Exploring structural properties of small carbon clusters Cn (n = 1, 2, 3) using molecular mechanics and energy minimization

NASA Astrophysics Data System (ADS)

Miswan, M. A.; Gopir, G.; Anas, M. M.

2016-11-01

Geometry optimization is one of the most widely used methods to study in carbon cluster Cn to understand its structural properties. The total energy for each of the structures was calculated using Octopus software with conjugate gradient Broyden-Fletcher-Goldfarb-Shanno (CG-BFGS). Our calculation and other studies indicate that the linear forms are the most stable structures. However, the C3 isomers have equal probability to form, as the differences in our calculation of total energy are statistically insignificant. Despite there are two cohort of total energy, the calculations are acceptable due to the energy ratio between C3 to C2 and C2 to C1 are comparable to others work. Meanwhile, the bond properties of the C2 and C3 bonds also gives significant difference between our work and previous study.

Portable microwave instrument for non-destructive evaluation of structural characteristics

DOEpatents

Bible, D.W.; Crutcher, R.I.; Sohns, C.W.; Maddox, S.R.

1995-01-24

A portable microwave instrument for evaluating characteristics of a structural member includes a source of microwave energy, a transmitter coupled to the source of microwave energy for transmitting a microwave signal at the structural member, and a receiver positioned on the same side of the structural member as the transmitter and being disposed to receive a microwave signal reflected by the structural member. A phase angle difference is determined between the transmitted microwave signal and the received microwave signal using a signal splitter and a balanced mixer. The difference in phase angle varies in accordance with differences in size, shape and locations of constituent materials within the structural member. 6 figures.

Free Energy and Structure of Helix-forming Peptides: A Theoretical Investigation

NASA Astrophysics Data System (ADS)

Karpusenka, Vadzim

This thesis focuses on the structure and free energy of helical secondary structures of short peptides in a variety of experimental settings. Specifically, the formation of alpha-, pi- and 310-helices was investigated using large-scale classical molecular dynamics simulations with state-of-the-art force fields. In addition, the recently developed Adaptively Biased Molecular Dynamics (ABMD) and Steered Molecular Dynamics (SMD) methods were used to calculate the corresponding free energies. The most important results are as follows. For the examined peptide homopolymers, the observed minima on the free energy landscapes (based on suitable collective variables such as the radius of gyration, number of hydrogen bonds, and handedness) were associated with alpha-helices and "globular" or "knot-like" configurations only. No evidence was found to indicate that 310- or pi-helices represent equilibrium structures for these systems. In addition, the free energy landscape of short peptide chains formed by mixing two different amino acids were also examined. These results too indicate that the alpha-helix is only equilibrium helical secondary structure, and that the mixing of different amino acids does not result in the introduction of any significant new minima into the free energy landscapes. These results are in agreement with experimental observations insofar as these indicate that helical structural motifs are primary based on alpha-helices, with 310- and pi-helices being observed only rarely. Although pi- and 310-helices represent nonequilibrium structures, we were still able to estimate their free energies by means of SMD simulations. The helical secondary structure of the examined polypeptide chains is due to the formation of hydrogen bonds. However, there are other mechanisms that may allow for the additional stabilization of these structures. Specifically, in the so-called AK-(4,7) protein, the possible presence of disulfide bonds connecting cysteine residues may significantly alter the free energy landscapes and therefore the stability of different helical structures. We therefore examined this issue with ABMD simulations. However, our results show that while the free energy landscapes are indeed significantly altered only the formation of alpha-helices is favored as a secondary structural motif. Since all the results indicate that alpha-helix formation dominates, it is natural to think in terms of an alpha-helix forming propensity for different amino acids. To address this question, we carried out an extensive residue-by-residue population analysis of different amino acid guests in an alanine-based host setting. Such an analysis allows us to rank the different amino acid guests based on whether they increased or decreased the population in the alpha-helix region of the corresponding Ramachandran plots. Our ranking of the different guest amino acids is in reasonable correspondence with the experimental results, although some differences are observed. Finally, using a four-beads coarse-grained model were have investigated the stability of GA88 and GB88 proteins, which are quite similar in terms of their amino acid sequence, by means of 10mus simulations. The results indicate that while the three alpha-helix bundle of the GA88 protein remains stable, the 2beta--alpha--2beta configuration of the GB88 protein does not: the latter rapidly converts to a structure consisting mostly of helices similar to the GA88 protein design. These results indicate that this particular four-bead coarse-grained model is not able to properly grasp the dynamics of the beta-sheet secondary structure and overstabilizes the corresponding helical content.

Global expression for representing cohesive-energy curves. II

NASA Technical Reports Server (NTRS)

Schlosser, Herbert; Ferrante, John

1993-01-01

Schlosser et al. (1991) showed that the R dependence of the cohesive energy of partially ionic solids may be characterized by a two-term energy relationship consisting of a Coulomb term arising from the charge transfer, delta-Z, and a scaled universal energy function, E*(a *), which accounts for the partially covalent character of the bond and for repulsion between the atomic cores for small R; a* is a scaled length. In the paper by Schlosser et al., the normalized cohesive-energy curves of NaCl-structure alkali-halide crystals were generated with this expression. In this paper we generate the cohesive-energy curves of several families of partially ionic solids with different crystal structures and differing degrees of ionicity. These include the CsCl-structure Cs halides, and the Tl and Ag halides, which have weaker ionic bonding than the alkali halides, and which have the CsCl and NaCl structures, respectively. The cohesive-energy-curve parameters are then used to generate theoretical isothermal compression curves for the Li, Na, K, Cs, and Ag halides. We find good agreement with the available experimental compression data.

Energy Services Company | Climate Neutral Research Campuses | NREL

Science.gov Websites

different corporate and ownership structures. While many are large engineering or equipment manufacturers Services Company Options Performance-based contracts can take different forms including guaranteed energy different financing options for energy performance contracting, please refer to page 13 of the April 2009

The role of confined collagen geometry in decreasing nucleation energy barriers to intrafibrillar mineralization.

PubMed

Kim, Doyoon; Lee, Byeongdu; Thomopoulos, Stavros; Jun, Young-Shin

2018-03-06

Mineralization of collagen is critical for the mechanical functions of bones and teeth. Calcium phosphate nucleation in collagenous structures follows distinctly different patterns in highly confined gap regions (nanoscale confinement) than in less confined extrafibrillar spaces (microscale confinement). Although the mechanism(s) driving these differences are still largely unknown, differences in the free energy for nucleation may explain these two mineralization behaviors. Here, we report on experimentally obtained nucleation energy barriers to intra- and extrafibrillar mineralization, using in situ X-ray scattering observations and classical nucleation theory. Polyaspartic acid, an extrafibrillar nucleation inhibitor, increases interfacial energies between nuclei and mineralization fluids. In contrast, the confined gap spaces inside collagen fibrils lower the energy barrier by reducing the reactive surface area of nuclei, decreasing the surface energy penalty. The confined gap geometry, therefore, guides the two-dimensional morphology and structure of bioapatite and changes the nucleation pathway by reducing the total energy barrier.

Structural expansions for the ground state energy of a simple metal

NASA Technical Reports Server (NTRS)

Hammerberg, J.; Ashcroft, N. W.

1973-01-01

A structural expansion for the static ground state energy of a simple metal is derived. An approach based on single particle band structure which treats the electron gas as a non-linear dielectric is presented, along with a more general many particle analysis using finite temperature perturbation theory. The two methods are compared, and it is shown in detail how band-structure effects, Fermi surface distortions, and chemical potential shifts affect the total energy. These are of special interest in corrections to the total energy beyond third order in the electron ion interaction, and hence to systems where differences in energies for various crystal structures are exceptionally small. Preliminary calculations using these methods for the zero temperature thermodynamic functions of atomic hydrogen are reported.

What can wave energy learn from offshore oil and gas?

PubMed

Jefferys, E R

2012-01-28

This title may appear rather presumptuous in the light of the progress made by the leading wave energy devices. However, there may still be some useful lessons to be learnt from current 'offshore' practice, and there are certainly some awful warnings from the past. Wave energy devices and the marine structures used in oil and gas exploration as well as production share a common environment and both are subject to wave, wind and current loads, which may be evaluated with well-validated, albeit imperfect, tools. Both types of structure can be designed, analysed and fabricated using similar tools and technologies. They fulfil very different missions and are subject to different economic and performance requirements; hence 'offshore' design tools must be used appropriately in wave energy project and system design, and 'offshore' cost data should be adapted for 'wave' applications. This article reviews the similarities and differences between the fields and highlights the differing economic environments; offshore structures are typically a small to moderate component of field development cost, while wave power devices will dominate overall system cost. The typical 'offshore' design process is summarized and issues such as reliability-based design and design of not normally manned structures are addressed. Lessons learned from poor design in the past are discussed to highlight areas where care is needed, and wave energy-specific design areas are reviewed. Opportunities for innovation and optimization in wave energy project and device design are discussed; wave energy projects must ultimately compete on a level playing field with other routes to low CO₂ energy and/or energy efficiency. This article is a personal viewpoint and not an expression of a ConocoPhillips position.

Characterization of Ultrasound Energy Diffusion Due to Small-Size Damage on an Aluminum Plate Using Piezoceramic Transducers

PubMed Central

Lu, Guangtao; Feng, Qian; Li, Yourong; Wang, Hao; Song, Gangbing

2017-01-01

During the propagation of ultrasonic waves in structures, there is usually energy loss due to ultrasound energy diffusion and dissipation. The aim of this research is to characterize the ultrasound energy diffusion that occurs due to small-size damage on an aluminum plate using piezoceramic transducers, for the future purpose of developing a damage detection algorithm. The ultrasonic energy diffusion coefficient is related to the damage distributed in the medium. Meanwhile, the ultrasonic energy dissipation coefficient is related to the inhomogeneity of the medium. Both are usually employed to describe the characteristics of ultrasound energy diffusion. The existence of multimodes of Lamb waves in metallic plate structures results in the asynchronous energy transport of different modes. The mode of Lamb waves has a great influence on ultrasound energy diffusion as a result, and thus has to be chosen appropriately. In order to study the characteristics of ultrasound energy diffusion in metallic plate structures, an experimental setup of an aluminum plate with a through-hole, whose diameter varies from 0.6 mm to 1.2 mm, is used as the test specimen with the help of piezoceramic transducers. The experimental results of two categories of damages at different locations reveal that the existence of damage changes the energy transport between the actuator and the sensor. Also, when there is only one dominate mode of Lamb wave excited in the structure, the ultrasound energy diffusion coefficient decreases approximately linearly with the diameter of the simulated damage. Meanwhile, the ultrasonic energy dissipation coefficient increases approximately linearly with the diameter of the simulated damage. However, when two or more modes of Lamb waves are excited, due to the existence of different group velocities between the different modes, the energy transport of the different modes is asynchronous, and the ultrasonic energy diffusion is not strictly linear with the size of the damage. Therefore, it is recommended that only one dominant mode of Lamb wave should be excited during the characterization process, in order to ensure that the linear relationship between the damage size and the characteristic parameters is maintained. In addition, the findings from this paper demonstrate the potential of developing future damage detection algorithms using the linear relationships between damage size and the ultrasound energy diffusion coefficient or ultrasonic energy dissipation coefficient when a single dominant mode is excited. PMID:29207530

The Power of Micro Urban Structures, Theory of EEPGC - the Micro Urban Energy Distribution Model as a Planning Tool for Sustainable City Development

NASA Astrophysics Data System (ADS)

Tkáč, Štefan

2015-11-01

To achieve the smart growth and equitable development in the region, urban planners should consider also lateral energies represented by the energy urban models like further proposed EEPGC focused on energy distribution via connections among micro-urban structures, their onsite renewable resources and the perception of micro-urban structures as decentralized energy carriers based on pre industrialized era. These structures are still variously bound when part of greater patterns. After the industrial revolution the main traded goods became energy in its various forms. The EEPGC is focused on sustainable energy transportation distances between the villages and the city, described by the virtual "energy circles". This more human scale urbanization, boost the economy in micro-urban areas, rising along with clean energy available in situ that surely gives a different perspective to human quality of life in contrast to overcrowded multicultural mega-urban structures facing generations of problems and struggling to survive as a whole.

Time tracking and interaction of energy-eddies at different scales

NASA Astrophysics Data System (ADS)

Cardesa, Jose I.; Vela-Martin, Alberto; Jimenez, Javier

2016-11-01

We study the energy cascade through coherent structures obtained in time-resolved simulations of incompressible, statistically steady isotropic turbulence. The structures are defined as geometrically connected regions of the flow with high kinetic energy. We compute the latter by band-pass filtering the velocity field around a scale r. We analyse the dynamics of structures extracted with different r, which are a proxy for eddies containing energy at those r. We find that the size of these "energy-eddies" scales with r, while their lifetime scales with the local eddy-turnover r 2 / 3ɛ - 1 / 3 , where ɛ is the energy dissipation averaged over all space and time. Furthermore, a statistical analysis over the lives of the eddies shows a slight predominance of the splitting over the merging process. When we isolate the eddies which do not interact with other eddies of the same scale, we observe a parent-child dependence by which, on average, structures are born at scale r during the decaying part of the life of a structure at scale r' > r . The energy-eddy at r' lives in the same region of space as that at r. Finally, we investigate how interactions between eddies at the same scale are echoed across other scales. Funded by the ERC project Coturb.

Effects of geometrical structure on spatial distribution of thermal energy in two-dimensional triangular lattices

NASA Astrophysics Data System (ADS)

Liu, Yong-Yang; Xu, Yu-Liang; Liu, Zhong-Qiang; Li, Jing; Wang, Chun-Yang; Kong, Xiang-Mu

2018-07-01

Employing the correlation matrix technique, the spatial distribution of thermal energy in two-dimensional triangular lattices in equilibrium, interacting with linear springs, is studied. It is found that the spatial distribution of thermal energy varies with the included angle of the springs. In addition, the average thermal energy of the longer springs is lower. Springs with different included angle and length will lead to an inhomogeneous spatial distribution of thermal energy. This suggests that the spatial distribution of thermal energy is affected by the geometrical structure of the system: the more asymmetric the geometrical structure of the system is, the more inhomogeneous is the spatial distribution of thermal energy.

Allosteric Ligand Binding and Anisotropic Energy Flow in Albumin

NASA Astrophysics Data System (ADS)

Dyer, Brian

2014-03-01

Protein allostery usually involves propagation of local structural changes through the protein to a remote site. Coupling of structural changes at remote sites is thought to occur through anisotropic energy transport, but the nature of this process is poorly understood. We have studied the relationship between allosteric interactions of remote ligand binding sites of the protein and energy flow through the structure of bovine serum albumin (BSA). We applied ultrafast infrared spectroscopy to probe the flow of energy through the protein backbone following excitation of a heater dye, a metalloporphyrin or malachite green, bound to different binding sites in the protein. We observe ballistic flow through the protein structure following input of thermal energy into the flexible ligand binding sites. We also observe anisotropic heat flow through the structure, without local heating of the rigid helix bundles that connect these sites. We will discuss the implications of this efficient energy transport mechanism with regard to the allosteric propagation of binding energy through the connecting helix structures.

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.

Modulation of Small-scale Turbulence Structure by Large-scale Motions in the Absence of Direct Energy Transfer.

NASA Astrophysics Data System (ADS)

Brasseur, James G.; Juneja, Anurag

1996-11-01

Previous DNS studies indicate that small-scale structure can be directly altered through ``distant'' dynamical interactions by energetic forcing of the large scales. To remove the possibility of stimulating energy transfer between the large- and small-scale motions in these long-range interactions, we here perturb the large scale structure without altering its energy content by suddenly altering only the phases of large-scale Fourier modes. Scale-dependent changes in turbulence structure appear as a non zero difference field between two simulations from identical initial conditions of isotropic decaying turbulence, one perturbed and one unperturbed. We find that the large-scale phase perturbations leave the evolution of the energy spectrum virtually unchanged relative to the unperturbed turbulence. The difference field, on the other hand, is strongly affected by the perturbation. Most importantly, the time scale τ characterizing the change in in turbulence structure at spatial scale r shortly after initiating a change in large-scale structure decreases with decreasing turbulence scale r. Thus, structural information is transferred directly from the large- to the smallest-scale motions in the absence of direct energy transfer---a long-range effect which cannot be explained by a linear mechanism such as rapid distortion theory. * Supported by ARO grant DAAL03-92-G-0117

Far-Zone Resonant Energy Transfer in X-ray Photoemission as a Structure Determination Tool.

PubMed

Céolin, Denis; Rueff, Jean-Pascal; Zimin, Andrey; Morin, Paul; Kimberg, Victor; Polyutov, Sergey; Ågren, Hans; Gel'mukhanov, Faris

2017-06-15

Near-zone Förster resonant energy transfer is the main effect responsible for excitation energy flow in the optical region and is frequently used to obtain structural information. In the hard X-ray region, the Förster law is inadequate because the wavelength is generally shorter than the distance between donors and acceptors; hence, far-zone resonant energy transfer (FZRET) becomes dominant. We demonstrate the characteristics of X-ray FZRET and its fundamental differences with the ordinary near-zone resonant energy-transfer process in the optical region by recording and analyzing two qualitatively different systems: high-density CuO polycrystalline powder and SF 6 diluted gas. We suggest a method to estimate geometrical structure using X-ray FZRET employing as a ruler the distance-dependent shift of the acceptor core ionization potential induced by the Coulomb field of the core-ionized donor.

Retrospective and Prospective Decomposition Analysis of Chinese Manufacturing Energy Use, 1995-2020

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

Hasanbeigi, Ali; Price, Lynn; Fino-Chen, Cecilia

In 2010, China was responsible for nearly 20 percent of global energy use and 25 percent of energy-related carbon dioxide (CO 2) emissions. Unlike most countries, China’s energy consumption pattern is unique because the industrial sector dominates the country’s total energy consumption, accounting for about 70 percent of energy use and 72 percent of CO 2 emissions in 2010. For this reason, the development path of China’s industrial sector will greatly affect future energy demand and dynamics of not only China, but the entire world. A number of analyses of historical trends have been conducted, but careful projections of themore » key factors affecting China’s industry sector energy use over the next decade are scarce. This study analyzes industrial energy use and the economic structure of the Chinese manufacturing sector in detail. First, the study analyzes the energy use of and output from 18 industry sub-sectors. Then, retrospective (1995-2010) and prospective (2010-2020) decomposition analyses are conducted for these industrial sectors in order to show how different factors (production growth, structural change, and energy intensity change) influenced industrial energy use trends in China over the last 15 years and how they will do so over the next 10 years. The results of this study will allow policy makers to quantitatively compare the level of structural change in the past and in the years to come and adjust their policies if needed to move towards the target of less energy-intensive industries. The scenario analysis shows the structural change achieved through different paths and helps to understand the consequences of supporting or limiting the growth of certain manufacturing subsectors from the point of view of energy use and structural change. The results point out the industries that have the largest influence in such structural change« less

Anisotropic energy flow and allosteric ligand binding in albumin

NASA Astrophysics Data System (ADS)

Li, Guifeng; Magana, Donny; Dyer, R. Brian

2014-01-01

Allosteric interactions in proteins generally involve propagation of local structural changes through the protein to a remote site. Anisotropic energy transport is thought to couple the remote sites, but the nature of this process is poorly understood. Here, we report the relationship between energy flow through the structure of bovine serum albumin and allosteric interactions between remote ligand binding sites of the protein. Ultrafast infrared spectroscopy is used to probe the flow of energy through the protein backbone following excitation of a heater dye, a metalloporphyrin or malachite green, bound to different binding sites in the protein. We observe ballistic and anisotropic energy flow through the protein structure following input of thermal energy into the flexible ligand binding sites, without local heating of the rigid helix bundles that connect these sites. This efficient energy transport mechanism enables the allosteric propagation of binding energy through the connecting helix structures.

Anisotropic energy flow and allosteric ligand binding in albumin.

PubMed

Li, Guifeng; Magana, Donny; Dyer, R Brian

2014-01-01

Allosteric interactions in proteins generally involve propagation of local structural changes through the protein to a remote site. Anisotropic energy transport is thought to couple the remote sites, but the nature of this process is poorly understood. Here, we report the relationship between energy flow through the structure of bovine serum albumin and allosteric interactions between remote ligand binding sites of the protein. Ultrafast infrared spectroscopy is used to probe the flow of energy through the protein backbone following excitation of a heater dye, a metalloporphyrin or malachite green, bound to different binding sites in the protein. We observe ballistic and anisotropic energy flow through the protein structure following input of thermal energy into the flexible ligand binding sites, without local heating of the rigid helix bundles that connect these sites. This efficient energy transport mechanism enables the allosteric propagation of binding energy through the connecting helix structures.

Anisotropic energy flow and allosteric ligand binding in albumin

PubMed Central

Li, Guifeng; Magana, Donny; Dyer, R. Brian

2014-01-01

Allosteric interactions in proteins generally involve propagation of local structural changes through the protein to a remote site. Anisotropic energy transport is thought to couple the remote sites, but the nature of this process is poorly understood. Here, we report the relationship between energy flow through the structure of bovine serum albumin and allosteric interactions between remote ligand binding sites of the protein. Ultrafast infrared spectroscopy is used to probe the flow of energy through the protein backbone following excitation of a heater dye, a metalloporphyrin or malachite green, bound to different binding sites in the protein. We observe ballistic and anisotropic energy flow through the protein structure following input of thermal energy into the flexible ligand binding sites, without local heating of the rigid helix bundles that connect these sites. This efficient energy transport mechanism enables the allosteric propagation of binding energy through the connecting helix structures. PMID:24445265

Protein loop modeling using a new hybrid energy function and its application to modeling in inaccurate structural environments.

PubMed

Park, Hahnbeom; Lee, Gyu Rie; Heo, Lim; Seok, Chaok

2014-01-01

Protein loop modeling is a tool for predicting protein local structures of particular interest, providing opportunities for applications involving protein structure prediction and de novo protein design. Until recently, the majority of loop modeling methods have been developed and tested by reconstructing loops in frameworks of experimentally resolved structures. In many practical applications, however, the protein loops to be modeled are located in inaccurate structural environments. These include loops in model structures, low-resolution experimental structures, or experimental structures of different functional forms. Accordingly, discrepancies in the accuracy of the structural environment assumed in development of the method and that in practical applications present additional challenges to modern loop modeling methods. This study demonstrates a new strategy for employing a hybrid energy function combining physics-based and knowledge-based components to help tackle this challenge. The hybrid energy function is designed to combine the strengths of each energy component, simultaneously maintaining accurate loop structure prediction in a high-resolution framework structure and tolerating minor environmental errors in low-resolution structures. A loop modeling method based on global optimization of this new energy function is tested on loop targets situated in different levels of environmental errors, ranging from experimental structures to structures perturbed in backbone as well as side chains and template-based model structures. The new method performs comparably to force field-based approaches in loop reconstruction in crystal structures and better in loop prediction in inaccurate framework structures. This result suggests that higher-accuracy predictions would be possible for a broader range of applications. The web server for this method is available at http://galaxy.seoklab.org/loop with the PS2 option for the scoring function.

The role of confined collagen geometry in decreasing nucleation energy barriers to intrafibrillar mineralization

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

Kim, Doyoon; Lee, Byeongdu; Thomopoulos, Stavros

Mineralization of collagen is critical for the mechanical functions of bones and teeth. Calcium phosphate nucleation in collagenous structures follows distinctly different patterns in highly confined gap regions (nanoscale confinement) than in less confined extrafibrillar spaces (microscale confinement). Although the mechanism(s) driving these differences are still largely unknown, differences in the free energy for nucleation may explain these two mineralization behaviors. Here, we report on experimentally obtained nucleation energy barriers to intra- and extrafibrillar mineralization, using in situ X-ray scattering observations and classical nucleation theory. Polyaspartic acid, an extrafibrillar nucleation inhibitor, increases interfacial energies between nuclei and mineralization fluids. Inmore » contrast, the confined gap spaces inside collagen fibrils lower the energy barrier by reducing the reactive surface area of nuclei, decreasing the surface energy penalty. The confined gap geometry, therefore, guides the two-dimensional morphology and structure of bioapatite and changes the nucleation pathway by reducing the total energy barrier.« less

The role of confined collagen geometry in decreasing nucleation energy barriers to intrafibrillar mineralization

DOE PAGES

Kim, Doyoon; Lee, Byeongdu; Thomopoulos, Stavros; ...

2018-03-06

Mineralization of collagen is critical for the mechanical functions of bones and teeth. Calcium phosphate nucleation in collagenous structures follows distinctly different patterns in highly confined gap regions (nanoscale confinement) than in less confined extrafibrillar spaces (microscale confinement). Although the mechanism(s) driving these differences are still largely unknown, differences in the free energy for nucleation may explain these two mineralization behaviors. Here, we report on experimentally obtained nucleation energy barriers to intra- and extrafibrillar mineralization, using in situ X-ray scattering observations and classical nucleation theory. Polyaspartic acid, an extrafibrillar nucleation inhibitor, increases interfacial energies between nuclei and mineralization fluids. Inmore » contrast, the confined gap spaces inside collagen fibrils lower the energy barrier by reducing the reactive surface area of nuclei, decreasing the surface energy penalty. The confined gap geometry, therefore, guides the two-dimensional morphology and structure of bioapatite and changes the nucleation pathway by reducing the total energy barrier.« less

Ground-state energies of simple metals

NASA Technical Reports Server (NTRS)

Hammerberg, J.; Ashcroft, N. W.

1974-01-01

A structural expansion for the static ground-state energy of a simple metal is derived. Two methods are presented, one an approach based on single-particle band structure which treats the electron gas as a nonlinear dielectric, the other a more general many-particle analysis using finite-temperature perturbation theory. The two methods are compared, and it is shown in detail how band-structure effects, Fermi-surface distortions, and chemical-potential shifts affect the total energy. These are of special interest in corrections to the total energy beyond third order in the electron-ion interaction and hence to systems where differences in energies for various crystal structures are exceptionally small. Preliminary calculations using these methods for the zero-temperature thermodynamic functions of atomic hydrogen are reported.

A study of photomodulated reflectance on staircase-like, n-doped GaAs/AlxGa1−xAs quantum well structures

PubMed Central

2012-01-01

In this study, photomodulated reflectance (PR) technique was employed on two different quantum well infrared photodetector (QWIP) structures, which consist of n-doped GaAs quantum wells (QWs) between undoped AlxGa1−xAs barriers with three different x compositions. Therefore, the barrier profile is in the form of a staircase-like barrier. The main difference between the two structures is the doping profile and the doping concentration of the QWs. PR spectra were taken at room temperature using a He-Ne laser as a modulation source and a broadband tungsten halogen lamp as a probe light. The PR spectra were analyzed using Aspnes’ third derivative functional form. Since the barriers are staircase-like, the structure has different ground state energies; therefore, several optical transitions take place in the spectrum which cannot be resolved in a conventional photoluminescence technique at room temperature. To analyze the experimental results, all energy levels in the conduction and in the valance band were calculated using transfer matrix technique, taking into account the effective mass and the parabolic band approximations. A comparison of the PR results with the calculated optical transition energies showed an excellent agreement. Several optical transition energies of the QWIP structures were resolved from PR measurements. It is concluded that PR spectroscopy is a very useful experimental tool to characterize complicated structures with a high accuracy at room temperature. PMID:23146126

A study of photomodulated reflectance on staircase-like, n-doped GaAs/AlxGa1-xAs quantum well structures.

PubMed

Donmez, Omer; Nutku, Ferhat; Erol, Ayse; Arikan, Cetin M; Ergun, Yuksel

2012-11-12

In this study, photomodulated reflectance (PR) technique was employed on two different quantum well infrared photodetector (QWIP) structures, which consist of n-doped GaAs quantum wells (QWs) between undoped AlxGa1-xAs barriers with three different x compositions. Therefore, the barrier profile is in the form of a staircase-like barrier. The main difference between the two structures is the doping profile and the doping concentration of the QWs. PR spectra were taken at room temperature using a He-Ne laser as a modulation source and a broadband tungsten halogen lamp as a probe light. The PR spectra were analyzed using Aspnes' third derivative functional form.Since the barriers are staircase-like, the structure has different ground state energies; therefore, several optical transitions take place in the spectrum which cannot be resolved in a conventional photoluminescence technique at room temperature. To analyze the experimental results, all energy levels in the conduction and in the valance band were calculated using transfer matrix technique, taking into account the effective mass and the parabolic band approximations. A comparison of the PR results with the calculated optical transition energies showed an excellent agreement. Several optical transition energies of the QWIP structures were resolved from PR measurements. It is concluded that PR spectroscopy is a very useful experimental tool to characterize complicated structures with a high accuracy at room temperature.

A study of photomodulated reflectance on staircase-like, n-doped GaAs/Al x Ga1- x As quantum well structures

NASA Astrophysics Data System (ADS)

Donmez, Omer; Nutku, Ferhat; Erol, Ayse; Arikan, Cetin M.; Ergun, Yuksel

2012-11-01

In this study, photomodulated reflectance (PR) technique was employed on two different quantum well infrared photodetector (QWIP) structures, which consist of n-doped GaAs quantum wells (QWs) between undoped Al x Ga1- x As barriers with three different x compositions. Therefore, the barrier profile is in the form of a staircase-like barrier. The main difference between the two structures is the doping profile and the doping concentration of the QWs. PR spectra were taken at room temperature using a He-Ne laser as a modulation source and a broadband tungsten halogen lamp as a probe light. The PR spectra were analyzed using Aspnes' third derivative functional form. Since the barriers are staircase-like, the structure has different ground state energies; therefore, several optical transitions take place in the spectrum which cannot be resolved in a conventional photoluminescence technique at room temperature. To analyze the experimental results, all energy levels in the conduction and in the valance band were calculated using transfer matrix technique, taking into account the effective mass and the parabolic band approximations. A comparison of the PR results with the calculated optical transition energies showed an excellent agreement. Several optical transition energies of the QWIP structures were resolved from PR measurements. It is concluded that PR spectroscopy is a very useful experimental tool to characterize complicated structures with a high accuracy at room temperature.

Predicting helix orientation for coiled-coil dimers

PubMed Central

Apgar, James R.; Gutwin, Karl N.; Keating, Amy E.

2008-01-01

The alpha-helical coiled coil is a structurally simple protein oligomerization or interaction motif consisting of two or more alpha helices twisted into a supercoiled bundle. Coiled coils can differ in their stoichiometry, helix orientation and axial alignment. Because of the near degeneracy of many of these variants, coiled coils pose a challenge to fold recognition methods for structure prediction. Whereas distinctions between some protein folds can be discriminated on the basis of hydrophobic/polar patterning or secondary structure propensities, the sequence differences that encode important details of coiled-coil structure can be subtle. This is emblematic of a larger problem in the field of protein structure and interaction prediction: that of establishing specificity between closely similar structures. We tested the behavior of different computational models on the problem of recognizing the correct orientation - parallel vs. antiparallel - of pairs of alpha helices that can form a dimeric coiled coil. For each of 131 examples of known structure, we constructed a large number of both parallel and antiparallel structural models and used these to asses the ability of five energy functions to recognize the correct fold. We also developed and tested three sequenced-based approaches that make use of varying degrees of implicit structural information. The best structural methods performed similarly to the best sequence methods, correctly categorizing ∼81% of dimers. Steric compatibility with the fold was important for some coiled coils we investigated. For many examples, the correct orientation was determined by smaller energy differences between parallel and antiparallel structures distributed over many residues and energy components. Prediction methods that used structure but incorporated varying approximations and assumptions showed quite different behaviors when used to investigate energetic contributions to orientation preference. Sequence based methods were sensitive to the choice of residue-pair interactions scored. PMID:18506779

Excitation energy shift and size difference of low-energy levels in p -shell Λ hypernuclei

NASA Astrophysics Data System (ADS)

Kanada-En'yo, Yoshiko

2018-02-01

Structures of low-lying 0 s -orbit Λ states in p -shell Λ hypernuclei (ZAΛ) are investigated by applying microscopic cluster models for nuclear structure and a single-channel folding potential model for a Λ particle. For A >10 systems, the size reduction of core nuclei is small, and the core polarization effect is regarded as a higher-order perturbation in the Λ binding. The present calculation qualitatively describes the systematic trend of experimental data for excitation energy change from Z-1A to ZAΛ, in A >10 systems. The energy change shows a clear correlation with the nuclear size difference between the ground and excited states. In Li7Λ and Be9Λ, the significant shrinkage of cluster structures occurs consistently with the prediction of other calculations.

Diagnosing the influence of model structure on the simulation of water, energy and carbon fluxes on bark beetle infested forests

NASA Astrophysics Data System (ADS)

Gochis, D. J.; Gutmann, E. D.; Brooks, P. D.; Reed, D. E.; Ewers, B. E.; Pendall, E.; Biederman, J. A.; Harpold, A. A.; Barnard, H. R.; Hu, J.

2011-12-01

Forest dynamics induced by insect infestation can have a significant, local impact on plant physiological regulation of water, energy and carbon fluxes. Rapid mortality succeeded by more gradually varying land cover changes are presently thought to initiate a cascade of changes to water, energy and carbon budgets at the forest stand scale. Initial model sensitivity results have suggested very strong changes in land-atmosphere exchanges of these variables. Specifically, model results from the Noah land surface model, a relatively simple model, have suggested that loss of transpiration function may result in a nearly 50% increase in seasonal soil moisture values and similar increases in runoff production for locations in the central Rocky Mountains. However, differing model structures, such as the representation of plant canopy architecture, snowpack dynamics, dynamic vegetation and hillslope hydrologic processes, may significantly confound the synthesis of results from different modeling systems. We assess the performance of new suite of model simulations from three different land surface models of differing model structures and complexity levels against a comprehensive set of field observations of land surface flux and state variables. The focus of the analysis is in diagnosing how model structure influences changes in energy, water and carbon budget partitioning prior to and following insect infestation. Specific emphasis in this presentation is placed on verifying variables that characterize top of canopy and within canopy energy and water fluxes. We conclude the presentation with a set of recommendations about the advantages and disadvantages of various model structures in their simulation of insect driven forest dynamics.

Characterization of seismic hazard and structural response by energy flux

USGS Publications Warehouse

Afak, E.

2000-01-01

Seismic safety of structures depends on the structure's ability to absorb the seismic energy that is transmitted from ground to structure. One parameter that can be used to characterize seismic energy is the energy flux. Energy flux is defined as the amount of energy transmitted per unit time through a cross-section of a medium, and is equal to kinetic energy multiplied by the propagation velocity of seismic waves. The peak or the integral of energy flux can be used to characterize ground motions. By definition, energy flux automatically accounts for site amplification. Energy flux in a structure can be studied by formulating the problem as a wave propagation problem. For buildings founded on layered soil media and subjected to vertically incident plane shear waves, energy flux equations are derived by modeling the buildings as an extension of the layered soil medium, and considering each story as another layer. The propagation of energy flux in the layers is described in terms of the upgoing and downgoing energy flux in each layer, and the energy reflection and transmission coefficients at each interface. The formulation results in a pair of simple finite-difference equations for each layer, which can be solved recursively starting from the bedrock. The upgoing and downgoing energy flux in the layers allows calculation of the energy demand and energy dissipation in each layer. The methodology is applicable to linear, as well as nonlinear structures. ?? 2000 Published by Elsevier Science Ltd.

Investigation of a cantilever structured piezoelectric energy harvester used for wearable devices with random vibration input

NASA Astrophysics Data System (ADS)

Bai, Yang; Tofel, Pavel; Hadas, Zdenek; Smilek, Jan; Losak, Petr; Skarvada, Pavel; Macku, Robert

2018-06-01

The capability of using a linear kinetic energy harvester - A cantilever structured piezoelectric energy harvester - to harvest human motions in the real-life activities is investigated. The whole loop of the design, simulation, fabrication and test of the energy harvester is presented. With the smart wristband/watch sized energy harvester, a root mean square of the output power of 50 μW is obtained from the real-life hand-arm motion in human's daily life. Such a power is enough to make some low power consumption sensors to be self-powered. This paper provides a good and reliable comparison to those with nonlinear structures. It also helps the designers to consider whether to choose a nonlinear structure or not in a particular energy harvester based on different application scenarios.

Complexes of a Zn-metalloenzyme binding site with hydroxamate-containing ligands. A case for detailed benchmarkings of polarizable molecular mechanics/dynamics potentials when the experimental binding structure is unknown.

PubMed

Gresh, Nohad; Perahia, David; de Courcy, Benoit; Foret, Johanna; Roux, Céline; El-Khoury, Lea; Piquemal, Jean-Philip; Salmon, Laurent

2016-12-15

Zn-metalloproteins are a major class of targets for drug design. They constitute a demanding testing ground for polarizable molecular mechanics/dynamics aimed at extending the realm of quantum chemistry (QC) to very long-duration molecular dynamics (MD). The reliability of such procedures needs to be demonstrated upon comparing the relative stabilities of competing candidate complexes of inhibitors with the recognition site stabilized in the course of MD. This could be necessary when no information is available regarding the experimental structure of the inhibitor-protein complex. Thus, this study bears on the phosphomannose isomerase (PMI) enzyme, considered as a potential therapeutic target for the treatment of several bacterial and parasitic diseases. We consider its complexes with 5-phospho-d-arabinonohydroxamate and three analog ligands differing by the number and location of their hydroxyl groups. We evaluate the energy accuracy expectable from a polarizable molecular mechanics procedure, SIBFA. This is done by comparisons with ab initio quantum-chemistry (QC) calculations in the following cases: (a) the complexes of the four ligands in three distinct structures extracted from the entire PMI-ligand energy-minimized structures, and totaling up to 264 atoms; (b) the solvation energies of several energy-minimized complexes of each ligand with a shell of 64 water molecules; (c) the conformational energy differences of each ligand in different conformations characterized in the course of energy-minimizations; and (d) the continuum solvation energies of the ligands in different conformations. The agreements with the QC results appear convincing. On these bases, we discuss the prospects of applying the procedure to ligand-macromolecule recognition problems. © 2016 Wiley Periodicals, Inc. © 2016 Wiley Periodicals, Inc.

An Energy Integrated Dispatching Strategy of Multi- energy Based on Energy Internet

NASA Astrophysics Data System (ADS)

Jin, Weixia; Han, Jun

2018-01-01

Energy internet is a new way of energy use. Energy internet achieves energy efficiency and low cost by scheduling a variety of different forms of energy. Particle Swarm Optimization (PSO) is an advanced algorithm with few parameters, high computational precision and fast convergence speed. By improving the parameters ω, c1 and c2, PSO can improve the convergence speed and calculation accuracy. The objective of optimizing model is lowest cost of fuel, which can meet the load of electricity, heat and cold after all the renewable energy is received. Due to the different energy structure and price in different regions, the optimization strategy needs to be determined according to the algorithm and model.

Intramolecular energies of the cytotoxic protein CagA of Helicobacter pylori as a possible descriptor of strains' pathogenicity level.

PubMed

Rojas-Rengifo, Diana F; Alvarez-Silva, Maria Camila; Ulloa-Guerrero, Cindy P; Nuñez-Velez, Vanessa Lucía; Del Pilar Delgado, Maria; Aguilera, Sonia Milena; Castro, Harold; Jaramillo, Carlos Alberto; Fernando González Barrios, Andrés

2018-05-25

The Helicobacter pylori cytotoxin-associated gene A (CagA) is known for causing gastroduodenal diseases, such as atrophic gastritis and peptic ulcerations. Furthermore Helicobacter pylori CagA positive strains has been reported as one of the main risk factors for gastric cancer (Parsonnet et al., 1997). Structural variations in the CagA structure can alter its affinity with the host proteins, inducing differences in the pathogenicity of H. pylori. CagA N-terminal region is characterized for be conserved among all H. pylori strains since the C-terminal region is characterized by an intrinsically disorder behavior. We generated complete structural models of CagA using different conformations of the C-terminal region for two H. pylori strains. These models contain the same EPIYA (ABC 1 C 2 ) motifs but different level of pathogenicity: gastric cancer and duodenal ulcer. Using these structural models we evaluated the pathogenicity level of the H. pylori strain, based on the affinity of the interaction with SHP-2 and Grb2 receptors and on the number of interactions with the EPIYA motif. We found that the main differences in the interaction was due to the contributions of certain types of energies from each strain and not from the total energy of the molecule. Specifically, the electrostatic energy, helix dipole energy, Wander Waals clashes, torsional clash, backbone clash and cis bond energy allowed a separation between severe and mild pathology for the interaction of only CagA with SHP2. Copyright © 2018 Elsevier Ltd. All rights reserved.

Thermodynamics of inversion-domain boundaries in aluminum nitride: Interplay between interface energy and electric dipole potential energy

NASA Astrophysics Data System (ADS)

Zhang, J. Y.; Xie, Y. P.; Guo, H. B.; Chen, Y. G.

2018-05-01

Aluminum nitride (AlN) has a polar crystal structure that is susceptible to electric dipolar interactions. The inversion domains in AlN, similar to those in GaN and other wurtzite-structure materials, decrease the energy associated with the electric dipolar interactions at the expense of inversion-domain boundaries, whose interface energy has not been quantified. We study the atomic structures of six different inversion-domain boundaries in AlN, and compare their interface energies from density functional theory calculations. The low-energy interfaces have atomic structures with similar bonding geometry as those in the bulk phase, while the high-energy interfaces contain N-N wrong bonds. We calculate the formation energy of an inversion domain using the interface energy and dipoles' electric-field energy, and find that the distribution of the inversion domains is an important parameter for the microstructures of AlN films. Using this thermodynamic model, it is possible to control the polarity and microstructure of AlN films by tuning the distribution of an inversion-domain nucleus and by selecting the low-energy synthesis methods.

Quantum chemical ab initio prediction of proton exchange barriers between CH{sub 4} and different H-zeolites

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

Tuma, Christian; Sauer, Joachim, E-mail: js@chemie.hu-berlin.de

2015-09-14

A hybrid MP2:DFT (second-order Møller–Plesset perturbation theory–density functional theory) method that combines MP2 calculations for cluster models with DFT calculations for the full periodic structure is used to localize minima and transition structures for proton jumps at different Brønsted sites in different frameworks (chabazite, faujasite, ferrierite, and ZSM-5) and at different crystallographic positions of a given framework. The MP2 limit for the periodic structures is obtained by extrapolating the results of a series of cluster models of increasing size. A coupled-cluster (CCSD(T)) correction to MP2 energies is calculated for cluster models consisting of three tetrahedra. For the adsorption energies, thismore » difference is small, between 0.1 and 0.9 kJ/mol, but for the intrinsic proton exchange barriers, this difference makes a significant (10.85 ± 0.25 kJ/mol) and almost constant contribution across different systems. The total values of the adsorption energies vary between 22 and 34 kJ/mol, whereas the total proton exchange energy barriers fall in the narrow range of 152–156 kJ/mol. After adding nuclear motion contributions (harmonic approximation, 298 K), intrinsic enthalpy barriers between 134 and 141 kJ/mol and apparent energy barriers between 105 and 118 kJ/mol are predicted for the different sites examined for the different frameworks. These predictions are consistent with experimental results available for faujasite, ferrierite, and ZSM-5.« less

Effects of dietary fibre on subjective appetite, energy intake and body weight: a systematic review of randomized controlled trials.

PubMed

Wanders, A J; van den Borne, J J G C; de Graaf, C; Hulshof, T; Jonathan, M C; Kristensen, M; Mars, M; Schols, H A; Feskens, E J M

2011-09-01

Dietary fibres are believed to reduce subjective appetite, energy intake and body weight. However, different types of dietary fibre may affect these outcomes differently. The aim of this review was to systematically investigate the available literature on the relationship between dietary fibre types, appetite, acute and long-term energy intake, and body weight. Fibres were grouped according to chemical structure and physicochemical properties (viscosity, solubility and fermentability). Effect rates were calculated as the proportion of all fibre-control comparisons that reduced appetite (n = 58 comparisons), acute energy intake (n = 26), long-term energy intake (n = 38) or body weight (n = 66). For appetite, acute energy intake, long-term energy intake and body weight, there were clear differences in effect rates depending on chemical structure. Interestingly, fibres characterized as being more viscous (e.g. pectins, β-glucans and guar gum) reduced appetite more often than those less viscous fibres (59% vs. 14%), which also applied to acute energy intake (69% vs. 30%). Overall, effects on energy intake and body weight were relatively small, and distinct dose-response relationships were not observed. Short- and long-term effects of dietary fibres appear to differ and multiple mechanisms relating to their different physicochemical properties seem to interplay. This warrants further exploration. © 2011 The Authors. obesity reviews © 2011 International Association for the Study of Obesity.

Parity-Violation Energy of Biomolecules - IV: Protein Secondary Structure

NASA Astrophysics Data System (ADS)

Faglioni, Francesco; Cuesta, Inmaculada García

2011-06-01

The parity-violation energy difference between enantiomeric forms of the same amino acid sequence, from the amyloid β-peptide involved in Alzheimer's desease, in both α-helix and β-sheet configurations, is investigated with ab-initio techniques. To this end, we develop an extension of the N2 computational scheme that selectively includes neighboring amino acids to preserve the relevant H-bonds. In agreement with previous speculations, it is found that the helical α structure is associated with larger parity-violation energy differences than the corresponding β form. Implications for the evolution of biological homochirality are discussed as well as the relative importance of various effects in determining the parity-violation energy.

Mechanical energy flow models of rods and beams

NASA Technical Reports Server (NTRS)

Wohlever, J. C.; Bernhard, R. J.

1992-01-01

It has been proposed that the flow of mechanical energy through a structural/acoustic system may be modeled in a manner similar to that of flow of thermal energy/in a heat conduction problem. If this hypothesis is true, it would result in relatively efficient numerical models of structure-borne energy in large built-up structures. Fewer parameters are required to approximate the energy solution than are required to model the characteristic wave behavior of structural vibration by using traditional displacement formulations. The energy flow hypothesis is tested in this investigation for both longitudinal vibration in rods and transverse flexural vibrations of beams. The rod is shown to behave approximately according to the thermal energy flow analogy. However, the beam solutions behave significantly differently than predicted by the thermal analogy unless locally-space-averaged energy and power are considered. Several techniques for coupling dissimilar rods and beams are also discussed. Illustrations of the solution accuracy of the methods are included.

An Experimental and Computational Investigation into the Gas-Phase Acidities of Tyrosine and Phenylalanine: Three Structures for Deprotonated Tyrosine

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

Bokatzian, Samantha S.; Stover, Michele L.; Plummer, Chelsea E.

Using mass spectrometry and correlated molecular orbital theory, three deprotonated structures were revealed for the amino acid tyrosine. The structures were distinguished experimentally by ion/molecule reactions involving proton transfer and trimethylsilyl azide. Gas-phase acidities from proton transfer reactions and from G3(MP2) calculations generally agree well. The lowest energy structure, which was only observed experimentally using electrospray ionization from aprotic solvents, is deprotonated at the carboxylic acid group and is predicted to be highly folded. A second unfolded carboxylate structure is several kcal/mol higher in energy and primarily forms from protic solvents. Protic solvents also yield a structure deprotonated at themore » phenolic side chain, which experiments find to be intermediate in energy to the two carboxylate forms. G3(MP2) calculations indicate that the three structures differ in energy by only 2.5 kcal/mol, yet they are readily distinguished experimentally. Structural abundance ratios are dependent upon experimental conditions, including the solvent and accumulation time of ions in a hexapole. Under some conditions, carboxylate ions may convert to phenolate ions. For phenylalanine, which lacks a phenolic group, only one deprotonated structure was observed experimentally when electrosprayed from protic solvent. This agrees with G3(MP2) calculations that find the folded and unfolded carboxylate forms to differ by 0.3 kcal/mol.« less

System, method and computer-readable medium for locating physical phenomena

DOEpatents

Weseman, Matthew T [Idaho Falls, ID; Rohrbaugh, David T [Idaho Falls, ID; Richardson, John G [Idaho Falls, ID

2008-02-26

A method, system and computer product for detecting the location of a deformation of a structure includes baselining a defined energy transmitting characteristic for each of the plurality of laterally adjacent conductors attached to the structure. Each of the plurality of conductors includes a plurality of segments coupled in series and having an associated unit value representative of the defined energy transmitting characteristic. The plurality of laterally adjacent conductors includes a plurality of identity groups with each identity group including at least one of the plurality of segments from each of the plurality of conductors. Each of the plurality of conductors are monitored for a difference in the defined energy transmitting characteristic when compared with a baseline energy transmitting characteristic for each of the plurality of conductors. When the difference exceeds a threshold value, a location of the deformation along the structure is calculated.

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.

Molecular Structure and Free Energy Landscape for Electron Transport in the Deca-Heme Cytochrome MtrF

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

Breuer, Marian; Zarzycki, Piotr P.; Shi, Liang

2012-12-01

The free energy profile for electron flow through the bacterial deca-heme cytochrome MtrF has been computed using thermodynamic integration and classical molecular dynamics. The extensive calculations on two versions of the structure help validate the method and results, because differences in the profiles can be related to differences in the charged amino acids local to specific heme groups. First estimates of reorganization free energies λ yield a range consistent with expectations for partially solvent exposed cofactors, and reveal an activation energy range surmountable for electron flow. Future work will aim at increasing the accuracy of λ with polarizable force fieldmore » dynamics and quantum chemical energy gap calculations, as well as quantum chemical computation of electronic coupling matrix elements.« less

Branch-point energies and the band-structure lineup at Schottky contacts and heterostrucures

NASA Astrophysics Data System (ADS)

Mönch, Winfried

2011-06-01

Empirical branch-point energies of Si, the group-III nitrides AlN, GaN, and InN, and the group-II and group-III oxides MgO, ZnO, Al2O3 and In2O3 are determined from experimental valance-band offsets of their heterostructures. For Si, GaN, and MgO, these values agree with the branch-point energies obtained from the barrier heights of their Schottky contacts. The empirical branch-point energies of Si and the group-III nitrides are in very good agreement with results of previously published calculations using quite different approaches such as the empirical tight-binding approximation and modern electronic-structure theory. In contrast, the empirical branch-point energies of the group-II and group-III oxides do not confirm the respective theoretical results. As at Schottky contacts, the band-structure lineup at heterostructures is also made up of a zero-charge-transfer term and an intrinsic electric-dipole contribution. Hence, valence-band offsets are not equal to the difference of the branch-point energies of the two semiconductors forming the heterostructure. The electric-dipole term may be described by the electronegativity difference of the two solids in contact. A detailed analysis of experimental Si Schottky barrier heights and heterostructure valence-band offsets explains and proves these conclusions.

Limited-angle multi-energy CT using joint clustering prior and sparsity regularization

NASA Astrophysics Data System (ADS)

Zhang, Huayu; Xing, Yuxiang

2016-03-01

In this article, we present an easy-to-implement Multi-energy CT scanning strategy and a corresponding reconstruction method, which facilitate spectral CT imaging by improving the data efficiency the number-of-energy- channel fold without introducing visible limited-angle artifacts caused by reducing projection views. Leveraging the structure coherence at different energies, we first pre-reconstruct a prior structure information image using projection data from all energy channels. Then, we perform a k-means clustering on the prior image to generate a sparse dictionary representation for the image, which severs as a structure information constraint. We com- bine this constraint with conventional compressed sensing method and proposed a new model which we referred as Joint Clustering Prior and Sparsity Regularization (CPSR). CPSR is a convex problem and we solve it by Alternating Direction Method of Multipliers (ADMM). We verify our CPSR reconstruction method with a numerical simulation experiment. A dental phantom with complicate structures of teeth and soft tissues is used. X-ray beams from three spectra of different peak energies (120kVp, 90kVp, 60kVp) irradiate the phantom to form tri-energy projections. Projection data covering only 75◦ from each energy spectrum are collected for reconstruction. Independent reconstruction for each energy will cause severe limited-angle artifacts even with the help of compressed sensing approaches. Our CPSR provides us with images free of the limited-angle artifact. All edge details are well preserved in our experimental study.

Folding a Protein with Equal Probability of Being Helix or Hairpin

PubMed Central

Lin, Chun-Yu; Chen, Nan-Yow; Mou, Chung Yu

2012-01-01

We explore the possibility for the native structure of a protein being inherently multiconformational in an ab initio coarse-grained model. Based on the Wang-Landau algorithm, the complete free energy landscape for the designed sequence 2DX4: INYWLAHAKAGYIVHWTA is constructed. It is shown that 2DX4 possesses two nearly degenerate native structures: one is a helix structure with the other a hairpinlike structure, and their free energy difference is <2% of that of local minima. Two degenerate native structures are stabilized by an energy barrier of ∼10 kcal/mol. Furthermore, the hydrogen-bond and dipole-dipole interactions are found to be two major competing interactions in transforming one conformation into the other. Our results indicate that two degenerate native structures are stabilized by subtle balance between different interactions in proteins. In particular, for small proteins, balance between the hydrogen-bond and dipole-dipole interactions happens for proteins of sizes being ∼18 amino acids and is shown to the main driving mechanism for the occurrence of degeneracy. These results provide important clues to the study of native structures of proteins. PMID:22828336

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.

Probing dark energy using convergence power spectrum and bi-spectrum

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

Dinda, Bikash R., E-mail: bikash@ctp-jamia.res.in

Weak lensing convergence statistics is a powerful tool to probe dark energy. Dark energy plays an important role to the structure formation and the effects can be detected through the convergence power spectrum, bi-spectrum etc. One of the most promising and simplest dark energy model is the ΛCDM . However, it is worth investigating different dark energy models with evolving equation of state of the dark energy. In this work, detectability of different dark energy models from ΛCDM model has been explored through convergence power spectrum and bi-spectrum.

Investigation of impact phenomena on the marine structures: Part II - Internal energy of the steel structure applied by selected materials in the ship-ship collision incidents

NASA Astrophysics Data System (ADS)

Prabowo, A. R.; Baek, S. J.; Lee, S. G.; Bae, D. M.; Sohn, J. M.

2018-01-01

Phenomena of impact loads on the marine structures has attracted attention to be predicted regarding its influences to structural damage. This part demands sustainable analysis and observation as tendency may vary from one to others since impact involves various scenario models and the structure itself experiences continuous development. Investigation of the damage extent can be conducted by observation on the energy behaviour during two entities involve in a contact. This study aimed to perform numerical investigation to predict structural damage by assessing absorbed strain energy represented by the internal energy during a series of ship collisions. The collision target in ship-ship interactions were determined on the single and double hulls part of a passenger ship. Tendency of the internal energy by the steel structures was summarized, and verification was presented by several crashworthiness criteria. It was found that steel structures applied by the material grades A and B produced different tendencies compared to the material grades D and E. Effect of the structural arrangement to structural responses in terms of strain and stress indicated that the single hull presented contour expansion mainly on the longitudinal directions.

Life comparative analysis of energy consumption and CO₂ emissions of different building structural frame types.

PubMed

Kim, Sangyong; Moon, Joon-Ho; Shin, Yoonseok; Kim, Gwang-Hee; Seo, Deok-Seok

2013-01-01

The objective of this research is to quantitatively measure and compare the environmental load and construction cost of different structural frame types. Construction cost also accounts for the costs of CO₂ emissions of input materials. The choice of structural frame type is a major consideration in construction, as this element represents about 33% of total building construction costs. In this research, four constructed buildings were analyzed, with these having either reinforced concrete (RC) or steel (S) structures. An input-output framework analysis was used to measure energy consumption and CO₂ emissions of input materials for each structural frame type. In addition, the CO₂ emissions cost was measured using the trading price of CO₂ emissions on the International Commodity Exchange. This research revealed that both energy consumption and CO₂ emissions were, on average, 26% lower with the RC structure than with the S structure, and the construction costs (including the CO₂ emissions cost) of the RC structure were about 9.8% lower, compared to the S structure. This research provides insights through which the construction industry will be able to respond to the carbon market, which is expected to continue to grow in the future.

Intersubband linear and nonlinear optical response of the delta-doped SiGe quantum well

NASA Astrophysics Data System (ADS)

Duque, C. A.; Akimov, V.; Demediuk, R.; Belykh, V.; Tiutiunnyk, A.; Morales, A. L.; Restrepo, R. L.; Mora-Ramos, M. E.; Fomina, O.; Tulupenko, V.

2015-11-01

The degree of ionization, controlled by external fields, of delta-doped layers inside the quantum wells can affect their energy structure, therefore delta-doped QWs can be used to engineer different kinds of tunable THz optical devices on intersubband transitions. Here it is calculated and analyzed the linear and nonlinear (Kerr-type) optical response, including absorption coefficient and refractive index change of 20 nm-wide Si0.8Ge0.2/Si/Si0.8Ge0.2 QW structures n-delta-doped either at the center or at the edge of the well under different temperatures. The conduction subband energy structure was found self-consistently, including the calculation of the impurity binding energy. Our results show that the degree of ionization of the impurity layer as well as the heterostructure symmetry has a strong influence on optical properties of the structures in THz region.

General Retarded Contact Self-energies in and beyond the Non-equilibrium Green's Functions Method

NASA Astrophysics Data System (ADS)

Kubis, Tillmann; He, Yu; Andrawis, Robert; Klimeck, Gerhard

2016-03-01

Retarded contact self-energies in the framework of nonequilibrium Green's functions allow to model the impact of lead structures on the device without explicitly including the leads in the actual device calculation. Most of the contact self-energy algorithms are limited to homogeneous or periodic, semi-infinite lead structures. In this work, the complex absorbing potential method is extended to solve retarded contact self-energies for arbitrary lead structures, including irregular and randomly disordered leads. This method is verified for regular leads against common approaches and on physically equivalent, but numerically different irregular leads. Transmission results on randomly alloyed In0.5Ga0.5As structures show the importance of disorder in the leads. The concept of retarded contact self-energies is expanded to model passivation of atomically resolved surfaces without explicitly increasing the device's Hamiltonian.

The dynamics, structure, and conformational free energy of proline-containing antifreeze glycoprotein.

PubMed Central

Nguyen, Dat H; Colvin, Michael E; Yeh, Yin; Feeney, Robert E; Fink, William H

2002-01-01

Recent NMR studies of the solution structure of the 14-amino acid antifreeze glycoprotein AFGP-8 have concluded that the molecule lacks long-range order. The implication that an apparently unstructured molecule can still have a very precise function as a freezing inhibitor seems startling at first consideration. To gain insight into the nature of conformations and motions in AFGP-8, we have undertaken molecular dynamics simulations augmented with free energy calculations using a continuum solvation model. Starting from 10 different NMR structures, 20 ns of dynamics of AFGP were explored. The dynamics show that AFGP structure is composed of four segments, joined by very flexible pivots positioned at alanine 5, 8, and 11. The dynamics also show that the presence of prolines in this small AFGP structure facilitates the adoption of the poly-proline II structure as its overall conformation, although AFGP does adopt other conformations during the course of dynamics as well. The free energies calculated using a continuum solvation model show that the lowest free energy conformations, while being energetically equal, are drastically different in conformations. In other words, this AFGP molecule has many structurally distinct and energetically equal minima in its energy landscape. In addition, conformational, energetic, and hydrogen bond analyses suggest that the intramolecular hydrogen bonds between the N-acetyl group and the protein backbone are an important integral part of the overall stability of the AFGP molecule. The relevance of these findings to the mechanism of freezing inhibition is discussed. PMID:12023212

The dynamics, structure, and conformational free energy of proline-containing antifreeze glycoprotein.

PubMed

Nguyen, Dat H; Colvin, Michael E; Yeh, Yin; Feeney, Robert E; Fink, William H

2002-06-01

Recent NMR studies of the solution structure of the 14-amino acid antifreeze glycoprotein AFGP-8 have concluded that the molecule lacks long-range order. The implication that an apparently unstructured molecule can still have a very precise function as a freezing inhibitor seems startling at first consideration. To gain insight into the nature of conformations and motions in AFGP-8, we have undertaken molecular dynamics simulations augmented with free energy calculations using a continuum solvation model. Starting from 10 different NMR structures, 20 ns of dynamics of AFGP were explored. The dynamics show that AFGP structure is composed of four segments, joined by very flexible pivots positioned at alanine 5, 8, and 11. The dynamics also show that the presence of prolines in this small AFGP structure facilitates the adoption of the poly-proline II structure as its overall conformation, although AFGP does adopt other conformations during the course of dynamics as well. The free energies calculated using a continuum solvation model show that the lowest free energy conformations, while being energetically equal, are drastically different in conformations. In other words, this AFGP molecule has many structurally distinct and energetically equal minima in its energy landscape. In addition, conformational, energetic, and hydrogen bond analyses suggest that the intramolecular hydrogen bonds between the N-acetyl group and the protein backbone are an important integral part of the overall stability of the AFGP molecule. The relevance of these findings to the mechanism of freezing inhibition is discussed.

Binding-affinity predictions of HSP90 in the D3R Grand Challenge 2015 with docking, MM/GBSA, QM/MM, and free-energy simulations

NASA Astrophysics Data System (ADS)

Misini Ignjatović, Majda; Caldararu, Octav; Dong, Geng; Muñoz-Gutierrez, Camila; Adasme-Carreño, Francisco; Ryde, Ulf

2016-09-01

We have estimated the binding affinity of three sets of ligands of the heat-shock protein 90 in the D3R grand challenge blind test competition. We have employed four different methods, based on five different crystal structures: first, we docked the ligands to the proteins with induced-fit docking with the Glide software and calculated binding affinities with three energy functions. Second, the docked structures were minimised in a continuum solvent and binding affinities were calculated with the MM/GBSA method (molecular mechanics combined with generalised Born and solvent-accessible surface area solvation). Third, the docked structures were re-optimised by combined quantum mechanics and molecular mechanics (QM/MM) calculations. Then, interaction energies were calculated with quantum mechanical calculations employing 970-1160 atoms in a continuum solvent, combined with energy corrections for dispersion, zero-point energy and entropy, ligand distortion, ligand solvation, and an increase of the basis set to quadruple-zeta quality. Fourth, relative binding affinities were estimated by free-energy simulations, using the multi-state Bennett acceptance-ratio approach. Unfortunately, the results were varying and rather poor, with only one calculation giving a correlation to the experimental affinities larger than 0.7, and with no consistent difference in the quality of the predictions from the various methods. For one set of ligands, the results could be strongly improved (after experimental data were revealed) if it was recognised that one of the ligands displaced one or two water molecules. For the other two sets, the problem is probably that the ligands bind in different modes than in the crystal structures employed or that the conformation of the ligand-binding site or the whole protein changes.

Binding-affinity predictions of HSP90 in the D3R Grand Challenge 2015 with docking, MM/GBSA, QM/MM, and free-energy simulations.

PubMed

Misini Ignjatović, Majda; Caldararu, Octav; Dong, Geng; Muñoz-Gutierrez, Camila; Adasme-Carreño, Francisco; Ryde, Ulf

2016-09-01

We have estimated the binding affinity of three sets of ligands of the heat-shock protein 90 in the D3R grand challenge blind test competition. We have employed four different methods, based on five different crystal structures: first, we docked the ligands to the proteins with induced-fit docking with the Glide software and calculated binding affinities with three energy functions. Second, the docked structures were minimised in a continuum solvent and binding affinities were calculated with the MM/GBSA method (molecular mechanics combined with generalised Born and solvent-accessible surface area solvation). Third, the docked structures were re-optimised by combined quantum mechanics and molecular mechanics (QM/MM) calculations. Then, interaction energies were calculated with quantum mechanical calculations employing 970-1160 atoms in a continuum solvent, combined with energy corrections for dispersion, zero-point energy and entropy, ligand distortion, ligand solvation, and an increase of the basis set to quadruple-zeta quality. Fourth, relative binding affinities were estimated by free-energy simulations, using the multi-state Bennett acceptance-ratio approach. Unfortunately, the results were varying and rather poor, with only one calculation giving a correlation to the experimental affinities larger than 0.7, and with no consistent difference in the quality of the predictions from the various methods. For one set of ligands, the results could be strongly improved (after experimental data were revealed) if it was recognised that one of the ligands displaced one or two water molecules. For the other two sets, the problem is probably that the ligands bind in different modes than in the crystal structures employed or that the conformation of the ligand-binding site or the whole protein changes.

Modeling the dynamic equilibrium between oligomers of (AlOCH3)n in methylaluminoxane (MAO). A theoretical study based on a combined quantum mechanical and statistical mechanical approach.

PubMed

Zurek, E; Woo, T K; Firman, T K; Ziegler, T

2001-01-15

Density functional theory (DFT) has been used to calculate the energies of 36 different methylaluminoxane (MAO) cage structures with the general formula (MeAlO)n, where n ranges from 4 to 16. A least-squares fit has been used to devise a formula which predicts the total energies of the MAO with different n's giving an rms deviation of 4.70 kcal/mol. These energies in conjunction with frequency calculations based on molecular mechanics have been used to estimate the finite temperature enthalpies, entropies, and free energies for these MAO structures. Furthermore, formulas have been devised which predict finite temperature enthalpies and entropies for MAO structures of any n for a temperature range of 198.15-598.15 K. Using these formulas, the free energies at different temperatures have been predicted for MAO structures where n ranges from 17 to 30. The free energy values were then used to predict the percentage of each n found at a given temperature. Our calculations give an average n value of 18.41, 17.23, 16.89, and 15.72 at 198.15, 298.15, 398.15, and 598.15 K, respectively. Topological arguments have also been used to show that the MAO cage structure contains a limited amount of square faces as compared to octagonal and hexagonal ones. It is also suggested that the limited number of square faces with their strained Al-O bonds explain the high molar Al:catalyst ratio required for activation. Moreover, in this study we outline a general methodology which may be used to calculate the percent abundance of an equilibrium mixture of oligomers with the general formula (X)n.

Low-Velocity Impact Behavior of Sandwich Structures with Additively Manufactured Polymer Lattice Cores

NASA Astrophysics Data System (ADS)

Turner, Andrew J.; Al Rifaie, Mohammed; Mian, Ahsan; Srinivasan, Raghavan

2018-05-01

Sandwich panel structures are widely used in aerospace, marine, and automotive applications because of their high flexural stiffness, strength-to-weight ratio, good vibration damping, and low through-thickness thermal conductivity. These structures consist of solid face sheets and low-density cellular core structures, which are traditionally based upon honeycomb folded-sheet topologies. The recent advances in additive manufacturing (AM) or 3D printing process allow lattice core configurations to be designed with improved mechanical properties. In this work, the sandwich core is comprised of lattice truss structures (LTS). Two different LTS designs are 3D-printed using acrylonitrile butadiene styrene (ABS) and are tested under low-velocity impact loads. The absorption energy and the failure mechanisms of lattice cells under such loads are investigated. The differences in energy-absorption capabilities are captured by integrating the load-displacement curve found from the impact response. It is observed that selective placement of vertical support struts in the unit-cell results in an increase in the absorption energy of the sandwich panels.

Low-Velocity Impact Behavior of Sandwich Structures with Additively Manufactured Polymer Lattice Cores

NASA Astrophysics Data System (ADS)

Turner, Andrew J.; Al Rifaie, Mohammed; Mian, Ahsan; Srinivasan, Raghavan

2018-04-01

Sandwich panel structures are widely used in aerospace, marine, and automotive applications because of their high flexural stiffness, strength-to-weight ratio, good vibration damping, and low through-thickness thermal conductivity. These structures consist of solid face sheets and low-density cellular core structures, which are traditionally based upon honeycomb folded-sheet topologies. The recent advances in additive manufacturing (AM) or 3D printing process allow lattice core configurations to be designed with improved mechanical properties. In this work, the sandwich core is comprised of lattice truss structures (LTS). Two different LTS designs are 3D-printed using acrylonitrile butadiene styrene (ABS) and are tested under low-velocity impact loads. The absorption energy and the failure mechanisms of lattice cells under such loads are investigated. The differences in energy-absorption capabilities are captured by integrating the load-displacement curve found from the impact response. It is observed that selective placement of vertical support struts in the unit-cell results in an increase in the absorption energy of the sandwich panels.

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

Petkov, Valeri; Hessel, Colin M.; Ovtchinnikoff, Justine

High-energy synchrotron X-ray diffraction coupled to atomic pair distribution function analysis and computer simulations is used to determine the atomic-scale structure of silicon (Si) nanoparticles obtained by two different synthetic routes. Results show that Si nanoparticles may have significant structural differences depending on the synthesis route and surface chemistry. In this case, one method produced Si nanoparticles that are highly crystalline but surface oxidized, whereas a different method yields organic ligand-passivated nanoparticles without surface oxide but that are structurally distorted at the atomic scale. Particular structural features of the oxide-free Si nanoparticles such as average first coordination numbers, length ofmore » structural coherence, and degree of local distortions are compared to their optical properties such as photoluminescence emission energy, quantum yield, and Raman spectra. A clear structure–properties correlation is observed indicating that the former may need to be taken into account when considering the latter.« less

Energy Efficiency and Renewables: Market and Behavioral Failures

ScienceCinema

James Sweeney

2017-12-09

Thursday, January 28, 2010: Policies to promote renewable energy and energy efficiency have been gaining momentum throughout the world, often justified by environmental and energy security concerns. This presentation first talks about energy efficiency options, then delves into the economic motivation for energy efficiency and renewable energy policies by articulating the classes of relevant behavioral failures and market failures. Such behavioral and market failures may vary intertemporally or atemporally; the temporal structure and the extent of the failures are the critical considerations in the development of energy policies. The talk discusses key policy instruments and assess the extent to which they are well-suited to correct for failures with different structures. http://eetd.lbl.gov/dls/lecture-01-28...

Low energy electron-impact ionization of hydrogen atom for coplanar equal-energy-sharing kinematics in Debye plasmas

NASA Astrophysics Data System (ADS)

Li, Jun; Zhang, Song Bin; Ye, Bang Jiao; Wang, Jian Guo; Janev, R. K.

2016-12-01

Low energy electron-impact ionization of hydrogen atom in Debye plasmas has been investigated by employing the exterior complex scaling method. The interactions between the charged particles in the plasma have been represented by Debye-Hückel potentials. Triple differential cross sections (TDCS) in the coplanar equal-energy-sharing geometry at an incident energy of 15.6 eV for different screening lengths are reported. As the screening strength increases, TDCS change significantly. The evolutions of dominant typical peak structures of the TDCS are studied in detail for different screening lengths and for different coplanar equal-energy-sharing geometries.

Green Banks | State, Local, and Tribal Governments | NREL

Science.gov Websites

, and a commercial property assessed clean energy (PACE) product for a variety of different energy , Green Banks can help to help secure private capital by a number of different means including lowering Formation State and local governments have established Green Banks under a variety of different structures

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

APPLICATION OF STATISTICAL ENERGY ANALYSIS TO VIBRATIONS OF MULTI-PANEL STRUCTURES.

DTIC Science & Technology

cylindrical shell are compared with predictions obtained from statistical energy analysis . Generally good agreement is observed. The flow of mechanical...the coefficients of proportionality between power flow and average modal energy difference, which one must know in order to apply statistical energy analysis . No

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

The effect of laser energy on V2O5 thin film growth prepared by laser assisted molecular beam deposition

NASA Astrophysics Data System (ADS)

Abdel Samad, B.; Ashrit, P. V.

2014-09-01

Vanadium pentoxide V2O5 thin films were grown on glass substrates by the LAMBD deposition system with different laser energies. The structure, composition and optical properties of the films have been investigated with atomic force microscopy, x-ray photoemission spectroscopy, ellipsometry and the transmittance analysis. Upon the increase of laser energy, the results showed that the changes in the optical constants are consistent with the thickness changes of the film. The refractive index increases and the absorption coefficient increases when the laser energy increases. The AFM analysis showed a change of the roughness and structure of the deposited films at different laser energies. The prepared films deposited by LAMBD showed interesting properties with correct V2O5 phase without need of annealing after deposition.

Method for fabricating an ignitable heterogeneous stratified metal structure

DOEpatents

Barbee, T.W. Jr.; Weihs, T.

1996-08-20

A multilayer structure has a selectable: (1) propagating reaction front velocity V; (2) reaction initiation temperature attained by application of external energy; and (3) amount of energy delivered by a reaction of alternating unreacted layers of the multilayer structure. Because V is selectable and controllable, a variety of different applications for the multilayer structures are possible, including but not limited to their use as igniters, in joining applications, in fabrication of new materials, as smart materials and in medical applications and devices. The multilayer structure has a period D, and an energy release rate constant K. Two or more alternating unreacted layers are made of different materials and separated by reacted zones. The period D is equal to a sum of the widths of each single alternating reaction layer of a particular material, and also includes a sum of reacted zone widths, t{sub i}, in the period D. The multilayer structure has a selectable propagating reaction front velocity V, where V=K(1/D{sup n}){times}[1-(t{sub i}/D)] and n is about 0.8 to 1.2. 8 figs.

Method for fabricating an ignitable heterogeneous stratified metal structure

DOEpatents

Barbee, Jr., Troy W.; Weihs, Timothy

1996-01-01

A multilayer structure has a selectable, (i) propagating reaction front velocity V, (ii) reaction initiation temperature attained by application of external energy and (iii) amount of energy delivered by a reaction of alternating unreacted layers of the multilayer structure. Because V is selectable and controllable, a variety of different applications for the multilayer structures are possible, including but not limited to their use as ignitors, in joining applications, in fabrication of new materials, as smart materials and in medical applications and devices. The multilayer structure has a period D, and an energy release rate constant K. Two or more alternating unreacted layers are made of different materials and separated by reacted zones. The period D is equal to a sum of the widths of each single alternating reaction layer of a particular material, and also includes a sum of reacted zone widths, t.sub.i, in the period D. The multilayer structure has a selectable propagating reaction front velocity V, where V=K(1/D.sup.n).times.[1-(t.sub.i /D)]and n is about 0.8 to 1.2.

The effects of alloying elements Al and In on Ni-Mn-Ga shape memory alloys, from first principles.

PubMed

Chen, Jie; Li, Yan; Shang, Jia-Xiang; Xu, Hui-Bin

2009-01-28

The electronic structures and formation energies of the Ni(9)Mn(4)Ga(3-x)Al(x) and Ni(9)Mn(4)Ga(3-x)In(x) alloys have been investigated using the first-principles pseudopotential plane-wave method based on density functional theory. The results show that both the austenite and martensite phases of Ni(9)Mn(4)Ga(3) alloy are stabilized by Al alloying, while they become unstable with In alloying. According to the partial density of states and structural energy analysis, different effects of Al and In alloying on the phase stability are mainly attributed to their chemical effects. The formation energy difference between the austenite and martensite phases decreases with Al or In alloying, correlating with the experimentally reported changes in martensitic transformation temperature. The shape factor plays an important role in the decrease of the formation energy difference.

Intelligent Energy Systems As a Modern Basis For Improving Energy Efficiency

NASA Astrophysics Data System (ADS)

Vidyaev, Igor G.; Ivashutenko, Alexandr S.; Samburskaya, Maria A.

2017-01-01

This work presents data on the share of energy costs in the cost structure for different countries. The information is provided on reducing the use of energy resources by means of introducing the intelligent control systems in the industrial enterprises. The structure and the use of such intelligent systems in the energy industry are under our consideration. It is shown that the constructing an intelligent system should be the strategic direction for the development of the distribution grid complex implying the four main areas for improvement: intellectualization of the equipment, management, communication and automation.

Photoelectron energy-loss study of the Bi2CaSr2Cu2O8 superconductor

NASA Astrophysics Data System (ADS)

Shen, Z.-X.; Lindberg, P. A. P.; Dessau, D. S.; Lindau, I.; Spicer, W. E.; Mitzi, D. B.; Bozovic, I.; Kapitulnik, A.

1989-03-01

Using energy-loss spectroscopy of photoelectrons from a single crystal of Bi2CaSr2Cu2O8, we show that the electronic structure of the near-surface region is the same as that of the bulk. Utilizing the fact that photoelectrons of different elements are excited at different locations in the unit cell, we identify the energy-loss features as due to valence plasmon excitations, and one-electron excitations by comparing the photoelectron energy-loss spectra of the different elements.

Synthesis of ceramic-based porous gradient structures for applications in energy conversion and related fields

NASA Astrophysics Data System (ADS)

Graule, Thomas; Ozog, Paulina; Durif, Caroline; Wilkens-Heinecke, Judit; Kata, Dariusz

2016-06-01

Porous, graded ceramic structures are of high relevance in the field of energy conversion as well as in catalysis, and additionally in filtration technology and in biomedical applications. Among different technologies for the tailored design for such structures we demonstrate here a new environmental friendly UV curing-based concept to prepare laminated structures with pore sizes ranging from a few microns up to 50 microns in diameter and with porosities ranging from 10% up to 75 vol.% porosity.

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.

Isolated glyoxylic acid-water 1:1 complexes in low temperature argon matrices.

PubMed

Lundell, Jan; Olbert-Majkut, Adriana

2015-02-05

The 1:1 hydrogen bonded complexes between glyoxylic acid (GA) and water are studied in low temperature argon matrices. Four different complex structures were found in deposited matrices. The lowest energy conformer (T1) of GA was found to form complex, where the water molecule was attached to the opposite side of the intramolecular hydrogen bond in the molecule (T1B). Interestingly, this complex was estimated to be+8.0 kJ mol(-1) higher in energy than the most stable structure (T1A), where the water is inserted into the internal hydrogen bond, and also found in solid argon but in smaller abundance. For the second-lowest energy conformer of GA (T2), the two lowest-energy complex structures were identified, with the most stable complex structure (T2A) also being the most abundant in the matrices. The difference between experiment and computational energetic order of the two complex structures of the same GA conformer is explained by contributions of deformation energy upon complexation and the effect of the environment. The computed BSSE-corrected interaction energies are for the two most stable complexes of the two GA conformers for T1A and T2A -42.11 and -45.03 kJ mol(-1), respectively, at the CCSD(T)/aug-cc-pVTZ//B3LYP/aug-cc-pVTZ level of theory. Copyright © 2013 Elsevier B.V. All rights reserved.

Efficient Construction of Free Energy Profiles of Breathing Metal–Organic Frameworks Using Advanced Molecular Dynamics Simulations

PubMed Central

2017-01-01

In order to reliably predict and understand the breathing behavior of highly flexible metal–organic frameworks from thermodynamic considerations, an accurate estimation of the free energy difference between their different metastable states is a prerequisite. Herein, a variety of free energy estimation methods are thoroughly tested for their ability to construct the free energy profile as a function of the unit cell volume of MIL-53(Al). The methods comprise free energy perturbation, thermodynamic integration, umbrella sampling, metadynamics, and variationally enhanced sampling. A series of molecular dynamics simulations have been performed in the frame of each of the five methods to describe structural transformations in flexible materials with the volume as the collective variable, which offers a unique opportunity to assess their computational efficiency. Subsequently, the most efficient method, umbrella sampling, is used to construct an accurate free energy profile at different temperatures for MIL-53(Al) from first principles at the PBE+D3(BJ) level of theory. This study yields insight into the importance of the different aspects such as entropy contributions and anharmonic contributions on the resulting free energy profile. As such, this thorough study provides unparalleled insight in the thermodynamics of the large structural deformations of flexible materials. PMID:29131647

Efficient Construction of Free Energy Profiles of Breathing Metal-Organic Frameworks Using Advanced Molecular Dynamics Simulations.

PubMed

Demuynck, Ruben; Rogge, Sven M J; Vanduyfhuys, Louis; Wieme, Jelle; Waroquier, Michel; Van Speybroeck, Veronique

2017-12-12

In order to reliably predict and understand the breathing behavior of highly flexible metal-organic frameworks from thermodynamic considerations, an accurate estimation of the free energy difference between their different metastable states is a prerequisite. Herein, a variety of free energy estimation methods are thoroughly tested for their ability to construct the free energy profile as a function of the unit cell volume of MIL-53(Al). The methods comprise free energy perturbation, thermodynamic integration, umbrella sampling, metadynamics, and variationally enhanced sampling. A series of molecular dynamics simulations have been performed in the frame of each of the five methods to describe structural transformations in flexible materials with the volume as the collective variable, which offers a unique opportunity to assess their computational efficiency. Subsequently, the most efficient method, umbrella sampling, is used to construct an accurate free energy profile at different temperatures for MIL-53(Al) from first principles at the PBE+D3(BJ) level of theory. This study yields insight into the importance of the different aspects such as entropy contributions and anharmonic contributions on the resulting free energy profile. As such, this thorough study provides unparalleled insight in the thermodynamics of the large structural deformations of flexible materials.

Missile impacts as sources of seismic energy on the moon

USGS Publications Warehouse

Latham, G.V.; McDonald, W.G.; Moore, H.J.

1970-01-01

Seismic signals recorded from impacts of missiles at the White Sands Missile Range are radically different from the signal recorded from the Apollo 12 lunar module impact. This implies that lunar structure to depths of at least 10 to 20 kilometers is quite different from the typical structure of the earth's crust. Results obtained from this study can be used to predict seismic wave amplitudes from future man-made lunar impacts. Seismic energy and crater dimensions from impacts are compared with measurements from chemical explosions.

Origins of the structural phase transitions in MoTe2 and WTe2

NASA Astrophysics Data System (ADS)

Kim, Hyun-Jung; Kang, Seoung-Hun; Hamada, Ikutaro; Son, Young-Woo

2017-05-01

Layered transition metal dichalcogenides MoTe2 and WTe2 share almost similar lattice constants as well as topological electronic properties except their structural phase transitions. While the former shows a first-order phase transition between monoclinic and orthorhombic structures, the latter does not. Using a recently proposed van der Waals density functional method, we investigate structural stability of the two materials and uncover that the disparate phase transitions originate from delicate differences between their interlayer bonding states near the Fermi energy. By exploiting the relation between the structural phase transitions and the low energy electronic properties, we show that a charge doping can control the transition substantially, thereby suggesting a way to stabilize or to eliminate their topological electronic energy bands.

Communication: Relationship between local structure and the stability of water in hydrophobic confinement

NASA Astrophysics Data System (ADS)

Altabet, Y. Elia; Debenedetti, Pablo G.

2017-12-01

Liquid water confined between nanoscale hydrophobic objects can become metastable with respect to its vapor at nanoscale separations. While the separations are only several molecular diameters, macroscopic theories are often invoked to interpret the thermodynamics and kinetics of water under confinement. We perform detailed rate and free energy calculations via molecular simulations in order to assess the dependence of the rate of evaporation, free energy barriers, and free energy differences between confined liquid and vapor upon object separation and compare them to the relevant macroscopic theories. At small enough separations, the rate of evaporation appears to deviate significantly from the predictions of classical nucleation theory, and we attribute such deviations to changes in the structure of the confined liquid film. However, the free energy difference between the confined liquid and vapor phases agrees quantitatively with macroscopic theory, and the free energy barrier to condensation displays qualitative agreement. Overall, the present work suggests that theories attempting to capture the kinetic behavior of nanoscale systems should incorporate structural details rather than treating it as a continuum.

Guanine base stacking in G-quadruplex nucleic acids

PubMed Central

Lech, Christopher Jacques; Heddi, Brahim; Phan, Anh Tuân

2013-01-01

G-quadruplexes constitute a class of nucleic acid structures defined by stacked guanine tetrads (or G-tetrads) with guanine bases from neighboring tetrads stacking with one another within the G-tetrad core. Individual G-quadruplexes can also stack with one another at their G-tetrad interface leading to higher-order structures as observed in telomeric repeat-containing DNA and RNA. In this study, we investigate how guanine base stacking influences the stability of G-quadruplexes and their stacked higher-order structures. A structural survey of the Protein Data Bank is conducted to characterize experimentally observed guanine base stacking geometries within the core of G-quadruplexes and at the interface between stacked G-quadruplex structures. We couple this survey with a systematic computational examination of stacked G-tetrad energy landscapes using quantum mechanical computations. Energy calculations of stacked G-tetrads reveal large energy differences of up to 12 kcal/mol between experimentally observed geometries at the interface of stacked G-quadruplexes. Energy landscapes are also computed using an AMBER molecular mechanics description of stacking energy and are shown to agree quite well with quantum mechanical calculated landscapes. Molecular dynamics simulations provide a structural explanation for the experimentally observed preference of parallel G-quadruplexes to stack in a 5′–5′ manner based on different accessible tetrad stacking modes at the stacking interfaces of 5′–5′ and 3′–3′ stacked G-quadruplexes. PMID:23268444

Exploring proton transfer in 1,2,3-triazole-triazolium dimer with ab initio method

NASA Astrophysics Data System (ADS)

Li, Ailin; Yan, Tianying; Shen, Panwen

Ab initio calculations are utilized to search for transition state structures for proton transfer in the 1,2,3-triazole-triazolium complexes on the basis of optimized dimers. The result suggests six transition state structures for single proton transfer in the complexes, most of which are coplanar. The energy barriers, between different stable and transition states structures with zero point energy (ZPE) corrections, show that proton transfer occurs at room temperature with coplanar configuration that has the lowest energy. The results clearly support that reorientation gives triazole flexibility for proton transfer.

Piezoelectrically enhanced photocathode

NASA Technical Reports Server (NTRS)

Beach, Robert A. (Inventor); Nikzad, Shouleh (Inventor); Strittmatter, Robert P. (Inventor); Bell, Lloyd Douglas (Inventor)

2009-01-01

A photocathode, for generating electrons in response to incident photons in a photodetector, includes a base layer having a first lattice structure and an active layer having a second lattice structure and epitaxially formed on the base layer, the first and second lattice structures being sufficiently different to create a strain in the active layer with a corresponding piezoelectrically induced polarization field in the active layer, the active layer having a band gap energy corresponding to a desired photon energy.

Data-Driven Learning of Total and Local Energies in Elemental Boron

NASA Astrophysics Data System (ADS)

Deringer, Volker L.; Pickard, Chris J.; Csányi, Gábor

2018-04-01

The allotropes of boron continue to challenge structural elucidation and solid-state theory. Here we use machine learning combined with random structure searching (RSS) algorithms to systematically construct an interatomic potential for boron. Starting from ensembles of randomized atomic configurations, we use alternating single-point quantum-mechanical energy and force computations, Gaussian approximation potential (GAP) fitting, and GAP-driven RSS to iteratively generate a representation of the element's potential-energy surface. Beyond the total energies of the very different boron allotropes, our model readily provides atom-resolved, local energies and thus deepened insight into the frustrated β -rhombohedral boron structure. Our results open the door for the efficient and automated generation of GAPs, and other machine-learning-based interatomic potentials, and suggest their usefulness as a tool for materials discovery.

Data-Driven Learning of Total and Local Energies in Elemental Boron.

PubMed

Deringer, Volker L; Pickard, Chris J; Csányi, Gábor

2018-04-13

The allotropes of boron continue to challenge structural elucidation and solid-state theory. Here we use machine learning combined with random structure searching (RSS) algorithms to systematically construct an interatomic potential for boron. Starting from ensembles of randomized atomic configurations, we use alternating single-point quantum-mechanical energy and force computations, Gaussian approximation potential (GAP) fitting, and GAP-driven RSS to iteratively generate a representation of the element's potential-energy surface. Beyond the total energies of the very different boron allotropes, our model readily provides atom-resolved, local energies and thus deepened insight into the frustrated β-rhombohedral boron structure. Our results open the door for the efficient and automated generation of GAPs, and other machine-learning-based interatomic potentials, and suggest their usefulness as a tool for materials discovery.

Energy capture and storage in asymmetrically multistable modular structures inspired by skeletal muscle

NASA Astrophysics Data System (ADS)

Kidambi, Narayanan; Harne, Ryan L.; Wang, K. W.

2017-08-01

The remarkable versatility and adaptability of skeletal muscle that arises from the assembly of its nanoscale cross-bridges into micro-scale assemblies known as sarcomeres provides great inspiration for the development of advanced adaptive structures and material systems. Motivated by the capability of cross-bridges to capture elastic strain energy to improve the energetic efficiency of sudden movements and repeated motions, and by models of cross-bridge power stroke motions and sarcomere contractile behaviors that incorporate asymmetric, bistable potential energy landscapes, this research develops and studies modular mechanical structures that trap and store energy in higher-energy configurations. Modules exhibiting tailorable asymmetric bistability are first designed and fabricated, revealing how geometric parameters influence the asymmetry of the resulting double-well energy landscapes. These experimentally-observed characteristics are then investigated with numerical and analytical methods to characterize the dynamics of asymmetrically bistable modules. The assembly of such modules into greater structures generates complex, multi-well energy landscapes with stable system configurations exhibiting different quantities of stored elastic potential energy. Dynamic analyses illustrate the ability of these structures to capture a portion of the initial kinetic energy due to impulsive excitations as recoverable strain potential energy, and reveal how stiffness parameters, damping, and the presence of thermal noise in micro- and nano-scale applications influence energy capture behaviors. The insights gained could foster the development of advanced structural/material systems inspired by skeletal muscle, including actuators that effectively capture, store, and release energy, as well as adaptive, robust, and reusable armors and protective devices.

Life Comparative Analysis of Energy Consumption and CO2 Emissions of Different Building Structural Frame Types

PubMed Central

Kim, Sangyong; Moon, Joon-Ho; Shin, Yoonseok; Kim, Gwang-Hee; Seo, Deok-Seok

2013-01-01

The objective of this research is to quantitatively measure and compare the environmental load and construction cost of different structural frame types. Construction cost also accounts for the costs of CO2 emissions of input materials. The choice of structural frame type is a major consideration in construction, as this element represents about 33% of total building construction costs. In this research, four constructed buildings were analyzed, with these having either reinforced concrete (RC) or steel (S) structures. An input-output framework analysis was used to measure energy consumption and CO2 emissions of input materials for each structural frame type. In addition, the CO2 emissions cost was measured using the trading price of CO2 emissions on the International Commodity Exchange. This research revealed that both energy consumption and CO2 emissions were, on average, 26% lower with the RC structure than with the S structure, and the construction costs (including the CO2 emissions cost) of the RC structure were about 9.8% lower, compared to the S structure. This research provides insights through which the construction industry will be able to respond to the carbon market, which is expected to continue to grow in the future. PMID:24227998

Energetics of the formation of Cu-Ag core–shell nanoparticles

DOE PAGES

Chandross, Michael

2014-10-06

Our work presents molecular dynamics and Monte Carlo simulations aimed at developing an understanding of the formation of core–shell Cu-Ag nanoparticles. The effects of surface and interfacial energies were considered and used to form a phenomenological model that calculates the energy gained upon the formation of a core–shell structure from two previously distinct, non-interacting nanoparticles. In most cases, the core–shell structure was found to be energetically favored. Specifically, the difference in energy as a function of the radii of the individual Cu and Ag particles was examined, with the assumption that a core–shell structure forms. In general, it was foundmore » that the energetic gain from forming such a structure increased with increasing size of the initial Ag particle. This result was interpreted as a result of the reduction in surface energy. Moreover, for two separate particles, both Cu and Ag contribute to the surface energy; however, for a core–shell structure, the only contribution to the surface energy is from the Ag shell and the Cu contribution is changed to a Cu–Ag interfacial energy, which is always smaller.« less

Operational management of offshore energy assets

NASA Astrophysics Data System (ADS)

Kolios, A. J.; Martinez Luengo, M.

2016-02-01

Energy assets and especially those deployed offshore are subject to a variety of harsh operational and environmental conditions which lead to deterioration of their performance and structural capacity over time. The aim of reduction of CAPEX in new installations shifts focus to operational management to monitor and assess performance of critical assets ensuring their fitness for service throughout their service life and also to provide appropriate and effective information towards requalification or other end of life scenarios, optimizing the OPEX. Over the last decades, the offshore oil & gas industry has developed and applied various approaches in operational management of assets through Structural Health and Condition Monitoring (SHM/CM) systems which can be, at a certain level, transferable to offshore renewable installations. This paper aims to highlight the key differences between offshore oil & gas and renewable energy assets from a structural integrity and reliability perspective, provide a comprehensive overview of different approaches that are available and applicable, and distinguish the benefits of such systems in the efficient operation of offshore energy assets.

Torsional wave band gap properties in a circular plate of a two-dimensional generalized phononic crystal

NASA Astrophysics Data System (ADS)

Zhao, Lei; Shu, Haisheng; Liang, Shanjun; Shi, Xiaona; An, Shuowei; Ren, Wanyue; Zhu, Jie

2018-05-01

The torsional wave band gap properties of a two-dimensional generalized phononic crystal (GPC) are investigated in this paper. The GPC structure considered is consisted of two different materials being arranged with radial and circumferential periodicities simultaneously. Based on the viewpoint of energy distribution and the finite element method, the power flow, energy density, sound intensity vector together with the stress field of the structure excited by torsional load are numerically calculated and discussed. Our results show that, the band gap of Bragg type exists in these two-dimensional composite structures, and the band gap range is mainly determined by radial periodicity while the circumferential periodicity would result in some transmission peaks within the band gap. These peaks are mainly produced by two different mechanisms, the energy leakage occurred in circumferential channels and the excitation of the local eigenmodes of certain scatterers. These results may be useful in torsional vibration control for various rotational parts and components, and in the application of energy harvesting, etc.

Effect of fabric structure and polymer matrix on flexural strength, interlaminar shear stress, and energy dissipation of glass fiber-reinforced polymer composites

USDA-ARS?s Scientific Manuscript database

We report the effect of glass fiber structure and the epoxy polymer system on the flexural strength, interlaminar shear stress (ILSS), and energy absorption properties of glass fiber-reinforced polymer (GFRP) composites. Four different GFRP composites were fabricated from two glass fiber textiles of...

Stability and free energy calculation of LNA modified quadruplex: a molecular dynamics study

NASA Astrophysics Data System (ADS)

Chaubey, Amit Kumar; Dubey, Kshatresh Dutta; Ojha, Rajendra Prasad

2012-03-01

Telomeric ends of chromosomes, which comprise noncoding repeat sequences of guanine-rich DNA, which are the fundamental in protecting the cell from recombination and degradation. Telomeric DNA sequences can form four stranded quadruplex structures, which are involved in the structure of telomere ends. The formation and stabilization of telomeric quadruplexes has been shown to inhibit the activity of telomerase, thus establishing telomeric DNA quadrulex as an attractive target for cancer therapeutic intervention. Molecular dynamic simulation offers the prospects of detailed description of the dynamical structure with ion and water at molecular level. In this work we have taken a oligomeric part of human telomeric DNA, d(TAGGGT) to form different monomeric quadruplex structures d(TAGGGT)4. Here we report the relative stabilities of these structures under K+ ion conditions and binding interaction between the strands, as determined by molecular dynamic simulations followed by energy calculation. We have taken locked nucleic acid (LNA) in this study. The free energy molecular mechanics Poission Boltzman surface area calculations are performed for the determination of most stable complex structure between all modified structures. We calculated binding free energy for the combination of different strands as the ligand and receptor for all structures. The energetic study shows that, a mixed hybrid type quadruplex conformation in which two parallel strands are bind with other two antiparallel strands, are more stable than other conformations. The possible mechanism for the inhibition of the cancerous growth has been discussed. Such studies may be helpful for the rational drug designing.

Data collection framework for energy efficient privacy preservation in wireless sensor networks having many-to-many structures.

PubMed

Bahşi, Hayretdin; Levi, Albert

2010-01-01

Wireless sensor networks (WSNs) generally have a many-to-one structure so that event information flows from sensors to a unique sink. In recent WSN applications, many-to-many structures evolved due to the need for conveying collected event information to multiple sinks. Privacy preserved data collection models in the literature do not solve the problems of WSN applications in which network has multiple un-trusted sinks with different level of privacy requirements. This study proposes a data collection framework bases on k-anonymity for preventing record disclosure of collected event information in WSNs. Proposed method takes the anonymity requirements of multiple sinks into consideration by providing different levels of privacy for each destination sink. Attributes, which may identify an event owner, are generalized or encrypted in order to meet the different anonymity requirements of sinks at the same anonymized output. If the same output is formed, it can be multicasted to all sinks. The other trivial solution is to produce different anonymized outputs for each sink and send them to related sinks. Multicasting is an energy efficient data sending alternative for some sensor nodes. Since minimization of energy consumption is an important design criteria for WSNs, multicasting the same event information to multiple sinks reduces the energy consumption of overall network.

Thermodynamics of manganese oxides: Sodium, potassium, and calcium birnessite and cryptomelane

PubMed Central

Birkner, Nancy; Navrotsky, Alexandra

2017-01-01

Manganese oxides with layer and tunnel structures occur widely in nature and inspire technological applications. Having variable compositions, these structures often are found as small particles (nanophases). This study explores, using experimental thermochemistry, the role of composition, oxidation state, structure, and surface energy in the their thermodynamic stability. The measured surface energies of cryptomelane, sodium birnessite, potassium birnessite and calcium birnessite are all significantly lower than those of binary manganese oxides (Mn3O4, Mn2O3, and MnO2), consistent with added stabilization of the layer and tunnel structures at the nanoscale. Surface energies generally decrease with decreasing average manganese oxidation state. A stabilizing enthalpy contribution arises from increasing counter-cation content. The formation of cryptomelane from birnessite in contact with aqueous solution is favored by the removal of ions from the layered phase. At large surface area, surface-energy differences make cryptomelane formation thermodynamically less favorable than birnessite formation. In contrast, at small to moderate surface areas, bulk thermodynamics and the energetics of the aqueous phase drive cryptomelane formation from birnessite, perhaps aided by oxidation-state differences. Transformation among birnessite phases of increasing surface area favors compositions with lower surface energy. These quantitative thermodynamic findings explain and support qualitative observations of phase-transformation patterns gathered from natural and synthetic manganese oxides. PMID:28130549

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

NASA Astrophysics Data System (ADS)

Ali Safaei

2010-03-01

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

Quasi-static energy absorption of hollow microlattice structures

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

Liu, YL; Schaedler, TA; Jacobsen, AJ

2014-12-01

We present a comprehensive modeling and numerical study focusing on the energy quasi-static crushing behavior and energy absorption characteristics of hollow tube microlattice structures. The peak stress and effective plateau stress of the hollow microlattice structures are deduced for different geometrical parameters which gives volume and mass densities of energy absorption, D-v and D-m, scale with the relative density, (rho) over bar, as D-v similar to (rho) over bar (1) (5) and D-m similar to (rho) over bar (0 5), respectively, fitting very well to the experimental results of both 60 degrees inclined and 90 degrees predominately microlattices. Then themore » strategies for energy absorption enhancement are proposed for the engineering design of microlattice structures. By introducing a gradient in the thickness or radius of the lattice members, the buckle propagation can be modulated resulting in an increase in energy absorption density that can exceed 40%. Liquid filler is another approach to improve energy absorption by strengthening the microtruss via circumference expansion, and the gain may be over 100% in terms of volume density. Insight into the correlations between microlattice architecture and energy absorption performance combined with the high degree of architecture control paves the way for designing high performance microlattice structures for a range of impact and impulse mitigation applications for vehicles and structures. (C) 2014 Elsevier Ltd. All rights reserved.« less

Inorganic and methane clathrates: Versatility of guest–host compounds for energy harvesting

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

Krishna, Lakshmi; Koh, Carolyn A.

ABSTRACT This review article evaluates the structure–property relations of inorganic clathrates and clathrate hydrates and their potential role in energy harvesting. There is potential cross-fertilization between the two research areas. Guest–host clathrate compounds exhibit unique structural and physical properties, which lead to their versatile roles in energy applications. Prominent classes of clathrate compounds are gas hydrates and inorganic clathrates. That said, there is limited cross-fertilization between the clathrate hydrate and inorganic clathrate communities, with researchers in the respective fields being less informed on the other field. Yet the structures and unique guest–host interactions in both these compounds are common importantmore » features of these clathrates. Common features and procedures can inspire and inform development between the compound classes, which may be important to the technological advancements for the different clathrate materials, e.g., structure characterization techniques and guest–host dynamics in which the “guest” tends to be imprisoned in the host structure, until external forces are applied. Conversely, the diversity in chemical compositions of these two classes of materials leads to the different applications from methane capture and storage to converting waste heat to electricity (thermoelectrics). This article highlights the structural and physical similarities and differences of inorganic and methane clathrates. The most promising state-of-the-art applications of the clathrates are highlighted for harvesting energy from methane (clathrate) hydrate deposits under the ocean and for inorganic clathrates as promising thermoelectric materials.« less

Inorganic and methane clathrates: Versatility of guest–host compounds for energy harvesting

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

Krishna, Lakshmi; Koh, Carolyn A.

2015-01-01

ABSTRACT This review article evaluates the structure–property relations of inorganic clathrates and clathrate hydrates and their potential role in energy harvesting. There is potential cross-fertilization between the two research areas. Guest–host clathrate compounds exhibit unique structural and physical properties, which lead to their versatile roles in energy applications. Prominent classes of clathrate compounds are gas hydrates and inorganic clathrates. That said, there is limited cross-fertilization between the clathrate hydrate and inorganic clathrate communities, with researchers in the respective fields being less informed on the other field. Yet the structures and unique guest–host interactions in both these compounds are common importantmore » features of these clathrates. Common features and procedures can inspire and inform development between the compound classes, which may be important to the technological advancements for the different clathrate materials, e.g., structure characterization techniques and guest–host dynamics in which the “guest” tends to be imprisoned in the host structure, until external forces are applied. Conversely, the diversity in chemical compositions of these two classes of materials leads to the different applications from methane capture and storage to converting waste heat to electricity (thermoelectrics). This article highlights the structural and physical similarities and differences of inorganic and methane clathrates. The most promising state-of-the-art applications of the clathrates are highlighted for harvesting energy from methane (clathrate) hydrate deposits under the ocean and for inorganic clathrates as promising thermoelectric materials.« less

Study of iridium silicide monolayers using density functional theory

NASA Astrophysics Data System (ADS)

Popis, Minh D.; Popis, Sylvester V.; Oncel, Nuri; Hoffmann, Mark R.; ćakır, Deniz

2018-02-01

In this study, we investigated physical and electronic properties of possible two-dimensional structures formed by Si (silicon) and Ir (iridium). To this end, different plausible structures were modeled by using density functional theory and the cohesive energies calculated for the geometry of optimized structures, with the lowest equilibrium lattice constants. Among several candidate structures, we identified three mechanically (via elastic constants and Young's modulus), dynamically (via phonon calculations), and thermodynamically stable iridium silicide monolayer structures. The lowest energy structure has a chemical formula of Ir2Si4 (called r-IrSi2), with a rectangular lattice (Pmmn space group). Its cohesive energy was calculated to be -0.248 eV (per IrSi2 unit) with respect to bulk Ir and bulk Si. The band structure indicates that the Ir2Si4 monolayer exhibits metallic properties. Other stable structures have hexagonal (P-3m1) and tetragonal (P4/nmm) cell structures with 0.12 and 0.20 eV/f.u. higher cohesive energies, respectively. Our calculations showed that Ir-Si monolayers are reactive. Although O2 molecules exothermically dissociate on the surface of the free-standing iridium silicide monolayers with large binding energies, H2O molecules bind to the monolayers with a rather weak interaction.

Folding Free Energy Landscape of the Decapeptide Chignolin

NASA Astrophysics Data System (ADS)

Dou, Xianghua; Wang, Jihua

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

Isospin-symmetry-breaking effects in A˜70 nuclei within beyond-mean-field approach

NASA Astrophysics Data System (ADS)

Petrovici, A.; Andrei, O.

2015-02-01

Particular isospin-symmetry-breaking probes including Coulomb energy differences (CED), mirror energy differences (MED), and triplet energy differences (TED) manifest anomalies in the A˜70 isovector triplets of nuclei. The structure of proton-rich nuclei in the A˜70 mass region suggests shape coexistence and competition between pairing correlations in different channels. Recent results concerning the interplay between isospin-mixing and shape-coexistence effects on exotic phenomena in A˜70 nuclei obtained within the beyond-mean-field complex Excited Vampir variational model with symmetry projection before variation using a realistic effective interaction in a relatively large model space are presented. Excited Vampir predictions concerning the Gamow-Teller β decay to the odd-odd N=Z 66As and 70Br nuclei correlated with the pair structure analysis in the T=1 and T=0 channel of the involved wave functions are discussed.

Isospin-symmetry-breaking effects in A∼70 nuclei within beyond-mean-field approach

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

Petrovici, A.; Andrei, O.

2015-02-24

Particular isospin-symmetry-breaking probes including Coulomb energy differences (CED), mirror energy differences (MED), and triplet energy differences (TED) manifest anomalies in the A∼70 isovector triplets of nuclei. The structure of proton-rich nuclei in the A∼70 mass region suggests shape coexistence and competition between pairing correlations in different channels. Recent results concerning the interplay between isospin-mixing and shape-coexistence effects on exotic phenomena in A∼70 nuclei obtained within the beyond-mean-field complex Excited Vampir variational model with symmetry projection before variation using a realistic effective interaction in a relatively large model space are presented. Excited Vampir predictions concerning the Gamow-Teller β decay to themore » odd-odd N=Z {sup 66}As and {sup 70}Br nuclei correlated with the pair structure analysis in the T=1 and T=0 channel of the involved wave functions are discussed.« less

THE INTERNAL STRUCTURE OF OVERPRESSURED, MAGNETIZED, RELATIVISTIC JETS

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

Martí, J. M.; Perucho, M.; Gómez, J. L.

This work presents the first characterization of the internal structure of overpressured, steady superfast-magnetosonic relativistic jets in connection with their dominant type of energy. To this aim, relativistic magnetohydrodynamic simulations of different jet models threaded by a helical magnetic field have been analyzed covering a wide region in the magnetosonic Mach number–specific internal energy plane. The merit of this plane is that models dominated by different types of energy (internal energy: hot jets; rest-mass energy: kinetically dominated jets; magnetic energy: Poynting-flux-dominated jets) occupy well-separated regions. The analyzed models also cover a wide range of magnetizations. Models dominated by the internalmore » energy (i.e., hot models, or Poynting-flux-dominated jets with magnetizations larger than but close to one) have a rich internal structure characterized by a series of recollimation shocks and present the largest variations in the flow Lorentz factor (and internal energy density). Conversely, in kinetically dominated models, there is not much internal or magnetic energy to be converted into kinetic, and the jets are featureless with small variations in the flow Lorentz factor. The presence of a significant toroidal magnetic field threading the jet produces large gradients in the transversal profile of the internal energy density. Poynting-flux-dominated models with high magnetization (≈10 or larger) are prone to be unstable against magnetic pinch modes, which sets limits on the expected magnetization in parsec-scale active galactic nucleus jets or constrains their magnetic field configuration.« less

Influence of Structural Heterogeneity on Diffusion of CH4 and CO2 in Silicon Carbide-Derived Nanoporous Carbon

PubMed Central

2015-01-01

We investigate the influence of structural heterogeneity on the transport properties of simple gases in a Hybrid Reverse Monte Carlo (HRMC) constructed model of silicon carbide-derived carbon (SiC-DC). The energy landscape of the system is determined based on free energy analysis of the atomistic model. The overall energy barriers of the system for different gases are computed along with important properties, such as Henry constant and differential enthalpy of adsorption at infinite dilution, and indicate hydrophobicity of the SiC-DC structure and its affinity for CO2 and CH4 adsorption. We also study the effect of molecular geometry, pore structure and energy heterogeneity considering different hopping scenarios for diffusion of CO2 and CH4 through ultramicropores using the Nudged Elastic Band (NEB) method. It is shown that the energy barrier of a hopping molecule is very sensitive to the shape of the pore entry. We provide evidence for the influence of structural heterogeneity on self-diffusivity of methane and carbon dioxide using molecular dynamics simulation, based on a maximum in the variation of self-diffusivity with loading. A comparison of the MD simulation results with self-diffusivities from quasi-elastic neutron scattering (QENS) measurements and, with macroscopic uptake-based low-density transport coefficients, reveals the existence of internal barriers not captured in MD simulation and QENS experiments. Nevertheless, the simulation and macroscopic uptake-based diffusion coefficients agree within a factor of 2–3, indicating that our HRMC model structure captures most of the important energy barriers affecting the transport of CH4 in the nanostructure of SiC-DC. PMID:24932319

Influence of Structural Heterogeneity on Diffusion of CH4 and CO2 in Silicon Carbide-Derived Nanoporous Carbon.

PubMed

Farmahini, Amir H; Shahtalebi, Ali; Jobic, Hervé; Bhatia, Suresh K

2014-06-05

We investigate the influence of structural heterogeneity on the transport properties of simple gases in a Hybrid Reverse Monte Carlo (HRMC) constructed model of silicon carbide-derived carbon (SiC-DC). The energy landscape of the system is determined based on free energy analysis of the atomistic model. The overall energy barriers of the system for different gases are computed along with important properties, such as Henry constant and differential enthalpy of adsorption at infinite dilution, and indicate hydrophobicity of the SiC-DC structure and its affinity for CO 2 and CH 4 adsorption. We also study the effect of molecular geometry, pore structure and energy heterogeneity considering different hopping scenarios for diffusion of CO 2 and CH 4 through ultramicropores using the Nudged Elastic Band (NEB) method. It is shown that the energy barrier of a hopping molecule is very sensitive to the shape of the pore entry. We provide evidence for the influence of structural heterogeneity on self-diffusivity of methane and carbon dioxide using molecular dynamics simulation, based on a maximum in the variation of self-diffusivity with loading. A comparison of the MD simulation results with self-diffusivities from quasi-elastic neutron scattering (QENS) measurements and, with macroscopic uptake-based low-density transport coefficients, reveals the existence of internal barriers not captured in MD simulation and QENS experiments. Nevertheless, the simulation and macroscopic uptake-based diffusion coefficients agree within a factor of 2-3, indicating that our HRMC model structure captures most of the important energy barriers affecting the transport of CH 4 in the nanostructure of SiC-DC.

The influence of renewable and non-renewable energy consumption and real income on CO2 emissions in the USA: evidence from structural break tests.

PubMed

Dogan, Eyup; Ozturk, Ilhan

2017-04-01

The objective of this study is to explore the influence of the real income (GDP), renewable energy consumption and non-renewable energy consumption on carbon dioxide (CO 2 ) emissions for the United States of America (USA) in the environmental Kuznets curve (EKC) model for the period 1980-2014. The Zivot-Andrews unit root test with a structural break and the Clemente-Montanes-Reyes unit root test with a structural break report that the analyzed variables become stationary at first-differences. The Gregory-Hansen cointegration test with a structural break and the bounds testing for cointegration in the presence of a structural break show CO 2 emissions, the real income, the quadratic real income, renewable and non-renewable energy consumption are cointegrated. The long-run estimates obtained from the ARDL model indicate that increases in renewable energy consumption mitigate environmental degradation whereas increases in non-renewable energy consumption contribute to CO 2 emissions. In addition, the EKC hypothesis is not valid for the USA. Since we use time-series econometric approaches that account for structural break in the data, findings of this study are robust, reliable and accurate. The US government is advised to put more weights on renewable sources in energy mix, to support and encourage the use and adoption of renewable energy and clean technologies, and to increase the public awareness of renewable energy for lower levels of emissions.

Scientific Benchmarks for Guiding Macromolecular Energy Function Improvement

PubMed Central

Leaver-Fay, Andrew; O’Meara, Matthew J.; Tyka, Mike; Jacak, Ron; Song, Yifan; Kellogg, Elizabeth H.; Thompson, James; Davis, Ian W.; Pache, Roland A.; Lyskov, Sergey; Gray, Jeffrey J.; Kortemme, Tanja; Richardson, Jane S.; Havranek, James J.; Snoeyink, Jack; Baker, David; Kuhlman, Brian

2013-01-01

Accurate energy functions are critical to macromolecular modeling and design. We describe new tools for identifying inaccuracies in energy functions and guiding their improvement, and illustrate the application of these tools to improvement of the Rosetta energy function. The feature analysis tool identifies discrepancies between structures deposited in the PDB and low energy structures generated by Rosetta; these likely arise from inaccuracies in the energy function. The optE tool optimizes the weights on the different components of the energy function by maximizing the recapitulation of a wide range of experimental observations. We use the tools to examine three proposed modifications to the Rosetta energy function: improving the unfolded state energy model (reference energies), using bicubic spline interpolation to generate knowledge based torisonal potentials, and incorporating the recently developed Dunbrack 2010 rotamer library (Shapovalov and Dunbrack, 2011). PMID:23422428

Photoelectron spectroscopy of nitromethane anion clusters

NASA Astrophysics Data System (ADS)

Pruitt, Carrie Jo M.; Albury, Rachael M.; Goebbert, Daniel J.

2016-08-01

Nitromethane anion and nitromethane dimer, trimer, and hydrated cluster anions were studied by photoelectron spectroscopy. Vertical detachment energies, estimated electron affinities, and solvation energies were obtained from the photoelectron spectra. Cluster structures were investigated using theoretical calculations. Predicted detachment energies agreed with experiment. Calculations show water binds to nitromethane anion through two hydrogen bonds. The dimer has a non-linear structure with a single ionic Csbnd H⋯O hydrogen bond. The trimer has two different solvent interactions, but both involve the weak Csbnd H⋯O hydrogen bond.

Field Evaluation of Four Novel Roof Designs for Energy-Efficient Manufactured Homes

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

Levy, E.; Dentz, J.; Ansanelli, E.

2015-12-03

"9A five-bay roof test structure was built, instrumented and monitored in an effort to determine through field testing and analysis the relative contributions of select technologies toward reducing energy use in new manufactured homes. The roof structure in Jamestown, California was designed to examine how differences in roof construction impact space conditioning loads, wood moisture content and attic humidity levels. Conclusions are drawn from the data on the relative energy and moisture performance of various configurations of vented and sealed attics.

Field Evaluation of Four Novel Roof Designs for Energy-Efficient Manufactured Homes

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

Levy, E.; Dentz, J.; Ansanelli, E.

2015-12-01

A five-bay roof test structure was built, instrumented and monitored in an effort to determine through field testing and analysis the relative contributions of select technologies toward reducing energy use in new manufactured homes. The roof structure in Jamestown, California was designed to examine how differences in roof construction impact space conditioning loads, wood moisture content and attic humidity levels. Conclusions are drawn from the data on the relative energy and moisture performance of various configurations of vented and sealed attics.

Actinide electronic structure and atomic forces

NASA Astrophysics Data System (ADS)

Albers, R. C.; Rudin, Sven P.; Trinkle, Dallas R.; Jones, M. D.

2000-07-01

We have developed a new method[1] of fitting tight-binding parameterizations based on functional forms developed at the Naval Research Laboratory.[2] We have applied these methods to actinide metals and report our success using them (see below). The fitting procedure uses first-principles local-density-approximation (LDA) linear augmented plane-wave (LAPW) band structure techniques[3] to first calculate an electronic-structure band structure and total energy for fcc, bcc, and simple cubic crystal structures for the actinide of interest. The tight-binding parameterization is then chosen to fit the detailed energy eigenvalues of the bands along symmetry directions, and the symmetry of the parameterization is constrained to agree with the correct symmetry of the LDA band structure at each eigenvalue and k-vector that is fit to. By fitting to a range of different volumes and the three different crystal structures, we find that the resulting parameterization is robust and appears to accurately calculate other crystal structures and properties of interest.

Structure-dependent vibrational dynamics of Mg(BH 4 ) 2 polymorphs probed with neutron vibrational spectroscopy and first-principles calculations

DOE PAGES

Dimitrievska, Mirjana; White, James L.; Zhou, Wei; ...

2016-08-19

We investigated the structure-dependent vibrational properties of different Mg(BH 4) 2 polymorphs (α, β, γ, and δ phases) with a combination of neutron vibrational spectroscopy (NVS) measurements and density functional theory (DFT) calculations, with emphasis placed on the effects of the local structure and orientation of the BH 4 - anions. DFT simulations closely match the neutron vibrational spectra. The main bands in the low-energy region (20–80 meV) are associated with the BH4 - librational modes. The features in the intermediate energy region (80–120 meV) are attributed to overtones and combination bands arising from the lower-energy modes. The features inmore » the high-energy region (120–200 meV) correspond to the BH 4 - symmetric and asymmetric bending vibrations, of which four peaks located at 140, 142, 160, and 172 meV are especially intense. There are noticeable intensity distribution variations in the vibrational bands for different polymorphs. We can explain these differences using the spatial distribution of BH 4 - anions within various structures. An example of the possible identification of products after the hydrogenation of MgB 2, using NVS measurements, is presented. Our results provide fundamental insights of benefit to researchers currently studying these promising hydrogen-storage materials.« less

Evolutionary, structural and biochemical evidence for a new interaction site of the leptin obesity protein

NASA Technical Reports Server (NTRS)

Gaucher, Eric A.; Miyamoto, Michael M.; Benner, Steven A.

2003-01-01

The Leptin protein is central to the regulation of energy metabolism in mammals. By integrating evolutionary, structural, and biochemical information, a surface segment, outside of its known receptor contacts, is predicted as a second interaction site that may help to further define its roles in energy balance and its functional differences between humans and other mammals.

Ignitable heterogeneous stratified structure for the propagation of an internal exothermic chemical reaction along an expanding wavefront and method of making same

DOEpatents

Barbee, T.W. Jr.; Weihs, T.

1996-07-23

A multilayer structure has a selectable, (1) propagating reaction front velocity V, (2) reaction initiation temperature attained by application of external energy, and (3) amount of energy delivered by a reaction of alternating unreacted layers of the multilayer structure. Because V is selectable and controllable, a variety of different applications for the multilayer structures are possible, including but not limited to their use as igniters, in joining applications, in fabrication of new materials, as smart materials and in medical applications and devices. The multilayer structure has a period D, and an energy release rate constant K. Two or more alternating unreacted layers are made of different materials and separated by reacted zones. The period D is equal to a sum of the widths of each single alternating reaction layer of a particular material, and also includes a sum of reacted zone widths, t{sub i}, in the period D. The multilayer structure has a selectable propagating reaction front velocity V, where V=K(1/D{sup n}){times}[1-(t{sub i}/D)] and n is about 0.8 to 1.2. 8 figs.

Ignitable heterogeneous stratified structure for the propagation of an internal exothermic chemical reaction along an expanding wavefront and method of making same

DOEpatents

Barbee, Jr., Troy W.; Weihs, Timothy

1996-01-01

A multilayer structure has a selectable, (i) propagating reaction front velocity V, (ii) reaction initiation temperature attained by application of external energy and (iii) amount of energy delivered by a reaction of alternating unreacted layers of the multilayer structure. Because V is selectable and controllable, a variety of different applications for the multilayer structures are possible, including but not limited to their use as ignitors, in joining applications, in fabrication of new materials, as smart materials and in medical applications and devices. The multilayer structure has a period D, and an energy release rate constant K. Two or more alternating unreacted layers are made of different materials and separated by reacted zones. The period D is equal to a sum of the widths of each single alternating reaction layer of a particular material, and also includes a sum of reacted zone widths, t.sub.i, in the period D. The multilayer structure has a selectable propagating reaction front velocity V, where V=K(1/D.sup.n).times.[1-(t.sub.i /D)] and n is about 0.8 to 1.2.

Magnon Splitting Induced by Charge Transfer in the Three-Orbital Hubbard Model

NASA Astrophysics Data System (ADS)

Wang, Yao; Huang, Edwin W.; Moritz, Brian; Devereaux, Thomas P.

2018-06-01

Understanding spin excitations and their connection to unconventional superconductivity have remained central issues since the discovery of cuprates. Direct measurement of the dynamical spin structure factor in the parent compounds can provide key information on important interactions relevant in the doped regime, and variations in the magnon dispersion have been linked closely to differences in crystal structure between families of cuprate compounds. Here, we elucidate the relationship between spin excitations and various controlling factors thought to be significant in high-Tc materials by systematically evaluating the dynamical spin structure factor for the three-orbital Hubbard model, revealing differences in the spin dispersion along the Brillouin zone axis and the diagonal. Generally, we find that the absolute energy scale and momentum dependence of the excitations primarily are sensitive to the effective charge-transfer energy, while changes in the on-site Coulomb interactions have little effect on the details of the dispersion. In particular, our result highlights the splitting between spin excitations along the axial and diagonal directions in the Brillouin zone. This splitting decreases with increasing charge-transfer energy and correlates with changes in the apical oxygen position, and general structural variations, for different cuprate families.

Ammonia-water cation and ammonia dimer cation.

PubMed

Kim, Hahn; Lee, Han Myoung

2009-06-25

We have investigated the structure, interaction energy, electronic properties, and IR spectra of the ammonia-water cation (NH(3)H(2)O)(+) using density functional theory (DFT) and high-level ab initio theory. The ammonia-water cation has three minimum-energy structures of (a) H(2)NH(+)...OH(2), (b) H(3)N(+)...OH(2), and (c) H(3)NH(+)...OH. The lowest-energy structure is (a), followed by (c) and (b). The ammonia dimer cation has two minimum-energy structures [the lowest H(3)NH(+)...NH(2) structure and the second lowest (H(3)N...NH(3))(+) structure]. The minimum transition barrier for the interconversion between (a), (b), and (c) is approximately 6 kcal/mol. Most DFT calculations with various functionals, except a few cases, overstabilize the N...O and N...N binding, predicting different structures from Moller-Plesset second-order perturbation (MP2) theory and the most reliable complete basis set (CBS) limit of coupled cluster theory with single, double, and perturbative triple excitations [CCSD(T)]. Thus, the validity test of the DFT functionals for these ionized molecular systems would be of importance.

Acoustic Mechanical Feed-Throughs for Producing Work Across a Structure

NASA Technical Reports Server (NTRS)

Sherril, Stewart (Inventor); Bar-Cohen, Yoseph (Inventor); Bao, Xiaoqi (Inventor)

2017-01-01

An apparatus that passes vibrational energy across a mechanical structure lacking a perforation. The disclosed apparatus and method provide the ability to transfer work (rotary or linear motion) across pressure or thermal barriers or in a sterile environment without generating contaminants; the presence of reflectors in the solid barrier to enhance the efficiency of the energy/power transmission, and the ability to produce a bi-directional driving mechanism using a plurality of different mode resonances, such as a fundamental frequency resonance and a higher frequency resonance. In some instances, a plane within the mechanical structure lacking a perforation is a nodal plane of the vibrational energy field.

Theoretical study of the influence of the electric field on the electronic properties of armchair boron nitride nanoribbon

NASA Astrophysics Data System (ADS)

Chegel, Raad; Behzad, Somayeh

2014-11-01

We have investigated the electronic properties of A-BNNRs in the external electric field using third nearest neighbor tight binding approximation including edge effects. We found that the dependence of on-site energy to the external electric field for edge atoms and center part atoms is different. By comparing the band structure in the different fields, several differences are clearly seen such as modification of energy dispersions, creation of additional band edge states and band gap reduction. By increasing the electric field the band gap reduces linearly until reaches zero and BNNRs with larger width are more sensitive than small ones. All changes in the band structure are directly reflected in the DOS spectrum. The numbers and the energies of the DOS peaks are dependent on the electric field strength.

Broadband piezoelectric energy harvesting devices using multiple bimorphs with different operating frequencies.

PubMed

Xue, Huan; Hu, Yuantai; Wang, Qing-Ming

2008-09-01

This paper presents a novel approach for designing broadband piezoelectric harvesters by integrating multiple piezoelectric bimorphs (PBs) with different aspect ratios into a system. The effect of 2 connecting patterns among PBs, in series and in parallel, on improving energy harvesting performance is discussed. It is found for multifrequency spectra ambient vibrations: 1) the operating frequency band (OFB) of a harvesting structure can be widened by connecting multiple PBs with different aspect ratios in series; 2) the OFB of a harvesting structure can be shifted to the dominant frequency domain of the ambient vibrations by increasing or decreasing the number of PBs in parallel. Numerical results show that the OFB of the piezoelectric energy harvesting devices can be tailored by the connection patterns (i.e., in series and in parallel) among PBs.

Fluorescence energy transfer as a probe for nucleic acid structures and sequences.

PubMed Central

Mergny, J L; Boutorine, A S; Garestier, T; Belloc, F; Rougée, M; Bulychev, N V; Koshkin, A A; Bourson, J; Lebedev, A V; Valeur, B

1994-01-01

The primary or secondary structure of single-stranded nucleic acids has been investigated with fluorescent oligonucleotides, i.e., oligonucleotides covalently linked to a fluorescent dye. Five different chromophores were used: 2-methoxy-6-chloro-9-amino-acridine, coumarin 500, fluorescein, rhodamine and ethidium. The chemical synthesis of derivatized oligonucleotides is described. Hybridization of two fluorescent oligonucleotides to adjacent nucleic acid sequences led to fluorescence excitation energy transfer between the donor and the acceptor dyes. This phenomenon was used to probe primary and secondary structures of DNA fragments and the orientation of oligodeoxynucleotides synthesized with the alpha-anomers of nucleoside units. Fluorescence energy transfer can be used to reveal the formation of hairpin structures and the translocation of genes between two chromosomes. PMID:8152922

When the lowest energy does not induce native structures: parallel minimization of multi-energy values by hybridizing searching intelligences.

PubMed

Lü, Qiang; Xia, Xiao-Yan; Chen, Rong; Miao, Da-Jun; Chen, Sha-Sha; Quan, Li-Jun; Li, Hai-Ou

2012-01-01

Protein structure prediction (PSP), which is usually modeled as a computational optimization problem, remains one of the biggest challenges in computational biology. PSP encounters two difficult obstacles: the inaccurate energy function problem and the searching problem. Even if the lowest energy has been luckily found by the searching procedure, the correct protein structures are not guaranteed to obtain. A general parallel metaheuristic approach is presented to tackle the above two problems. Multi-energy functions are employed to simultaneously guide the parallel searching threads. Searching trajectories are in fact controlled by the parameters of heuristic algorithms. The parallel approach allows the parameters to be perturbed during the searching threads are running in parallel, while each thread is searching the lowest energy value determined by an individual energy function. By hybridizing the intelligences of parallel ant colonies and Monte Carlo Metropolis search, this paper demonstrates an implementation of our parallel approach for PSP. 16 classical instances were tested to show that the parallel approach is competitive for solving PSP problem. This parallel approach combines various sources of both searching intelligences and energy functions, and thus predicts protein conformations with good quality jointly determined by all the parallel searching threads and energy functions. It provides a framework to combine different searching intelligence embedded in heuristic algorithms. It also constructs a container to hybridize different not-so-accurate objective functions which are usually derived from the domain expertise.

When the Lowest Energy Does Not Induce Native Structures: Parallel Minimization of Multi-Energy Values by Hybridizing Searching Intelligences

PubMed Central

Lü, Qiang; Xia, Xiao-Yan; Chen, Rong; Miao, Da-Jun; Chen, Sha-Sha; Quan, Li-Jun; Li, Hai-Ou

2012-01-01

Background Protein structure prediction (PSP), which is usually modeled as a computational optimization problem, remains one of the biggest challenges in computational biology. PSP encounters two difficult obstacles: the inaccurate energy function problem and the searching problem. Even if the lowest energy has been luckily found by the searching procedure, the correct protein structures are not guaranteed to obtain. Results A general parallel metaheuristic approach is presented to tackle the above two problems. Multi-energy functions are employed to simultaneously guide the parallel searching threads. Searching trajectories are in fact controlled by the parameters of heuristic algorithms. The parallel approach allows the parameters to be perturbed during the searching threads are running in parallel, while each thread is searching the lowest energy value determined by an individual energy function. By hybridizing the intelligences of parallel ant colonies and Monte Carlo Metropolis search, this paper demonstrates an implementation of our parallel approach for PSP. 16 classical instances were tested to show that the parallel approach is competitive for solving PSP problem. Conclusions This parallel approach combines various sources of both searching intelligences and energy functions, and thus predicts protein conformations with good quality jointly determined by all the parallel searching threads and energy functions. It provides a framework to combine different searching intelligence embedded in heuristic algorithms. It also constructs a container to hybridize different not-so-accurate objective functions which are usually derived from the domain expertise. PMID:23028708

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.

Lost in folding space? Comparing four variants of the thermodynamic model for RNA secondary structure prediction.

PubMed

Janssen, Stefan; Schudoma, Christian; Steger, Gerhard; Giegerich, Robert

2011-11-03

Many bioinformatics tools for RNA secondary structure analysis are based on a thermodynamic model of RNA folding. They predict a single, "optimal" structure by free energy minimization, they enumerate near-optimal structures, they compute base pair probabilities and dot plots, representative structures of different abstract shapes, or Boltzmann probabilities of structures and shapes. Although all programs refer to the same physical model, they implement it with considerable variation for different tasks, and little is known about the effects of heuristic assumptions and model simplifications used by the programs on the outcome of the analysis. We extract four different models of the thermodynamic folding space which underlie the programs RNAFOLD, RNASHAPES, and RNASUBOPT. Their differences lie within the details of the energy model and the granularity of the folding space. We implement probabilistic shape analysis for all models, and introduce the shape probability shift as a robust measure of model similarity. Using four data sets derived from experimentally solved structures, we provide a quantitative evaluation of the model differences. We find that search space granularity affects the computed shape probabilities less than the over- or underapproximation of free energy by a simplified energy model. Still, the approximations perform similar enough to implementations of the full model to justify their continued use in settings where computational constraints call for simpler algorithms. On the side, we observe that the rarely used level 2 shapes, which predict the complete arrangement of helices, multiloops, internal loops and bulges, include the "true" shape in a rather small number of predicted high probability shapes. This calls for an investigation of new strategies to extract high probability members from the (very large) level 2 shape space of an RNA sequence. We provide implementations of all four models, written in a declarative style that makes them easy to be modified. Based on our study, future work on thermodynamic RNA folding may make a choice of model based on our empirical data. It can take our implementations as a starting point for further program development.

Electronic Structure of C60/Zinc Phthalocyanine/V₂O₅ Interfaces Studied Using Photoemission Spectroscopy for Organic Photovoltaic Applications.

PubMed

Lim, Chang Jin; Park, Min Gyu; Kim, Min Su; Han, Jeong Hwa; Cho, Soohaeng; Cho, Mann-Ho; Yi, Yeonjin; Lee, Hyunbok; Cho, Sang Wan

2018-02-18

The interfacial electronic structures of a bilayer of fullerene (C 60 ) and zinc phthalocyanine (ZnPc) grown on vanadium pentoxide (V₂O₅) thin films deposited using radio frequency sputtering under various conditions were studied using X-ray and ultraviolet photoelectron spectroscopy. The energy difference between the highest occupied molecular orbital (HOMO) level of the ZnPc layer and the lowest unoccupied molecular orbital (LUMO) level of the C 60 layer was determined and compared with that grown on an indium tin oxide (ITO) substrate. The energy difference of a heterojunction on all V₂O₅ was found to be 1.3~1.4 eV, while that on ITO was 1.1 eV. This difference could be due to the higher binding energy of the HOMO of ZnPc on V₂O₅ than that on ITO regardless of work functions of the substrates. We also determined the complete energy level diagrams of C 60 /ZnPc on V₂O₅ and ITO.

Structural transition of (InSb)n clusters at n = 6-10

NASA Astrophysics Data System (ADS)

Lu, Qi Liang; Luo, Qi Quan; Huang, Shou Guo; Li, Yi De

2016-10-01

An optimization strategy combining global semi-empirical quantum mechanical search with all-electron density functional theory was adopted to determine the lowest energy structure of (InSb)n clusters with n = 6-10. A new structural growth pattern of the clusters was observed. The lowest energy structures of (InSb)6 and (InSb)8 were different from that of previously reported results. Competition existed between core-shell and cage-like structures of (InSb)8. The structural transition of (InSb)n clusters occurred at size n = 8-9. For (InSb)9 and (InSb)10 clusters, core-shell structure were more energetically favorable than the cage. The corresponding electronic properties were investigated.

Determining the phonon energy of highly oriented pyrolytic graphite by scanning tunneling microscope light emission spectroscopy

NASA Astrophysics Data System (ADS)

Uehara, Yoichi; Michimata, Junichi; Watanabe, Shota; Katano, Satoshi; Inaoka, Takeshi

2018-03-01

We have investigated the scanning tunneling microscope (STM) light emission spectra of isolated single Ag nanoparticles lying on highly oriented pyrolytic graphite (HOPG). The STM light emission spectra exhibited two types of spectral structures (step-like and periodic). Comparisons of the observed structures and theoretical predictions indicate that the phonon energy of the ZO mode of HOPG [M. Mohr et al., Phys. Rev. B 76, 035439 (2007)] can be determined from the energy difference between the cutoff of STM light emission and the step in the former structure, and from the period of the latter structure. Since the role of the Ag nanoparticles does not depend on the substrate materials, this method will enable the phonon energies of various materials to be measured by STM light emission spectroscopy. The spatial resolution is comparable to the lateral size of the individual Ag nanoparticles (that is, a few nm).

Energy dependent track structure parametrisations for protons and carbon ions based on nanometric simulations

NASA Astrophysics Data System (ADS)

Alexander, Frauke; Villagrasa, Carmen; Rabus, Hans; Wilkens, Jan J.

2015-09-01

The BioQuaRT project within the European Metrology Research Programme aims at correlating ion track structure characteristics with the biological effects of radiation and develops measurement and simulation techniques for determining ion track structure on different length scales from about 2 nm to about 10 μm. Within this framework, we investigate methods to translate track-structure quantities derived on a nanometre scale to macroscopic dimensions. Input data sets were generated by simulations of ion tracks of protons and carbon ions in liquid water using the Geant 4 Monte Carlo toolkit with the Geant4-DNA processes. Based on the energy transfer points - recorded with nanometre resolution - we investigated parametrisations of overall properties of ion track structure. Three different track structure parametrisations have been developed using the distances to the 10 next neighbouring ionisations, the radial energy distribution and ionisation cluster size distributions. These parametrisations of nanometric track structure build a basis for deriving biologically relevant mean values which are essential in the clinical situation where each voxel is exposed to a mixed radiation field. Contribution to the Topical Issue "COST Action Nano-IBCT: Nano-scale Processes Behind Ion-Beam Cancer Therapy", edited by Andrey Solov'yov, Nigel Mason, Gustavo García, Eugene Surdutovich.

Band structure of an electron in a kind of periodic potentials with singularities

NASA Astrophysics Data System (ADS)

Hai, Kuo; Yu, Ning; Jia, Jiangping

2018-06-01

Noninteracting electrons in some crystals may experience periodic potentials with singularities and the governing Schrödinger equation cannot be defined at the singular points. The band structure of a single electron in such a one-dimensional crystal has been calculated by using an equivalent integral form of the Schrödinger equation. Both the perturbed and exact solutions are constructed respectively for the cases of a general singular weak-periodic system and its an exactly solvable version, Kronig-Penney model. Any one of them leads to a special band structure of the energy-dependent parameter, which results in an effective correction to the previous energy-band structure and gives a new explanation for forming the band structure. The used method and obtained results could be a valuable aid in the study of energy bands in solid-state physics, and the new explanation may trigger investigation to different physical mechanism of electron band structures.

Long-range energy transfer in self-assembled quantum dot-DNA cascades

NASA Astrophysics Data System (ADS)

Goodman, Samuel M.; Siu, Albert; Singh, Vivek; Nagpal, Prashant

2015-11-01

The size-dependent energy bandgaps of semiconductor nanocrystals or quantum dots (QDs) can be utilized in converting broadband incident radiation efficiently into electric current by cascade energy transfer (ET) between layers of different sized quantum dots, followed by charge dissociation and transport in the bottom layer. Self-assembling such cascade structures with angstrom-scale spatial precision is important for building realistic devices, and DNA-based QD self-assembly can provide an important alternative. Here we show long-range Dexter energy transfer in QD-DNA self-assembled single constructs and ensemble devices. Using photoluminescence, scanning tunneling spectroscopy, current-sensing AFM measurements in single QD-DNA cascade constructs, and temperature-dependent ensemble devices using TiO2 nanotubes, we show that Dexter energy transfer, likely mediated by the exciton-shelves formed in these QD-DNA self-assembled structures, can be used for efficient transport of energy across QD-DNA thin films.The size-dependent energy bandgaps of semiconductor nanocrystals or quantum dots (QDs) can be utilized in converting broadband incident radiation efficiently into electric current by cascade energy transfer (ET) between layers of different sized quantum dots, followed by charge dissociation and transport in the bottom layer. Self-assembling such cascade structures with angstrom-scale spatial precision is important for building realistic devices, and DNA-based QD self-assembly can provide an important alternative. Here we show long-range Dexter energy transfer in QD-DNA self-assembled single constructs and ensemble devices. Using photoluminescence, scanning tunneling spectroscopy, current-sensing AFM measurements in single QD-DNA cascade constructs, and temperature-dependent ensemble devices using TiO2 nanotubes, we show that Dexter energy transfer, likely mediated by the exciton-shelves formed in these QD-DNA self-assembled structures, can be used for efficient transport of energy across QD-DNA thin films. Electronic supplementary information (ESI) available. See DOI: 10.1039/c5nr04778a

Methylene blue binding to DNA with alternating AT base sequence: minor groove binding is favored over intercalation.

PubMed

Rohs, Remo; Sklenar, Heinz

2004-04-01

The results presented in this paper on methylene blue (MB) binding to DNA with AT alternating base sequence complement the data obtained in two former modeling studies of MB binding to GC alternating DNA. In the light of the large amount of experimental data for both systems, this theoretical study is focused on a detailed energetic analysis and comparison in order to understand their different behavior. Since experimental high-resolution structures of the complexes are not available, the analysis is based on energy minimized structural models of the complexes in different binding modes. For both sequences, four different intercalation structures and two models for MB binding in the minor and major groove have been proposed. Solvent electrostatic effects were included in the energetic analysis by using electrostatic continuum theory, and the dependence of MB binding on salt concentration was investigated by solving the non-linear Poisson-Boltzmann equation. We find that the relative stability of the different complexes is similar for the two sequences, in agreement with the interpretation of spectroscopic data. Subtle differences, however, are seen in energy decompositions and can be attributed to the change from symmetric 5'-YpR-3' intercalation to minor groove binding with increasing salt concentration, which is experimentally observed for the AT sequence at lower salt concentration than for the GC sequence. According to our results, this difference is due to the significantly lower non-electrostatic energy for the minor groove complex with AT alternating DNA, whereas the slightly lower binding energy to this sequence is caused by a higher deformation energy of DNA. The energetic data are in agreement with the conclusions derived from different spectroscopic studies and can also be structurally interpreted on the basis of the modeled complexes. The simple static modeling technique and the neglect of entropy terms and of non-electrostatic solute-solvent interactions, which are assumed to be nearly constant for the compared complexes of MB with DNA, seem to be justified by the results.

Glucose, Lactate, and Shuttling of Metabolites in Vertebrate Retinas

PubMed Central

Hurley, James B.; Lindsay, Kenneth J.; Du, Jianhai

2016-01-01

The vertebrate retina has specific functions and structures that give it a unique set of constraints on the way in which it can produce and use metabolic energy. The retina’s response to illumination influences its energy requirements, and the retina’s laminated structure influences the extent to which neurons and glia can access metabolic fuels. There are fundamental differences between energy metabolism in retina and that in brain. The retina relies on aerobic glycolysis much more than the brain does, and morphological differences between retina and brain limit the types of metabolic relationships that are possible between neurons and glia. This Mini-Review summarizes the unique metabolic features of the retina with a focus on the role of lactate shuttling. PMID:25801286

Structural Break, Stock Prices of Clean Energy Firms and Carbon Market

NASA Astrophysics Data System (ADS)

Wang, Yubao; Cai, Junyu

2018-03-01

This paper uses EU ETS carbon future price and Germany/UK clean energy firms stock indices to study the relationship between carbon market and clean energy market. By structural break test, it is found that the ‘non-stationary’ variables judged by classical unit root test do own unit roots and need taking first difference. After analysis of VAR and Granger causality test, no causal relationships are found between the two markets. However, when Hsiao’s version of causality test is employed, carbon market is found to have power in explaining the movement of stock prices of clean energy firms, and stock prices of clean energy firms also affect the carbon market.

High Energy Density in Azobenzene-based Materials for Photo-Thermal Batteries via Controlled Polymer Architecture and Polymer-Solvent Interactions.

PubMed

Jeong, Seung Pyo; Renna, Lawrence A; Boyle, Connor J; Kwak, Hyunwook S; Harder, Edward; Damm, Wolfgang; Venkataraman, Dhandapani

2017-12-19

Energy densities of ~510 J/g (max: 698 J/g) have been achieved in azobenzene-based syndiotactic-rich poly(methacrylate) polymers. The processing solvent and polymer-solvent interactions are important to achieve morphologically optimal structures for high-energy density materials. This work shows that morphological changes of solid-state syndiotactic polymers, driven by different solvent processings play an important role in controlling the activation energy of Z-E isomerization as well as the shape of the DSC exotherm. Thus, this study shows the crucial role of processing solvents and thin film structure in achieving higher energy densities.

First-principle modelling of forsterite surface properties: Accuracy of methods and basis sets.

PubMed

Demichelis, Raffaella; Bruno, Marco; Massaro, Francesco R; Prencipe, Mauro; De La Pierre, Marco; Nestola, Fabrizio

2015-07-15

The seven main crystal surfaces of forsterite (Mg2 SiO4 ) were modeled using various Gaussian-type basis sets, and several formulations for the exchange-correlation functional within the density functional theory (DFT). The recently developed pob-TZVP basis set provides the best results for all properties that are strongly dependent on the accuracy of the wavefunction. Convergence on the structure and on the basis set superposition error-corrected surface energy can be reached also with poorer basis sets. The effect of adopting different DFT functionals was assessed. All functionals give the same stability order for the various surfaces. Surfaces do not exhibit any major structural differences when optimized with different functionals, except for higher energy orientations where major rearrangements occur around the Mg sites at the surface or subsurface. When dispersions are not accounted for, all functionals provide similar surface energies. The inclusion of empirical dispersions raises the energy of all surfaces by a nearly systematic value proportional to the scaling factor s of the dispersion formulation. An estimation for the surface energy is provided through adopting C6 coefficients that are more suitable than the standard ones to describe O-O interactions in minerals. A 2 × 2 supercell of the most stable surface (010) was optimized. No surface reconstruction was observed. The resulting structure and surface energy show no difference with respect to those obtained when using the primitive cell. This result validates the (010) surface model here adopted, that will serve as a reference for future studies on adsorption and reactivity of water and carbon dioxide at this interface. © 2015 Wiley Periodicals, Inc.

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.

Parameter optimization on the convergence surface of path simulations

NASA Astrophysics Data System (ADS)

Chandrasekaran, Srinivas Niranj

Computational treatments of protein conformational changes tend to focus on the trajectories themselves, despite the fact that it is the transition state structures that contain information about the barriers that impose multi-state behavior. PATH is an algorithm that computes a transition pathway between two protein crystal structures, along with the transition state structure, by minimizing the Onsager-Machlup action functional. It is rapid but depends on several unknown input parameters whose range of different values can potentially generate different transition-state structures. Transition-state structures arising from different input parameters cannot be uniquely compared with those generated by other methods. I outline modifications that I have made to the PATH algorithm that estimates these input parameters in a manner that circumvents these difficulties, and describe two complementary tests that validate the transition-state structures found by the PATH algorithm. First, I show that although the PATH algorithm and two other approaches to computing transition pathways produce different low-energy structures connecting the initial and final ground-states with the transition state, all three methods agree closely on the configurations of their transition states. Second, I show that the PATH transition states are close to the saddle points of free-energy surfaces connecting initial and final states generated by replica-exchange Discrete Molecular Dynamics simulations. I show that aromatic side-chain rearrangements create similar potential energy barriers in the transition-state structures identified by PATH for a signaling protein, a contractile protein, and an enzyme. Finally, I observed, but cannot account for, the fact that trajectories obtained for all-atom and Calpha-only simulations identify transition state structures in which the Calpha atoms are in essentially the same positions. The consistency between transition-state structures derived by different algorithms for unrelated protein systems argues that although functionally important protein conformational change trajectories are to a degree stochastic, they nonetheless pass through a well-defined transition state whose detailed structural properties can rapidly be identified using PATH. In the end, I outline the strategies that could enhance the efficiency and applicability of PATH.

Temporal Control over Transient Chemical Systems using Structurally Diverse Chemical Fuels.

PubMed

Chen, Jack L-Y; Maiti, Subhabrata; Fortunati, Ilaria; Ferrante, Camilla; Prins, Leonard J

2017-08-25

The next generation of adaptive, intelligent chemical systems will rely on a continuous supply of energy to maintain the functional state. Such systems will require chemical methodology that provides precise control over the energy dissipation process, and thus, the lifetime of the transiently activated function. This manuscript reports on the use of structurally diverse chemical fuels to control the lifetime of two different systems under dissipative conditions: transient signal generation and the transient formation of self-assembled aggregates. The energy stored in the fuels is dissipated at different rates by an enzyme, which installs a dependence of the lifetime of the active system on the chemical structure of the fuel. In the case of transient signal generation, it is shown that different chemical fuels can be used to generate a vast range of signal profiles, allowing temporal control over two orders of magnitude. Regarding self-assembly under dissipative conditions, the ability to control the lifetime using different fuels turns out to be particularly important as stable aggregates are formed only at well-defined surfactant/fuel ratios, meaning that temporal control cannot be achieved by simply changing the fuel concentration. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Recent research progress on iron- and manganese-based positive electrode materials for rechargeable sodium batteries

PubMed Central

Yabuuchi, Naoaki; Komaba, Shinichi

2014-01-01

Large-scale high-energy batteries with electrode materials made from the Earth-abundant elements are needed to achieve sustainable energy development. On the basis of material abundance, rechargeable sodium batteries with iron- and manganese-based positive electrode materials are the ideal candidates for large-scale batteries. In this review, iron- and manganese-based electrode materials, oxides, phosphates, fluorides, etc, as positive electrodes for rechargeable sodium batteries are reviewed. Iron and manganese compounds with sodium ions provide high structural flexibility. Two layered polymorphs, O3- and P2-type layered structures, show different electrode performance in Na cells related to the different phase transition and sodium migration processes on sodium extraction/insertion. Similar to layered oxides, iron/manganese phosphates and pyrophosphates also provide the different framework structures, which are used as sodium insertion host materials. Electrode performance and reaction mechanisms of the iron- and manganese-based electrode materials in Na cells are described and the similarities and differences with lithium counterparts are also discussed. Together with these results, the possibility of the high-energy battery system with electrode materials made from only Earth-abundant elements is reviewed. PMID:27877694

Recent research progress on iron- and manganese-based positive electrode materials for rechargeable sodium batteries.

PubMed

Yabuuchi, Naoaki; Komaba, Shinichi

2014-08-01

Large-scale high-energy batteries with electrode materials made from the Earth-abundant elements are needed to achieve sustainable energy development. On the basis of material abundance, rechargeable sodium batteries with iron- and manganese-based positive electrode materials are the ideal candidates for large-scale batteries. In this review, iron- and manganese-based electrode materials, oxides, phosphates, fluorides, etc, as positive electrodes for rechargeable sodium batteries are reviewed. Iron and manganese compounds with sodium ions provide high structural flexibility. Two layered polymorphs, O3- and P2-type layered structures, show different electrode performance in Na cells related to the different phase transition and sodium migration processes on sodium extraction/insertion. Similar to layered oxides, iron/manganese phosphates and pyrophosphates also provide the different framework structures, which are used as sodium insertion host materials. Electrode performance and reaction mechanisms of the iron- and manganese-based electrode materials in Na cells are described and the similarities and differences with lithium counterparts are also discussed. Together with these results, the possibility of the high-energy battery system with electrode materials made from only Earth-abundant elements is reviewed.

Effects of radiation reaction in the interaction between cluster media and high intensity lasers in the radiation dominant regime

NASA Astrophysics Data System (ADS)

Iwata, Natsumi; Nagatomo, Hideo; Fukuda, Yuji; Matsui, Ryutaro; Kishimoto, Yasuaki

2016-06-01

Interaction between media composed of clusters and high intensity lasers in the radiation dominant regime, i.e., intensity of 10 22 - 23 W / cm 2 , is studied based on the particle-in-cell simulation that includes the radiation reaction. By introducing target materials that have the same total mass but different internal structures, i.e., uniform plasma and cluster media with different cluster radii, we investigate the effect of the internal structure on the interaction dynamics, high energy radiation emission, and its reaction. Intense radiation emission is found in the cluster media where electrons exhibit non-ballistic motions suffering from strong accelerations by both the penetrated laser field and charge separation field of clusters. As a result, the clustered structure increases the energy conversion into high energy radiations significantly at the expense of the conversion into particles, while the total absorption rate into radiation and particles remains unchanged from the absorption rate into particles in the case without radiation reaction. The maximum ion energy achieved in the interaction with cluster media is found to be decreased through the radiation reaction to electrons into the same level with that achieved in the interaction with the uniform plasma. The clustered structure thus enhances high energy radiation emission rather than the ion acceleration in the considered intensity regime.

Leaving Group Ability Observably Affects Transition State Structure in a Single Enzyme Active Site.

PubMed

Roston, Daniel; Demapan, Darren; Cui, Qiang

2016-06-15

A reaction's transition state (TS) structure plays a critical role in determining reactivity and has important implications for the design of catalysts, drugs, and other applications. Here, we explore TS structure in the enzyme alkaline phosphatase using hybrid Quantum Mechanics/Molecular Mechanics simulations. We find that minor perturbations to the substrate have major effects on TS structure and the way the enzyme stabilizes the TS. Substrates with good leaving groups (LGs) have little cleavage of the phosphorus-LG bond at the TS, while substrates with poor LGs have substantial cleavage of that bond. The results predict nonlinear free energy relationships for a single rate-determining step, and substantial differences in kinetic isotope effects for different substrates; both trends were observed in previous experimental studies, although the original interpretations differed from the present model. Moreover, due to different degrees of phosphorus-LG bond cleavage at the TS for different substrates, the LG is stabilized by different interactions at the TS: while a poor LG is directly stabilized by an active site zinc ion, a good LG is mainly stabilized by active site water molecules. Our results demonstrate the considerable plasticity of TS structure and stabilization in enzymes. Furthermore, perturbations to reactivity that probe TS structure experimentally (i.e., substituent effects) may substantially perturb the TS they aim to probe, and thus classical experimental approaches such as free energy relations should be interpreted with care.

Hydroxyl migration disorders the surface structure of hydroxyapatite nanoparticles

NASA Astrophysics Data System (ADS)

Cheng, Xiajie; Wu, Hong; Zhang, Li; Ma, Xingtao; Zhang, Xingdong; Yang, Mingli

2017-09-01

The surface structure of nano-hydroxyapatite (HAP) was investigated using a combined simulated annealing and molecular dynamics method. The stationary structures of nano-HAP with 4-7 nm in diameter and annealed under different temperatures were analyzed in terms of pair distribution function, structural factor, mean square displacement and atomic coordination number. The particles possess different structures from bulk crystal. A clear radial change in their atomic arrangements was noted. From core to surface the structures change from ordered to disordered. A three-shell model was proposed to describe the structure evolution of nano-HAP. Atoms in the core zone keep their arrangements as in crystal, while atoms in the surface shell are in short-range order and long-range disorder, adopting a typically amorphous structure. Atoms in the middle shell have small displacements and/or deflections but basically retain their original locations as in crystal. The disordered shell is about 1 nm in thickness, in agreement with experimental observations. The disordering mainly stems from hydroxyl migration during which hydroxyls move to the surface and bond with the exposed Ca ions, and their left vacancies bring about a rearrangement of nearby atoms. The disordering is to some extent different for particles unannealed under different temperatures, resulting from fewer number of migrated hydroxyls at lower temperatures. Particles with different sizes have similar surface structures, and their surface energy decreases with increasing size. Moreover, the surface energy is reduced by hydroxyl migration because the exposed Ca ions on the surface are ionically bonded with the migrated hydroxyls. Our calculations proposed a new structure model for nano-HAP, which indicates a surface structure with activities different from those without surface reorganization. This is particularly interesting because most bioactivities of biomaterials are dominated by their surface activity.

THz emission of donor and acceptor doped GaAs/AlGaAs quantum well structures with inserted thin AlAs monolayer

NASA Astrophysics Data System (ADS)

van Dommelen, Paphavee; Daengngam, Chalongrat; Kalasuwan, Pruet

2018-04-01

In this paper, we explore THz range optical intersubband transition energies in a donor doped quantum well of a GaAs/AlGaAs system as a function of the insertion position of an AlAs monolayer in the GaAs quantum well. In simulated models, the optical transition energies between electron subband levels 1 and 2 were higher in the doped structure than in the undoped structure. This may be because the envelope wave function of the second electron subband strongly overlapped the envelope wave function of the first electron subband and influenced the optical intersubband transition between the two levels in the THz range. At different levels of bias voltage at the Schottky barrier on the donor doped structure, the electric field in the growth direction of the structure linearly increased the further away the AlAs monolayer was placed from the reference position. We also simulated the optical transition energies between acceptor energy levels of the acceptor doped structure as a function of the insertion position of the AlAs monolayer. The acceptor doped structure induced THz range emission whereas the undoped structure induced mid-IR emission.

Structure and vibrational spectra of low-energy silicon clusters

NASA Astrophysics Data System (ADS)

Sieck, A.; Porezag, D.; Frauenheim, Th.; Pederson, M. R.; Jackson, K.

1997-12-01

We have identified low-energy structures of silicon clusters with 9 to 14 atoms using a nonorthogonal tight-binding method (TB) based on density-functional theory (DF). We have further investigated the resulting structures with an accurate all-electron first-principles technique. The results for cohesive energies, cluster geometries, and highest occupied to lowest unoccupied molecular orbital (HOMO-LUMO) gaps show an overall good agreement between DF-TB and self-consistent-field (SCF) DF theory. For Si9 and Si14, we have found equilibrium structures, whereas for Si11, Si12, and Si13, we present clusters with energies close to that of the corresponding ground-state structure recently proposed in the literature. The bonding scheme of clusters in this size range is different from the bulk tetrahedral symmetry. The most stable structures, characterized by low energies and large HOMO-LUMO gaps, have similar common subunits. To aid in their experimental identification, we have computed the full vibrational spectra of the structures, along with the Raman activities, IR intensities, and static polarizabilities, using SCF-DF theory within the local-density approximation (LDA). This method has already been successfully applied to the determination of Raman and IR spectra of silicon clusters with 3-8, 10, 13, 20, and 21 atoms.

A study of structural and mechanical properties of nano-crystalline tungsten nitride film synthesis by plasma focus

NASA Astrophysics Data System (ADS)

Hussnain, Ali; Singh Rawat, Rajdeep; Ahmad, Riaz; Hussain, Tousif; Umar, Z. A.; Ikhlaq, Uzma; Chen, Zhong; Shen, Lu

2015-02-01

Nano-crystalline tungsten nitride thin films are synthesized on AISI-304 steel at room temperature using Mather-type plasma focus system. The surface properties of the exposed substrate against different deposition shots are examined for crystal structure, surface morphology and mechanical properties using X-ray diffraction (XRD), atomic force microscope, field emission scanning electron microscope and nano-indenter. The XRD results show the growth of WN and WN2 phases and the development of strain/stress in the deposited films by varying the number of deposition shots. Morphology of deposited films shows the significant change in the surface structure with different ion energy doses (number of deposition shots). Due to the effect of different ion energy doses, the strain/stress developed in the deposited film leads to an improvement of hardness of deposited films.

Hierarchical structure and compressive deformation mechanisms of bighorn sheep (Ovis canadensis) horn.

PubMed

Huang, Wei; Zaheri, Alireza; Jung, Jae-Young; Espinosa, Horacio D; Mckittrick, Joanna

2017-12-01

Bighorn sheep (Ovis canadensis) rams hurl themselves at each other at speeds of ∼9 m/s (20 mph) to fight for dominance and mating rights. This necessitates impact resistance and energy absorption mechanisms, which stem from material-structure components in horns. In this study, the material hierarchical structure as well as correlations between the structure and mechanical properties are investigated. The major microstructural elements of horns are found as tubules and cell lamellae, which are oriented with (∼30⁰) angle with respect to each other. The cell lamellae contain keratin cells, in the shape of pancakes, possessing an average thickness of ∼2 µm and diameter of ∼20-30 µm. The morphology of keratin cells reveals the presence of keratin fibers and intermediate filaments with diameter of ∼200 nm and ∼12 nm, respectively, parallel to the cell surface. Quasi-static and high strain rate impact experiments, in different loading directions and hydration states, revealed a strong strain rate dependency for both dried and hydrated conditions. A strong anisotropy behavior was observed under impact for the dried state. The results show that the radial direction is the most preferable impact orientation because of its superior energy absorption. Detailed failure mechanisms under the aforementioned conditions are examined by bar impact recovery experiments. Shear banding, buckling of cell lamellae, and delamination in longitudinal and transverse direction were identified as the cause for strain softening under high strain rate impact. While collapse of tubules occurs in both quasi-static and impact tests, in radial and transverse directions, the former leads to more energy absorption and impact resistance. Bighorn sheep (Ovis canadensis) horns show remarkable impact resistance and energy absorption when undergoing high speed impact during the intraspecific fights. The present work illustrates the hierarchical structure of bighorn sheep horn at different length scales and investigates the energy dissipation mechanisms under different strain rates, loading orientations and hydration states. These results demonstrate how horn dissipates large amounts of energy, thus provide a new path to fabricate energy absorbent and crashworthiness engineering materials. Copyright © 2017 Acta Materialia Inc. Published by Elsevier Ltd. All rights reserved.

Metamorphic quantum dots: Quite different nanostructures

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

Seravalli, L.; Frigeri, P.; Nasi, L.

In this work, we present a study of InAs quantum dots deposited on InGaAs metamorphic buffers by molecular beam epitaxy. By comparing morphological, structural, and optical properties of such nanostructures with those of InAs/GaAs quantum dot ones, we were able to evidence characteristics that are typical of metamorphic InAs/InGaAs structures. The more relevant are: the cross-hatched InGaAs surface overgrown by dots, the change in critical coverages for island nucleation and ripening, the nucleation of new defects in the capping layers, and the redshift in the emission energy. The discussion on experimental results allowed us to conclude that metamorphic InAs/InGaAs quantummore » dots are rather different nanostructures, where attention must be put to some issues not present in InAs/GaAs structures, namely, buffer-related defects, surface morphology, different dislocation mobility, and stacking fault energies. On the other hand, we show that metamorphic quantum dot nanostructures can provide new possibilities of tailoring various properties, such as dot positioning and emission energy, that could be very useful for innovative dot-based devices.« less

Structure-affinity relationships for the binding of actinomycin D to DNA

NASA Astrophysics Data System (ADS)

Gallego, José; Ortiz, Angel R.; de Pascual-Teresa, Beatriz; Gago, Federico

1997-03-01

Molecular models of the complexes between actinomycin D and 14 different DNA hexamers were built based on the X-ray crystal structure of the actinomycin-d(GAAGCTTC)2 complex. The DNA sequences included the canonical GpC binding step flanked by different base pairs, nonclassical binding sites such as GpG and GpT, and sites containing 2,6-diamino- purine. A good correlation was found between the intermolecular interaction energies calculated for the refined complexes and the relative preferences of actinomycin binding to standard and modified DNA. A detailed energy decomposition into van der Waals and electrostatic components for the interactions between the DNA base pairs and either the chromophore or the peptidic part of the antibiotic was performed for each complex. The resulting energy matrix was then subjected to principal component analysis, which showed that actinomycin D discriminates among different DNA sequences by an interplay of hydrogen bonding and stacking interactions. The structure-affinity relationships for this important antitumor drug are thus rationalized and may be used to advantage in the design of novel sequence-specific DNA-binding agents.

Effects of hydrophobic and dipole-dipole interactions on the conformational transitions of a model polypeptide

NASA Astrophysics Data System (ADS)

Mu, Yan; Gao, Yi Qin

2007-09-01

We studied the effects of hydrophobicity and dipole-dipole interactions between the nearest-neighbor amide planes on the secondary structures of a model polypeptide by calculating the free energy differences between different peptide structures. The free energy calculations were performed with low computational costs using the accelerated Monte Carlo simulation (umbrella sampling) method, with a bias-potential method used earlier in our accelerated molecular dynamics simulations. It was found that the hydrophobic interaction enhances the stability of α helices at both low and high temperatures but stabilizes β structures only at high temperatures at which α helices are not stable. The nearest-neighbor dipole-dipole interaction stabilizes β structures under all conditions, especially in the low temperature region where α helices are the stable structures. Our results indicate clearly that the dipole-dipole interaction between the nearest neighboring amide planes plays an important role in determining the peptide structures. Current research provides a more unified and quantitative picture for understanding the effects of different forms of interactions on polypeptide structures. In addition, the present model can be extended to describe DNA/RNA, polymer, copolymer, and other chain systems.

Enhancement of electron correlation due to the molecular dimerization in organic superconductors β -(BDA-TTP )2X (X =I3, SbF6)

NASA Astrophysics Data System (ADS)

Aizawa, Hirohito; Kuroki, Kazuhiko; Yamada, Jun-ichi

2015-10-01

We perform a first-principles band calculation for quasi-two-dimensional organic superconductors β -(BDA -TTP) 2I3 and β -(BDA -TTP) 2SbF6. The first-principles band structures between the I3 and SbF6 salts are apparently different. We construct a tight-binding model for each material which accurately reproduces the first-principles band structure. The obtained transfer energies give the differences as follows: (i) larger dimerization in the I3 salt than the SbF6 salt, and (ii) different signs and directions of the interstacking transfer energies. To decompose the origin of the difference into the dimerization and the interstacking transfer energies, we adopt a simplified model by eliminating the dimerization effect and focus only on the difference caused by the interstacking transfer energies. From the analysis using the simplified model, we find that the difference of the band structure comes mainly from the strength of the dimerization. To compare the strength of the electron correlation having roots in the band structure, we calculate the physical properties originating from the effect of the electron correlation such as the spin susceptibility applying the two-particle self-consistent method. We find that the maximum value of the spin susceptibility for the I3 salt is larger than that of the SbF6 salt. Hypothetically decreasing the dimerization within the model of the I3 salt, the spin susceptibility takes almost the same value as that of the SbF6 salt for the same magnitude of the dimerization. We expect that the different ground state between the I3 and SbF6 salt mainly comes from the strength of the dimerization which is apparently masked in the band calculation along a particular k path.

Site-specific electronic structure analysis by channeling EELS and first-principles calculations.

PubMed

Tatsumi, Kazuyoshi; Muto, Shunsuke; Yamamoto, Yu; Ikeno, Hirokazu; Yoshioka, Satoru; Tanaka, Isao

2006-01-01

Site-specific electronic structures were investigated by electron energy loss spectroscopy (EELS) under electron channeling conditions. The Al-K and Mn-L(2,3) electron energy loss near-edge structure (ELNES) of, respectively, NiAl2O4 and Mn3O4 were measured. Deconvolution of the raw spectra with the instrumental resolution function restored the blunt and hidden fine features, which allowed us to interpret the experimental spectral features by comparing with theoretical spectra obtained by first-principles calculations. The present method successfully revealed the electronic structures specific to the differently coordinated cationic sites.

Vertical coupling and transition energies in multilayer InAs/GaAs quantum-dot structures

NASA Astrophysics Data System (ADS)

Taddei, S.; Colocci, M.; Vinattieri, A.; Bogani, F.; Franchi, S.; Frigeri, P.; Lazzarini, L.; Salviati, G.

2000-10-01

Vertically ordered quantum dots in multilayer InAs/GaAs structures have attracted large interest in recent years for device application as light emitters. Contradictory claims on the dependence of the fundamental transition energy on the interlayer separation and number of dot layers have been reported in the literature. We show that either a blueshift or a redshift of the fundamental transition energy can be observed in different coupling conditions and straightforwardly explained by including strain, indium segregation, and electron-hole Coulomb interaction, in good agreement with experimental results.

Accurate calibration for the quantification of the Al content in AlGaN epitaxial layers by energy-dispersive X-ray spectroscopy in a Transmission Electron Microscope

NASA Astrophysics Data System (ADS)

Amari, H.; Lari, L.; Zhang, H. Y.; Geelhaar, L.; Chèze, C.; Kappers, M. J.; McAleese, C.; Humphreys, C. J.; Walther, T.

2011-11-01

Since the band structure of group III- nitrides presents a direct electronic transition with a band-gap energy covering the range from 3.4 eV for (GaN) to 6.2 eV (for AlN) at room temperature as well as a high thermal conductivity, aluminium gallium nitride (AlGaN) is a strong candidate for high-power and high-temperature electronic devices and short-wavelength (visible and ultraviolet) optoelectronic devices. We report here a study by energy-filtered transmission electron microscopy (EFTEM) and energy-dispersive X-ray spectroscopy (EDXS) of the micro structure and elemental distribution in different aluminium gallium nitride epitaxial layers grown by different research groups. A calibration procedure is out-lined that yields the Al content from EDXS to within ~1 at % precision.

Halo-substituted azobenzenes adsorbed at Ag(111) and Au(111) interfaces: Structures and optical properties

NASA Astrophysics Data System (ADS)

Hughes, Zak E.; Baev, Alexander; Prasad, Paras N.; Walsh, Tiffany R.

2017-05-01

The adsorption of azobenzene (AB), ortho fluoro-azobenzene (FAB) and ortho chlor-azobenzol (ClAB), in both the cis and trans isomers, at the Au(111) and Ag(111) surfaces is investigated using plane-wave density functional calculations with the revPBE-vdW-DF functional. The resulting adsorption energies and internal structures of AB adsorbed to both metal surfaces are in broad agreement with available experimental data. In the gas phase, FAB and ClAB feature a significant reduction in the energy difference between the two isomeric states, compared with AB. This relative reduction in the energy difference is still significant for the adsorbed form of FAB but is only weakly apparent for ClAB. The absorption spectra of the molecules have also been calculated, with the halogen substituents generating significant changes in the gas phase, but only a modest difference for the adsorbed molecules.

The dynamical conductance of graphene tunnelling structures.

PubMed

Zhang, Huan; Chan, K S; Lin, Zijing

2011-12-16

The dynamical conductances of graphene tunnelling structures were numerically calculated using the scattering matrix method with the interaction effect included in a phenomenological approach. The overall single-barrier dynamical conductance is capacitative. Transmission resonances in the single-barrier structure lead to dips in the capacitative imaginary part of the response. This is different from the ac responses of typical semiconductor nanostructures, where transmission resonances usually lead to inductive peaks. The features of the dips depend on the Fermi energy. When the Fermi energy is below half of the barrier height, the dips are sharper. When the Fermi energy is higher than half of the barrier height, the dips are broader. Inductive behaviours can be observed in a double-barrier structure due to the resonances formed by reflection between the two barriers.

First-principles study of structure, electronic properties and stability of tungsten adsorption on TiC(111) surface with disordered vacancies

NASA Astrophysics Data System (ADS)

Ilyasov, Victor V.; Pham, Khang D.; Zhdanova, Tatiana P.; Phuc, Huynh V.; Hieu, Nguyen N.; Nguyen, Chuong V.

2017-12-01

In this paper, we systematically investigate the atomic structure, electronic and thermodynamic properties of adsorbed W atoms on the polar Ti-terminated TixCy (111) surface with different configurations of adsorptions using first principle calculations. The bond length, adsorption energy, and formation energy for different reconstructions of the atomic structure of the W/TixCy (111) systems were established. The effect of the tungsten coverage on the electronic structure and the adsorption mechanism of tungsten atom on the TixCy (111) are also investigated. We also suggest the possible mechanisms of W nucleation on the TixCy (111) surface. The effective charges on W atoms and nearest-neighbor atoms in the examined reconstructions were identified. Additionally, we have established the charge transfer from titanium atom to tungsten and carbon atoms which determine by the reconstruction of the local atomic and electronic structures. Our calculations showed that the charge transfer correlates with the electronegativity of tungsten and nearest-neighbor atoms. We also determined the effective charge per atom of titanium, carbon atoms, and neighboring adsorbed tungsten atom in different binding configurations. We found that, with reduction of the lattice symmetry associated with titanium and carbon vacancies, the adsorption energy increases by 1.2 times in the binding site A of W/TixCy systems.

Understanding the structure and functioning of polar pelagic ecosystems to predict the impacts of change

PubMed Central

Drinkwater, K. F.; Grant, S. M.; Heymans, J. J.; Hofmann, E. E.; Hunt, G. L.; Johnston, N. M.

2016-01-01

The determinants of the structure, functioning and resilience of pelagic ecosystems across most of the polar regions are not well known. Improved understanding is essential for assessing the value of biodiversity and predicting the effects of change (including in biodiversity) on these ecosystems and the services they maintain. Here we focus on the trophic interactions that underpin ecosystem structure, developing comparative analyses of how polar pelagic food webs vary in relation to the environment. We highlight that there is not a singular, generic Arctic or Antarctic pelagic food web, and, although there are characteristic pathways of energy flow dominated by a small number of species, alternative routes are important for maintaining energy transfer and resilience. These more complex routes cannot, however, provide the same rate of energy flow to highest trophic-level species. Food-web structure may be similar in different regions, but the individual species that dominate mid-trophic levels vary across polar regions. The characteristics (traits) of these species are also different and these differences influence a range of food-web processes. Low functional redundancy at key trophic levels makes these ecosystems particularly sensitive to change. To develop models for projecting responses of polar ecosystems to future environmental change, we propose a conceptual framework that links the life histories of pelagic species and the structure of polar food webs. PMID:27928038

Understanding the structure and functioning of polar pelagic ecosystems to predict the impacts of change.

PubMed

Murphy, E J; Cavanagh, R D; Drinkwater, K F; Grant, S M; Heymans, J J; Hofmann, E E; Hunt, G L; Johnston, N M

2016-12-14

The determinants of the structure, functioning and resilience of pelagic ecosystems across most of the polar regions are not well known. Improved understanding is essential for assessing the value of biodiversity and predicting the effects of change (including in biodiversity) on these ecosystems and the services they maintain. Here we focus on the trophic interactions that underpin ecosystem structure, developing comparative analyses of how polar pelagic food webs vary in relation to the environment. We highlight that there is not a singular, generic Arctic or Antarctic pelagic food web, and, although there are characteristic pathways of energy flow dominated by a small number of species, alternative routes are important for maintaining energy transfer and resilience. These more complex routes cannot, however, provide the same rate of energy flow to highest trophic-level species. Food-web structure may be similar in different regions, but the individual species that dominate mid-trophic levels vary across polar regions. The characteristics (traits) of these species are also different and these differences influence a range of food-web processes. Low functional redundancy at key trophic levels makes these ecosystems particularly sensitive to change. To develop models for projecting responses of polar ecosystems to future environmental change, we propose a conceptual framework that links the life histories of pelagic species and the structure of polar food webs. © 2016 The Authors.

Templating effect of the substrate on the structure of Cu-phthalocyanine thin film

NASA Astrophysics Data System (ADS)

Pierantozzi, Gian Marco; Sbroscia, Marco; Ruocco, Alessandro

2018-03-01

An experimental study of electronic properties, structure and morphology of Copper-phthalocyanine films deposited onto Al(100) and Au(110), as a function of thickness up to tens of nanometers, is presented. The monolayers grown on these two model substrates are already known to exhibit very different behavior for what concerns both the degree of interaction with the substrate and the formation of long range order; in this experiment, by means of low energy electron scattering and Electron Energy Loss Spectroscopy (EELS), remarkable differences are revealed also in the successive growth. Exploiting the link between the crystal structure and the lineshape of HOMO-LUMO transition in EELS spectrum, two different structural phases are identified, compatible with α and β phases, respectively in the case of the film grown on aluminum and on gold. Besides, the evolution of the specular reflection elastic peak indicates the formation of islands on the gold substrate and a more homogeneous growth on the aluminum one.

Evaluation of multiple-scale 3D characterization for coal physical structure with DCM method and synchrotron X-ray CT.

PubMed

Wang, Haipeng; Yang, Yushuang; Yang, Jianli; Nie, Yihang; Jia, Jing; Wang, Yudan

2015-01-01

Multiscale nondestructive characterization of coal microscopic physical structure can provide important information for coal conversion and coal-bed methane extraction. In this study, the physical structure of a coal sample was investigated by synchrotron-based multiple-energy X-ray CT at three beam energies and two different spatial resolutions. A data-constrained modeling (DCM) approach was used to quantitatively characterize the multiscale compositional distributions at the two resolutions. The volume fractions of each voxel for four different composition groups were obtained at the two resolutions. Between the two resolutions, the difference for DCM computed volume fractions of coal matrix and pores is less than 0.3%, and the difference for mineral composition groups is less than 0.17%. This demonstrates that the DCM approach can account for compositions beyond the X-ray CT imaging resolution with adequate accuracy. By using DCM, it is possible to characterize a relatively large coal sample at a relatively low spatial resolution with minimal loss of the effect due to subpixel fine length scale structures.

Kinesin Motor Enzymology: Chemistry, Structure, and Physics of Nanoscale Molecular Machines.

PubMed

Cochran, J C

2015-09-01

Molecular motors are enzymes that convert chemical potential energy into controlled kinetic energy for mechanical work inside cells. Understanding the biophysics of these motors is essential for appreciating life as well as apprehending diseases that arise from motor malfunction. This review focuses on kinesin motor enzymology with special emphasis on the literature that reports the chemistry, structure and physics of several different kinesin superfamily members.

Numerical study for identification of influence of energy absorption and frontal crush for vehicle crashworthiness

NASA Astrophysics Data System (ADS)

Suman, Shwetabh; Shah, Haard; Susarla, Vaibhav; Ravi, K.

2017-11-01

According to the statistics it has been seen that everyday nearly 400 people are killed due to road accidents. Due to this it has become an important concern to concentrate on the safety of the passengers which can be done by improving the crashworthiness of the vehicle. During the impact, a large amount of energy is released which if not absorbed, will be transmitted to the passenger compartment. For the safety of the passenger this energy has to be absorbed. Front rail is one of the main energy absorbing components in the vehicle front structure. When it comes to the structure and material of the part or component of the vehicle that is to be designed for crash, it is done based on three parameters: Specific Energy of Absorption, Mass of the front rail and maximum crush force. In this work, we are considering different internal geometries with different materials to increase the energy absorbing capacity of the front rail. Based on the extensive analysis carried aluminium seizes to be the opt material for frontal crash.

Structure of an energetic narrow discrete arc

NASA Technical Reports Server (NTRS)

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

1990-01-01

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

Mechanism and energetics of dislocation cross-slip in hcp metals

NASA Astrophysics Data System (ADS)

Wu, Zhaoxuan; Curtin, W. A.

2016-10-01

Hexagonal close-packed (hcp) metals such as Mg, Ti, and Zr are lightweight and/or durable metals with critical structural applications in the automotive (Mg), aerospace (Ti), and nuclear (Zr) industries. The hcp structure, however, brings significant complications in the mechanisms of plastic deformation, strengthening, and ductility, and these complications pose significant challenges in advancing the science and engineering of these metals. In hcp metals, generalized plasticity requires the activation of slip on pyramidal planes, but the structure, motion, and cross-slip of the associated dislocations are not well established even though they determine ductility and influence strengthening. Here, atomistic simulations in Mg reveal the unusual mechanism of dislocation cross-slip between pyramidal I and II planes, which occurs by cross-slip of the individual partial dislocations. The energy barrier is controlled by a fundamental step/jog energy and the near-core energy difference between pyramidal dislocations. The near-core energy difference can be changed by nonglide stresses, leading to tension-compression asymmetry and even a switch in absolute stability from one glide plane to the other, both features observed experimentally in Mg, Ti, and their alloys. The unique cross-slip mechanism is governed by common features of the generalized stacking fault energy surfaces of hcp pyramidal planes and is thus expected to be generic to all hcp metals. An analytical model is developed to predict the cross-slip barrier as a function of the near-core energy difference and applied stresses and quantifies the controlling features of cross-slip and pyramidal I/II stability across the family of hcp metals.

Light Absorption Enhancement of Silicon-Based Photovoltaic Devices with Multiple Bandgap Structures of Porous Silicon

PubMed Central

Wu, Kuen-Hsien; Li, Chong-Wei

2015-01-01

Porous-silicon (PS) multi-layered structures with three stacked PS layers of different porosity were prepared on silicon (Si) substrates by successively tuning the electrochemical-etching parameters in an anodization process. The three PS layers have different optical bandgap energy and construct a triple-layered PS (TLPS) structure with multiple bandgap energy. Photovoltaic devices were fabricated by depositing aluminum electrodes of Schottky contacts on the surfaces of the developed TLPS structures. The TLPS-based devices exhibit broadband photoresponses within the spectrum of the solar irradiation and get high photocurrent for the incident light of a tungsten lamp. The improved spectral responses of devices are owing to the multi-bandgap structures of TLPS, which are designed with a layered configuration analog to a tandem cell for absorbing a wider energy range of the incidental sun light. The large photocurrent is mainly ascribed to an enhanced light-absorption ability as a result of applying nanoporous-Si thin films as the surface layers to absorb the short-wavelength light and to improve the Schottky contacts of devices. Experimental results reveal that the multi-bandgap PS structures produced from electrochemical-etching of Si wafers are potentially promising for development of highly efficient Si-based solar cells. PMID:28793542

Silicide/Silicon Hetero-Junction Structure for Thermoelectric Applications.

PubMed

Jun, Dongsuk; Kim, Soojung; Choi, Wonchul; Kim, Junsoo; Zyung, Taehyoung; Jang, Moongyu

2015-10-01

We fabricated silicide/silicon hetero-junction structured thermoelectric device by CMOS process for the reduction of thermal conductivity with the scatterings of phonons at silicide/silicon interfaces. Electrical conductivities, Seebeck coefficients, power factors, and temperature differences are evaluated using the steady state analysis method. Platinum silicide/silicon multilayered structure showed an enhanced Seebeck coefficient and power factor characteristics, which was considered for p-leg element. Also, erbium silicide/silicon structure showed an enhanced Seebeck coefficient, which was considered for an n-leg element. Silicide/silicon multilayered structure is promising for thermoelectric applications by reducing thermal conductivity with an enhanced Seebeck coefficient. However, because of the high thermal conductivity of the silicon packing during thermal gradient is not a problem any temperature difference. Therefore, requires more testing and analysis in order to overcome this problem. Thermoelectric generators are devices that based on the Seebeck effect, convert temperature differences into electrical energy. Although thermoelectric phenomena have been used for heating and cooling applications quite extensively, it is only in recent years that interest has increased in energy generation.

[Energy Conservation and Emissions Reduction Benefits Analysis for Battery Electric Buses Based on Travel Services].

PubMed

Lin, Xiao-dan; Tian, Liang; Lü, Bin; Yang, Jian-xin

2015-09-01

Battery Electric Bus (BEB) has become one of prior options of urban buses for its "zero emission" during the driving stage. However, the environmental performance of electric buses is affected by multi-factors from the point of whole life cycle. In practice, carrying capacity of BEB and power generation structures can both implement evident effects on the energy consumption and pollutants emission of BEB. Therefore, take the above factors into consideration, in this article, Life Cycle Assessment is employed to evaluate the energy conservation and emissions reduction benefits of BEB. Results indicate that, travel service is more reasonable as the functional unit, rather than mileage, since the carrying capacity of BEB is 15% lower than the diesel buses. Moreover, compared with diesel buses, the energy conservation and emissions reduction benefits of battery electric buses are all different due to different regional power structures. Specifically, the energy benefits are 7. 84%, 11. 91%, 26. 90%, 11. 15%, 19. 55% and 20. 31% respectively in Huabei, Huadong, Huazhong, Dongbei, Xibei and Nanfang power structure. From the point of comprehensive emissions reduction benefits, there is no benefit in Huabei power structure, as it depends heavily on coal. But in other areas, the comprehensive emissions reduction benefits of BEB are separately 3. 46%, 26. 81%, 1. 17%, 13. 74% and 17. 48% in Huadong, Huazhong, Dongbei, Xibei and Nanfang. Therefore, it suggests that, enlargement of carrying capacity should be taken as the most prior technology innovation direction for BEB, and the grids power structure should be taken into consideration when the development of BEB is in planning.

Investigation of thermal energy transport interface of hybrid graphene-carbon nanotube/polyethylene nanocomposites.

PubMed

Liu, Feng; Liu, Xuyang; Hu, Ning; Ning, Huiming; Atobe, Satoshi; Yan, Cheng; Mo, Fuhao; Fu, Shaoyun; Zhang, Jianyu; Wang, Yu; Mu, Xiaojing

2017-10-31

It is well known the thermal properties of three-dimensional (3-D) hybrid graphene (GR)-carbon nanotube (CNT) structures are not superior to that of the individual GR and CNT, however, the 3-D hybrid GR-CNT structures can effectively improve the thermal properties of polymer matrix. Therefore, understanding the thermal energy transport in the interface between polymer matrix and 3-D hybrid GR-CNT structure is essential. Here, the enhancement mechanism of interfacial thermal transport of hybrid GR-CNT structure was explored by applying non-equilibrium molecular dynamics (NEMD) simulations. Three different types of hybrid GR-CNT structures were built. The influences of CNT radius and CNT type for the hybrid GR-CNT on the interfacial thermal properties were also analyzed. Computational results show that among the three different types of hybrid GR-CNT structures, the Model-I, i.e., the covalent bond hybrid GR-CNT structures are of the best interfacial thermal properties. Meanwhile, the CNT radius of hybrid GR-CNT structure has a great influence on the interfacial thermal properties.

Magnetar Giant Flares in Multipolar Magnetic Fields. III. Multipolar Magnetic Field Structure Variations

NASA Astrophysics Data System (ADS)

Yao, Guang-Rui; Huang, Lei; Yu, Cong; Shen, Zhi-Qiang

2018-02-01

We have analyzed the multipolar magnetic field structure variation at neutron star surface by means of the catastrophic eruption model and find that the variation of the geometry of multipolar fields on the magnetar surface could result in the catastrophic rearrangement of the magnetosphere, which provides certain physical mechanism for the outburst of giant flares. The magnetospheric model we adopted consists of two assumptions: (1) a helically twisted flux rope is suspended in an ideal force-free magnetosphere around the magnetar, and (2) a current sheet emerges during the flux rope evolution. Magnetic energy accumulates during the flux rope’s gradual evolution along with the variation of magnetar surface magnetic structure before the eruption. The two typical behaviors, either state transition or catastrophic escape, would take place once the flux rope loses equilibrium; thus, tremendous accumulated energy is radiated. We have investigated the equilibrium state of the flux rope and the energy release affected by different multipolar structures and find structures that could trigger violent eruption and provide the radiation approximately 0.5% of the total magnetic energy during the giant flare outburst. Our results provide certain multipolar structures of the neutron star’s magnetic field with an energy release percentage 0.42% in the state transition and 0.51% in the catastrophic escape case, which are sufficient for the previously reported energy release from SGR 1806–20 giant flares.

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.

Combined MCD/DFT/TDDFT Study of the Electronic Structure of Axially Pyridine Coordinated Metallocorroles.

PubMed

Rhoda, Hannah M; Crandall, Laura A; Geier, G Richard; Ziegler, Christopher J; Nemykin, Victor N

2015-05-18

A series of metallocorroles were investigated by UV-vis and magnetic circular dichroism spectroscopies. The diamagnetic distorted square-pyramidal main-group corrole Ga(tpfc)py (2), the diamagnetic distorted octahedral transition-metal adduct Co(tpfc)(py)2 (3), and paramagnetic distorted octahedral transition-metal complex Fe(tpfc)(py)2 (4) [H3tpfc = tris(perfluorophenyl)corrole] were studied to investigate similarities and differences in the electronic structure and spectroscopy of the closed- and open-shell metallocorroles. Similar to the free-base H3tpfc (1), inspection of the MCD Faraday B-terms for all of the macrocycles presented in this report revealed that a ΔHOMO < ΔLUMO [ΔHOMO is the energy difference between two highest energy corrole-centered π-orbitals and ΔLUMO is the energy difference between two lowest energy corrole-centered π*-orbitals originating from ML ± 4 and ML ± 5 pairs of perimeter] condition is present for each complex, which results in an unusual sign-reversed sequence for π-π* transitions in their MCD spectra. In addition, the MCD spectra of the cobalt and the iron complexes were also complicated by a number of charge-transfer states in the visible region. Iron complex 4 also exhibits a low-energy absorption in the NIR region (1023 nm). DFT and TDDFT calculations were used to elaborate the electronic structures and provide band assignments in UV-vis and MCD spectra of the metallocorroles. DFT and TDDFT calculations predict that the orientation of the axial pyridine ligand(s) has a very minor influence on the calculated electronic structures and absorption spectra in the target systems.

Advances in Spiropyrans/Spirooxazines and Applications Based on Fluorescence Resonance Energy Transfer (FRET) with Fluorescent Materials.

PubMed

Xia, Hongyan; Xie, Kang; Zou, Gang

2017-12-18

Studies on the following were reviewed: (1) the structure of spiropyrans and spirooxazines (two kinds of spiro compounds) under external stimuli and (2) the construction and applications of composite systems based on fluorescence resonance energy transfer (FRET) with fluorescent materials. When treated with different stimuli (light, acids and bases, solvents, metal ions, temperature, redox potential, and so on), spiropyrans/spirooxazines undergo transformations between the ring-closed form (SP), the ring-opened merocyanine (MC) form, and the protonated ring-opened form (MCH). This is due to the breakage of the spiro C-O bond and the protonation of MC, along with a color change. Various novel, multifunctional materials based on photochromic spiropyrans and spirooxazines have been successfully developed because of the vastly differently physiochemical properties posssed by the SP, MC and MCH forms. Among the three different structural forms, the MC form has been studied most extensively. The MC form not only gives complexes with various inorganic particles, biological molecules, and organic chemicals but also acts as the energy acceptor (of energy from fluorescent molecules) during energy transfer processes that take place under proper conditions. Furthermore, spiropyran and spirooxazine compounds exhibit reversible physicochemical property changes under proper stimuli; this provides more advantages compared with other photochromic compounds. Additionally, the molecular structures of spiropyrans and spirooxazines can be easily modified and extended, so better compounds can be obtained to expand the scope of already known applications. Described in detail are: (1) the structural properties of spiropyrans and spirooxazines and related photochromic mechanisms; (2) composite systems based on spiropyrans and spirooxazines, and (3) fluorescent materials which have potential applications in sensing, probing, and a variety of optical elements.

Liquid-phase tuning of porous PVDF-TrFE film on flexible substrate for energy harvesting

NASA Astrophysics Data System (ADS)

Chen, Dajing; Chen, Kaina; Brown, Kristopher; Hang, Annie; Zhang, John X. J.

2017-04-01

Emerging wearable and implantable biomedical energy harvesting devices demand efficient power conversion, flexible structures, and lightweight construction. This paper presents Polyvinylidene fluoride-trifluoroethylene (PVDF-TrFE) micro-porous structures, which can be tuned to specific mechanical flexibilities and optimized for piezoelectric power conversion. Specifically, the water vapor phase separation method was developed to control microstructure formation, pore diameter, porosity, and mechanical flexibility. Furthermore, we investigated the effects of the piezoelectric layer to supporting layer Young's modulus ratio, through using both analytical calculation and experimentation. Both structure flexibility and stress-induced voltage were considered in the analyses. Specification of electromechanical coupling efficiency, made possible by carefully designed three-dimensional porous structures, was shown to increase the power output by five-fold relative to uncoupled structures. Therefore, flexible PVDF-TrFE films with tunable microstructures, paired with substrates of different rigidities, provide highly efficient designs of compact piezoelectric energy generating devices.

The establishment and application of direct coupled electrostatic-structural field model in electrostatically controlled deployable membrane antenna

NASA Astrophysics Data System (ADS)

Gu, Yongzhen; Duan, Baoyan; Du, Jingli

2018-05-01

The electrostatically controlled deployable membrane antenna (ECDMA) is a promising space structure due to its low weight, large aperture and high precision characteristics. However, it is an extreme challenge to describe the coupled field between electrostatic and membrane structure accurately. A direct coupled method is applied to solve the coupled problem in this paper. Firstly, the membrane structure and electrostatic field are uniformly described by energy, considering the coupled problem is an energy conservation phenomenon. Then the direct coupled electrostatic-structural field governing equilibrium equations are obtained by energy variation approach. Numerical results show that the direct coupled method improves the computing efficiency by 36% compared with the traditional indirect coupled method with the same level accuracy. Finally, the prototype has been manufactured and tested and the ECDMA finite element simulations show good agreement with the experiment results as the maximum surface error difference is 6%.

Solid energy calibration standards for P K-edge XANES: electronic structure analysis of PPh4Br.

PubMed

Blake, Anastasia V; Wei, Haochuan; Donahue, Courtney M; Lee, Kyounghoon; Keith, Jason M; Daly, Scott R

2018-03-01

P K-edge X-ray absorption near-edge structure (XANES) spectroscopy is a powerful method for analyzing the electronic structure of organic and inorganic phosphorus compounds. Like all XANES experiments, P K-edge XANES requires well defined and readily accessible calibration standards for energy referencing so that spectra collected at different beamlines or under different conditions can be compared. This is especially true for ligand K-edge X-ray absorption spectroscopy, which has well established energy calibration standards for Cl (Cs 2 CuCl 4 ) and S (Na 2 S 2 O 3 ·5H 2 O), but not neighboring P. This paper presents a review of common P K-edge XANES energy calibration standards and analysis of PPh 4 Br as a potential alternative. The P K-edge XANES region of commercially available PPh 4 Br revealed a single, highly resolved pre-edge feature with a maximum at 2146.96 eV. PPh 4 Br also showed no evidence of photodecomposition when repeatedly scanned over the course of several days. In contrast, we found that PPh 3 rapidly decomposes under identical conditions. Density functional theory calculations performed on PPh 3 and PPh 4 + revealed large differences in the molecular orbital energies that were ascribed to differences in the phosphorus oxidation state (III versus V) and molecular charge (neutral versus +1). Time-dependent density functional theory calculations corroborated the experimental data and allowed the spectral features to be assigned. The first pre-edge feature in the P K-edge XANES spectrum of PPh 4 Br was assigned to P 1s → P-C π* transitions, whereas those at higher energy were P 1s → P-C σ*. Overall, the analysis suggests that PPh 4 Br is an excellent alternative to other solid energy calibration standards commonly used in P K-edge XANES experiments.

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.

Energy consumption analysis for various memristive networks under different learning strategies

NASA Astrophysics Data System (ADS)

Deng, Lei; Wang, Dong; Zhang, Ziyang; Tang, Pei; Li, Guoqi; Pei, Jing

2016-02-01

Recently, various memristive systems emerge to emulate the efficient computing paradigm of the brain cortex; whereas, how to make them energy efficient still remains unclear, especially from an overall perspective. Here, a systematical and bottom-up energy consumption analysis is demonstrated, including the memristor device level and the network learning level. We propose an energy estimating methodology when modulating the memristive synapses, which is simulated in three typical neural networks with different synaptic structures and learning strategies for both offline and online learning. These results provide an in-depth insight to create energy efficient brain-inspired neuromorphic devices in the future.

[Research on the photoelectric conversion efficiency of grating antireflective layer solar cells].

PubMed

Zhong, Hui; Gao, Yong-Yi; Zhou, Ren-Long; Zhou, Bing-ju; Tang, Li-qiang; Wu, Ling-xi; Li, Hong-jian

2011-07-01

A numerical investigation of the effect of grating antireflective layer structure on the photoelectric conversion efficiency of solar cells was carried out by the finite-difference time-domain method. The influence of grating shape, height and the metal film thickness coated on grating surface on energy storage was analyzed in detail. It was found that the comparison between unoptimized and optimized surface grating structure on solar cells shows that the optimization of surface by grating significantly increases the energy storage capability and greatly improves the efficiency, especially of the photoelectric conversion efficiency and energy storage of the triangle grating. As the film thickness increases, energy storage effect increases, while as the film thickness is too thick, energy storage effect becomes lower and lower.

Human development VII: a spiral fractal model of fine structure of physical energy could explain central aspects of biological information, biological organization and biological creativity.

PubMed

Ventegodt, Søren; Hermansen, Tyge Dahl; Flensborg-Madsen, Trine; Rald, Erik; Nielsen, Maj Lyck; Merrick, Joav

2006-11-14

In this paper we have made a draft of a physical fractal essence of the universe, a sketch of a new cosmology, which we believe to lay at the root of our new holistic biological paradigm. We present the fractal roomy spiraled structures and the energy-rich dancing "infinite strings" or lines of the universe that our hypothesis is based upon. The geometric language of this cosmology is symbolic and both pre-mathematical and pre-philosophical. The symbols are both text and figures, and using these we step by step explain the new model that at least to some extent is able to explain the complex informational system behind morphogenesis, ontogenesis, regeneration and healing. We suggest that it is from this highly dynamic spiraled structure that organization of cells, organs, and the wholeness of the human being including consciousness emerge. The model of "dancing fractal spirals" carries many similarities to premodern cultures descriptions of the energy of the life and universe. Examples are the Native American shamanistic descriptions of their perception of energy and the old Indian Yogis descriptions of the life-energy within the body and outside. Similar ideas of energy and matter are found in the modern superstring theories. The model of the informational system of the organism gives new meaning to Bateson's definition of information: "A difference that makes a difference", and indicates how information-directed self-organization can exist on high structural levels in living organisms, giving birth to their subjectivity and consciousness.

Phase competition in the growth of SrCoOx/LaAlO3 thin films

NASA Astrophysics Data System (ADS)

Zhang, Jie; Meng, Dechao; Huang, Haoliang; Cai, Honglei; Huang, Qiuping; Wang, Jianlin; Yang, Yuanjun; Zhai, Xiaofang; Fu, Zhengping; Lu, Yalin

2018-02-01

The reversible topotactic phase transformation between brownmillerite SrCoO2.5 to perovskite SrCoO3 has attracted more and more attention for potential applications as solid oxide fuels and electrolysis cells. However, the relatively easy transformation result from small thermal stable energy barriers between the two phases leads to unstable the structures. In the paper, amounts of SrCoO3-δ films have been prepared by pulsed laser deposition at optimized growth conditions with the temperature range of 590-720°C. The X-ray diffraction (XRD) results demonstrated that a phase competition emerged around 650°C. The Gibbs free energies of two phases at high temperature revealed the difference of stability of these two phases under different growth temperature. The optical spectroscopies and X-ray photoelectron spectroscopies were used to verify the electronic structure and chemical state differences between the two phases with distinct crystal structures.

On the use of big-bang method to generate low-energy structures of atomic clusters modeled with pair potentials of different ranges.

PubMed

Marques, J M C; Pais, A A C C; Abreu, P E

2012-02-05

The efficiency of the so-called big-bang method for the optimization of atomic clusters is analysed in detail for Morse pair potentials with different ranges; here, we have used Morse potentials with four different ranges, from long- ρ = 3) to short-ranged ρ = 14) interactions. Specifically, we study the efficacy of the method in discovering low-energy structures, including the putative global minimum, as a function of the potential range and the cluster size. A new global minimum structure for long-ranged ρ = 3) Morse potential at the cluster size of n= 240 is reported. The present results are useful to assess the maximum cluster size for each type of interaction where the global minimum can be discovered with a limited number of big-bang trials. Copyright © 2011 Wiley Periodicals, Inc.

Short-Term Energy Outlook Model Documentation: Electricity Generation and Fuel Consumption Models

EIA Publications

2014-01-01

The electricity generation and fuel consumption models of the Short-Term Energy Outlook (STEO) model provide forecasts of electricity generation from various types of energy sources and forecasts of the quantities of fossil fuels consumed for power generation. The structure of the electricity industry and the behavior of power generators varies between different areas of the United States. In order to capture these differences, the STEO electricity supply and fuel consumption models are designed to provide forecasts for the four primary Census regions.

Relationship Study on Land Use Spatial Distribution Structure and Energy-Related Carbon Emission Intensity in Different Land Use Types of Guangdong, China, 1996–2008

PubMed Central

Huang, Yi; Yang, Lei

2013-01-01

This study attempts to discuss the relationship between land use spatial distribution structure and energy-related carbon emission intensity in Guangdong during 1996–2008. We quantized the spatial distribution structure of five land use types including agricultural land, industrial land, residential and commercial land, traffic land, and other land through applying spatial Lorenz curve and Gini coefficient. Then the corresponding energy-related carbon emissions in each type of land were calculated in the study period. Through building the reasonable regression models, we found that the concentration degree of industrial land is negatively correlated with carbon emission intensity in the long term, whereas the concentration degree is positively correlated with carbon emission intensity in agricultural land, residential and commercial land, traffic land, and other land. The results also indicate that land use spatial distribution structure affects carbon emission intensity more intensively than energy efficiency and production efficiency do. These conclusions provide valuable reference to develop comprehensive policies for energy conservation and carbon emission reduction in a new perspective. PMID:23476128

Relationship study on land use spatial distribution structure and energy-related carbon emission intensity in different land use types of Guangdong, China, 1996-2008.

PubMed

Huang, Yi; Xia, Bin; Yang, Lei

2013-01-01

This study attempts to discuss the relationship between land use spatial distribution structure and energy-related carbon emission intensity in Guangdong during 1996-2008. We quantized the spatial distribution structure of five land use types including agricultural land, industrial land, residential and commercial land, traffic land, and other land through applying spatial Lorenz curve and Gini coefficient. Then the corresponding energy-related carbon emissions in each type of land were calculated in the study period. Through building the reasonable regression models, we found that the concentration degree of industrial land is negatively correlated with carbon emission intensity in the long term, whereas the concentration degree is positively correlated with carbon emission intensity in agricultural land, residential and commercial land, traffic land, and other land. The results also indicate that land use spatial distribution structure affects carbon emission intensity more intensively than energy efficiency and production efficiency do. These conclusions provide valuable reference to develop comprehensive policies for energy conservation and carbon emission reduction in a new perspective.

Interfacial and thermal energy driven growth and evolution of Langmuir-Schaefer monolayers of Au-nanoparticles.

PubMed

Mukhopadhyay, Mala; Hazra, S

2018-01-03

Structures of Langmuir-Schaefer (LS) monolayers of thiol-coated Au-nanoparticles (DT-AuNPs) deposited on H-terminated and OTS self-assembled Si substrates (of different hydrophobic strength and stability) and their evolution with time under ambient conditions, which plays an important role for their practical use as 2D-nanostructures over large areas, were investigated using the X-ray reflectivity technique. The strong effect of substrate surface energy (γ) on the initial structures and the competitive role of room temperature thermal energy (kT) and the change in interfacial energy (Δγ) at ambient conditions on the evolution and final structures of the DT-AuNP LS monolayers are evident. The strong-hydrophobic OTS-Si substrate, during transfer, seems to induce strong attraction towards hydrophobic DT-AuNPs on hydrophilic (repulsive) water to form vertically compact partially covered (with voids) monolayer structures (of perfect monolayer thickness) at low pressure and nearly covered buckled monolayer structures (of enhanced monolayer thickness) at high pressure. After transfer, the small kT-energy (in absence of repulsive water) probably fluctuates the DT-AuNPs to form vertically expanded monolayer structures, through systematic exponential growth with time. The effect is prominent for the film deposited at low pressure, where the initial film-coverage and film-thickness are low. On the other hand, the weak-hydrophobic H-Si substrate, during transfer, appears to induce optimum attraction towards DT-AuNPs to better mimic the Langmuir monolayer structures on it. After transfer, the change in the substrate surface nature, from weak-hydrophobic to weak-hydrophilic with time (i.e. Δγ-energy, apart from the kT-energy), enhances the size of the voids and weakens the monolayer/bilayer structure to form a similar expanded monolayer structure, the thickness of which is probably optimized by the available thermal energy.

Structural and electronic properties of high pressure phases of lead chalcogenides

NASA Astrophysics Data System (ADS)

Petersen, John; Scolfaro, Luisa; Myers, Thomas

2012-10-01

Lead chalcogenides, most notably PbTe and PbSe, have become an active area of research due to their thermoelectric properties. The high figure of merit (ZT) of these materials has brought much attention to them, due to their ability to convert waste heat into electricity. Variation in synthesis conditions gives rise to a need for analysis of structural and thermoelectric properties of these materials at different pressures. In addition to the NaCl structure at ambient conditions, lead chalcogenides have a dynamic orthorhombic (Pnma) intermediate phase and a higher pressure yet stable CsCl phase. By altering the lattice constant, we simulate the application of external pressure; this has notable effects on ground state total energy, band gap, and structural phase. Using the General Gradient Approximation (GGA) in Density Functional Theory (DFT), we calculate the phase transition pressures by finding the differences in enthalpy from total energy calculations. For each phase, elastic constants, bulk modulus, shear modulus, Young's modulus, and hardness are calculated, using two different approaches. In addition to structural properties, we analyze the band structure and density of states at varying pressures, paying special note to thermoelectric implications.

Long-range empirical potential model: extension to hexagonal close-packed metals.

PubMed

Dai, Y; Li, J H; Liu, B X

2009-09-23

An n-body potential is developed and satisfactorily applied to hcp metals, Co, Hf, Mg, Re, Ti, and Zr, in the form of long-range empirical potential. The potential can well reproduce the lattice constants, c/a ratios, cohesive energies, and the bulk modulus for their stable structures (hcp) and metastable structures (bcc or fcc). Meanwhile, the potential can correctly predict the order of structural stability and distinguish the energy differences between their stable hcp structure and other structures. The energies and forces derived by the potential can smoothly go to zero at cutoff radius, thus completely avoiding the unphysical behaviors in the simulations. The developed potential is applied to study the vacancy, surface fault, stacking fault and self-interstitial atom in the hcp metals. The calculated formation energies of vacancy and divacancy and activation energies of self-diffusion by vacancies are in good agreement with the values in experiments and in other works. The calculated surface energies and stacking fault energies are also consistent with the experimental data and those obtained in other theoretical works. The calculated formation energies generally agree with the results in other works, although the stable configurations of self-interstitial atoms predicted in this work somewhat contrast with those predicted by other methods. The proposed potential is shown to be relevant for describing the interaction of bcc, fcc and hcp metal systems, bringing great convenience for researchers in constructing potentials for metal systems constituted by any combination of bcc, fcc and hcp metals.

Influence of material structure on air-borne ultrasonic application in drying.

PubMed

Ozuna, César; Gómez Álvarez-Arenas, Tomás; Riera, Enrique; Cárcel, Juan A; Garcia-Perez, Jose V

2014-05-01

This work aims to contribute to the understanding of how the properties of the material being dried affect air-borne ultrasonic application. To this end, the experimental drying kinetics (40°C and 1m/s) of cassava (Manihot esculenta) and apple (Malus domestica var. Granny Smith) were carried out applying different ultrasonic powers (0, 6, 12, 19, 25 and 31 kW/m(3)). Furthermore, the power ultrasound-assisted drying kinetics of different fruits and vegetables (potato, eggplant, carrot, orange and lemon peel) already reported in previous studies were also analyzed. The structural, textural and acoustic properties of all these products were assessed, and the drying kinetics modeled by means of the diffusion theory. A significant linear correlation (r>0.95) was established between the identified effective diffusivity (DW) and the applied ultrasonic power for the different products. The slope of this relationship (SDUP) was used as an index of the effectiveness of the ultrasonic application; thus the higher the SDUP, the more effective the ultrasound application. SDUP was well correlated (r ⩾ 0.95) with the porosity and hardness. In addition, SDUP was largely affected by the acoustic impedance of the material being dried, showing a similar pattern with the impedance than the transmission coefficient of the acoustic energy on the interface. Thus, soft and open-porous product structures exhibited a better transmission of acoustic energy and were more prone to the mechanical effects of ultrasound. However, materials with a hard and closed-compact structure were less affected by acoustic energy due to the fact that the significant impedance differences between the product and the air cause high energy losses on the interface. Copyright © 2013 Elsevier B.V. All rights reserved.

Structure and energy of non-canonical basepairs: comparison of various computational chemistry methods with crystallographic ensembles.

PubMed

Panigrahi, Swati; Pal, Rahul; Bhattacharyya, Dhananjay

2011-12-01

Different types of non-canonical basepairs, in addition to the Watson-Crick ones, are observed quite frequently in RNA. Their importance in the three dimensional structure is not fully understood, but their various roles have been proposed by different groups. We have analyzed the energetics and geometry of 32 most frequently observed basepairs in the functional RNA crystal structures using different popular empirical, semi-empirical and ab initio quantum chemical methods and compared their optimized geometry with the crystal data. These basepairs are classified into three categories: polar, non-polar and sugar-mediated, depending on the types of atoms involved in hydrogen bonding. In case of polar basepairs, most of the methods give rise to optimized structures close to their initial geometry. The interaction energies also follow similar trends, with the polar ones having more attractive interaction energies. Some of the C-H...O/N hydrogen bond mediated non-polar basepairs are also found to be significantly stable in terms of their interaction energy values. Few polar basepairs, having amino or carboxyl groups not hydrogen bonded to anything, such as G:G H:W C, show large flexibility. Most of the non-polar basepairs, except A:G s:s T and A:G w:s C, are found to be stable; indicating C-H...O/N interaction also plays a prominent role in stabilizing the basepairs. The sugar mediated basepairs show variability in their structures, due to the involvement of flexible ribose sugar. These presumably indicate that the most of the polar basepairs along with few non-polar ones act as seed for RNA folding while few may act as some conformational switch in the RNA.

A density functional theory study on the structural and electronic properties of PbxSbySez (x + y + z = 2, 3) clusters

NASA Astrophysics Data System (ADS)

Peköz, Rengi˙n; Erkoç, Şaki˙r

2018-01-01

The structural and electronic properties of neutral ternary PbxSbySez clusters (x + y + z = 2, 3) in their ground states have been explored by means of density functional theory calculations. The geometric structures and binding energies are systematically explored and for the most stable configurations of each cluster type vibrational frequencies, charges on atoms, energy difference between highest occupied and lowest unoccupied molecular orbitals, and the possible dissociations channels have been analyzed. Depending on being binary or ternary cluster and composition, the most energetic structures have singlet, doublet or triplet ground states, and trimers prefer to form isosceles, equilateral or scalene triangle structure.

Defect formation energy in pyrochlore: the effect of crystal size

NASA Astrophysics Data System (ADS)

Wang, Jianwei; Ewing, Rodney C.; Becker, Udo

2014-09-01

Defect formation energies of point defects of two pyrochlores Gd2Ti2O7 and Gd2Zr2O7 as a function of crystal size were calculated. Density functional theory with plane-wave basis sets and the projector-augmented wave method were used in the calculations. The results show that the defect formation energies of the two pyrochlores diverge as the size decreases to the nanometer range. For Gd2Ti2O7 pyrochlore, the defect formation energy is higher at nanometers with respect to that of the bulk, while it is lower for Gd2Zr2O7. The lowest defect formation energy for Gd2Zr2O7 is found at 15-20 Å. The different behaviors of the defect formation energies as a function of crystal size are caused by different structural adjustments around the defects as the size decreases. For both pyrochlore compositions at large sizes, the defect structures are similar to those of the bulk. As the size decreases, for Gd2Ti2O7, additional structure distortions appear at the surfaces, which cause the defect formation energy to increase. For Gd2Zr2O7, additional oxygen Frenkel pair defects are introduced, which reduce the defect formation energy. As the size further decreases, increased structure distortions occur at the surfaces, which cause the defect formation energy to increase. Based on a hypothesis that correlates the energetics of defect formation and radiation response for complex oxides, the calculated results suggest that at nanometer range Gd2Ti2O7 pyrochlore is expected to have a lower radiation tolerance, and those of Gd2Zr2O7 pyrochlore to have a higher radiation tolerance. The highest radiation tolerance for Gd2Zr2O7 pyrochlore is expected to be found at ˜2 nanometers.

Modification of WS2 nanosheets with controllable layers via oxygen ion irradiation

NASA Astrophysics Data System (ADS)

Song, Honglian; Yu, Xiaofei; Chen, Ming; Qiao, Mei; Wang, Tiejun; Zhang, Jing; Liu, Yong; Liu, Peng; Wang, Xuelin

2018-05-01

As one kind of two-dimensional materials, WS2 nanosheets have drawn much attention with different kinds of research methods. Yet ion irradiation method was barely used for WS2 nanosheets. In this paper, the structure, composition and optical band gap (Eg) of the multilayer WS2 films deposited by chemical vapor deposition (CVD) method on sapphire substrates before and after oxygen ion irradiation with different energy and fluences were studied. Precise tailored layer-structures and a controllable optical band gap of WS2 nanosheets were achieved after oxygen ion irradiation. The results shows higher energy oxygen irradiation changed the shape from triangular shaped grains to irregular rectangle shape but did not change 2H-WS2 phase structure. The intensity of E2g1 (Г) and A1g (Г) modes decreased and have small shifts after oxygen ion irradiation. The peak frequency difference between the E2g1 (Г) and A1g (Г) modes (Δω) decreased after oxygen ion irradiation, and this result indicates the number of layers decreased after oxygen ion irradiation. The Eg decreased with the increase of the energy and the fluence of oxygen ions. The number of layers, thickness and optical band gap changed after ion irradiation with different ion fluences and energies. The results proposed a new strategy for precise control of multilayer nanosheets and demonstrated the high applicability of ion irradiation in super-capacitors, field effect transistors and other applications.

Ab initio and DFT study of hydrogen bond interactions between ascorbic acid and dimethylsulfoxide based on FT-IR and FT-Raman spectra

NASA Astrophysics Data System (ADS)

Niazazari, Naser; Zatikyan, Ashkhen L.; Markarian, Shiraz A.

2013-06-01

The hydrogen bonding of 1:1 complexes formed between L-ascorbic acid (LAA) and dimethylsulfoxide (DMSO) has been studied by means of ab initio and density functional theory (DFT) calculations. Solutions of L-ascorbic acid (AA) in dimethylsulfoxide (DMSO) have been studied by means of both FT-IR (4000-220 cm-1) and FT-Raman spectroscopy. Ab initio Hartree-Fock (HF) and DFT methods have been used to determine the structure and energies of stable conformers of various types of L-AA/DMSO complexes in gas phase and solution. The basis sets 6-31++G∗∗ and 6-311+G∗ were used to describe the structure, energy, charges and vibrational frequencies of interacting complexes in the gas phase. The optimized geometric parameters and interaction energies for various complexes at different theories have been estimated. Binding energies have been corrected for basis set superposition error (BSSE) and harmonic vibrational frequencies of the structures have been calculated to obtain the stable forms of the complexes. The self-consistent reaction field (SCRF) has been used to calculate the effect of DMSO as the solvent on the geometry, energy and charges of complexes. The solvent effect has been studied using the Onsager models. It is shown that the polarity of the solvent plays an important role on the structures and relative stabilities of different complexes. The results obtained show that there is a satisfactory correlation between experimental and theoretical predictions.

Spatial and temporal benthic species assemblage responses with a deployed marine tidal energy device: a small scaled study.

PubMed

Broadhurst, Melanie; Orme, C David L

2014-08-01

The addition of man-made structures to the marine environment is known to increase the physical complexity of the seafloor, which can influence benthic species community patterns and habitat structure. However, knowledge of how deployed tidal energy device structures influence benthic communities is currently lacking. Here we examined species biodiversity, composition and habitat type surrounding a tidal energy device within the European Marine Energy Centre test site, Orkney. Commercial fishing and towed video camera techniques were used over three temporal periods, from 2009 to 2010. Our results showed increased species biodiversity and compositional differences within the device site, compared to a control site. Both sites largely comprised of crustacean species, omnivore or predatory feeding regimes and marine tide-swept EUNIS habitat types, which varied over the time. We conclude that the device could act as a localised artificial reef structure, but that further in-depth investigations are required. Copyright © 2014 Elsevier Ltd. All rights reserved.

Vibrational Fingerprints of Low-Lying Pt(n)P(2n) (n = 1-5) Cluster Structures from Global Optimization Based on Density Functional Theory Potential Energy Surfaces.

PubMed

Jedidi, Abdesslem; Li, Rui; Fornasiero, Paolo; Cavallo, Luigi; Carbonniere, Philippe

2015-12-03

Vibrational fingerprints of small Pt(n)P(2n) (n = 1-5) clusters were computed from their low-lying structures located from a global exploration of their DFT potential energy surfaces with the GSAM code. Five DFT methods were assessed from the CCSD(T) wavenumbers of PtP2 species and CCSD relative energies of Pt2P4 structures. The eight first Pt(n)P(2n) isomers found are reported. The vibrational computations reveal (i) the absence of clear signatures made by overtone or combination bands due to very weak mechanical and electrical anharmonicities and (ii) some significant and recurrent vibrational fingerprints in correlation with the different PP bonding situations in the Pt(n)P(2n) structures.

Conformational Phase Diagram for Polymers Adsorbed on Ultrathin Nanowires

NASA Astrophysics Data System (ADS)

Vogel, Thomas; Bachmann, Michael

2010-05-01

We study the conformational behavior of a polymer adsorbed at an attractive stringlike nanowire and construct the complete structural phase diagram in dependence of the binding strength and effective thickness of the nanowire. For this purpose, Monte Carlo optimization techniques are employed to identify lowest-energy structures for a coarse-grained model of a polymer in contact with the nanowire. Among the representative conformations in the different phases are, for example, compact droplets attached to the wire and also nanotubelike monolayer films wrapping it in a very ordered way. We here systematically analyze low-energy shapes and structural order parameters to elucidate the transitions between the structural phases.

Conformational phase diagram for polymers adsorbed on ultrathin nanowires.

PubMed

Vogel, Thomas; Bachmann, Michael

2010-05-14

We study the conformational behavior of a polymer adsorbed at an attractive stringlike nanowire and construct the complete structural phase diagram in dependence of the binding strength and effective thickness of the nanowire. For this purpose, Monte Carlo optimization techniques are employed to identify lowest-energy structures for a coarse-grained model of a polymer in contact with the nanowire. Among the representative conformations in the different phases are, for example, compact droplets attached to the wire and also nanotubelike monolayer films wrapping it in a very ordered way. We here systematically analyze low-energy shapes and structural order parameters to elucidate the transitions between the structural phases.

Ecological characteristics of old-growth Douglas-fir forests.

Treesearch

Jerry F. Franklin; Kermit Jr. Cromack; William Denison; Arthur McKee; Chris Maser; James Sedell; Fred Swanson; Glen Juday

1981-01-01

Old-growth coniferous forests differ significantly from young-growth forests in species composition, function (rate and paths of energy flow and nutrient and water cycling), and structure. Most differences can be related to four key structural components of old growth: large live trees, large snags, large logs on land, and large logs in streams. Foresters wishing to...

Nickel-aluminum alloy clusters -- structural and dynamical properties

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

Jellinek, J.; Krissinel, E.B.

1997-08-01

Structural and dynamical properties of mixed Ni{sub n}Al{sub m} alloy clusters mimicked by a many-body potential are studied computationally for all the possible compositions n and m such that n + m = 13. It is shown that the manifold of the usually very large number of the different possible structural forms can be systematized by introducing classes of structures corresponding to the same concentration of the components, geometry and type of the central atom. General definitions of mixing energy and mixing coefficient are introduced, and it is shown that the energy ordering of the structural forms within each classmore » is governed by the mixing coefficient. The peculiarities of the solid-to-liquid-like transition are described as a function of the concentration of the two types of atoms. These peculiarities are correlated with and explained in terms of the energy spectra of the structural forms. Class-dependent features of the dynamics are described and analyzed.« less

The Effects of Dietary Macronutrient Balance on Skin Structure in Aging Male and Female Mice

PubMed Central

McMahon, Aisling C.; Ruohonen, Kari; Raubenheimer, David; Ballard, J. William O.; Le Couteur, David G.; Nicholls, Caroline; Li, Zhe; Maitz, Peter K. M.; Wang, Yiwei; Simpson, Stephen J.

2016-01-01

Nutrition influences skin structure; however, a systematic investigation into how energy and macronutrients (protein, carbohydrate and fat) affects the skin has yet to be conducted. We evaluated the associations between macronutrients, energy intake and skin structure in mice fed 25 experimental diets and a control diet for 15 months using the Geometric Framework, a novel method of nutritional analysis. Skin structure was associated with the ratio of dietary macronutrients eaten, not energy intake, and the nature of the effect differed between the sexes. In males, skin structure was primarily associated with protein intake, whereas in females carbohydrate intake was the primary correlate. In both sexes, the dermis and subcutaneous fat thicknesses were inversely proportional. Subcutaneous fat thickness varied positively with fat intake, due to enlarged adipocytes rather than increased adipocyte number. We therefore demonstrated clear interactions between skin structure and macronutrient intakes, with the associations being sex-specific and dependent on dietary macronutrient balance. PMID:27832138

Pseudopotential plane-wave calculation of the structural properties of yttrium

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

Wang, Y.; Chou, M.Y.

1991-11-01

The structural properties of hexagonal-close-packed yttrium are studied by using the plane-wave basis within the pseudopotential method and local-density-functional approximation. By employing a soft'' pseudopotential proposed by Troullier and Martins, satisfactory convergence is achieved with a plane-wave energy cutoff of 30--40 Ry for this early-transition-metal element. The overall results for the structural properties are in good agreement with experiment. It is found that the charge overlap between core and valence electrons has a substantial effect on the accuracy of the calculated structural properties. Two different calculations are performed with and without the outer-core 4{ital p} orbital included as a valencemore » state. In addition, as found in some other local-density calculations, the uncertainty in the results due to different exchange-correlation energy functionals may not be negligible in transition metals.« less

Simulation of Surface Energy Fluxes and Snow Interception Using a Higher Order Closure Multi-Layer Soil-Vegetation-Atmospheric Model: The Effect of Canopy Shape and Structure

NASA Astrophysics Data System (ADS)

McGowan, L. E.; Dahlke, H. E.; Paw U, K. T.

2015-12-01

Snow cover is a critical driver of the Earth's surface energy budget, climate change, and water resources. Variations in snow cover not only affect the energy budget of the land surface but also represent a major water supply source. In California, US estimates of snow depth, extent, and melt in the Sierra Nevada are critical to estimating the amount of water available for both California agriculture and urban users. However, accurate estimates of snow cover and snow melt processes in forested area still remain a challenge. Canopy structure influences the vertical and spatiotemporal distribution of snow, and therefore ultimately determines the degree and extent by which snow alters both the surface energy balance and water availability in forested regions. In this study we use the Advanced Canopy-Atmosphere-Soil algorithm (ACASA), a multi-layer soil-vegetation-atmosphere numerical model, to simulate the effect of different snow-covered canopy structures on the energy budget, and temperature and other scalar profiles within different forest types in the Sierra Nevada, California. ACASA incorporates a higher order turbulence closure scheme which allows the detailed simulation of turbulent fluxes of heat and water vapor as well as the CO2 exchange of several layers within the canopy. As such ACASA can capture the counter gradient fluxes within canopies that may occur frequently, but are typically unaccounted for, in most snow hydrology models. Six different canopy types were modeled ranging from coniferous forests (e.g. most biomass near the ground) to top-heavy (e.g. most biomass near the top of the crown) deciduous forests to multi-layered forest canopies (e.g. mixture of young and mature trees). Preliminary results indicate that the canopy shape and structure associated with different canopy types fundamentally influence the vertical scalar profiles (including those of temperature, moisture, and wind speed) in the canopy and thus alter the interception and snow melt dynamics in forested land surfaces. The turbulent transport dynamics, including counter-gradient fluxes, and radiation features including land surface albedo, are discussed in the context of the snow energy balance.

Controlling Structure and Properties of High Surface Area Nonwoven Materials via Hydroentangling

NASA Astrophysics Data System (ADS)

Luzius, Dennis

Hydroentangling describes a technique using a series of high-velocity water jets to mechanically interlock and entangle fibers. Over the last decades researchers worked on a fundamental understanding of the process and the factors influencing the properties of the final nonwoven material. Recent studies discovered hydroentangling to be capable to create unique, knot-like structures characterized by high- and low density regions, which are believed to have interesting properties for filtration applications. However, just little is known about the impact of hydroentangling parameters on the properties of filtration media to this day. In this study we report on the effect of various hydroentangling parameters, such as jet spacing, manifold pressure, number of manifolds but also specific energy on the structure and properties of high surface area nonwoven materials. Latter was achieved by different bicomponent fiber technologies and subsequent treatments removing the sacrificial compound from the structure. The highest BET surface area was measured to be 3.5 m2 g-1 and the smallest mean fiber size about 0.5 mum. Hydroentangling with large jet spacing was found to be a parameter significantly enhancing the filtration properties of caustic-treated island-in-the-sea nonwoven materials. Moreover, improved capture efficiencies and reduced pressure drops were achieved by reducing the manifold pressure and therefore specific energy during hydroentangling. Jet spacing but not island count was found to be the dominant factor influencing the structure and properties of island-in-the-sea nonwovens. Contrary to our initial expectations increasing the island count and thus decreasing the fiber size did not result in better filtration properties. Mixed media nonwoven structures made from homocomponent and island-in-the-sea fibers were found to have lower densities, higher air permeabilities and better quality factors compared to island-in-the-sea structures hydroentangled under the exact same conditions. Study showed the specific energy to not be an adequate measure for describing the process-structure relationship in hydroentangling. Hydroentangling with same specific energy but different manifold pressures revealed the structure and properties to be different and the peak manifold pressure to be the dominant parameter. It was further shown that hydroentangling with multiple manifolds but same water pressure influences the structure and properties of mono- and bicomponent nonwoven materials. Hydroentangling with three manifolds having the same water pressure resulted in stronger, less permeable fabrics compared to two manifolds or one manifold with the same water pressure. Necessary hydroentangling intensity for winged and island-in-the-sea nonwoven materials was found to be different. Winged fiber nonwovens required higher manifold pressures and a different energy ratio than island-in-in-the-sea nonwovens. Hydroentangling winged fiber webs with jet spacing larger than 600 mum resulted in materials too weak to withstand the caustic-treatment. Study indicated the charging potential of winged fiber nonwovens to be superior compared to island-in-the-sea-structures. In contrast to winged fiber nonwovens, island-in-the-sea structures showed higher pressure drops after corona discharge. Loading winged fiber nonwovens with potassium chloride revealed caustic-treated, IPA discharged materials to show the highest loading capacity.

Dimerization and conformation-related free energy landscapes of dye-tagged amyloid-β12-28 linked to FRET experiments.

PubMed

Kulesza, Alexander; Daly, Steven; Dugourd, Philippe

2017-04-05

We have investigated the free energy landscape of Aβ-peptide dimer models in connection to gas-phase FRET experiments. We use a FRET-related distance coordinate and one conformation-related coordinate per monomer for accelerated structural exploration with well-tempered metadynamics in solvent and in vacuo. The free energy profiles indicate that FRET under equilibrium conditions should be significantly affected by the de-solvation upon the transfer of ions to the gas-phase. In contrast, a change in the protonation state is found to be less impacting once de-solvated. Comparing F19P and WT alloforms, for which we measure different FRET efficiencies in the gas-phase, we predict only the relevant structural differences in the solution populations, not under gas-phase equilibrium conditions. This finding supports the hypothesis that the gas-phase action-FRET measurement after ESI operates under non-equilibrium conditions, with a memory of the solution conditions - even for the dimer of this relatively short peptide. The structural differences in solution are rationalized in terms of conformational propensities around residue 19, which show a transition to a poly-proline type of pattern upon mutation to F19P - a difference that gets lost in the gas-phase.

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.

Estimation of effect of hydrogen on the parameters of magnetoacoustic emission signals

NASA Astrophysics Data System (ADS)

Skalskyi, Valentyn; Stankevych, Olena; Dubytskyi, Olexandr

2018-05-01

The features of the magnetoacoustic emission (MAE) signals during magnetization of structural steels with the different degree of hydrogenating were investigated by the wavelet transform. The dominant frequency ranges of MAE signals for the different magnetic field strength were determined using Discrete Wavelet Transform (DWT), and the energy and spectral parameters of MAE signals were determined using Continuous Wavelet Transform (CWT). The characteristic differences of the local maximums of signals according to energy, bandwidth, duration and frequency were found. The methodology of estimation of state of local degradation of materials by parameters of wavelet transform of MAE signals was proposed. This methodology was approbated for investigate of state of long-time exploitations structural steels of oil and gas pipelines.

Structural and electrical properties of Se-hyperdoped Si via ion implantation and flash lamp annealing

NASA Astrophysics Data System (ADS)

Liu, Fang; Prucnal, S.; Yuan, Ye; Heller, R.; Berencén, Y.; Böttger, R.; Rebohle, L.; Skorupa, W.; Helm, M.; Zhou, S.

2018-06-01

We report on the hyperdoping of silicon with selenium obtained by ion implantation followed by flash lamp annealing. It is shown that the degree of crystalline lattice recovery of the implanted layers and the Se substitutional fraction depend on the pulse duration and energy density of the flash. While the annealing at low energy densities leads to an incomplete recrystallization, annealing at high energy densities results in a decrease of the substitutional fraction of impurities. The electrical properties of the implanted layers are well-correlated with the structural properties resulting from different annealing processing.

Analysis of Crushing Response of Composite Crashworthy Structures

NASA Astrophysics Data System (ADS)

David, Matthew; Johnson, Alastair F.; Voggenreiter, H.

2013-10-01

The paper describes quasi-static and dynamic tests to characterise the energy absorption properties of polymer composite crash energy absorbing segment elements under axial loads. Detailed computer tomography scans of failed specimens are used to identify local compression crush failure mechanisms at the crush front. The varied crushing morphology between the compression strain rates identified in this paper is observed to be due to the differences in the response modes and mechanical properties of the strain dependent epoxy matrix. The importance of understanding the role of strain rate effects in composite crash energy absorbing structures is highlighted in this paper.

Electron trapping in evolving coronal structures during a large gradual hard X-ray/radio burst

NASA Technical Reports Server (NTRS)

Bruggmann, G.; Vilmer, N.; Klein, K.-L.; Kane, S. R.

1994-01-01

Gradual hard X-ray/radio bursts are characterized by their long duration, smooth time profile, time delays between peaks at different hard X-ray energies and microwaves, and radiation from extended sources in the low and middle corona. Their characteristic properties have been ascribed to the dynamic evolution of the accelerated electrons in coronal magnetic traps or to the separate acceleration of high-energy electrons in a 'second step' process. The information available so far was drawn from quality considerations of time profiles or even only from the common occurrence of emissions in different spectral ranges. This paper presents model computations of the temporal evolution of hard X-ray and microwave spectra, together with a qualitative discussion of radio lightcurves over a wide spectral range, and metric imaging observations. The basis hypothesis investigated is that the peculiar 'gradual' features can be related to the dynamical evolution of electrons injected over an extended time interval in a coronal trap, with electrons up to relativistic energies being injected simultaneously. The analyzed event (26 April. 1981) is particularly challenging to this hypothesis because of the long time delays between peaks at different X-ray energies and microwave frequencies. The observations are shown to be consistent with the hypothesis, provided that the electrons lose their energy by Coulomb collisions and possibly betatron deceleration. The access of the electrons to different coronal structures varies in the course of the event. The evolution and likely destabilization of part of the coronal plasma-magnetic field configuration is of crucial influence in determining the access to these structures and possibly the dynamical evolution of the trapped electrons through betatron deceleration in the late phase of the event.

Compositional and Ionic-Size Controls on the Diffusion of Divalent Cations in Garnet: Insights from Atomistic Simulations

NASA Astrophysics Data System (ADS)

Carlson, W. D.

2012-12-01

Divalent cations in garnet (Mg, Fe, Mn, Ca) diffuse at rates that depend strongly on the host-crystal composition and on the ionic radius of the diffusant. Understanding of the nanoscale basis for these behaviors comes from atomistic simulations that calculate energies in the static limit for the defects and transition-state configurations associated with each diffusive step. Diffusion of divalent cations requires (a) creation of a cation-vacancy defect in a dodecahedral site and of a charge-compensating oxygen-vacancy defect that may or may not be in close spatial association; (b) except in the case of self-diffusion, creation of an impurity defect in which a foreign atom replaces the normal atom in a dodecahedral site adjacent to the vacancy; and (c) during the diffusive process, motion of the diffusing atom to a 'saddlepoint' position that represents the transition-state configuration. Comparisons of the system's energy in these various states, in structures of different composition and for ions of different ionic size, allows assessment of the nanoscale controls on diffusion kinetics. Molecular-statics calculations quantify defect energies and identify the transition-state configuration: the maximum energy along the diffusion path between two adjacent dodecahedral sites results when the diffusing ion is surrounded symmetrically by the six oxygen atoms that lie between the two sites. Across the range of end-member compositions, self-diffusion coefficients measured at identical conditions, and the tracer diffusivity of a single ion measured at identical conditions, can each vary by five orders of magnitude or more. Measured activation energies for these motions, however, are all equivalent to within ±6%. Calculated activation energies are in agreement with observations, in that they vary by only ±10%. Calculated vacancy-formation energies, on the other hand, are significantly larger in expanded structures; for example, that energy is greater for Prp than for Grs by ~ 470 kJ/mol. Thus in expanded structures, much higher vacancy concentrations can be produced at the same energetic cost, greatly enhancing rates of diffusion. The primary explanation for the more rapid diffusion of divalent cations in structures with larger cell dimensions therefore comes not from reduced saddlepoint strain energies in more compliant structures, but instead from the smaller energy required to create vacancy defects. Diffusivities of divalent cations exhibit a curious parabolic dependence on ionic size: for each structure, an optimally-sized ion exists, close in size to the dominant ion, that exhibits the fastest diffusion. Larger ions — and enigmatically, smaller ions — both diffuse more slowly. Calculated impurity-defect energies show that undersized impurity ions are bound more tightly in their sites, but the effects are too small in comparison to corresponding reductions in strain energy for the transition-state configuration to account for observed rate differences. Calculated vacancy-association energies reveal a slight tendency for vacancies to associate preferentially with larger impurity ions, but again the effect appears to be too small to provide a full explanation for observed behaviors.

Vibration Response Models of a Stiffened Aluminum Plate Excited by a Shaker

NASA Technical Reports Server (NTRS)

Cabell, Randolph H.

2008-01-01

Numerical models of structural-acoustic interactions are of interest to aircraft designers and the space program. This paper describes a comparison between two energy finite element codes, a statistical energy analysis code, a structural finite element code, and the experimentally measured response of a stiffened aluminum plate excited by a shaker. Different methods for modeling the stiffeners and the power input from the shaker are discussed. The results show that the energy codes (energy finite element and statistical energy analysis) accurately predicted the measured mean square velocity of the plate. In addition, predictions from an energy finite element code had the best spatial correlation with measured velocities. However, predictions from a considerably simpler, single subsystem, statistical energy analysis model also correlated well with the spatial velocity distribution. The results highlight a need for further work to understand the relationship between modeling assumptions and the prediction results.

Multicriteria Decision Analysis of Material Selection of High Energy Performance Residential Building

NASA Astrophysics Data System (ADS)

Čuláková, Monika; Vilčeková, Silvia; Katunská, Jana; Krídlová Burdová, Eva

2013-11-01

In world with limited amount of energy sources and with serious environmental pollution, interest in comparing the environmental embodied impacts of buildings using different structure systems and alternative building materials will be increased. This paper shows the significance of life cycle energy and carbon perspective and the material selection in reducing energy consumption and emissions production in the built environment. The study evaluates embodied environmental impacts of nearly zero energy residential structures. The environmental assessment uses framework of LCA within boundary: cradle to gate. Designed alternative scenarios of material compositions are also assessed in terms of energy effectiveness through selected thermal-physical parameters. This study uses multi-criteria decision analysis for making clearer selection between alternative scenarios. The results of MCDA show that alternative E from materials on nature plant base (wood, straw bales, massive wood panel) present possible way to sustainable perspective of nearly zero energy houses in Slovak republic

"Trunk-like" heavy ion structures observed by the Van Allen Probes

NASA Astrophysics Data System (ADS)

Zhang, J.-C.; Kistler, L. M.; Spence, H. E.; Wolf, R. A.; Reeves, G.; Skoug, R.; Funsten, H.; Larsen, B. A.; Niehof, J. T.; MacDonald, E. A.; Friedel, R.; Ferradas, C. P.; Luo, H.

2015-10-01

Dynamic ion spectral features in the inner magnetosphere are the observational signatures of ion acceleration, transport, and loss in the global magnetosphere. We report "trunk-like" ion structures observed by the Van Allen Probes on 2 November 2012. This new type of ion structure looks like an elephant's trunk on an energy-time spectrogram, with the energy of the peak flux decreasing Earthward. The trunks are present in He+ and O+ ions but not in H+. During the event, ion energies in the He+ trunk, located at L = 3.6-2.6, magnetic local time (MLT) = 9.1-10.5, and magnetic latitude (MLAT) = -2.4-0.09°, vary monotonically from 3.5 to 0.04 keV. The values at the two end points of the O+ trunk are energy = 4.5-0.7 keV, L = 3.6-2.5, MLT = 9.1-10.7, and MLAT = -2.4-0.4°. Results from backward ion drift path tracings indicate that the trunks are likely due to (1) a gap in the nightside ion source or (2) greatly enhanced impulsive electric fields associated with elevated geomagnetic activity. Different ion loss lifetimes cause the trunks to differ among ion species.

Hysteretic energy prediction method for mainshock-aftershock sequences

NASA Astrophysics Data System (ADS)

Zhai, Changhai; Ji, Duofa; Wen, Weiping; Li, Cuihua; Lei, Weidong; Xie, Lili

2018-04-01

Structures located in seismically active regions may be subjected to mainshock-aftershock (MSAS) sequences. Strong aftershocks significantly affect the hysteretic energy demand of structures. The hysteretic energy, E H,seq, is normalized by mass m and expressed in terms of the equivalent velocity, V D,seq, to quantitatively investigate aftershock effects on the hysteretic energy of structures. The equivalent velocity, V D,seq, is computed by analyzing the response time-history of an inelastic single-degree-of-freedom (SDOF) system with a varying vibration period subjected to 309 MSAS sequences. The present study selected two kinds of MSAS sequences, with one aftershock and two aftershocks, respectively. The aftershocks are scaled to maintain different relative intensities. The variation of the equivalent velocity, V D,seq, is studied for consideration of the ductility values, site conditions, relative intensities, number of aftershocks, hysteretic models, and damping ratios. The MSAS sequence with one aftershock exhibited a 10% to 30% hysteretic energy increase, whereas the MSAS sequence with two aftershocks presented a 20% to 40% hysteretic energy increase. Finally, a hysteretic energy prediction equation is proposed as a function of the vibration period, ductility value, and damping ratio to estimate hysteretic energy for mainshock-aftershock sequences.

Conformational Sampling of a Biomolecular Rugged Energy Landscape.

PubMed

Rydzewski, Jakub; Jakubowski, Rafal; Nicosia, Giuseppe; Nowak, Wieslaw

2018-01-01

The protein structure refinement using conformational sampling is important in hitherto protein studies. In this paper, we examined the protein structure refinement by means of potential energy minimization using immune computing as a method of sampling conformations. The method was tested on the x-ray structure and 30 decoys of the mutant of [Leu]Enkephalin, a paradigmatic example of the biomolecular multiple-minima problem. In order to score the refined conformations, we used a standard potential energy function with the OPLSAA force field. The effectiveness of the search was assessed using a variety of methods. The robustness of sampling was checked by the energy yield function which measures quantitatively the number of the peptide decoys residing in an energetic funnel. Furthermore, the potential energy-dependent Pareto fronts were calculated to elucidate dissimilarities between peptide conformations and the native state as observed by x-ray crystallography. Our results showed that the probed potential energy landscape of [Leu]Enkephalin is self-similar on different metric scales and that the local potential energy minima of the peptide decoys are metastable, thus they can be refined to conformations whose potential energy is decreased by approximately 250 kJ/mol.

Two types of energy-dispersed ion structures at the plasma sheet boundary

NASA Astrophysics Data System (ADS)

Sauvaud, J.-A.; Kovrazhkin, R. A.

2004-12-01

We study two main types of ion energy dispersions observed in the energy range ˜1 to 14 keV on board the Interball-Auroral (IA) satellite at altitudes 2-3 RE at the poleward boundary of the plasma sheet. The first type of structure is named velocity dispersed ion structures (VDIS). It is known that VDIS represent a global proton structure with a latitudinal width of ˜0.7-2.5°, where the ion overall energy increases with latitude. IA data allow to show that VDIS are made of substructures lasting for ˜1-3 min. Inside each substructure, high-energy protons arrive first, regardless of the direction of the plasma sheet boundary crossing. A near-continuous rise of the maximal and minimal energies of consecutive substructures with invariant latitude characterizes VDIS. The second type of dispersed structure is named time-of-flight dispersed ion structures (TDIS). TDIS are recurrent sporadic structures in H+ (and also O+) with a quasi-period of ˜3 min and a duration of ˜1-3 min. The maximal energy of TDIS is rather constant and reaches ≥14 keV. During both poleward and equatorward crossings of the plasma sheet boundary, inside each TDIS, high-energy ions arrive first. These structures are accompanied by large fluxes of upflowing H+ and O+ ions with maximal energies up to 5-10 keV. In association with TDIS, bouncing H+ clusters are observed in quasi-dipolar magnetic field tubes, i.e., equatorward from TDIS. The electron populations generally have different properties during observations of VDIS and TDIS. The electron flux accompanying VDIS first increases smoothly and then decreases after Interball-Auroral has passed through the proton structure. The average electron energy in the range ˜0.5-2 keV is typical for electrons from the plasma sheet boundary layer (PSBL). The electron fluxes associated with TDIS increases suddenly at the polar boundary of the auroral zone. Their average energy, reaching ˜5-8 keV, is typical for CPS. A statistical analysis shows that VDIS are observed mainly during magnetically quiet times and during the recovery phase of substorms, while sporadic and recurrent TDIS are observed during the onset and main phases of substorms and magnetic storms and, although less frequently, during substorm recovery phases. From the slope of the (velocity)-1 versus time dispersions of TDIS, we conclude that they have a sporadic source located at the outer boundary of the central plasma sheet, at distances from 8 to 40 RE in the equatorial plane. The disappearance of the PSBL associated with TDIS can be tentatively linked to a reconfiguration of the magnetotail, which disconnects from the Earth the field lines forming the "quiet" PSBL. We show that VDIS consist of ion beams ejected from an extended current sheet at different distances. These ion beams could be formed in the neutral sheet at distance ranging from ˜30 RE to ˜100 RE from the Earth. Inside each substructure the time-of-flight dispersion of ions generally dominate over any latitudinal dispersion induced by a dawn-dusk electric field. These two main types of energy-dispersed ion structures reflect probably two main states of the magnetotail, quiet and active. Finally, it must be stressed that only ˜49% (246 over 501) of the Interball-Auroral auroral zone-polar cap boundary crossings can be described as VDIS or TDIS. On the other 51% of the crossings of the plasma sheet boundary, no well-defined ion dispersed structures were observed.

GAtor: A First-Principles Genetic Algorithm for Molecular Crystal Structure Prediction.

PubMed

Curtis, Farren; Li, Xiayue; Rose, Timothy; Vázquez-Mayagoitia, Álvaro; Bhattacharya, Saswata; Ghiringhelli, Luca M; Marom, Noa

2018-04-10

We present the implementation of GAtor, a massively parallel, first-principles genetic algorithm (GA) for molecular crystal structure prediction. GAtor is written in Python and currently interfaces with the FHI-aims code to perform local optimizations and energy evaluations using dispersion-inclusive density functional theory (DFT). GAtor offers a variety of fitness evaluation, selection, crossover, and mutation schemes. Breeding operators designed specifically for molecular crystals provide a balance between exploration and exploitation. Evolutionary niching is implemented in GAtor by using machine learning to cluster the dynamically updated population by structural similarity and then employing a cluster-based fitness function. Evolutionary niching promotes uniform sampling of the potential energy surface by evolving several subpopulations, which helps overcome initial pool biases and selection biases (genetic drift). The various settings offered by GAtor increase the likelihood of locating numerous low-energy minima, including those located in disconnected, hard to reach regions of the potential energy landscape. The best structures generated are re-relaxed and re-ranked using a hierarchy of increasingly accurate DFT functionals and dispersion methods. GAtor is applied to a chemically diverse set of four past blind test targets, characterized by different types of intermolecular interactions. The experimentally observed structures and other low-energy structures are found for all four targets. In particular, for Target II, 5-cyano-3-hydroxythiophene, the top ranked putative crystal structure is a Z' = 2 structure with P1̅ symmetry and a scaffold packing motif, which has not been reported previously.

Modification of Structure and Tribological Properties of the Surface Layer of Metal-Ceramic Composite under Electron Irradiation in the Plasmas of Inert Gases

NASA Astrophysics Data System (ADS)

Ovcharenko, V. E.; Ivanov, K. V.; Mohovikov, A. A.; Yu, B.; Xu, Yu; Zhong, L.

2018-01-01

Metal-ceramic composites are the main materials for high-load parts in tribomechanical systems. Modern approaches to extend the operation life of tribomechanical systems are based on increasing the strength and tribological properties of the surface layer having 100 to 200 microns in depth. The essential improvement of the properties occurs when high dispersed structure is formed in the surface layer using high-energy processing. As a result of the dispersed structure formation the more uniform distribution of elastic stresses takes place under mechanical or thermal action, the energy of stress concentrators emergence significantly increases and the probability of internal defects formation reduces. The promising method to form the dispersed structure in the surface layer is pulse electron irradiation in the plasmas of inert gases combining electron irradiation and ion bombardment in one process. The present work reports upon the effect of pulse electron irradiation in plasmas of different inert gases with different atomic mass and ionization energy on the structure and tribological properties of the surface layer of TiC/(Ni-Cr) metal-ceramic composite with the volume ratio of the component being 50:50. It is experimentally shown that high-dispersed heterophase structure with a fraction of nanosized particles is formed during the irradiation. Electron microscopy study reveals that refining of the initial coarse TiC particles occurs via their dissolution in the molten metal binder followed by the precipitation of secondary fine particles in the interparticle layers of the binder. The depth of modified layer and the fraction of nanosized particles increase when the atomic number of the plasma gas increases and ionization energy decreases. The wear resistance of metal-ceramic composite improves in accordance to the formation of nanocrystalline structure in the surface layer.

NMR comparison of the native energy landscapes of DLC8 dimer and monomer.

PubMed

Krishna Mohan, P M; Barve, Maneesha; Chatterjee, Amarnath; Ghosh-Roy, Anindya; Hosur, Ramakrishna V

2008-04-01

Characterization of the low energy excited states on the energy landscape of a protein is one of the exciting and challenging problems in structural biology today. In this context, we present here residue level NMR description of the low energy excited states representing locally different alternative conformations in the dynein light chain protein, in its dimeric as well as monomeric forms. Important differences have been observed between the two cases and these are not necessarily restricted to the dimer interface. Simulations indicate that the low energy excited states are within a free energy of 2-3 kcal/mol above the native state. In both the monomer and the dimer the energy landscape is very sensitive to small pH perturbations. Nearly 25% of the residues (total of residues at pH 3.0 and 3.5 for the monomer, and at pH 7.0 and 6.0 for the dimer) access alternative conformations. The observations have been rationalized on the basis of protonation-deprotonation equilibria in the side chains; histidines in the case of the dimer and aspartates/glutamates in the case of the monomer. The possible relationship of the observed ruggedness of the native energy landscape with the protein structure, and its implications to protein adaptability and unfolding have been discussed.

Cascaded exciton energy transfer in a monolayer semiconductor lateral heterostructure assisted by surface plasmon polariton.

PubMed

Shi, Jinwei; Lin, Meng-Hsien; Chen, I-Tung; Mohammadi Estakhri, Nasim; Zhang, Xin-Quan; Wang, Yanrong; Chen, Hung-Ying; Chen, Chun-An; Shih, Chih-Kang; Alù, Andrea; Li, Xiaoqin; Lee, Yi-Hsien; Gwo, Shangjr

2017-06-26

Atomically thin lateral heterostructures based on transition metal dichalcogenides have recently been demonstrated. In monolayer transition metal dichalcogenides, exciton energy transfer is typically limited to a short range (~1 μm), and additional losses may be incurred at the interfacial regions of a lateral heterostructure. To overcome these challenges, here we experimentally implement a planar metal-oxide-semiconductor structure by placing a WS 2 /MoS 2 monolayer heterostructure on top of an Al 2 O 3 -capped Ag single-crystalline plate. We find that the exciton energy transfer range can be extended to tens of microns in the hybrid structure mediated by an exciton-surface plasmon polariton-exciton conversion mechanism, allowing cascaded exciton energy transfer from one transition metal dichalcogenides region supporting high-energy exciton resonance to a different transition metal dichalcogenides region in the lateral heterostructure with low-energy exciton resonance. The realized planar hybrid structure combines two-dimensional light-emitting materials with planar plasmonic waveguides and offers great potential for developing integrated photonic and plasmonic devices.Exciton energy transfer in monolayer transition metal dichalcogenides is limited to short distances. Here, Shi et al. fabricate a planar metal-oxide-semiconductor structure and show that exciton energy transfer can be extended to tens of microns, mediated by an exciton-surface-plasmon-polariton-exciton conversion mechanism.

Substrate temperature effect on the structural anisotropy in amorphous Tb-Fe films

NASA Astrophysics Data System (ADS)

Harris, V. G.; Hellman, F.; Elam, W. T.; Koon, N. C.

1993-05-01

Using extended x-ray absorption fine structures (EXAFS) measurements we have investigated the atomic environment around the Fe atom in a series of amorphous Tb0.26Fe0.74 films having different magnetic anisotropy energies owing to different deposition temperatures. The polarization properties of synchrotron radiation allowed the separate study of structure parallel and perpendicular to the sample plane. An anisotropy between these two structures was observed. Modeling results indicate this anisotropy is due to anisotropic pair correlations where the Fe-Fe pairs are statistically preferred in-plane and the Fe-Tb pairs out-of-plane. The amplitude of this anisotropy scales with both the substrate temperature and the magnetic anisotropy energy. A ≊1% in-plane compression of the Fe-Fe distance was measured between the in-plane and out-of-plane structure of the sample grown at 77 K. This sample had no detectable local chemical anisotropy suggesting that intrinsic stress plays an important role in determining its magnetic anisotropy.

Research on the calibration of ultraviolet energy meters

NASA Astrophysics Data System (ADS)

Lin, Fangsheng; Yin, Dejin; Li, Tiecheng; Lai, Lei; Xia, Ming

2016-10-01

Ultraviolet (UV) radiation is a kind of non-lighting radiation with the wavelength range from 100nm to 400nm. Ultraviolet irradiance meters are now widely used in many areas. However, as the development of science and technology, especially in the field of light-curing industry, there are more and more UV energy meters or UV-integrators need to be measured. Because the structure, wavelength band and measured power intensity of UV energy meters are different from traditional UV irradiance meters, it is important for us to take research on the calibration. With reference to JJG879-2002, we SIMT have independently developed the UV energy calibration device and the standard of operation and experimental methods for UV energy calibration in detail. In the calibration process of UV energy meter, many influencing factors will affect the final results, including different UVA-band UV light sources, different spectral response for different brands of UV energy meters, instability and no uniformity of UV light source and temperature. Therefore we need to take all of these factors into consideration to improve accuracy in UV energy calibration.

Confined-Volume Effect on the Thermal Properties of Encapsulated Phase Change Materials for Thermal Energy Storage.

PubMed

De Castro, Paula F; Ahmed, Adham; Shchukin, Dmitry G

2016-03-18

We have encapsulated the heat exchange material, n-docosane, into polyurethane capsules of different sizes. Decreasing the size of the capsules leads to changes of the crystallinity of phase-change material as well as melting/crystallization temperature. The novelty of the paper includes 1) protection of the nanostructured energy-enriched materials against environment during storage and controlled release of the encapsulated energy on demand and 2) study of the structure and surface-to-volume properties of the energy-enriched materials dispersed in capsules of different sizes. The stability of energy nanomaterials, influence of capsule diameter on their energy capacity, homogeneity and operation lifetime are investigated. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Mechanism and energetics of 〈c + a〉 dislocation cross-slip in hcp metals.

PubMed

Wu, Zhaoxuan; Curtin, W A

2016-10-04

Hexagonal close-packed (hcp) metals such as Mg, Ti, and Zr are lightweight and/or durable metals with critical structural applications in the automotive (Mg), aerospace (Ti), and nuclear (Zr) industries. The hcp structure, however, brings significant complications in the mechanisms of plastic deformation, strengthening, and ductility, and these complications pose significant challenges in advancing the science and engineering of these metals. In hcp metals, generalized plasticity requires the activation of slip on pyramidal planes, but the structure, motion, and cross-slip of the associated [Formula: see text] dislocations are not well established even though they determine ductility and influence strengthening. Here, atomistic simulations in Mg reveal the unusual mechanism of [Formula: see text] dislocation cross-slip between pyramidal I and II planes, which occurs by cross-slip of the individual partial dislocations. The energy barrier is controlled by a fundamental step/jog energy and the near-core energy difference between pyramidal [Formula: see text] dislocations. The near-core energy difference can be changed by nonglide stresses, leading to tension-compression asymmetry and even a switch in absolute stability from one glide plane to the other, both features observed experimentally in Mg, Ti, and their alloys. The unique cross-slip mechanism is governed by common features of the generalized stacking fault energy surfaces of hcp pyramidal planes and is thus expected to be generic to all hcp metals. An analytical model is developed to predict the cross-slip barrier as a function of the near-core energy difference and applied stresses and quantifies the controlling features of cross-slip and pyramidal I/II stability across the family of hcp metals.

Mechanism and energetics of 〈c + a〉 dislocation cross-slip in hcp metals

PubMed Central

Wu, Zhaoxuan; Curtin, W. A.

2016-01-01

Hexagonal close-packed (hcp) metals such as Mg, Ti, and Zr are lightweight and/or durable metals with critical structural applications in the automotive (Mg), aerospace (Ti), and nuclear (Zr) industries. The hcp structure, however, brings significant complications in the mechanisms of plastic deformation, strengthening, and ductility, and these complications pose significant challenges in advancing the science and engineering of these metals. In hcp metals, generalized plasticity requires the activation of slip on pyramidal planes, but the structure, motion, and cross-slip of the associated 〈c+a〉 dislocations are not well established even though they determine ductility and influence strengthening. Here, atomistic simulations in Mg reveal the unusual mechanism of 〈c+a〉 dislocation cross-slip between pyramidal I and II planes, which occurs by cross-slip of the individual partial dislocations. The energy barrier is controlled by a fundamental step/jog energy and the near-core energy difference between pyramidal 〈c+a〉 dislocations. The near-core energy difference can be changed by nonglide stresses, leading to tension–compression asymmetry and even a switch in absolute stability from one glide plane to the other, both features observed experimentally in Mg, Ti, and their alloys. The unique cross-slip mechanism is governed by common features of the generalized stacking fault energy surfaces of hcp pyramidal planes and is thus expected to be generic to all hcp metals. An analytical model is developed to predict the cross-slip barrier as a function of the near-core energy difference and applied stresses and quantifies the controlling features of cross-slip and pyramidal I/II stability across the family of hcp metals. PMID:27647908

Performance comparison of two fuel cell hybrid buses with different powertrain and energy management strategies

NASA Astrophysics Data System (ADS)

Ouyang, Minggao; Xu, Liangfei; Li, Jianqiu; Lu, Languang; Gao, Dawei; Xie, Qicheng

In order to assess the influences of different powertrain structures and energy management strategies on the performance of hybrid fuel cell buses (FCB), two buses (FCB A and FCB B) were constructed with a "energy hybrid structure" and "power hybrid structure", respectively. Different energy management strategies were investigated based on analysis of the two systems. And the two buses were compared with each other in a bus cycle and constant speed testing. The Polymer Electrolyte Membrane Fuel Cell (PEMFC) in FCB A showed an advantage in fuel economy for it worked usually in the high efficient range of the PEMFC engine. The hydrogen consumption rate in the cycle testing was 7.9 kg/100 km and 9.8 kg/100 km for FCB A and FCB B, and in the 40 kmph constant speed testing it was 3.3 kg/100 km and 4.0 kg/100 km, respectively. The fuel economy could be improved when the hydrogen and air supply subsystems are optimized and controlled with an advanced algorithm. It could also benefit from a braking energy regeneration system. Compared with FCB A, the PEMFC in FCB B worked under unfavorable operation conditions because its working range was comparatively wide, and the power changing rate was relatively large from a statistical point of view, which resulted in performance recession of the PEMFC in FCB B. After a mileage of 7000 km, the output power of the PEMFC in FCB B was reduced by 10%, compared with 2.4% in FCB A. An advanced energy management strategy is necessary to split the power between the PEMFC and a battery suitable for long durability of a PEMFC.

Combined electron energy-loss and cathodoluminescence spectroscopy on individual and composite plasmonic nanostructures

NASA Astrophysics Data System (ADS)

Coenen, Toon; Schoen, David T.; Brenny, Benjamin J. M.; Polman, Albert; Brongersma, Mark L.

2016-05-01

We systematically investigate the plasmonic "dolmen" geometry and its constituent elements using electron energy-loss spectroscopy and cathodoluminescence spectroscopy. In particular, we study the effects of the particle size and spacing on the resonant behavior and interparticle coupling. Because we apply both techniques on the same structures we can directly compare the results and investigate the radiative versus nonradiative character of the different modes. We find that the cathodoluminescence response is significantly lower than the electron energy-loss response for higher-energy modes because strong absorption reduces the scattering efficiency in this regime. Furthermore, we show that the overall resonant response roughly scales with size as expected for plasmonic structures but that the transverse resonant modes do become more dominant in larger structures due to a relative reduction in Ohmic dissipation. Using EELS and CL we can rigorously study coupling between the elements and show that the coupling diminishes for larger spacings.

Characterization of multifunctional structural capacitors for embedded energy storage

NASA Astrophysics Data System (ADS)

Lin, Yirong; Sodano, Henry A.

2009-12-01

Multifunctional composites are a class of materials that combine structural and other functionalities such as sensing, actuation, energy harvesting, and vibration control in order to maximize structural performance while minimizing weight and complexity. Among all the multifunctional composites developed so far, piezoelectric composites have been widely studied due to the high coupling of energy between the electrical and mechanical domains and the inherently high dielectric constant. Several piezoelectric fiber composites have been developed for sensing and actuation applications; however, none of the previously studied composites fully embed all components of an energy storage device as load bearing members of the structure. A multifunctional fiber that can be embedded in a composite material to perform sensing and actuation has been recently developed [Y. Lin and H. A. Sodano, Adv. Funct. Mater. 18, 592 (2008)], in addition to providing load bearing functionality. The design was achieved by coating a common structural fiber, silicon carbide, with a barium titanate piezoelectric shell, and poling the active material radically by employing the structural fiber as one of the electrodes. The silicon carbide core fiber also carries external mechanical loading to protect the brittle barium titanate shell from fracture. The excellent piezoelectric and dielectric properties of the barium titanate material make the active structural fiber an outstanding candidate for converting and storing ambient mechanical energy into electrical energy to power other electric devices in the system. This paper focuses on the characterization of energy storage capability of the multifunctional fiber provided by the dielectric properties of the barium titanate shell. The capacitances of the multifunctional fibers with four different aspect ratios are tested and compared with the theoretical expressions for the cylindrical capacitor, while the breakdown voltages of the multifunctional fibers are tested according to American Society for Testing and Materials standards (ASTM D 149-97a). The stored energy is calculated from the testing results and the best aspect ratio for energy storage application can be determined. The resulting capacitive fiber is shown to have an energy density approximately two orders of magnitude higher than structural capacitors in the literature.

Protein surface roughness accounts for binding free energy of Plasmepsin II-ligand complexes.

PubMed

Valdés-Tresanco, Mario E; Valdés-Tresanco, Mario S; Valiente, Pedro A; Cocho, Germinal; Mansilla, Ricardo; Nieto-Villar, J M

2018-01-01

The calculation of absolute binding affinities for protein-inhibitor complexes remains as one of the main challenges in computational structure-based ligand design. The present work explored the calculations of surface fractal dimension (as a measure of surface roughness) and the relationship with experimental binding free energies of Plasmepsin II complexes. Plasmepsin II is an attractive target for novel therapeutic compounds to treat malaria. However, the structural flexibility of this enzyme is a drawback when searching for specific inhibitors. Concerning that, we performed separate explicitly solvated molecular dynamics simulations using the available high-resolution crystal structures of different Plasmepsin II complexes. Molecular dynamics simulations allowed a better approximation to systems dynamics and, therefore, a more reliable estimation of surface roughness. This constitutes a novel approximation in order to obtain more realistic values of fractal dimension, because previous works considered only x-ray structures. Binding site fractal dimension was calculated considering the ensemble of structures generated at different simulation times. A linear relationship between binding site fractal dimension and experimental binding free energies of the complexes was observed within 20 ns. Previous studies of the subject did not uncover this relationship. Regression model, coined FD model, was built to estimate binding free energies from binding site fractal dimension values. Leave-one-out cross-validation showed that our model reproduced accurately the absolute binding free energies for our training set (R 2  = 0.76; <|error|> =0.55 kcal/mol; SD error  = 0.19 kcal/mol). The fact that such a simple model may be applied raises some questions that are addressed in the article. Copyright © 2017 John Wiley & Sons, Ltd.

Demonstrating the Uneven Importance of Fine-Scale Forest Structure on Snow Distributions using High Resolution Modeling

NASA Astrophysics Data System (ADS)

Broxton, P. D.; Harpold, A. A.; van Leeuwen, W.; Biederman, J. A.

2016-12-01

Quantifying the amount of snow in forested mountainous environments, as well as how it may change due to warming and forest disturbance, is critical given its importance for water supply and ecosystem health. Forest canopies affect snow accumulation and ablation in ways that are difficult to observe and model. Furthermore, fine-scale forest structure can accentuate or diminish the effects of forest-snow interactions. Despite decades of research demonstrating the importance of fine-scale forest structure (e.g. canopy edges and gaps) on snow, we still lack a comprehensive understanding of where and when forest structure has the largest impact on snowpack mass and energy budgets. Here, we use a hyper-resolution (1 meter spatial resolution) mass and energy balance snow model called the Snow Physics and Laser Mapping (SnowPALM) model along with LIDAR-derived forest structure to determine where spatial variability of fine-scale forest structure has the largest influence on large scale mass and energy budgets. SnowPALM was set up and calibrated at sites representing diverse climates in New Mexico, Arizona, and California. Then, we compared simulations at different model resolutions (i.e. 1, 10, and 100 m) to elucidate the effects of including versus not including information about fine scale canopy structure. These experiments were repeated for different prescribed topographies (i.e. flat, 30% slope north, and south-facing) at each site. Higher resolution simulations had more snow at lower canopy cover, with the opposite being true at high canopy cover. Furthermore, there is considerable scatter, indicating that different canopy arrangements can lead to different amounts of snow, even when the overall canopy coverage is the same. This modeling is contributing to the development of a high resolution machine learning algorithm called the Snow Water Artificial Network (SWANN) model to generate predictions of snow distributions over much larger domains, which has implications for improving land surface models that do not currently resolve or parameterize fine-scale canopy structure. In addition, these findings have implications for understanding the potential of different forest management strategies (i.e. thinning) based on local topography and climate to maximize the amount and retention of snow.

Defining the Biological Effectiveness of Components of High-LET Track Structure.

PubMed

Sridharan, Deepa M; Chappell, Lori J; Whalen, Mary K; Cucinotta, Francis A; Pluth, Janice M

2015-07-01

During space travel, astronauts are exposed to a wide array of high-linear energy transfer (LET) particles, with differing energies and resulting biological effects. Risk assessment of these exposures carries a large uncertainty predominantly due to the unique track structure of the particle's energy deposition. The complex damage elicited by high charge and energy (HZE) particles results from both lesions along the track core and from energetic electrons, δ rays, generated as a consequence of particle traversal. To better define how cells respond to this complex radiation exposure, a normal hTERT immortalized skin fibroblast cell line was exposed to a defined panel of particles carefully chosen to tease out track structure effects. Phosphorylation kinetics for several key double-strand break (DSB) response proteins (γ-H2AX, pATF2 and pSMC1) were defined after exposure to ten different high-LET radiation qualities and one low-LET radiation (X ray), at two doses (0.5-2 Gy) and time points (2 and 24 h). The results reveal that the lower energy particles (Fe 300, Si 93 and Ti 300 MeV/u), with a narrower track width and higher number and intensity of δ rays, cause the highest degree of persistent damage response. The persistent γ-H2AX signal at lower energies suggests that damage from these exposures are more difficult to resolve, likely due to the greater complexity of the associated DNA lesions. However, different kinetics were observed for the solely ATM-mediated phosphorylations (pATF2 and pSMC1), revealing a shallow induction at early times and a higher level of residual phosphorylation compared to γ-H2AX. The differing phospho-protein profiles exhibited, compared to γ-H2AX, suggests additional functions for these proteins within the cell. The strong correspondence between the predicted curves for energy deposition per nucleosome for each ion/energy combination and the persistent levels of γ-H2AX indicates that the nature of energy distribution defines residual levels of γ-H2AX, an indicator of unrepaired DSBs. Our results suggest that decreasing the energy of a particle results in more complex damage that may increase genomic instability and increase the risk of carcinogenesis.

Track structure in radiation biology: theory and applications.

PubMed

Nikjoo, H; Uehara, S; Wilson, W E; Hoshi, M; Goodhead, D T

1998-04-01

A brief review is presented of the basic concepts in track structure and the relative merit of various theoretical approaches adopted in Monte-Carlo track-structure codes are examined. In the second part of the paper, a formal cluster analysis is introduced to calculate cluster-distance distributions. Total experimental ionization cross-sections were least-square fitted and compared with the calculation by various theoretical methods. Monte-Carlo track-structure code Kurbuc was used to examine and compare the spectrum of the secondary electrons generated by using functions given by Born-Bethe, Jain-Khare, Gryzinsky, Kim-Rudd, Mott and Vriens' theories. The cluster analysis in track structure was carried out using the k-means method and Hartigan algorithm. Data are presented on experimental and calculated total ionization cross-sections: inverse mean free path (IMFP) as a function of electron energy used in Monte-Carlo track-structure codes; the spectrum of secondary electrons generated by different functions for 500 eV primary electrons; cluster analysis for 4 MeV and 20 MeV alpha-particles in terms of the frequency of total cluster energy to the root-mean-square (rms) radius of the cluster and differential distance distributions for a pair of clusters; and finally relative frequency distribution for energy deposited in DNA, single-strand break and double-strand breaks for 10MeV/u protons, alpha-particles and carbon ions. There are a number of Monte-Carlo track-structure codes that have been developed independently and the bench-marking presented in this paper allows a better choice of the theoretical method adopted in a track-structure code to be made. A systematic bench-marking of cross-sections and spectra of the secondary electrons shows differences between the codes at atomic level, but such differences are not significant in biophysical modelling at the macromolecular level. Clustered-damage evaluation shows: that a substantial proportion of dose ( 30%) is deposited by low-energy electrons; the majority of DNA damage lesions are of simple type; the complexity of damage increases with increased LET, while the total yield of strand breaks remains constant; and at high LET values nearly 70% of all double-strand breaks are of complex type.

Space-planning and structural solutions of low-rise buildings: Optimal selection methods

NASA Astrophysics Data System (ADS)

Gusakova, Natalya; Minaev, Nikolay; Filushina, Kristina; Dobrynina, Olga; Gusakov, Alexander

2017-11-01

The present study is devoted to elaboration of methodology used to select appropriately the space-planning and structural solutions in low-rise buildings. Objective of the study is working out the system of criteria influencing the selection of space-planning and structural solutions which are most suitable for low-rise buildings and structures. Application of the defined criteria in practice aim to enhance the efficiency of capital investments, energy and resource saving, create comfortable conditions for the population considering climatic zoning of the construction site. Developments of the project can be applied while implementing investment-construction projects of low-rise housing at different kinds of territories based on the local building materials. The system of criteria influencing the optimal selection of space-planning and structural solutions of low-rise buildings has been developed. Methodological basis has been also elaborated to assess optimal selection of space-planning and structural solutions of low-rise buildings satisfying the requirements of energy-efficiency, comfort and safety, and economical efficiency. Elaborated methodology enables to intensify the processes of low-rise construction development for different types of territories taking into account climatic zoning of the construction site. Stimulation of low-rise construction processes should be based on the system of approaches which are scientifically justified; thus it allows enhancing energy efficiency, comfort, safety and economical effectiveness of low-rise buildings.

Density functional calculations on structural materials for nuclear energy applications and functional materials for photovoltaic energy applications (abstract only).

PubMed

Domain, C; Olsson, P; Becquart, C S; Legris, A; Guillemoles, J F

2008-02-13

Ab initio density functional theory calculations are carried out in order to predict the evolution of structural materials under aggressive working conditions such as cases with exposure to corrosion and irradiation, as well as to predict and investigate the properties of functional materials for photovoltaic energy applications. Structural metallic materials used in nuclear facilities are subjected to irradiation which induces the creation of large amounts of point defects. These defects interact with each other as well as with the different elements constituting the alloys, which leads to modifications of the microstructure and the mechanical properties. VASP (Vienna Ab initio Simulation Package) has been used to determine the properties of point defect clusters and also those of extended defects such as dislocations. The resulting quantities, such as interaction energies and migration energies, are used in larger scale simulation methods in order to build predictive tools. For photovoltaic energy applications, ab initio calculations are used in order to search for new semiconductors and possible element substitutions for existing ones in order to improve their efficiency.

A theoretical study on the geometry and spectroscopic properties of ground-state and local minima isomers of (CuS)n=2-6 clusters

NASA Astrophysics Data System (ADS)

Luque-Ceballos, Jonathan C.; Posada-Borbón, Alvaro; Herrera-Urbina, Ronaldo; Aceves, R.; Juárez-Sánchez, J. Octavio; Posada-Amarillas, Alvaro

2018-03-01

Spectroscopic properties of gas-phase copper sulfide clusters (CuS)n (n = 2-6) are calculated using Density Functional Theory (DFT) and time-dependent (TD) DFT approaches. The energy landscape of the potential energy surface is explored through a basin-hopping DFT methodology. Ground-state and low-lying isomer structures are obtained. The global search was performed at the B3PW91/SDD level of theory. Normal modes are calculated to validate the existence of optimal cluster structures. Energetic properties are obtained for the ground-state and isomer clusters and their relative energies are evaluated for probing isomerization. This is a few tenths of an eV, except for (CuS)2 cluster, which presents energy differences of ∼1 eV. Notable differences in the infrared spectra exist between the ground-state and first isomer structures, even for the (CuS)5 cluster, which has in both configurations a core copper pyramid. TDDFT provides the simulated absorption spectrum, presenting a theoretical description of optical absorption bands in terms of electronic excitations in the UV and visible regions. Results exhibit a significant dependence of the calculated UV/vis spectra on clusters size and shape regarding the ground state structures. Optical absorption is strong in the UV region, and weak or forbidden in the visible region of the spectrum.

Accelerating atomic structure search with cluster regularization

NASA Astrophysics Data System (ADS)

Sørensen, K. H.; Jørgensen, M. S.; Bruix, A.; Hammer, B.

2018-06-01

We present a method for accelerating the global structure optimization of atomic compounds. The method is demonstrated to speed up the finding of the anatase TiO2(001)-(1 × 4) surface reconstruction within a density functional tight-binding theory framework using an evolutionary algorithm. As a key element of the method, we use unsupervised machine learning techniques to categorize atoms present in a diverse set of partially disordered surface structures into clusters of atoms having similar local atomic environments. Analysis of more than 1000 different structures shows that the total energy of the structures correlates with the summed distances of the atomic environments to their respective cluster centers in feature space, where the sum runs over all atoms in each structure. Our method is formulated as a gradient based minimization of this summed cluster distance for a given structure and alternates with a standard gradient based energy minimization. While the latter minimization ensures local relaxation within a given energy basin, the former enables escapes from meta-stable basins and hence increases the overall performance of the global optimization.

Titanium embedded cage structure formation in Al{sub n}Ti{sup +} clusters and their interaction with Ar

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

Torres, M. B., E-mail: begonia@ubu.es; Vega, A.; Balbás, L. C.

2014-05-07

Recently, Ar physisorption was used as a structural probe for the location of the Ti dopant atom in aluminium cluster cations, Al{sub n}Ti{sup +} [Lang et al., J. Am. Soc. Mass Spectrom. 22, 1508 (2011)]. As an experiment result, the lack of Ar complexes for n > n{sub c} determines the cluster size for which the Ti atom is located inside of an Al cage. To elucidate the decisive factors for the formation of endohedrally Al{sub n}Ti{sup +}, experimentalists proposed detailed computational studies as indispensable. In this work, we investigated, using the density functional theory, the structural and electronic propertiesmore » of singly titanium doped cationic clusters, Al{sub n}Ti{sup +} (n = 16–21) as well as the adsorption of an Ar atom on them. The first endohedral doped cluster, with Ti encapsulated in a fcc-like cage skeleton, appears at n{sub c} = 21, which is the critical number consistent with the exohedral-endohedral transition experimentally observed. At this critical size the non-crystalline icosahedral growth pattern, related to the pure aluminium clusters, with the Ti atom in the surface, changes into a endohedral fcc-like pattern. The map of structural isomers, relative energy differences, second energy differences, and structural parameters were determined and analyzed. Moreover, we show the critical size depends on the net charge of the cluster, being different for the cationic clusters (n{sub c} = 21) and their neutral counterparts (n{sub c} = 20). For the Al {sub n} Ti {sup +} · Ar complexes, and for n < 21, the preferred Ar adsorption site is on top of the exohedral Ti atom, with adsorption energy in very good agreement with the experimental value. Instead, for n = 21, the Ar adsorption occurs on the top an Al atom with very low absorption energy. For all sizes the geometry of the Al{sub n}Ti{sup +} clusters keeps unaltered in the Ar-cluster complexes. This fact indicates that Ar adsorption does not influence the cluster structure, providing support to the experimental technique used. For n{sub c} = 21, the smallest size of endohedral Ti doped cationic clusters, the Ar binding energy decreases drastically, whereas the Ar-cluster distance increases substantially, point to Ar physisorption, as assumed by the experimentalists. Calculated Ar adsorption energies agree well with available experimental binding energies.« less

Chemical, structural and combustion characteristics of carbonaceous products obtained by hydrothermal carbonization of palm empty fruit bunches.

PubMed

Parshetti, Ganesh K; Kent Hoekman, S; Balasubramanian, Rajasekhar

2013-05-01

A carbon-rich solid product, denoted as hydrochar, was synthesized by hydrothermal carbonization (HTC) of palm oil empty fruit bunch (EFB), at different pre-treatment temperatures of 150, 250 and 350 °C. The conversion of the raw biomass to its hydrochar occurred via dehydration and decarboxylation processes. The hydrochar produced at 350 °C had the maximum energy-density (>27 MJ kg(-1)) with 68.52% of raw EFB energy retained in the char. To gain a detailed insight into the chemical and structural properties, carbonaceous hydrochar materials were characterized by FE-SEM, FT-IR, XRD and Brunauer-Emmett-Teller (BET) analyses. This work also investigated the influence of hydrothermally treated hydrochars on the co-combustion characteristics of low rank Indonesian coal. Conventional thermal gravimetric analysis (TGA) parameters, kinetics and activation energy of different hydrochar and coal blends were estimated. Our results show that solid hydrochars improve the combustion of low rank coals for energy generation. Copyright © 2012 Elsevier Ltd. All rights reserved.

Dynamics of C2H 2 3 +→H++H++C 2 + investigated by 50-keV/u Ne8 + impact

NASA Astrophysics Data System (ADS)

Xu, S.; Zhu, X. L.; Feng, W. T.; Guo, D. L.; Zhao, Q.; Yan, S.; Zhang, P.; Zhao, D. M.; Gao, Y.; Zhang, S. F.; Yang, J.; Ma, X.

2018-06-01

Breakup dynamics of C2H 2 3 + → H++H++C 2 + induced by 50-keV/u Ne8 + ion impact is investigated employing a reaction microscope. All three ionic fragments in the final state are detected in coincidence, and their momentum vectors as well as the kinetic energies are determined. The kinetic-energy correlation spectrum of the two protons displays very rich structures. Utilizing the Newton diagrams and the Dalitz plots, different dissociation mechanisms corresponding to these structures are identified. It was found that, besides the concerted and sequential breakup, fragmentation mechanisms associated with different vibration modes including molecular bending and asymmetric stretching also make significant contributions. We analyzed the correlation between different fragmentation mechanisms and the kinetic-energy release (KER) and found that the sequential process occurs with higher KER while, in contrast, the concerted process mainly contributes to the lower KER. This behavior is entirely opposite to the breakup of the CO2 molecule.

Dopant-Modulating Mechanism of Lithium Adsorption and Diffusion at the Graphene /Li2S Interface

NASA Astrophysics Data System (ADS)

Guo, Lichao; Li, Jiajun; Wang, Huayu; Zhao, Naiqin; Shi, Chunsheng; Ma, Liying; He, Chunnian; He, Fang; Liu, Enzuo

2018-02-01

Graphene modification is one of the most effective routes to enhance the electrochemical properties of the transition-metal sulfide anode for Li-ion batteries and the Li2S cathode for Li-S batteries. Boron, nitrogen, oxygen, phosphorus, and sulfur doping greatly affect the electrochemical properties of Li2S /graphene . Here, we investigate the interfacial binding energy, lithium adsorption energy, interface diffusion barrier, and electronic structure by first-principles calculations to unveil the diverse effects of different dopants during interfacial lithiation reactions. The interfacial lithium storage follows the pseudocapacitylike mechanism with intercalation character. Two different mechanisms are revealed to enhance the interfacial lithium adsorption and diffusion, which are the electron-deficiency host doping and the vacancylike structure evolutions with bond breaking. The synergistic effect between different dopants with diverse doping effects is also proposed. The results give a theoretical basis for the materials design with doped graphene as advanced materials modification for energy storage.

Molecular structure and the EPR calculation of the gas phase succinonitrile molecule

NASA Astrophysics Data System (ADS)

Kepceoǧlu, A.; Kılıç, H. Ş.; Dereli, Ö.

2017-02-01

Succinonitrile (i.e. butanedinitrile) is a colorless nitrile compound that can be used in the gel polymer batteries as a solid-state solvent electrolytes and has a plastic crystal structure. Prior to the molecular structure calculation of the succinonitrile molecule, the conformer analysis were calculated by using semi empirical method PM3 core type Hamiltonian and eight different conformer structures were determined. Molecular structure with energy related properties of these conformers having the lowest energy was calculated by using DFT (B3LYP) methods with 6-311++G(d,p) basis set. Possible radicals, can be formed experimentally, were modeled in this study. EPR parameters of these model radicals were calculated and then compared with that obtained experimentally.

Electronic structure and properties of lanthanum

NASA Astrophysics Data System (ADS)

Nixon, Lane; Papaconstantopoulos, Dimitrios

2008-03-01

The total energy and electronic structure of lanthanum have been calculated in the bcc, fcc, hcp and dhcp structures for pressures up to 50 GPa. The full potential linearized-augmented-planewave method was used with both the local-density and general-gradient approximations. The correct phase ordering has been found, with lattice parameters and bulk moduli in good agreement with experimental data. The GGA method shows excellent agreement overall while the LDA results show larger discrepancies. The calculated strain energies for the fcc and bcc structures demonstrate the respective stable and unstable configurations at ambient conditions. The calculated superconductivity properties under pressure for the fcc structure are also found to agree well with measurements. Both LDA and GGA, with minor differences, reproduce well the experimental results for Tc.

A thermally driven differential mutation approach for the structural optimization of large atomic systems

NASA Astrophysics Data System (ADS)

Biswas, Katja

2017-09-01

A computational method is presented which is capable to obtain low lying energy structures of topological amorphous systems. The method merges a differential mutation genetic algorithm with simulated annealing. This is done by incorporating a thermal selection criterion, which makes it possible to reliably obtain low lying minima with just a small population size and is suitable for multimodal structural optimization. The method is tested on the structural optimization of amorphous graphene from unbiased atomic starting configurations. With just a population size of six systems, energetically very low structures are obtained. While each of the structures represents a distinctly different arrangement of the atoms, their properties, such as energy, distribution of rings, radial distribution function, coordination number, and distribution of bond angles, are very similar.

Two-order-parameter description of liquid Al under five different pressures

NASA Astrophysics Data System (ADS)

Li, Y. D.; Hao, Qing-Hai; Cao, Qi-Long; Liu, C. S.

2008-11-01

In the present work, using the glue potential, the constant pressure molecular-dynamics simulations of liquid Al under five various pressures and a systematic analysis of the local atomic structures have been performed in order to test the two-order-parameter model proposed by Tanaka [Phys. Rev. Lett. 80, 5750 (1998)] originally for explaining the unusual behaviors of liquid water. The temperature dependence of the bond order parameter Q6 in liquid Al under five different pressures can be well fitted by the functional expression (Q6)/(1-Q6)=Q60exp((ΔE-PΔV)/(kBT)) which produces the energy gain ΔE and the volume change upon the formation of a locally favored structure: ΔE=0.025eV and ΔV=-0.27(Å)3 . ΔE is nearly equal to the difference between the average bond energy of the other type I bonds and the average bond energy of 1551 bonds (characterizing the icosahedronlike local structure); ΔV could be explained as the average volume occupied by one atom in icosahedra minus that occupied by one atom in other structures. With the obtained ΔE and ΔV , it is satisfactorily explained that the density of liquid Al displays a much weaker nonlinear dependence on temperature under lower pressures. So it is demonstrated that the behavior of liquid Al can be well described by the two-order-parameter model.

Evolutionary interplay between structure, energy and epistasis in the coat protein of the ϕX174 phage family.

PubMed

Redondo, Rodrigo A F; de Vladar, Harold P; Włodarski, Tomasz; Bollback, Jonathan P

2017-01-01

Viral capsids are structurally constrained by interactions among the amino acids (AAs) of their constituent proteins. Therefore, epistasis is expected to evolve among physically interacting sites and to influence the rates of substitution. To study the evolution of epistasis, we focused on the major structural protein of the ϕX174 phage family by first reconstructing the ancestral protein sequences of 18 species using a Bayesian statistical framework. The inferred ancestral reconstruction differed at eight AAs, for a total of 256 possible ancestral haplotypes. For each ancestral haplotype and the extant species, we estimated, in silico, the distribution of free energies and epistasis of the capsid structure. We found that free energy has not significantly increased but epistasis has. We decomposed epistasis up to fifth order and found that higher-order epistasis sometimes compensates pairwise interactions making the free energy seem additive. The dN/dS ratio is low, suggesting strong purifying selection, and that structure is under stabilizing selection. We synthesized phages carrying ancestral haplotypes of the coat protein gene and measured their fitness experimentally. Our findings indicate that stabilizing mutations can have higher fitness, and that fitness optima do not necessarily coincide with energy minima. © 2017 The Authors.

Cinetica de oxidacion de polimeros conductores: poli-3,4- etilendioxitiofeno

NASA Astrophysics Data System (ADS)

Caballero Romero, Maria

Films of poly-3,4-ethylenedioxythiophene (PEDOT) perchlorate used as electrodes in liquid electrolytes incorporate anions and solvent during oxidation for charge and osmotic balance: the film swells. During reduction the film shrinks, closes its structure trapping counterions getting then rising conformational packed states by expulsion of counterions and solvent. Here by potential step from the same reduced initial state to the same oxidized final state the rate coefficient, the activation energy and reaction orders related to the counterion concentration in solution and to the concentration of active centers in the polymer film, were attained following the usual methodology used for chemical and electrochemical kinetics. Now the full methodology was repeated using different reduced-shrunk or reduced-conformational compacted initial states every time. Those initial states were attained by reduction of the oxidized film at rising cathodic potentials for the same reduction time each. Rising reduced and conformational compacted states give slower subsequent oxidation rates by potential step to the same anodic potential every time. The activation energy, the reaction coefficient and reaction orders change for rising conformational compacted initial states. Decreasing rate constants and increasing activation energies are obtained for the PEDOT oxidation from increasing conformational compacted initial states. The experimental activation energy presents two linear ranges as a function of the initial reduced-compacted state. Using as initial states for the oxidation open structures attained by reduction at low cathodic potentials, activation energies attained were constant: namely the chemical activation energy. Using as initial states for the oxidation deeper reduced, closed and packed conformational structures, the activation energy includes two components: the constant chemical energy plus the conformational energy required to relax the conformational structure generating free volume which allows the entrance of the balancing counterions required for the reaction. The conformational energy increases linearly as a function of the reduction-compaction potential. The kinetic magnitudes include conformational and structural information. The Chemical Kinetics becomes Structural (or conformational) Chemical Kinetics.

Electron bunch structure in energy recovery linac with high-voltage dc photoelectron gun

NASA Astrophysics Data System (ADS)

Saveliev, Y. M.; Jackson, F.; Jones, J. K.; McKenzie, J. W.

2016-09-01

The internal structure of electron bunches generated in an injector line with a dc photoelectron gun is investigated. Experiments were conducted on the ALICE (accelerators and lasers in combined experiments) energy recovery linac at Daresbury Laboratory. At a relatively low dc gun voltage of 230 kV, the bunch normally consisted of two beamlets with different electron energies, as well as transverse and longitudinal characteristics. The beamlets are formed at the head and the tail of the bunch. At a higher gun voltage of 325 kV, the beam substructure is much less pronounced and could be observed only at nonoptimal injector settings. Experiments and computer simulations demonstrated that the bunch structure develops during the initial beam acceleration in the superconducting rf booster cavity and can be alleviated either by increasing the gun voltage to the highest possible level or by controlling the beam acceleration from the gun voltage in the first accelerating structure.

Data-driven spectral filters for decomposing the streamwise turbulent kinetic energy in turbulent boundary layers

NASA Astrophysics Data System (ADS)

Baars, Woutijn J.; Hutchins, Nicholas; Marusic, Ivan

2017-11-01

An organization in wall-bounded turbulence is evidenced by the classification of distinctly different flow structures, including large-scale motions such as hairpin packets and very large-scale motions or superstructures. In conjunction with less organized turbulence, these flow structures all contribute to the streamwise turbulent kinetic energy . Since different class structures comprise dissimilar scalings of their overlapping imprints in the streamwise velocity spectra, their coexistence complicates the interpretation of the wall-normal trend in and its Reynolds number dependence. Via coherence analyses of two-point data in boundary layers we derive spectral filters for stochastically decomposing the streamwise spectra into sub-components, representing different types of statistical flow structures. It is also explored how the decomposition reflects the spectral break-down following the modeling attempts of Perry et al. 1986 and Marusic & Perry 1995. In the process we reveal a universal wall-scaling for a portion of the outer-region turbulence that is coherent with the near-wall region for Reτ O(103) to O(106) , which is described as a wall-attached self-similar structure embedded within the logarithmic region.

Design of a Conceptual Bumper Energy Absorber Coupling Pedestrian Safety and Low-Speed Impact Requirements

PubMed Central

Mo, Fuhao; Zhao, Siqi; Yu, Chuanhui; Duan, Shuyong

2018-01-01

The car front bumper system needs to meet the requirements of both pedestrian safety and low-speed impact which are somewhat contradicting. This study aims to design a new kind of modular self-adaptive energy absorber of the front bumper system which can balance the two performances. The X-shaped energy-absorbing structure was proposed which can enhance the energy absorption capacity during impact by changing its deformation mode based on the amount of external collision energy. Then, finite element simulations with a realistic vehicle bumper system are performed to demonstrate its crashworthiness in comparison with the traditional foam energy absorber, which presents a significant improvement of the two performances. Furthermore, the structural parameters of the X-shaped energy-absorbing structure including thickness (t u), side arc radius (R), and clamping boost beam thickness (t b) are analyzed using a full factorial method, and a multiobjective optimization is implemented regarding evaluation indexes of both pedestrian safety and low-speed impact. The optimal parameters are then verified, and the feasibility of the optimal results is confirmed. In conclusion, the new X-shaped energy absorber can meet both pedestrian safety and low-speed impact requirements well by altering the main deformation modes according to different impact energy levels. PMID:29581728

Design of a Conceptual Bumper Energy Absorber Coupling Pedestrian Safety and Low-Speed Impact Requirements.

PubMed

Mo, Fuhao; Zhao, Siqi; Yu, Chuanhui; Xiao, Zhi; Duan, Shuyong

2018-01-01

The car front bumper system needs to meet the requirements of both pedestrian safety and low-speed impact which are somewhat contradicting. This study aims to design a new kind of modular self-adaptive energy absorber of the front bumper system which can balance the two performances. The X-shaped energy-absorbing structure was proposed which can enhance the energy absorption capacity during impact by changing its deformation mode based on the amount of external collision energy. Then, finite element simulations with a realistic vehicle bumper system are performed to demonstrate its crashworthiness in comparison with the traditional foam energy absorber, which presents a significant improvement of the two performances. Furthermore, the structural parameters of the X-shaped energy-absorbing structure including thickness ( t u ), side arc radius ( R ), and clamping boost beam thickness ( t b ) are analyzed using a full factorial method, and a multiobjective optimization is implemented regarding evaluation indexes of both pedestrian safety and low-speed impact. The optimal parameters are then verified, and the feasibility of the optimal results is confirmed. In conclusion, the new X-shaped energy absorber can meet both pedestrian safety and low-speed impact requirements well by altering the main deformation modes according to different impact energy levels.

Effect of Topology Structure on the Output Performance of an Automobile Exhaust Thermoelectric Generator

NASA Astrophysics Data System (ADS)

Fang, W.; Quan, S. H.; Xie, C. J.; Ran, B.; Li, X. L.; Wang, L.; Jiao, Y. T.; Xu, T. W.

2017-05-01

The majority of the thermal energy released in an automotive internal combustion cycle is exhausted as waste heat through the tail pipe. This paper describes an automobile exhaust thermoelectric generator (AETEG), designed to recycle automobile waste heat. A model of the output characteristics of each thermoelectric device was established by testing their open circuit voltage and internal resistance, and combining the output characteristics. To better describe the relationship, the physical model was transformed into a topological model. The connection matrix was used to describe the relationship between any two thermoelectric devices in the topological structure. Different topological structures produced different power outputs; their output power was maximised by using an iterative algorithm to optimize the series-parallel electrical topology structure. The experimental results have shown that the output power of the optimal topology structure increases by 18.18% and 29.35% versus that of a pure in-series or parallel topology, respectively, and by 10.08% versus a manually defined structure (based on user experience). The thermoelectric conversion device increased energy efficiency by 40% when compared with a traditional car.

Computational investigation of large-scale vortex interaction with flexible bodies

NASA Astrophysics Data System (ADS)

Connell, Benjamin; Yue, Dick K. P.

2003-11-01

The interaction of large-scale vortices with flexible bodies is examined with particular interest paid to the energy and momentum budgets of the system. Finite difference direct numerical simulation of the Navier-Stokes equations on a moving curvilinear grid is coupled with a finite difference structural solver of both a linear membrane under tension and linear Euler-Bernoulli beam. The hydrodynamics and structural dynamics are solved simultaneously using an iterative procedure with the external structural forcing calculated from the hydrodynamics at the surface and the flow-field velocity boundary condition given by the structural motion. We focus on an investigation into the canonical problem of a vortex-dipole impinging on a flexible membrane. It is discovered that the structural properties of the membrane direct the interaction in terms of the flow evolution and the energy budget. Pressure gradients associated with resonant membrane response are shown to sustain the oscillatory motion of the vortex pair. Understanding how the key mechanisms in vortex-body interactions are guided by the structural properties of the body is a prerequisite to exploiting these mechanisms.

Contribution of energy values to the analysis of global searching molecular dynamics simulations of transmembrane helical bundles.

PubMed Central

Torres, Jaume; Briggs, John A G; Arkin, Isaiah T

2002-01-01

Molecular interactions between transmembrane alpha-helices can be explored using global searching molecular dynamics simulations (GSMDS), a method that produces a group of probable low energy structures. We have shown previously that the correct model in various homooligomers is always located at the bottom of one of various possible energy basins. Unfortunately, the correct model is not necessarily the one with the lowest energy according to the computational protocol, which has resulted in overlooking of this parameter in favor of experimental data. In an attempt to use energetic considerations in the aforementioned analysis, we used global searching molecular dynamics simulations on three homooligomers of different sizes, the structures of which are known. As expected, our results show that even when the conformational space searched includes the correct structure, taking together simulations using both left and right handedness, the correct model does not necessarily have the lowest energy. However, for the models derived from the simulation that uses the correct handedness, the lowest energy model is always at, or very close to, the correct orientation. We hypothesize that this should also be true when simulations are performed using homologous sequences, and consequently lowest energy models with the right handedness should produce a cluster around a certain orientation. In contrast, using the wrong handedness the lowest energy structures for each sequence should appear at many different orientations. The rationale behind this is that, although more than one energy basin may exist, basins that do not contain the correct model will shift or disappear because they will be destabilized by at least one conservative (i.e. silent) mutation, whereas the basin containing the correct model will remain. This not only allows one to point to the possible handedness of the bundle, but can be used to overcome ambiguities arising from the use of homologous sequences in the analysis of global searching molecular dynamics simulations. In addition, because clustering of lowest energy models arising from homologous sequences only happens when the estimation of the helix tilt is correct, it may provide a validation for the helix tilt estimate. PMID:12023229

Optimization of SMA layers in composite structures to enhance damping

NASA Astrophysics Data System (ADS)

Haghdoust, P.; Cinquemani, S.; Lecis, N.; Bassani, P.

2016-04-01

The performance of lightweight structures can be severely affected by vibration. New design concepts leading to lightweight, slender structural components can increase the vulnerability of the components to failure due to excessive vibration. The intelligent approach to address the problem would be the use of materials which are more capable in dissipating the energy due to their high value of loss factor. Among the different materials available to achieve damping, much attention has been attached to the use of shape memory alloys (SMAs) because of their unique microstructure, leading to good damping capacity. This work describes the design and optimization of a hybrid layered composite structure for the passive suppression of flexural vibrations in slender and light structures. Embedding the SMA layers in composite structure allows to combine different properties: the lightness of the base composite (e.g. fiber glass), the mechanical strength of the insert of metallic material and the relevant damping properties of SMA, in the martensitic phase. In particular, we put our attention on embedding the CuZnAl in the form of thin sheet in a layered composite made by glass fiber reinforced epoxy. By appropriately positioning of the SMA sheets so that they are subjected to the maximum curvature, the damping of the hybrid system can be considerably enhanced. Accordingly analytical method for evaluating the energy dissipation of the thin sheets with different shapes and patterns is developed and is followed by a shape optimization based on genetic algorithm. Eventually different configurations of the hybrid beam structure with different patterns of SMA layer are proposed and compared in the term of damping capacity.

Transformation between divacancy defects induced by an energy pulse in graphene.

PubMed

Xia, Jun; Liu, XiaoYi; Zhou, Wei; Wang, FengChao; Wu, HengAn

2016-07-08

The mutual transformations among the four typical divacancy defects induced by a high-energy pulse were studied via molecular dynamics simulation. Our study revealed all six possible mutual transformations and found that defects transformed by absorbing energy to overcome the energy barrier with bonding, debonding, and bond rotations. The reversibility of defect transformations was also investigated by potential energy analysis. The energy difference was found to greatly influence the transformation reversibility. The direct transformation path was irreversible if the energy difference was too large. We also studied the correlation between the transformation probability and the input energy. It was found that the transformation probability had a local maxima at an optimal input energy. The introduction of defects and their structural evolutions are important for tailoring the exceptional properties and thereby performances of graphene-based devices, such as nanoporous membranes for the filtration and desalination of water.

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.

Crashworthy airframe design concepts: Fabrication and testing

NASA Technical Reports Server (NTRS)

Cronkhite, J. D.; Berry, V. L.

1982-01-01

Crashworthy floor concepts applicable to general aviation aircraft metal airframe structures were investigated. Initially several energy absorbing lower fuselage structure concepts were evaluated. Full scale floor sections representative of a twin engine, general aviation airplane lower fuselage structure were designed and fabricated. The floors featured an upper high strength platform with an energy absorbing, crushable structure underneath. Eighteen floors were fabricated that incorporated five different crushable subfloor concepts. The floors were then evaluated through static and dynamic testing. Computer programs NASTRAN and KRASH were used for the static and dynamic analysis of the floor section designs. Two twin engine airplane fuselages were modified to incorporate the most promising crashworthy floor sections for test evaluation.

The two-dimensional hybrid surface plasma micro-cavity

NASA Astrophysics Data System (ADS)

Kai, Tong; Mei-yu, Wang; Fu-cheng, Wang; Jia, Guo

2018-07-01

A hybrid surface plasma micro-cavity structure with a defect cavity is formed based on the two-dimensional surface plasmon resonance photonic crystal waveguide structure. A cell defect is introduced in the centre of the photonic crystal layer to build the hybrid surface plasma micro-cavity structure. This work is numerical based on the finite-difference time-domain method. The photon energy is confined to the micro-cavity and the photon energy is strongest at the interface between the insulating layer and the metal layer. The micro-cavity structure has a very small mode volume of sub-wavelength scale in the 1550 nm communication band. The value of Q/V is up to 7132.08 λ/n-3.

Hierarchical Coupling of First-Principles Molecular Dynamics with Advanced Sampling Methods.

PubMed

Sevgen, Emre; Giberti, Federico; Sidky, Hythem; Whitmer, Jonathan K; Galli, Giulia; Gygi, Francois; de Pablo, Juan J

2018-05-14

We present a seamless coupling of a suite of codes designed to perform advanced sampling simulations, with a first-principles molecular dynamics (MD) engine. As an illustrative example, we discuss results for the free energy and potential surfaces of the alanine dipeptide obtained using both local and hybrid density functionals (DFT), and we compare them with those of a widely used classical force field, Amber99sb. In our calculations, the efficiency of first-principles MD using hybrid functionals is augmented by hierarchical sampling, where hybrid free energy calculations are initiated using estimates obtained with local functionals. We find that the free energy surfaces obtained from classical and first-principles calculations differ. Compared to DFT results, the classical force field overestimates the internal energy contribution of high free energy states, and it underestimates the entropic contribution along the entire free energy profile. Using the string method, we illustrate how these differences lead to different transition pathways connecting the metastable minima of the alanine dipeptide. In larger peptides, those differences would lead to qualitatively different results for the equilibrium structure and conformation of these molecules.

Key issues in theoretical and functional pneumatic design

NASA Astrophysics Data System (ADS)

Xu, Z. G.; Yang, D. Y.; Liu, W. M.; Liu, T. T.

2017-10-01

This paper studies the energy release of the pneumatic engine in different thermodynamic processes, the isothermal process is the highest power output process, while adiabatic process is the lowest energy output process, and the energy release of the pneumatic engine is a multi-state thermodynamic process between them. Therefore heat exchanging should be increased between the pneumatic engine and the outer space, the gas expansion process in the cylinder should be as close as possible to the isothermal process. Heat exchange should be increased between the cylinder and the external spaces. Secondly, the fin structure is studied to increase the heat exchanging between the cylinder body and the outside space. The upper part has fin structures and the lower cylinder has no fin structure, this structure improved the working efficiency of pneumatic engine. Finally the cam and the hydraulic bottle of pneumatic engines are designed. Simulation and theoretical calculation are used to the analysis of the whole structure, which lay the foundation for the manufacturing and design of the pneumatic engines.

Ferrocene Orientation Determined Intramolecular Interactions Using Energy Decomposition Analysis.

PubMed

Wang, Feng; Islam, Shawkat; Vasilyev, Vladislav

2015-11-16

Two very different quantum mechanically based energy decomposition analyses (EDA) schemes are employed to study the dominant energy differences between the eclipsed and staggered ferrocene conformers. One is the extended transition state (ETS) based on the Amsterdam Density Functional (ADF) package and the other is natural EDA (NEDA) based in the General Atomic and Molecular Electronic Structure System (GAMESS) package. It reveals that in addition to the model (theory and basis set), the fragmentation channels more significantly affect the interaction energy terms (Δ E ) between the conformers. It is discovered that such an interaction energy can be absorbed into the pre-partitioned fragment channels so that to affect the interaction energies in a particular conformer of Fc. To avoid this, the present study employs a complete fragment channel-the fragments of ferrocene are individual neutral atoms. It therefore discovers that the major difference between the ferrocene conformers is due to the quantum mechanical Pauli repulsive energy and orbital attractive energy, leading to the eclipsed ferrocene the energy preferred structure. The NEDA scheme further indicates that the sum of attractive (negative) polarization (POL) and charge transfer (CL) energies prefers the eclipsed ferrocene. The repulsive (positive) deformation (DEF) energy, which is dominated by the cyclopentadienyle (Cp) rings, prefers the staggered ferrocene. Again, the cancellation results in a small energy residue in favour of the eclipsed ferrocene, in agreement with the ETS scheme. Further Natural Bond Orbital (NBO) analysis indicates that all NBO energies, total Lewis (no Fe) and lone pair (LP) deletion all prefer the eclipsed Fc conformer. The most significant energy preferring the eclipsed ferrocene without cancellation is the interactions between the donor lone pairs (LP) of the Fe atom and the acceptor antibond (BD*) NBOs of all C-C and C-H bonds in the ligand, LP(Fe)-BD*(C-C & C-H), which strongly stabilizes the eclipsed (D 5h ) conformation by -457.6 kcal·mol -1 .

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.

Orientation-dependent structural and photocatalytic properties of LaCoO3 epitaxial nano-thin films

NASA Astrophysics Data System (ADS)

Zhang, Yan-ping; Liu, Hai-feng; Hu, Hai-long; Xie, Rui-shi; Ma, Guo-hua; Huo, Ji-chuan; Wang, Hai-bin

2018-02-01

LaCoO3 epitaxial films were grown on (100), (110) and (111) oriented LaAlO3 substrates by the polymer-assisted deposition method. Crystal structure measurement and cross-section observation indicate that all the LaCoO3 films are epitaxially grown in accordance with the orientation of LaAlO3 substrates, with biaxial compressive strain in the ab plane. Owing to the different strain directions of CoO6 octahedron, the mean Co-O bond length increases by different amounts in (100), (110) and (111) oriented films compared with that of bulk LaCoO3, and the (100) oriented LaCoO3 has the largest increase. Photocatalytic degradation of methyl orange indicates that the order of photocatalytic activity of the three oriented films is (100) > (111) > (110). Combined with analysis of electronic nature and band structure for LaCoO3 films, it is found that the change of the photocatalytic activity is closely related to the crystal field splitting energy of Co3+ and Co-O binding energy. The increase in the mean Co-O bond length will decrease the crystal field splitting energy of Co3+ and Co-O binding energy and further reduce the value of band gap energy, thus improving the photocatalytic activity. This may also provide a clue for expanding the visible-light-induced photocatalytic application of LaCoO3.

Structural evolution study of 1-2 nm gold clusters

NASA Astrophysics Data System (ADS)

Beltrán, M. R.; Suárez Raspopov, R.; González, G.

2011-12-01

We have explored lowest energy minima structures of gold atom clusters both, charged and neutral (Aun^{ν}νn with n = 20, 28, 34, 38, 55, 75, 101, 146, 147, 192, 212 atoms and ν = 0, ±1). The structures have been obtained from first principles generalized gradient approximation, density functional theory (DFT) calculations based on norm-conserving pseudopotentials and numerical atomic basis sets. We have found two new disordered or defective isomers lower in energy than their ordered counterparts for n = 101, 147. The purpose of this work is to systematically study the difference between the electronic properties of the two lowest ordered and disordered isomers for each size. Our results agree with previous first principle calculations and with some recent experimental results (Au20 and Au101). For each case we report total energies, binding energies, ionization potentials, electron affinities, density of states, highest occupied molecular orbital-lowest unoccupied molecular orbital (HOMO-LUMO) gaps, Housdorff chirality measure index and their simulated image in a high resolution transmission electron microscopy (HRTEM). The calculated properties of the two low lying (ordered and disordered) isomers show clear differences as to be singled out in a suitable experimental setting. An extensive discussion on the evolution with size of the cohesive energy, the ionization potentials, the electron affinities, the HOMO-LUMO gaps and their index of chirality to determine the crossover between them is given.

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

A combined crossed molecular beams and theoretical study of the reaction CN + C2H4

NASA Astrophysics Data System (ADS)

Balucani, Nadia; Leonori, Francesca; Petrucci, Raffaele; Wang, Xingan; Casavecchia, Piergiorgio; Skouteris, Dimitrios; Albernaz, Alessandra F.; Gargano, Ricardo

2015-03-01

The CN + C2H4 reaction has been investigated experimentally, in crossed molecular beam (CMB) experiments at the collision energy of 33.4 kJ/mol, and theoretically, by electronic structure calculations of the relevant potential energy surface and Rice-Ramsperger-Kassel-Marcus (RRKM) estimates of the product branching ratio. Differently from previous CMB experiments at lower collision energies, but similarly to a high energy study, we have some indication that a second reaction channel is open at this collision energy, the characteristics of which are consistent with the channel leading to CH2CHNC + H. The RRKM estimates using M06L electronic structure calculations qualitatively support the experimental observation of C2H3NC formation at this and at the higher collision energy of 42.7 kJ/mol of previous experiments.

Destabilization of Human Serum Albumin by Ionic Liquids Studied Using Enhanced Molecular Dynamics Simulations.

PubMed

Jaeger, Vance W; Pfaendtner, Jim

2016-12-01

Ionic liquid (IL) containing solvents can change the structure, dynamics, function, and stability of proteins. In order to investigate the mechanisms by which ILs induce structural changes in a large multidomain protein, we study the interactions of human serum albumin (HSA) with two different ILs, 1-butyl-3-methylimidazolium tetrafluoroborate and choline dihydrogen phosphate. Root mean square deviation and fluctuation calculations indicate that high concentrations of ILs in mixtures with water lead to protein structures that remain close to their crystallographic structures on time scales of hundreds of nanoseconds. To overcome potential time scale limitations due to the high viscosity of the solvent, we employed enhanced sampling techniques to estimate the free energy of an experimentally determined important transition within the protein structure. Metadynamics simulations show that the free energy landscape of the unfolding of loop 1 of domain I is different in the presence of ILs than it is in water, consistent with previously published experimental evidence. We then apply essential dynamics coarse graining to systematically predict differences in the dynamics of proteins solvated in IL-water mixtures versus pure water systems. We also demonstrate that the presence of ionic liquids changes the distribution of intermolecular distances among several ligands, indicating that the protein structure swells in the presence of certain ILs, consistent with experimental evidence.

The Sound Broadcasting System of the Bullfrog

NASA Astrophysics Data System (ADS)

Purgue, Alejandro P.

1995-01-01

This work presents a comparison across selected species of several aspects of the mechanism of sound broadcasting in anuran amphibians. These studies indicate that all anuran species studied to date broadcast their calls through structures that resonate at the dominant frequency in their calls. Measurements of the magnitude of the transfer function of the radiating structures show that the structures responsible for radiating the bulk of the energy present in the call vary depending on the species considered. Bullfrogs (Rana catesbeiana) radiate most of the energy (89% sound level) present in their calls through their eardrums. In this species the transfer function of the eardrum displays several peaks coincident in frequency and amplitude with the energy distribution observed in the mating and release call of the species. The vocal sac and gular area contribute energy only in the lower band (150 to 400 Hz) of the call. The ears are responsible for radiating additional frequency bands to the ones being radiated through the gular area and vocal sacs. This condition appears to be derived. In Rana pipiens the ears also broadcast a significant portion of the energy present in the call (63% sound level) but the frequencies of the aural emissions are a subset of those frequencies radiated through the vocal sac and gular area. Character optimization suggests that this is the primitive condition for ranid frogs. Finally, the barking treefrog (Hyla gratiosa) appears to use two different structures to radiate different portions of the call. The low frequency band appears to be preferentially radiated through the lungs while the high frequency components of the call are radiated through the vocal sac.

Toward Fully in Silico Melting Point Prediction Using Molecular Simulations

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

Zhang, Y; Maginn, EJ

2013-03-01

Melting point is one of the most fundamental and practically important properties of a compound. Molecular computation of melting points. However, all of these methods simulation methods have been developed for the accurate need an experimental crystal structure as input, which means that such calculations are not really predictive since the melting point can be measured easily in experiments once a crystal structure is known. On the other hand, crystal structure prediction (CSP) has become an active field and significant progress has been made, although challenges still exist. One of the main challenges is the existence of many crystal structuresmore » (polymorphs) that are very close in energy. Thermal effects and kinetic factors make the situation even more complicated, such that it is still not trivial to predict experimental crystal structures. In this work, we exploit the fact that free energy differences are often small between crystal structures. We show that accurate melting point predictions can be made by using a reasonable crystal structure from CSP as a starting point for a free energy-based melting point calculation. The key is that most crystal structures predicted by CSP have free energies that are close to that of the experimental structure. The proposed method was tested on two rigid molecules and the results suggest that a fully in silico melting point prediction method is possible.« less

A multi-stakeholder framework for sustainable energy behavior: A multidisciplinary systems study

NASA Astrophysics Data System (ADS)

Khansari, Nasrin

Growth of population and moving towards over-consumption and over-pollution are significant threats to the environment and therefore necessitate moving towards sustainability approaches. CO2 emissions are considered to be the main basis of the incredible increase in the earth's surface temperature in recent years. Most emissions result from human activities. Thus, developing a detailed framework representing the parameters affecting individuals' energy behaviors is required. This dissertation offers an integrated conceptual framework to increase the efficiency of energy systems under complex and uncertainty conditions, facilitate energy consumption problem solving, and support the development of capacities at the individual, social, and technical levels to improve managing energy consumptions in the future. This research presents a conceptual soft systems model to explore the process of individuals' energy behavior change based on socio-structural and techno-structural contexts. In addition, a comprehensive model based on systems dynamics principles is presented to address the issue of CO2 emissions related to the households' energy consumption behavior. The proposed systems dynamics model provides a broad overview of the key agents affecting energy consumption, including government/public sector, households, and power industry. The model is created based on the research in the literature discussing the causal relations between various variables. The proposed systems dynamics model is verified by simulating different scenarios. In this research a survey is designed and conducted to investigate the role of individual, social and technical behaviors in reducing energy consumption, energy costs and carbon footprints based on the energy use profile. In sum, this study investigates the process of energy behavior change based on socio-structural and techno-structural contexts.

Atomic Layer-Deposited Molybdenum Oxide/Carbon Nanotube Hybrid Electrodes: The Influence of Crystal Structure on Lithium-Ion Capacitor Performance.

PubMed

Fleischmann, Simon; Zeiger, Marco; Quade, Antje; Kruth, Angela; Presser, Volker

2018-06-06

Merging of supercapacitors and batteries promises the creation of electrochemical energy storage devices that combine high specific energy, power, and cycling stability. For that purpose, lithium-ion capacitors (LICs) that store energy by lithiation reactions at the negative electrode and double-layer formation at the positive electrode are currently investigated. In this study, we explore the suitability of molybdenum oxide as a negative electrode material in LICs for the first time. Molybdenum oxide-carbon nanotube hybrid materials were synthesized via atomic layer deposition, and different crystal structures and morphologies were obtained by post-deposition annealing. These model materials are first structurally characterized and electrochemically evaluated in half-cells. Benchmarking in LIC full-cells revealed the influences of crystal structure, half-cell capacity, and rate handling on the actual device level performance metrics. The energy efficiency, specific energy, and power are mainly influenced by the overpotential and kinetics of the lithiation reaction during charging. Optimized LIC cells show a maximum specific energy of about 70 W·h·kg -1 and a high specific power of 4 kW·kg -1 at 34 W·h·kg -1 . The longevity of the LIC cells is drastically increased without significantly reducing the energy by preventing a deep cell discharge, hindering the negative electrode from crossing its anodic potential limit.

Ion spectral structures observed by the Van Allen Probes

NASA Astrophysics Data System (ADS)

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

2015-12-01

During the last decades several missions have recorded the presence of dynamic spectral features of energetic ions in the inner magnetosphere. Previous studies have reported single "nose-like" structures occurring alone and simultaneous nose-like structures (up to three). These ion structures are named after the characteristic shapes of energy bands or gaps in the energy-time spectrograms of in situ measured ion fluxes. They constitute the observational signatures of ion acceleration, transport, and loss in the global magnetosphere. The HOPE mass spectrometer onboard the Van Allen Probes measures energetic hydrogen, helium, and oxygen ions near the inner edge of the plasma sheet, where these ion structures are observed. We present a statistical study of nose-like structures, using 2-years measurements from the HOPE instrument. The results provide important details about the spatial distribution (dependence on geocentric distance), spectral features of the structures (differences among species), and geomagnetic conditions under which these structures occur.

Crush analysis of the foam-filled bitubal circular tube under oblique impact

NASA Astrophysics Data System (ADS)

Djamaluddin, F.; Abdullah, S.; Arrifin, A. K.; Nopiah, Z. M.

2018-02-01

This paper presents crashworthiness analysis of bitubal cylindrical tubes under different impact angular. The numerical solution of double cylindrical tubes are determined by finite element analysis (FEA). Moreover, the structure was impacted by mass block as impactor respect to longitudinal direction of the tubes. The model of structure was developed by non-linear ABAQUS sofware with variations of load angle and dimensions of tube. The outcome of this study is the respons parameters such as the peak crusing force (PCF), energy absorption (EA) and specific energy absorption (SEA), thus it can be expected this tube as the great energy absorber.

Connecting Interface Structure to Energy Level Alignment at Aqueous Semiconductor Interfaces

NASA Astrophysics Data System (ADS)

Hybertsen, Mark

Understanding structure-function relationships at aqueous semiconductor interfaces presents fundamental challenges, including the discovery of the key interface structure motifs themselves. Important examples include the alignment of electrochemical redox levels with the semiconductor band edges and the identification of catalytic active sites. We have developed a multistep approach, initially demonstrated for GaN, ZnO and their alloys, motivated by measured high efficiency for photocatalytic water oxidation. The interface structure is simulated using ab initio molecular dynamics (AIMD). The calculated, average interface dipole is combined with the GW approach from many-body perturbation theory to calculate the energy level alignment between the semiconductor band edges and the centroid of the occupied 1b1 energy level of water and thus, the electrochemical levels. Cluster models are used to study reaction pathways. The emergent interface motif is the full (GaN) or partial (ZnO) dissociated interface water layer. Here I will focus on the aqueous interfaces to the stable TiO2 anatase (101) and rutile (110) facets. The AIMD calculations reveal interface water dissociation and reassociation processes through distinct pathways: one direct at the interface and the other via a spectator water molecule from the hydration layer. Comparisons between the two interfaces shows that the energy landscape for these pathways depends on the local hydrogen bonding patterns and the interplay with the interface template. Combined results from different initial conditions and AIMD temperatures demonstrate a partially dissociated interface water layer in both cases. Specifically for rutile, structure and the GW-based analysis of the interface energy level alignment agree with experiment. Finally, hole localization at different interface structure motifs will be discussed. Work performed in collaboration with J. Lyons, N. Kharche, M. Ertem and J. Muckerman, done in part at the CFN, which is a U.S. DOE Office of Science Facility, at BNL under Contract No. DE-SC0012704 and with resources from NERSC under Contract No. DE-AC02-05CH11231.

Evaluation of Shear Strength of RC Beams with Multiple Interfaces Formed before Initial Setting Using 3D Printing Technology

PubMed Central

Kim, Kyeongjin; Park, Sangmin; Jeong, Yoseok; Lee, Jaeha

2017-01-01

With the recent development of 3D printing technology, concrete materials are sometimes used in 3D printing. Concrete structures based on 3D printing have been characterized to have the form of multiple layer build-up. Unlike general concrete structures, therefore, the 3D-printed concrete can be regarded as an orthotropic material. The material property of the 3D-printed concrete’s interface between layers is expected to be far different from that of general concrete bodies since there are no aggregate interlocks and weak chemical bonding. Such a difference finally affects the structural performance of concrete structures even though the interfaces are formed before initial setting of the concrete. The current study mainly reviewed the changes in fracture energy (toughness) with respect to various environmental conditions of such interface. Changes in fracture energies of interfaces between concrete layers were measured using low-speed Crack Mouth Opening Displacement (CMOD) closed loop concrete fracture test. The experimental results indicated reduction in fracture energy as well as tensile strengths. To improve the tensile strength of interfaces, the use of bridging materials is suggested. Since it was assumed that reduction in fracture energy could be a cause of shear strength, to evaluate the reduced structural performance of concrete structure constructed with multiple interfaces by 3D printing technology, the shear strength of RC beam by 3D printing technology was predicted and compared with that of plain RC beam. Based on the fracture energy measured in this study, Modified Compression Field Theory (MCFT) theory-applied Vector 2 program was employed to predict the degree of reduction in shear strength without considering stirrups. Reduction factors were presented based on the obtained results to predict the reduction in shear strength due to interfaces before initial setting of the concrete.

Foraging on the potential energy surface: a swarm intelligence-based optimizer for molecular geometry.

PubMed

Wehmeyer, Christoph; Falk von Rudorff, Guido; Wolf, Sebastian; Kabbe, Gabriel; Schärf, Daniel; Kühne, Thomas D; Sebastiani, Daniel

2012-11-21

We present a stochastic, swarm intelligence-based optimization algorithm for the prediction of global minima on potential energy surfaces of molecular cluster structures. Our optimization approach is a modification of the artificial bee colony (ABC) algorithm which is inspired by the foraging behavior of honey bees. We apply our modified ABC algorithm to the problem of global geometry optimization of molecular cluster structures and show its performance for clusters with 2-57 particles and different interatomic interaction potentials.

Foraging on the potential energy surface: A swarm intelligence-based optimizer for molecular geometry

NASA Astrophysics Data System (ADS)

Wehmeyer, Christoph; Falk von Rudorff, Guido; Wolf, Sebastian; Kabbe, Gabriel; Schärf, Daniel; Kühne, Thomas D.; Sebastiani, Daniel

2012-11-01

We present a stochastic, swarm intelligence-based optimization algorithm for the prediction of global minima on potential energy surfaces of molecular cluster structures. Our optimization approach is a modification of the artificial bee colony (ABC) algorithm which is inspired by the foraging behavior of honey bees. We apply our modified ABC algorithm to the problem of global geometry optimization of molecular cluster structures and show its performance for clusters with 2-57 particles and different interatomic interaction potentials.

Ab-initio study of electronic structure and elastic properties of ZrC

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

Mund, H. S., E-mail: hmoond@gmail.com; Ahuja, B. L.

2016-05-23

The electronic and elastic properties of ZrC have been investigated using the linear combination of atomic orbitals method within the framework of density functional theory. Different exchange-correlation functionals are taken into account within generalized gradient approximation. We have computed energy bands, density of states, elastic constants, bulk modulus, shear modulus, Young’s modulus, Poisson’s ratio, lattice parameters and pressure derivative of the bulk modulus by calculating ground state energy of the rock salt structure type ZrC.

Influence of Endo- and Exocyclic Heteroatoms on Stabilities and 1,3-Dipolar Cycloaddition Reactivities of Mesoionic Azomethine Ylides and Imines.

PubMed

Champagne, Pier Alexandre; Houk, K N

2017-10-20

The geometries, stabilities, and 1,3-dipolar cycloaddition reactivities of 24 mesoionic azomethine ylides and imines were investigated using density functional theory calculations at the M06-2X/6-311+G-(d,p)/M06-2X/6-31G-(d) level. The computed structures highlight how the commonly used "aromatic" resonance form should be replaced by two more accurate resonance structures. Stabilities of the dipoles were assessed by various homodesmotic schemes and are consistent with these compounds being nonaromatic. The activation free energies with ethylene or acetylene range from 11.8 to 36.6 kcal/mol. Within each dipole type, the predicted cycloaddition reactivities correlate with the reaction energies and the resonance stabilization energies provided by the various substituents. Endocyclic (X) heteroatoms increase the reactivity of the 1,3-dipoles in the order of O > NH ≅ S, whereas exocyclic (Y) substituents increase it in the order of CH 2 > NH > O > S. Distortion/interaction analysis indicated that the difference in reactivity between differently substituted 1,3-dipoles is driven by distortion, whereas the difference between azomethine ylides and imines is related to lower interaction energies of imines with the dipolarophiles.

Structures, vibrational frequencies, and infrared spectra of the hexa-hydrated benzene clusters

NASA Astrophysics Data System (ADS)

Lee, Jin Yong; Kim, Jongseob; Lee, Han Myoung; Tarakeshwar, P.; Kim, Kwang S.

2000-10-01

The water hexamer is known to have a number of isoenergetic structures. The first experimental identification of the O-H stretching vibrational spectra of the water hexamer was done in the presence of benzene. It was followed by the identification of the pure water hexamer structure by vibration-rotational tunneling (VRT) spectroscopy. Although both experiments seem to have located only the Cage structure, the structure of the benzene-water hexamer complex is not clearly known, and the effect of benzene in the water hexamer is unclear. In particular, it is not obvious how the energy difference between nearly isoenergetic water hexamer conformers changes in the presence of benzene. Thus, we have compared the benzene complexes with four low-lying isoenergetic water hexamers, Ring, Book, Cage, and Prism structures, using ab initio calculations. We also investigated the effects of the presence of benzene on the structures, harmonic vibrational frequencies, and infrared (IR) intensities for the four low-lying energy conformers. There is little change in the structure of the water hexamer upon its interaction with the benzene molecule. Hence the deformation energies are very small. The dominant contribution to the benzene-water cluster interaction mainly comes from the π-H interactions between benzene and a single water molecule. As a result of this π-H interaction, O-Hπ bond length increases and the corresponding stretching vibrational frequencies are redshifted. The IR spectral features of both (H2O)6 and benzene-(H2O)6 are quite similar. From both the energetics and the comparison of calculated and experimental spectra of the benzene-(H2O)6, the water structure in these complexes is found to have the Cage form. In particular, among the four different Cage structures, only one conformer matches the experimental O-H vibrational frequencies.

Ion Spectral Structures Observed by the Van Allen Probes and Cluster

NASA Astrophysics Data System (ADS)

Ferradas, C.; Zhang, J.; Luo, H.; Kistler, L. M.; Spence, H. E.; Larsen, B.; Skoug, R. M.; Funsten, H. O.; Reeves, G. D.

2014-12-01

During the last decades several missions have recorded the presence of dynamic spectral features of energetic ions in the inner magnetosphere. Previous studies have revealed single "nose-like" structures occurring alone and simultaneous nose-like structures (up to three). In this study we also include signatures of new types of ion structure, namely "trunk-like" and "tusk-like" structures. All the ion structures are named after the characteristic shapes of energy bands or gaps in the energy-time spectrograms of in situ measured ion fluxes. They constitute the observational signatures of ion acceleration, transport, and loss in the global magnetosphere. Multi-spacecraft analysis of these structures is important to understand their spatial distribution and temporal evolution. Mass spectrometers onboard Cluster (in a polar orbit) and the Van Allen Probes (in an equatorial orbit) measure energetic hydrogen, helium, and oxygen ions near the inner edge of the plasma sheet, where these ion structures are observed. We present a statistical study of the ion structures, using >1-year measurements from the two missions during the Van Allen Probes era. The results provide important details about the spatial distribution (dependence on geocentric distance and magnetic local time), spectral features of the structures (e.g., characteristic energy and differences among species), and geomagnetic and solar wind conditions under which these structures occur.

New mechanism of structuring associated with the quasi-merohedral twinning by an example of Ca{sub 1–x}La{sub x}F{sub 2+x} ordered solid solutions

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

Maksimov, S. K., E-mail: maksimov-sk@comtv.ru; Maksimov, K. S., E-mail: kuros@rambler.ru; Sukhov, N. D.

Merohedry is considered an inseparable property of atomic structures, and uses for the refinement of structural data in a process of correct determination of structure of compounds. Transformation of faulty structures stimulated by decreasing of systemic cumulative energy leads to generation of merohedral twinning type. Ordering is accompanied by origin of antiphase domains. If ordering belongs to the CuAu type, it is accompanied by tetragonal distortions along different (100) directions. If a crystal consists of mosaic of nanodimensional antiphase domains, the conjugation of antiphase domains with different tetragonality leads to monoclinic distortions, at that, conjugated domains are distorted mirrorly. Similarmore » system undergoes further transformation by means of quasi-merohedral twinning. As a result of quasi-merohedry, straight-lines of lattices with different monoclinic distortions are transformed into coherent lattice broken-lines providing minimization of the cumulative energy. Structuring is controlled by regularities of the self-organization. However stochasticity of ordering predetermines the origin areas where few domains with different tetragonality contact which leads to the origin of faulty fields braking regular passage of structuring. Resulting crystal has been found structurally non-uniform, furthermore structural non-uniformity permits identifying elements and stages of a process. However there is no precondition preventing arising the origin of homogenous states. Effect has been revealed in Ca{sub 1–x}La{sub x}F{sub 2+x} solid solution, but it can be expected that distortions of regular alternation of ions similar to antiphase domains can be obtained in non-equilibrium conditions in compounds and similar effect of the quasi-merohedry can falsify results of structural analysis.« less

Energy literacy of Indiana high school practical arts and vocational teachers

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

Emshousen, F.W. Jr.

The purpose of the study was to develop an energy knowledge examination, investigate the extent high school teachers of home economics, agriculture, and industrial arts differ in their knowledge of energy, and to ascertain the extent their knowledge of energy differs with personal, educational, and geographic characteristics. Based upon literature review, a subject model was structured according to Bloom's (1956) taxonomy category of Knowledge and Hauenstein's (1972) procedure for classifying knowledges. Energy experts critically evaluated this model, which after refinement, was used to develop an Energy Knowledge Examination. The model consisted of six primary elements: sources, uses, costs, conservation, conversion,more » and policy issues. Energy experts reviewed items for accuracy, relevance, reading level, and clarity. The final instrument (65 multiple choice questions), was administered to a stratified random sample of Indiana public high school (IPHS) teachers from selected disciplines. Findings revealed significant biases among energy experts regarding relevance of specific subject content to the needs of teachers and students. Significant differences in the energy knowledge of IPHS teachers existed only in specific areas of the subject.« less

Applicability of LET to single events in microelectronic structures

NASA Astrophysics Data System (ADS)

Xapsos, Michael A.

1992-12-01

LET is often used as a single parameter to determine the energy deposited in a microelectronic structure by a single event. The accuracy of this assumption is examined for ranges of ion energies and volumes of silicon appropriate for modern microelectronics. It is shown to be accurate only under very restricted conditions. Significant differences arise because (1) LET is related to energy lost by the ion, not energy deposited in the volume; and (2) LET is an average value and does not account for statistical variations in energy deposition. Criteria are suggested for determining when factors other than LET should be considered, and new analytical approaches are presented to account for them. One implication of these results is that improvements can be made in space upset rate predictions by incorporating the new methods into currently used codes such as CREME and CRUP.

Anisotropy modulations of femtosecond laser pulse induced periodic surface structures on silicon by adjusting double pulse delay.

PubMed

Han, Weina; Jiang, Lan; Li, Xiaowei; Wang, Qingsong; Li, Hao; Lu, YongFeng

2014-06-30

We demonstrate that the polarization-dependent anisotropy of the laser-induced periodic surface structure (LIPSS) on silicon can be adjusted by designing a femtosecond laser pulse train (800 nm, 50 fs, 1 kHz). By varying the pulse delay from 100 to 1600 fs within a double pulse train to reduce the deposited pulse energy, which weakens the directional surface plasmon polarition (SPP)-laser energy coupling based on the initial formed ripple structure, the polarization-dependent geometrical morphology of the LIPSS evolves from a nearly isotropic circular shape to a somewhat elongated elliptical shape. Meanwhile, the controllable anisotropy of the two-dimensional scanned-line widths with different directions is achieved based on a certain pulse delay combined with the scanning speed. This can effectively realize better control over large-area uniform LIPSS formation. As an example, we further show that the large-area LIPSS can be formed with different scanning times under different pulse delays.

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.

Structural Dynamics in Metal Tris-hydroxyquinolines: Interconversion of Meridianal and Facial Alq3 Isomers

NASA Astrophysics Data System (ADS)

Ferris, Kim; Sapochak, Linda; Burrows, Paul; Rodovsky, Deanna; Marmolejo, Theresa

2004-03-01

While previous work investigating the charge transport properties of Alq3 has indicated that the meridianal (mer) conformation of Alq3 is predominant species, recent work suggesting identification of a facial (fac) form raises again the question of heterogeneity. Electronic structure computations from our group have noted that the energy difference(in parenthesis) between the mer and fac conformations is highly sensitive to basis set description (8.6 kcal/mol//3-21g*/SCF; 6.9 kcal/mol//6-31g*/SCF), electron correlation (6.0 kcal/mol//3-21g*/MP2; 4.7 kcal/mol//6-31g*/MP2), and solvent effects (4.4 kcal/mol/3-21g*/SCF/DMSO). Given these small energy differences, we have conducted a series of Hartree-Fock and first principles electronic structure computations on the interconversion of these structural forms, and will report on the structural and energetic aspects of the transformation. The likely reaction path involves lengthening of the Al-N bond to the point where a pentacoordinate intermediate or transition state would be formed, followed by flipping of the ligand through rotation around the Al-O bond. Following Schmidbauer's earlier work, we note that transformation involving only one ligand will actually lead to a facial isomer. Preliminary characterization of this transition state suggests that the activation energy is approximately 20-25 kcal/mol above the mer conformation. The authors gratefully acknowledge financial support from PNNL Laboratory Directed Research and Development Project and the U.S. Department of Energy, Office of Science, Materials Sciences Division.

Nanostructured Coatings of Inner Surfaces in Microporous Matrixes

DTIC Science & Technology

2000-01-01

SURFACE ENERGY _.I", DISPERSED MATERIAL............................ ,BULK MATERIp,’ t. i02 10’ iol LM Figure 1. a) Surface arising due to process of...material dispersion . b) Surface energy per cm3 of dispersed material versus characteristic size of dispersed particles - nanostructures with different...growth and lateral microstructuring techniques have made it possible to realise low-dimensional electronic systems with quantum confined energy structure

Theoretical study of EAS hadronic structure

NASA Technical Reports Server (NTRS)

Popova, L.

1985-01-01

The structure of extensive air showers (EAS) is determined mainly by the energetic hadrons. They are strongly collimated in the core of the shower and essential difficulties are encountered for resolution of individual hadrons. The properties for resolution are different from the variety of hadron detectors used in EAS experiments. This is the main difficulty in obtaining a general agreement between actually registered data with different detectors. The most plausible source for disagreement is the uncertainty in determination of the energy of individual hadrons. This research demonstrates that a better agreement can be obtained with the average tendency of hadronic measurements if one assumes a larger coefficient of inelasticity and stronger energy increase of the total inelastic cross section in high energy pion interactions. EAS data above 10 to the 5th power GeV are revealing a faster development of hadronic cascades in the air then can be expected by extrapolating the parameters of hadron interactions obtained in accelerator measurements.

Ab initio study of the molecular structure and vibrational spectrum of nitric acid and its protonated forms

NASA Technical Reports Server (NTRS)

Lee, Timothy J.; Rice, Julia E.

1992-01-01

The equilibrium structures, harmonic vibrational frequencies, IR intensities, and relative energetics of HNO3 and its protonated form H2NO3+ were investigated using double-zeta plus polarization and triple-zeta plus polarization basis sets in conjunction with high-level ab initio methods. The latter include second-order Moller-Plesset perturbation theory, the single and double excitation coupled cluster (CCSD) methods, a perturbational estimate of the effects of connected triple excitations (CCSD(T)), and the self-consistent field. To determine accurate energy differences CCSD(T) energies were computed using large atomic natural orbital basis sets. Four different isomers of H2NO3+ were considered. The lowest energy form of protonated nitric acid was found to correspond to a complex between H2O and NO2+, which is consistent with earlier theoretical and experimental studies.

Microdosimetry of low-energy electrons.

PubMed

Liamsuwan, Thiansin; Emfietzoglou, Dimitris; Uehara, Shuzo; Nikjoo, Hooshang

2012-12-01

To investigate differences in energy depositions and microdosimetric parameters of low-energy electrons in liquid and gaseous water using Monte Carlo track structure simulations. KURBUC-liq (Kyushu University and Radiobiology Unit Code for liquid water) was used for simulating electron tracks in liquid water. The inelastic scattering cross sections of liquid water were obtained from the dielectric response model of Emfietzoglou et al. (Radiation Research 2005;164:202-211). Frequencies of energy deposited in nanometre-size cylindrical targets per unit absorbed dose and associated lineal energies were calculated for 100-5000 eV monoenergetic electrons and the electron spectrum of carbon K edge X-rays. The results for liquid water were compared with those for water vapour. Regardless of electron energy, there is a limit how much energy electron tracks can deposit in a target. Phase effects on the frequencies of energy depositions are largely visible for the targets with diameters and heights smaller than 30 nm. For the target of 2.3 nm by 2.3 nm (similar to dimension of DNA segments), the calculated frequency- and dose-mean lineal energies for liquid water are up to 40% smaller than those for water vapour. The corresponding difference is less than 12% for the targets with diameters ≥ 30 nm. Condensed-phase effects are non-negligible for microdosimetry of low-energy electrons for targets with sizes smaller than a few tens of nanometres, similar to dimensions of DNA molecular structures and nucleosomes.

Genarris: Random generation of molecular crystal structures and fast screening with a Harris approximation

NASA Astrophysics Data System (ADS)

Li, Xiayue; Curtis, Farren S.; Rose, Timothy; Schober, Christoph; Vazquez-Mayagoitia, Alvaro; Reuter, Karsten; Oberhofer, Harald; Marom, Noa

2018-06-01

We present Genarris, a Python package that performs configuration space screening for molecular crystals of rigid molecules by random sampling with physical constraints. For fast energy evaluations, Genarris employs a Harris approximation, whereby the total density of a molecular crystal is constructed via superposition of single molecule densities. Dispersion-inclusive density functional theory is then used for the Harris density without performing a self-consistency cycle. Genarris uses machine learning for clustering, based on a relative coordinate descriptor developed specifically for molecular crystals, which is shown to be robust in identifying packing motif similarity. In addition to random structure generation, Genarris offers three workflows based on different sequences of successive clustering and selection steps: the "Rigorous" workflow is an exhaustive exploration of the potential energy landscape, the "Energy" workflow produces a set of low energy structures, and the "Diverse" workflow produces a maximally diverse set of structures. The latter is recommended for generating initial populations for genetic algorithms. Here, the implementation of Genarris is reported and its application is demonstrated for three test cases.

Synergy and Self-organization in Tribosystem’s evolution. Energy Model of Friction

NASA Astrophysics Data System (ADS)

Fedorov, S. V.; Assenova, E.

2018-01-01

Different approaches are known to treat self-organization in tribosystems, related to the structural adaptation in the formation of dissipative surface structures and of frictional or tribo-films, using of synergistic modifying of layers and coatings, e.g. of the selective material transfer during friction, etc. Regarding tribological processes in contact systems, self-organization is observed as spontaneous creation of higher ordered structures during the contact interaction. The proposed paper considers friction as process of transformation and dissipation of energy and process of elasto-plastic deformation localized in thin surface layers of the interacting bodies. Еnergetic interpretation of friction is proposed. Based on the energy balance equations of friction, the evolution of tribosystems is followed in its adaptive-dissipative character. It reflects the variable friction surfaces compatibility and the nonlinear dynamics of friction evolution. Structural-energy relationships in the contacting surfaces evolution are obtained. Maximum of tribosystem’s efficiency during the evolution is the stage of self-organzation of the friction surface layers, which is a state of abnormal low friction and wear.

Impedance measures in analysis and characterization of multistable structures subjected to harmonic excitation

NASA Astrophysics Data System (ADS)

Harne, Ryan L.; Goodpaster, Benjamin A.

2018-01-01

Structural components susceptible to adverse, post-buckled dynamic behaviors have long challenged the success of applications requiring lightweight, slender curved structures, while researchers have begun to leverage such bistable systems in emerging applications for novel energy attenuation and shape-changing properties. To expedite development and deployment of these built-up platforms containing post-buckled constituents, efficient approaches are required to complement time-consuming full-field models in the prediction of the near- and far-from-equilibrium dynamics. This research meets the need by introducing a semi-analytical model framework to enable the characterization of steady-state responses in multi degree-of-freedom (DOF) and multistable structural systems subjected to harmonic excitation. In so doing, the pathway for assessing impedance measures is created here so as to identify how energy travels and returns within built-up multistable structures. Verified by simulations and qualitatively validated by experiments, the analysis is shown to accurately reproduce both near- and far-from-equilibrium responses including different classes of energetic snap-through dynamics that only exist in such multistable structures. A first look at the impedance measures of different dynamic regimes reveals a connection between damping in multistable structures and the sustainability of far-from-equilibrium oscillations.

A thermodynamic approach to link self-organization, preferential flow and rainfall-runoff behaviour

NASA Astrophysics Data System (ADS)

Zehe, E.; Ehret, U.; Blume, T.; Kleidon, A.; Scherer, U.; Westhoff, M.

2013-11-01

This study investigates whether a thermodynamically optimal hillslope structure can, if existent, serve as a first guess for uncalibrated predictions of rainfall-runoff. To this end we propose a thermodynamic framework to link rainfall-runoff processes and dynamics of potential energy, kinetic energy and capillary binding energy in catchments and hillslopes. The starting point is that hydraulic equilibrium in soil corresponds to local thermodynamic equilibrium (LTE), characterized by a local maximum entropy/minimum of free energy of soil water. Deviations from LTE occur either due to evaporative losses, which increase absolute values of negative capillary binding energy of soil water and reduce its potential energy, or due to infiltration of rainfall, which increases potential energy of soil water and reduces the strength of capillary binding energy. The amplitude and relaxation time of these deviations depend on climate, vegetation, soil hydraulic functions, topography and density of macropores. Based on this framework we analysed the free energy balance of hillslopes within numerical experiments that perturbed model structures with respect to the surface density of macropores. These model structures have been previously shown to allow successful long-term simulations of the water balances of the Weiherbach and the Malalcahuello catchments, which are located in distinctly different pedological and climatic settings. Our findings offer a new perspective on different functions of preferential flow paths depending on the pedological setting. Free energy dynamics of soil water in the cohesive soils of the Weiherbach is dominated by dynamics of capillary binding energy. Macropores act as dissipative wetting structures by enlarging water flows against steep gradients in soil water potential after long dry spells. This implies accelerated depletion of these gradients and faster relaxation back towards LTE. We found two local optima in macropore density that maximize reduction rates of free energy of soil water during rainfall-driven conditions. These two optima exist because reduction rates of free energy are, in this case, a second-order polynomial of the wetting rate, which implicitly depends on macroporosity. An uncalibrated long-term simulation of the water balance of the Weiherbach catchment based on the first optimum macroporosity performed almost as well as the best fit when macroporosity was calibrated to match rainfall-runoff. In the Malalcahuello catchment we did not find an apparent optimum density of macropores, because free energy dynamics of soil water during rainfall-driven conditions is dominated by increases of potential energy. Macropores act as dissipative drainage structures by enhancing export of potential energy. No optimum macropore density exists in this case because potential energy change rates scale linearly with the wetting rate. We found, however, a distinguished macroporosity that assures steady-state conditions of the potential energy balance of the soil, in the sense that average storage of potential energy is compensated by average potential energy export. This distinguished macroporosity was close to the value that yielded the best fit of rainfall-runoff behaviour during a calibration exercise and allowed a robust estimate of the annual runoff coefficient. Our findings are promising for predictions in ungauged catchments (PUB) as the optimal/distinguished model structures can serve as a first guess for uncalibrated predictions of rainfall-runoff. They also offer an alternative for classifying catchments according to their similarity of the free energy balance components.

Computational assessment of folding energy landscapes in heterodimeric coiled coils.

PubMed

André, Ingemar; Bjelic, Sinisa

2018-07-01

The coiled coil structural motif consists of alpha helices supercoiling around each other to form staggered knobs-into-holes packing. Such structures are deceptively simple, especially as they often can be described with parametric equations, but are known to exist in various conformations. Even the simplest systems, consisting of 2 monomers, can assemble into a wide range of states. They can form canonical as well as noncanonical coiled coils, be parallel or antiparallel, where helices associate with different degrees of shift, tilt, and rotation. Here, we investigate the energy landscape of heterodimeric coiled coils by carrying out de novo folding simulations starting from amino acid sequence. We folded a diverse set of 22 heterodimers and demonstrate that the approach is capable of identifying the atomic details in the experimental structure in the majority of cases. Our methodology also enables exploration of alternative states that can be accessible in solution beyond the experimentally determined structure. For many systems, we observe folding energy landscapes with multiple energy minima and several isoenergetic states. By comparing coiled coils from single domains and those extracted from larger proteins, we find that standalone coiled coils have deeper energy wells at the experimentally determined conformation. By folding the competing homodimeric states in addition to the heterodimers, we observe that the structural specificity towards the heteromeric state is often small. Taken together, our results demonstrate that de novo folding simulations can be a powerful tool to characterize structural specificity of coiled coils when coupled to assessment of energy landscapes. © 2018 Wiley Periodicals, Inc.

Free energy landscapes of RNA/RNA complexes: with applications to snRNA complexes in spliceosomes.

PubMed

Cao, Song; Chen, Shi-Jie

2006-03-17

We develop a statistical mechanical model for RNA/RNA complexes with both intramolecular and intermolecular interactions. As an application of the model, we compute the free energy landscapes, which give the full distribution for all the possible conformations, for U4/U6 and U2/U6 in major spliceosome and U4atac/U6atac and U12/U6atac in minor spliceosome. Different snRNA experiments found contrasting structures, our free energy landscape theory shows why these structures emerge and how they compete with each other. For yeast U2/U6, the model predicts that the two distinct experimental structures, the four-helix junction structure and the helix Ib-containing structure, can actually coexist and specifically compete with each other. In addition, the energy landscapes suggest possible mechanisms for the conformational switches in splicing. For instance, our calculation shows that coaxial stacking is essential for stabilizing the four-helix junction in yeast U2/U6. Therefore, inhibition of the coaxial stacking possibly by protein-binding may activate the conformational switch from the four-helix junction to the helix Ib-containing structure. Moreover, the change of the energy landscape shape gives information about the conformational changes. We find multiple (native-like and misfolded) intermediates formed through base-pairing rearrangements in snRNA complexes. For example, the unfolding of the U2/U6 undergoes a transition to a misfolded state which is functional, while in the unfolding of U12/U6atac, the functional helix Ib is found to be the last one to unfold and is thus the most stable structural component. Furthermore, the energy landscape gives the stabilities of all the possible (functional) intermediates and such information is directly related to splicing efficiency.

Structural and Functional Hierarchy in Photosynthetic Energy Conversion—from Molecules to Nanostructures

NASA Astrophysics Data System (ADS)

Szabó, Tibor; Magyar, Melinda; Hajdu, Kata; Dorogi, Márta; Nyerki, Emil; Tóth, Tünde; Lingvay, Mónika; Garab, Győző; Hernádi, Klára; Nagy, László

2015-12-01

Basic principles of structural and functional requirements of photosynthetic energy conversion in hierarchically organized machineries are reviewed. Blueprints of photosynthesis, the energetic basis of virtually all life on Earth, can serve the basis for constructing artificial light energy-converting molecular devices. In photosynthetic organisms, the conversion of light energy into chemical energy takes places in highly organized fine-tunable systems with structural and functional hierarchy. The incident photons are absorbed by light-harvesting complexes, which funnel the excitation energy into reaction centre (RC) protein complexes containing redox-active chlorophyll molecules; the primary charge separations in the RCs are followed by vectorial transport of charges (electrons and protons) in the photosynthetic membrane. RCs possess properties that make their use in solar energy-converting and integrated optoelectronic systems feasible. Therefore, there is a large interest in many laboratories and in the industry toward their use in molecular devices. RCs have been bound to different carrier matrices, with their photophysical and photochemical activities largely retained in the nano-systems and with electronic connection to conducting surfaces. We show examples of RCs bound to carbon-based materials (functionalized and non-functionalized single- and multiwalled carbon nanotubes), transitional metal oxides (ITO) and conducting polymers and porous silicon and characterize their photochemical activities. Recently, we adapted several physical and chemical methods for binding RCs to different nanomaterials. It is generally found that the P+(QAQB)- charge pair, which is formed after single saturating light excitation is stabilized after the attachment of the RCs to the nanostructures, which is followed by slow reorganization of the protein structure. Measuring the electric conductivity in a direct contact mode or in electrochemical cell indicates that there is an electronic interaction between the protein and the inorganic carrier matrices. This can be a basis of sensing element of bio-hybrid device for biosensor and/or optoelectronic applications.

Thermodynamics of the living organisms. Allometric relationship between the total metabolic energy, chemical energy and body temperature in mammals

NASA Astrophysics Data System (ADS)

Atanasov, Atanas Todorov

2017-11-01

The study present relationship between the total metabolic energy (ETME(c), J) derived as a function of body chemical energy (Gchem, J) and absolute temperature (Tb, K) in mammals: ETME(c) =Gchem (Tb/Tn). In formula the temperature Tn =2.73K appears normalization temperature. The calculated total metabolic energy ETME(c) differs negligible from the total metabolic energy ETME(J), received as a product between the basal metabolic rate (Pm, J/s) and the lifespan (Tls, s) of mammals: ETME = Pm×Tls. The physical nature and biological mean of the normalization temperature (Tn, K) is unclear. It is made the hypothesis that the kTn energy (where k= 1.3806×10-23 J/K -Boltzmann constant) presents energy of excitation states (modes) in biomolecules and body structures that could be in equilibrium with chemical energy accumulated in body. This means that the accumulated chemical energy allows trough all body molecules and structures to propagate excitations states with kTn energy with wavelength in the rage of width of biological membranes. The accumulated in biomolecules chemical energy maintains spread of the excited states through biomolecules without loss of energy.

“Trunk-like” heavy ion structures observed by the Van Allen Probes

DOE PAGES

Zhang, J. -C.; Kistler, L. M.; Spence, H. E.; ...

2015-10-27

Dynamic ion spectral features in the inner magnetosphere are the observational signatures of ion acceleration, transport, and loss in the global magnetosphere. Here, we report “trunk-like” ion structures observed by the Van Allen Probes on 2 November 2012. This new type of ion structure looks like an elephant's trunk on an energy-time spectrogram, with the energy of the peak flux decreasing Earthward. The trunks are present in He + and O + ions but not in H +. During the event, ion energies in the He+ trunk, located at L=3.6–2.6, magnetic local time (MLT)=9.1–10.5, and magnetic latitude (MLAT) =-2.4–0.09°, varymore » monotonically from 3.5 to 0.04 keV. Values at the two end points of the O + trunk are energy=4.5–0.7keV, L=3.6–2.5, MLT=9.1–10.7, and MLAT=-2.4–0.4°. Our results from backward ion drift path tracings indicate that the trunks are likely due to (1) a gap in the nightside ion source or (2) greatly enhanced impulsive electric fields associated with elevated geomagnetic activity. Different ion loss lifetimes cause the trunks to differ among ion species.« less

Biotemplated materials for sustainable energy and environment: current status and challenges.

PubMed

Zhou, Han; Fan, Tongxiang; Zhang, Di

2011-10-17

Materials science will play a key role in the further development of emerging solutions for the increasing problems of energy and environment. Materials found in nature have many inspiring structures, such as hierarchical organizations, periodic architectures, or nanostructures, that endow them with amazing functions, such as energy harvesting and conversion, antireflection, structural coloration, superhydrophobicity, and biological self-assembly. Biotemplating is an effective strategy to obtain morphology-controllable materials with structural specificity, complexity, and related unique functions. Herein, we highlight the synthesis and application of biotemplated materials for six key areas of energy and environment technologies, namely, photocatalytic hydrogen evolution, CO(2) reduction, solar cells, lithium-ion batteries, photocatalytic degradation, and gas/vapor sensing. Although the applications differ from each other, a common fundamental challenge is to realize optimum structures for improved performances. We highlight the role of four typical structures derived from biological systems exploited to optimize properties: hierarchical (porous) structures, periodic (porous) structures, hollow structures, and nanostructures. We also provide examples of using biogenic elements (e.g., C, Si, N, I, P, S) for the creation of active materials. Finally, we disscuss the challenges of achieving the desired performance for large-scale commercial applications and provide some useful prototypes from nature for the biomimetic design of new materials or systems. The emphasis is mainly focused on the structural effects and compositional utilization of biotemplated materials. Copyright © 2011 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Assessment of SIP Buildings for Sustainable Development in Rural China Using AHP-Grey Correlation Analysis.

PubMed

Bai, Libiao; Wang, Hailing; Shi, Chunming; Du, Qiang; Li, Yi

2017-10-25

Traditional rural residential construction has the problems of high energy consumption and severe pollution. In general, with sustainable development in the construction industry, rural residential construction should be aimed towards low energy consumption and low carbon emissions. To help achieve this objective, in this paper, we evaluated four different possible building structures using AHP-Grey Correlation Analysis, which consists of the Analytic Hierarchy Process (AHP) and the Grey Correlation Analysis. The four structures included the traditional and currently widely used brick and concrete structure, as well as structure insulated panels (SIPs). Comparing the performances of economic benefit and carbon emission, the conclusion that SIPs have the best overall performance can be obtained, providing a reference to help builders choose the most appropriate building structure in rural China.

Probing disorder in isometric pyrochlore and related complex oxides

NASA Astrophysics Data System (ADS)

Shamblin, Jacob; Feygenson, Mikhail; Neuefeind, Joerg; Tracy, Cameron L.; Zhang, Fuxiang; Finkeldei, Sarah; Bosbach, Dirk; Zhou, Haidong; Ewing, Rodney C.; Lang, Maik

2016-05-01

There has been an increased focus on understanding the energetics of structures with unconventional ordering (for example, correlated disorder that is heterogeneous across different length scales). In particular, compounds with the isometric pyrochlore structure, A2B2O7, can adopt a disordered, isometric fluorite-type structure, (A, B)4O7, under extreme conditions. Despite the importance of the disordering process there exists only a limited understanding of the role of local ordering on the energy landscape. We have used neutron total scattering to show that disordered fluorite (induced intrinsically by composition/stoichiometry or at far-from-equilibrium conditions produced by high-energy radiation) consists of a local orthorhombic structural unit that is repeated by a pseudo-translational symmetry, such that orthorhombic and isometric arrays coexist at different length scales. We also show that inversion in isometric spinel occurs by a similar process. This insight provides a new basis for understanding order-to-disorder transformations important for applications such as plutonium immobilization, fast ion conduction, and thermal barrier coatings.

General theoretical description of angle-resolved photoemission spectroscopy of van der Waals structures

NASA Astrophysics Data System (ADS)

Amorim, B.

2018-04-01

We develop a general theory to model the angle-resolved photoemission spectroscopy (ARPES) of commensurate and incommensurate van der Waals (vdW) structures, formed by lattice mismatched and/or misaligned stacked layers of two-dimensional materials. The present theory is based on a tight-binding description of the structure and the concept of generalized umklapp processes, going beyond previous descriptions of ARPES in incommensurate vdW structures, which are based on continuous, low-energy models, being limited to structures with small lattice mismatch/misalignment. As applications of the general formalism, we study the ARPES bands and constant energy maps for two structures: twisted bilayer graphene and twisted bilayer MoS2. The present theory should be useful in correctly interpreting experimental results of ARPES of vdW structures and other systems displaying competition between different periodicities, such as two-dimensional materials weakly coupled to a substrate and materials with density wave phases.

Atomic resolution Z-contrast imaging and energy loss spectroscopy of carbon nanotubes and bundles

NASA Astrophysics Data System (ADS)

Lupini, A. R.; Chisholm, M. F.; Puretzky, A. A.; Eres, G.; Melechko, A. V.; Schaaff, G.; Lowndes, D. H.; Geohegan, D. B.; Schittenhelm, H.; Pennycook, S. J.; Wang, Y.; Smalley, R. E.

2002-03-01

Single-wall carbon nanotubes and bundles were studied by a combination of techniques, including conventional imaging and diffraction, atomic resolution Z-contrast imaging in an aberration corrected STEM and electron energy loss spectroscopy (EELS). EELS is ideally suited for the analysis of carbon based structures because of the ability to distinguish between the different forms, specifically nanotubes, graphite, amorphous carbon and diamond. Numerous attempts were made to synthesize crystals of single walled carbon nanotubes, using both solution and vapor deposition of precursor structures directly onto TEM grids for in-situ annealing. The range of structures produced will be discussed.

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

Xiong, L. H.; Wang, X. D.; Yu, Q.

Temperature-dependent atomistic structure evolution of liquid gallium (Ga) has been investigated by using in situ high energy X-ray diffraction experiment and ab initio molecular dynamics simulation. Both experimental and theoretical results reveal the existence of a liquid structural change around 1000 K in liquid Ga. Below and above this temperature the liquid exhibits differences in activation energy for selfdiffusion, temperature-dependent heat capacity, coordination numbers, density, viscosity, electric resistivity and thermoelectric power, which are reflected from structural changes of the bond-orientational order parameter Q6, fraction of covalent dimers, averaged string length and local atomic packing. This finding will trigger more studiesmore » on the liquid-to-liquid crossover in metallic melts.« less

Navigating ligand protein binding free energy landscapes: universality and diversity of protein folding and molecular recognition mechanisms

NASA Astrophysics Data System (ADS)

Verkhivker, Gennady M.; Rejto, Paul A.; Bouzida, Djamal; Arthurs, Sandra; Colson, Anthony B.; Freer, Stephan T.; Gehlhaar, Daniel K.; Larson, Veda; Luty, Brock A.; Marrone, Tami; Rose, Peter W.

2001-03-01

Thermodynamic and kinetic aspects of ligand-protein binding are studied for the methotrexate-dihydrofolate reductase system from the binding free energy profile constructed as a function of the order parameter. Thermodynamic stability of the native complex and a cooperative transition to the unique native structure suggest the nucleation kinetic mechanism at the equilibrium transition temperature. Structural properties of the transition state ensemble and the ensemble of nucleation conformations are determined by kinetic simulations of the transmission coefficient and ligand-protein association pathways. Structural analysis of the transition states and the nucleation conformations reconciles different views on the nucleation mechanism in protein folding.

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

Altay, A.; Carter, C.B., E-mail: cbcarter@engr.uconn.ed; Rulis, P.

Calcium aluminates, compounds in the CaO-Al{sub 2}O{sub 3} phase system, are used in high-temperature cements and refractory oxides and have wide range of potential technological applications due to their interesting optical, electrical, thermal, and mechanical properties. They are used in both crystalline and glassy form; the glass is an isotropic material while the crystalline materials may be highly anisotropic. This paper will consider two particular crystalline materials, CA{sub 2} and CA{sub 6}, but the results should be applicable to all calcium aluminates. Although CA{sub 2} and CA{sub 6} crystals contain the same chemical species, Ca, Al, and O, the coordinationmore » and local environments of these species are different in the two structures and hence they show very different energy-loss near-edge structures (ELNES) when examined by electron energy-loss spectroscopy (EELS) in the TEM. The data obtained using ELNES can effectively provide a fingerprint for each compound and a map for their electronic structure. Once such fingerprints are obtained, they can be used to identify nano-sized particles/grains or material at interfaces and grain boundaries. In the present study, the local symmetry fingerprints for CA{sub 2} and CA{sub 6} structures are reported combining experimental spectra with electronic-structure calculations that allow the different features in the spectra to be interpreted. Al-L{sub 2,3} and O-K edge core-loss spectra from CA{sub 2} and CA{sub 6} were measured experimentally using electron energy-loss spectroscopy in a monochromated scanning transmission electron microscope. The near-edge structures were calculated for the different phases using the orthogonalized linear combination of atomic-orbitals method, and took account of core-hole interactions. It is shown that CA{sub 2} and CA{sub 6} structures exhibit distinctive experimental ELNES fingerprints so that these two phases can be separately identified even when present in small volumes. - Graphical abstract: Projection of the CA{sub 2} structure viewed in the [010] direction. Green atoms represent the Ca{sup 2+} ions and blue atoms represent the Al{sup 3+} ions. Two unit cells are outlined..« less

Structural health monitoring and damage evaluation for steel confined reinforced concrete column using the acoustic emission technique

NASA Astrophysics Data System (ADS)

Du, Fangzhu; Li, Dongsheng

2018-03-01

As a new kind of composite structures, the using of steel confined reinforced concrete column attract increasing attention in civil engineer. During the damage process, this new structure offers highly complex and invisible failure mechanism due to the combination effects of steel tubes, concrete, and steel rebar. Acoustic emission (AE) technique has been extensively studied in nondestructive testing (NDT) and is currently applied in civil engineering for structural health monitoring (SHM) and damage evaluation. In the present study, damage property and failure evolution of steel confined and unconfined reinforced concrete (RC) columns are investigated under quasi-static loading through (AE) signal. Significantly improved loading capacity and excellent energy dissipation characteristic demonstrated the practicality of that proposed structure. AE monitoring results indicated that the progressive deformation of the test specimens occur in three stages representing different damage conditions. Sentry function compares the logarithm ratio between the stored strain energy (Es) and the released acoustic energy (Ea); explicitly disclose the damage growth and failure mechanism of the test specimens. Other extended AE features including index of damage (ID), and relax ratio are calculated to quantitatively evaluate the damage severity and critical point. Complicated temporal evolution of different AE features confirms the potential importance of integrated analysis of two or more parameters. The proposed multi-indicators analysis is capable of revealing the damage growth and failure mechanism for steel confined RC columns, and providing critical warning information for structure failure.

Light Irradiation as Key to Shape and Function of Nano-Assemblies in Solution

NASA Astrophysics Data System (ADS)

Groehn, Franziska

Developing strategies to exploit solar energy become more and more important. Inspired by natural systems it is highly promising to self-assemble functional species into effective tailored supramolecular units. Here we report self-assembled polymer structures in solution, taking advantage of optical properties of hybrid structures and light responsiveness. A new type of photocatalytically active self-assembled polymer structure in aqueous solution consists of supramolecular nano-objects obtained from macroions and multivalent inorganic ``counterions'' such as nanoparticles or clusters. These can exhibit expressed selectivity or even allow catalytic reactions in solution that are not possible with the building blocks only. Further, polyelectrolyte-porphyrin nanoscale assemblies exhibit tunable optical properties including strong fluorescence and an up to 20-fold higher photocatalytic activity than without polymeric template. A different approach is to transfer light energy into mechanical energy. Here, light energy is converted into nanoscale shape changes. This route for the conversion of light is highly promising for applications in drug delivery, nanosensors and solar energy conversion. Membership of DPG, Germany ID 153159-.

Ligand solvation in molecular docking.

PubMed

Shoichet, B K; Leach, A R; Kuntz, I D

1999-01-01

Solvation plays an important role in ligand-protein association and has a strong impact on comparisons of binding energies for dissimilar molecules. When databases of such molecules are screened for complementarity to receptors of known structure, as often occurs in structure-based inhibitor discovery, failure to consider ligand solvation often leads to putative ligands that are too highly charged or too large. To correct for the different charge states and sizes of the ligands, we calculated electrostatic and non-polar solvation free energies for molecules in a widely used molecular database, the Available Chemicals Directory (ACD). A modified Born equation treatment was used to calculate the electrostatic component of ligand solvation. The non-polar component of ligand solvation was calculated based on the surface area of the ligand and parameters derived from the hydration energies of apolar ligands. These solvation energies were subtracted from the ligand-receptor interaction energies. We tested the usefulness of these corrections by screening the ACD for molecules that complemented three proteins of known structure, using a molecular docking program. Correcting for ligand solvation improved the rankings of known ligands and discriminated against molecules with inappropriate charge states and sizes.

Deployable System for Crash-Load Attenuation

NASA Technical Reports Server (NTRS)

Kellas, Sotiris; Jackson, Karen E.

2007-01-01

An externally deployable honeycomb structure is investigated with respect to crash energy management for light aircraft. The new concept utilizes an expandable honeycomb-like structure to absorb impact energy by crushing. Distinguished by flexible hinges between cell wall junctions that enable effortless deployment, the new energy absorber offers most of the desirable features of an external airbag system without the limitations of poor shear stability, system complexity, and timing sensitivity. Like conventional honeycomb, once expanded, the energy absorber is transformed into a crush efficient and stable cellular structure. Other advantages, afforded by the flexible hinge feature, include a variety of deployment options such as linear, radial, and/or hybrid deployment methods. Radial deployment is utilized when omnidirectional cushioning is required. Linear deployment offers better efficiency, which is preferred when the impact orientation is known in advance. Several energy absorbers utilizing different deployment modes could also be combined to optimize overall performance and/or improve system reliability as outlined in the paper. Results from a series of component and full scale demonstration tests are presented as well as typical deployment techniques and mechanisms. LS-DYNA analytical simulations of selected tests are also presented.

Towards a microscopic description of the free-energy landscape of water.

PubMed

Prada-Gracia, Diego; Shevchuk, Roman; Hamm, Peter; Rao, Francesco

2012-10-14

Free-energy landscape theory is often used to describe complex molecular systems. Here, a microscopic description of water structure and dynamics based on configuration-space-networks and molecular dynamics simulations of the TIP4P/2005 model is applied to investigate the free-energy landscape of water. The latter is built on top of a large set of water microstates describing the kinetic stability of local hydrogen-bond arrangements up to the second solvation shell. In temperature space, the landscape displays three different regimes. At around ambient conditions, the free-energy surface is characterized by many short-lived basins of attraction which are structurally well-defined (inhomogeneous regime). At lower temperatures instead, the liquid rapidly becomes homogeneous. In this regime, the free energy is funneled-like, with fully coordinated water arrangements at the bottom of the funnel. Finally, a third regime develops below the temperature of maximal compressibility (Widom line) where the funnel becomes steeper with few interconversions between microstates other than the fully coordinated ones. Our results present a way to manage the complexity of water structure and dynamics, connecting microscopic properties to its ensemble behavior.

Quasiparticle energy bands and Fermi surfaces of monolayer NbSe2

NASA Astrophysics Data System (ADS)

Kim, Sejoong; Son, Young-Woo

2017-10-01

A quasiparticle band structure of a single layer 2 H -NbSe2 is reported by using first-principles G W calculation. We show that a self-energy correction increases the width of a partially occupied band and alters its Fermi surface shape when comparing those using conventional mean-field calculation methods. Owing to a broken inversion symmetry in the trigonal prismatic single layer structure, the spin-orbit interaction is included and its impact on the Fermi surface and quasiparticle energy bands are discussed. We also calculate the doping dependent static susceptibilities from the band structures obtained by the mean-field calculation as well as G W calculation with and without spin-orbit interactions. A complete tight-binding model is constructed within the three-band third nearest neighbor hoppings and is shown to reproduce our G W quasiparticle energy bands and Fermi surface very well. Considering variations of the Fermi surface shapes depending on self-energy corrections and spin-orbit interactions, we discuss the formations of charge density wave (CDW) with different dielectric environments and their implications on recent controversial experimental results on CDW transition temperatures.

Energy Absorption Capacity in Natural Fiber Reinforcement Composites Structures

PubMed Central

López-Alba, Elías; Díaz, Francisco

2018-01-01

The study of natural fiber reinforcement composite structures has focused the attention of the automobile industry due to the new regulation in relation to the recyclability and the reusability of the materials preserving and/or improving the mechanical characteristics. The influence of different parameters on the material behavior of natural fiber reinforced plastic structures has been investigated, showing the potential for transport application in energy absorbing structures. Two different woven fabrics (twill and hopsack) made of flax fibers as well as a non-woven mat made of a mixture of hemp and kenaf fibers were employed as reinforcing materials. These reinforcing textiles were impregnated with both HD-PE (high-density polyethylen) and PLA (polylactic acid) matrix, using a continuous compression molding press. The impregnated semi-finished laminates (so-called organic sheets) were thermoformed in a second step to half-tubes that were assembled through vibration-welding process to cylindric crash absorbers. The specimens were loaded by compression to determine the specific energy absorption capacity. Quasi-static test results were compared to dynamic test data obtained on a catapult arrangement. The differences on the specific energies absorption (SEA) as a function of different parameters, such as the wall thickness, the weave material type, the reinforced textiles, and the matrix used, depending on the velocity rate application were quantified. In the case of quasi-static analysis it is observed a 20% increment in the SEA value when wove Hopsack fabric reinforcement is employed. No velocity rate influence from the material was observed on the SEA evaluation at higher speeds used to perform the experiments. The influence of the weave configuration (Hopsack) seems to be more stable against buckling effects at low loading rates with 10% higher SEA values. An increase of SEA level of up to 72% for PLA matrix was observed when compared with HD-PE matrix. PMID:29534003

Energy Absorption Capacity in Natural Fiber Reinforcement Composites Structures.

PubMed

López-Alba, Elías; Schmeer, Sebastian; Díaz, Francisco

2018-03-13

The study of natural fiber reinforcement composite structures has focused the attention of the automobile industry due to the new regulation in relation to the recyclability and the reusability of the materials preserving and/or improving the mechanical characteristics. The influence of different parameters on the material behavior of natural fiber reinforced plastic structures has been investigated, showing the potential for transport application in energy absorbing structures. Two different woven fabrics (twill and hopsack) made of flax fibers as well as a non-woven mat made of a mixture of hemp and kenaf fibers were employed as reinforcing materials. These reinforcing textiles were impregnated with both HD-PE (high-density polyethylen) and PLA (polylactic acid) matrix, using a continuous compression molding press. The impregnated semi-finished laminates (so-called organic sheets) were thermoformed in a second step to half-tubes that were assembled through vibration-welding process to cylindric crash absorbers. The specimens were loaded by compression to determine the specific energy absorption capacity. Quasi-static test results were compared to dynamic test data obtained on a catapult arrangement. The differences on the specific energies absorption (SEA) as a function of different parameters, such as the wall thickness, the weave material type, the reinforced textiles, and the matrix used, depending on the velocity rate application were quantified. In the case of quasi-static analysis it is observed a 20% increment in the SEA value when wove Hopsack fabric reinforcement is employed. No velocity rate influence from the material was observed on the SEA evaluation at higher speeds used to perform the experiments. The influence of the weave configuration (Hopsack) seems to be more stable against buckling effects at low loading rates with 10% higher SEA values. An increase of SEA level of up to 72% for PLA matrix was observed when compared with HD-PE matrix.

Long-term change of the atmospheric energy cycles and weather disturbances

NASA Astrophysics Data System (ADS)

Kim, WonMoo; Choi, Yong-Sang

2017-11-01

Weather disturbances are the manifestation of mean atmospheric energy cascading into eddies, thus identifying atmospheric energy structure is of fundamental importance to understand the weather variability in a changing climate. The question is whether our observational data can lead to a consistent diagnosis on the energy conversion characteristics. Here we investigate the atmospheric energy cascades by a simple framework of Lorenz energy cycle, and analyze the energy distribution in mean and eddy fields as forms of potential and kinetic energy. It is found that even the widely utilized independent reanalysis datasets, NCEP-DOE AMIP-II Reanalysis (NCEP2) and ERA-Interim (ERA-INT), draw different conclusions on the change of weather variability measured by eddy-related kinetic energy. NCEP2 shows an increased mean-to-eddy energy conversion and enhanced eddy activity due to efficient baroclinic energy cascade, but ERA-INT shows relatively constant energy cascading structure between the 1980s and the 2000s. The source of discrepancy mainly originates from the uncertainties in hydrological variables in the mid-troposphere. Therefore, much efforts should be made to improve mid-tropospheric observations for more reliable diagnosis of the weather disturbances as a consequence of man-made greenhouse effect.

Two formalisms, one renormalized stress-energy tensor

NASA Astrophysics Data System (ADS)

Barceló, C.; Carballo, R.; Garay, L. J.

2012-04-01

We explicitly compare the structure of the renormalized stress-energy tensor of a massless scalar field in a (1+1) curved spacetime as obtained by two different strategies: normal-mode construction of the field operator and one-loop effective action. We pay special attention to where and how the information related to the choice of vacuum state in both formalisms is encoded. By establishing a clear translation map between both procedures, we show that these two potentially different renormalized stress-energy tensors are actually equal, when using vacuum-state choices related by this map. One specific aim of the analysis is to facilitate the comparison of results regarding semiclassical effects in gravitational collapse as obtained within these different formalisms.

Insulating phases of vanadium dioxide are Mott-Hubbard insulators

DOE PAGES

Huffman, T. J.; Hendriks, C.; Walter, E. J.; ...

2017-02-15

Here, we present comprehensive broadband optical spectroscopy data on two insulating phases of vanadium dioxide (VO 2): monoclinic M 2 and triclinic. The main result of our work is that the energy gap and the electronic structure are essentially unaltered by the first-order structural phase transition between the M 2 and triclinic phases. Moreover, the optical interband features in the M 2 and triclinic phases are remarkably similar to those observed in the well-studied monoclinic M 1 insulating phase of VO 2. As the energy gap is insensitive to the different lattice structures of the three insulating phases, we rulemore » out vanadium-vanadium pairing (the Peierls component) as the dominant contributor to the opening of the gap. Rather, the energy gap arises primarily from intra-atomic Coulomb correlations.« less

Coupled Finite Element ? Potts Model Simulations of Grain Growth in Copper Interconnects

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

Radhakrishnan, Balasubramaniam; Gorti, Sarma B

The paper addresses grain growth in copper interconnects in the presence of thermal expansion mismatch stresses. The evolution of grain structure and texture in copper in the simultaneous presence of two driving forces, curvature and elastic stored energy difference, is modeled by using a hybrid Potts model simulation approach. The elastic stored energy is calculated by using the commercial finite element code ABAQUS, where the effect of elastic anisotropy on the thermal mismatch stress and strain distribution within a polycrystalline grain structure is modeled through a user material (UMAT) interface. Parametric studies on the effect of trench width and themore » height of the overburden were carried out. The results show that the grain structure and texture evolution are significantly altered by the presence of elastic strain energy.« less

Developing a structure-function model for the cryptophyte phycoerythrin 545 using ultrahigh resolution crystallography and ultrafast laser spectroscopy.

PubMed

Doust, Alexander B; Marai, Christopher N J; Harrop, Stephen J; Wilk, Krystyna E; Curmi, Paul M G; Scholes, Gregory D

2004-11-12

Cryptophyte algae differ from cyanobacteria and red algae in the architecture of their photosynthetic light harvesting systems, even though all three are evolutionarily related. Central to cryptophyte light harvesting is the soluble antenna protein phycoerythrin 545 (PE545). The ultrahigh resolution crystal structure of PE545, isolated from a unicellular cryptophyte Rhodomonas CS24, is reported at both 1.1A and 0.97A resolution, revealing details of the conformation and environments of the chromophores. Absorption, emission and polarized steady state spectroscopy (298K, 77K), as well as ultrafast (20fs time resolution) measurements of population dynamics are reported. Coupled with complementary quantum chemical calculations of electronic transitions of the bilins, these enable assignment of spectral absorption characteristics to each chromophore in the structure. Spectral differences between the tetrapyrrole pigments due to chemical differences between bilins, as well as their binding and interaction with the local protein environment are described. Based on these assignments, and considering customized optical properties such as strong coupling, a model for light harvesting by PE545 is developed which explains the fast, directional harvesting of excitation energy. The excitation energy is funnelled from four peripheral pigments (beta158,beta82) into a central chromophore dimer (beta50/beta61) in approximately 1ps. Those chromophores, in turn, transfer the excitation energy to the red absorbing molecules located at the periphery of the complex in approximately 4ps. A final resonance energy transfer step sensitizes just one of the alpha19 bilins on a time scale of 22ps. Furthermore, it is concluded that binding of PE545 to the thylakoid membrane is not essential for efficient energy transfer to the integral membrane chlorophyll a-containing complexes associated with PS-II.

Coulomb energy differences in isobaric multiplets

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

Lenzi, S. M.; Farnea, E.; Bazzacco, D.

2007-02-12

By comparing the excitation energies of analogue states in isobaric multiplets, several nuclear structure properties can be studied as a function of the angular momentum up to high spin states. In particular, the mirror nuclei 35Ar and 35Cl show large differences between the excitation energies of analogue negative-parity states at high spin, confirming the important contribution of the relativistic electromagnetic spin-orbit interaction to the Coulomb energy. The single-particle character of the configuration of these states is reproduced with very good accuracy by shell model calculations in the sd and pf shells valence space. In addition, evidence of isospin mixing ismore » deduced from the El transitions linking positive and negative parity states.« less

Prediction of molecular crystal structures by a crystallographic QM/MM model with full space-group symmetry.

PubMed

Mörschel, Philipp; Schmidt, Martin U

2015-01-01

A crystallographic quantum-mechanical/molecular-mechanical model (c-QM/MM model) with full space-group symmetry has been developed for molecular crystals. The lattice energy was calculated by quantum-mechanical methods for short-range interactions and force-field methods for long-range interactions. The quantum-mechanical calculations covered the interactions within the molecule and the interactions of a reference molecule with each of the surrounding 12-15 molecules. The interactions with all other molecules were treated by force-field methods. In each optimization step the energies in the QM and MM shells were calculated separately as single-point energies; after adding both energy contributions, the crystal structure (including the lattice parameters) was optimized accordingly. The space-group symmetry was maintained throughout. Crystal structures with more than one molecule per asymmetric unit, e.g. structures with Z' = 2, hydrates and solvates, have been optimized as well. Test calculations with different quantum-mechanical methods on nine small organic molecules revealed that the density functional theory methods with dispersion correction using the B97-D functional with 6-31G* basis set in combination with the DREIDING force field reproduced the experimental crystal structures with good accuracy. Subsequently the c-QM/MM method was applied to nine compounds from the CCDC blind tests resulting in good energy rankings and excellent geometric accuracies.

Price Elasticities for Energy Use in Buildings of the United States

EIA Publications

2014-01-01

Energy demand tends to be responsive to changes in energy prices, a concept in economics known as price elasticity. Generally, an increase in a fuel price causes users to use less of that fuel or switch to a different fuel. The extent to which each of these changes takes place is of high importance to stakeholders in the energy sector and especially in energy planning. The purpose of this analysis is to determine fuel-price elasticities in stationary structures, particularly in the residential and commercial sectors.

Towards a mature offshore wind energy technology - guidelines from the opti-OWECS project

NASA Astrophysics Data System (ADS)

Kühn, M.; Bierbooms, W. A. A. M.; van Bussel, G. J. W.; Cockerill, T. T.; Harrison, R.; Ferguson, M. C.; Göransson, B.; Harland, L. A.; Vugts, J. H.; Wiecherink, R.

1999-01-01

The article reviews the main results of the recent European research project Opti-OWECS (Structural and Economic Optimisation of Bottom-Mounted Offshore Wind Energy Converters'), which has significantly improved the understanding of the requirements for a large-scale utilization of offshore wind energy. An integrated design approach was demonstrated for a 300 MW offshore wind farm at a demanding North Sea site. Several viable solutions were obtained and one was elaborated to include the design of all major components. Simultaneous structural and economic optimization took place during the different design stages. An offshore wind energy converter founded on a soft-soft monopile was tailored with respect to the distinct characteristics of dynamic wind and wave loading. The operation and maintenance behaviour of the wind farm was analysed by Monte Carlo simulations. With an optimized maintenance strategy and suitable hardware a high availability was achieved. Based upon the experience from the structural design, cost models for offshore wind farms were developed and linked to a European database of the offshore wind energy potential. This enabled the first consistent estimate of cost of offshore wind energy for entire European regions.

Binary colloidal structures assembled through Ising interactions

NASA Astrophysics Data System (ADS)

Khalil, Karim S.; Sagastegui, Amanda; Li, Yu; Tahir, Mukarram A.; Socolar, Joshua E. S.; Wiley, Benjamin J.; Yellen, Benjamin B.

2012-04-01

New methods for inducing microscopic particles to assemble into useful macroscopic structures could open pathways for fabricating complex materials that cannot be produced by lithographic methods. Here we demonstrate a colloidal assembly technique that uses two parameters to tune the assembly of over 20 different pre-programmed structures, including kagome, honeycomb and square lattices, as well as various chain and ring configurations. We programme the assembled structures by controlling the relative concentrations and interaction strengths between spherical magnetic and non-magnetic beads, which behave as paramagnetic or diamagnetic dipoles when immersed in a ferrofluid. A comparison of our experimental observations with potential energy calculations suggests that the lowest energy configuration within binary mixtures is determined entirely by the relative dipole strengths and their relative concentrations.

Vibration control in smart coupled beams subjected to pulse excitations

NASA Astrophysics Data System (ADS)

Pisarski, Dominik; Bajer, Czesław I.; Dyniewicz, Bartłomiej; Bajkowski, Jacek M.

2016-10-01

In this paper, a control method to stabilize the vibration of adjacent structures is presented. The control is realized by changes of the stiffness parameters of the structure's couplers. A pulse excitation applied to the coupled adjacent beams is imposed as the kinematic excitation. For such a representation, the designed control law provides the best rate of energy dissipation. By means of a stability analysis, the performance in different structural settings is studied. The efficiency of the proposed strategy is examined via numerical simulations. In terms of the assumed energy metric, the controlled structure outperforms its passively damped equivalent by over 50 percent. The functionality of the proposed control strategy should attract the attention of practising engineers who seek solutions to upgrade existing damping systems.

Transport properties of electrons in fractal magnetic-barrier structures

NASA Astrophysics Data System (ADS)

Sun, Lifeng; Fang, Chao; Guo, Yong

2010-09-01

Quantum transport properties in fractal magnetically modulated structures are studied by the transfer-matrix method. It is found that the transmission spectra depend sensitively not only on the incident energy and the direction of the wave vector but also on the stage of the fractal structures. Resonance splitting, enhancement, and position shift of the resonance peaks under different magnetic modulation are observed at four different fractal stages, and the relationship between the conductance in the fractal structure and magnetic modulation is also revealed. The results indicate the spectra of the transmission can be considered as fingerprints for the fractal structures, which show the subtle correspondence between magnetic structures and transport behaviors.

Ab initio study of the alkali and alkaline-earth monohydroxides

NASA Technical Reports Server (NTRS)

Bauschlicher, C. W., Jr.; Langhoff, S. R.; Partridge, H.

1986-01-01

A systematic study of the structures and dissociation energies of all the alkali and alkaline-earth monohydroxides is conducted. A theoretical model for determining accurate dissociation energies of ionic molecules is discussed. The obtained theoretical structures and dissociation energies of the alkali and alkaline-earth monohydroxides, respectively, are compared with experimental data. It is found that the theoretical studies of the bending potentials of BeOH, MgOH, and CaOH reveal the different admixture of covalent character in these systems. The BeOH molecule with the largest degree of covalent character is found to be bent (theta equals 147 deg). The MgOH is also linear. The theoretical dissociation energies for the alkali and akaline-earth hydroxides are thought to be accurate to 0.1 eV.

Ion energy/momentum effects during ion assisted growth of niobium nitride films

NASA Astrophysics Data System (ADS)

Klingenberg, Melissa L.

The research described herein was performed to better understand and discern ion energy vs. ion momentum effects during ion beam assisted (IBAD) film growth and their effects on residual stress, crystalline structure, morphology, and composition, which influence film tribological properties. NbxN y was chosen for this research because it is a refractory material that can possess a large number of crystalline structures, and it has been found to have good tribological properties. To separate the effects of momentum transfer per arriving atom (p/a), which considers bombarding species mass, energy, and ion-to-atom transport ratio, from those of energy deposition per arriving atom (E/a), a mass independent parameter, different inert ion beams (krypton, argon, and neon) were used to create a matrix of coatings formed using similar energy deposition, but different momentum transfer and vice versa. Deposition was conducted in a research-scale IBAD system using electron beam evaporation, a radio frequency ion source, and a neutral nitrogen gas backfill. Films were characterized using x-ray diffraction, atomic force microscopy, Rutherford backscattering spectrometry, and residual stress analysis. Direct and quantifiable effects of bombardment were observed; however, energy deposition and momentum transfer effects could not be completely separated, confirming that thin film processes are complex. Complexities arose from ion-specific interactions (ion size, recoil energy, per cent reflected neutrals, Penning ionization, etc.) and chemistry effects that are not considered by the simple models. Overall, it can be stated that bombardment promoted nitride formation, nanocrystallinity, and compressive stress formation; influenced morphology (which influenced post-deposition oxygen uptake) and stress evolution; increased lattice parameter; modified crystalline phase and texture; and led to inert gas incorporation. High stress levels correlated strongly with material disorder and closed-structured morphologies.

Application of the advanced engineering environment for optimization energy consumption in designed vehicles

NASA Astrophysics Data System (ADS)

Monica, Z.; Sękala, A.; Gwiazda, A.; Banaś, W.

2016-08-01

Nowadays a key issue is to reduce the energy consumption of road vehicles. In particular solution one could find different strategies of energy optimization. The most popular but not sophisticated is so called eco-driving. In this strategy emphasized is particular behavior of drivers. In more sophisticated solution behavior of drivers is supported by control system measuring driving parameters and suggesting proper operation of the driver. The other strategy is concerned with application of different engineering solutions that aid optimization the process of energy consumption. Such systems take into consideration different parameters measured in real time and next take proper action according to procedures loaded to the control computer of a vehicle. The third strategy bases on optimization of the designed vehicle taking into account especially main sub-systems of a technical mean. In this approach the optimal level of energy consumption by a vehicle is obtained by synergetic results of individual optimization of particular constructional sub-systems of a vehicle. It is possible to distinguish three main sub-systems: the structural one the drive one and the control one. In the case of the structural sub-system optimization of the energy consumption level is related with the optimization or the weight parameter and optimization the aerodynamic parameter. The result is optimized body of a vehicle. Regarding the drive sub-system the optimization of the energy consumption level is related with the fuel or power consumption using the previously elaborated physical models. Finally the optimization of the control sub-system consists in determining optimal control parameters.

New crystal structures in hexagonal CuInS2 nanocrystals

NASA Astrophysics Data System (ADS)

Shen, Xiao; Hernández-Pagan, Emil A.; Zhou, Wu; Puzyrev, Yevgeniy S.; Idrobo, Juan C.; MacDonald, Janet E.; Pennycook, Stephen J.; Pantelides, Sokrates T.

2013-03-01

CuInS2 is one of the best candidate materials for solar energy harvesting. Its nanocrystals with a hexagonal lattice structure that is different from the bulk chalcopyrite phase have been synthesized by many groups. The structure of these CuInS2 nanocrystals has been previously identified as the wurtzite structure in which the copper and indium atoms randomly occupy the cation sites. Using first-principles total energy and electronic structure calculations based on density functional theory, UV-vis absorption spectroscopy, X-ray diffraction, and atomic resolution Z-contrast images obtained in an aberration-corrected scanning transmission electron microscope, we show that CuInS2 nanocrystals do not form random wurtzite structure. Instead, the CuInS2 nanocrystals consist of several wurtzite- related crystal structures with ordered cation sublattices, some of which are reported for the first time here. This work is supported by the NSF TN-SCORE (JEM), by NSF (WZ), by ORNL's Shared Research Equipment User Program (JCI) sponsored by DOE BES, by DOE BES Materials Sciences and Engineering Division (SJP, STP), and used resources of the National Energy Research Scientific Computing Center, supported by the DOE Office of Science under Contract No. DE-AC02-05CH11231.

Replica Exchange Simulations of the Thermodynamics of Aβ Fibril Growth

PubMed Central

Takeda, Takako; Klimov, Dmitri K.

2009-01-01

Abstract Replica exchange molecular dynamics and an all-atom implicit solvent model are used to probe the thermodynamics of deposition of Alzheimer's Aβ monomers on preformed amyloid fibrils. Consistent with the experiments, two deposition stages have been identified. The docking stage occurs over a wide temperature range, starting with the formation of the first peptide-fibril interactions at 500 K. Docking is completed when a peptide fully adsorbs on the fibril edge at the temperature of 380 K. The docking transition appears to be continuous, and occurs without free energy barriers or intermediates. During docking, incoming Aβ monomer adopts a disordered structure on the fibril edge. The locking stage occurs at the temperature of ≈360 K and is characterized by the rugged free energy landscape. Locking takes place when incoming Aβ peptide forms a parallel β-sheet structure on the fibril edge. Because the β-sheets formed by locked Aβ peptides are typically off-registry, the structure of the locked phase differs from the structure of the fibril interior. The study also reports that binding affinities of two distinct fibril edges with respect to incoming Aβ peptides are different. The peptides bound to the concave edge have significantly lower free energy compared to those bound on the convex edge. Comparison with the available experimental data is discussed. PMID:19167295

Evolution and Control of Electronic Structures near the Interface of Complex Oxide Heterostructure SmTiO3/SrTiO3

NASA Astrophysics Data System (ADS)

Mori, Ryo; Marshall, Patrick; Isaac, Brandon; Denlinger, Jonathan; Stemmer, Susanne; Lanzara, Alessandra

The confined electron system in the quantum well of the transition metal oxide, SrTiO3, embedded in the rare earth titanate, SmTiO3, shows unique properties, such as high carrier density, fermi liquid to non-fermi liquid transition, and pseudo-gap, which can be controlled by changing the shape of the quantum well. We will present a distinct difference in the electronic structures between the different quantum well structures obtained by angle-resolved photoemission spectroscopy (ARPES) measurements, suggesting the possibility to control the orbital character and the electron correlation near the interface as well as carrier density. The work was supported by the Quantum Materials Program at LBNL, funded by the U.S. Department of Energy, Office of Science, Office of Basic Energy Sciences, Materials Sciences and Engineering Division, under Contract No. DE-AC02-05CH11231.

Surface and ultrastructural characterization of raw and pretreated switchgrass.

PubMed

Donohoe, Bryon S; Vinzant, Todd B; Elander, Richard T; Pallapolu, Venkata Ramesh; Lee, Y Y; Garlock, Rebecca J; Balan, Venkatesh; Dale, Bruce E; Kim, Youngmi; Mosier, Nathan S; Ladisch, Michael R; Falls, Matthew; Holtzapple, Mark T; Sierra-Ramirez, Rocio; Shi, Jian; Ebrik, Mirvat A; Redmond, Tim; Yang, Bin; Wyman, Charles E; Hames, Bonnie; Thomas, Steve; Warner, Ryan E

2011-12-01

The US Department of Energy-funded Biomass Refining CAFI (Consortium for Applied Fundamentals and Innovation) project has developed leading pretreatment technologies for application to switchgrass and has evaluated their effectiveness in recovering sugars from the coupled operations of pretreatment and enzymatic hydrolysis. Key chemical and physical characteristics have been determined for pretreated switchgrass samples. Several analytical microscopy approaches utilizing instruments in the Biomass Surface Characterization Laboratory (BSCL) at the National Renewable Energy Laboratory (NREL) have been applied to untreated and CAFI-pretreated switchgrass samples. The results of this work have shown that each of the CAFI pretreatment approaches on switchgrass result in different structural impacts at the plant tissue, cellular, and cell wall levels. Some of these structural changes can be related to changes in chemical composition upon pretreatment. There are also apparently different structural mechanisms that are responsible for achieving the highest enzymatic hydrolysis sugar yields. Copyright © 2011. Published by Elsevier Ltd.

Research on Impact Stress and Fatigue Simulation of a New Down-to-the-Hole Impactor Based on ANSYS

NASA Astrophysics Data System (ADS)

Wu, Tao; Wang, Wei; Yao, Aiguo; Li, Yongbo; He, Wangyong; Fei, Dongdong

2018-06-01

In the present work, a down-to-the-hole electric hammer driven by linear motor is reported for drilling engineering. It differs from the common hydraulic or pneumatic hammers in that it can be applied to some special occasions without circulating medium due to its independence of the drilling fluid. The impact stress caused by the reciprocating motion between stator and rotor and the fatigue damage in key components of linear motor are analyzed by the ANSYS Workbench software and 3D model. Based on simulation results, the hammer's structure is optimized by using special sliding bearing, increasing the wall thickness of key and multilayer buffer gasket. Fatigue life and coefficient issues of the new structure are dramatically improved. However buffer gasket reduces the impactor's energy, different bumper structure effect on life improving and energy loss have also been elaborated.

The Calculation Study of Electronic Properties of Doped RE (Eu, Er and Tm)-GaN using Density Functional Theory

NASA Astrophysics Data System (ADS)

Zaharo, Aflah; Purqon, Acep

2017-07-01

The calculation of the structure and electronic properties of Rare Earth (RE) at the wurtzite Gallium Nitride (GaN) based on DFT has completed. GGA approximation used for exchange correlation and Ultra soft pseudo potential too. The stability structure of GaN is seen that difference lattice parameter 11% lower than another calculation and experiment result. It is shown the stability structure GaN have direct band gap energy on Gamma point hexagonal lattice Brillouin zone. The width Eg is 2.6 eV. When one atom Ga is substituted with one atom RE, the bond length is change 12 % longest. An in good agreement with theoretical doping RE concentration increases, the edge of energy level shifted towards to make the band gap narrow which is allow the optical transitions and help to improve the optical performance of GaN. The RE doped GaN is potentially applicable for various color of LED with lower energy consumption and potentially energy saving application

Simultaneous NMR characterisation of multiple minima in the free energy landscape of an RNA UUCG tetraloop.

PubMed

Borkar, Aditi N; Vallurupalli, Pramodh; Camilloni, Carlo; Kay, Lewis E; Vendruscolo, Michele

2017-01-25

RNA molecules in solution tend to undergo structural fluctuations of relatively large amplitude and to populate a range of different conformations some of which with low populations. It is still very challenging, however, to characterise the structures of these low populated states and to understand their functional roles. In the present study, we address this problem by using NMR residual dipolar couplings (RDCs) as structural restraints in replica-averaged metadynamics (RAM) simulations. By applying this approach to a 14-mer RNA hairpin containing the prototypical UUCG tetraloop motif, we show that it is possible to construct the free energy landscape of this RNA molecule. This free energy landscapes reveals the surprisingly rich dynamics of the UUCG tetraloop and identifies the multiple substates that exist in equilibrium owing to thermal fluctuations. The approach that we present is general and can be applied to the study of the free energy landscapes of other RNA or RNA-protein systems.

Tailored interphase structure for improved strength and energy absorption of composites

NASA Astrophysics Data System (ADS)

Gao, Xiao

Fiber reinforced polymeric composites are lightweight, high-strength and high impact-resistant materials used widely for various applications. It has been shown that the mechanical performance of composites are dependent on the interphase, a three-dimensional region of nanometer size in the vicinity of the fiber-matrix boundary that possesses properties different from those of either the fiber reinforcement or the matrix resin and governs the load transfer from matrix to fiber. This research conducts a systematic study on glass fiber-epoxy interphase structure by tailoring adhesion between constituents and the creation of textures to control strength and energy absorption through mechanical interlocking between glass fiber and epoxy matrix. Our objective is to establish the foundation for microstructural design and optimization of the composite's structural and impact performance. Two ways of roughening the glass fiber surface have been studied to create the mechanical interlocking between fiber and resin; the first technique involves forming in-situ islands on the glass fiber surface by using silane blends of Glycidoxypropyltrimethoxy silane (GPS) and Tetraethoxy silane (TEOS); the second technique applies a silane coupling agents based sizing with the incorporation of silica nanoparticles (Ludox TMA, 22 nm) onto the fiber surface. The microdroplet test was selected to characterize the influence of adhesion and mechanical interlocking effects on interphase properties of different sizing sized glass fiber reinforced epoxy systems. A suitable data reduction scheme enables the strength and specified energy absorbed due to debonding, dynamic sliding, and quasi-static sliding to be quantified. In order to validate the effect of tailored interphase structure, which is induced by creating mechanical interlocking between fiber and resin, on macroscopic composite properties, composite panels were made from these four different sizing sized glass fibers and tested using the punch shear test. The composite panel made from the hybrid sizing sized glass fiber exhibited improved strength and energy absorption consistent with the trends in micromechanical measurements. Through all failure stages under macromechanical testing, hybrid sizing sized glass fiber/epoxyamine composite panel shows an increase in the strength and total energy absorption by 13% and 26%, respectively, compared to the compatible sizing sized baseline. Both micromechanical and macromechanical tests demonstrate the significant influence of tailoring the interphase structure on improving the impact performance of the composites. The hybrid sizing with the incorporation of nanoparticles, in particular, can greatly improve the impact resistance (i.e. energy absorption) of composites without sacrificing its structural performance (i.e. strength).

Impact localization and energy quantification based on the power flow: A low-power requirement approach

NASA Astrophysics Data System (ADS)

Guyomar, Daniel; Lallart, Mickaël; Petit, Lionel; Wang, Xing-Jun

2011-06-01

The increasing use of composite materials has led to a dramatic change in the definition of safety standards. In particular, composite structures may be subjected to internal damages caused by external impacts that may not be detected by classical inspection methods. Additional constraints related to energy requirements may also be considered in order to make the system autonomous and possibly self-powered. The purpose of this paper is to present a low-cost impact detection and quantification scheme for thin plates or shells giving the whole history of the structure solicitation. Based on the analysis of the energy that has flown over a monitored area through the use of the elastic Poynting vector (that relates the mechanical power density of travelling waves), it is shown that this global energy balance may be linked in a simple way to the voltage output of piezoelectric elements in open-circuit condition. From this estimation, it is therefore possible to detect if an impact occurred inside the monitored area (in this case, the global energy balance would be positive) as well as its associated energy. If the impact occurs out of the frame, the global energy (and thus the obtained estimator) would be negative because of energy dissipation caused by internal losses and almost null. Thanks to this energy flow approach, the system is also independent from the boundary conditions of the structure. Experimental measurements aiming at validating the theoretical predictions showed that the technique permits detecting the impact area (inside/outside the frame) as well as an accurate estimation of the impact energy if the latter occurred inside the frame, both on a steel plate (with different boundary conditions) and an anisotropic composite structure.

Two alternative solar energy scenarios for Western Europe

NASA Astrophysics Data System (ADS)

Nakicenovic, N.

1982-11-01

Two limiting scenarios that lead to a sustainable energy system in Western Europe toward the end of the next century are described. The scenarios consider exclusively solar energy futures: one based on centralized solar technologies (hard scenario) and the other on decentralized user-oriented technologies (soft scenario). While both scenarios eliminate Western Europe's dependence on domestic and foreign fossil energy sources, the hard solar scenario requires substantial imports of solar produced hydrogen. Fundamental but different changes of the whole energy system, economic structure and lifestyles are necessary in order to achieve sustainable solar energy futures in the scenarios.

Modelling of Surfaces. Part 2: Metallic Alloy Surfaces Using the BFS Method

NASA Technical Reports Server (NTRS)

Bozzolo, Guillermo; Ferrante, John; Kobistek, Robert J.

1994-01-01

Using BFS, a new semiempirical method for alloys, we study the surface structure of fcc ordered binary alloys. We concentrate on the calculation of surface energies and surface relaxations for the L1(sub 0) and L1(sub 2) ordered structures. Different terminations of the low-index faces are studied. Also, we present results for the interlayer relaxations for planes close to the surface, revealing different relaxations for atoms of different species producing a rippled surface layer.

Molecular structure and interactions in the ionic liquid 1-ethyl-3-methylimidazolium bis(trifluoromethylsulfonyl)imide.

PubMed

Dhumal, Nilesh R; Noack, Kristina; Kiefer, Johannes; Kim, Hyung J

2014-04-03

Electronic structure theory (density functional and Møller-Plesset perturbation theory) and vibrational spectroscopy (FT-IR and Raman) are employed to study molecular interactions in the room-temperature ionic liquid 1-ethyl-3-methylimidazolium bis(trifluoromethylsulfonyl)imide. Different conformers of a cation-anion pair based on their molecular interactions are simulated in the gas phase and in a dielectric continuum solvent environment. Although the ordering of conformers in energy varies with theoretical methods, their predictions for three lowest energy conformers in the gas phase are similar. Strong C-H---N interactions between the acidic hydrogen atom of the cation imidazole ring and the nitrogen atom of the anion are predicted for either the lowest or second lowest energy conformer. In a continuum solvent, different theoretical methods yield the same ion-pair conformation for the lowest energy state. In both phases, the density functional method predicts that the anion is in a trans conformation in the lowest energy ion pair state. The theoretical results are compared with experimental observations from Raman scattering and IR absorption spectroscopies and manifestations of the molecular interactions in the vibrational spectra are discussed. The directions of the frequency shifts of the characteristic vibrations relative to the free anion and cation are explained by calculating the difference electron density coupled with electron density topography.

Energy for Wild-Type Acetylcholine Receptor Channel Gating from Different Choline Derivatives

PubMed Central

Bruhova, Iva; Gregg, Timothy; Auerbach, Anthony

2013-01-01

Agonists, including the neurotransmitter acetylcholine (ACh), bind at two sites in the neuromuscular ACh receptor channel (AChR) to promote a reversible, global change in protein conformation that regulates the flow of ions across the muscle cell membrane. In the synaptic cleft, ACh is hydrolyzed to acetate and choline. Replacement of the transmitter’s ester acetyl group with a hydroxyl (ACh→choline) results in a +1.8 kcal/mol reduction in the energy for gating generated by each agonist molecule from a low- to high-affinity change of the transmitter binding site (ΔGB). To understand the distinct actions of structurally related agonist molecules, we measured ΔGB for 10 related choline derivatives. Replacing the hydroxyl group of choline with different substituents, such as hydrogen, chloride, methyl, or amine, increased the energy for gating (i.e., it made ΔGB more negative relative to choline). Extending the ethyl hydroxide tail of choline to propyl and butyl hydroxide also increased this energy. Our findings reveal the amount of energy that is available for the AChR conformational change provided by different, structurally related agonists. We speculate that a hydrogen bond between the choline hydroxyl and the backbone carbonyl of αW149 positions this agonist’s quaternary ammonium group so as to reduce the cation-π interaction between this moiety and the aromatic groups at the binding site. PMID:23442907

Using peer-to-peer energy-trading platforms to incentivize prosumers to form federated power plants

NASA Astrophysics Data System (ADS)

Morstyn, Thomas; Farrell, Niall; Darby, Sarah J.; McCulloch, Malcolm D.

2018-02-01

Power networks are undergoing a fundamental transition, with traditionally passive consumers becoming `prosumers' — proactive consumers with distributed energy resources, actively managing their consumption, production and storage of energy. A key question that remains unresolved is: how can we incentivize coordination between vast numbers of distributed energy resources, each with different owners and characteristics? Virtual power plants and peer-to-peer (P2P) energy trading offer different sources of value to prosumers and the power network, and have been proposed as different potential structures for future prosumer electricity markets. In this Perspective, we argue they can be combined to capture the benefits of both. We thus propose the concept of the federated power plant, a virtual power plant formed through P2P transactions between self-organizing prosumers. This addresses social, institutional and economic issues faced by top-down strategies for coordinating virtual power plants, while unlocking additional value for P2P energy trading.

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

Reconstructing Folding Energy Landscapes by Single-Molecule Force Spectroscopy

PubMed Central

Woodside, Michael T.; Block, Steven M.

2015-01-01

Folding may be described conceptually in terms of trajectories over a landscape of free energies corresponding to different molecular configurations. In practice, energy landscapes can be difficult to measure. Single-molecule force spectroscopy (SMFS), whereby structural changes are monitored in molecules subjected to controlled forces, has emerged as a powerful tool for probing energy landscapes. We summarize methods for reconstructing landscapes from force spectroscopy measurements under both equilibrium and nonequilibrium conditions. Other complementary, but technically less demanding, methods provide a model-dependent characterization of key features of the landscape. Once reconstructed, energy landscapes can be used to study critical folding parameters, such as the characteristic transition times required for structural changes and the effective diffusion coefficient setting the timescale for motions over the landscape. We also discuss issues that complicate measurement and interpretation, including the possibility of multiple states or pathways and the effects of projecting multiple dimensions onto a single coordinate. PMID:24895850

Stacking faults density driven collapse of magnetic energy in hcp-cobalt nano-magnets

NASA Astrophysics Data System (ADS)

Nong, H. T. T.; Mrad, K.; Schoenstein, F.; Piquemal, J.-Y.; Jouini, N.; Leridon, B.; Mercone, S.

2017-06-01

Cobalt nanowires with different shape parameters were synthesized via the polyol process. By calculating the magnetic energy product (BH max) both for dried nano-powder and for nanowires in their synthesis solution, we observed unexpected independent BH max values from the nanowires shape. A good alignment of the nanowires leads to a higher BH max value. Our results show that the key parameter driving the magnetic energy product of the cobalt nanowires is the stacking fault density. An exponential collapse of the magnetic energy is observed at very low percentage of structural faults. Cobalt nanowires with almost perfect hcp crystalline structures should present high magnetic energy, which is promising for application in rare earth-free permanent magnets. Oral talk at 8th International Workshop on Advanced Materials Science and Nanotechnology (IWAMSN2016), 8-12 November 2016, Ha Long City, Vietnam.

Investigation of ionic transport in sodium scandium phosphate (NSP) and related compounds

NASA Astrophysics Data System (ADS)

Bhat, Kaustubh; Blügel, Stefan; Lustfeld, Hans

Sodium ionic conductors offer significant advantages for application in large scale energy storage systems. In this study, we investigate the different pathways available for sodium ion conduction in NSP and calculate energy barriers for ionic transport using Density Functional Theory (DFT) and the Nudged Elastic Band Method. We identify the structural parameters that reduce the energy barrier, by calculating the influence of positive and negative external pressure on the energy barrier. Lattice strain can be introduced by cation or anion substitution within the NASICON structure. We substitute the scandium atom with other trivalent atoms such as aluminium and yttrium, and calculate the resulting energy barriers. Sodium thiophosphate (Na3PS4) has previously shown about two orders of magnitude higher ionic conductivity than sodium phosphate (Na3PO4). We investigate the effect of substituting oxygen with sulphur in NSP. We acknowledge discussions with our experimental colleagues F. Tietz and M. Guin toward this work

Method, apparatus and system for low-energy beta particle detection

DOEpatents

Akers, Douglas W.; Drigert, Mark W.

2012-09-25

An apparatus, method, and system relating to radiation detection of low-energy beta particles are disclosed. An embodiment includes a radiation detector with a first scintillator and a second scintillator operably coupled to each other. The first scintillator and the second scintillator are each structured to generate a light pulse responsive to interaction with beta particles. The first scintillator is structured to experience full energy deposition of low-energy beta particles, and permit a higher-energy beta particle to pass therethrough and interact with the second scintillator. The radiation detector further includes a light-to-electrical converter operably coupled to the second scintillator and configured to convert light pulses generated by the first scintillator and the second scintillator into electrical signals. The first scintillator and the second scintillator have at least one mutually different characteristic to enable an electronic system to determine whether a given light pulse is generated in the first scintillator or the second scintillator.

Characterisation of the biofouling community on a floating wave energy device.

PubMed

Nall, Christopher R; Schläppy, Marie-Lise; Guerin, Andrew J

2017-05-01

Wave energy devices are novel structures in the marine environment and, as such, provide a unique habitat for biofouling organisms. In this study, destructive scrape samples and photoquadrats were used to characterise the temperate epibenthic community present on prototypes of the Pelamis wave energy converter. The biofouling observed was extensive and diverse with 115 taxa recorded including four non-native species. Vertical zonation was identified on the sides of the device, with an algae-dominated shallow subtidal area and a deeper area characterised by a high proportion of suspension-feeding invertebrates. Differences in species composition and biomass were also observed between devices, along the length of the device and between sampling dates. This research provides an insight into the variation of biofouling assemblages on a wave energy device as well as the potential technical and ecological implications associated with biofouling on marine renewable energy structures.

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.

Effects of ion concentration on thermally-chargeable double-layer supercapacitors

NASA Astrophysics Data System (ADS)

Lim, Hyuck; Lu, Weiyi; Chen, Xi; Qiao, Yu

2013-11-01

The concept of thermally-chargeable supercapacitor was discussed and validated experimentally. As two double-layer supercapacitor-type devices were placed at different temperatures and connected, due to the thermal dependence of surface charge structures, the electrode potentials became different, and thermal energy could be harvested and stored as electric energy. The important effect of ion concentration was investigated. The results were quite different from the prediction of conventional surface theory, which should be attributed to the unique behaviors of the ions confined in the nanoporous electrodes.

Effects of ion concentration on thermally-chargeable double-layer supercapacitors.

PubMed

Lim, Hyuck; Lu, Weiyi; Chen, Xi; Qiao, Yu

2013-11-22

The concept of thermally-chargeable supercapacitor was discussed and validated experimentally. As two double-layer supercapacitor-type devices were placed at different temperatures and connected, due to the thermal dependence of surface charge structures, the electrode potentials became different, and thermal energy could be harvested and stored as electric energy. The important effect of ion concentration was investigated. The results were quite different from the prediction of conventional surface theory, which should be attributed to the unique behaviors of the ions confined in the nanoporous electrodes.

Structure and chemical reactivity of the polar three-fold surfaces of GaPd: A density-functional study

NASA Astrophysics Data System (ADS)

Krajčí, M.; Hafner, J.

2013-03-01

The polar threefold surfaces of the GaPd compound crystallizing in the B20 (FeSi-type) structure (space group P213) have been investigated using density-functional methods. Because of the lack of inversion symmetry the B20 structure exists in two enantiomorphic forms denoted as A and B. The threefold {111} surfaces have polar character. In both nonequivalent (111) and (bar{1}bar{1}bar{1}) directions several surface terminations differing in structure and chemical composition are possible. The formation of the threefold surfaces has been studied by simulated cleavage experiments and by calculations of the surface energies. Because of the polar character of the threefold surfaces calculations for stoichiometric slabs permit only the determination of the average energy of the surfaces exposed on both sides of the slab. Calculations for nonstoichiometric slabs performed in the grand canonical ensemble yield differences of the surface energies for the possible terminations as a function of the chemical potential in the reactive atmosphere above the surface and predict a transition between Ga- and Pd-terminated surfaces as a function of the chemical potential. The {100} surfaces are stoichiometric and uniquely defined. The calculated surface energies are identical to the average energies of the {100} surfaces of the pure metals. The {210} surfaces are also stoichiometric, with an energy very close to that of the {100} surfaces. Assuming that for the {111} surfaces the energies of different possible terminations are in a proportion equal to that of the concentration-weighted energies of the {111} surfaces of the pure metals, surface energies for all possible {111} terminations may be calculated. The preferable termination perpendicular to the A⟨111⟩ direction consists of a bilayer with three Ga atoms in the upper and three Pd atoms in the lower part. The surface energy of this termination further decreases if the Pd triplet is covered by additional Ga atom. Perpendicular to the A< bar{1}bar{1}bar{1} > direction the lowest energy has been found for a bilayer with three Ga atoms per surface cell in the upper layer and one Ga and one Pd in the lower part. The calculated surface energies are in agreement with a simulated cleavage experiment. However, cleavage does not result in the formation of the lowest-energy surfaces, because all possible {111} cleavage planes expose a low-energy surface on one, and a high-energy surface on the other side. The prediction of Ga-terminated surfaces has been tested against the available experimental information. The calculated surface electronic density of states is in very good agreement with photo-emission spectroscopy. Calculated STM images of the most stable surfaces agree with all details of the available experimental images. The chemical reactivity of the most stable surfaces has been studied by the adsorption of CO molecules. The adsorption energies and maximum coverages calculated for the Ga-terminated surfaces permit a reasonable interpretation of the observed thermal desorption spectra, whereas for the Pd-terminated surfaces the calculated adsorption energies are far too high.

The observed characteristics of flare energy release. I - Magnetic structure at the energy release site

NASA Technical Reports Server (NTRS)

Machado, Marcos E.; Moore, Ronald L.; Hagyard, Mona J.; Hernandez, Ana M.; Rovira, Marta G.

1988-01-01

It is shown that flaring activity as seen in X-rays usually encompasses two or more interacting magnetic bipoles within an active region. Soft and hard X-ray spatiotemporal evolution is considered as well as the time dependence of the thermal energy content in different magnetic bipoles participating in the flare, the hardness and impulsivity of the hard X-ray emission, and the relationship between the X-ray behavior and the strength and 'observable shear' of the magnetic field. It is found that the basic structure of a flare usually consists of an initiating closed bipole plus one or more adjacent closed bipoles impacted against it.

Coupling continuous damage and debris fragmentation for energy absorption prediction by cfrp structures during crushing

NASA Astrophysics Data System (ADS)

Espinosa, Christine; Lachaud, Frédéric; Limido, Jérome; Lacome, Jean-Luc; Bisson, Antoine; Charlotte, Miguel

2015-05-01

Energy absorption during crushing is evaluated using a thermodynamic based continuum damage model inspired from the Matzenmiller-Lubliner-Taylors model. It was found that for crash-worthiness applications, it is necessary to couple the progressive ruin of the material to a representation of the matter openings and debris generation. Element kill technique (erosion) and/or cohesive elements are efficient but not predictive. A technique switching finite elements into discrete particles at rupture is used to create debris and accumulated mater during the crushing of the structure. Switching criteria are evaluated using the contribution of the different ruin modes in the damage evolution, energy absorption, and reaction force generation.

MEMS for vibration energy harvesting

NASA Astrophysics Data System (ADS)

Li, Lin; Zhang, Yangjian; San, Haisheng; Guo, Yinbiao; Chen, Xuyuan

2008-03-01

In this paper, a capacitive vibration-to-electrical energy harvester was designed. An integrated process flow for fabricating the designed capacitive harvester is presented. For overcoming the disadvantage of depending on external power source in capacitive energy harvester, two parallel electrodes with different work functions are used as the two electrodes of the capacitor to generate a build-in voltage for initially charging the capacitor. The device is a sandwich structure of silicon layer in two glass layers with area of about 1 cm2. The silicon structure is fabricated by using silicon-on-insulator (SOI) wafer. The glass wafers are anodic bonded on to both sides of the SOI wafer to create a vacuum sealed package.

Molecular dynamics calculation on structures, stabilities, mechanical properties, and energy density of CL-20/FOX-7 cocrystal explosives.

PubMed

Hang, Gui-Yun; Yu, Wen-Li; Wang, Tao; Wang, Jin-Tao; Li, Zhen

2017-11-30

In this article, different CL-20/FOX-7 cocrystal models were established by the substitution method based on the molar ratios of CL-20:FOX-7. The structures and comprehensive properties, including mechanical properties, stabilities, and energy density, of different cocrystal models were obtained and compared with each other. The main aim was to estimate the influence of molar ratios on properties of cocrystal explosives. The molecular dynamics (MD) simulation results show that the cocrystal model with molar ratio 1:1 has the best mechanical properties and highest binding energy, so the CL-20/FOX-7 cocrystal model is more likely to form in 1:1 M ratio. The detonation parameters show that the cocrystal explosive exhibited preferable energy density and excellent detonation performance. In a word, the 1:1 cocrystal model has the best comprehensive properties, is very promising, and worth more theoretical investigations and experimental tests. This paper gives some original theories to better understand the cocrystal mechanism and provides some helpful guidance and useful instructions to help design CL-20 cocrystal explosives.

The relationship between structural and optical properties of Se-Ge-As glasses

NASA Astrophysics Data System (ADS)

Ghayebloo, M.; Rezvani, M.; Tavoosi, M.

2018-05-01

In this study, the structural and optical characterization of bulk Se-Ge-As glasses has been investigated. In this regards, six different Se60Ge40-xAsx (0 ≤ x ≤ 25) glasses were prepared by conventional melt quenching technique in quartz ampoule. The produced samples were characterized using X-ray diffraction (XRD), Raman spectroscopy, differential thermal analysis (DTA), ultraviolet-visible (UV-Vis) and Fourier transform infrared (FTIR) spectroscopy. The fundamental absorption edge for all the glasses was analyzed in terms of the theory proposed by Davis and Mott. According to achieved results, fully amorphous phase can easily form in different Se-Ge-As systems. The thermal and optical characteristic of Se60Ge40-xAsx glasses shows anomalous behavior at 5 mol% of As for the glass transition temperature, transmittance, absorption edge, optical energy gap and Urbach energy. The highest glass transition temperature, transmittance, optical energy gap and Urbach energy properties were achieved in Se60Ge35As5 glass as a result of the highest connectivity of cations and anions in glass network.

Effect on structure and mechanical property of tungsten irradiated by high intensity pulsed ion beam

NASA Astrophysics Data System (ADS)

Mei, Xianxiu; Zhang, Xiaonan; Liu, Xiaofei; Wang, Younian

2017-09-01

The anti-thermal radiation performance of tungsten was investigated by high intensity pulsed ion beam technology. The ion beam was mainly composed of Cn+ (70%) and H+ (30%) at an acceleration voltage of 250 kV under different energy densities for different number of pulses. GIXRD analysis showed that no obvious phase structural changes occurred on the tungsten, and microstress generated. SEM analysis exhibited that there was no apparent irradiation damage on the surface of tungsten at the low irradiation frequency (3 times and 10 times) and at the low energy density (0.25 J/cm2 and 0.7 J/cm2). Cracks appeared on the surface of tungsten after 100-time and 300-time irradiation. Shedding phenomenon even appeared on the surface of tungsten at the energy densities of 1.4 J/cm2 and 2.0 J/cm2. The surface nano-hardness of tungsten decreased with the increase of the pulse times and the energy density. The tungsten has good anti-thermal radiation properties under certain heat load environment.

Orientation-dependent structural and photocatalytic properties of LaCoO3 epitaxial nano-thin films

PubMed Central

Zhang, Yan-ping; Hu, Hai-long; Xie, Rui-shi; Ma, Guo-hua; Huo, Ji-chuan; Wang, Hai-bin

2018-01-01

LaCoO3 epitaxial films were grown on (100), (110) and (111) oriented LaAlO3 substrates by the polymer-assisted deposition method. Crystal structure measurement and cross-section observation indicate that all the LaCoO3 films are epitaxially grown in accordance with the orientation of LaAlO3 substrates, with biaxial compressive strain in the ab plane. Owing to the different strain directions of CoO6 octahedron, the mean Co–O bond length increases by different amounts in (100), (110) and (111) oriented films compared with that of bulk LaCoO3, and the (100) oriented LaCoO3 has the largest increase. Photocatalytic degradation of methyl orange indicates that the order of photocatalytic activity of the three oriented films is (100) > (111) > (110). Combined with analysis of electronic nature and band structure for LaCoO3 films, it is found that the change of the photocatalytic activity is closely related to the crystal field splitting energy of Co3+ and Co–O binding energy. The increase in the mean Co–O bond length will decrease the crystal field splitting energy of Co3+ and Co–O binding energy and further reduce the value of band gap energy, thus improving the photocatalytic activity. This may also provide a clue for expanding the visible-light-induced photocatalytic application of LaCoO3. PMID:29515854

Orientation-dependent structural and photocatalytic properties of LaCoO3 epitaxial nano-thin films.

PubMed

Zhang, Yan-Ping; Liu, Hai-Feng; Hu, Hai-Long; Xie, Rui-Shi; Ma, Guo-Hua; Huo, Ji-Chuan; Wang, Hai-Bin

2018-02-01

LaCoO 3 epitaxial films were grown on (100), (110) and (111) oriented LaAlO 3 substrates by the polymer-assisted deposition method. Crystal structure measurement and cross-section observation indicate that all the LaCoO 3 films are epitaxially grown in accordance with the orientation of LaAlO 3 substrates, with biaxial compressive strain in the ab plane. Owing to the different strain directions of CoO 6 octahedron, the mean Co-O bond length increases by different amounts in (100), (110) and (111) oriented films compared with that of bulk LaCoO 3 , and the (100) oriented LaCoO 3 has the largest increase. Photocatalytic degradation of methyl orange indicates that the order of photocatalytic activity of the three oriented films is (100) > (111) > (110). Combined with analysis of electronic nature and band structure for LaCoO 3 films, it is found that the change of the photocatalytic activity is closely related to the crystal field splitting energy of Co 3+ and Co-O binding energy. The increase in the mean Co-O bond length will decrease the crystal field splitting energy of Co 3+ and Co-O binding energy and further reduce the value of band gap energy, thus improving the photocatalytic activity. This may also provide a clue for expanding the visible-light-induced photocatalytic application of LaCoO 3 .

Quantum transport in new two-dimensional heterostructures: Thin films of topological insulators, phosphorene

NASA Astrophysics Data System (ADS)

Majidi, Leyla; Zare, Moslem; Asgari, Reza

2018-06-01

The unusual features of the charge and spin transport characteristics are investigated in new two-dimensional heterostructures. Intraband specular Andreev reflection is realized in a topological insulator thin film normal/superconducting junction in the presence of a gate electric field. Perfect specular electron-hole conversion is shown for different excitation energy values in a wide experimentally available range of the electric field and also for all angles of incidence when the excitation energy has a particular value. It is further demonstrated that the transmission probabilities of the incoming electrons from different spin subbands to the monolayer phosphorene ferromagnetic/normal/ferromagnetic (F/N/F) hybrid structure have different behavior with the angle of incidence and perfect transmission occurs at defined angles of incidence to the proposed structure with different length of the N region, and different alignments of magnetization vectors. Moreover, the sign change of the spin-current density is demonstrated by tuning the chemical potential and exchange field of the F region.

Anharmonic and Quantum Fluctuations in Molecular Crystals from Ab Initio Simulations

NASA Astrophysics Data System (ADS)

Rossi, Mariana; Gasparotto, Piero; Ceriotti, Michele

Molecular crystals often exist in multiple competing polymorphs which are challenging to be predicted computationally, but show significantly different physicochemical properties. This challenge is not due only to the combinatorial search space, but also to the complex interplay of subtle effects determine the relative stability of different structures. Here we estimate all contributions to the free energies of these systems with density-functional theory, including the oft-neglected anharmonic contributions and nuclear quantum effects, by using a series of different flavors of thermodynamic integration. As an example, for the two most stable forms of paracetamol we find that anharmonic contributions, different descriptions of van der Waals interactions, and nuclear quantum effects all matter to quantitatively determine the stability of different phases. Our studies indicate that anharmonic free energies could play an important role for molecular crystals composed by large molecules and opens the way for a systematic inclusion of these effects in order to obtain a predictive screening of structures.

Resonant Soft X-ray Scattering of Cellulose Microstructure in Plant Primary Cell Walls

NASA Astrophysics Data System (ADS)

Ye, Dan; Kiemle, Sarah N.; Wang, Cheng; Cosgrove, Daniel J.; Gomez, Esther W.; Gomez, Enrique D.

Cellulosic biomass is the most abundant raw material available for the production of renewable and sustainable biofuels. Breaking down cellulose is the rate-limiting step in economical biofuel production; therefore, a detailed understanding of the microscopic structure of plant cell walls is required to develop efficient biofuel conversion methods. Primary cell walls are key determinants of plant growth and mechanics. Their structure is complex and heterogeneous, making it difficult to elucidate how various components such as pectin, hemicellulose, and cellulose contribute to the overall structure. The electron density of these wall components is similar; such that conventional hard X-ray scattering does not generate enough contrast to resolve the different elements of the polysaccharide network. The chemical specificity of resonant soft X-ray scattering allows contrast to be generated based on differences in chemistry of the different polysaccharides. By varying incident X-ray energies, we have achieved increased scattering contrast between cellulose and other polysaccharides from primary cell walls of onions. By performing scattering at certain energies, features of the network structure of the cell wall are resolved. From the soft X-ray scattering results, we obtained the packing distance of cellulose microfibrils embedded in the polysaccharide network.

Atypical behavior in the electron capture induced dissociation of biologically relevant transition metal ion complexes of the peptide hormone oxytocin

NASA Astrophysics Data System (ADS)

Kleinnijenhuis, Anne J.; Mihalca, Romulus; Heeren, Ron M. A.; Heck, Albert J. R.

2006-07-01

Doubly protonated ions of the disulfide bond containing nonapeptide hormone oxytocin and oxytocin complexes with different transition metal ions, that have biological relevance under physiological conditions, were subjected to electron capture dissociation (ECD) to probe their structural features in the gas phase. Although, all the ECD spectra were strikingly different, typical ECD behavior was observed for complexes of the nonapeptide hormone oxytocin with Ni2+, Co2+ and Zn2+, i.e., abundant c/z' and a'/y backbone cleavages and ECD characteristic S-S and S-C bond cleavages were observed. We propose that, although in the oxytocin-transition metal ion complexes the metal ions serve as the main initial capture site, the captured electron is transferred to other sites in the complex to form a hydrogen radical, which drives the subsequent typical ECD fragmentations. The complex of oxytocin with Cu2+ displayed noticeably different ECD behavior. The fragment ions were similar to fragment ions typically observed with low-energy collision induced dissociation (CID). We propose that the electrons captured by the oxytocin-Cu2+ complex might be favorably involved in reducing the Cu2+ metal ion to Cu+. Subsequent energy redistribution would explain the observed low-energy CID-type fragmentations. Electron capture resulted also in quite different specific cleavage sites for the complexes of oxytocin with Ni2+, Co2+ and Zn2+. This is an indication for structural differences in these complexes possibly linked to their significantly different biological effects on oxytocin-receptor binding, and suggests that ECD may be used to study subtle structural differences in transition metal ion-peptide complexes.

Surface modification of EPDM rubber by plasma treatment.

PubMed

Grythe, Kai Frode; Hansen, Finn Knut

2006-07-04

The effect of argon, oxygen, and nitrogen plasma treatment of solvent cast EPDM rubber films has been investigated by means of atomic force microscopy (AFM), X-ray photoelectron spectroscopy (XPS), and surface energy measurements. Plasma treatment leads to changes in the surface energy from 25 to 70 mN/m. Treatment conditions influenced both the changes in surface energy and the stability, and it became more difficult to obtain good contact angle measurements after longer (> ca. 4 min) treatment times, probably because of an increasingly uneven surface structure. XPS analyses revealed that up to 20 at. % oxygen can be easily incorporated and that variations of approximately 5% can be controlled by the plasma conditions. Oxygen was mainly found in hydroxyl groups, but also as carbonyl and carboxyl. XPS analyses showed more stable surfaces than expected from contact angles, probably because XPS analysis is less surface sensitive than contact angle measurements. AFM measurements revealed different surface structures with the three gases. The surface roughness increased generally with treatment time, and dramatic changes could be observed at longer times. At short times, surface energy changes were much faster than the changes in surface structure, showing that plasma treatment conditions can be utilized to tailor both surface energies and surface structure of EPDM rubber.

Track Structure and the Biological Effectiveness of Accelerated Particles for the Induction of Chromosome Damage

NASA Technical Reports Server (NTRS)

George, K.; Hada, M.; Chappell, L.; Cucinotta, F. A.

2011-01-01

Track structure models predict that at a fixed value of LET, particles with lower charge number, Z will have a higher biological effectiveness compared to particles with a higher Z. In this report we investigated how track structure effects induction of chromosomal aberration in human cells. Human lymphocytes were irradiated in vitro with various energies of accelerated iron, silicon, neon, or titanium ions and chromosome damage was assessed in using three color FISH chromosome painting in chemically induced PCC samples collected a first cell division post irradiation. The LET values for these ions ranged from 30 to195 keV/micron. Of the particles studied, Neon ions have the highest biological effectiveness for induction of total chromosome damage, which is consistent with track structure model predictions. For complex-type exchanges 64 MeV/ u Neon and 450 MeV/u Iron were equally effective and induced the most complex damage. In addition we present data on chromosomes exchanges induced by six different energies of protons (5 MeV/u to 2.5 GeV/u). The linear dose response term was similar for all energies of protons suggesting that the effect of the higher LET at low proton energies is balanced by the production of nuclear secondaries from the high energy protons.

Secondary structure encodes a cooperative tertiary folding funnel in the Azoarcus ribozyme

PubMed Central

Mustoe, Anthony M.; Al-Hashimi, Hashim M.; Brooks, Charles L.

2016-01-01

A requirement for specific RNA folding is that the free-energy landscape discriminate against non-native folds. While tertiary interactions are critical for stabilizing the native fold, they are relatively non-specific, suggesting additional mechanisms contribute to tertiary folding specificity. In this study, we use coarse-grained molecular dynamics simulations to explore how secondary structure shapes the tertiary free-energy landscape of the Azoarcus ribozyme. We show that steric and connectivity constraints posed by secondary structure strongly limit the accessible conformational space of the ribozyme, and that these so-called topological constraints in turn pose strong free-energy penalties on forming different tertiary contacts. Notably, native A-minor and base-triple interactions form with low conformational free energy, while non-native tetraloop/tetraloop–receptor interactions are penalized by high conformational free energies. Topological constraints also give rise to strong cooperativity between distal tertiary interactions, quantitatively matching prior experimental measurements. The specificity of the folding landscape is further enhanced as tertiary contacts place additional constraints on the conformational space, progressively funneling the molecule to the native state. These results indicate that secondary structure assists the ribozyme in navigating the otherwise rugged tertiary folding landscape, and further emphasize topological constraints as a key force in RNA folding. PMID:26481360

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

Marana, Naiara L.; Albuquerque, Anderson R.; La Porta, Felipe A.

Periodic density functional theory calculations with the B3LYP hybrid functional and all-electron Gaussian basis set were performed to simulate the structural and electronic properties as well as the strain and formation energies of single-walled ZnO nanotubes (SWZnONTs) and Carbon nanotubes (SWCNTs) with different chiralities as functions of their diameters. For all SWZnONTs, the band gap, strain energy, and formation energy converge to ~4.5 eV, 0.0 eV/atom, and 0.40 eV/atom, respectively. This result suggests that the nanotubes are formed more easily from the surface than from the bulk. For SWCNTs, the strain energy is always positive, while the formation energy ismore » negative for armchair and zigzag nanotubes, therefore suggesting that these types of nanotubes can be preferentially formed from the bulk. The electronic properties of SWCNTs depend on the chirality; all armchair nanotubes are metallic, while zigzag and chiral nanotubes can be metallic or semiconducting, depending on the n and m vectors. - Graphical abstract: DFT/B3LYP were performed to simulate the structural and electronic properties as well as the strain and formation energies of SWZnONTs and SWCNTs with different chiralities as functions of their diameters. - Highlights: • The energies of SWZnONTs converge for chirality with diameters up 20 Å. • SWCNTs electronic properties depend on the chirality. • The properties of SWZnONTs are very similar to those of monolayer surface.« less

Inherent Structure versus Geometric Metric for State Space Discretization

PubMed Central

Liu, Hanzhong; Li, Minghai; Fan, Jue; Huo, Shuanghong

2016-01-01

Inherent structure (IS) and geometry-based clustering methods are commonly used for analyzing molecular dynamics trajectories. ISs are obtained by minimizing the sampled conformations into local minima on potential/effective energy surface. The conformations that are minimized into the same energy basin belong to one cluster. We investigate the influence of the applications of these two methods of trajectory decomposition on our understanding of the thermodynamics and kinetics of alanine tetrapeptide. We find that at the micro cluster level, the IS approach and root-mean-square deviation (RMSD) based clustering method give totally different results. Depending on the local features of energy landscape, the conformations with close RMSDs can be minimized into different minima, while the conformations with large RMSDs could be minimized into the same basin. However, the relaxation timescales calculated based on the transition matrices built from the micro clusters are similar. The discrepancy at the micro cluster level leads to different macro clusters. Although the dynamic models established through both clustering methods are validated approximately Markovian, the IS approach seems to give a meaningful state space discretization at the macro cluster level. PMID:26915811

Electronic properties of diphenyl-s-tetrazine and some related oligomers. An spectroscopic and theoretical study

NASA Astrophysics Data System (ADS)

Moral, Mónica; García, Gregorio; Peñas, Antonio; Garzón, Andrés; Granadino-Roldán, José M.; Melguizo, Manuel; Fernández-Gómez, Manuel

2012-10-01

This work presents a theoretical and spectroscopic study on the electronic and structural properties of the diphenyl-s-tetrazine molecule (Ph2Tz) and some oligomeric derivatives. Ph2Tz was synthesized through a variation of Pinner-type reaction which uses N-acetylcysteine as catalyst. Insight into the structure and electronic properties of the title compound was obtained through IR, Raman, UV-Vis spectra in different solvents, and theoretical calculations. Theoretical studies have been extended to different n-mers derivatives up to an ideal molecular wire through the oligomeric approximation, predicting this way electronic properties such as LUMO energy levels, electron affinity and reorganization energy in order to assess their possible applications in molecular electronics.

Energy Efficiency and Sustainability of Different Building Structures in Latvian Climate

NASA Astrophysics Data System (ADS)

Jakovičs, A.; Gendelis, S.; Bandeniece, L.

2015-11-01

Five experimental test buildings have been built in Riga, Latvia. They are identical except external walls for which different mainly regional building materials are used. Calculated U-values of the other walls, floor and ceiling are the same for each test building. Initial moisture influences the relative humidity of indoor air, which can be higher in the initial time period; as a result, heat transmittances are also very different and cause different heating/cooling energy consumption. Overheating risk in summer exists for test buildings with the smallest thermal inertia. Both summer and heating seasons have been analysed and differences between five test houses have been discussed in details.

Lessons learned from comparing molecular dynamics engines on the SAMPL5 dataset.

PubMed

Shirts, Michael R; Klein, Christoph; Swails, Jason M; Yin, Jian; Gilson, Michael K; Mobley, David L; Case, David A; Zhong, Ellen D

2017-01-01

We describe our efforts to prepare common starting structures and models for the SAMPL5 blind prediction challenge. We generated the starting input files and single configuration potential energies for the host-guest in the SAMPL5 blind prediction challenge for the GROMACS, AMBER, LAMMPS, DESMOND and CHARMM molecular simulation programs. All conversions were fully automated from the originally prepared AMBER input files using a combination of the ParmEd and InterMol conversion programs. We find that the energy calculations for all molecular dynamics engines for this molecular set agree to better than 0.1 % relative absolute energy for all energy components, and in most cases an order of magnitude better, when reasonable choices are made for different cutoff parameters. However, there are some surprising sources of statistically significant differences. Most importantly, different choices of Coulomb's constant between programs are one of the largest sources of discrepancies in energies. We discuss the measures required to get good agreement in the energies for equivalent starting configurations between the simulation programs, and the energy differences that occur when simulations are run with program-specific default simulation parameter values. Finally, we discuss what was required to automate this conversion and comparison.

Lessons learned from comparing molecular dynamics engines on the SAMPL5 dataset

PubMed Central

Shirts, Michael R.; Klein, Christoph; Swails, Jason M.; Yin, Jian; Gilson, Michael K.; Mobley, David L.; Case, David A.; Zhong, Ellen D.

2017-01-01

We describe our efforts to prepare common starting structures and models for the SAMPL5 blind prediction challenge. We generated the starting input files and single configuration potential energies for the host-guest in the SAMPL5 blind prediction challenge for the GROMACS, AMBER, LAMMPS, DESMOND and CHARMM molecular simulation programs. All conversions were fully automated from the originally prepared AMBER input files using a combination of the ParmEd and InterMol conversion programs. We find that the energy calculations for all molecular dynamics engines for this molecular set agree to a better than 0.1% relative absolute energy for all energy components, and in most cases an order of magnitude better, when reasonable choices are made for different cutoff parameters. However, there are some surprising sources of statistically significant differences. Most importantly, different choices of Coulomb’s constant between programs are one of the largest sources of discrepancies in energies. We discuss the measures required to get good agreement in the energies for equivalent starting configurations between the simulation programs, and the energy differences that occur when simulations are run with program-specific default simulation parameter values. Finally, we discuss what was required to automate this conversion and comparison. PMID:27787702

Lessons learned from comparing molecular dynamics engines on the SAMPL5 dataset

NASA Astrophysics Data System (ADS)

Shirts, Michael R.; Klein, Christoph; Swails, Jason M.; Yin, Jian; Gilson, Michael K.; Mobley, David L.; Case, David A.; Zhong, Ellen D.

2017-01-01

We describe our efforts to prepare common starting structures and models for the SAMPL5 blind prediction challenge. We generated the starting input files and single configuration potential energies for the host-guest in the SAMPL5 blind prediction challenge for the GROMACS, AMBER, LAMMPS, DESMOND and CHARMM molecular simulation programs. All conversions were fully automated from the originally prepared AMBER input files using a combination of the ParmEd and InterMol conversion programs. We find that the energy calculations for all molecular dynamics engines for this molecular set agree to better than 0.1 % relative absolute energy for all energy components, and in most cases an order of magnitude better, when reasonable choices are made for different cutoff parameters. However, there are some surprising sources of statistically significant differences. Most importantly, different choices of Coulomb's constant between programs are one of the largest sources of discrepancies in energies. We discuss the measures required to get good agreement in the energies for equivalent starting configurations between the simulation programs, and the energy differences that occur when simulations are run with program-specific default simulation parameter values. Finally, we discuss what was required to automate this conversion and comparison.

Structural morphology of crystals with the barite (BaSO 4) structure: A revision and extension

NASA Astrophysics Data System (ADS)

Hartman, P.; Strom, C. S.

1989-09-01

The structural morphology of crystals with the barite (BaSO 4) structure (sulphates, chromates, perchlorates, permanganates and tetrafluoroborates) has been determined with the use of computer programs. Uniquely defined F forms are {002}, {210}, {211}, {020} and {201}. Two different F slices were found for {101} and {200}, 33 for {011}. Attachment energies and specific surface energies have been calculated for an electrostatic point charge model as a function of the charge distribution in the anion. On this basis it is concluded that {101} behaves as an F form, {200} as an S form and {011} as a K form. The theoretical growth form shows {210}, {101} and {002} as main forms. A comparison is made with habits of natural and synthetic crystals. Experiments on KCIO 4 show that {011} appears at high supersaturations (>38; ;20%). It is shown that a broken bond model provides relative attachment energies that are higher by a factor of about three.

Efficient Structure Resonance Energy Transfer from Microwaves to Confined Acoustic Vibrations in Viruses

PubMed Central

Yang, Szu-Chi; Lin, Huan-Chun; Liu, Tzu-Ming; Lu, Jen-Tang; Hung, Wan-Ting; Huang, Yu-Ru; Tsai, Yi-Chun; Kao, Chuan-Liang; Chen, Shih-Yuan; Sun, Chi-Kuang

2015-01-01

Virus is known to resonate in the confined-acoustic dipolar mode with microwave of the same frequency. However this effect was not considered in previous virus-microwave interaction studies and microwave-based virus epidemic prevention. Here we show that this structure-resonant energy transfer effect from microwaves to virus can be efficient enough so that airborne virus was inactivated with reasonable microwave power density safe for the open public. We demonstrate this effect by measuring the residual viral infectivity of influenza A virus after illuminating microwaves with different frequencies and powers. We also established a theoretical model to estimate the microwaves power threshold for virus inactivation and good agreement with experiments was obtained. Such structure-resonant energy transfer induced inactivation is mainly through physically fracturing the virus structure, which was confirmed by real-time reverse transcription polymerase chain reaction. These results provide a pathway toward establishing a new epidemic prevention strategy in open public for airborne virus. PMID:26647655

Efficient Structure Resonance Energy Transfer from Microwaves to Confined Acoustic Vibrations in Viruses.

PubMed

Yang, Szu-Chi; Lin, Huan-Chun; Liu, Tzu-Ming; Lu, Jen-Tang; Hung, Wan-Ting; Huang, Yu-Ru; Tsai, Yi-Chun; Kao, Chuan-Liang; Chen, Shih-Yuan; Sun, Chi-Kuang

2015-12-09

Virus is known to resonate in the confined-acoustic dipolar mode with microwave of the same frequency. However this effect was not considered in previous virus-microwave interaction studies and microwave-based virus epidemic prevention. Here we show that this structure-resonant energy transfer effect from microwaves to virus can be efficient enough so that airborne virus was inactivated with reasonable microwave power density safe for the open public. We demonstrate this effect by measuring the residual viral infectivity of influenza A virus after illuminating microwaves with different frequencies and powers. We also established a theoretical model to estimate the microwaves power threshold for virus inactivation and good agreement with experiments was obtained. Such structure-resonant energy transfer induced inactivation is mainly through physically fracturing the virus structure, which was confirmed by real-time reverse transcription polymerase chain reaction. These results provide a pathway toward establishing a new epidemic prevention strategy in open public for airborne virus.

Interaction of water with (silico)aluminophosphate zeotypes: a comparative investigation using dispersion-corrected DFT.

PubMed

Fischer, Michael

2016-06-21

Porous aluminophosphates (AlPOs) and silicoaluminophosphates (SAPOs) with zeolite-like structures have received considerable attention as potential adsorbents for heat transformation applications using water adsorption/desorption cycles. Since a detailed experimental characterisation of the water adsorption properties has only been performed for some of these materials, such as AlPO-18 (AEI topology) and SAPO-34 (CHA topology), more systematic insights regarding the influence of the pore topology and (for SAPOs) the arrangement of the framework protons on the affinity towards water are lacking. To study the relationships between structure and properties in more detail, the interaction of water with six structurally different AlPOs (with AEI, AFX, CHA, ERI, GIS, RHO topologies) and their SAPO analogues was investigated using dispersion-corrected density-functional theory (DFT-D) calculations. Different possible locations of silicon atoms and charge-balancing protons were considered for the SAPO systems. The calculations for SAPOs at low water loadings (one H2O molecule per framework proton) revealed that the interaction energies exhibit a considerable variation, ranging from -75 to -100 kJ mol(-1) (per water molecule). The differences in interaction energy were rationalised with the different structural environment of the framework protons at which the water molecules are adsorbed. At high water uptakes (near saturation), interaction energies in the range of -65 kJ mol(-1) were obtained for all AlPOs, and there was no evidence for a marked influence of pore size and/or topology on the interaction strength. The interaction of water with SAPOs was found to be approximately 5 kJ mol(-1) stronger than for AlPOs due to an increased contribution of electrostatic interactions. An analysis of the structural changes upon water adsorption revealed striking differences between the distinct topologies, with the materials with GIS and RHO topologies being distorted much more drastically than the systems based on double six-ring (d6r) units. Moreover, the direct coordination of water molecules to framework aluminium atoms occurs more frequently in these materials, an observation that points towards a reduced structural stability upon hydration.

Crash energy management on the base of Movable cellular automata method

NASA Astrophysics Data System (ADS)

Psakhie, Serguei; Dmitriev, Andrei; Shilko, Evgueni; Tatarintsev, Evgueni; Korostelev, Serguei

2001-06-01

One of the main problems of materials science is increasing of structure's viability under dynamic loading. In general, a solution is the management of transformation of the energy of loading to the energy of destroying of the least important parts and details of the structure. It has to be noted that similar problem also exists in materials science, since a majority of modern materials are heterogeneous and have a complex internal structure. To optimize this structure for working under dynamic loading it is necessary to take into account the redistribution of elastic energy including phase transformation, generation and accumulation of micro-damages, etc. As far as real experiments on destroying the complex objects are sufficiently expensive and getting of detailed information is often associates with essential difficulties, the methods of computer modeling are used in solving the similar problems. As a rule, these are the methods of continuum mechanics. Although essential achievements have been obtained on the basis of these methods the continuum approach has several limitations, connected first of all with the possibility of description of generation of damages, formation and development of cracks and mass mixing effects. These problems may be solved on the basis of the Movable Cellular Automata (MCA) method, which has been successfully used for modeling fracture of the different material and structures In the paper behavior and peculiarities of failure of complex structures and materials under dynamic loading are studied on the basis of computer modeling. The results shown that sometimes even small changes of the internal structure leads to the significant increasing of the viability of the complex structures and materials. It is due to the elastic energy flux change over during the dynamical loading. This effect may be explained by the fact that elastic energy fluxes define the current stress concentration. Namely, because the area of inclusions are subjected by the largest displacement and due to less Young modulus of inclusions the loading pulses are transferred towards the other parts of the sample. This leads to "blurring" of the stress concentrators and conservation of wholeness of the structure. In its turn, this leads to essential raising up of threshold value of "injected" energy, i.e. the energy absorbed by the structure before loss of its carrying capacity. Practically, elastic energy "circulates" in the structure until a stress concentrator appears, which power will be sufficient for forming a macro-cracks. The results demonstrate a possibility of managing the fracture process under dynamic loading and raising viability of structures and heterogeneous materials by changing their internal structure, geometry, so by entering the specific inclusions.

An Integrated, Layered-Spinel Composite Cathode for Energy Storage Applications

NASA Technical Reports Server (NTRS)

Hagh, Nader; Skandan, Ganesh

2012-01-01

At low operating temperatures, commercially available electrode materials for lithium-ion batteries do not fully meet the energy and power requirements for NASA fs exploration activities. The composite cathode under development is projected to provide the required energy and power densities at low temperatures and its usage will considerably reduce the overall volume and weight of the battery pack. The newly developed composite electrode material can provide superior electrochemical performance relative to a commercially available lithium cobalt system. One advantage of using a composite cathode is its higher energy density, which can lead to smaller and lighter battery packs. In the current program, different series of layered-spinel composite materials with at least two different systems in an integrated structure were synthesized, and the volumetric and gravimetric energy densities were evaluated. In an integrated network of a composite electrode, the effect of the combined structures is to enhance the capacity and power capabilities of the material to levels greater than what is possible in current state-of-the-art cathode systems. The main objective of the current program is to implement a novel cathode material that meets NASA fs low temperature energy density requirements. An important feature of the composite cathode is that it has at least two components (e.g., layered and spinel) that are structurally integrated. The layered material by itself is electrochemically inactive; however, upon structural integration with a spinel material, the layered material can be electrochemically activated, thereby delivering a large amount of energy with stable cycling. A key aspect of the innovation has been the development of a scalable process to produce submicronand micron-scale particles of these composite materials. An additional advantage of using such a composite electrode material is its low irreversible loss (.5%), which is primarily due to the unique activation of the composite. High columbic efficiency (greater than 99%) upon cycling may indicate the formation of a stable SEI (solid-electrolyte interface) layer, which can contribute to long cycle life. The innovation in the current program, when further developed, will enable the system to maintain high energy and power densities at low temperatures, improve efficiency, and further stabilize and enhance the safety of the cell.

Revised Atomistic Models of the Crystal Structure of C-S-H with high C/S Ratio

NASA Astrophysics Data System (ADS)

Kovačević, Goran; Nicoleau, Luc; Nonat, André; Veryazov, Valera

2016-09-01

The atomic structure of calcium-silicate-hydrate (C1.67-S-Hx) has been studied. Atomistic C-S-H models suggested in our previous study have been revised in order to perform a direct comparison of energetic stability of the different structures. An extensive set of periodic structures of C-S-H with variation of water content was created, and then optimized using molecular dynamics with reactive force field ReaxFF and quantum chemical semiempirical method PM6. All models show organization of water molecules inside the structure of C-S-H. The new geometries of C-S-H, reported in this paper, show lower relative energy with respect to the geometries from the original definition of C-S-H models. Model that corresponds to calcium enriched tobermorite structure has the lowest relative energy and the density closest to the experimental values.

Understanding the sensitivity of nucleation free energies: The role of supersaturation and temperature

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

Keasler, Samuel J., E-mail: samuel.keasler@vcsu.edu; Department of Science, Valley City State University, 101 College Street SW, Valley City, North Dakota 58072; Siepmann, J. Ilja

2015-10-28

Simulations are used to investigate the vapor-to-liquid nucleation of water for several different force fields at various sets of physical conditions. The nucleation free energy barrier is found to be extremely sensitive to the force field at the same absolute conditions. However, when the results are compared at the same supersaturation and reduced temperature or the same metastability parameter and reduced temperature, then the differences in the nucleation free energies of the different models are dramatically reduced. This finding suggests that comparisons of experimental data and computational predictions are most meaningful at the same relative conditions and emphasizes the importancemore » of knowing the phase diagram of a given computational model, but such information is usually not available for models where the interaction energy is determined directly from electronic structure calculations.« less

Mechanism of heterogeneous catalytic oxidation of organic compounds to carboxylic acids

NASA Astrophysics Data System (ADS)

Andrushkevich, T. V.; Chesalov, Yu A.

2018-06-01

The results of studies on the mechanism of heterogeneous catalytic oxidation of organic compounds of different chemical structure to carboxylic acids are analyzed and generalized. The concept developed by Academician G.K.Boreskov, according to which the direction of the reaction is governed by the structure and bond energy of surface intermediates, was confirmed taking the title processes as examples. Quantitative criteria of the bond energies of surface compounds of oxidizable reactants, reaction products and oxygen that determine the selective course of the reaction are presented. The bibliography includes 195 references.

Computer simulation of formation and decomposition of Au13 nanoparticles

NASA Astrophysics Data System (ADS)

Stishenko, P.; Svalova, A.

2017-08-01

To study the Ostwald ripening process of Au13 nanoparticles a two-scale model is constructed: analytical approximation of average nanoparticle energy as function of nanoparticle size and structural motive, and the Monte Carlo model of 1000 particles ensemble. Simulation results show different behavior of particles of different structural motives. The change of the distributions of atom coordination numbers during the Ostwald ripening process was observed. The nanoparticles of the equal size and shape with the face-centered cubic structure of the largest sizes appeared to be the most stable.

Ultrafast Dynamics of 1,3-Cyclohexadiene in Highly Excited States

DOE PAGES

Bühler, Christine C.; Minitti, Michael P.; Deb, Sanghamitra; ...

2011-01-01

The ultrafast dynamics of 1,3-cyclohexadiene has been investigated via structurally sensitive Rydberg electron binding energies and shown to differ upon excitation to the 1B state and the 3p Rydberg state. Excitation of the molecule with 4.63 eV photons into the ultrashort-lived 1B state yields the well-known ring opening to 1,3,5-hexatriene, while a 5.99 eV photon lifts the molecule directly into the 3p-Rydberg state. Excitation to 3p does not induce ring opening. In both experiments, time-dependent shifts of the Rydberg electron binding energy reflect the structural dynamics of the molecular core. Structural distortions associated with 3p-excitation cause a dynamical shift in the -more » and -binding energies by 10 and 26 meV/ps, respectively, whereas after excitation into 1B, more severe structural transformations along the ring-opening coordinate produce shifts at a rate of 40 to 60 meV/ps. The experiment validates photoionization-photoelectron spectroscopy via Rydberg states as a powerful technique to observe structural dynamics of polyatomic molecules.« less

Growth and structural evolution of Sn on Ag(001): Epitaxial monolayer to thick alloy film

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

Chakraborty, Suvankar; Menon, Krishnakumar S. R., E-mail: krishna.menon@saha.ac.in

The growth and structure of Sn on Ag(001), from submonolayer to thick film coverages at room temperature, are studied using low energy electron diffraction, x-ray photoemission spectroscopy and angle-resolved photoemission spectroscopy (ARPES) techniques. The authors observe different growth modes for submonolayer Sn coverages and for higher Sn coverages. Systematic surface structural evolution, consistent with the substitution of surface Ag atoms by Sn atoms, is observed for submonolayer Sn coverages while an ordered Ag-Sn bulk alloy film is formed for higher Sn coverages with an Ag overlayer. For monolayer coverage of Sn, a pseudomorphic growth of a Sn layer without alloyingmore » is determined. ARPES results also confirm the presence of an ordered Ag overlayer on the bulk Ag-Sn alloy film, suggesting the formation of an Ag/Ag{sub 3}Sn/Ag(001) sandwich structure at the surface for higher Sn coverages. The present results illustrate the complex interplay of atomic mobilities, surface free-energies, and alloy formation energies in determining the growth and structural properties of the system.« less

T- and Y-splitters based on an Au/SiO2 nanoring chain at an optical communication band.

PubMed

Ahmadivand, A; Golmohammadi, S; Rostami, A

2012-05-20

In this paper, we have utilized Au nanoring chains in an SiO2 host to design certain T-and Y-structures, and expanded it to transport and split the electromagnetic energy in integrated nanophotonic devices operating at an optical communication band (λ≈1550 nm). We compared two structures and tried to choose the best one, with lower losses and higher efficiency at the output branches, in order to split and transport the optical energy. Comparing the different types of nanoparticles corroborates that nanorings have an extra degree of tunability in their geometrical components. Meanwhile, nanorings show strong confinement in near-field coupling, less extinction coefficient, and also lower scattering into the far field during energy transportation at the C-band spectrum. Due to the nanoring's particular properties, transportation losses would be lower than in other nanoparticle-based structures like nanospheres, nanorods, and nanodisks. We demonstrate that Au nanorings surrounded by an SiO2 host yield suitable conditions to excite surface Plasmons inside the metal. Comparison between Y-and T-splitters shows that the Y-splitter is a more suitable alternative than the T-splitter, with higher transmission efficiency and lower losses. In the Y-structure, the power ratio (time-averaged power across the surface) is 24.7%, and electromagnetic energy transportation takes place at group velocities in the vicinity of 30% of the velocity of light; transmission losses are γT=3 dB/655 nm and γT=3 dB/443 nm. In this work, we have applied the finite-difference time-domain method (FDTD) to simulate and indicate the properties of structures.

Atmospheric Energy Deposition Modeling and Inference for Varied Meteoroid Structures

NASA Technical Reports Server (NTRS)

Wheeler, Lorien; Mathias, Donovan; Stokan, Edward; Brown, Peter

2018-01-01

Asteroids populations are highly diverse, ranging from coherent monoliths to loosely-bound rubble piles with a broad range of material and compositional properties. These different structures and properties could significantly affect how an asteroid breaks up and deposits energy in the atmosphere, and how much ground damage may occur from resulting blast waves. We have previously developed a fragment-cloud model (FCM) for assessing the atmospheric breakup and energy deposition of asteroids striking Earth. The approach represents ranges of breakup characteristics by combining progressive fragmentation with releases of variable fractions of debris and larger discrete fragments. In this work, we have extended the FCM to also represent asteroids with varied initial structures, such as rubble piles or fractured bodies. We have used the extended FCM to model the Chelyabinsk, Benesov, Kosice, and Tagish Lake meteors, and have obtained excellent matches to energy deposition profiles derived from their light curves. These matches provide validation for the FCM approach, help guide further model refinements, and enable inferences about pre-entry structure and breakup behavior. Results highlight differences in the amount of small debris vs. discrete fragments in matching the various flare characteristics of each meteor. The Chelyabinsk flares were best represented using relatively high debris fractions, while Kosice and Benesov cases were more notably driven by their discrete fragmentation characteristics, perhaps indicating more cohesive initial structures. Tagish Lake exhibited a combination of these characteristics, with lower-debris fragmentation at high altitudes followed by sudden disintegration into small debris in the lower flares. Results from all cases also suggest that lower ablation coefficients and debris spread rates may be more appropriate for the way in which debris clouds are represented in FCM, offering an avenue for future model refinement.

Assessment of SIP Buildings for Sustainable Development in Rural China Using AHP-Grey Correlation Analysis

PubMed Central

Wang, Hailing; Shi, Chunming; Li, Yi

2017-01-01

Traditional rural residential construction has the problems of high energy consumption and severe pollution. In general, with sustainable development in the construction industry, rural residential construction should be aimed towards low energy consumption and low carbon emissions. To help achieve this objective, in this paper, we evaluated four different possible building structures using AHP-Grey Correlation Analysis, which consists of the Analytic Hierarchy Process (AHP) and the Grey Correlation Analysis. The four structures included the traditional and currently widely used brick and concrete structure, as well as structure insulated panels (SIPs). Comparing the performances of economic benefit and carbon emission, the conclusion that SIPs have the best overall performance can be obtained, providing a reference to help builders choose the most appropriate building structure in rural China. PMID:29068420

Energy Transformations of Soil Organic Matter in a Changing World

NASA Astrophysics Data System (ADS)

Herrmann, A. M.; Coucheney, E.; Grice, S. M.; Ritz, K.; Harris, J.

2011-12-01

The role of soils in governing the terrestrial carbon balance is acknowledged as being important but remains poorly understood within the context of climate change. Soils exchange energy with their surroundings and are therefore open systems thermodynamically, but little is known how energy transformations of decomposition processes are affected by temperature. Soil organic matter and the soil biomass can be conceptualised as analogous to the 'fuel' and 'biological engine' of the earth, respectively, and are pivotal in driving the belowground carbon cycle. Thermodynamic principles of soil organic matter decomposition were evaluated by means of isothermal microcalorimetry (TAM Air, TA Instruments, Sollentuna Sweden: (i) Mineral forest soils from the Flakaliden long-term nitrogen fertilisation experiment (Sweden) were amended with a range of different substrates representing structurally simple to complex, ecologically pertinent organic matter and heat signatures were determined at temperatures between 5 and 25°C. (ii) Thermodynamic and resource-use efficiencies of the biomass were determined in arable soils which received contrasting long-term management regimes with respect to organic matter and nitrogen since 1956. The work showed that (i) structurally labile components have higher activation energy and temperature dependence than structurally more complex organic components. This is, however, in contrast to the thermodynamic argument which suggests the opposite that reactions metabolising structurally complex, aromatic components have higher temperature dependence than reactions metabolising structurally more labile components. (ii) Microbial communities exposed to long-term stress by heavy metal and low pH were less thermodynamic efficient and showed a decrease in resource-use efficiency in comparison with conventional input regimes. Differences in efficiencies were mirrored in both the phenotypic and functional profiles of the communities. We will present our findings illustrating the capacity of isothermal microcalorimetry to evaluate temperature dependencies of soil organic matter decomposition, associated energy transformations and thermodynamic principles in soil ecosystems.

Effects of chemical fuel composition on energy generation from thermopower waves

NASA Astrophysics Data System (ADS)

Yeo, Taehan; Hwang, Hayoung; Jeong, Dong-Cheol; Lee, Kang Yeol; Hong, Jongsup; Song, Changsik; Choi, Wonjoon

2014-11-01

Thermopower waves, which occur during combustion within hybrid structures formed from nanomaterials and chemical fuels, result in a self-propagating thermal reaction and concomitantly generate electrical energy from the acceleration of charge carriers along the nanostructures. The hybrid structures for thermopower waves are composed of two primary components: the core thermoelectric material and the combustible fuel. So far, most studies have focused on investigating various nanomaterials for improving energy generation. Herein, we report that the composition of the chemical fuel used has a significant effect on the power generated by thermopower waves. Hybrid nanostructures consisting of mixtures of picric acid and picramide with sodium azide were synthesized and used to generate thermopower waves. A maximum voltage of ˜2 V and an average peak specific power as high as 15 kW kg-1 were obtained using the picric acid/sodium azide/multiwalled carbon nanotubes (MWCNTs) array composite. The average reaction velocity and the output voltage in the case of the picric acid/sodium azide were 25 cm s-1 and 157 mV, while they were 2 cm s-1 and 3 mV, in the case of the picramide/sodium azide. These marked differences are attributable to the chemical and structural differences of the mixtures. Mixing picric acid and sodium azide in deionized water resulted in the formation of 2,4,6-trinitro sodium phenoxide and hydrogen azide (H-N3), owing to the exchange of H+ and Na+ ions, as well as the formation of fiber-like structures, because of benzene π stacking. The negative enthalpy of formation of the new compounds and the fiber-like structures accelerate the reaction and increase the output voltage. Elucidating the effects of the composition of the chemical fuel used in the hybrid nanostructures will allow for the control of the combustion process and help optimize the energy generated from thermopower waves, furthering the development of thermopower waves as an energy source.

Understanding the structure and structural degradation mechanisms in high-voltage lithium-ion battery cathode oxides. A review of materials diagnostics

DOE PAGES

Mohanty, Debasish; Li, Jianlin; Nagpure, Shrikant C; ...

2015-12-21

Materials diagnostic techniques are the principal tools used in the development of low-cost, high-performance electrodes for next-generation lithium-based energy storage technologies. Also, this review highlights the importance of materials diagnostic techniques in unraveling the structure and the structural degradation mechanisms in high-voltage, high-capacity oxides that have the potential to be implemented in high-energy-density lithium-ion batteries for transportation that can use renewable energy and is less-polluting than today. The rise in CO 2 concentration in the earth’s atmosphere due to the use of petroleum products in vehicles and the dramatic increase in the cost of gasoline demand the replacement of currentmore » internal combustion engines in our vehicles with environmentally friendly, carbon free systems. Therefore, vehicles powered fully/partially by electricity are being introduced into today’s transportation fleet. As power requirements in all-electric vehicles become more demanding, lithium-ion battery (LiB) technology is now the potential candidate to provide higher energy density. Moreover, discovery of layered high-voltage lithium-manganese–rich (HV-LMR) oxides has provided a new direction toward developing high-energy-density LiBs because of their ability to deliver high capacity (~250 mA h/g) and to be operated at high operating voltage (~4.7 V). Unfortunately, practical use of HV-LMR electrodes is not viable because of structural changes in the host oxide during operation that can lead to fundamental and practical issues. This article provides the current understanding on the structure and structural degradation pathways in HV-LMR oxides, and manifests the importance of different materials diagnostic tools to unraveling the key mechanism(s). Furthermore, the fundamental insights reported, might become the tools to manipulate the chemical and/or structural aspects of HV-LMR oxides for low cost, high-energy-density LiB applications.« less

WE-EF-207-07: Dual Energy CT with One Full Scan and a Second Sparse-View Scan Using Structure Preserving Iterative Reconstruction (SPIR)

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

Wang, T; Zhu, L

Purpose: Conventional dual energy CT (DECT) reconstructs CT and basis material images from two full-size projection datasets with different energy spectra. To relax the data requirement, we propose an iterative DECT reconstruction algorithm using one full scan and a second sparse-view scan by utilizing redundant structural information of the same object acquired at two different energies. Methods: We first reconstruct a full-scan CT image using filtered-backprojection (FBP) algorithm. The material similarities of each pixel with other pixels are calculated by an exponential function about pixel value differences. We assume that the material similarities of pixels remains in the second CTmore » scan, although pixel values may vary. An iterative method is designed to reconstruct the second CT image from reduced projections. Under the data fidelity constraint, the algorithm minimizes the L2 norm of the difference between pixel value and its estimation, which is the average of other pixel values weighted by their similarities. The proposed algorithm, referred to as structure preserving iterative reconstruction (SPIR), is evaluated on physical phantoms. Results: On the Catphan600 phantom, SPIR-based DECT method with a second 10-view scan reduces the noise standard deviation of a full-scan FBP CT reconstruction by a factor of 4 with well-maintained spatial resolution, while iterative reconstruction using total-variation regularization (TVR) degrades the spatial resolution at the same noise level. The proposed method achieves less than 1% measurement difference on electron density map compared with the conventional two-full-scan DECT. On an anthropomorphic pediatric phantom, our method successfully reconstructs the complicated vertebra structures and decomposes bone and soft tissue. Conclusion: We develop an effective method to reduce the number of views and therefore data acquisition in DECT. We show that SPIR-based DECT using one full scan and a second 10-view scan can provide high-quality DECT images and accurate electron density maps as conventional two-full-scan DECT.« less

Distributions of experimental protein structures on coarse-grained free energy landscapes

PubMed Central

Liu, Jie; Jernigan, Robert L.

2015-01-01

Predicting conformational changes of proteins is needed in order to fully comprehend functional mechanisms. With the large number of available structures in sets of related proteins, it is now possible to directly visualize the clusters of conformations and their conformational transitions through the use of principal component analysis. The most striking observation about the distributions of the structures along the principal components is their highly non-uniform distributions. In this work, we use principal component analysis of experimental structures of 50 diverse proteins to extract the most important directions of their motions, sample structures along these directions, and estimate their free energy landscapes by combining knowledge-based potentials and entropy computed from elastic network models. When these resulting motions are visualized upon their coarse-grained free energy landscapes, the basis for conformational pathways becomes readily apparent. Using three well-studied proteins, T4 lysozyme, serum albumin, and sarco-endoplasmic reticular Ca2+ adenosine triphosphatase (SERCA), as examples, we show that such free energy landscapes of conformational changes provide meaningful insights into the functional dynamics and suggest transition pathways between different conformational states. As a further example, we also show that Monte Carlo simulations on the coarse-grained landscape of HIV-1 protease can directly yield pathways for force-driven conformational changes. PMID:26723638

Comparison of electronic structure between monolayer silicenes on Ag (111)

NASA Astrophysics Data System (ADS)

Chun-Liang, Lin; Ryuichi, Arafune; Maki, Kawai; Noriaki, Takagi

2015-08-01

The electronic structures of monolayer silicenes (4 × 4 and ) grown on Ag (111) surface are studied by scanning tunneling spectroscopy (STS) and density functional theory (DFT) calculations. While both phases have similar electronic structures around the Fermi level, significant differences are observed in the higher energy unoccupied states. The DFT calculations show that the contributions of Si 3pz orbitals to the unoccupied states are different because of their different buckled configurations. Project supported by the Ministry of Education, Culture, Sports, Science and Technology (MEXT) through Grants-in-Aid for Scientific Research (Grant Nos. 24241040 and 25110008) and the World Premier International Research Center Initiative (WPI), MEXT, Japan.

Surface wave energy absorption by a partially submerged bio-inspired canopy.

PubMed

Nové-Josserand, C; Castro Hebrero, F; Petit, L-M; Megill, W M; Godoy-Diana, R; Thiria, B

2018-03-27

Aquatic plants are known to protect coastlines and riverbeds from erosion by damping waves and fluid flow. These flexible structures absorb the fluid-borne energy of an incoming fluid by deforming mechanically. In this paper we focus on the mechanisms involved in these fluid-elasticity interactions, as an efficient energy harvesting system, using an experimental canopy model in a wave tank. We study an array of partially-submerged flexible structures that are subjected to the action of a surface wave field, investigating in particular the role of spacing between the elements of the array on the ability of our system to absorb energy from the flow. The energy absorption potential of the canopy model is examined using global wave height measurements for the wave field and local measurements of the elastic energy based on the kinematics of each element of the canopy. We study different canopy arrays and show in particular that flexibility improves wave damping by around 40%, for which half is potentially harvestable.

Non-resonant energy harvester with elastic constraints for low rotating frequencies

NASA Astrophysics Data System (ADS)

Machado, Sebastián P.; Febbo, Mariano; Gatti, Claudio D.; Ramirez, José M.

2017-11-01

This paper presents a non-resonant piezoelectric energy harvester (PEH) which is designed to capture energy from low frequency rotational vibration. The proposed device works out of the plane of rotation where the motion of a mass-spring system is transferred to a piezoelectric layer with the intention to generate energy to power wireless structural monitoring systems or sensors. The mechanical structure is formed by two beams with rigid and elastic boundary conditions at the clamped end. On the free boundaries, heavy masses connected by a spring are placed in order to increase voltage generation and diminish the natural frequency. A mathematical framework and the equations governing the energy-harvesting system are presented. Numerical simulations and experimental verifications are performed for different rotation speeds ranging from 0.7 to 2.5 Hz. An output power of 125 μW is obtained for maximum rotating frequency demonstrating that the proposed design can collect enough energy for the suggested application.

Prediction of Ras-effector interactions using position energy matrices.

PubMed

Kiel, Christina; Serrano, Luis

2007-09-01

One of the more challenging problems in biology is to determine the cellular protein interaction network. Progress has been made to predict protein-protein interactions based on structural information, assuming that structural similar proteins interact in a similar way. In a previous publication, we have determined a genome-wide Ras-effector interaction network based on homology models, with a high accuracy of predicting binding and non-binding domains. However, for a prediction on a genome-wide scale, homology modelling is a time-consuming process. Therefore, we here successfully developed a faster method using position energy matrices, where based on different Ras-effector X-ray template structures, all amino acids in the effector binding domain are sequentially mutated to all other amino acid residues and the effect on binding energy is calculated. Those pre-calculated matrices can then be used to score for binding any Ras or effector sequences. Based on position energy matrices, the sequences of putative Ras-binding domains can be scanned quickly to calculate an energy sum value. By calibrating energy sum values using quantitative experimental binding data, thresholds can be defined and thus non-binding domains can be excluded quickly. Sequences which have energy sum values above this threshold are considered to be potential binding domains, and could be further analysed using homology modelling. This prediction method could be applied to other protein families sharing conserved interaction types, in order to determine in a fast way large scale cellular protein interaction networks. Thus, it could have an important impact on future in silico structural genomics approaches, in particular with regard to increasing structural proteomics efforts, aiming to determine all possible domain folds and interaction types. All matrices are deposited in the ADAN database (http://adan-embl.ibmc.umh.es/). Supplementary data are available at Bioinformatics online.

Protein-ligand binding free energy estimation using molecular mechanics and continuum electrostatics. Application to HIV-1 protease inhibitors

NASA Astrophysics Data System (ADS)

Zoete, V.; Michielin, O.; Karplus, M.

2003-12-01

A method is proposed for the estimation of absolute binding free energy of interaction between proteins and ligands. Conformational sampling of the protein-ligand complex is performed by molecular dynamics (MD) in vacuo and the solvent effect is calculated a posteriori by solving the Poisson or the Poisson-Boltzmann equation for selected frames of the trajectory. The binding free energy is written as a linear combination of the buried surface upon complexation, SAS bur, the electrostatic interaction energy between the ligand and the protein, Eelec, and the difference of the solvation free energies of the complex and the isolated ligand and protein, ΔGsolv. The method uses the buried surface upon complexation to account for the non-polar contribution to the binding free energy because it is less sensitive to the details of the structure than the van der Waals interaction energy. The parameters of the method are developed for a training set of 16 HIV-1 protease-inhibitor complexes of known 3D structure. A correlation coefficient of 0.91 was obtained with an unsigned mean error of 0.8 kcal/mol. When applied to a set of 25 HIV-1 protease-inhibitor complexes of unknown 3D structures, the method provides a satisfactory correlation between the calculated binding free energy and the experimental pIC 50 without reparametrization.

Magnitude Differences in Bioactive Compounds, Chemical Functional Groups, Fatty Acid Profiles, Nutrient Degradation and Digestion, Molecular Structure, and Metabolic Characteristics of Protein in Newly Developed Yellow-Seeded and Black-Seeded Canola Lines.

PubMed

Theodoridou, Katerina; Zhang, Xuewei; Vail, Sally; Yu, Peiqiang

2015-06-10

Recently, new lines of yellow-seeded (CS-Y) and black-seeded canola (CS-B) have been developed with chemical and structural alteration through modern breeding technology. However, no systematic study was found on the bioactive compounds, chemical functional groups, fatty acid profiles, inherent structure, nutrient degradation and absorption, or metabolic characteristics between the newly developed yellow- and black-seeded canola lines. This study aimed to systematically characterize chemical, structural, and nutritional features in these canola lines. The parameters accessed include bioactive compounds and antinutrition factors, chemical functional groups, detailed chemical and nutrient profiles, energy value, nutrient fractions, protein structure, degradation kinetics, intestinal digestion, true intestinal protein supply, and feed milk value. The results showed that the CS-Y line was lower (P ≤ 0.05) in neutral detergent fiber (122 vs 154 g/kg DM), acid detergent fiber (61 vs 99 g/kg DM), lignin (58 vs 77 g/kg DM), nonprotein nitrogen (56 vs 68 g/kg DM), and acid detergent insoluble protein (11 vs 35 g/kg DM) than the CS-B line. There was no difference in fatty acid profiles except C20:1 eicosenoic acid content (omega-9) which was in lower in the CS-Y line (P < 0.05) compared to the CS-B line. The glucosinolate compounds differed (P < 0.05) in terms of 4-pentenyl, phenylethyl, 3-CH3-indolyl, and 3-butenyl glucosinolates (2.9 vs 1.0 μmol/g) between the CS-Y and CS-B lines. For bioactive compounds, total polyphenols tended to be different (6.3 vs 7.2 g/kg DM), but there were no differences in erucic acid and condensed tannins with averages of 0.3 and 3.1 g/kg DM, respectively. When protein was portioned into five subfractions, significant differences were found in PA, PB1 (65 vs 79 g/kg CP), PB2, and PC fractions (10 vs 33 g/kg CP), indicating protein degradation and supply to small intestine differed between two new lines. In terms of protein structure spectral profile, there were no significant differences in functional groups of amides I and II, α helix, and β-sheet structure as well as their ratio between the two new lines, indicating no difference in protein structure makeup and conformation between the two lines. In terms of energy values, there were significant differences in total digestible nutrient (TDN; 149 vs 133 g/kg DM), metabolizable energy (ME; 58 vs 52 MJ/kg DM), and net energy for lactation (NEL; 42 vs 37 MJ/kg DM) between CS-Y and CS-B lines. For in situ rumen degradation kinetics, the two lines differed in soluble fraction (S; 284 vs 341 g/kg CP), potential degradation fraction (D; 672 vs 590 g/kg CP), and effective degraded organic matter (EDOM; 710 vs 684 g/kg OM), but no difference in degradation rate. CS-Y had higher digestibility of rumen bypass protein in the intestine than CS-B (566 vs 446 g/kg of RUP, P < 0.05). Modeling nutrient supply results showed that microbial protein synthesis (MCP; 148 vs 171 g/kg DM) and rumen protein degraded balance (DPB; 108 vs 127 g/kg DM) were lower in the CS-Y line, but there were no differences in total truly digested protein in small intestine (DVE) and feed milk value (FMV) between the two lines. In conclusion, the new yellow line had different nutritional, chemical, and structural features compared to the black line. CS-Y provided better nutrient utilization and availability.

Gamma-ray energy buildup factor calculations and shielding effects of some Jordanian building structures

NASA Astrophysics Data System (ADS)

Sharaf, J. M.; Saleh, H.

2015-05-01

The shielding properties of three different construction styles, and building materials, commonly used in Jordan, were evaluated using parameters such as attenuation coefficients, equivalent atomic number, penetration depth and energy buildup factor. Geometric progression (GP) method was used to calculate gamma-ray energy buildup factors of limestone, concrete, bricks, cement plaster and air for the energy range 0.05-3 MeV, and penetration depths up to 40 mfp. It has been observed that among the examined building materials, limestone offers highest value for equivalent atomic number and linear attenuation coefficient and the lowest values for penetration depth and energy buildup factor. The obtained buildup factors were used as basic data to establish the total equivalent energy buildup factors for three different multilayer construction styles using an iterative method. The three styles were then compared in terms of fractional transmission of photons at different incident photon energies. It is concluded that, in case of any nuclear accident, large multistory buildings with five layers exterior walls, style A, could effectively attenuate radiation more than small dwellings of any construction style.

Offshore Energy Mapping for Northeast Atlantic and Mediterranean: MARINA PLATFORM project

NASA Astrophysics Data System (ADS)

Kallos, G.; Galanis, G.; Spyrou, C.; Kalogeri, C.; Adam, A.; Athanasiadis, P.

2012-04-01

Deep offshore ocean energy mapping requires detailed modeling of the wind, wave, tidal and ocean circulation estimations. It requires also detailed mapping of the associated extremes. An important issue in such work is the co-generation of energy (generation of wind, wave, tides, currents) in order to design platforms on an efficient way. For example wind and wave fields exhibit significant phase differences and therefore the produced energy from both sources together requires special analysis. The other two sources namely tides and currents have different temporal scales from the previous two. Another important issue is related to the estimation of the environmental frequencies in order to avoid structural problems. These are issues studied at the framework of the FP7 project MARINA PLATFORM. The main objective of the project is to develop deep water structures that can exploit the energy from wind, wave, tidal and ocean current energy sources. In particular, a primary goal will be the establishment of a set of equitable and transparent criteria for the evaluation of multi-purpose platforms for marine renewable energy. Using these criteria, a novel system set of design and optimisation tools will be produced addressing new platform design, component engineering, risk assessment, spatial planning, platform-related grid connection concepts, all focussed on system integration and reducing costs. The University of Athens group is in charge for estimation and mapping of wind, wave, tidal and ocean current resources, estimate available energy potential, map extreme event characteristics and provide any additional environmental parameter required.

Exploration of tetrahedral structures in silicate cathodes using a motif-network scheme

PubMed Central

Zhao, Xin; Wu, Shunqing; Lv, Xiaobao; Nguyen, Manh Cuong; Wang, Cai-Zhuang; Lin, Zijing; Zhu, Zi-Zhong; Ho, Kai-Ming

2015-01-01

Using a motif-network search scheme, we studied the tetrahedral structures of the dilithium/disodium transition metal orthosilicates A2MSiO4 with A = Li or Na and M = Mn, Fe or Co. In addition to finding all previously reported structures, we discovered many other different tetrahedral-network-based crystal structures which are highly degenerate in energy. These structures can be classified into structures with 1D, 2D and 3D M-Si-O frameworks. A clear trend of the structural preference in different systems was revealed and possible indicators that affect the structure stabilities were introduced. For the case of Na systems which have been much less investigated in the literature relative to the Li systems, we predicted their ground state structures and found evidence for the existence of new structural motifs. PMID:26497381

Study of heavy metals and other elements in macrophyte algae using energy-dispersive X-ray fluorescence

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

Carvalho, M.L.; Amorim, P.; Marques, M.I.M.

1997-04-01

Fucus vesiculosus L. seaweeds from three estuarine stations were analyzed by X-ray fluorescence, providing results for the concentration of total K, Ca, Ti, Mn, Fe, Co, Ni, Cu, Zn, As, Br, Sr, and Pb. Four different structures of the algae (base, stipe, reproductive organs, and growing tips) were analyzed to study the differential accumulation of heavy metals by different parts of Fucus. Some elements (e.g., Cu and Fe) are preferentially accumulated in the base of the algae, whereas others (e.g., As) exhibit higher concentrations in the reproductive organs and growing tips. The pattern of accumulation in different structures is similarmore » for Cu, Zn, and Pb, but for other metals there is considerable variability in accumulation between parts of the plant. This is important in determining which structures of the plant should be used for biomonitoring. For samples collected at stations subject to differing metal loads, the relative elemental composition is approximately constant, notwithstanding significant variation in absolute values. The proportion of metals in Fucus is similar to that found in other estuaries, where metal concentrations are significantly lower. Energy-dispersive X-ray fluorescence has been shown to be a suitable technique for multielement analysis in this type of sample. No chemical pretreatment is required, minimizing sample contamination. The small amount of sample required, and the wide range of elements that can be detected simultaneously make energy-dispersive X-ray fluorescence a valuable tool for pollution studies.« less

Future energy system in environment, economy, and energy problems (2) various nuclear energy system evaluations

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

Matsui, Kazuaki; Ujita, Hiroshi; Tashimo, Masanori

2006-07-01

Role and potentials of nuclear energy system in the energy options are discussed from the viewpoint of sustainable development with protecting from global warming by using the energy module structure of GRAPE model. They change and are affected dramatically by different sets of energy characteristics, nuclear behavior and energy policy even under the moderate set of presumptions. Introduction of thousands of reactors in the end of the century seems inevitable for better life and cleaner earth, but it will not come without efforts and cost. The analysis suggests the need of long term planning and R and D efforts undermore » the wisdom. (authors)« less

Design and fabrication of non silicon substrate based MEMS energy harvester for arbitrary surface applications

NASA Astrophysics Data System (ADS)

Balpande, Suresh S.; Pande, Rajesh S.

2016-04-01

Internet of Things (IoT) uses MEMS sensor nodes and actuators to sense and control objects through Internet. IOT deploys millions of chemical battery driven sensors at different locations which are not reliable many times because of frequent requirement of charging & battery replacement in case of underground laying, placement at harsh environmental conditions, huge count and difference between demand (24 % per year) and availability (energy density growing rate 8% per year). Energy harvester fabricated on silicon wafers have been widely used in manufacturing MEMS structures. These devices require complex fabrication processes, costly chemicals & clean room. In addition to this silicon wafer based devices are not suitable for curved surfaces like pipes, human bodies, organisms, or other arbitrary surface like clothes, structure surfaces which does not have flat and smooth surface always. Therefore, devices based on rigid silicon wafers are not suitable for these applications. Flexible structures are the key solution for this problems. Energy transduction mechanism generates power from free surrounding vibrations or impact. Sensor nodes application has been purposefully selected due to discrete power requirement at low duty cycle. Such nodes require an average power budget in the range of about 0.1 microwatt to 1 mW over a period of 3-5 seconds. Energy harvester is the best alternate source in contrast with battery for sensor node application. Novel design of Energy Harvester based on cheapest flexible non silicon substrate i.e. cellulose acetate substrate have been modeled, simulated and analyzed on COMSOL multiphysics and fabricated using sol-gel spin coating setup. Single cantilever based harvester generates 60-75 mV peak electric potential at 22Hz frequency and approximately 22 µW power at 1K-Ohm load. Cantilever array can be employed for generating higher voltage by replicating this structure. This work covers design, optimization, fabrication of harvester and schottky diodes based voltage multiplier.

Design and fabrication of non silicon substrate based MEMS energy harvester for arbitrary surface applications

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

Balpande, Suresh S., E-mail: balpandes@rknec.edu; Pande, Rajesh S.

Internet of Things (IoT) uses MEMS sensor nodes and actuators to sense and control objects through Internet. IOT deploys millions of chemical battery driven sensors at different locations which are not reliable many times because of frequent requirement of charging & battery replacement in case of underground laying, placement at harsh environmental conditions, huge count and difference between demand (24 % per year) and availability (energy density growing rate 8% per year). Energy harvester fabricated on silicon wafers have been widely used in manufacturing MEMS structures. These devices require complex fabrication processes, costly chemicals & clean room. In addition tomore » this silicon wafer based devices are not suitable for curved surfaces like pipes, human bodies, organisms, or other arbitrary surface like clothes, structure surfaces which does not have flat and smooth surface always. Therefore, devices based on rigid silicon wafers are not suitable for these applications. Flexible structures are the key solution for this problems. Energy transduction mechanism generates power from free surrounding vibrations or impact. Sensor nodes application has been purposefully selected due to discrete power requirement at low duty cycle. Such nodes require an average power budget in the range of about 0.1 microwatt to 1 mW over a period of 3-5 seconds. Energy harvester is the best alternate source in contrast with battery for sensor node application. Novel design of Energy Harvester based on cheapest flexible non silicon substrate i.e. cellulose acetate substrate have been modeled, simulated and analyzed on COMSOL multiphysics and fabricated using sol-gel spin coating setup. Single cantilever based harvester generates 60-75 mV peak electric potential at 22Hz frequency and approximately 22 µW power at 1K-Ohm load. Cantilever array can be employed for generating higher voltage by replicating this structure. This work covers design, optimization, fabrication of harvester and schottky diodes based voltage multiplier.« less

The Energy Economics of Financial Structuring for Renewable Energy Projects

NASA Astrophysics Data System (ADS)

Rana, Vishwajeet

2011-12-01

This dissertation focuses on the various financial structuring options for the renewable energy sector. The projects in this sector are capital-intensive to build but have relatively low operating costs in the long run when compared to traditional energy resources. The large initial capital requirements tend to discourage investors. To encourage renewable investments the government needs to provide financial incentives. Since these projects ultimately generate returns, the government's monetary incentives go to the sponsors and tax equity investors who build and operate such projects and invest capital in them. These incentives are usually in the form of ITCs, PTCs and accelerated depreciation benefits. Also, in some parts of the world, carbon credits are another form of incentive for the sponsors and equity investors to invest in such turnkey projects. The relative importance of these various considerations, however, differs from sponsor to sponsor, investor to investor and from project to project. This study focuses mainly on the US market, the federal tax benefits and incentives provided by the government. This study focuses on the energy economics that are used for project decision-making and parties involved in the transaction as: Project Developer/Sponsor, Tax equity investor, Debt investor, Energy buyer and Tax regulator. The study fulfils the knowledge gap in the decision making process that takes advantage of tax monetization in traditional after-tax analysis for renewable energy projects if the sponsors do not have the tax capacity to realize the total benefits of the project. A case-study for a wind farm, using newly emerging financial structures, validates the hypothesis that these renewable energy sources can meet energy industry economic criteria. The case study also helps to validate the following hypotheses: a) The greater a sponsor's tax appetite, the tower the sponsor's equity dilution. b) The use of leverage increases the cost of equity financing and the financing fee. c) Capital contributions by the sponsor are not relevant to the rate of return (IRR) over the life of the project. Overall conclusion is that financial structures can have a major impact on renewable energy, meeting energy demand in an economic manner. At the end, the dissertation lays down the foundation for future research that can be conducted in this field. Key Words: Renewable energy investments, structured finance, financial structuring

The track structure in condensed matter

NASA Astrophysics Data System (ADS)

Kaplan, I. G.

1995-11-01

The physical stage of track formation in a condensed phase is discussed. For interaction of charged particles with condensed molecular media its most important specific features are: (a) the continuous oscillator strength distribution with the broak peak in the energy range 21-22 eV attributed to the collective plasmon-type state; (b) the lowering of ionization potential compared to a gas phase. These specific features must be taken into account for simulation of track structures. The great difference in mass and charge for a electron and heavy ions cause a qualitative difference in their track structures. We analyse the structure of heavy ion tracks and prove the impossibility to use the LET as a universal characteristic for the radiation action of different ions.

Vibrational Study of Melatonin and its Radioprotective Activity towards Hydroxyl Radical

NASA Astrophysics Data System (ADS)

Singh, Gurpreet; Kaur, Sarvpreet; Saini, G. S. S.

2011-12-01

Vibrational study of Melatonin (N-acetyl 5-methoxytrypatamin) was done using FTIR and Raman spectroscopy. DFT calculations were employed to the structural analysis of melatonin and to the end products. The theoretical calculations confirmed the different observed vibrational modes. The optimized structure energy calculations of the different end products confirmed the most probable site of the hydroxyl radical attack is the hydrogen attached to nitrogen present in the indole ring.

Characterization of scintillator-based detectors for few-ten-keV high-spatial-resolution x-ray imaging

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

Larsson, Jakob C., E-mail: jakob.larsson@biox.kth.se; Lundström, Ulf; Hertz, Hans M.

2016-06-15

Purpose: High-spatial-resolution x-ray imaging in the few-ten-keV range is becoming increasingly important in several applications, such as small-animal imaging and phase-contrast imaging. The detector properties critically influence the quality of such imaging. Here the authors present a quantitative comparison of scintillator-based detectors for this energy range and at high spatial frequencies. Methods: The authors determine the modulation transfer function, noise power spectrum (NPS), and detective quantum efficiency for Gadox, needle CsI, and structured CsI scintillators of different thicknesses and at different photon energies. An extended analysis of the NPS allows for direct measurements of the scintillator effective absorption efficiency andmore » effective light yield as well as providing an alternative method to assess the underlying factors behind the detector properties. Results: There is a substantial difference in performance between the scintillators depending on the imaging task but in general, the CsI based scintillators perform better than the Gadox scintillators. At low energies (16 keV), a thin needle CsI scintillator has the best performance at all frequencies. At higher energies (28–38 keV), the thicker needle CsI scintillators and the structured CsI scintillator all have very good performance. The needle CsI scintillators have higher absorption efficiencies but the structured CsI scintillator has higher resolution. Conclusions: The choice of scintillator is greatly dependent on the imaging task. The presented comparison and methodology will assist the imaging scientist in optimizing their high-resolution few-ten-keV imaging system for best performance.« less

Characterization of scintillator-based detectors for few-ten-keV high-spatial-resolution x-ray imaging.

PubMed

Larsson, Jakob C; Lundström, Ulf; Hertz, Hans M

2016-06-01

High-spatial-resolution x-ray imaging in the few-ten-keV range is becoming increasingly important in several applications, such as small-animal imaging and phase-contrast imaging. The detector properties critically influence the quality of such imaging. Here the authors present a quantitative comparison of scintillator-based detectors for this energy range and at high spatial frequencies. The authors determine the modulation transfer function, noise power spectrum (NPS), and detective quantum efficiency for Gadox, needle CsI, and structured CsI scintillators of different thicknesses and at different photon energies. An extended analysis of the NPS allows for direct measurements of the scintillator effective absorption efficiency and effective light yield as well as providing an alternative method to assess the underlying factors behind the detector properties. There is a substantial difference in performance between the scintillators depending on the imaging task but in general, the CsI based scintillators perform better than the Gadox scintillators. At low energies (16 keV), a thin needle CsI scintillator has the best performance at all frequencies. At higher energies (28-38 keV), the thicker needle CsI scintillators and the structured CsI scintillator all have very good performance. The needle CsI scintillators have higher absorption efficiencies but the structured CsI scintillator has higher resolution. The choice of scintillator is greatly dependent on the imaging task. The presented comparison and methodology will assist the imaging scientist in optimizing their high-resolution few-ten-keV imaging system for best performance.

Photonics walking up a human hair

NASA Astrophysics Data System (ADS)

Zeng, Hao; Parmeggiani, Camilla; Martella, Daniele; Wasylczyk, Piotr; Burresi, Matteo; Wiersma, Diederik S.

2016-03-01

While animals have access to sugars as energy source, this option is generally not available to artificial machines and robots. Energy delivery is thus the bottleneck for creating independent robots and machines, especially on micro- and nano- meter length scales. We have found a way to produce polymeric nano-structures with local control over the molecular alignment, which allowed us to solve the above issue. By using a combination of polymers, of which part is optically sensitive, we can create complex functional structures with nanometer accuracy, responsive to light. In particular, this allowed us to realize a structure that can move autonomously over surfaces (it can "walk") using the environmental light as its energy source. The robot is only 60 μm in total length, thereby smaller than any known terrestrial walking species, and it is capable of random, directional walking and rotating on different dry surfaces.

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

Lima, Jonas R. F., E-mail: jonas.iasd@gmail.com

We study the electronic and transport properties of a graphene-based superlattice theoretically by using an effective Dirac equation. The superlattice consists of a periodic potential applied on a single-layer graphene deposited on a substrate that opens an energy gap of 2Δ in its electronic structure. We find that extra Dirac points appear in the electronic band structure under certain conditions, so it is possible to close the gap between the conduction and valence minibands. We show that the energy gap E{sub g} can be tuned in the range 0 ≤ E{sub g} ≤ 2Δ by changing the periodic potential. We analyze the low energymore » electronic structure around the contact points and find that the effective Fermi velocity in very anisotropic and depends on the energy gap. We show that the extra Dirac points obtained here behave differently compared to previously studied systems.« less

Improvement of energy conversion effectiveness and maximum output power of electrostatic induction-type MEMS energy harvesters by using symmetric comb-electrode structures

NASA Astrophysics Data System (ADS)

Honma, H.; Mitsuya, H.; Hashiguchi, G.; Fujita, H.; Toshiyoshi, H.

2018-06-01

We introduce symmetric comb-electrode structures for the electrostatic vibrational MEMS energy harvester to lower the electrostatic constraint force attributed to the built-in electret potential, thereby allowing the harvester device to operate in a small acceleration range of 0.05 g or lower (1 g  =  9.8 m s‑2). Given the same device structure, two different potentials for the electret are tested to experimentally confirm that the output induction current is enhanced 4.2 times by increasing the electret potential from  ‑60 V to  ‑250 V. At the same time, the harvester effectiveness has been improved to as high as 93%. The device is used to swiftly charge a 470 µF storage capacitor to 3.3 V in 120 s from small sinusoidal vibrations of 0.6 g at 124 Hz.

The energy spectrum and geometrical structure of Galactic turbulent magnetic field

NASA Astrophysics Data System (ADS)

Sun, Xiaohui; Gaensler, Bryan; Mcclure-Griffiths, Naomi; Purcell, Cormac; Hill, Alex; Burkhart, Blakesley; Lazarian, Alex

2012-10-01

The energy spectrum and geometrical structure of the turbulent magnetic field can offer a solid test of different theoretical models on the generation and evolution of Galactic magnetic fields. They are also pivotal to understanding the propagation of cosmic-ray particles. However, the energy spectrum has been difficult to determine and the geometrical structure has never been obtained so far, due to lack of proper methods and observations. We aim to infer these quantities by applying our newly developed techniques to polarisation images. These images are required to be observed with high angular resolution and broadband multi-channel polarimetry, which is possible only recently using the ATCA. As a pilot study, we plan to map the 2X2 degree high-latitude field centred at l=255.5 degree and b=-38 degree at 1.1-3.1 GHz in total intensity and polarisation.

The energy spectrum and geometrical structure of Galactic turbulent magnetic field

NASA Astrophysics Data System (ADS)

Sun, Xiaohui; Gaensler, Bryan; Mcclure-Griffiths, Naomi; Purcell, Cormac; Hill, Alex; Burkhart, Blakesley; Lazarian, Alex

2012-04-01

The energy spectrum and geometrical structure of the turbulent magnetic field can offer a solid test of different theoretical models on the generation and evolution of Galactic magnetic fields. They are also pivotal to understanding the propagation of cosmic-ray particles. However, the energy spectrum has been difficult to determine and the geometrical structure has never been obtained so far, due to lack of proper methods and observations. We aim to infer these quantities by applying our newly developed techniques to polarisation images. These images are required to be observed with high angular resolution and broadband multi-channel polarimetry, which is possible only recently using the ATCA. As a pilot study, we plan to map the 2X2 degree high-latitude field centred at l=255.5 degree and b=-38 degree at 1.1-3.1 GHz in total intensity and polarisation.

Bismuth doping strategies in GeTe nanowires to promote high-temperature phase transition from rhombohedral to face-centered cubic structure

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

Zhang, Jie; Huang, Rong; Wei, Fenfen

2014-11-17

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

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

NASA Astrophysics Data System (ADS)

Adlakha, I.; Solanki, K. N.

2015-03-01

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

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

NASA Astrophysics Data System (ADS)

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

2018-02-01

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

Conformational landscape of the HIV-V3 hairpin loop from all-atom free-energy simulations

NASA Astrophysics Data System (ADS)

Verma, Abhinav; Wenzel, Wolfgang

2008-03-01

Small beta hairpins have many distinct biological functions, including their involvement in chemokine and viral receptor recognition. The relevance of structural similarities between different hairpin loops with near homologous sequences is not yet understood, calling for the development of methods for de novo hairpin structure prediction and simulation. De novo folding of beta strands is more difficult than that of helical proteins because of nonlocal hydrogen bonding patterns that connect amino acids that are distant in the amino acid sequence and there is a large variety of possible hydrogen bond patterns. Here we use a greedy version of the basin hopping technique with our free-energy forcefield PFF02 to reproducibly and predictively fold the hairpin structure of a HIV-V3 loop. We performed 20 independent basin hopping runs for 500cycles corresponding to 7.4×107 energy evaluations each. The lowest energy structure found in the simulation has a backbone root mean square deviation (bRMSD) of only 2.04Å to the native conformation. The lowest 9 out of the 20 simulations converged to conformations deviating less than 2.5Å bRMSD from native.

Conformational landscape of the HIV-V3 hairpin loop from all-atom free-energy simulations.

PubMed

Verma, Abhinav; Wenzel, Wolfgang

2008-03-14

Small beta hairpins have many distinct biological functions, including their involvement in chemokine and viral receptor recognition. The relevance of structural similarities between different hairpin loops with near homologous sequences is not yet understood, calling for the development of methods for de novo hairpin structure prediction and simulation. De novo folding of beta strands is more difficult than that of helical proteins because of nonlocal hydrogen bonding patterns that connect amino acids that are distant in the amino acid sequence and there is a large variety of possible hydrogen bond patterns. Here we use a greedy version of the basin hopping technique with our free-energy forcefield PFF02 to reproducibly and predictively fold the hairpin structure of a HIV-V3 loop. We performed 20 independent basin hopping runs for 500 cycles corresponding to 7.4 x 10(7) energy evaluations each. The lowest energy structure found in the simulation has a backbone root mean square deviation (bRMSD) of only 2.04 A to the native conformation. The lowest 9 out of the 20 simulations converged to conformations deviating less than 2.5 A bRMSD from native.

Track-structure simulations for charged particles.

PubMed

Dingfelder, Michael

2012-11-01

Monte Carlo track-structure simulations provide a detailed and accurate picture of radiation transport of charged particles through condensed matter of biological interest. Liquid water serves as a surrogate for soft tissue and is used in most Monte Carlo track-structure codes. Basic theories of radiation transport and track-structure simulations are discussed and differences compared to condensed history codes highlighted. Interaction cross sections for electrons, protons, alpha particles, and light and heavy ions are required input data for track-structure simulations. Different calculation methods, including the plane-wave Born approximation, the dielectric theory, and semi-empirical approaches are presented using liquid water as a target. Low-energy electron transport and light ion transport are discussed as areas of special interest.

Structural makeup, biopolymer conformation, and biodegradation characteristics of a newly developed super genotype of oats (CDC SO-I versus conventional varieties): a novel approach.

PubMed

Damiran, Daalkhaijav; Yu, Peiqiang

2010-02-24

Recently, a new "super" genotype of oats (CDC SO-I or SO-I) has been developed. The objectives of this study were to determine structural makeup (features) of oat grain in endosperm and pericarp regions and to reveal and identify differences in protein amide I and II and carbohydrate structural makeup (conformation) between SO-I and two conventional oats (CDC Dancer and Derby) grown in western Canada in 2006, using advanced synchrotron radiation based Fourier transform infrared microspectroscopy (SRFTIRM). The SRFTIRM experiments were conducted at National Synchrotron Light Sources, Brookhaven National Laboratory (NSLS, BNL, U.S. Department of Energy). From the results, it was observed that comparison between the new genotype oats and conventional oats showed (1) differences in basic chemical and protein subfraction profiles and energy values with the new SO-I oats containing lower lignin (21 g/kg of DM) and higher soluble crude protein (530 g/kg CP), crude fat (59 g/kg of DM), and energy values (TDN, 820 g/kg of DM; NE(L3x), 7.8 MJ/kg of DM); (2) significant differences in rumen biodegradation kinetics of dry matter, starch, and protein with the new SO-I oats containing lower EDDM (638 g/kg of DM) and higher EDCP (103 g/kg of DM); (3) significant differences in nutrient supply with highest truly absorbed rumen undegraded protein (ARUP, 23 g/kg of DM) and total metabolizable protein supply (MP, 81 g/kg of DM) from the new SO-I oats; and (4) significant differences in structural makeup in terms of protein amide I in the endosperm region (with amide I peak height from 0.13 to 0.22 IR absorbance unit) and cellulosic compounds to carbohydrate ratio in the pericarp region (ratio from 0.02 to 0.06). The results suggest that with the SRFTIRM technique, the structural makeup differences between the new genotype oats (SO-I) and two conventional oats (Dancer and Derby) could be revealed.

Structural Make-up, Biopolymer Conformation, and Biodegradation Characteristics of Newly Developed Super Genotype of Oats (CDC SO-I vs. Conventional Varieties): Novel Approach

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

Damiran, D.; Yu, P

Recently, a new 'super' genotype of oats (CDC SO-I or SO-I) has been developed. The objectives of this study were to determine structural makeup (features) of oat grain in endosperm and pericarp regions and to reveal and identify differences in protein amide I and II and carbohydrate structural makeup (conformation) between SO-I and two conventional oats (CDC Dancer and Derby) grown in western Canada in 2006, using advanced synchrotron radiation based Fourier transform infrared microspectroscopy (SRFTIRM). The SRFTIRM experiments were conducted at National Synchrotron Light Sources, Brookhaven National Laboratory (NSLS, BNL, U.S. Department of Energy). From the results, it wasmore » observed that comparison between the new genotype oats and conventional oats showed (1) differences in basic chemical and protein subfraction profiles and energy values with the new SO-I oats containing lower lignin (21 g/kg of DM) and higher soluble crude protein (530 g/kg CP), crude fat (59 g/kg of DM), and energy values (TDN, 820 g/kg of DM; NE{sub L3x}, 7.8 MJ/kg of DM); (2) significant differences in rumen biodegradation kinetics of dry matter, starch, and protein with the new SO-I oats containing lower EDDM (638 g/kg of DM) and higher EDCP (103 g/kg of DM); (3) significant differences in nutrient supply with highest truly absorbed rumen undegraded protein (ARUP, 23 g/kg of DM) and total metabolizable protein supply (MP, 81 g/kg of DM) from the new SO-I oats; and (4) significant differences in structural makeup in terms of protein amide I in the endosperm region (with amide I peak height from 0.13 to 0.22 IR absorbance unit) and cellulosic compounds to carbohydrate ratio in the pericarp region (ratio from 0.02 to 0.06). The results suggest that with the SRFTIRM technique, the structural makeup differences between the new genotype oats (SO-I) and two conventional oats (Dancer and Derby) could be revealed.« less

Effects of surface stability on the morphological transformation of metals and metal oxides as investigated by first-principles calculations.

PubMed

Andrés, Juan; Gracia, Lourdes; Gouveia, Amanda Fernandes; Ferrer, Mateus Meneghetti; Longo, Elson

2015-10-09

Morphology is a key property of materials. Owing to their precise structure and morphology, crystals and nanocrystals provide excellent model systems for joint experimental and theoretical investigations into surface-related properties. Faceted polyhedral crystals and nanocrystals expose well-defined crystallographic planes depending on the synthesis method, which allow for thoughtful investigations into structure-reactivity relationships under practical conditions. This feature article introduces recent work, based on the combined use of experimental findings and first-principles calculations, to provide deeper knowledge of the electronic, structural, and energetic properties controlling the morphology and the transformation mechanisms of different metals and metal oxides: Ag, anatase TiO2, BaZrO3, and α-Ag2WO4. According to the Wulff theorem, the equilibrium shapes of these systems are obtained from the values of their respective surface energies. These investigations are useful to gain further understanding of how to achieve morphological control of complex three-dimensional crystals by tuning the ratio of the surface energy values of the different facets. This strategy allows the prediction of possible morphologies for a crystal and/or nanocrystal by controlling the relative values of surface energies.

Some metal oxides and their applications for creation of Microsystems (MEMS) and Energy Harvesting Devices (EHD)

NASA Astrophysics Data System (ADS)

Denishev, K.

2016-10-01

This is a review of a part of the work of the Technological Design Group at Technical University of Sofia, Faculty of Electronic Engineering and Technologies, Department of Microelectronics. It is dealing with piezoelectric polymer materials and their application in different microsystems (MEMS) and Energy Harvesting Devices (EHD), some organic materials and their applications in organic (OLED) displays, some transparent conductive materials etc. The metal oxides Lead Zirconium Titanate (PZT) and Zinc Oxide (ZnO) are used as piezoelectric layers - driving part of different sensors, actuators and EHD. These materials are studied in term of their performance in dependence on the deposition conditions and parameters. They were deposited as thin films by using RF Sputtering System. As technological substrates, glass plates and Polyethylenetherephtalate (PET) foils were used. For characterization of the materials, a test structure, based on Surface Acoustic Waves (SAW), was designed and prepared. The layers were characterized by Fourier Transform Infrared spectroscopy (FTIR). The piezoelectric response was tested at variety of mechanical loads (tensile strain, stress) in static and dynamic (multiple bending) mode. The single-layered and double-layered structures were prepared for piezoelectric efficiency increase. A structure of piezoelectric energy transformer is proposed and investigated.

Topological ring currents in the "empty" ring of benzo-annelated perylenes.

PubMed

Dickens, Timothy K; Mallion, Roger B

2011-01-27

Cyclic conjugation in benzo-annelated perylenes is examined by means of the topological π-electron ring currents calculated for each of their constituent rings, in a study that is an exact analogy of a recent investigation by Gutman et al. based on energy-effect values for the corresponding rings in each of these structures. "Classical" approaches, such as Kekulé structures, Clar "sextet" formulas, and circuits of conjugation, predict that the central ring in perylene is "empty" and thus contributes negligibly to cyclic conjugation. However, conclusions from the present calculations of topological ring currents agree remarkably with those arising from the earlier study involving energy-effect values in that, contrary to what would be predicted from the classical approaches, rings annelated in an angular fashion relative to the central ring of these perylene structures materially increase the extent of that ring's involvement in cyclic conjugation. It is suggested that such close quantitative agreement between the predictions of these two superficially very different indices (energy effect and topological ring current) might be due to the fact that, ultimately, both depend, albeit in ostensibly quite different ways, only on an adjacency matrix that contains information about the carbon-carbon connectivity of the conjugated system in question.

On the Origin of the Methyl Radical Loss from Deprotonated Ferulic and Isoferulic Acids: Electronic Excitation of a Transient Structure

NASA Astrophysics Data System (ADS)

Zhang, Xiaoping; Li, Fei; Lv, Huiqing; Wu, Yanqing; Bian, Gaofeng; Jiang, Kezhi

2013-06-01

Formation of radical fragments from even-electron ions is an exception to the "even-electron rule". In this work, ferulic acid (FA) and isoferulic acid (IFA) were used as the model compounds to probe the fragmentation mechanisms and the isomeric effects on homolytic cleavage. Elimination of methyl radical and CO2 are the two competing reactions observed in the CID-MS of [FA - H]- and [IFA - H]-, of which losing methyl radical violates the "even-electron rule". The relative intensity of their product ions is significantly different, and thereby the two isomeric compounds can be differentiated by tandem MS. Theoretical calculations indicate that both the singlet-triplet gap and the excitation energy decrease in the transient structures, as the breaking C-O bond is lengthened. The methyl radical elimination has been rationalized as the intramolecular electronic excitation of a transient structure with an elongating C-O bond. The potential energy diagrams, completed by the addition of the energy barrier of the radical elimination, have provided a reasonable explanation of the different CID-MS behaviors of [FA - H]- and [IFA - H]-.

Ground state structure of high-energy-density polymeric carbon monoxide

NASA Astrophysics Data System (ADS)

Xia, Kang; Sun, Jian; Pickard, Chris J.; Klug, Dennis D.; Needs, Richard J.

2017-04-01

Crystal structure prediction methods and first-principles calculations have been used to explore low-energy structures of carbon monoxide (CO). Contrary to the standard wisdom, the most stable structure of CO at ambient pressure was found to be a polymeric structure of P n a 21 symmetry rather than a molecular solid. This phase is formed from six-membered (four carbon + two oxygen) rings connected by C=C double bonds with two double-bonded oxygen atoms attached to each ring. Interestingly, the polymeric P n a 21 phase of CO has a much higher energy density than trinitrotoluene (TNT). On compression to about 7 GPa, P n a 21 is found to transform into another chainlike phase of C c symmetry which has similar ring units to P n a 21 . On compression to 12 GPa, it is energetically favorable for CO to polymerize into a purely single bonded C m c a phase, which is stable over a wide pressure range and transforms into the previously known C m c m phase at around 100 GPa. Thermodynamic stability of these structures was verified using calculations with different density functionals, including hybrid and van der Waals corrected functionals.

Silicene-terminated surface of calcium and strontium disilicides: properties and comparison with bulk structures by computational methods

NASA Astrophysics Data System (ADS)

Brázda, Petr; Mutombo, Pingo; Ondráček, Martin; Corrêa, Cinthia Antunes; Kopeček, Jaromír; Palatinus, Lukáš

2018-05-01

The bulk and surface structures of calcium and strontium disilicides are investigated by computational methods using density functional theory. The investigated structures are R6, R3 and P1-CaSi2 and P1-SrSi2. The investigated properties are the cleavage energy at the silicene sheet, buckling of the bulk and surface silicene layers, charge transfer from calcium to silicon, band structure of bulk and surface-terminated structures and adsorption energies on H atoms and H2 molecules on the silicene-terminated surface of the R3 phase. The cleavage energy at the silicene surface is low in all cases. Structures P1-CaSi2 and R3-CaSi2 contain silicene sheets with different coordination to Ca, while R6-CaSi2 contains both types of the sheets. It is shown that the properties of the two types of silicene-like sheets in R6-CaSi2 are similar to those of the corresponding sheets in P1-CaSi2 and R3-CaSi2, and the thermodynamically stable R6 phase is a good candidate for experimental investigation of silicene-terminated surface in calcium disilicide.

Interdisciplinary design study of a high-rise integrated roof wind energy system

NASA Astrophysics Data System (ADS)

Dekker, R. W. A.; Ferraro, R. M.; Suma, A. B.; Moonen, S. P. G.

2012-10-01

Today's market in micro-wind turbines is in constant development introducing more efficient solutions for the future. Besides the private use of tower supported turbines, opportunities to integrate wind turbines in the built environment arise. The Integrated Roof Wind Energy System (IRWES) presented in this work is a modular roof structure integrated on top of existing or new buildings. IRWES is build up by an axial array of skewed shaped funnels used for both wind inlet and outlet. This inventive use of shape and geometry leads to a converging air capturing inlet to create high wind mass flow and velocity toward a Vertical Axis Wind Turbine (VAWT) in the center-top of the roof unit for the generation of a relatively high amount of energy. The scope of this research aims to make an optimized structural design of IRWES to be placed on top of the Vertigo building in Eindhoven; analysis of the structural performance; and impact to the existing structure by means of Finite Element Modeling (FEM). Results show that the obvious impact of wind pressure to the structural design is easily supported in different configurations of fairly simple lightweight structures. In particular, the weight addition to existing buildings remains minimal.

Generalized Kinetic Description of Steady-State Collisionless Plasmas

NASA Technical Reports Server (NTRS)

Khazanov, G. V.; Liemohn, M. W.; Krivorutsky, E. N.

1997-01-01

We present a general solution to the collisionless Boltzmann (Vlasov) equation for a free-flowing plasma along a magnetic field line using Liouville's theorem, allowing for an arbitrary potential structure including non-monotonicities. The constraints of the existing collisionless kinetic transport models are explored, and the need for a more general approach to the problem of self- consistent potential energy calculations is described. Then a technique that handles an arbitrary potential energy distribution along the field line is presented and discussed. For precipitation of magnetospherically trapped hot plasma, this model yields moment calculations that vary by up to a factor of two for various potential energy structures with the same total potential drop. The differences are much greater for the high-latitude outflow scenario, giving order of magnitude variations depending on the shape of the potential energy distribution.

Models of charge pair generation in organic solar cells.

PubMed

Few, Sheridan; Frost, Jarvist M; Nelson, Jenny

2015-01-28

Efficient charge pair generation is observed in many organic photovoltaic (OPV) heterojunctions, despite nominal electron-hole binding energies which greatly exceed the average thermal energy. Empirically, the efficiency of this process appears to be related to the choice of donor and acceptor materials, the resulting sequence of excited state energy levels and the structure of the interface. In order to establish a suitable physical model for the process, a range of different theoretical studies have addressed the nature and energies of the interfacial states, the energetic profile close to the heterojunction and the dynamics of excited state transitions. In this paper, we review recent developments underpinning the theory of charge pair generation and phenomena, focussing on electronic structure calculations, electrostatic models and approaches to excited state dynamics. We discuss the remaining challenges in achieving a predictive approach to charge generation efficiency.

Dual structure in the charge excitation spectrum of electron-doped cuprates

NASA Astrophysics Data System (ADS)

Bejas, Matías; Yamase, Hiroyuki; Greco, Andrés

2017-12-01

Motivated by the recent resonant x-ray scattering (RXS) and resonant inelastic x-ray scattering (RIXS) experiments for electron-doped cuprates, we study the charge excitation spectrum in a layered t -J model with the long-range Coulomb interaction. We show that the spectrum is not dominated by a specific type of charge excitations, but by different kinds of charge fluctuations, and is characterized by a dual structure in the energy space. Low-energy charge excitations correspond to various types of bond-charge fluctuations driven by the exchange term (J term), whereas high-energy charge excitations are due to usual on-site charge fluctuations and correspond to plasmon excitations above the particle-hole continuum. The interlayer coupling, which is frequently neglected in many theoretical studies, is particularly important to the high-energy charge excitations.

An empirical potential for simulating vacancy clusters in tungsten.

PubMed

Mason, D R; Nguyen-Manh, D; Becquart, C S

2017-12-20

We present an empirical interatomic potential for tungsten, particularly well suited for simulations of vacancy-type defects. We compare energies and structures of vacancy clusters generated with the empirical potential with an extensive new database of values computed using density functional theory, and show that the new potential predicts low-energy defect structures and formation energies with high accuracy. A significant difference to other popular embedded-atom empirical potentials for tungsten is the correct prediction of surface energies. Interstitial properties and short-range pairwise behaviour remain similar to the Ackford-Thetford potential on which it is based, making this potential well-suited to simulations of microstructural evolution following irradiation damage cascades. Using atomistic kinetic Monte Carlo simulations, we predict vacancy cluster dissociation in the range 1100-1300 K, the temperature range generally associated with stage IV recovery.

Energy Dissipation in Earthquake Soil Structure Interaction: The September 3rd, 2016 M5.8 Pawnee Oklahoma Earthquake

NASA Astrophysics Data System (ADS)

Yang, H.; Sinha, S. K.; Feng, Y.; Jeremic, B.

2016-12-01

The M5.8 earthquake occurred in Pawnee, Oklahoma on September 3rd 2016 is the strongest seismic event recorded in Oklahoma. Soil structure interaction (SSI) played an important role in this tragic event. As a major aspect of SSI analysis, the propagation and dissipation of seismic energy will be studied in depth, with particular focus on the ground motion recorded in this earthquake. Seismic energy propagates from seismic source to the SSI system and is dissipated within and around the SSI system. Energy dissipation with the SSI system is related to inelastic behavior of soil, rock, contact zone (foundation-soil/rock), structural components and energy dissipators. Accurate evaluation of seismic energy can be used to optimize SSI system for safety and economy. The SSI system can be designed so that majority of seismic energy is dissipated within soil and soil-foundation contact zone, away from the structure.Accurate and theoretically sound modeling of propagation and dissipation is essential to use of seismic energy for design and assessment. The rate of plastic work is defined as the product of stress and the rate of plastic strain. On the other hand, plastic dissipation is defined as a form of heat transfer. The difference between these two quantities, which has been neglected in many studies, is a plastic part of the free energy. By considering energy storage and dissipation at both micro (particle) scale and macro (continuum) scale, it can be shown that the plastic free energy is an intrinsic attribute at the continuum scale due to particle rearrangement. Proper application of thermodynamics to finite element simulations, plastic dissipation can be correctly modeled. Examples will be used to illustrate above point on both constitutive, single element and SSI model scales. In addition, propagation of seismic energy, its dissipation (timing and location) will be used to illustrate use in design and assessment.

DYNECHARM++: a toolkit to simulate coherent interactions of high-energy charged particles in complex structures

NASA Astrophysics Data System (ADS)

Bagli, Enrico; Guidi, Vincenzo

2013-08-01

A toolkit for the simulation of coherent interactions between high-energy charged particles and complex crystal structures, called DYNECHARM++ has been developed. The code has been written in C++ language taking advantage of this object-oriented programing method. The code is capable to evaluating the electrical characteristics of complex atomic structures and to simulate and track the particle trajectory within them. Calculation method of electrical characteristics based on their expansion in Fourier series has been adopted. Two different approaches to simulate the interaction have been adopted, relying on the full integration of particle trajectories under the continuum potential approximation and on the definition of cross-sections of coherent processes. Finally, the code has proved to reproduce experimental results and to simulate interaction of charged particles with complex structures.

Organic molecules as tools to control the growth, surface structure, and redox activity of colloidal quantum dots.

PubMed

Weiss, Emily A

2013-11-19

In order to achieve efficient and reliable technology that can harness solar energy, the behavior of electrons and energy at interfaces between different types or phases of materials must be understood. Conversion of light to chemical or electrical potential in condensed phase systems requires gradients in free energy that allow the movement of energy or charge carriers and facilitate redox reactions and dissociation of photoexcited states (excitons) into free charge carriers. Such free energy gradients are present at interfaces between solid and liquid phases or between inorganic and organic materials. Nanostructured materials have a higher density of these interfaces than bulk materials. Nanostructured materials, however, have a structural and chemical complexity that does not exist in bulk materials, which presents a difficult challenge: to lower or eliminate energy barriers to electron and energy flux that inevitably result from forcing different materials to meet in a spatial region of atomic dimensions. Chemical functionalization of nanostructured materials is perhaps the most versatile and powerful strategy for controlling the potential energy landscape of their interfaces and for minimizing losses in energy conversion efficiency due to interfacial structural and electronic defects. Colloidal quantum dots are semiconductor nanocrystals synthesized with wet-chemical methods and coated in organic molecules. Chemists can use these model systems to study the effects of chemical functionalization of nanoscale organic/inorganic interfaces on the optical and electronic properties of a nanostructured material, and the behavior of electrons and energy at interfaces. The optical and electronic properties of colloidal quantum dots have an intense sensitivity to their surface chemistry, and their organic adlayers make them dispersible in solvent. This allows researchers to use high signal-to-noise solution-phase spectroscopy to study processes at interfaces. In this Account, I describe the varied roles of organic molecules in controlling the structure and properties of colloidal quantum dots. Molecules serve as surfactant that determines the mechanism and rate of nucleation and growth and the final size and surface structure of a quantum dot. Anionic surfactant in the reaction mixture allows precise control over the size of the quantum dot core but also drives cation enrichment and structural disordering of the quantum dot surface. Molecules serve as chemisorbed ligands that dictate the energetic distribution of surface states. These states can then serve as thermodynamic traps for excitonic charge carriers or couple to delocalized states of the quantum dot core to change the confinement energy of excitonic carriers. Ligands, therefore, in some cases, dramatically shift the ground state absorption and photoluminescence spectra of quantum dots. Molecules also act as protective layers that determine the probability of redox processes between quantum dots and other molecules. How much the ligand shell insulates the quantum dot from electron exchange with a molecular redox partner depends less on the length or degree of conjugation of the native ligand and more on the density and packing structure of the adlayer and the size and adsorption mode of the molecular redox partner. Control of quantum dot properties in these examples demonstrates that nanoscale interfaces, while complex, can be rationally designed to enhance or specify the functionality of a nanostructured system.

Effects of experimental conditions on the morphologies, structures and growth modes of pulsed laser-deposited CdS nanoneedles

PubMed Central

2014-01-01

CdS nanoneedles with different morphologies, structures, and growth modes have been grown on Ni-coated Si(100) surface under different experimental conditions by pulsed laser deposition method. The effects of catalyst layer, substrate temperature, and laser pulse energy on the growth of the CdS nanoneedles were studied in detail. It was confirmed that the formation of the molten catalyst spheres is the key to the nucleation of the CdS nanoneedles by observing the morphologies of the Ni catalyst thin films annealed at different substrate temperatures. Both the substrate temperature and laser pulse energy strongly affected the growth modes of the CdS nanoneedles. The secondary growth of the smaller nanoneedles on the top of the main nanoneedles was found at appropriate conditions. A group of more completed pictures of the growth modes of the CdS nanoneedles were presented. PMID:24559455

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.

Machine learning for the structure-energy-property landscapes of molecular crystals.

PubMed

Musil, Félix; De, Sandip; Yang, Jack; Campbell, Joshua E; Day, Graeme M; Ceriotti, Michele

2018-02-07

Molecular crystals play an important role in several fields of science and technology. They frequently crystallize in different polymorphs with substantially different physical properties. To help guide the synthesis of candidate materials, atomic-scale modelling can be used to enumerate the stable polymorphs and to predict their properties, as well as to propose heuristic rules to rationalize the correlations between crystal structure and materials properties. Here we show how a recently-developed machine-learning (ML) framework can be used to achieve inexpensive and accurate predictions of the stability and properties of polymorphs, and a data-driven classification that is less biased and more flexible than typical heuristic rules. We discuss, as examples, the lattice energy and property landscapes of pentacene and two azapentacene isomers that are of interest as organic semiconductor materials. We show that we can estimate force field or DFT lattice energies with sub-kJ mol -1 accuracy, using only a few hundred reference configurations, and reduce by a factor of ten the computational effort needed to predict charge mobility in the crystal structures. The automatic structural classification of the polymorphs reveals a more detailed picture of molecular packing than that provided by conventional heuristics, and helps disentangle the role of hydrogen bonded and π-stacking interactions in determining molecular self-assembly. This observation demonstrates that ML is not just a black-box scheme to interpolate between reference calculations, but can also be used as a tool to gain intuitive insights into structure-property relations in molecular crystal engineering.

A minimal peptide scaffold for beta-turn display: optimizing a strand position in disulfide-cyclized beta-hairpins.

PubMed

Cochran, A G; Tong, R T; Starovasnik, M A; Park, E J; McDowell, R S; Theaker, J E; Skelton, N J

2001-01-31

Phage display of peptide libraries has become a powerful tool for the evolution of novel ligands that bind virtually any protein target. However, the rules governing conformational preferences in natural peptides are poorly understood, and consequently, structure-activity relationships in these molecules can be difficult to define. In an effort to simplify this process, we have investigated the structural stability of 10-residue, disulfide-constrained beta-hairpins and assessed their suitability as scaffolds for beta-turn display. Using disulfide formation as a probe, relative free energies of folding were measured for 19 peptides that differ at a one strand position. A tryptophan substitution promotes folding to a remarkable degree. NMR analysis confirms that the measured energies correlate well with the degree of beta-hairpin structure in the disulfide-cyclized peptides. Reexamination of a subset of the strand substitutions in peptides with different turn sequences reveals linear free energy relationships, indicating that turns and strand-strand interactions make independent, additive contributions to hairpin stability. Significantly, the tryptophan strand substitution is highly stabilizing with all turns tested, and peptides that display model turns or the less stable C'-C' ' turn of CD4 on this tryptophan "stem" are highly structured beta-hairpins in water. Thus, we have developed a small, structured beta-turn scaffold, containing only natural L-amino acids, that may be used to display peptide libraries of limited conformational diversity on phage.

Energy distributions in rods and beams

NASA Technical Reports Server (NTRS)

Wohlever, J. C.; Bernhard, R. J.

1989-01-01

A hypothesis proposed by Nefske and Sung (1987) that the mechanical energy flow in acoustic/structural systems can be modeled using a thermal energy flow analogy was tested for both longitudinal vibration in rods and transverse flexural vibrations in beams. It was found that the rod behaves according to the energy flow analogy. However, the beam solutions behaved significantly differently than predicted by the thermal analogy, unless spatially averaged energy and power flow were considered. Otherwise, the beam analysis is restricted to frequencies where the near-field terms in the displacement solution are negligible over most of the beam.

Efficient near-field wireless energy transfer using adiabatic system variations

DOEpatents

Hamam, Rafif E.; Karalis, Aristeidis; Joannopoulos, John D.; Soljacic, Marin

2013-01-29

Disclosed is a method for transferring energy wirelessly including transferring energy wirelessly from a first resonator structure to an intermediate resonator structure, wherein the coupling rate between the first resonator structure and the intermediate resonator structure is .kappa..sub.1B, transferring energy wirelessly from the intermediate resonator structure to a second resonator structure, wherein the coupling rate between the intermediate resonator structure and the second resonator structure is .kappa..sub.B2, and during the wireless energy transfers, adjusting at least one of the coupling rates .kappa..sub.1B and .kappa..sub.B2 to reduce energy accumulation in the intermediate resonator structure and improve wireless energy transfer from the first resonator structure to the second resonator structure through the intermediate resonator structure.

Efficient near-field wireless energy transfer using adiabatic system variations

DOEpatents

Hamam, Rafif E; Karalis, Aristeidis; Joannopoulos, John D; Soljacic, Marin

2014-09-16

Disclosed is a method for transferring energy wirelessly including transferring energy wirelessly from a first resonator structure to an intermediate resonator structure, wherein the coupling rate between the first resonator structure and the intermediate resonator structure is .kappa..sub.1B, transferring energy wirelessly from the intermediate resonator structure to a second resonator structure, wherein the coupling rate between the intermediate resonator structure and the second resonator structure is .kappa..sub.B2, and during the wireless energy transfers, adjusting at least one of the coupling rates .kappa..sub.1B and .kappa..sub.B2 to reduce energy accumulation in the intermediate resonator structure and improve wireless energy transfer from the first resonator structure to the second resonator structure through the intermediate resonator structure.

Simulations of Collisional Disruption at the Catastrophic Impact Energy Threshold: Effect of the Target's Internal Structure and Diameter

NASA Astrophysics Data System (ADS)

Michel, P.; Benz, W.; Richardson, D. C.

2005-08-01

Recent simulations of asteroid break-ups, including both the fragmentation of the parent body and the gravitational interactions of the fragments, have allowed to reproduced successfully the main properties of asteroid families formed in different regimes of impact energy. Here, using the same kind of simulations, we concentrate on a single regime of impact energy, the so-called catastrophic threshold usually designated by Qcrit, which results in the escape of half of the target's mass. Considering a wide range of diameter values and two kinds of internal structures of the parent body, monolithic and pre-shattered, we analyse their potential influences on the value of Qcrit and on the collisional outcome limited here to the fragment size and ejection speed distributions, which are the main outcome properties used by collisional models to study the evolutions of the different populations of small bodies. For all the considered diameters and the two internal structures of the parent body, we confirm that the process of gravitational reaccumulation is at the origin of the largest remnant's mass. We then find that, for a given diameter of the parent body, the impact energy corresponding to the catastrophic disruption threshold is highly dependent on the internal structure of the parent body. In particular, a pre-shattered parent body containing only damaged zones but no macroscopic voids is easier to disrupt than a monolithic parent body. Other kinds of internal properties that can also characterize small bodies in real populations will be investigated in a future work.

The mechanics and energetics of soil bioturbation by earthworms and plant roots - Impacts on soil structure generation and maintenance

NASA Astrophysics Data System (ADS)

Or, Dani; Ruiz, Siul; Schymanski, Stanlislaus

2015-04-01

Soil structure is the delicate arrangement of solids and voids that facilitate numerous hydrological and ecological soil functions ranging from water infiltration and retention to gaseous exchange and mechanical anchoring of plant roots. Many anthropogenic activities affect soil structure, e.g. via tillage and compaction, and by promotion or suppression of biological activity and soil carbon pools. Soil biological activity is critical to the generation and maintenance of favorable soil structure, primarily through bioturbation by earthworms and root proliferation. The study aims to quantify the mechanisms, rates, and energetics associated with soil bioturbation, using a new biomechanical model to estimate stresses required to penetrate and expand a cylindrical cavity in a soil under different hydration and mechanical conditions. The stresses and soil displacement involved are placed in their ecological context (typical sizes, population densities, burrowing rates and behavior) enabling estimation of mechanical energy requirements and impacts on soil organic carbon pool (in the case of earthworms). We consider steady state plastic cavity expansion to determine burrowing pressures of earthworms and plant roots, akin to models of cone penetration representing initial burrowing into soil volumes. Results show that with increasing water content the strain energy decreases and suggest trade-offs between cavity expansion pressures and energy investment for different root and earthworm geometries and soil hydration. The study provides a quantitative framework for estimating energy costs of bioturbation in terms of soil organic carbon or the mechanical costs of soil exploration by plant roots as well as mechanical and hydration limits to such activities.

Experimental Investigation on Laser Impact Welding of Fe-Based Amorphous Alloys to Crystalline Copper

PubMed Central

Wang, Xiao; Luo, Yapeng; Huang, Tao; Liu, Huixia

2017-01-01

Recently, amorphous alloys have attracted many researchers’ attention for amorphous structures and excellent properties. However, the welding of amorphous alloys to traditional metals in the microscale is not easy to realize in the process with amorphous structures unchanged, which restrains the application in industry. In this paper, a new method of welding Fe-based amorphous alloys (GB1K101) to crystalline copper by laser impact welding (LIW) is investigated. A series of experiments was conducted under different laser energies, during which Fe-based amorphous alloys and crystalline copper were welded successfully by LIW. In addition, the microstructure and mechanical properties of welding joints were observed and measured, respectively. The results showed that the surface wave and springback were observed on the flyer plate after LIW. The welding interface was straight or wavy due to different plastic deformation under different laser energies. The welding interface was directly bonded tightly without visible defects. No visible element diffusion and intermetallic phases were found in the welding interface. The Fe-based amorphous alloys retained amorphous structures after LIW under the laser energy of 835 mJ. The nanoindentation hardness across the welding interface showed an increase on both sides of the welding interface. The results of the lap shearing test showed that the fracture position was on the side of copper coil. PMID:28772886

Experimental Investigation on Laser Impact Welding of Fe-Based Amorphous Alloys to Crystalline Copper.

PubMed

Wang, Xiao; Luo, Yapeng; Huang, Tao; Liu, Huixia

2017-05-12

Recently, amorphous alloys have attracted many researchers' attention for amorphous structures and excellent properties. However, the welding of amorphous alloys to traditional metals in the microscale is not easy to realize in the process with amorphous structures unchanged, which restrains the application in industry. In this paper, a new method of welding Fe-based amorphous alloys (GB1K101) to crystalline copper by laser impact welding (LIW) is investigated. A series of experiments was conducted under different laser energies, during which Fe-based amorphous alloys and crystalline copper were welded successfully by LIW. In addition, the microstructure and mechanical properties of welding joints were observed and measured, respectively. The results showed that the surface wave and springback were observed on the flyer plate after LIW. The welding interface was straight or wavy due to different plastic deformation under different laser energies. The welding interface was directly bonded tightly without visible defects. No visible element diffusion and intermetallic phases were found in the welding interface. The Fe-based amorphous alloys retained amorphous structures after LIW under the laser energy of 835 mJ. The nanoindentation hardness across the welding interface showed an increase on both sides of the welding interface. The results of the lap shearing test showed that the fracture position was on the side of copper coil.

Evolution of the properties of Al(n)N(n) clusters with size.

PubMed

Costales, Aurora; Blanco, M A; Francisco, E; Pandey, Ravindra; Martín Pendás, A

2005-12-29

A global optimization of stoichiometric (AlN)(n) clusters (n = 1-25, 30, 35, ..., 95, 100) has been performed using the basin-hopping (BH) method and describing the interactions with simple and yet realistic interatomic potentials. The results for the smaller isomers agree with those of previous electronic structure calculations, thus validating the present scheme. The lowest-energy isomers found can be classified in three different categories according to their structural motifs: (i) small clusters (n = 2-5), with planar ring structures and 2-fold coordination, (ii) medium clusters (n = 6-40), where a competition between stacked rings and globular-like empty cages exists, and (iii) large clusters (n > 40), large enough to mix different elements of the previous stage. All the atoms in small and medium-sized clusters are in the surface, while large clusters start to display interior atoms. Large clusters display a competition between tetrahedral and octahedral-like features: the former lead to a lower energy interior in the cluster, while the latter allow for surface terminations with a lower energy. All of the properties studied present different regimes according to the above classification. It is of particular interest that the local properties of the interior atoms do converge to the bulk limit. The isomers with n = 6 and 12 are specially stable with respect to the gain or loss of AlN molecules.

Molecular structure, chemical and nutrient profiles, and metabolic characteristics of the proteins and energy in new cool-season corn varieties harvested as fresh forage for dairy cattle.

PubMed

Abeysekara, Saman; Christensen, David A; Niu, Zhiyuan; Theodoridou, Katerina; Yu, Peiqiang

2013-10-01

To our knowledge, no previous research exists concerning the molecular structure and metabolic characteristics of the proteins and energy that new cool-season corn varieties provide for dairy cattle. The objectives of this study were to identify the differences in the molecular structures of proteins among several new cool-season corn varieties [Pioneer P7443R, Pioneer P7213R, Pioneer P7535R (Pioneer Hi-Bred International Inc., Johnston, IA), Hyland Baxxos RR, Hyland SR22, and Hyland SR06 (Hyland Seeds, Blenheim, ON, Canada)] using Fourier transform infrared attenuated total reflectance (FT/IR-ATR) molecular spectroscopy, and to determine the nutrient profile and supply that each variety provided for dairy cattle. The protein molecular structure studies showed that the amide I to amide II ratio ranged from 1.09 to 1.66 and that the α-helix to β-sheet ratio ranged from 0.95 to 1.01 among the new cool-season corn varieties. Energy content was significantly different among the new varieties. We found significant differences in the protein and carbohydrate subfractions and in the ruminal degradation kinetics of the organic matter, crude protein, starch, and neutral detergent fiber of the new varieties. The new varieties had similar estimated intestinal digestibilities for rumen undegraded crude protein. However, the new varieties had significant differences in predicted total truly absorbable protein, ranging from 39 to 57 g/kg of dry matter, indicating that these newly developed varieties are satisfactory sources of truly absorbed protein for dairy cattle. Further study on the molecular structure profiles of cool-season corn in relation to its nutrient utilization and availability in dairy cattle is necessary. Copyright © 2013 American Dairy Science Association. Published by Elsevier Inc. All rights reserved.

Energy behavior on side structure in event of ship collision subjected to external parameters.

PubMed

Prabowo, Aditya Rio; Bae, Dong Myung; Sohn, Jung Min; Cao, Bo

2016-11-01

The safety of ships in regards to collisions and groundings, as well as the navigational and structural aspects of ships, has been improved and developed up to this day by technical, administrative and nautical parties. The damage resulting from collisions could be reduced through several techniques such as designing appropriate hull structures, ensuring tightness of cargo tanks as well as observation and review on structural behaviors, whilst accounting for all involved parameters. The position during a collision can be influenced by the collisions' location and angle as these parts are included in the external dynamics of ship collisions. In this paper, the results of several collision analyses using the finite element method were used and reviewed regarding the effect of location and angle on energy characteristic. Firstly, the capabilities of the structure and its ability to resist destruction in a collision process were presented and comparisons were made to other collision cases. Three types of collisions were identified based on the relative location of contact points to each other. From the results, it was found that the estimation of internal energy by the damaged ships differed in range from 12%-24%. In the second stage, the results showed that a collision between 30 to 60 degrees produced higher level energy than a collision in the perpendicular position. Furthermore, it was concluded that striking and struck objects in collision contributed to energy and damage shape.

Evolution of displacement cascades in Fe-Cr structures with different [001] tilt grain boundaries

NASA Astrophysics Data System (ADS)

Abu-Shams, M.; Haider, W.; Shabib, I.

2017-06-01

Reduced-activation ferritic/martensitic steels of Cr concentration between 2.25 and 12 wt% are candidate structural materials for next-generation nuclear reactors. In this study, molecular dynamics (MD) simulation is used to generate the displacement cascades in Fe-Cr structures with different Cr concentrations by using different primary knock-on atom (PKA) energies between 2 and 10 keV. A concentration-dependent model potential has been used to describe the interactions between Fe and Cr. Single crystals (SCs) of three different coordinate bases (e.g. [310], [510], and [530]) and bi-crystal (BC) structures with three different [001] tilt grain boundaries (GBs) (e.g. Σ5, Σ13, and Σ17) have been simulated. The Wigner-Seitz cell criterion has been used to identify the produced Frenkel pairs. The results show a marked difference between collisions observed in SCs and those in BC structures. The numbers of vacancies and interstitials are found to be significantly higher in BC structures than those found in SCs. The number of point defects exhibits a power relationship with the PKA energies; however, the Cr concentration does not seem to have any influence on the number of survived point defects. In BC models, a large fraction of the total survived point defects (between 59% and 93%) tends accumulate at the GBs, which seem to trap the generated point defects. The BC structure with Σ17 GB is found to trap more defects than Σ5 and Σ13 GBs. The defect trapping is found to be dictated by the crystallographic parameters of the GBs. For all studied GBs, self-interstitial atoms (SIAs) are easily trapped within the GB region than vacancies. An analysis of defect composition reveals an enrichment of Cr in SIAs, and in BC cases, more than half of the Cr-SIAs are found to be located within the GB region.

Characterization of the free-energy landscapes of proteins by NMR-guided metadynamics

PubMed Central

Granata, Daniele; Camilloni, Carlo; Vendruscolo, Michele; Laio, Alessandro

2013-01-01

The use of free-energy landscapes rationalizes a wide range of aspects of protein behavior by providing a clear illustration of the different states accessible to these molecules, as well as of their populations and pathways of interconversion. The determination of the free-energy landscapes of proteins by computational methods is, however, very challenging as it requires an extensive sampling of their conformational spaces. We describe here a technique to achieve this goal with relatively limited computational resources by incorporating nuclear magnetic resonance (NMR) chemical shifts as collective variables in metadynamics simulations. As in this approach the chemical shifts are not used as structural restraints, the resulting free-energy landscapes correspond to the force fields used in the simulations. We illustrate this approach in the case of the third Ig-binding domain of protein G from streptococcal bacteria (GB3). Our calculations reveal the existence of a folding intermediate of GB3 with nonnative structural elements. Furthermore, the availability of the free-energy landscape enables the folding mechanism of GB3 to be elucidated by analyzing the conformational ensembles corresponding to the native, intermediate, and unfolded states, as well as the transition states between them. Taken together, these results show that, by incorporating experimental data as collective variables in metadynamics simulations, it is possible to enhance the sampling efficiency by two or more orders of magnitude with respect to standard molecular dynamics simulations, and thus to estimate free-energy differences among the different states of a protein with a kBT accuracy by generating trajectories of just a few microseconds. PMID:23572592

Structure and stability of clusters of β-alanine in the gas phase: importance of the nature of intermolecular interactions.

PubMed

Piekarski, Dariusz Grzegorz; Díaz-Tendero, Sergio

2017-02-15

We present a theoretical study of neutral clusters of β-alanine molecules in the gas phase, (β-ala) n n ≤ 5. Classical molecular dynamics simulations carried out with different internal excitation energies provide information on the clusters formation and their thermal decomposition limits. We also present an assessment study performed with different families of density functionals using the dimer, (β-ala) 2 , as a benchmark system. The M06-2X functional provides the best agreement in geometries and relative energies in comparison with the reference values computed with the MP2 and CCSD(T) methods. The structure, stability, dissociation energies and vertical ionization potentials of the studied clusters have been investigated using this functional in combination with the 6-311++G(d,p) basis set. An exhaustive analysis of intermolecular interactions is also presented. These results provide new insights into the stability, interaction nature and formation mechanisms of clusters of amino acids in the gas phase.

Strong CH/O interactions between polycyclic aromatic hydrocarbons and water: Influence of aromatic system size.

PubMed

Veljković, Dušan Ž

2018-03-01

Energies of CH/O interactions between water molecule and polycyclic aromatic hydrocarbons with a different number of aromatic rings were calculated using ab initio calculations at MP2/cc-PVTZ level. Results show that an additional aromatic ring in structure of polycyclic aromatic hydrocarbons significantly strengthens CH/O interactions. Calculated interaction energies in optimized structures of the most stable tetracene/water complex is -2.27 kcal/mol, anthracene/water is -2.13 kcal/mol and naphthalene/water is -1.97 kcal/mol. These interactions are stronger than CH/O contacts in benzene/water complex (-1.44 kcal/mol) while CH/O contacts in tetracene/water complex are even stronger than CH/O contacts in pyridine/water complexes (-2.21 kcal/mol). Electrostatic potential maps for different polycyclic aromatic hydrocarbons were calculated and used to explain trends in the energies of interactions. Copyright © 2017 Elsevier Inc. All rights reserved.

Supratransmission in a metastable modular metastructure for tunable non-reciprocal wave transmission

NASA Astrophysics Data System (ADS)

Wu, Zhen; Wang, K. W.

2018-03-01

In this research, we numerically and analytically investigate the nonlinear energy transmission phenomenon in a metastable modular metastructure. Numerical studies on a 1D metastable chain provide clear evidence that when driving frequency is within the stopband of the periodic structure, there exists a threshold for the driving amplitude, above which sudden increase in the energy transmission can be observed. This onset of transmission is due to nonlinear instability and is known as supratransmission. We discover that due to spatial asymmetry of strategically configured constituents, such transmission thresholds are considerably different when structure is excited from different ends and this discrepancy creates a region of non-reciprocal energy transmission. We demonstrate that when the loss of stability is due to saddlenode bifurcation, the transmission threshold can be predicted analytically using a localized nonlinear-linear system model, and analyzed via combining harmonic balancing and transfer matrix methods. These investigations elucidate the rich and complex dynamics achievable by nonlinearity and metastabilities, and provide synthesize tools for tunable bandgaps and non-reciprocal wave transmissions.

Free energy determinants of secondary structure formation: III. beta-turns and their role in protein folding.

PubMed

Yang, A S; Hitz, B; Honig, B

1996-06-21

The stability of beta-turns is calculated as a function of sequence and turn type with a Monte Carlo sampling technique. The conformational energy of four internal hydrogen-bonded turn types, I, I', II and II', is obtained by evaluating their gas phase energy with the CHARMM force field and accounting for solvation effects with the Finite Difference Poisson-Boltzmann (FDPB) method. All four turn types are found to be less stable than the coil state, independent of the sequence in the turn. The free-energy penalties associated with turn formation vary between 1.6 kcal/mol and 7.7 kcal/mol, depending on the sequence and turn type. Differences in turn stability arise mainly from intraresidue interactions within the two central residues of the turn. For each combination of the two central residues, except for -Gly-Gly-, the most stable beta-turn type is always found to occur most commonly in native proteins. The fact that a model based on local interactions accounts for the observed preference of specific sequences suggests that long-range tertiary interactions tend to play a secondary role in determining turn conformation. In contrast, for beta-hairpins, long-range interactions appear to dominate. Specifically, due to the right-handed twist of beta-strands, type I' turns for -Gly-Gly- are found to occur with high frequency, even when local energetics would dictate otherwise. The fact that any combination of two residues is found able to adopt a relatively low-energy turn structure explains why the amino acid sequence in turns is highly variable. The calculated free-energy cost of turn formation, when combined with related numbers obtained for alpha-helices and beta-sheets, suggests a model for the initiation of protein folding based on metastable fragments of secondary structure.

A bio-inspired study on tidal energy extraction with flexible flapping wings.

PubMed

Liu, Wendi; Xiao, Qing; Cheng, Fai

2013-09-01

Previous research on the flexible structure of flapping wings has shown an improved propulsion performance in comparison to rigid wings. However, not much is known about this function in terms of power efficiency modification for flapping wing energy devices. In order to study the role of the flexible wing deformation in the hydrodynamics of flapping wing energy devices, we computationally model the two-dimensional flexible single and twin flapping wings in operation under the energy extraction conditions with a large Reynolds number of 106. The flexible motion for the present study is predetermined based on a priori structural result which is different from a passive flexibility solution. Four different models are investigated with additional potential local distortions near the leading and trailing edges. Our simulation results show that the flexible structure of a wing is beneficial to enhance power efficiency by increasing the peaks of lift force over a flapping cycle, and tuning the phase shift between force and velocity to a favourable trend. Moreover, the impact of wing flexibility on efficiency is more profound at a low nominal effective angle of attack (AoA). At a typical flapping frequency f * = 0.15 and nominal effective AoA of 10°, a flexible integrated wing generates 7.68% higher efficiency than a rigid wing. An even higher increase, around six times that of a rigid wing, is achievable if the nominal effective AoA is reduced to zero degrees at feathering condition. This is very attractive for a semi-actuated flapping energy system, where energy input is needed to activate the pitching motion. The results from our dual-wing study found that a parallel twin-wing device can produce more power compared to a single wing due to the strong flow interaction between the two wings.

Characterization of prepared In2O3 thin films: The FT-IR, FT-Raman, UV-Visible investigation and optical analysis.

PubMed

Panneerdoss, I Joseph; Jeyakumar, S Johnson; Ramalingam, S; Jothibas, M

2015-08-05

In this original work, the Indium oxide (In2O3) thin film is deposited cleanly on microscope glass substrate at different temperatures by spray pyrolysis technique. The physical properties of the films are characterized by XRD, SEM, AFM and AFM measurements. The spectroscopic investigation has been carried out on the results of FT-IR, FT-Raman and UV-Visible. XRD analysis exposed that the structural transformation of films from stoichiometric to non-stoichiometric orientation of the plane vice versa and also found that, the film is polycrystalline in nature having cubic crystal structure with a preferred grain orientation along (222) plane. SEM and AFM studies revealed that, the film with 0.1M at 500°C has spherical grains with uniform dimension. The complete vibrational analysis has been carried out and the optimized parameters are calculated using HF and DFT (CAM-B3LYP, B3LYP and B3PW91) methods with 3-21G(d,p) basis set. Furthermore, NMR chemical shifts are calculated by using the gauge independent atomic orbital (GIAO) technique. The molecular electronic properties; absorption wavelengths, excitation energy, dipole moment and frontier molecular orbital energies, molecular electrostatic potential energy (MEP) analysis and Polarizability first order hyperpolarizability calculations are performed by time dependent DFT (TD-DFT) approach. The energy excitation on electronic structure is investigated and the assignment of the absorption bands in the electronic spectra of steady compound is discussed. The calculated HOMO and LUMO energies showed the enhancement of energy gap by the addition of substitutions with the base molecule. The thermodynamic properties (heat capacity, entropy, and enthalpy) at different temperatures are calculated and interpreted in gas phase. Crown Copyright © 2015. Published by Elsevier B.V. All rights reserved.

On the Monte Carlo simulation of electron transport in the sub-1 keV energy range.

PubMed

Thomson, Rowan M; Kawrakow, Iwan

2011-08-01

The validity of "classic" Monte Carlo (MC) simulations of electron and positron transport at sub-1 keV energies is investigated in the context of quantum theory. Quantum theory dictates that uncertainties on the position and energy-momentum four-vectors of radiation quanta obey Heisenberg's uncertainty relation; however, these uncertainties are neglected in "classical" MC simulations of radiation transport in which position and momentum are known precisely. Using the quantum uncertainty relation and electron mean free path, the magnitudes of uncertainties on electron position and momentum are calculated for different kinetic energies; a validity bound on the classical simulation of electron transport is derived. In order to satisfy the Heisenberg uncertainty principle, uncertainties of 5% must be assigned to position and momentum for 1 keV electrons in water; at 100 eV, these uncertainties are 17 to 20% and are even larger at lower energies. In gaseous media such as air, these uncertainties are much smaller (less than 1% for electrons with energy 20 eV or greater). The classical Monte Carlo transport treatment is questionable for sub-1 keV electrons in condensed water as uncertainties on position and momentum must be large (relative to electron momentum and mean free path) to satisfy the quantum uncertainty principle. Simulations which do not account for these uncertainties are not faithful representations of the physical processes, calling into question the results of MC track structure codes simulating sub-1 keV electron transport. Further, the large difference in the scale at which quantum effects are important in gaseous and condensed media suggests that track structure measurements in gases are not necessarily representative of track structure in condensed materials on a micrometer or a nanometer scale.

Thermoelectric Energy Harvesting Using Phase Change Materials (PCMs) in High Temperature Environments in Aircraft

NASA Astrophysics Data System (ADS)

Elefsiniotis, A.; Becker, Th.; Schmid, U.

2014-06-01

Wireless, energy-autonomous structural health-monitoring systems in aircraft have the potential of reducing total maintenance costs. Thermoelectric energy harvesting, which seems the best choice for creating truly autonomous health monitoring sensors, is the principle behind converting waste heat to useful electrical energy through the use of thermoelectric generators. To enhance the temperature difference across the two sides of a thermoelectric generator, i.e. increasing heat flux and energy production, a phase change material acting as thermal mass is attached on one side of the thermoelectric generators while the other side is placed on the aircraft structure. The application area under investigation for this paper is the pylon aft fairing, located near the engine of an aircraft, with temperatures reaching on the inside up to 350 °C. Given these harsh operational conditions, the performance of a device, containing erythritol as a phase change material, is evaluated. The harvested energy reaching values up to 81.4 J can be regulated by a power management module capable of storing the excess energy and recovering it from the medium powering a sensor node and a wireless transceiver.

Photoelectron Spectroscopy of Substituted Phenylnitrenes

NASA Astrophysics Data System (ADS)

Wijeratne, Neloni R.; Da Fonte, Maria; Wenthold, Paul G.

2009-06-01

Nitrenes are unusual molecular structures with unfilled electronic valences that are isoelectronic with carbenes. Although, both can be generated by either thermal or photochemical decomposition of appropriate precursors they usually exhibit different reactivities. In this work, we carry out spectroscopic studies of substituted phenylnitrene to determine how the introduction of substituents will affect the reactivity and its thermochemical properties. All studies were carried out by using the newly constructed time-of-flight negative ion photoelectron spectrometer (NIPES) at Purdue University. The 355 nm photoelectron spectra of the o-, m-, and p-chlorophenyl nitrene anions are fairly similar to that measured for phenylnitrene anion. All spectra show low energy triplet state and a high energy singlet state. The singlet state for the meta isomer is well-resolved, with a well defined origin and observable vibrational structure. Whereas the singlet states for the ortho and para isomers have lower energy onsets and no resolved structure. The isomeric dependence suggests that the geometry differences result from the resonance interaction between the nitrogen and the substituent. Quinoidal resonance structures are possible for the open-shell singlet states of the o- and p-chlorinated phenyl nitrenes. The advantages of this type of electronic structures for the open-shell singlet states is that the unpaired electrons can be more localized on separate atoms in the molecules, minimizing the repulsion between. Because the meta position is not in resonance with the nitrenes, substitution at that position should not affect the structure of the open-shell singlet state. The measured electron affinities (EA) of the triplet phenylnitrenes are in excellent agreement with the values predicted by electronic structure calculations. The largest EA, 1.82 eV is found for the meta isomer, with para being the smallest, 1.70 eV.

Anisotropy and the knee of the energy spectrum

NASA Technical Reports Server (NTRS)

Clay, R. W.

1985-01-01

The measured cosmic ray energy spectrum exhibits clear structure (the knee) at approx 3 x 10 to the 15th power eV (sea level shower size approx 3 x 10 to the 5th power particles). Additionally, at energies in this general region, there occur apparent changes in shower development such that the observed characteristics of showers at this energy appear different to those characteristics observed at somewhat higher energies. At energies just below this region, the cosmic ray anisotropy amplitude apparently begins a progressive increase with energy. The latter effect does not clearly fit with the first two since there appears to be no significant change exactly at the knee. However, the phase of the first harmonic of the anisotropy appears to show a substantial change just where the energy spectrum shows structure and in the middle of the shower development changes. The first harmonic phase appears to change from approx. 18 hours R.A. to approx. 5 hours R.A. as the energy of observation moves through the knee. In this paper the latter change is examined in some detail by taking into account information contained in the second harmonic of the anisotropy.

Nonplanar core structure of the screw dislocations in tantalum from the improved Peierls-Nabarro theory

NASA Astrophysics Data System (ADS)

Hu, Xiangsheng; Wang, Shaofeng

2018-02-01

The extended structure of ? screw dislocation in Ta has been studied theoretically using the improved Peierls-Nabarro model combined with the first principles calculation. An instructive way to derive the fundamental equation for dislocations with the nonplanar structure is presented. The full ?-surface of ? plane in tantalum is evaluated from the first principles. In order to compare the energy of the screw dislocation with different structures, the structure parameter is introduced to describe the core configuration. Each kind of screw dislocation is described by an overall-shape component and a core component. Far from the dislocation centre, the asymptotic behaviour of dislocation is uniquely controlled by the overall-shape component. Near the dislocation centre, the structure detail is described by the core component. The dislocation energy is explicitly plotted as a function of the core parameter for the nonplanar dislocation as well as for the planar dislocation. It is found that in the physical regime of the core parameter, the sixfold nonplanar structure always has the lowest energy. Our result clearly confirms that the sixfold nonplanar structure is the most stable. Furthermore, the pressure effect on the dislocation structure is explored up to 100 GPa. The stability of the sixfold nonplanar structure is not changed by the applied pressure. The equilibrium structure and the related stress field are calculated, and a possible mechanism of the dislocation movement is discussed briefly based on the structure deformation caused by the external stress.

Free-energy landscape of the GB1 hairpin in all-atom explicit solvent simulations with different force fields: Similarities and differences.

PubMed

Best, Robert B; Mittal, Jeetain

2011-04-01

Although it is now possible to fold peptides and miniproteins in molecular dynamics simulations, it is well appreciated that force fields are not all transferable to different proteins. Here, we investigate the influence of the protein force field and the solvent model on the folding energy landscape of a prototypical two-state folder, the GB1 hairpin. We use extensive replica-exchange molecular dynamics simulations to characterize the free-energy surface as a function of temperature. Most of these force fields appear similar at a global level, giving a fraction folded at 300 K between 0.2 and 0.8 in all cases, which is a difference in stability of 2.8 kT, and are generally consistent with experimental data at this temperature. The most significant differences appear in the unfolded state, where there are different residual secondary structures which are populated, and the overall dimensions of the unfolded states, which in most of the force fields are too collapsed relative to experimental Förster Resonance Energy Transfer (FRET) data.

A Gas-Actuated Projectile Launcher for High-Energy Impact Testing of Structures

NASA Technical Reports Server (NTRS)

Ambur, Damodar R.; Jaunky, Navin; Lawson, Robin E.; Knight, Norman F., Jr.; Lyle, Karen H.

1999-01-01

A gas-act,uated penetration device has been developed for high-energy impact testing of structures. The high-energy impact. t,estiiig is for experimental simulation of uncontained engine failures. The non-linear transient finite element, code LS-DYNA3D has been used in the numerical simula.tions of a titanium rectangular blade with a.n aluminum target, plate. Threshold velocities for different combinations of pitch and yaw angles of the impactor were obtained for the impactor-target, t8est configuration in the numerica.1 simulations. Complet,e penet,ration of the target plate was also simulat,ed numerically. Finally, limited comparison of analytical and experimental results is presented for complete penetration of the target by the impactor.

Theoretical Study of Fe(CO)n-

NASA Technical Reports Server (NTRS)

Ricca, Alessandra; Baushlicher, Charles W., Jr.

1995-01-01

The structures and CO binding energies are computed for Fe(CO)n- using a hybrid density functional theory (DFT) approach. The structures and ground states can be explained in terms of maximizing the Fe to CO 2pi* donation and minimizing Fe-CO 5 sigma repulsion. The trends in the CO binding energies for Fe(CO)n- and the differences between the trends for Fe(CO)n- and Fe(CO)n are also explained. For Fe(CO)n-, the second, third, and fourth CO bonding energies are in good agreement with experiment, while the first is too small. The first CO binding is also too small using the coupled cluster singles and doubles approach including a perturbation estimate of the connected triple excitations.

Nuclear Data Sheets for A=40

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

Chen, Jun

The experimental nuclear structure data and decay data are evaluated for the known nuclides of mass 40 (Mg, Al, Si, P, S, Cl, Ar, K, Ca, Sc, Ti). Detailed evaluated nuclear structure information is presented with the best values recommended for level energies, half-lives, γ-ray energies and intensities, decay properties (energies, intensities and placement of radiations), and other spectroscopic data. The {sup 40}Ca and {sup 40}K nuclides remain as the most extensively studied from many different reactions and decays; no excited states are known in {sup 40}Mg, {sup 40}Al, {sup 40}P and {sup 40}Ti. This work supersedes the earlier fullmore » evaluation of A=40 by J. Cameron and B. Singh (2004Ca38).« less

Stochastic annealing simulations of defect interactions among subcascades

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

Heinisch, H.L.; Singh, B.N.

1997-04-01

The effects of the subcascade structure of high energy cascades on the temperature dependencies of annihilation, clustering and free defect production are investigated. The subcascade structure is simulated by closely spaced groups of lower energy MD cascades. The simulation results illustrate the strong influence of the defect configuration existing in the primary damage state on subsequent intracascade evolution. Other significant factors affecting the evolution of the defect distribution are the large differences in mobility and stability of vacancy and interstitial defects and the rapid one-dimensional diffusion of small, glissile interstitial loops produced directly in cascades. Annealing simulations are also performedmore » on high-energy, subcascade-producing cascades generated with the binary collision approximation and calibrated to MD results.« less