling of the sharp tip with terminator species on the top and underneath material surface at in-depth friction measurements from 20 to 200 nm. Experimentally, the friction coefficient decreases when nitrogen atoms are substituted for oxygen in the iron network. This effect is interpreted as due to energy losses through phonons whilst lower vibrational frequency excitation modes imply lower friction coefficients and a more accurate adjustment is obtained when a theoretical model with longitudinal adsorbate vibration is used.« less

Green Energy in New Construction: Maximize Energy Savings and Minimize Cost

ERIC Educational Resources Information Center

Ventresca, Joseph

2010-01-01

People often use the term "green energy" to refer to alternative energy technologies. But green energy doesn't guarantee maximum energy savings at a minimum cost--a common misconception. For school business officials, green energy means getting the lowest energy bills for the lowest construction cost, which translates into maximizing green energy…

Inflation and dark energy from the Brans-Dicke theory

NASA Astrophysics Data System (ADS)

Artymowski, Michał; Lalak, Zygmunt; Lewicki, Marek

2015-06-01

We consider the Brans-Dicke theory motivated by the f(R) = R + α Rn - β R2-n model to obtain a stable minimum of the Einstein frame scalar potential of the Brans-Dicke field. As a result we have obtained an inflationary scalar potential with non-zero value of residual vacuum energy, which may be a source of dark energy. In addition we discuss the probability of quantum tunnelling from the minimum of the potential. Our results can be easily consistent with PLANCK or BICEP2 data for appropriate choices of the value of n and ω.

Structural mechanics of DNA wrapping in the nucleosome.

PubMed

Battistini, Federica; Hunter, Christopher A; Gardiner, Eleanor J; Packer, Martin J

2010-02-19

Experimental X-ray crystal structures and a database of calculated structural parameters of DNA octamers were used in combination to analyse the mechanics of DNA bending in the nucleosome core complex. The 1kx5 X-ray crystal structure of the nucleosome core complex was used to determine the relationship between local structure at the base-step level and the global superhelical conformation observed for nucleosome-bound DNA. The superhelix is characterised by a large curvature (597 degrees) in one plane and very little curvature (10 degrees) in the orthogonal plane. Analysis of the curvature at the level of 10-step segments shows that there is a uniform curvature of 30 degrees per helical turn throughout most of the structure but that there are two sharper kinks of 50 degrees at +/-2 helical turns from the central dyad base pair. The curvature is due almost entirely to the base-step parameter roll. There are large periodic variations in roll, which are in phase with the helical twist and account for 500 degrees of the total curvature. Although variations in the other base-step parameters perturb the local path of the DNA, they make minimal contributions to the total curvature. This implies that DNA bending in the nucleosome is achieved using the roll-slide-twist degree of freedom previously identified as the major degree of freedom in naked DNA oligomers. The energetics of bending into a nucleosome-bound conformation were therefore analysed using a database of structural parameters that we have previously developed for naked DNA oligomers. The minimum energy roll, the roll flexibility force constant and the maximum and minimum accessible roll values were obtained for each base step in the relevant octanucleotide context to account for the effects of conformational coupling that vary with sequence context. The distribution of base-step roll values and corresponding strain energy required to bend DNA into the nucleosome-bound conformation defined by the 1kx5 structure were obtained by applying a constant bending moment. When a single bending moment was applied to the entire sequence, the local details of the calculated structure did not match the experiment. However, when local 10-step bending moments were applied separately, the calculated structure showed excellent agreement with experiment. This implies that the protein applies variable bending forces along the DNA to maintain the superhelical path required for nucleosome wrapping. In particular, the 50 degrees kinks are constraints imposed by the protein rather than a feature of the 1kx5 DNA sequence. The kinks coincide with a relatively flexible region of the sequence, and this is probably a prerequisite for high-affinity nucleosome binding, but the bending strain energy is significantly higher at these points than for the rest of the sequence. In the most rigid regions of the sequence, a higher strain energy is also required to achieve the standard 30 degrees curvature per helical turn. We conclude that matching of the DNA sequence to the local roll periodicity required to achieve bending, together with the increased flexibility required at the kinks, determines the sequence selectivity of DNA wrapping in the nucleosome. 2009 Elsevier Ltd. All rights reserved.

Energy balance in high-quality cutting of steel by fiber and CO2 lasers

NASA Astrophysics Data System (ADS)

Fomin, V. M.; Golyshev, A. A.; Orishich, A. M.; Shulyat'ev, V. B.

2017-03-01

The energy balance of laser cutting of low-carbon and stainless steel sheets with the minimum roughness of the cut surface is experimentally studied. Experimental data obtained in wide ranges of cutting parameters are generalized with the use of dimensionless parameters (Peclet number and absorbed laser energy). It is discovered for the first time that the minimum roughness is ensured at a certain value of energy per unit volume of the melt (approximately 26 J/mm3), regardless of the gas type (oxygen or nitrogen) and laser type (fiber laser with a wavelength of 1.07 μm or CO2 laser with a wavelength of 10.6 μm).

Computational domain length and Reynolds number effects on large-scale coherent motions in turbulent pipe flow

NASA Astrophysics Data System (ADS)

Feldmann, Daniel; Bauer, Christian; Wagner, Claus

2018-03-01

We present results from direct numerical simulations (DNS) of turbulent pipe flow at shear Reynolds numbers up to Reτ = 1500 using different computational domains with lengths up to ?. The objectives are to analyse the effect of the finite size of the periodic pipe domain on large flow structures in dependency of Reτ and to assess a minimum ? required for relevant turbulent scales to be captured and a minimum Reτ for very large-scale motions (VLSM) to be analysed. Analysing one-point statistics revealed that the mean velocity profile is invariant for ?. The wall-normal location at which deviations occur in shorter domains changes strongly with increasing Reτ from the near-wall region to the outer layer, where VLSM are believed to live. The root mean square velocity profiles exhibit domain length dependencies for pipes shorter than 14R and 7R depending on Reτ. For all Reτ, the higher-order statistical moments show only weak dependencies and only for the shortest domain considered here. However, the analysis of one- and two-dimensional pre-multiplied energy spectra revealed that even for larger ?, not all physically relevant scales are fully captured, even though the aforementioned statistics are in good agreement with the literature. We found ? to be sufficiently large to capture VLSM-relevant turbulent scales in the considered range of Reτ based on our definition of an integral energy threshold of 10%. The requirement to capture at least 1/10 of the global maximum energy level is justified by a 14% increase of the streamwise turbulence intensity in the outer region between Reτ = 720 and 1500, which can be related to VLSM-relevant length scales. Based on this scaling anomaly, we found Reτ⪆1500 to be a necessary minimum requirement to investigate VLSM-related effects in pipe flow, even though the streamwise energy spectra does not yet indicate sufficient scale separation between the most energetic and the very long motions.

Multidimensionally constrained relativistic mean-field study of triple-humped barriers in actinides

NASA Astrophysics Data System (ADS)

Zhao, Jie; Lu, Bing-Nan; Vretenar, Dario; Zhao, En-Guang; Zhou, Shan-Gui

2015-01-01

Background: Potential energy surfaces (PES's) of actinide nuclei are characterized by a two-humped barrier structure. At large deformations beyond the second barrier, the occurrence of a third barrier was predicted by macroscopic-microscopic model calculations in the 1970s, but contradictory results were later reported by a number of studies that used different methods. Purpose: Triple-humped barriers in actinide nuclei are investigated in the framework of covariant density functional theory (CDFT). Methods: Calculations are performed using the multidimensionally constrained relativistic mean field (MDC-RMF) model, with the nonlinear point-coupling functional PC-PK1 and the density-dependent meson exchange functional DD-ME2 in the particle-hole channel. Pairing correlations are treated in the BCS approximation with a separable pairing force of finite range. Results: Two-dimensional PES's of 226,228,230,232Th and 232,235,236,238U are mapped and the third minima on these surfaces are located. Then one-dimensional potential energy curves along the fission path are analyzed in detail and the energies of the second barrier, the third minimum, and the third barrier are determined. The functional DD-ME2 predicts the occurrence of a third barrier in all Th nuclei and 238U . The third minima in 230 ,232Th are very shallow, whereas those in 226 ,228Th and 238U are quite prominent. With the functional PC-PK1 a third barrier is found only in 226 ,228 ,230Th . Single-nucleon levels around the Fermi surface are analyzed in 226Th, and it is found that the formation of the third minimum is mainly due to the Z =90 proton energy gap at β20≈1.5 and β30≈0.7 . Conclusions: The possible occurrence of a third barrier on the PES's of actinide nuclei depends on the effective interaction used in multidimensional CDFT calculations. More pronounced minima are predicted by the DD-ME2 functional, as compared to the functional PC-PK1. The depth of the third well in Th isotopes decreases with increasing neutron number. The origin of the third minimum is due to the proton Z =90 shell gap at relevant deformations.

Identification of the protein folding transition state from molecular dynamics trajectories

NASA Astrophysics Data System (ADS)

Muff, S.; Caflisch, A.

2009-03-01

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

Peierls-Nabarro barrier and protein loop propagation

NASA Astrophysics Data System (ADS)

Sieradzan, Adam K.; Niemi, Antti; Peng, Xubiao

2014-12-01

When a self-localized quasiparticle excitation propagates along a discrete one-dimensional lattice, it becomes subject to a dissipation that converts the kinetic energy into lattice vibrations. Eventually the kinetic energy no longer enables the excitation to cross over the minimum energy barrier between neighboring sites, and the excitation becomes localized within a lattice cell. In the case of a protein, the lattice structure consists of the Cα backbone. The self-localized quasiparticle excitation is the elemental building block of loops. It can be modeled by a kink that solves a variant of the discrete nonlinear Schrödinger equation. We study the propagation of such a kink in the case of the protein G related albumin-binding domain, using the united residue coarse-grained molecular-dynamics force field. We estimate the height of the energy barriers that the kink needs to cross over in order to propagate along the backbone lattice. We analyze how these barriers give rise to both stresses and reliefs, which control the kink movement. For this, we deform a natively folded protein structure by parallel translating the kink along the backbone away from its native position. We release the transposed kink, and we follow how it propagates along the backbone toward the native location. We observe that the dissipative forces that are exerted on the kink by the various energy barriers have a pivotal role in determining how a protein folds toward its native state.

Neutral and charged gallium clusters: structures, physical properties and implications for the melting features

NASA Astrophysics Data System (ADS)

Núñez, Sara; López, José M.; Aguado, Andrés

2012-09-01

We report the putative Global Minimum (GM) structures and electronic properties of GaN+, GaN and GaN- clusters with N = 13-37 atoms, obtained from first-principles density functional theory structural optimizations. The calculations include spin polarization and employ an exchange-correlation functional which accounts for van der Waals dispersion interactions (vdW-DFT). We find a wide diversity of structural motifs within the located GM, including decahedral, polyicosahedral, polytetrahedral and layered structures. The GM structures are also extremely sensitive to the number of electrons in the cluster, so that the structures of neutral and charged clusters differ for most sizes. The main magic numbers (clusters with an enhanced stability) are identified and interpreted in terms of electronic and geometric shell closings. The theoretical results are consistent with experimental abundance mass spectra of GaN+ and with photoelectron spectra of GaN-. The size dependence of the latent heats of melting, the shape of the heat capacity peaks, and the temperature dependence of the collision cross-sections, all measured for GaN+ clusters, are properly interpreted in terms of the calculated cohesive energies, spectra of configurational excitations, and cluster shapes, respectively. The transition from ``non-melter'' to ``magic-melter'' behaviour, experimentally observed between Ga30+ and Ga31+, is traced back to a strong geometry change. Finally, the higher-than-bulk melting temperatures of gallium clusters are correlated with a more typically metallic behaviour of the clusters as compared to the bulk, contrary to previous theoretical claims.We report the putative Global Minimum (GM) structures and electronic properties of GaN+, GaN and GaN- clusters with N = 13-37 atoms, obtained from first-principles density functional theory structural optimizations. The calculations include spin polarization and employ an exchange-correlation functional which accounts for van der Waals dispersion interactions (vdW-DFT). We find a wide diversity of structural motifs within the located GM, including decahedral, polyicosahedral, polytetrahedral and layered structures. The GM structures are also extremely sensitive to the number of electrons in the cluster, so that the structures of neutral and charged clusters differ for most sizes. The main magic numbers (clusters with an enhanced stability) are identified and interpreted in terms of electronic and geometric shell closings. The theoretical results are consistent with experimental abundance mass spectra of GaN+ and with photoelectron spectra of GaN-. The size dependence of the latent heats of melting, the shape of the heat capacity peaks, and the temperature dependence of the collision cross-sections, all measured for GaN+ clusters, are properly interpreted in terms of the calculated cohesive energies, spectra of configurational excitations, and cluster shapes, respectively. The transition from ``non-melter'' to ``magic-melter'' behaviour, experimentally observed between Ga30+ and Ga31+, is traced back to a strong geometry change. Finally, the higher-than-bulk melting temperatures of gallium clusters are correlated with a more typically metallic behaviour of the clusters as compared to the bulk, contrary to previous theoretical claims. Electronic supplementary information (ESI) available: Atomic coordinates (in xyz format and Å units) and point group symmetries for the global minimum structures reported in this paper. See DOI: 10.1039/c2nr31222k

The energy requirements of an aircraft triggered discharge

NASA Astrophysics Data System (ADS)

Bicknell, J. A.; Shelton, R. W.

The corona produced at aircraft surfaces requires an energy input before the corona can develop into a high current discharge and, thus, a possible lightning stroke. This energy must be drawn from the space charge field of the thundercloud and, since this is of low density, the unique propagation characteristics of positive corona streamers may be important. Estimates of the energy made available by the propagation are compared with laboratory measurements of the minimum energy input required to trigger a breakdown. The comparison indicates a minimum streamer range for breakdown of several tens of meters. Also estimated is the energy released as a consequence of streamer-hydrometer interactions; this is shown to be significant so that breakdown could depend upon the precipitation rate within the cloud. Inhibiting streamer production may therefore provide an aircraft with a degree of corona protection.

A hierarchical approach for the design improvements of an Organocat biorefinery.

PubMed

Abdelaziz, Omar Y; Gadalla, Mamdouh A; El-Halwagi, Mahmoud M; Ashour, Fatma H

2015-04-01

Lignocellulosic biomass has emerged as a potentially attractive renewable energy source. Processing technologies of such biomass, particularly its primary separation, still lack economic justification due to intense energy requirements. Establishing an economically viable and energy efficient biorefinery scheme is a significant challenge. In this work, a systematic approach is proposed for improving basic/existing biorefinery designs. This approach is based on enhancing the efficiency of mass and energy utilization through the use of a hierarchical design approach that involves mass and energy integration. The proposed procedure is applied to a novel biorefinery called Organocat to minimize its energy and mass consumption and total annualized cost. An improved heat exchanger network with minimum energy consumption of 4.5 MJ/kgdry biomass is designed. An optimal recycle network with zero fresh water usage and minimum waste discharge is also constructed, making the process more competitive and economically attractive. Copyright © 2015 Elsevier Ltd. All rights reserved.

The structure of high-temperature solar flare plasma in non-thermal flare models

NASA Technical Reports Server (NTRS)

Emslie, A. G.

1985-01-01

Analytic differential emission measure distributions have been derived for coronal plasma in flare loops heated both by collisions of high-energy suprathermal electrons with background plasma, and by ohmic heating by the beam-normalizing return current. For low densities, reverse current heating predominates, while for higher densities collisional heating predominates. There is thus a minimum peak temperature in an electron-heated loop. In contrast to previous approximate analyses, it is found that a stable reverse current can dominate the heating rate in a flare loop, especially in the low corona. Two 'scaling laws' are found which relate the peak temperature in the loop to the suprathermal electron flux. These laws are testable observationally and constitute a new diagnostic procedure for examining modes of energy transport in flaring loops.

River landscapes and optimal channel networks.

PubMed

Balister, Paul; Balogh, József; Bertuzzo, Enrico; Bollobás, Béla; Caldarelli, Guido; Maritan, Amos; Mastrandrea, Rossana; Morris, Robert; Rinaldo, Andrea

2018-06-26

We study tree structures termed optimal channel networks (OCNs) that minimize the total gravitational energy loss in the system, an exact property of steady-state landscape configurations that prove dynamically accessible and strikingly similar to natural forms. Here, we show that every OCN is a so-called natural river tree, in the sense that there exists a height function such that the flow directions are always directed along steepest descent. We also study the natural river trees in an arbitrary graph in terms of forbidden substructures, which we call k-path obstacles, and OCNs on a d-dimensional lattice, improving earlier results by determining the minimum energy up to a constant factor for every [Formula: see text] Results extend our capabilities in environmental statistical mechanics. Copyright © 2018 the Author(s). Published by PNAS.

Ab initio/DFT/GIAO-CCSD(T) calculational study of the t-butyl cation: comparison of experimental data with structures, energetics, IR vibrational frequencies, and 13C NMR chemical shifts indicating preferred C(s) conformation.

PubMed

Rasul, Golam; Chen, Jonathan L; Prakash, G K Surya; Olah, George A

2009-06-18

The C(s) conformation of the tert-butyl cation 3 was established to be the preferred global energy minimum using a combination of ab initio, DFT, and CCSD(T) methodology with correlation-consistent basis sets. The potential energy surface of methyl rotation involving the C(3v), C(s), and C(3h) forms, however, in accord with previous studies, is quite flat. The computed IR absorptions of 3 indicate that it has the greatest degree of electron donation from C-H bonds into the C(+)-C bonds. The experimental (13)C NMR chemical shifts also agree very well with the experimental data.

A theoretical study of bond selective photochemistry in CH2BrI

NASA Astrophysics Data System (ADS)

Liu, Kun; Zhao, Hongmei; Wang, Caixia; Zhang, Aihua; Ma, Siyu; Li, Zonghe

2005-01-01

Bromoiodomethane photodissociation in the low-lying excited states has been characterized using unrestricted Hartree-Fock, configuration-interaction-singles, and complete active space self-consistent field calculations with the SDB-aug-cc-pVTZ, aug-cc-pVTZ, and 3-21g** basis sets. According to the results of the vertical excited energies and oscillator strengths of these low-lying excited states, bond selectivity is predicted. Subsequently, the minimum energy paths of the first excited singlet state and the third excited state for the dissociation reactions were calculated using the complete active space self-consistent field method with 3-21g** basis set. Good agreement is found between the calculations and experimental data. The relationships of excitations, the electronic structures at Franck-Condon points, and bond selectivity are discussed.

A Subspace Semi-Definite programming-based Underestimation (SSDU) method for stochastic global optimization in protein docking*

PubMed Central

Nan, Feng; Moghadasi, Mohammad; Vakili, Pirooz; Vajda, Sandor; Kozakov, Dima; Ch. Paschalidis, Ioannis

2015-01-01

We propose a new stochastic global optimization method targeting protein docking problems. The method is based on finding a general convex polynomial underestimator to the binding energy function in a permissive subspace that possesses a funnel-like structure. We use Principal Component Analysis (PCA) to determine such permissive subspaces. The problem of finding the general convex polynomial underestimator is reduced into the problem of ensuring that a certain polynomial is a Sum-of-Squares (SOS), which can be done via semi-definite programming. The underestimator is then used to bias sampling of the energy function in order to recover a deep minimum. We show that the proposed method significantly improves the quality of docked conformations compared to existing methods. PMID:25914440

Relaxation dynamics of C60

NASA Astrophysics Data System (ADS)

Walsh, Tiffany R.; Wales, David J.

1998-10-01

The relaxation dynamics of C60 from high-energy isomers to Buckminsterfullerene is examined using a master equation approach. An exhaustive catalog of the C60 fullerene isomers containing only five- and six-membered rings is combined with knowledge of the Stone-Wales rearrangements that connect all such isomers. Full geometry optimizations have been performed for all the minima and the transition states which connect them up to six Stone-Wales steps away from the global minimum. A density-functional tight-binding potential was employed to provide a quantum mechanical description of the bonding. The resulting picture of the potential energy landscape reveals a "weeping willow" structure which offers a clear explanation for the relatively long relaxation times observed experimentally. We also predict the most important transient local minima on the annealing pathway.

RNA design using simulated SHAPE data.

PubMed

Lotfi, Mohadeseh; Zare-Mirakabad, Fatemeh; Montaseri, Soheila

2018-05-03

It has long been established that in addition to being involved in protein translation, RNA plays essential roles in numerous other cellular processes, including gene regulation and DNA replication. Such roles are known to be dictated by higher-order structures of RNA molecules. It is therefore of prime importance to find an RNA sequence that can fold to acquire a particular function that is desirable for use in pharmaceuticals and basic research. The challenge of finding an RNA sequence for a given structure is known as the RNA design problem. Although there are several algorithms to solve this problem, they mainly consider hard constraints, such as minimum free energy, to evaluate the predicted sequences. Recently, SHAPE data has emerged as a new soft constraint for RNA secondary structure prediction. To take advantage of this new experimental constraint, we report here a new method for accurate design of RNA sequences based on their secondary structures using SHAPE data as pseudo-free energy. We then compare our algorithm with four others: INFO-RNA, ERD, MODENA and RNAifold 2.0. Our algorithm precisely predicts 26 out of 29 new sequences for the structures extracted from the Rfam dataset, while the other four algorithms predict no more than 22 out of 29. The proposed algorithm is comparable to the above algorithms on RNA-SSD datasets, where they can predict up to 33 appropriate sequences for RNA secondary structures out of 34.

Structure, energetics and vibrational spectra of dimers, trimers, and tetramers of HX (X = Cl, Br, I)

NASA Astrophysics Data System (ADS)

Latajka, Zdzislaw; Scheiner, Steve

1997-03-01

The title complexes are studied by correlated ab initio methods using a pseudopotential double-ζ basis set, augmented by diffuse sp and two sets of polarization functions. The binding energies of the complexes decrease in the order HCl > HBr > HI. In the mixed HX…HX' dimers, the nature of the proton-donor molecule is more important than is the proton-acceptor with respect to the strength of the interaction. Only one minimum is found on the potential energy surface of the trimers and tetramers, which corresponds to the C nh cyclic structure. Enlargement of the complex leads to progressively greater individual H-bond energy and HX bond stretch, coupled with reduced intermolecular separation and smaller nonlinearity of each H-bond. Electron correlation makes a larger contribution as the atomic number of X increases. The highest degree of cooperativity is noted for oligomers of HCl and HBr, as compared to HI. The nonadditivity is dominated by terms present at the SCF level. The vibrational frequencies exhibit trends that generally parallel the energetics and geometry patterns, particularly the red shifts of the HX stretches and the intermolecular modes.

Protein side chain rotational isomerization: A minimum perturbation mapping study

NASA Astrophysics Data System (ADS)

Haydock, Christopher

1993-05-01

A theory of the rotational isomerization of the indole side chain of tryptophan-47 of variant-3 scorpion neurotoxin is presented. The isomerization potential energy, entropic part of the isomerization free energy, isomer probabilities, transition state theory reaction rates, and indole order parameters are calculated from a minimum perturbation mapping over tryptophan-47 χ1×χ2 torsion space. A new method for calculating the fluorescence anisotropy from molecular dynamics simulations is proposed. The method is based on an expansion that separates transition dipole orientation from chromophore dynamics. The minimum perturbation potential energy map is inverted and applied as a bias potential for a 100 ns umbrella sampling simulation. The entropic part of the isomerization free energy as calculated by minimum perturbation mapping and umbrella sampling are in fairly close agreement. Throughout, the approximation is made that two glutamine and three tyrosine side chains neighboring tryptophan-47 are truncated at the Cβ atom. Comparison with the previous combination thermodynamic perturbation and umbrella sampling study suggests that this truncated neighbor side chain approximation leads to at least a qualitatively correct theory of tryptophan-47 rotational isomerization in the wild type variant-3 scorpion neurotoxin. Analysis of van der Waals interactions in a transition state region indicates that for the simulation of barrier crossing trajectories a linear combination of three specially defined dihedral angles will be superior to a simple side chain dihedral reaction coordinate.

Reaction of hydrogen with Ag(111): binding states, minimum energy paths, and kinetics.

PubMed

Montoya, Alejandro; Schlunke, Anna; Haynes, Brian S

2006-08-31

The interaction of atomic and molecular hydrogen with the Ag(111) surface is studied using periodic density functional total-energy calculations. This paper focuses on the site preference for adsorption, ordered structures, and energy barriers for H diffusion and H recombination. Chemisorbed H atoms are unstable with respect to the H(2) molecule in all adsorption sites below monolayer coverage. The three-hollow sites are energetically the most favorable for H chemisorption. The binding energy of H to the surface decreases slightly up to one monolayer, suggesting a small repulsive H-H interaction on nonadjacent sites. Subsurface and vacancy sites are energetically less favorable for H adsorption than on-top sites. Recombination of chemisorbed H atoms leads to the formation of gas-phase H(2) with no molecular chemisorbed state. Recombination is an exothermic process and occurs on the bridge site with a pronounced energy barrier. This energy barrier is significantly higher than that inferred from experimental temperature-programmed desorption (TPD) studies. However, there is significant permeability of H atoms through the recombination energy barrier at low temperatures, thus increasing the rate constant for H(2) desorption due to quantum tunneling effects, and improving the agreement between experiment and theory.

Uncertainty of the potential curve minimum for diatomic molecules extrapolated from Dunham type coefficients

NASA Astrophysics Data System (ADS)

Ilieva, T.; Iliev, I.; Pashov, A.

2016-12-01

In the traditional description of electronic states of diatomic molecules by means of molecular constants or Dunham coefficients, one of the important fitting parameters is the value of the zero point energy - the minimum of the potential curve or the energy of the lowest vibrational-rotational level - E00 . Their values are almost always the result of an extrapolation and it may be difficult to estimate their uncertainties, because they are connected not only with the uncertainty of the experimental data, but also with the distribution of experimentally observed energy levels and the particular realization of set of Dunham coefficients. This paper presents a comprehensive analysis based on Monte Carlo simulations, which aims to demonstrate the influence of all these factors on the uncertainty of the extrapolated minimum of the potential energy curve U (Re) and the value of E00 . The very good extrapolation properties of the Dunham coefficients are quantitatively confirmed and it is shown that for a proper estimate of the uncertainties, the ambiguity in the composition of the Dunham coefficients should be taken into account.

10 CFR 429.44 - Commercial water heating equipment.

Code of Federal Regulations, 2013 CFR

2013-01-01

... of minimum thermal efficiency or other measure of energy consumption of a basic model for which... 10 Energy 3 2013-01-01 2013-01-01 false Commercial water heating equipment. 429.44 Section 429.44 Energy DEPARTMENT OF ENERGY ENERGY CONSERVATION CERTIFICATION, COMPLIANCE, AND ENFORCEMENT FOR CONSUMER...

Quantification of feather structure, wettability and resistance to liquid penetration.

PubMed

Srinivasan, Siddarth; Chhatre, Shreerang S; Guardado, Jesus O; Park, Kyoo-Chul; Parker, Andrew R; Rubner, Michael F; McKinley, Gareth H; Cohen, Robert E

2014-07-06

Birds in the cormorant (Phalacrocoracidae) family dive tens of metres into water to prey on fish while entraining a thin layer of air (a plastron film) within the microstructures of their feathers. In addition, many species within the family spread their wings for long periods of time upon emerging from water. To investigate whether wetting and wing-spreading are related to feather structure, microscopy and photographic studies have previously been used to extract structural parameters for barbs and barbules. In this work, we describe a systematic methodology to characterize the quasi-hierarchical topography of bird feathers that is based on contact angle measurements using a set of polar and non-polar probing liquids. Contact angle measurements on dip-coated feathers of six aquatic bird species (including three from the Phalacrocoracidae family) are used to extract two distinguishing structural parameters, a dimensionless spacing ratio of the barbule (D*) and a characteristic length scale corresponding to the spacing of defect sites. The dimensionless spacing parameter can be used in conjunction with a model for the surface topography to enable us to predict a priori the apparent contact angles of water droplets on feathers as well as the water breakthrough pressure required for the disruption of the plastron on the feather barbules. The predicted values of breakthrough depths in water (1-4 m) are towards the lower end of typical diving depths for the aquatic bird species examined here, and therefore a representative feather is expected to be fully wetted in a typical deep dive. However, thermodynamic surface energy analysis based on a simple one-dimensional cylindrical model of the feathers using parameters extracted from the goniometric analysis reveals that for water droplets on feathers of all six species under consideration, the non-wetting 'Cassie-Baxter' composite state represents the global energy minimum of the system. By contrast, for other wetting liquids, such as alkanes and common oils, the global energy minimum corresponds to a fully wetted or Wenzel state. For diving birds, individual feathers therefore spontaneously dewet once the bird emerges out of water, and the 'wing-spreading' posture might assist in overcoming kinetic barriers associated with pinning of liquid droplets that retard the rate of drying of the wet plumage of diving birds.

Quantification of feather structure, wettability and resistance to liquid penetration

PubMed Central

Srinivasan, Siddarth; Chhatre, Shreerang S.; Guardado, Jesus O.; Park, Kyoo-Chul; Parker, Andrew R.; Rubner, Michael F.; McKinley, Gareth H.; Cohen, Robert E.

2014-01-01

Birds in the cormorant (Phalacrocoracidae) family dive tens of metres into water to prey on fish while entraining a thin layer of air (a plastron film) within the microstructures of their feathers. In addition, many species within the family spread their wings for long periods of time upon emerging from water. To investigate whether wetting and wing-spreading are related to feather structure, microscopy and photographic studies have previously been used to extract structural parameters for barbs and barbules. In this work, we describe a systematic methodology to characterize the quasi-hierarchical topography of bird feathers that is based on contact angle measurements using a set of polar and non-polar probing liquids. Contact angle measurements on dip-coated feathers of six aquatic bird species (including three from the Phalacrocoracidae family) are used to extract two distinguishing structural parameters, a dimensionless spacing ratio of the barbule (D*) and a characteristic length scale corresponding to the spacing of defect sites. The dimensionless spacing parameter can be used in conjunction with a model for the surface topography to enable us to predict a priori the apparent contact angles of water droplets on feathers as well as the water breakthrough pressure required for the disruption of the plastron on the feather barbules. The predicted values of breakthrough depths in water (1–4 m) are towards the lower end of typical diving depths for the aquatic bird species examined here, and therefore a representative feather is expected to be fully wetted in a typical deep dive. However, thermodynamic surface energy analysis based on a simple one-dimensional cylindrical model of the feathers using parameters extracted from the goniometric analysis reveals that for water droplets on feathers of all six species under consideration, the non-wetting ‘Cassie–Baxter’ composite state represents the global energy minimum of the system. By contrast, for other wetting liquids, such as alkanes and common oils, the global energy minimum corresponds to a fully wetted or Wenzel state. For diving birds, individual feathers therefore spontaneously dewet once the bird emerges out of water, and the ‘wing-spreading’ posture might assist in overcoming kinetic barriers associated with pinning of liquid droplets that retard the rate of drying of the wet plumage of diving birds. PMID:24789563

B11-: a moving subnanoscale tank tread

NASA Astrophysics Data System (ADS)

Wang, Ying-Jin; Zhao, Xiao-Yun; Chen, Qiang; Zhai, Hua-Jin; Li, Si-Dian

2015-09-01

We present a concept that an elongated, planar boron cluster can serve as a ``tank tread'' at the sub-nanometer scale, a novel propulsion system for potential nanomachines. Density functional calculations at the PBE0/6-311+G* level for the global-minimum B11-C2v (1A1) and B11C2v (2B2) structures along the soft in-plane rotational mode allow the identification of their corresponding B11-C2v and B11C2v transition states, with small rotational energy barriers of 0.42 and 0.55 kcal mol-1, respectively. The energy barriers are refined to 0.35 and 0.60 kcal mol-1 at the single-point CCSD(T) level, suggesting that the clusters are structurally fluxional at room temperature. Molecular dynamics simulations show that B11- and B11 behave exactly like a tank tread, in which the peripheral B9 ring rotates almost freely around the B2 core. A full turn of rotation may be accomplished in around 2 ps. In contrast to molecular wheels or Wankel motors, the peripheral boron atoms in the tank tread behave as a flexible chain gliding around, rather than as a rigid wheel rotation. This finding is beyond imagination, which expands the concepts of molecular wheels and Wankel motors.We present a concept that an elongated, planar boron cluster can serve as a ``tank tread'' at the sub-nanometer scale, a novel propulsion system for potential nanomachines. Density functional calculations at the PBE0/6-311+G* level for the global-minimum B11-C2v (1A1) and B11C2v (2B2) structures along the soft in-plane rotational mode allow the identification of their corresponding B11-C2v and B11C2v transition states, with small rotational energy barriers of 0.42 and 0.55 kcal mol-1, respectively. The energy barriers are refined to 0.35 and 0.60 kcal mol-1 at the single-point CCSD(T) level, suggesting that the clusters are structurally fluxional at room temperature. Molecular dynamics simulations show that B11- and B11 behave exactly like a tank tread, in which the peripheral B9 ring rotates almost freely around the B2 core. A full turn of rotation may be accomplished in around 2 ps. In contrast to molecular wheels or Wankel motors, the peripheral boron atoms in the tank tread behave as a flexible chain gliding around, rather than as a rigid wheel rotation. This finding is beyond imagination, which expands the concepts of molecular wheels and Wankel motors. Electronic supplementary information (ESI) available: A short movie extracted from the molecular dynamics (MD) simulation for B11- optimized structures of the C2v (1A1) global minimum (GM) and C2v (1A1) transition state (TS) of B11- and those of their corresponding B11 neutral clusters at the PBE0/6-311+G* level; the total electron localization function (ELF) of the GM of B11-C2v (1A1); chemical bonding in the C2v TS of B11- as revealed from the ELF and adaptive natural density partitioning (AdNDP) analyses; the structural evolution of B11 during the peripheral rotation; and the Cartesian coordinates for the GM structures of B11-C2v (1A1), B11C2v (2B2), and their C2v TS states at the PBE0/6-311+G* level. See DOI: 10.1039/c5nr03732h

K + block is the mechanism of functional asymmetry in bacterial Na v channels

DOE PAGES

Ngo, Van; Wang, Yibo; Haas, Stephan; ...

2016-01-04

Crystal structures of several bacterial Na v channels have been recently published and molecular dynamics simulations of ion permeation through these channels are consistent with many electrophysiological properties of eukaryotic channels. Bacterial Na v channels have been characterized as functionally asymmetric, and the mechanism of this asymmetry has not been clearly understood. To address this question, we combined non-equilibrium simulation data with two-dimensional equilibrium unperturbed landscapes generated by umbrella sampling and Weighted Histogram Analysis Methods for multiple ions traversing the selectivity filter of bacterial Na vAb channel. This approach provided new insight into the mechanism of selective ion permeation inmore » bacterial Nav channels. The non-equilibrium simulations indicate that two or three extracellular K + ions can block the entrance to the selectivity filter of Na vAb in the presence of applied forces in the inward direction, but not in the outward direction. The block state occurs in an unstable local minimum of the equilibrium unperturbed free-energy landscape of two K+ ions that can be ‘locked’ in place bymodest applied forces. In contrast to K +, three Na + ions move favorably through the selectivity filter together as a unit in a loose “knock-on” mechanism of permeation in both inward and outward directions, and there is no similar local minimum in the two-dimensional free-energy landscape of two Na + ions for a block state. The useful work predicted by the non-equilibrium simulations that is required to break the K + block is equivalent to large applied potentials experimentally measured for two bacterial Na v channels to induce inward currents of K + ions. Here, these results illustrate how inclusion of non-equilibrium factors in the simulations can provide detailed information about mechanisms of ion selectivity that is missing from mechanisms derived from either crystal structures or equilibrium unperturbed free-energy landscapes.« less

K+ Block Is the Mechanism of Functional Asymmetry in Bacterial Nav Channels

PubMed Central

Ngo, Van; Wang, Yibo; Haas, Stephan; Noskov, Sergei Y.; Farley, Robert A.

2016-01-01

Crystal structures of several bacterial Nav channels have been recently published and molecular dynamics simulations of ion permeation through these channels are consistent with many electrophysiological properties of eukaryotic channels. Bacterial Nav channels have been characterized as functionally asymmetric, and the mechanism of this asymmetry has not been clearly understood. To address this question, we combined non-equilibrium simulation data with two-dimensional equilibrium unperturbed landscapes generated by umbrella sampling and Weighted Histogram Analysis Methods for multiple ions traversing the selectivity filter of bacterial NavAb channel. This approach provided new insight into the mechanism of selective ion permeation in bacterial Nav channels. The non-equilibrium simulations indicate that two or three extracellular K+ ions can block the entrance to the selectivity filter of NavAb in the presence of applied forces in the inward direction, but not in the outward direction. The block state occurs in an unstable local minimum of the equilibrium unperturbed free-energy landscape of two K+ ions that can be ‘locked’ in place by modest applied forces. In contrast to K+, three Na+ ions move favorably through the selectivity filter together as a unit in a loose “knock-on” mechanism of permeation in both inward and outward directions, and there is no similar local minimum in the two-dimensional free-energy landscape of two Na+ ions for a block state. The useful work predicted by the non-equilibrium simulations that is required to break the K+ block is equivalent to large applied potentials experimentally measured for two bacterial Nav channels to induce inward currents of K+ ions. These results illustrate how inclusion of non-equilibrium factors in the simulations can provide detailed information about mechanisms of ion selectivity that is missing from mechanisms derived from either crystal structures or equilibrium unperturbed free-energy landscapes. PMID:26727271

Evolved Minimal Frustration in Multifunctional Biomolecules.

PubMed

Röder, Konstantin; Wales, David J

2018-05-25

Protein folding is often viewed in terms of a funnelled potential or free energy landscape. A variety of experiments now indicate the existence of multifunnel landscapes, associated with multifunctional biomolecules. Here, we present evidence that these systems have evolved to exhibit the minimal number of funnels required to fulfil their cellular functions, suggesting an extension to the principle of minimum frustration. We find that minimal disruptive mutations result in additional funnels, and the associated structural ensembles become more diverse. The same trends are observed in an atomic cluster. These observations suggest guidelines for rational design of engineered multifunctional biomolecules.

Waveguide and active region structure optimization for low-divergence InAs/InGaAs quantum dot comb lasers

NASA Astrophysics Data System (ADS)

Korenev, Vladimir V.; Savelyev, Artem V.; Zhukov, Alexey E.; Maximov, Mikhail V.; Omelchenko, Alexander V.

2015-05-01

Ways to improve beam divergence and energy consumption of quantum dot lasers emitting via the ground-state optical transitions by optimization of the key parameters of laser active region are discussed. It is shown that there exist an optimal cavity length, dispersion of inhomogeneous broadening and number of QD layers in active region allowing to obtain lasing spectrum of a given width at minimum injection current. The planar dielectric waveguide of the laser is optimized by analytical means for a better trade-off between high Γ-factor and low beam divergence.

Cosmic 21 cm delensing of microwave background polarization and the minimum detectable energy scale of inflation.

PubMed

Sigurdson, Kris; Cooray, Asantha

2005-11-18

We propose a new method for removing gravitational lensing from maps of cosmic microwave background (CMB) polarization anisotropies. Using observations of anisotropies or structures in the cosmic 21 cm radiation, emitted or absorbed by neutral hydrogen atoms at redshifts 10 to 200, the CMB can be delensed. We find this method could allow CMB experiments to have increased sensitivity to a background of inflationary gravitational waves (IGWs) compared to methods relying on the CMB alone and may constrain models of inflation which were heretofore considered to have undetectable IGW amplitudes.

Building Better: Advanced Energy Design Guides - Continuum Magazine |

Science.gov Websites

NREL Building Better: Advanced Energy Design Guides Building Better: Advanced Energy Design Greensburg be constructed to meet Leadership in Energy and Environmental Design (LEED) Platinum ratings from design needs to incorporate a number of recommendations for achieving energy savings over the minimum

Specific energy contributions from competing hydrogen-bonded structures in six polymorphs of phenobarbital.

PubMed

Gelbrich, Thomas; Braun, Doris E; Griesser, Ulrich J

2016-01-01

In solid state structures of organic molecules, identical sets of H-bond donor and acceptor functions can result in a range of distinct H-bond connectivity modes. Specifically, competing H-bond structures (HBSs) may differ in the quantitative proportion between one-point and multiple-point H-bond connections. For an assessment of such HBSs, the effects of their internal as well as external (packing) interactions need to be taken into consideration. The semi-classical density sums (SCDS-PIXEL) method, which enables the calculation of interaction energies for molecule-molecule pairs, was used to investigate six polymorphs of phenobarbital (Pbtl) with different quantitative proportions of one-point and two-point H-bond connections. The structures of polymorphs V and VI of Pbtl were determined from single crystal data. Two-point H-bond connections are inherently inflexible in their geometry and lie within a small PIXEL energy range (-45.7 to -49.7 kJ mol(-1)). One-point H-bond connections are geometrically less restricted and subsequently show large variations in their dispersion terms and total energies (-23.1 to -40.5 kJ mol(-1)). The comparison of sums of interaction energies in small clusters containing only the strongest intermolecular interactions showed an advantage for compact HBSs with multiple-point connections, whereas alternative HBSs based on one-point connections may enable more favourable overall packing interactions (i.e. V vs. III). Energy penalties associated with experimental intramolecular geometries relative to the global conformational energy minimum were calculated and used to correct total PIXEL energies. The estimated order of stabilities (based on PIXEL energies) is III > I > II > VI > X > V, with a difference of just 1.7 kJ mol(-1) between the three most stable forms. For an analysis of competing HBSs, one has to consider the contributions from internal H-bond and non-H-bond interactions, from the packing of multiple HBS instances and intramolecular energy penalties. A compact HBS based on multiple-point H-bond connections should typically lead to more packing alternatives and ultimately to a larger number of viable low-energy structures than a competing one-point HBS (i.e. dimer vs. catemer). Coulombic interaction energies associated with typical short intermolecular C-H···O contact geometries are small in comparison with dispersion effects associated with the packing complementary molecular shapes.Graphical abstractCompeting H-bond motifs can differ markedly in their energy contributions.

Investigation of Quasi-Static Indentation Response of Inkjet Printed Sandwich Structures under Various Indenter Geometries

PubMed Central

Dikshit, Vishwesh; Nagalingam, Arun Prasanth; Yap, Yee Ling; Sing, Swee Leong; Yeong, Wai Yee; Wei, Jun

2017-01-01

The objective of this investigation was to determine the quasi-static indentation response and failure mode in three-dimensional (3D) printed trapezoidal core structures, and to characterize the energy absorbed by the structures. In this work, the trapezoidal sandwich structure was designed in the following two ways. Firstly, the trapezoidal core along with its facesheet was 3D printed as a single element comprising a single material for both core and facesheet (type A); Secondly, the trapezoidal core along with facesheet was 3D printed, but with variation in facesheet materials (type B). Quasi-static indentation was carried out using three different indenters, namely standard hemispherical, conical, and flat indenters. Acoustic emission (AE) technique was used to capture brittle cracking in the specimens during indentation. The major failure modes were found to be brittle failure and quasi-brittle fractures. The measured indentation energy was at a maximum when using a conical indenter at 9.40 J and 9.66 J and was at a minimum when using a hemispherical indenter at 6.87 J and 8.82 J for type A and type B series specimens respectively. The observed maximum indenter displacements at failure were the effect of material variations and composite configurations in the facesheet. PMID:28772649

B80 and B101-103 clusters: Remarkable stability of the core-shell structures established by validated density functionalsa)

NASA Astrophysics Data System (ADS)

Li, Fengyu; Jin, Peng; Jiang, De-en; Wang, Lu; Zhang, Shengbai B.; Zhao, Jijun; Chen, Zhongfang

2012-02-01

Prompted by the very recent claim that the volleyball-shaped B80 fullerene [X. Wang, Phys. Rev. B 82, 153409 (2010), 10.1103/PhysRevB.82.153409] is lower in energy than the B80 buckyball [N. G. Szwacki, A. Sadrzadeh, and B. I. Yakobson, Phys. Rev. Lett. 98, 166804 (2007), 10.1103/PhysRevLett.98.166804] and core-shell structure [J. Zhao, L. Wang, F. Li, and Z. Chen, J. Phys. Chem. A 114, 9969 (2010), 10.1021/jp1018873], and inspired by the most recent finding of another core-shell isomer as the lowest energy B80 isomer [S. De, A. Willand, M. Amsler, P. Pochet, L. Genovese, and S. Goedecher, Phys. Rev. Lett. 106, 225502 (2011), 10.1103/PhysRevLett.106.225502], we carefully evaluated the performance of the density functional methods in the energetics of boron clusters and confirmed that the core-shell construction (stuffed fullerene) is thermodynamically the most favorable structural pattern for B80. Our global minimum search showed that both B101 and B103 also prefer a core-shell structure and that B103 can reach the complete core-shell configuration. We called for great attention to the theoretical community when using density functionals to investigate boron-related nanomaterials.

Investigation of Quasi-Static Indentation Response of Inkjet Printed Sandwich Structures under Various Indenter Geometries.

PubMed

Dikshit, Vishwesh; Nagalingam, Arun Prasanth; Yap, Yee Ling; Sing, Swee Leong; Yeong, Wai Yee; Wei, Jun

2017-03-14

The objective of this investigation was to determine the quasi-static indentation response and failure mode in three-dimensional (3D) printed trapezoidal core structures, and to characterize the energy absorbed by the structures. In this work, the trapezoidal sandwich structure was designed in the following two ways. Firstly, the trapezoidal core along with its facesheet was 3D printed as a single element comprising a single material for both core and facesheet (type A); Secondly, the trapezoidal core along with facesheet was 3D printed, but with variation in facesheet materials (type B). Quasi-static indentation was carried out using three different indenters, namely standard hemispherical, conical, and flat indenters. Acoustic emission (AE) technique was used to capture brittle cracking in the specimens during indentation. The major failure modes were found to be brittle failure and quasi-brittle fractures. The measured indentation energy was at a maximum when using a conical indenter at 9.40 J and 9.66 J and was at a minimum when using a hemispherical indenter at 6.87 J and 8.82 J for type A and type B series specimens respectively. The observed maximum indenter displacements at failure were the effect of material variations and composite configurations in the facesheet.

Ab initio conformational analysis of N-formyl ?-alanine amide including electron correlation

NASA Astrophysics Data System (ADS)

Yu, Ching-Hsing; Norman, Mya A.; Schäfer, Lothar; Ramek, Michael; Peeters, Anik; van Alsenoy, Christian

2001-06-01

The conformational properties of N-formyl L-alanine amide (ALA) were investigated using RMP2/6-311G∗∗ ab initio gradient geometry optimization. One hundred forty four structures of ALA were optimized at 30° grid points in its φ(N-C(α)), ψ(C(α)-C‧) conformational space. Using cubic spline functions, the grid structures were then used to construct analytical representations of complete surfaces, in φ,ψ-space, of bond lengths, bond angles, torsional sensitivity and electrostatic atomic charges. Analyses show that, in agreement with previous studies, the right-handed helical conformation, αR, is not a local energy minimum of the potential energy surface of ALA. Comparisons with protein crystallographic data show that the characteristic differences between geometrical trends in dipeptides and proteins, previously found for ab initio dipeptide structures obtained without electron correlation, are also found in the electron-correlated geometries. In contrast to generally accepted features of force fields used in empirical molecular modeling, partial atomic charges obtained by the CHELPG method are found to be not constant, but to vary significantly throughout the φ,ψ-space. By comparing RHF and MP2 structures, the effects of dispersion forces on ALA were studied, revealing molecular contractions for those conformations, in which small adjustments of torsional angles entail large changes in non-bonded distances.

Evaluation of Structural Robustness against Column Loss: Methodology and Application to RC Frame Buildings

PubMed Central

Bao, Yihai; Main, Joseph A.; Noh, Sam-Young

2017-01-01

A computational methodology is presented for evaluating structural robustness against column loss. The methodology is illustrated through application to reinforced concrete (RC) frame buildings, using a reduced-order modeling approach for three-dimensional RC framing systems that includes the floor slabs. Comparisons with high-fidelity finite-element model results are presented to verify the approach. Pushdown analyses of prototype buildings under column loss scenarios are performed using the reduced-order modeling approach, and an energy-based procedure is employed to account for the dynamic effects associated with sudden column loss. Results obtained using the energy-based approach are found to be in good agreement with results from direct dynamic analysis of sudden column loss. A metric for structural robustness is proposed, calculated by normalizing the ultimate capacities of the structural system under sudden column loss by the applicable service-level gravity loading and by evaluating the minimum value of this normalized ultimate capacity over all column removal scenarios. The procedure is applied to two prototype 10-story RC buildings, one employing intermediate moment frames (IMFs) and the other employing special moment frames (SMFs). The SMF building, with its more stringent seismic design and detailing, is found to have greater robustness. PMID:28890599

Wing flapping with minimum energy. [minimize the drag for a bending moment at the wing root

NASA Technical Reports Server (NTRS)

Jones, R. T.

1980-01-01

For slow flapping motions it is found that the minimum energy loss occurs when the vortex wake moves as a rigid surface that rotates about the wing root - a condition analogous to that determined for a slow-turning propeller. The optimum circulation distribution determined by this condition differs from the elliptic distribution, showing a greater concentration of lift toward the tips. It appears that very high propulsive efficiencies are obtained by flapping.

From brittle to ductile fracture in disordered materials.

PubMed

Picallo, Clara B; López, Juan M; Zapperi, Stefano; Alava, Mikko J

2010-10-08

We introduce a lattice model able to describe damage and yielding in heterogeneous materials ranging from brittle to ductile ones. Ductile fracture surfaces, obtained when the system breaks once the strain is completely localized, are shown to correspond to minimum energy surfaces. The similarity of the resulting fracture paths to the limits of brittle fracture or minimum energy surfaces is quantified. The model exhibits a smooth transition from brittleness to ductility. The dynamics of yielding exhibits avalanches with a power-law distribution.

Planning Minimum-Energy Paths in an Off-Road Environment with Anisotropic Traversal Costs and Motion Constraints

DTIC Science & Technology

1989-06-01

problems, and (3) weighted-region problems. Since the minimum-energy path-planning problem addressed in this dissertation is a hybrid between the two...contains components that are strictly vehicle dependent, components that are strictly terrain dependent, and components representing a hybrid of...Single Segment Braking/Multiple Segment Hybrid Using Eq. (3.46), the traversal cost U 1,.-1 can be rewritten as Uop- 1 = mgD Itan01 , (4.12a) and the

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

Altabet, Y. Elia; Debenedetti, Pablo G., E-mail: pdebene@princeton.edu; Stillinger, Frank H.

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

First-principles study of hydrogen-bonded molecular conductor κ -H3(Cat-EDT-TTF/ST)2

NASA Astrophysics Data System (ADS)

Tsumuraya, Takao; Seo, Hitoshi; Kato, Reizo; Miyazaki, Tsuyoshi

2015-07-01

We theoretically study hydrogen-bonded molecular conductors synthesized recently, κ -H3(Cat-EDT-TTF) 2 and its diselena analog, κ -H3(Cat-EDT-ST) 2, by first-principles density functional theory calculations. In these crystals, two H(Cat-EDT-TTF/ST) units share a hydrogen atom with a short O-H-O hydrogen bond. The calculated band structure near the Fermi level shows a quasi-two-dimensional character with a rather large interlayer dispersion due to the absence of insulating layers, in contrast with conventional molecular conductors. We discuss effective low-energy models based on H(Cat-EDT-TTF/ST) units and its dimers, respectively, where the microscopic character of the orbitals composing them are analyzed. Furthermore, we find a stable structure which is different from the experimentally determined structure, where the shared hydrogen atom becomes localized to one of the oxygen atoms, in which charge disproportionation between the two types of H(Cat-EDT-TTF) units is associated. The calculated potential energy surface for the H atom is very shallow near the minimum points; therefore the probability of the H atom can be delocalized between the two O atoms.

Ab initio investigation of the first hydration shell of protonated glycine

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

Wei, Zhichao; Chen, Dong, E-mail: dongchen@henu.edu.cn, E-mail: boliu@henu.edu.cn; Zhao, Huiling

2014-02-28

The first hydration shell of the protonated glycine is built up using Monte Carlo multiple minimum conformational search analysis with the MMFFs force field. The potential energy surfaces of the protonated glycine and its hydration complexes with up to eight water molecules have been scanned and the energy-minimized structures are predicted using the ab initio calculations. First, three favorable structures of protonated glycine were determined, and the micro-hydration processes showed that water can significantly stabilize the unstable conformers, and then their first hydration shells were established. Finally, we found that seven water molecules are required to fully hydrate the firstmore » hydration shell for the most stable conformer of protonated glycine. In order to analyse the hydration process, the dominant hydration sites located around the ammonium and carboxyl groups are studied carefully and systemically. The results indicate that, water molecules hydrate the protonated glycine in an alternative dynamic hydration process which is driven by the competition between different hydration sites. The first three water molecules are strongly attached by the ammonium group, while only the fourth water molecule is attached by the carboxyl group in the ultimate first hydration shell of the protonated glycine. In addition, the first hydration shell model has predicted most identical structures and a reasonable accord in hydration energy and vibrational frequencies of the most stable conformer with the conductor-like polarizable continuum model.« less

Development of piezoelectric bistable energy harvester based on buckled beam with axially constrained end condition for human motion

NASA Astrophysics Data System (ADS)

Eltanany, Ali M.; Yoshimura, Takeshi; Fujimura, Norifumi; Ebied, Mohamed R.; Ali, Mohamed G. S.

2017-10-01

In this study, we aim to examine the triggering force for an efficient snap-through solution of hand shaking vibrations of a piezoelectric bistable energy harvester. The proposed structure works at very low frequencies with nearly continuous periodic vibrations. The static characterizations are presented as well as the dynamic characterizations based on the phase diagrams of velocity vs displacement, voltage vs displacement, and voltage vs input acceleration. The mass attached to the bistable harvester plays an important role in determining the acceleration needed for the snap-through action, and the explanation for this role is complex because of mass dependence on frequency/amplitude vibration. Various hand shaking vibration tests are performed to demonstrate the advantage of the proposed structure in harvesting energy from hand shaking vibration. The minimum input acceleration for snap-through action was 11.59 m/s2 with peaks of 15.76 and 2 m/s2 in the frequency range of 1.3-2.7 Hz, when an attached mass of 14.6 g is used. The maximum generated power at a buckling state of 0.5 mm is 11.3 µW for the test structure at 26 g. The experimental results obtained in this study indicate that power output harvesting of slow hand shaking vibrations at 10 µW and a load resistance of 1 MΩ.

[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.

Energy-efficient constellations design and fast decoding for space-collaborative MIMO visible light communications

NASA Astrophysics Data System (ADS)

Zhu, Yi-Jun; Liang, Wang-Feng; Wang, Chao; Wang, Wen-Ya

2017-01-01

In this paper, space-collaborative constellations (SCCs) for indoor multiple-input multiple-output (MIMO) visible light communication (VLC) systems are considered. Compared with traditional VLC MIMO techniques, such as repetition coding (RC), spatial modulation (SM) and spatial multiplexing (SMP), SCC achieves the minimum average optical power for a fixed minimum Euclidean distance. We have presented a unified SCC structure for 2×2 MIMO VLC systems and extended it to larger MIMO VLC systems with more transceivers. Specifically for 2×2 MIMO VLC, a fast decoding algorithm is developed with decoding complexity almost linear in terms of the square root of the cardinality of SCC, and the expressions of symbol error rate of SCC are presented. In addition, bit mappings similar to Gray mapping are proposed for SCC. Computer simulations are performed to verify the fast decoding algorithm and the performance of SCC, and the results demonstrate that the performance of SCC is better than those of RC, SM and SMP for indoor channels in general.

Home | BEopt

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BEopt - Building Energy Optimization BEopt NREL - National Renewable Energy Laboratory Primary Energy Optimization) software provides capabilities to evaluate residential building designs and identify sequential search optimization technique used by BEopt: Finds minimum-cost building designs at different

Character of intermolecular interaction in pyridine-argon complex: Ab initio potential energy surface, internal dynamics, and interrelations between SAPT energy components.

PubMed

Makarewicz, Jan; Shirkov, Leonid

2016-05-28

The pyridine-Ar (PAr) van der Waals (vdW) complex is studied using a high level ab initio method. Its structure, binding energy, and intermolecular vibrational states are determined from the analytical potential energy surface constructed from interaction energy (IE) values computed at the coupled cluster level of theory with single, double, and perturbatively included triple excitations with the augmented correlation consistent polarized valence double-ζ (aug-cc-pVDZ) basis set complemented by midbond functions. The structure of the complex at its global minimum with Ar at a distance of 3.509 Å from the pyridine plane and shifted by 0.218 Å from the center of mass towards nitrogen agrees well with the corresponding equilibrium structure derived previously from the rotational spectrum of PAr. The PAr binding energy De of 392 cm(-1) is close to that of 387 cm(-1) calculated earlier at the same ab initio level for the prototypical benzene-Ar (BAr) complex. However, under an extension of the basis set, De for PAr becomes slightly lower than De for BAr. The ab initio vdW vibrational energy levels allow us to estimate the reliability of the methods for the determination of the vdW fundamentals from the rotational spectra. To disclose the character of the intermolecular interaction in PAr, the symmetry-adapted perturbation theory (SAPT) is employed for the analysis of different physical contributions to IE. It is found that SAPT components of IE can be approximately expressed in the binding region by only two of them: the exchange repulsion and dispersion energy. The total induction effect is negligible. The interrelations between various SAPT components found for PAr are fulfilled for a few other complexes involving aromatic molecules and Ar or Ne, which indicates that they are valid for all rare gas (Rg) atoms and aromatics.

Stacked endoplasmic reticulum sheets are connected by helicoidal membrane motifs

PubMed Central

Terasaki, Mark; Shemesh, Tom; Kasthuri, Narayanan; Klemm, Robin W.; Schalek, Richard; Hayworth, Kenneth J.; Hand, Arthur R.; Yankova, Maya; Huber, Greg; Lichtman, Jeff W.; Rapoport, Tom A.; Kozlov, Michael M.

2013-01-01

The endoplasmic reticulum (ER) often forms stacked membrane sheets, an arrangement that is likely required to accommodate a maximum of membrane-bound polysomes for secretory protein synthesis. How sheets are stacked is unknown. Here, we used novel staining and automated ultra-thin sectioning electron microscopy methods to analyze stacked ER sheets in neuronal cells and secretory salivary gland cells of mice. Our results show that stacked ER sheets form a continuous membrane system in which the sheets are connected by twisted membrane surfaces with helical edges of left- or right-handedness. The three-dimensional structure of tightly stacked ER sheets resembles a parking garage, in which the different levels are connected by helicoidal ramps. A theoretical model explains the experimental observations and indicates that the structure corresponds to a minimum of elastic energy of sheet edges and surfaces. The structure allows the dense packing of ER sheets in the restricted space of a cell. PMID:23870120

Structural Expression of Exo-Anomeric Effect.

PubMed

Alonso, Elena R; Peña, Isabel; Cabezas, Carlos; Alonso, José L

2016-03-03

Structural signatures for exo-anomeric effect have been extracted from the archetypal methyl-β-D-xyloside using broadband Fourier transform microwave spectroscopy combined with laser ablation. Spectrum analysis allows the determination of a set of rotational constants, which has been unequivocally attributed to conformer cc-β-(4)C1 g-, corresponding to the global minimum of the potential energy surface, where the aglycon residue (CH3) orientation contributes to maximization of the exo-anomeric effect. Further analysis allowed the determination of the rs structure, based on the detection of 11 isotopologues--derived from the presence of six (13)C and five (18)O atoms--observed in their natural abundances. The observed glycosidic C1-O1 bond length decrease (1.38 Å) can be interpreted in terms of the exo-anomeric effect. As such, the exo-anomeric effect presents itself as one of the main driving forces controlling the shape of many biologically important oligosaccharides.

Ion acoustic solitons in an electronegative plasma with electron trapping and nonextensivity effects

NASA Astrophysics Data System (ADS)

Ali Shan, S.

2018-03-01

The impact of electron trapping and nonextensivity on the low frequency ion acoustic solitary waves in an electronegative plasma is investigated. The energy integral equation with the Sagdeev truncated approach is derived, which is then solved with the help of suitable parameters and necessary conditions to get the solitary structures. The minimum Mach (M) number needed to calculate the solitary structures is found to be varying under the impact of trapping efficiency determining factor β and entropic index q. The results have been illustrated with the help of physically acceptable parameters and the amplitude of nonlinear solitary structures is found to be modified significantly because of electron trapping efficiency β and entropic index q. This study has been made with reference to Laboratory observation, which can also be helpful in Space and astrophysical plasmas where electronegative plasmas have been reported.

Molecular tools for investigating microbial community structure and function in oxygen-deficient marine waters.

PubMed

Hawley, Alyse K; Kheirandish, Sam; Mueller, Andreas; Leung, Hilary T C; Norbeck, Angela D; Brewer, Heather M; Pasa-Tolic, Ljiljana; Hallam, Steven J

2013-01-01

Water column oxygen (O2)-deficiency shapes food-web structure by progressively directing nutrients and energy away from higher trophic levels into microbial community metabolism resulting in fixed nitrogen loss and greenhouse gas production. Although respiratory O2 consumption during organic matter degradation is a natural outcome of a productive surface ocean, global-warming-induced stratification intensifies this process leading to oxygen minimum zone (OMZ) expansion. Here, we describe useful tools for detection and quantification of potential key microbial players and processes in OMZ community metabolism including quantitative polymerase chain reaction primers targeting Marine Group I Thaumarchaeota, SUP05, Arctic96BD-19, and SAR324 small-subunit ribosomal RNA genes and protein extraction methods from OMZ waters compatible with high-resolution mass spectrometry for profiling microbial community structure and functional dynamics. © 2013 Elsevier Inc. All rights reserved.