Energy Landscape of All-Atom Protein-Protein Interactions Revealed by Multiscale Enhanced Sampling
Moritsugu, Kei; Terada, Tohru; Kidera, Akinori
2014-01-01
Protein-protein interactions are regulated by a subtle balance of complicated atomic interactions and solvation at the interface. To understand such an elusive phenomenon, it is necessary to thoroughly survey the large configurational space from the stable complex structure to the dissociated states using the all-atom model in explicit solvent and to delineate the energy landscape of protein-protein interactions. In this study, we carried out a multiscale enhanced sampling (MSES) simulation of the formation of a barnase-barstar complex, which is a protein complex characterized by an extraordinary tight and fast binding, to determine the energy landscape of atomistic protein-protein interactions. The MSES adopts a multicopy and multiscale scheme to enable for the enhanced sampling of the all-atom model of large proteins including explicit solvent. During the 100-ns MSES simulation of the barnase-barstar system, we observed the association-dissociation processes of the atomistic protein complex in solution several times, which contained not only the native complex structure but also fully non-native configurations. The sampled distributions suggest that a large variety of non-native states went downhill to the stable complex structure, like a fast folding on a funnel-like potential. This funnel landscape is attributed to dominant configurations in the early stage of the association process characterized by near-native orientations, which will accelerate the native inter-molecular interactions. These configurations are guided mostly by the shape complementarity between barnase and barstar, and lead to the fast formation of the final complex structure along the downhill energy landscape. PMID:25340714
Genheden, Samuel; Cabedo Martinez, Ana I; Criddle, Michael P; Essex, Jonathan W
2014-03-01
We present our predictions for the SAMPL4 hydration free energy challenge. Extensive all-atom Monte Carlo simulations were employed to sample the compounds in explicit solvent. While the focus of our study was to demonstrate well-converged and reproducible free energies, we attempted to address the deficiencies in the general Amber force field force field with a simple QM/MM correction. We show that by using multiple independent simulations, including different starting configurations, and enhanced sampling with parallel tempering, we can obtain well converged hydration free energies. Additional analysis using dihedral angle distributions, torsion-root mean square deviation plots and thermodynamic cycles support this assertion. We obtain a mean absolute deviation of 1.7 kcal mol(-1) and a Kendall's τ of 0.65 compared with experiment. PMID:24488307
NASA Astrophysics Data System (ADS)
Takemura, Kazuhiro; Guo, Hao; Sakuraba, Shun; Matubayasi, Nobuyuki; Kitao, Akio
2012-12-01
We propose a method to evaluate binding free energy differences among distinct protein-protein complex model structures through all-atom molecular dynamics simulations in explicit water using the solution theory in the energy representation. Complex model structures are generated from a pair of monomeric structures using the rigid-body docking program ZDOCK. After structure refinement by side chain optimization and all-atom molecular dynamics simulations in explicit water, complex models are evaluated based on the sum of their conformational and solvation free energies, the latter calculated from the energy distribution functions obtained from relatively short molecular dynamics simulations of the complex in water and of pure water based on the solution theory in the energy representation. We examined protein-protein complex model structures of two protein-protein complex systems, bovine trypsin/CMTI-1 squash inhibitor (PDB ID: 1PPE) and RNase SA/barstar (PDB ID: 1AY7), for which both complex and monomer structures were determined experimentally. For each system, we calculated the energies for the crystal complex structure and twelve generated model structures including the model most similar to the crystal structure and very different from it. In both systems, the sum of the conformational and solvation free energies tended to be lower for the structure similar to the crystal. We concluded that our energy calculation method is useful for selecting low energy complex models similar to the crystal structure from among a set of generated models.
NASA Astrophysics Data System (ADS)
Takemura, Kazuhiro; Burri, Raghunadha Reddy; Ishikawa, Takeshi; Ishikura, Takakazu; Sakuraba, Shun; Matubayasi, Nobuyuki; Kuwata, Kazuo; Kitao, Akio
2013-02-01
We propose a method for calculating the binding free energy of protein-ligand complexes using all-atom molecular dynamics simulation combined with the solution theory in the energy representation. Four distinct modes for the binding of tri-N-acetyl-D-glucosamine (triNAG) to hen egg-white lysozyme were investigated, one from the crystal structure and three generated by docking predictions. The proposed method was demonstrated to be used to distinguish the most plausible binding mode (crystal model) as the lowest binding energy mode.
Woo, Sun Young; Lee, Hwankyu
2016-01-01
Peptides E and K, which are synthetic coiled-coil peptides for membrane fusion, were simulated with lipid bilayers composed of lipids and cholesterols at different ratios using all-atom models. We first calculated free energies of binding from umbrella sampling simulations, showing that both E and K peptides tend to adsorb onto the bilayer surface, which occurs more strongly in the bilayer composed of smaller lipid headgroups. Then, unrestrained simulations show that K peptides more deeply insert into the bilayer with partially retaining the helical structure, while E peptides less insert and predominantly become random coils, indicating the structural transition from helices to random coils, in quantitative agreement with experiments. This is because K peptides electrostatically interact with lipid phosphates, as well as because hydrocarbons of lysines of K peptide are longer than those of glutamic acids of E peptide and thus form stronger hydrophobic interactions with lipid tails. This deeper insertion of K peptide increases the bilayer dynamics and a vacancy below the peptide, leading to the rearrangement of smaller lipids. These findings help explain the experimentally observed or proposed differences in the insertion depth, binding strength, and structural transition of E and K peptides, and support the snorkeling effect. PMID:26926570
Woo, Sun Young; Lee, Hwankyu
2016-01-01
Peptides E and K, which are synthetic coiled-coil peptides for membrane fusion, were simulated with lipid bilayers composed of lipids and cholesterols at different ratios using all-atom models. We first calculated free energies of binding from umbrella sampling simulations, showing that both E and K peptides tend to adsorb onto the bilayer surface, which occurs more strongly in the bilayer composed of smaller lipid headgroups. Then, unrestrained simulations show that K peptides more deeply insert into the bilayer with partially retaining the helical structure, while E peptides less insert and predominantly become random coils, indicating the structural transition from helices to random coils, in quantitative agreement with experiments. This is because K peptides electrostatically interact with lipid phosphates, as well as because hydrocarbons of lysines of K peptide are longer than those of glutamic acids of E peptide and thus form stronger hydrophobic interactions with lipid tails. This deeper insertion of K peptide increases the bilayer dynamics and a vacancy below the peptide, leading to the rearrangement of smaller lipids. These findings help explain the experimentally observed or proposed differences in the insertion depth, binding strength, and structural transition of E and K peptides, and support the snorkeling effect. PMID:26926570
NASA Astrophysics Data System (ADS)
Woo, Sun Young; Lee, Hwankyu
2016-03-01
Peptides E and K, which are synthetic coiled-coil peptides for membrane fusion, were simulated with lipid bilayers composed of lipids and cholesterols at different ratios using all-atom models. We first calculated free energies of binding from umbrella sampling simulations, showing that both E and K peptides tend to adsorb onto the bilayer surface, which occurs more strongly in the bilayer composed of smaller lipid headgroups. Then, unrestrained simulations show that K peptides more deeply insert into the bilayer with partially retaining the helical structure, while E peptides less insert and predominantly become random coils, indicating the structural transition from helices to random coils, in quantitative agreement with experiments. This is because K peptides electrostatically interact with lipid phosphates, as well as because hydrocarbons of lysines of K peptide are longer than those of glutamic acids of E peptide and thus form stronger hydrophobic interactions with lipid tails. This deeper insertion of K peptide increases the bilayer dynamics and a vacancy below the peptide, leading to the rearrangement of smaller lipids. These findings help explain the experimentally observed or proposed differences in the insertion depth, binding strength, and structural transition of E and K peptides, and support the snorkeling effect.
Whitford, Paul C; Noel, Jeffrey K; Gosavi, Shachi; Schug, Alexander; Sanbonmatsu, Kevin Y; Onuchic, José N
2009-05-01
Protein dynamics take place on many time and length scales. Coarse-grained structure-based (Go) models utilize the funneled energy landscape theory of protein folding to provide an understanding of both long time and long length scale dynamics. All-atom empirical forcefields with explicit solvent can elucidate our understanding of short time dynamics with high energetic and structural resolution. Thus, structure-based models with atomic details included can be used to bridge our understanding between these two approaches. We report on the robustness of folding mechanisms in one such all-atom model. Results for the B domain of Protein A, the SH3 domain of C-Src Kinase, and Chymotrypsin Inhibitor 2 are reported. The interplay between side chain packing and backbone folding is explored. We also compare this model to a C(alpha) structure-based model and an all-atom empirical forcefield. Key findings include: (1) backbone collapse is accompanied by partial side chain packing in a cooperative transition and residual side chain packing occurs gradually with decreasing temperature, (2) folding mechanisms are robust to variations of the energetic parameters, (3) protein folding free-energy barriers can be manipulated through parametric modifications, (4) the global folding mechanisms in a C(alpha) model and the all-atom model agree, although differences can be attributed to energetic heterogeneity in the all-atom model, and (5) proline residues have significant effects on folding mechanisms, independent of isomerization effects. Because this structure-based model has atomic resolution, this work lays the foundation for future studies to probe the contributions of specific energetic factors on protein folding and function. PMID:18837035
Mishra, Avdesh; Iqbal, Sumaiya; Hoque, Md Tamjidul
2016-06-01
The success of solving the protein folding and structure prediction problems in molecular and structural biology relies on an accurate energy function. With the rapid advancement in the computational biology and bioinformatics fields, there is a growing need of solving unknown fold and structure faster and thus an accurate energy function is indispensable. To address this need, we develop a new potential function, namely 3DIGARS3.0, which is a linearly weighted combination of 3DIGARS, mined accessible surface area (ASA) and ubiquitously computed Phi (uPhi) and Psi (uPsi) energies - optimized by a Genetic Algorithm (GA). We use a dataset of 4332 protein-structures to generate uPhi and uPsi based score libraries to be used within the core 3DIGARS method. The optimized weight of each component is obtained by applying Genetic Algorithm based optimization on three challenging decoy sets. The improved 3DIGARS3.0 outperformed state-of-the-art methods significantly based on a set of independent test datasets. PMID:27029514
Improving an all-atom force field.
Mohanty, Sandipan; Hansmann, U H E
2007-07-01
Experimentally well-characterized proteins that are small enough to be computationally tractable provide useful information for refining existing all-atom force fields. This is used by us for reparametrizing a recently developed all-atom force field. Relying on high statistics parallel tempering simulations of a designed 20 residue beta-sheet peptide, we propose incremental changes that improve the force field's range of applicability. PMID:17677516
An effective all-atom potential for proteins
Irbäck, Anders; Mitternacht, Simon; Mohanty, Sandipan
2009-01-01
We describe and test an implicit solvent all-atom potential for simulations of protein folding and aggregation. The potential is developed through studies of structural and thermodynamic properties of 17 peptides with diverse secondary structure. Results obtained using the final form of the potential are presented for all these peptides. The same model, with unchanged parameters, is furthermore applied to a heterodimeric coiled-coil system, a mixed α/β protein and a three-helix-bundle protein, with very good results. The computational efficiency of the potential makes it possible to investigate the free-energy landscape of these 49–67-residue systems with high statistical accuracy, using only modest computational resources by today's standards. PACS Codes: 87.14.E-, 87.15.A-, 87.15.Cc PMID:19356242
Ab initio prediction of protein structure with both all-atom and simplified force fields
NASA Astrophysics Data System (ADS)
Scheraga, Harold
2004-03-01
Using only a physics-based ab initio method, and both all-atom (ECEPP/3) and simplified united-residue (UNRES) force fields, global optimization of both potential functions with Monte Carlo-plus-Minimization (MCM) and Conformational Space Annealing (CSA), respectively, provides predicted structures of proteins without use of knowledge-based information. The all-atom approach has been applied to the 46-residue protein A, and the UNRES approach has been applied to larger CASP targets. The predicted structures will be described.
All-atom simulations of crowding effects on ubiquitin dynamics
NASA Astrophysics Data System (ADS)
Abriata, Luciano A.; Spiga, Enrico; Dal Peraro, Matteo
2013-08-01
It is well-known that crowded environments affect the stability of proteins, with strong biological and biotechnological implications; however, beyond this, crowding is also expected to affect the dynamic properties of proteins, an idea that is hard to probe experimentally. Here we report on a simulation study aimed at evaluating the effects of crowding on internal protein dynamics, based on fully all-atom descriptions of the protein, the solvent and the crowder. Our model system consists of ubiquitin, a protein whose dynamic features are closely related to its ability to bind to multiple partners, in a 325 g L-1 solution of glucose in water, a condition widely employed in in vitro studies of crowding effects. We observe a slight reduction in loop flexibility accompanied by a dramatic restriction of the conformational space explored in the timescale of the simulations (˜0.5 µs), indicating that crowding slows down collective motions and the rate of exploration of the conformational space. This effect is attributed to the extensive and long-lasting interactions observed between protein residues and glucose molecules throughout the entire protein surface. Potential implications of the observed effects are discussed.
An all-atom force field developed for Zn₄O(RCO₂)₆ metal organic frameworks.
Sun, Yingxin; Sun, Huai
2014-03-01
An all-atom force field is developed for metal organic frameworks Zn₄O(RCO₂)₆ by fitting to quantum mechanics data. Molecular simulations are conducted to validate the force field by calculating thermal expansion coefficients, crystal bulk and Young's moduli, power spectra, self-diffusion coefficients, and activation energies of self-diffusions for benzene and n-hexane. The calculated results are in good agreement with available experimental data. The proposed force field is suitable for simulations of adsorption or diffusion of organic molecules with flexible frameworks. PMID:24562858
An All-Atom Force Field for Tertiary Structure Prediction of Helical Proteins
Herges, T.; Wenzel, W.
2004-01-01
We have developed an all-atom free-energy force field (PFF01) for protein tertiary structure prediction. PFF01 is based on physical interactions and was parameterized using experimental structures of a family of proteins believed to span a wide variety of possible folds. It contains empirical, although sequence-independent terms for hydrogen bonding. Its solvent-accessible surface area solvent model was first fit to transfer energies of small peptides. The parameters of the solvent model were then further optimized to stabilize the native structure of a single protein, the autonomously folding villin headpiece, against competing low-energy decoys. Here we validate the force field for five nonhomologous helical proteins with 20–60 amino acids. For each protein, decoys with 2–3 Å backbone root mean-square deviation and correct experimental Cβ–Cβ distance constraints emerge as those with the lowest energy. PMID:15507688
Hydration Properties and Solvent Effects for All-Atom Solutes in Polarizable Coarse-Grained Water.
Yan, Xin Cindy; Tirado-Rives, Julian; Jorgensen, William L
2016-08-25
Due to the importance of water in chemical and biological systems, a coarse-grained representation of the solvent can greatly simplify the description of the system while retaining key thermodynamic properties of the medium. A multiscale solvation model that couples all-atom solutes and polarizable Martini coarse-grained water (AAX/CGS) is developed to reproduce free energies of hydration of organic solutes. Using Monte Carlo/free energy perturbation (MC/FEP) calculations, results from multiscale and all-atom simulations are compared. Improved accuracy is obtained with the AAX/CGS approach for hydrophobic and sulfur- or halogen-containing solutes, but larger deviations are found for polar solute molecules where hydrogen bonding is featured. Furthermore, solvent effects on conformational and tautomeric equilibria of AA solutes were investigated using AA, CG, and GB/SA solvent models. It is found that the CG solvent model can reproduce well the medium effects from experiment and AA simulations; however, the GB/SA solvent model fails in some cases. A 7-30-fold reduction in computational cost is found for the present AAX/CGS multiscale simulations compared to the AA alternative. PMID:26901452
NASA Astrophysics Data System (ADS)
Cui, Qizhi; Smith, Vedene H.
2001-08-01
Following our previous paper on methane [Cui and Smith, J. Chem. Phys. 113, 10240 (2000)], we study the solvation structures and thermodynamics of ethane and propane in water at the infinite dilution limit by using the hypernetted chain closure reference interaction site model (HNC-RISM) theory with all-atom representations for solute molecules. At four thermodynamic states: temperature T=283.15, 298.15, 313.15, 328.15 K and the corresponding bulk water density ρ=0.9997, 0.9970, 0.9922, 0.9875 g cm-3, all the atomic solute-solvent radial distribution functions are obtained, and the corresponding running coordination numbers and the hydration free energies, energies, enthalpies, and entropies are calculated with the radial distribution functions as input. The hydration structures of ethane and propane are presented and analyzed at the atomic level in terms of the atomic solute-solvent radial distribution functions. With the optimized nonbonded potential parameters based on the CHARMM96 all-atom model for alkanes [Yin and Mackerell, J. Comput. Chem. 19, 334 (1998)], the ethane and propane hydration thermodynamic properties predicted by the HNC-RISM theory are improved in the specified temperature range (10-55 °C).
All-atom simulation study of protein PTH(1-34) by using the Wang-Landau sampling method
NASA Astrophysics Data System (ADS)
Kim, Seung-Yeon; Kwak, Wooseop
2014-12-01
We perform simulations of the N-terminal 34-residue protein fragment PTH(1-34), consisting of 581 atoms, of the 84-residue human parathyroid hormone by using the all-atom ECEPP/3 force field and the Wang-Landau sampling method. Through a massive high-performance computation, the density of states and the partition function Z( T), as a continuous function of T, are obtained for PTH(1-34). From the continuous partition function Z( T), the partition function zeros of PTH(1-34) are evaluated for the first time. From both the specific heat and the partition function zeros, two characteristic transition temperatures are obtained for the all-atom protein PTH(1-34). The higher transition temperature T 1 and the lower transition temperature T 2 of PTH(1-34) can be interpreted as the collapse temperature T θ and the folding temperature T f , respectively.
Benchmarking all-atom simulations using hydrogen exchange
Skinner, John J.; Yu, Wookyung; Gichana, Elizabeth K.; Baxa, Michael C.; Hinshaw, James R.; Freed, Karl F.; Sosnick, Tobin R.
2014-01-01
Long-time molecular dynamics (MD) simulations are now able to fold small proteins reversibly to their native structures [Lindorff-Larsen K, Piana S, Dror RO, Shaw DE (2011) Science 334(6055):517–520]. These results indicate that modern force fields can reproduce the energy surface near the native structure. To test how well the force fields recapitulate the other regions of the energy surface, MD trajectories for a variant of protein G are compared with data from site-resolved hydrogen exchange (HX) and other biophysical measurements. Because HX monitors the breaking of individual H-bonds, this experimental technique identifies the stability and H-bond content of excited states, thus enabling quantitative comparison with the simulations. Contrary to experimental findings of a cooperative, all-or-none unfolding process, the simulated denatured state ensemble, on average, is highly collapsed with some transient or persistent native 2° structure. The MD trajectories of this protein G variant and other small proteins exhibit excessive intramolecular H-bonding even for the most expanded conformations, suggesting that the force fields require improvements in describing H-bonding and backbone hydration. Moreover, these comparisons provide a general protocol for validating the ability of simulations to accurately capture rare structural fluctuations. PMID:25349413
All-Atom Molecular Dynamics of Virus Capsids as Drug Targets.
Perilla, Juan R; Hadden, Jodi A; Goh, Boon Chong; Mayne, Christopher G; Schulten, Klaus
2016-05-19
Virus capsids are protein shells that package the viral genome. Although their morphology and biological functions can vary markedly, capsids often play critical roles in regulating viral infection pathways. A detailed knowledge of virus capsids, including their dynamic structure, interactions with cellular factors, and the specific roles that they play in the replication cycle, is imperative for the development of antiviral therapeutics. The following Perspective introduces an emerging area of computational biology that focuses on the dynamics of virus capsids and capsid-protein assemblies, with particular emphasis on the effects of small-molecule drug binding on capsid structure, stability, and allosteric pathways. When performed at chemical detail, molecular dynamics simulations can reveal subtle changes in virus capsids induced by drug molecules a fraction of their size. Here, the current challenges of performing all-atom capsid-drug simulations are discussed, along with an outlook on the applicability of virus capsid simulations to reveal novel drug targets. PMID:27128262
All-atom homology model of the Escherichia coli 30S ribosomal subunit.
Tung, Chang-Shung; Joseph, Simpson; Sanbonmatsu, Kevin Y
2002-10-01
Understanding the structural basis of ribosomal function requires close comparison between biochemical and structural data. Although a large amount of biochemical data are available for the Escherichia coli ribosome, the structure has not been solved to atomic resolution. Using a new RNA homology procedure, we have modeled the all-atom structure of the E. coli 30S ribosomal subunit. We find that the tertiary structure of the ribosome core, including the A-, P- and E-sites, is highly conserved. The hypervariable regions in our structure, which differ from the structure of the 30S ribosomal subunit from Thermus thermophilus, are consistent with the cryo-EM map of the E. coli ribosome. PMID:12244297
All-Atom Molecular Dynamics of Virus Capsids as Drug Targets
2016-01-01
Virus capsids are protein shells that package the viral genome. Although their morphology and biological functions can vary markedly, capsids often play critical roles in regulating viral infection pathways. A detailed knowledge of virus capsids, including their dynamic structure, interactions with cellular factors, and the specific roles that they play in the replication cycle, is imperative for the development of antiviral therapeutics. The following Perspective introduces an emerging area of computational biology that focuses on the dynamics of virus capsids and capsid–protein assemblies, with particular emphasis on the effects of small-molecule drug binding on capsid structure, stability, and allosteric pathways. When performed at chemical detail, molecular dynamics simulations can reveal subtle changes in virus capsids induced by drug molecules a fraction of their size. Here, the current challenges of performing all-atom capsid–drug simulations are discussed, along with an outlook on the applicability of virus capsid simulations to reveal novel drug targets. PMID:27128262
Folding peptides and proteins with all-atom physics: methods and applications
NASA Astrophysics Data System (ADS)
Shell, M. Scott
2008-03-01
Computational methods offer powerful tools for investigating proteins and peptides at the molecular-level; however, it has proven challenging to reproduce the long time scale folding processes of these molecules at a level that is both faithful to the atomic driving forces and attainable with modern commodity cluster computing. Alternatively, the past decade has seen significant progress in using bioinformatics-based approaches to infer the three dimensional native structures of proteins, drawing upon extensive knowledge databases of known protein structures [1]. These methods work remarkably well when a homologous protein can be found to provide a structural template for a candidate sequence. However, in cases where homology to database proteins is low, where the folding pathway is of interest, or where conformational flexibility is substantial---as in many emerging protein and peptide technologies---bioinformatics methods perform poorly. There is therefore great interest in seeing purely physics-based approaches succeed. We discuss a purely physics-based, database-free folding method, relying on proper thermal sampling (replica exchange molecular dynamics) and molecular potential energy functions. In order to surmount the tremendous computational demands of all-atom folding simulations, our approach implements a conformational search strategy based on a putative protein folding mechanism called zipping and assembly [2-4]. That is, we explicitly seek out potential folding pathways inferred from short simulations, and iteratively pursue all such routes by coaxing a polypeptide chain along them. The method is called the Zipping and Assembly Method (ZAM) and it works in two parts: (1) the full polypeptide chain is broken into small fragments that are first simulated independently and then successively re-assembled into larger segments with further sampling, and (2) consistently stable structure in fragments is detected and locked into place, in order to avoid re
CHARMM Additive All-Atom Force Field for Phosphate and Sulfate Linked to Carbohydrates
Mallajosyula, Sairam S.; Guvench, Olgun; Hatcher, Elizabeth; MacKerell, Alexander D.
2012-01-01
Presented is an extension of the CHARMM additive all-atom carbohydrate force field to enable the modeling of phosphate and sulfate linked to carbohydrates. The parameters are developed in a hierarchical fashion using model compounds containing the key atoms in the full carbohydrates. Target data for parameter optimization included full two-dimensional energy surfaces defined by the glycosidic dihedral angle pairs in the phosphate/sulfate model compound analogs of hexopyranose monosaccharide phosphates and sulfates, as determined by quantum mechanical (QM) MP2/cc-pVTZ single point energies on MP2/6-31+G(d) optimized structures. In order to achieve balanced, transferable dihedral parameters for the dihedral angles, surfaces for all possible anomeric and conformational states were included during the parametrization process. In addition, to model physiologically relevant systems both the mono- and di-anionic charged states were studied for the phosphates. This resulted in over 7000 MP2/cc-pVTZ//MP2/6-31G+(d) model compound conformational energies which, supplemented with QM geometries, were the main target data for the parametrization. Parameters were validated against crystals of relevant monosaccharide derivatives obtained from the Cambridge Structural Database (CSD) and larger systems, namely inositol-(tri/tetra/penta) phosphates non-covalently bound to the pleckstrin homology (PH) domain and oligomeric chondroitin sulfate in solution and in complex with cathepsin K protein. PMID:22685386
Local order parameters for use in driving homogeneous ice nucleation with all-atom models of water.
Reinhardt, Aleks; Doye, Jonathan P K; Noya, Eva G; Vega, Carlos
2012-11-21
We present a local order parameter based on the standard Steinhardt-Ten Wolde approach that is capable both of tracking and of driving homogeneous ice nucleation in simulations of all-atom models of water. We demonstrate that it is capable of forcing the growth of ice nuclei in supercooled liquid water simulated using the TIP4P/2005 model using over-biassed umbrella sampling Monte Carlo simulations. However, even with such an order parameter, the dynamics of ice growth in deeply supercooled liquid water in all-atom models of water are shown to be very slow, and so the computation of free energy landscapes and nucleation rates remains extremely challenging. PMID:23181323
Na, Hyuntae; Jernigan, Robert L.; Song, Guang
2015-01-01
Dynamics can provide deep insights into the functional mechanisms of proteins and protein complexes. For large protein complexes such as GroEL/GroES with more than 8,000 residues, obtaining a fine-grained all-atom description of its normal mode motions can be computationally prohibitive and is often unnecessary. For this reason, coarse-grained models have been used successfully. However, most existing coarse-grained models use extremely simple potentials to represent the interactions within the coarse-grained structures and as a result, the dynamics obtained for the coarse-grained structures may not always be fully realistic. There is a gap between the quality of the dynamics of the coarse-grained structures given by all-atom models and that by coarse-grained models. In this work, we resolve an important question in protein dynamics computations—how can we efficiently construct coarse-grained models whose description of the dynamics of the coarse-grained structures remains as accurate as that given by all-atom models? Our method takes advantage of the sparseness of the Hessian matrix and achieves a high efficiency with a novel iterative matrix projection approach. The result is highly significant since it can provide descriptions of normal mode motions at an all-atom level of accuracy even for the largest biomolecular complexes. The application of our method to GroEL/GroES offers new insights into the mechanism of this biologically important chaperonin, such as that the conformational transitions of this protein complex in its functional cycle are even more strongly connected to the first few lowest frequency modes than with other coarse-grained models. PMID:26473491
All-atom molecular dynamics simulation studies of fully hydrated gel phase DPPG and DPPE bilayers
NASA Astrophysics Data System (ADS)
Pimthon, Jutarat; Willumeit, Regine; Lendlein, Andreas; Hofmann, Dieter
2009-03-01
Here in silico lipid membranes are described providing a structural background of the organization of the lipid components of membranes and aiding further biological or biophysical studies. An all-atom molecular dynamics simulations has been performed to investigate structural and dynamical properties of two fully hydrated gel-phase bilayers of 1,2-dipalmitoyl- sn-glycero-3-phosphoglycerol (DPPG) and 1,2-dipalmitoyl- sn-glycero-3-phospho-ethanolamine (DPPE) bilayers at 303 K. The respective starting configuration of lipids in the simulation bilayer unit cells were taken on the basis of scattering data. In both simulations, we found overall reasonably good agreement with the available experimental data (area per lipid, phosphorus-phosphorus distance). The distribution of the water/counterions at the membrane interface, interactions/orientations of lipid headgroups, and hydrocarbon chain organization were extensively studied in terms of pair distribution functions between main structural components of the system. Intra/intermolecular hydrogen bond formation was discussed in detail. The water orientation at the lipid membrane interface was explored thoroughly in terms of dipole moment as a function of the water molecule positions along the membrane, where we found that the counterions changed the orientation of the water at the interface. Special attention has been devoted to the distribution of the sodium counterions around the DPPG headgroup. We found preferential binding of Na + ions to the phosphate oxygen species.
Hatcher, Elizabeth; Guvench, Olgun; MacKerell, Alexander D.
2009-01-01
An additive all-atom empirical force field for aldopentofuranoses, methyl-aldopentofuranosides (Me-aldopentofuranosides) and fructofuranose carbohydrates, compatible with existing CHARMM carbohydrate parameters, is presented. Building on existing parameters transferred from cyclic ethers and hexopyranoses, parameters were further developed using target data for complete furanose carbohydrates as well as O-methyl tetrahydrofuran. The bond and angle equilibrium parameters were adjusted to reproduce target geometries from a survey of furanose crystal structures, and dihedral parameters were fit to over 1700 quantum mechanical (QM) MP2/cc-pVTZ//MP2/6-31G(d) conformational energies. The conformational energies were for a variety of complete furanose monosaccharides, and included two-dimensional ring pucker energy surfaces. Bonded parameter optimization led to the correct description of the ring pucker for a large set of furanose compounds, while furanose-water interaction energies and distances reproduced QM HF/6-31G(d) results for a number of furanose monosaccharides, thereby validating the nonbonded parameters. Crystal lattice unit cell parameters and volumes, aqueous-phase densities, and aqueous NMR ring pucker and exocyclic data were used to validate the parameters in condensed-phase environments. Conformational sampling analysis of the ring pucker and exocyclic group showed excellent agreement with experimental NMR data, demonstrating that the conformational energetics in aqueous solution are accurately described by the optimized force field. Overall, the parameters reproduce available experimental data well and are anticipated to be of utility in future computational studies of carbohydrates, including in the context of proteins, nucleic acids and/or lipids when combined with existing CHARMM biomolecular force fields. PMID:19694450
CHARMM Additive All-Atom Force Field for Acyclic Polyalcohols, Acyclic Carbohydrates and Inositol
Hatcher, Elizabeth; Guvench, Olgun; MacKerell, Alexander D.
2009-01-01
Parametrization of the additive all-atom CHARMM force field for acyclic polyalcohols, acyclic carbohydrates and inositol is conducted. Initial parameters were transferred from the alkanes and hexopyranose carbohydrates, with subsequent development and optimization of parameters unique to the molecules considered in this study. Using the model compounds acetone and acetaldehyde, nonbonded parameters for carbonyls were optimized targeting quantum mechanical interaction data for solute-water pairs and pure solvent thermodynamic data. Bond and angle parameters were adjusted by comparing optimized geometries to small molecule crystal survey data and by performing vibrational analyses on acetone, acetaldehyde and glycerol. C-C-C-C, C-C-C-O, C-C-OH and O-C-C-O torsional parameters for polyol chains were fit to quantum mechanical dihedral potential energy scans comprising over 1500 RIMP2/cc-pVTZ//MP2/6-31G(d) conformations using an automated Monte Carlo simulated annealing procedure. Comparison of computed condensed-phase data, including crystal lattice parameters and densities, NMR proton-proton couplings, densities and diffusion coefficients of aqueous solutions, to experimental data validated the optimized parameters. Parameter development for these compounds proved particularly challenging because of the flexibility of the acyclic sugars and polyalcohols as well as the intramolecular hydrogen bonding between vicinal hydroxyls for all of the compounds. The newly optimized additive CHARMM force field parameters are anticipated to be of utility for atomic level of detail simulations of acyclic polyalcohols, acyclic carbohydrates and inositol in solution. PMID:20160980
All-atom molecular dynamics calculation study of entire poliovirus empty capsids in solution
Andoh, Y.; Yoshii, N.; Yamada, A.; Kojima, H.; Mizutani, K.; Okazaki, S.; Fujimoto, K.; Nakagawa, A.; Nomoto, A.
2014-10-28
Small viruses that belong, for example, to the Picornaviridae, such as poliovirus and foot-and-mouth disease virus, consist simply of capsid proteins and a single-stranded RNA (ssRNA) genome. The capsids are quite stable in solution to protect the genome from the environment. Here, based on long-time and large-scale 6.5 × 10{sup 6} all-atom molecular dynamics calculations for the Mahoney strain of poliovirus, we show microscopic properties of the viral capsids at a molecular level. First, we found equilibrium rapid exchange of water molecules across the capsid. The exchange rate is so high that all water molecules inside the capsid (about 200 000) can leave the capsid and be replaced by water molecules from the outside in about 25 μs. This explains the capsid's tolerance to high pressures and deactivation by exsiccation. In contrast, the capsid did not exchange ions, at least within the present simulation time of 200 ns. This implies that the capsid can function, in principle, as a semipermeable membrane. We also found that, similar to the xylem of trees, the pressure of the solution inside the capsid without the genome was negative. This is caused by coulombic interaction of the solution inside the capsid with the capsid excess charges. The negative pressure may be compensated by positive osmotic pressure by the solution-soluble ssRNA and the counter ions introduced into it.
Refined OPLS all-atom force field for saturated phosphatidylcholine bilayers at full hydration.
Maciejewski, Arkadiusz; Pasenkiewicz-Gierula, Marta; Cramariuc, Oana; Vattulainen, Ilpo; Rog, Tomasz
2014-05-01
We report parametrization of dipalmitoyl-phosphatidylcholine (DPPC) in the framework of the Optimized Parameters for Liquid Simulations all-atom (OPLS-AA) force field. We chose DPPC as it is one of the most studied phospholipid species and thus has plenty of experimental data necessary for model validation, and it is also one of the highly important and abundant lipid types, e.g., in lung surfactant. Overall, PCs have not been previously parametrized in the OPLS-AA force field; thus, there is a need to derive its bonding and nonbonding parameters for both the polar and nonpolar parts of the molecule. In the present study, we determined the parameters for torsion angles in the phosphatidylcholine and glycerol moieties and in the acyl chains, as well the partial atomic charges. In these calculations, we used three methods: (1) Hartree-Fock (HF), (2) second order Møller-Plesset perturbation theory (MP2), and (3) density functional theory (DFT). We also tested the effect of the polar environment by using the polarizable continuum model (PCM), and for acyl chains the van der Waals parameters were also adjusted. In effect, six parameter sets were generated and tested on a DPPC bilayer. Out of these six sets, only one was found to be able to satisfactorily reproduce experimental data for the lipid bilayer. The successful DPPC model was obtained from MP2 calculations in an implicit polar environment (PCM). PMID:24745688
All-atom molecular dynamics calculation study of entire poliovirus empty capsids in solution
NASA Astrophysics Data System (ADS)
Andoh, Y.; Yoshii, N.; Yamada, A.; Fujimoto, K.; Kojima, H.; Mizutani, K.; Nakagawa, A.; Nomoto, A.; Okazaki, S.
2014-10-01
Small viruses that belong, for example, to the Picornaviridae, such as poliovirus and foot-and-mouth disease virus, consist simply of capsid proteins and a single-stranded RNA (ssRNA) genome. The capsids are quite stable in solution to protect the genome from the environment. Here, based on long-time and large-scale 6.5 × 106 all-atom molecular dynamics calculations for the Mahoney strain of poliovirus, we show microscopic properties of the viral capsids at a molecular level. First, we found equilibrium rapid exchange of water molecules across the capsid. The exchange rate is so high that all water molecules inside the capsid (about 200 000) can leave the capsid and be replaced by water molecules from the outside in about 25 μs. This explains the capsid's tolerance to high pressures and deactivation by exsiccation. In contrast, the capsid did not exchange ions, at least within the present simulation time of 200 ns. This implies that the capsid can function, in principle, as a semipermeable membrane. We also found that, similar to the xylem of trees, the pressure of the solution inside the capsid without the genome was negative. This is caused by coulombic interaction of the solution inside the capsid with the capsid excess charges. The negative pressure may be compensated by positive osmotic pressure by the solution-soluble ssRNA and the counter ions introduced into it.
Local elasticity of strained DNA studied by all-atom simulations
NASA Astrophysics Data System (ADS)
Mazur, Alexey K.
2011-08-01
Genomic DNA is constantly subjected to various mechanical stresses arising from its biological functions and cell packaging. If the local mechanical properties of DNA change under torsional and tensional stress, the activity of DNA-modifying proteins and transcription factors can be affected and regulated allosterically. To check this possibility, appropriate steady forces and torques were applied in the course of all-atom molecular dynamics simulations of DNA with AT- and GC-alternating sequences. It is found that the stretching rigidity grows with tension as well as twisting. The torsional rigidity is not affected by stretching, but it varies with twisting very strongly, and differently for the two sequences. Surprisingly, for AT-alternating DNA it passes through a minimum with the average twist close to the experimental value in solution. For this fragment, but not for the GC-alternating sequence, the bending rigidity noticeably changes with both twisting and stretching. The results have important biological implications and shed light on earlier experimental observations.
On Using Atomistic Solvent Layers in Hybrid All-Atom/Coarse-Grained Molecular Dynamics Simulations.
Kuhn, Alexander B; Gopal, Srinivasa M; Schäfer, Lars V
2015-09-01
Hybrid all-atom/coarse-grained (AA-CG) simulations in which AA solutes are embedded in a CG environment can provide a significant computational speed-up over conventional fully atomistic simulations and thus alleviate the current length and time scale limitations of molecular dynamics (MD) simulations of large biomolecular systems. On one hand, coarse graining the solvent is particularly appealing, since it typically constitutes the largest part of the simulation system and thus dominates computational cost. On the other hand, retaining atomic-level solvent layers around the solute is desirable for a realistic description of hydrogen bonds and other local solvation effects. Here, we devise and systematically validate fixed resolution AA-CG schemes, both with and without atomistic water layers. To quantify the accuracy and diagnose possible pitfalls, Gibbs free energies of solvation of amino acid side chain analogues were calculated, and the influence of the nature of the CG solvent surrounding (polarizable vs nonpolarizable CG water) and the size of the AA solvent region was investigated. We show that distance restraints to keep the AA solvent around the solute lead to too high of a density in the inner shell. Together with a long-ranged effect due to orientational ordering of water molecules at the AA-CG boundary, this affects solvation free energies. Shifting the onset of the distance restraints slightly away from the central solute significantly improves solvation free energies, down to mean unsigned errors with respect to experiment of 2.3 and 2.6 kJ/mol for the polarizable and nonpolarizable CG water surrounding, respectively. The speed-up of the nonpolarizable model renders it computationally more attractive. The present work thus highlights challenges, and outlines possible solutions, involved with modeling the boundary between different levels of resolution in hybrid AA-CG simulations. PMID:26575936
Nicolaï, Adrien; Senet, Patrick; Delarue, Patrice; Ripoll, Daniel R
2010-08-10
The 70 kDa human heat shock protein is a major molecular chaperone involved in de novo folding of proteins in vivo and refolding of proteins under stress conditions. Hsp70 is related to several "misfolding diseases" and other major pathologies, such as cancer, and is a target for new therapies. Hsp70 is comprised of two main domains: an N-terminal nucleotide binding domain (NBD) and a C-terminal substrate protein binding domain (SBD). The chaperone function of Hsp70 is based on an allosteric mechanism. Binding of ATP in NBD decreases the affinity of the substrate for SBD, and hydrolysis of ATP is promoted by binding of polypeptide segments in the SBD. No complete structure of human Hsp70 is known. Here, we report two models of human Hsp70, constructed by homology with Saccharomyces cerevisiae cochaperone protein Hsp110 (open model) and with Escherichia coli 70 kDa DnaK (closed model) and relaxed for several tens to hundreds of nanoseconds by using all-atom molecular dynamics simulations in explicit solvent. We obtain two stable states, Hsp70 with SBD open and SBD closed, which agree with experimental and structural information for ATP-Hsp70 and ADP-Hsp70, respectively. The dynamics of the transition from the open to closed states is investigated with a coarse-grained model and normal-mode analysis. The results show that the conformational change between the two states can be represented by a relatively small number of collective modes which involved major conformational changes in the two domains. These modes provide a mechanistic representation of the communication between NBD and SBD and allow us to identify subdomains and residues that appear to have a critical role in the conformational change mechanism that guides the chaperoning cycle of Hsp70. PMID:26613502
All-atom 3D structure prediction of transmembrane β-barrel proteins from sequences
Hayat, Sikander; Sander, Chris; Marks, Debora S.
2015-01-01
Transmembrane β-barrels (TMBs) carry out major functions in substrate transport and protein biogenesis but experimental determination of their 3D structure is challenging. Encouraged by successful de novo 3D structure prediction of globular and α-helical membrane proteins from sequence alignments alone, we developed an approach to predict the 3D structure of TMBs. The approach combines the maximum-entropy evolutionary coupling method for predicting residue contacts (EVfold) with a machine-learning approach (boctopus2) for predicting β-strands in the barrel. In a blinded test for 19 TMB proteins of known structure that have a sufficient number of diverse homologous sequences available, this combined method (EVfold_bb) predicts hydrogen-bonded residue pairs between adjacent β-strands at an accuracy of ∼70%. This accuracy is sufficient for the generation of all-atom 3D models. In the transmembrane barrel region, the average 3D structure accuracy [template-modeling (TM) score] of top-ranked models is 0.54 (ranging from 0.36 to 0.85), with a higher (44%) number of residue pairs in correct strand–strand registration than in earlier methods (18%). Although the nonbarrel regions are predicted less accurately overall, the evolutionary couplings identify some highly constrained loop residues and, for FecA protein, the barrel including the structure of a plug domain can be accurately modeled (TM score = 0.68). Lower prediction accuracy tends to be associated with insufficient sequence information and we therefore expect increasing numbers of β-barrel families to become accessible to accurate 3D structure prediction as the number of available sequences increases. PMID:25858953
All-atom and coarse-grained simulations of the forced unfolding pathways of the SNARE complex.
Zheng, Wenjun
2014-07-01
The SNARE complex, consisting of three proteins (VAMP2, syntaxin, and SNAP-25), is thought to drive membrane fusion by assembling into a four-helix bundle through a zippering process. In support of the above zippering model, a recent single-molecule optical tweezers experiment by Gao et al. revealed a sequential unzipping of SNARE along VAMP2 in the order of the linker domain → the C-terminal domain → the N-terminal domain. To offer detailed structural insights to this unzipping process, we have performed all-atom and coarse-grained steered molecular dynamics (sMD) simulations of the forced unfolding pathways of SNARE using different models and force fields. Our findings are summarized as follows: First, the sMD simulations based on either an all-atom force field (with an implicit solvent model) or a coarse-grained Go model were unable to capture the forced unfolding pathway of SNARE as observed by Gao et al., which may be attributed to insufficient simulation time and inaccurate force fields. Second, the sMD simulations based on a reparameterized coarse-grained model (i.e., modified elastic network model) were able to predict a sequential unzipping of SNARE in good agreement with the findings by Gao et al. The key to this success is to reparameterize the intrahelix and interhelix nonbonded force constants against the pair-wise residue-residue distance fluctuations collected from all-atom MD simulations of SNARE. Therefore, our finding supports the importance of accurately describing the inherent dynamics/flexibility of SNARE (in the absence of force), in order to correctly simulate its unfolding behaviors under force. This study has established a useful computational framework for future studies of the zippering function of SNARE and its perturbations by point mutations with amino-acid level of details, and more generally the forced unfolding pathways of other helix bundle proteins. PMID:24403006
All-Atom Internal Coordinate Mechanics (ICM) Force Field for Hexopyranoses and Glycoproteins
2016-01-01
We present an extension of the all-atom internal-coordinate force field, ICMFF, that allows for simulation of heterogeneous systems including hexopyranose saccharides and glycan chains in addition to proteins. A library of standard glycan geometries containing α- and β-anomers of the most common hexapyranoses, i.e., d-galactose, d-glucose, d-mannose, d-xylose, l-fucose, N-acetylglucosamine, N-acetylgalactosamine, sialic, and glucuronic acids, is created based on the analysis of the saccharide structures reported in the Cambridge Structural Database. The new force field parameters include molecular electrostatic potential-derived partial atomic charges and the torsional parameters derived from quantum mechanical data for a collection of minimal molecular fragments and related molecules. The ϕ/ψ torsional parameters for different types of glycosidic linkages are developed using model compounds containing the key atoms in the full carbohydrates, i.e., glycosidic-linked tetrahydropyran–cyclohexane dimers. Target data for parameter optimization include two-dimensional energy surfaces corresponding to the ϕ/ψ glycosidic dihedral angles in the disaccharide analogues, as determined by quantum mechanical MP2/6-31G** single-point energies on HF/6-31G** optimized structures. To achieve better agreement with the observed geometries of glycosidic linkages, the bond angles at the O-linkage atoms are added to the internal variable set and the corresponding bond bending energy term is parametrized using quantum mechanical data. The resulting force field is validated on glycan chains of 1–12 residues from a set of high-resolution X-ray glycoprotein structures based on heavy atom root-mean-square deviations of the lowest-energy glycan conformations generated by the biased probability Monte Carlo (BPMC) molecular mechanics simulations from the native structures. The appropriate BPMC distributions for monosaccharide–monosaccharide and protein–glycan linkages are derived
Coupling all-atom molecular dynamics simulations of ions in water with Brownian dynamics
2016-01-01
Molecular dynamics (MD) simulations of ions (K+, Na+, Ca2+ and Cl−) in aqueous solutions are investigated. Water is described using the SPC/E model. A stochastic coarse-grained description for ion behaviour is presented and parametrized using MD simulations. It is given as a system of coupled stochastic and ordinary differential equations, describing the ion position, velocity and acceleration. The stochastic coarse-grained model provides an intermediate description between all-atom MD simulations and Brownian dynamics (BD) models. It is used to develop a multiscale method which uses all-atom MD simulations in parts of the computational domain and (less detailed) BD simulations in the remainder of the domain. PMID:27118886
2015-01-01
Using the translocation of short, charged cationic oligo-arginine peptides (mono-, di-, and triarginine) from bulk aqueous solution into model DMPC bilayers, we explore the question of the similarity of thermodynamic and structural predictions obtained from molecular dynamics simulations using all-atom and Martini coarse-grain force fields. Specifically, we estimate potentials of mean force associated with translocation using standard all-atom (CHARMM36 lipid) and polarizable and nonpolarizable Martini force fields, as well as a series of modified Martini-based parameter sets. We find that we are able to reproduce qualitative features of potentials of mean force of single amino acid side chain analogues into model bilayers. In particular, modifications of peptide–water and peptide–membrane interactions allow prediction of free energy minima at the bilayer–water interface as obtained with all-atom force fields. In the case of oligo-arginine peptides, the modified parameter sets predict interfacial free energy minima as well as free energy barriers in almost quantitative agreement with all-atom force field based simulations. Interfacial free energy minima predicted by a modified coarse-grained parameter set are −2.51, −4.28, and −5.42 for mono-, di-, and triarginine; corresponding values from all-atom simulations are −0.83, −3.33, and −3.29, respectively, all in units of kcal/mol. We found that a stronger interaction between oligo-arginine and the membrane components and a weaker interaction between oligo-arginine and water are crucial for producing such minima in PMFs using the polarizable CG model. The difference between bulk aqueous and bilayer center states predicted by the modified coarse-grain force field are 11.71, 14.14, and 16.53 kcal/mol, and those by the all-atom model are 6.94, 8.64, and 12.80 kcal/mol; those are of almost the same order of magnitude. Our simulations also demonstrate a remarkable similarity in the structural aspects of
The energy landscape for folding and function
NASA Astrophysics Data System (ADS)
Onuchic, Jose
2006-03-01
computationally-expensive all-atom simulations, we are now obtaining a quantitative understanding of the folding problem, which allows for a direct comparison to a new generation of folding experiments. Connections between the folding landscape and protein function will also be discussed.
Bell, Jeffrey A.; Ho, Kenneth L.; Farid, Ramy
2012-08-01
All-atom models derived from moderate-resolution protein crystal structures contain a high frequency of close nonbonded contacts, independent of the major refinement program used for structure determination. All-atom refinement with PrimeX corrects many of these problematic interactions, producing models that are better suited for use in computational chemistry and related applications. All-atom models are essential for many applications in molecular modeling and computational chemistry. Nonbonded atomic contacts much closer than the sum of the van der Waals radii of the two atoms (clashes) are commonly observed in such models derived from protein crystal structures. A set of 94 recently deposited protein structures in the resolution range 1.5–2.8 Å were analyzed for clashes by the addition of all H atoms to the models followed by optimization and energy minimization of the positions of just these H atoms. The results were compared with the same set of structures after automated all-atom refinement with PrimeX and with nonbonded contacts in protein crystal structures at a resolution equal to or better than 0.9 Å. The additional PrimeX refinement produced structures with reasonable summary geometric statistics and similar R{sub free} values to the original structures. The frequency of clashes at less than 0.8 times the sum of van der Waals radii was reduced over fourfold compared with that found in the original structures, to a level approaching that found in the ultrahigh-resolution structures. Moreover, severe clashes at less than or equal to 0.7 times the sum of atomic radii were reduced 15-fold. All-atom refinement with PrimeX produced improved crystal structure models with respect to nonbonded contacts and yielded changes in structural details that dramatically impacted on the interpretation of some protein–ligand interactions.
A simple and transferable all-atom/coarse-grained hybrid model to study membrane processes.
Genheden, Samuel; Essex, Jonathan W
2015-10-13
We present an efficient all-atom/coarse-grained hybrid model and apply it to membrane processes. This model is an extension of the all-atom/ELBA model applied previously to processes in water. Here, we improve the efficiency of the model by implementing a multiple-time step integrator that allows the atoms and the coarse-grained beads to be propagated at different timesteps. Furthermore, we fine-tune the interaction between the atoms and the coarse-grained beads by computing the potential of mean force of amino acid side chain analogs along the membrane normal and comparing to atomistic simulations. The model was independently validated on the calculation of small-molecule partition coefficients. Finally, we apply the model to membrane peptides. We studied the tilt angle of the Walp23 and Kalp23 helices in two different model membranes and the stability of the glycophorin A dimer. The model is efficient, accurate, and straightforward to use, as it does not require any extra interaction particles, layers of atomistic solvent molecules or tabulated potentials, thus offering a novel, simple approach to study membrane processes. PMID:26574264
An All-Atom Model of the Structure of Human Copper Transporter 1
Sharikov, Yuriy; Greenberg, Jerry P.; Miller, Mark A.; Kouznetsova, Valentina L.; Larson, Christopher A.; Howell, Stephen B.
2013-01-01
Human copper transporter 1 (hCTR1) is the major high affinity copper influx transporter in mammalian cells that also mediates uptake of the cancer chemotherapeutic agent cisplatin. A low resolution structure of hCTR1 determined by cryoelectron microscopy was recently published. Several protein structure simulation techniques were used to create an all-atom model of this important transporter using the low resolution structure as a starting point. The all-atom model provides new insights into the roles of specific residues of the N-terminal extracellular domain, the intracellular loop, and C-terminal region in metal ion transport. In particular, the model demonstrates that the central region of the pore contains four sets of methionine triads in the intramembranous region. The structure confirms that two triads of methionine residues delineate the intramembranous region of the transporter, and further identifies two additional methionine triads that are located in the extracellular N-terminal part of the transporter. Together, the four triads create a structure that promotes stepwise transport of metal ions into and then through the intramembranous channel of the transporter via transient thioether bonds to methionine residues. Putative copper-binding sites in the hCTR1 trimer were identified by a program developed by us for prediction of metal-binding sites. These sites correspond well with the known effects of mutations on the ability of the protein to transport copper and cisplatin. PMID:22569840
Roberts, Christopher C; Chang, Chia-En A
2016-08-25
We present the second-generation GeomBD Brownian dynamics software for determining interenzyme intermediate transfer rates and substrate association rates in biomolecular complexes. Substrate and intermediate association rates for a series of enzymes or biomolecules can be compared between the freely diffusing disorganized configuration and various colocalized or complexed arrangements for kinetic investigation of enhanced intermediate transfer. In addition, enzyme engineering techniques, such as synthetic protein conjugation, can be computationally modeled and analyzed to better understand changes in substrate association relative to native enzymes. Tools are provided to determine nonspecific ligand-receptor association residence times, and to visualize common sites of nonspecific association of substrates on receptor surfaces. To demonstrate features of the software, interenzyme intermediate substrate transfer rate constants are calculated and compared for all-atom models of DNA origami scaffold-bound bienzyme systems of glucose oxidase and horseradish peroxidase. Also, a DNA conjugated horseradish peroxidase enzyme was analyzed for its propensity to increase substrate association rates and substrate local residence times relative to the unmodified enzyme. We also demonstrate the rapid determination and visualization of common sites of nonspecific ligand-receptor association by using HIV-1 protease and an inhibitor, XK263. GeomBD2 accelerates simulations by precomputing van der Waals potential energy grids and electrostatic potential grid maps, and has a flexible and extensible support for all-atom and coarse-grained force fields. Simulation software is written in C++ and utilizes modern parallelization techniques for potential grid preparation and Brownian dynamics simulation processes. Analysis scripts, written in the Python scripting language, are provided for quantitative simulation analysis. GeomBD2 is applicable to the fields of biophysics, bioengineering
Phenomenological Relativistic Energy Density Functionals
Lalazissis, G. A.; Kartzikos, S.; Niksic, T.; Paar, N.; Vretenar, D.; Ring, P.
2009-08-26
The framework of relativistic nuclear energy density functionals is applied to the description of a variety of nuclear structure phenomena, not only in spherical and deformed nuclei along the valley of beta-stability, but also in exotic systems with extreme isospin values and close to the particle drip-lines. Dynamical aspects of exotic nuclear structure is explored using the fully consistent quasiparticle random-phase approximation based on the relativistic Hartree-Bogoliubov model. Recent applications of energy density functionals with explicit density dependence of the meson-nucleon couplings are presented.
All-atomic generation and noise-quadrature filtering of squeezed vacuum in hot Rb vapor
NASA Astrophysics Data System (ADS)
Horrom, Travis; Romanov, Gleb; Novikova, Irina; Mikhailov, Eugeniy E.
2013-01-01
With our all-atomic squeezing and filtering setup, we demonstrate control over the noise amplitudes and manipulation of the frequency-dependent squeezing angle of a squeezed vacuum quantum state by passing it through an atomic medium with electromagnetically induced transparency (EIT). We generate low sideband frequency squeezed vacuum using the polarization self-rotation effect in a hot Rb vapor cell, and direct it through a second atomic vapor subject to EIT conditions. We use the frequency-dependent absorption of the EIT window to demonstrate an example of squeeze amplitude attenuation and squeeze angle rotation of the quantum noise quadratures of the squeezed probe. These studies have implications for quantum memory and storage as well as gravitational wave interferometric detectors.
Hoang Man, Viet; Van-Oanh, Nguyen-Thi; Derreumaux, Philippe; Li, Mai Suan; Roland, Christopher; Sagui, Celeste; Nguyen, Phuong H
2016-04-28
Since the discovery of the plant pathogen tobacco mosaic virus as the first viral entity in the late 1800s, viruses traditionally have been mainly thought of as pathogens for disease-resistances. However, viruses have recently been exploited as nanoplatforms with applications in biomedicine and materials science. To this aim, a large majority of current methods and tools have been developed to improve the physical stability of viral particles, which may be critical to the extreme physical or chemical conditions that viruses may encounter during purification, fabrication processes, storage and use. However, considerably fewer studies are devoted to developing efficient methods to degrade or recycle such enhanced stability biomaterials. With this in mind, we carry out all-atom nonequilibrium molecular dynamics simulation, inspired by the recently developed mid-infrared free-electron laser pulse technology, to dissociate viruses. Adopting the poliovirus as a representative example, we find that the primary step in the dissociation process is due to the strong resonance between the amide I vibrational modes of the virus and the tuned laser frequencies. This process is determined by a balance between the formation and dissociation of the protein shell, reflecting the highly plasticity of the virus. Furthermore, our method should provide a feasible approach to simulate viruses, which is otherwise too expensive for conventional equilibrium all-atom simulations of such very large systems. Our work shows a proof of concept which may open a new, efficient way to cleave or to recycle virus-based materials, provide an extremely valuable tool for elucidating mechanical aspects of viruses, and may well play an important role in future fighting against virus-related diseases. PMID:27071540
Learning Protein Folding Energy Functions
Guan, Wei; Ozakin, Arkadas; Gray, Alexander; Borreguero, Jose; Pandit, Shashi; Jagielska, Anna; Wroblewska, Liliana; Skolnick, Jeffrey
2014-01-01
A critical open problem in ab initio protein folding is protein energy function design, which pertains to defining the energy of protein conformations in a way that makes folding most efficient and reliable. In this paper, we address this issue as a weight optimization problem and utilize a machine learning approach, learning-to-rank, to solve this problem. We investigate the ranking-via-classification approach, especially the RankingSVM method and compare it with the state-of-the-art approach to the problem using the MINUIT optimization package. To maintain the physicality of the results, we impose non-negativity constraints on the weights. For this we develop two efficient non-negative support vector machine (NNSVM) methods, derived from L2-norm SVM and L1-norm SVMs, respectively. We demonstrate an energy function which maintains the correct ordering with respect to structure dissimilarity to the native state more often, is more efficient and reliable for learning on large protein sets, and is qualitatively superior to the current state-of-the-art energy function. PMID:25311546
Bell, Jeffrey A; Ho, Kenneth L; Farid, Ramy
2012-08-01
All-atom models are essential for many applications in molecular modeling and computational chemistry. Nonbonded atomic contacts much closer than the sum of the van der Waals radii of the two atoms (clashes) are commonly observed in such models derived from protein crystal structures. A set of 94 recently deposited protein structures in the resolution range 1.5-2.8 Å were analyzed for clashes by the addition of all H atoms to the models followed by optimization and energy minimization of the positions of just these H atoms. The results were compared with the same set of structures after automated all-atom refinement with PrimeX and with nonbonded contacts in protein crystal structures at a resolution equal to or better than 0.9 Å. The additional PrimeX refinement produced structures with reasonable summary geometric statistics and similar R(free) values to the original structures. The frequency of clashes at less than 0.8 times the sum of van der Waals radii was reduced over fourfold compared with that found in the original structures, to a level approaching that found in the ultrahigh-resolution structures. Moreover, severe clashes at less than or equal to 0.7 times the sum of atomic radii were reduced 15-fold. All-atom refinement with PrimeX produced improved crystal structure models with respect to nonbonded contacts and yielded changes in structural details that dramatically impacted on the interpretation of some protein-ligand interactions. PMID:22868759
Qin, Sanbo; Zhou, Huan-Xiang
2013-10-01
It is now well recognized that macromolecular crowding can exert significant effects on protein folding and binding stability. In order to calculate such effects in direct simulations of proteins mixed with bystander macromolecules, the latter (referred to as crowders) are usually modeled as spheres and the proteins represented at a coarse-grained level. Our recently developed postprocessing approach allows the proteins to be represented at the all-atom level but, for computational efficiency, has only been implemented for spherical crowders. Modeling crowder molecules in cellular environments and in vitro experiments as spheres may distort their effects on protein stability. Here we present a new method that is capable for treating aspherical crowders. The idea, borrowed from protein-protein docking, is to calculate the excess chemical potential of the proteins in crowded solution by fast Fourier transform (FFT). As the first application, we studied the effects of ellipsoidal crowders on the folding and binding free energies of all-atom proteins, and found, in agreement with previous direct simulations with coarse-grained protein models, that the aspherical crowders exert greater stabilization effects than spherical crowders of the same volume. Moreover, as demonstrated here, the FFT-based method has the important property that its computational cost does not increase strongly even when the level of details in representing the crowders is increased all the way to all-atom, thus significantly accelerating realistic modeling of protein folding and binding in cell-like environments. PMID:24187527
A Real-Time All-Atom Structural Search Engine for Proteins
Gonzalez, Gabriel; Hannigan, Brett; DeGrado, William F.
2014-01-01
Protein designers use a wide variety of software tools for de novo design, yet their repertoire still lacks a fast and interactive all-atom search engine. To solve this, we have built the Suns program: a real-time, atomic search engine integrated into the PyMOL molecular visualization system. Users build atomic-level structural search queries within PyMOL and receive a stream of search results aligned to their query within a few seconds. This instant feedback cycle enables a new “designability”-inspired approach to protein design where the designer searches for and interactively incorporates native-like fragments from proven protein structures. We demonstrate the use of Suns to interactively build protein motifs, tertiary interactions, and to identify scaffolds compatible with hot-spot residues. The official web site and installer are located at http://www.degradolab.org/suns/ and the source code is hosted at https://github.com/godotgildor/Suns (PyMOL plugin, BSD license), https://github.com/Gabriel439/suns-cmd (command line client, BSD license), and https://github.com/Gabriel439/suns-search (search engine server, GPLv2 license). PMID:25079944
ALMOST: an all atom molecular simulation toolkit for protein structure determination.
Fu, Biao; Sahakyan, Aleksandr B; Camilloni, Carlo; Tartaglia, Gian Gaetano; Paci, Emanuele; Caflisch, Amedeo; Vendruscolo, Michele; Cavalli, Andrea
2014-05-30
Almost (all atom molecular simulation toolkit) is an open source computational package for structure determination and analysis of complex molecular systems including proteins, and nucleic acids. Almost has been designed with two primary goals: to provide tools for molecular structure determination using various types of experimental measurements as conformational restraints, and to provide methods for the analysis and assessment of structural and dynamical properties of complex molecular systems. The methods incorporated in Almost include the determination of structural and dynamical features of proteins using distance restraints derived from nuclear Overhauser effect measurements, orientational restraints obtained from residual dipolar couplings and the structural restraints from chemical shifts. Here, we present the first public release of Almost, highlight the key aspects of its computational design and discuss the main features currently implemented. Almost is available for the most common Unix-based operating systems, including Linux and Mac OS X. Almost is distributed free of charge under the GNU Public License, and is available both as a source code and as a binary executable from the project web site at http://www.open-almost.org. Interested users can follow and contribute to the further development of Almost on http://sourceforge.net/projects/almost. PMID:24676684
Molecular jamming—The cystine slipknot mechanical clamp in all-atom simulations
NASA Astrophysics Data System (ADS)
Pepłowski, Łukasz; Sikora, Mateusz; Nowak, Wiesław; Cieplak, Marek
2011-02-01
A recent survey of 17 134 proteins has identified a new class of proteins which are expected to yield stretching induced force peaks in the range of 1 nN. Such high force peaks should be due to forcing of a slip-loop through a cystine ring, i.e., by generating a cystine slipknot. The survey has been performed in a simple coarse grained model. Here, we perform all-atom steered molecular dynamics simulations on 15 cystine knot proteins and determine their resistance to stretching. In agreement with previous studies within a coarse grained structure based model, the level of resistance is found to be substantially higher than in proteins in which the mechanical clamp operates through shear. The large stretching forces arise through formation of the cystine slipknot mechanical clamp and the resulting steric jamming. We elucidate the workings of such a clamp in an atomic detail. We also study the behavior of five top strength proteins with the shear-based mechanostability in which no jamming is involved. We show that in the atomic model, the jamming state is relieved by moving one amino acid at a time and there is a choice in the selection of the amino acid that advances the first. In contrast, the coarse grained model also allows for a simultaneous passage of two amino acids.
Molecular jamming--the cystine slipknot mechanical clamp in all-atom simulations.
Pepłowski, Lukasz; Sikora, Mateusz; Nowak, Wiesław; Cieplak, Marek
2011-02-28
A recent survey of 17 134 proteins has identified a new class of proteins which are expected to yield stretching induced force peaks in the range of 1 nN. Such high force peaks should be due to forcing of a slip-loop through a cystine ring, i.e., by generating a cystine slipknot. The survey has been performed in a simple coarse grained model. Here, we perform all-atom steered molecular dynamics simulations on 15 cystine knot proteins and determine their resistance to stretching. In agreement with previous studies within a coarse grained structure based model, the level of resistance is found to be substantially higher than in proteins in which the mechanical clamp operates through shear. The large stretching forces arise through formation of the cystine slipknot mechanical clamp and the resulting steric jamming. We elucidate the workings of such a clamp in an atomic detail. We also study the behavior of five top strength proteins with the shear-based mechanostability in which no jamming is involved. We show that in the atomic model, the jamming state is relieved by moving one amino acid at a time and there is a choice in the selection of the amino acid that advances the first. In contrast, the coarse grained model also allows for a simultaneous passage of two amino acids. PMID:21361557
All-atom Multiscale Simulation of Cowpea Chlorotic Mottle Virus Capsid Swelling
Miao, Yinglong; Johnson, John E.; Ortoleva, Peter J.
2010-01-01
An all-atom multiscale computational modeling approach, Molecular Dynamics/Order Parameter eXtrapolation (MD/OPX), has recently been developed for simulating large bionanosystems. It accelerates MD simulations and addresses rapid atomistic fluctuations and slowly-varying nanoscale dynamics of bionanosystems simultaneously. With modules added to account for water molecules and ions, MD/OPX is applied to simulate the swelling of cowpea chlorotic mottle virus (CCMV) capsid solvated in a host medium in this study. Simulation results show that the N-terminal arms of capsid proteins undergo large deviations from the initial configurations with their length extended quickly during the early stage of capsid swelling. The capsid swelling is a symmetry-breaking process involving local initiation and front propagation. The capsid swelling rate is ~0.25 nm/ns (npn) during early stage of the simulation and propagation of the structural transition across the capsid is roughly 0.6npn. The system conditions that affect swelling of the capsid are analyzed. Prospects for creating a phase diagram for CCMV capsid swelling and using predictions to guide experiments are discussed. PMID:20695471
NASA Astrophysics Data System (ADS)
Cui, Qizhi; Smith, Vedene H.
2000-12-01
An all-atom molecular model and optimized site-site pair potential parameters are employed for methane solute. By use of the reference interaction site model theory, the methane hydration structure is analyzed at the atomic level and its hydration free energies, energies, enthalpies, and entropies for four different thermodynamic states: temperature T=283.15, 298.15, 313.15, 328.15 K and the corresponding bulk water density ρ=0.9997, 0.9970, 0.9922, 0.9875 g cm-3 are calculated. Our calculated thermodynamic properties are in rather good agreement with experiments.
2015-01-01
We describe the derivation of a set of bonded and nonbonded coarse-grained (CG) potential functions for use in implicit-solvent Brownian dynamics (BD) simulations of proteins derived from all-atom explicit-solvent molecular dynamics (MD) simulations of amino acids. Bonded potential functions were derived from 1 μs MD simulations of each of the 20 canonical amino acids, with histidine modeled in both its protonated and neutral forms; nonbonded potential functions were derived from 1 μs MD simulations of every possible pairing of the amino acids (231 different systems). The angle and dihedral probability distributions and radial distribution functions sampled during MD were used to optimize a set of CG potential functions through use of the iterative Boltzmann inversion (IBI) method. The optimized set of potential functions—which we term COFFDROP (COarse-grained Force Field for Dynamic Representation Of Proteins)—quantitatively reproduced all of the “target” MD distributions. In a first test of the force field, it was used to predict the clustering behavior of concentrated amino acid solutions; the predictions were directly compared with the results of corresponding all-atom explicit-solvent MD simulations and found to be in excellent agreement. In a second test, BD simulations of the small protein villin headpiece were carried out at concentrations that have recently been studied in all-atom explicit-solvent MD simulations by Petrov and Zagrovic (PLoS Comput. Biol.2014, 5, e1003638). The anomalously strong intermolecular interactions seen in the MD study were reproduced in the COFFDROP simulations; a simple scaling of COFFDROP’s nonbonded parameters, however, produced results in better accordance with experiment. Overall, our results suggest that potential functions derived from simulations of pairwise amino acid interactions might be of quite broad applicability, with COFFDROP likely to be especially useful for modeling unfolded or intrinsically
Kuroda, Yutaka; Suenaga, Atsushi; Sato, Yuji; Kosuda, Satoshi; Taiji, Makoto
2016-01-01
In order to investigate the contribution of individual amino acids to protein and peptide solubility, we carried out 100 ns molecular dynamics (MD) simulations of 106 Å3 cubic boxes containing ~3 × 104 water molecules and 27 tetra-peptides regularly positioned at 23 Å from each other and composed of a single amino acid type for all natural amino acids but cysteine and glycine. The calculations were performed using Amber with a standard force field on a special purpose MDGRAPE-3 computer, without introducing any “artificial” hydrophobic interactions. Tetra-peptides composed of I, V, L, M, N, Q, F, W, Y, and H formed large amorphous clusters, and those containing A, P, S, and T formed smaller ones. Tetra-peptides made of D, E, K, and R did not cluster at all. These observations correlated well with experimental solubility tendencies as well as hydrophobicity scales with correlation coefficients of 0.5 to > 0.9. Repulsive Coulomb interactions were dominant in ensuring high solubility, whereas both Coulomb and van der Waals (vdW) energies contributed to the aggregations of low solubility amino acids. Overall, this very first all-atom molecular dynamics simulation of a multi-peptide system appears to reproduce the basic properties of peptide solubility, essentially in line with experimental observations. PMID:26817663
Zhu, Yuzhen; Ma, Buyong; Qi, Ruxi; Nussinov, Ruth; Zhang, Qingwen
2016-04-14
Neuronal calcium sensor-1 (NCS-1) protein has orthologues from Saccharomyces cerevisiae to human with highly conserved amino acid sequences. NCS-1 is an important factor controlling the animal's response to temperature change. This leads us to investigate the temperature effects on the conformational dynamics of human NCS-1 at 310 and 316 K by all-atom molecular dynamics (MD) simulations and dynamic community network analysis. Four independent 500 ns MD simulations show that secondary structure content at 316 K is similar to that at 310 K, whereas the global protein structure is expanded. Loop 3 (L3) adopts an extended state occuping the hydrophobic crevice, and the number of suboptimal communication paths between residue D176 and V190 is reduced at 316 K. The dynamic community network analysis suggests that the interdomain correlation is weakened, and the intradomain coupling is strengthened at 316 K. The elevated temperature reduces the number of the salt bridges, especially in C-domain. This study suggests that the elevated temperature affects the conformational dynamics of human NCS-1 protein. Comparison of the structural dynamics of R102Q mutant and Δ176-190 truncated NCS-1 suggests that the structural and dynamical response of NCS-1 protein to elevated temperature may be one of its intrinsic functional properties. PMID:27007011
Lei, Dongsheng; Rames, Matthew; Zhang, Xing; Zhang, Lei; Zhang, Shengli; Ren, Gang
2016-07-01
Cholesteryl ester transfer protein (CETP) mediates cholesteryl ester (CE) transfer from the atheroprotective high density lipoprotein (HDL) cholesterol to the atherogenic low density lipoprotein cholesterol. In the past decade, this property has driven the development of CETP inhibitors, which have been evaluated in large scale clinical trials for treating cardiovascular diseases. Despite the pharmacological interest, little is known about the fundamental mechanism of CETP in CE transfer. Recent electron microscopy (EM) experiments have suggested a tunnel mechanism, and molecular dynamics simulations have shown that the flexible N-terminal distal end of CETP penetrates into the HDL surface and takes up a CE molecule through an open pore. However, it is not known whether a CE molecule can completely transfer through an entire CETP molecule. Here, we used all-atom molecular dynamics simulations to evaluate this possibility. The results showed that a hydrophobic tunnel inside CETP is sufficient to allow a CE molecule to completely transfer through the entire CETP within a predicted transfer time and at a rate comparable with those obtained through physiological measurements. Analyses of the detailed interactions revealed several residues that might be critical for CETP function, which may provide important clues for the effective development of CETP inhibitors and treatment of cardiovascular diseases. PMID:27143480
Lei, Dongsheng; Rames, Matthew; Zhang, Xing; Zhang, Lei; Zhang, Shengli; Ren, Gang
2016-01-01
Cholesteryl ester transfer protein (CETP) mediates cholesteryl ester (CE) transfer from the atheroprotective high density lipoprotein (HDL) cholesterol to the atherogenic low density lipoprotein cholesterol. In the past decade, this property has driven the development of CETP inhibitors, which have been evaluated in large scale clinical trials for treating cardiovascular diseases. Despite the pharmacological interest, little is known about the fundamental mechanism of CETP in CE transfer. Recent electron microscopy (EM) experiments have suggested a tunnel mechanism, and molecular dynamics simulations have shown that the flexible N-terminal distal end of CETP penetrates into the HDL surface and takes up a CE molecule through an open pore. However, it is not known whether a CE molecule can completely transfer through an entire CETP molecule. Here, we used all-atom molecular dynamics simulations to evaluate this possibility. The results showed that a hydrophobic tunnel inside CETP is sufficient to allow a CE molecule to completely transfer through the entire CETP within a predicted transfer time and at a rate comparable with those obtained through physiological measurements. Analyses of the detailed interactions revealed several residues that might be critical for CETP function, which may provide important clues for the effective development of CETP inhibitors and treatment of cardiovascular diseases. PMID:27143480
Preformed template fluctuations promote fibril formation: Insights from lattice and all-atom models
Kouza, Maksim Kolinski, Andrzej; Co, Nguyen Truong; Nguyen, Phuong H.; Li, Mai Suan
2015-04-14
Fibril formation resulting from protein misfolding and aggregation is a hallmark of several neurodegenerative diseases such as Alzheimer’s and Parkinson’s diseases. Despite the fact that the fibril formation process is very slow and thus poses a significant challenge for theoretical and experimental studies, a number of alternative pictures of molecular mechanisms of amyloid fibril formation have been recently proposed. What seems to be common for the majority of the proposed models is that fibril elongation involves the formation of pre-nucleus seeds prior to the creation of a critical nucleus. Once the size of the pre-nucleus seed reaches the critical nucleus size, its thermal fluctuations are expected to be small and the resulting nucleus provides a template for sequential (one-by-one) accommodation of added monomers. The effect of template fluctuations on fibril formation rates has not been explored either experimentally or theoretically so far. In this paper, we make the first attempt at solving this problem by two sets of simulations. To mimic small template fluctuations, in one set, monomers of the preformed template are kept fixed, while in the other set they are allowed to fluctuate. The kinetics of addition of a new peptide onto the template is explored using all-atom simulations with explicit water and the GROMOS96 43a1 force field and simple lattice models. Our result demonstrates that preformed template fluctuations can modulate protein aggregation rates and pathways. The association of a nascent monomer with the template obeys the kinetics partitioning mechanism where the intermediate state occurs in a fraction of routes to the protofibril. It was shown that template immobility greatly increases the time of incorporating a new peptide into the preformed template compared to the fluctuating template case. This observation has also been confirmed by simulation using lattice models and may be invoked to understand the role of template fluctuations in
Preformed template fluctuations promote fibril formation: Insights from lattice and all-atom models
NASA Astrophysics Data System (ADS)
Kouza, Maksim; Co, Nguyen Truong; Nguyen, Phuong H.; Kolinski, Andrzej; Li, Mai Suan
2015-04-01
Fibril formation resulting from protein misfolding and aggregation is a hallmark of several neurodegenerative diseases such as Alzheimer's and Parkinson's diseases. Despite the fact that the fibril formation process is very slow and thus poses a significant challenge for theoretical and experimental studies, a number of alternative pictures of molecular mechanisms of amyloid fibril formation have been recently proposed. What seems to be common for the majority of the proposed models is that fibril elongation involves the formation of pre-nucleus seeds prior to the creation of a critical nucleus. Once the size of the pre-nucleus seed reaches the critical nucleus size, its thermal fluctuations are expected to be small and the resulting nucleus provides a template for sequential (one-by-one) accommodation of added monomers. The effect of template fluctuations on fibril formation rates has not been explored either experimentally or theoretically so far. In this paper, we make the first attempt at solving this problem by two sets of simulations. To mimic small template fluctuations, in one set, monomers of the preformed template are kept fixed, while in the other set they are allowed to fluctuate. The kinetics of addition of a new peptide onto the template is explored using all-atom simulations with explicit water and the GROMOS96 43a1 force field and simple lattice models. Our result demonstrates that preformed template fluctuations can modulate protein aggregation rates and pathways. The association of a nascent monomer with the template obeys the kinetics partitioning mechanism where the intermediate state occurs in a fraction of routes to the protofibril. It was shown that template immobility greatly increases the time of incorporating a new peptide into the preformed template compared to the fluctuating template case. This observation has also been confirmed by simulation using lattice models and may be invoked to understand the role of template fluctuations in
Preformed template fluctuations promote fibril formation: insights from lattice and all-atom models.
Kouza, Maksim; Co, Nguyen Truong; Nguyen, Phuong H; Kolinski, Andrzej; Li, Mai Suan
2015-04-14
Fibril formation resulting from protein misfolding and aggregation is a hallmark of several neurodegenerative diseases such as Alzheimer's and Parkinson's diseases. Despite the fact that the fibril formation process is very slow and thus poses a significant challenge for theoretical and experimental studies, a number of alternative pictures of molecular mechanisms of amyloid fibril formation have been recently proposed. What seems to be common for the majority of the proposed models is that fibril elongation involves the formation of pre-nucleus seeds prior to the creation of a critical nucleus. Once the size of the pre-nucleus seed reaches the critical nucleus size, its thermal fluctuations are expected to be small and the resulting nucleus provides a template for sequential (one-by-one) accommodation of added monomers. The effect of template fluctuations on fibril formation rates has not been explored either experimentally or theoretically so far. In this paper, we make the first attempt at solving this problem by two sets of simulations. To mimic small template fluctuations, in one set, monomers of the preformed template are kept fixed, while in the other set they are allowed to fluctuate. The kinetics of addition of a new peptide onto the template is explored using all-atom simulations with explicit water and the GROMOS96 43a1 force field and simple lattice models. Our result demonstrates that preformed template fluctuations can modulate protein aggregation rates and pathways. The association of a nascent monomer with the template obeys the kinetics partitioning mechanism where the intermediate state occurs in a fraction of routes to the protofibril. It was shown that template immobility greatly increases the time of incorporating a new peptide into the preformed template compared to the fluctuating template case. This observation has also been confirmed by simulation using lattice models and may be invoked to understand the role of template fluctuations in
Yuan, Shuguang; Wu, Rongliang; Latek, Dorota; Trzaskowski, Bartosz; Filipek, Slawomir
2013-01-01
Sphingosine 1-phosphate (S1P) is a lysophospholipid mediator which activates G protein-coupled sphingosine 1-phosphate receptors and thus evokes a variety of cell and tissue responses including lymphocyte trafficking, endothelial development, integrity, and maturation. We performed five all-atom 700 ns molecular dynamics simulations of the sphingosine 1-phosphate receptor 1 (S1P₁) based on recently released crystal structure of that receptor with an antagonist. We found that the initial movements of amino acid residues occurred in the area of highly conserved W269⁶·⁴⁸ in TM6 which is close to the ligand binding location. Those residues located in the central part of the receptor and adjacent to kinks of TM helices comprise of a transmission switch. Side chains movements of those residues were coupled to the movements of water molecules inside the receptor which helped in the gradual opening of intracellular part of the receptor. The most stable parts of the protein were helices TM1 and TM2, while the largest movement was observed for TM7, possibly due to the short intracellular part starting with a helix kink at P⁷·⁵⁰, which might be the first helix to move at the intracellular side. We show for the first time the detailed view of the concerted action of the transmission switch and Trp (W⁶·⁴⁸) rotamer toggle switch leading to redirection of water molecules flow in the central part of the receptor. That event is a prerequisite for subsequent changes in intracellular part of the receptor involving water influx and opening of the receptor structure. PMID:24098103
Probing the Huntingtin 1-17 Membrane Anchor on a Phospholipid Bilayer by Using All-Atom Simulations
Côté, Sébastien; Binette, Vincent; Salnikov, Evgeniy S.; Bechinger, Burkhard; Mousseau, Normand
2015-01-01
Mislocalization and aggregation of the huntingtin protein are related to Huntington’s disease. Its first exon—more specifically the first 17 amino acids (Htt17)—is crucial for the physiological and pathological functions of huntingtin. It regulates huntingtin’s activity through posttranslational modifications and serves as an anchor to membrane-containing organelles of the cell. Recently, structure and orientation of the Htt17 membrane anchor were determined using a combined solution and solid-state NMR approach. This prompted us to refine this model by investigating the dynamics and thermodynamics of this membrane anchor on a POPC bilayer using all-atom, explicit solvent molecular dynamics and Hamiltonian replica exchange. Our simulations are combined with various experimental measurements to generate a high-resolution atomistic model for the huntingtin Htt17 membrane anchor on a POPC bilayer. More precisely, we observe that the single α-helix structure is more stable in the phospholipid membrane than the NMR model obtained in the presence of dodecylphosphocholine detergent micelles. The resulting Htt17 monomer has its hydrophobic plane oriented parallel to the bilayer surface. Our results further unveil the key residues interacting with the membrane in terms of hydrogen bonds, salt-bridges, and nonpolar contributions. We also observe that Htt17 equilibrates at a well-defined insertion depth and that it perturbs the physical properties—order parameter, thickness, and area per lipid—of the bilayer in a manner that could favor its dimerization. Overall, our observations reinforce and refine the NMR measurements on the Htt17 membrane anchor segment of huntingtin that is of fundamental importance to its biological functions. PMID:25762330
Dissociation of a Dynamic Protein Complex Studied by All-Atom Molecular Simulations.
Zhang, Liqun; Borthakur, Susmita; Buck, Matthias
2016-02-23
The process of protein complex dissociation remains to be understood at the atomic level of detail. Computers now allow microsecond timescale molecular-dynamics simulations, which make the visualization of such processes possible. Here, we investigated the dissociation process of the EphA2-SHIP2 SAM-SAM domain heterodimer complex using unrestrained all-atom molecular-dynamics simulations. Previous studies on this system have shown that alternate configurations are sampled, that their interconversion can be fast, and that the complex is dynamic by nature. Starting from different NMR-derived structures, mutants were designed to stabilize a subset of configurations by swapping ion pairs across the protein-protein interface. We focused on two mutants, K956D/D1235K and R957D/D1223R, with attenuated binding affinity compared with the wild-type proteins. In contrast to calculations on the wild-type complexes, the majority of simulations of these mutants showed protein dissociation within 2.4 μs. During the separation process, we observed domain rotation and pivoting as well as a translation and simultaneous rolling, typically to alternate and weaker binding interfaces. Several unsuccessful recapturing attempts occurred once the domains were moderately separated. An analysis of protein solvation suggests that the dissociation process correlates with a progressive loss of protein-protein contacts. Furthermore, an evaluation of internal protein dynamics using quasi-harmonic and order parameter analyses indicates that changes in protein internal motions are expected to contribute significantly to the thermodynamics of protein dissociation. Considering protein association as the reverse of the separation process, the initial role of charged/polar interactions is emphasized, followed by changes in protein and solvent dynamics. The trajectories show that protein separation does not follow a single distinct pathway, but suggest that the mechanism of dissociation is common in
Hierarchical atom type definitions and extensible all-atom force fields.
Jin, Zhao; Yang, Chunwei; Cao, Fenglei; Li, Feng; Jing, Zhifeng; Chen, Long; Shen, Zhe; Xin, Liang; Tong, Sijia; Sun, Huai
2016-03-15
The extensibility of force field is a key to solve the missing parameter problem commonly found in force field applications. The extensibility of conventional force fields is traditionally managed in the parameterization procedure, which becomes impractical as the coverage of the force field increases above a threshold. A hierarchical atom-type definition (HAD) scheme is proposed to make extensible atom type definitions, which ensures that the force field developed based on the definitions are extensible. To demonstrate how HAD works and to prepare a foundation for future developments, two general force fields based on AMBER and DFF functional forms are parameterized for common organic molecules. The force field parameters are derived from the same set of quantum mechanical data and experimental liquid data using an automated parameterization tool, and validated by calculating molecular and liquid properties. The hydration free energies are calculated successfully by introducing a polarization scaling factor to the dispersion term between the solvent and solute molecules. © 2015 Wiley Periodicals, Inc. PMID:26537332
Exploring the protein funnel energy landscape for folding and function
NASA Astrophysics Data System (ADS)
Onuchic, Jose
2005-03-01
Globally the energy landscape of a folding protein resembles a partially rough funnel. Using minimalist model simulations together with analytical theory, we learn about good (minimally frustrated) folding sequences and non-folding (frustrated) sequences In addition to the need to minimize energetic frustration, the fold topology also plays a major role in the folding mechanism. Some folding motifs are easier to design than others, suggesting the possibility that evolution not only selected sequences with sufficiently small energetic frustration but also more easily designable native structures. We have demonstrated for several proteins (such as CI2 and SH3) that they are sufficiently well designed (i.e., reduced energetic frustration) that much of the heterogeneity observed in their transition state ensemble (TSE) is determined by topology. Topological effects go beyond the TSE. The overall structure of the on-route and off-route (traps) intermediates for the folding of more complex proteins and protein dimers is also strongly influenced by topology.this theoretical framework, simulations of minimalist models and their connections to more computationally-expensive all-atom simulations, we are now in the process of obtaining a quantitative understanding of the folding problem, which allows for a direct comparison to a new generation of folding experiments. Connections between the folding landscape and protein function will also be discussed.
Murtola, Teemu; Vattulainen, Ilpo; Falck, Emma
2008-06-01
Tryptophan biosynthesis in Bacillus stearothermophilus is regulated by a trp RNA binding attenuation protein (TRAP). It is a ring-shaped 11-mer of identical 74 residue subunits. Tryptophan binding pockets are located between adjacent subunits, and tryptophan binding activates TRAP to bind RNA. Here, we report results from all-atom molecular dynamics simulations of the system, complementing existing extensive experimental studies. We focus on two questions. First, we look at the activation mechanism, of which relatively little is known experimentally. We find that the absence of tryptophan allows larger motions close to the tryptophan binding site, and we see indication of a conformational change in the BC loop. However, complete deactivation seems to occur on much longer time scales than the 40 ns studied here. Second, we study the TRAP-RNA interactions. We look at the relative flexibilities of the different bases in the complex and analyze the hydrogen bonds between the protein and RNA. We also study the role of Lys37, Lys56, and Arg58, which have been experimentally identified as essential for RNA binding. Hydrophobic stacking of Lys37 with the nearby RNA base is confirmed, but we do not see direct hydrogen bonding between RNA and the other two residues, in contrast to the crystal structure. Rather, these residues seem to stabilize the RNA-binding surface, and their positive charge may also play a role in RNA binding. Simulations also indicate that TRAP is able to attract RNA nonspecifically, and the interactions are quantified in more detail using binding energy calculations. The formation of the final binding complex is a very slow process: within the simulation time scale of 40 ns, only two guanine bases become bound (and no others), indicating that the binding initiates at these positions. In general, our results are in good agreement with experimental studies, and provide atomic-scale insights into the processes. PMID:18186477
A combined coarse-grained and all-atom simulation of TRPV1 channel gating and heat activation
Qin, Feng
2015-01-01
The transient receptor potential (TRP) channels act as key sensors of various chemical and physical stimuli in eukaryotic cells. Despite years of study, the molecular mechanisms of TRP channel activation remain unclear. To elucidate the structural, dynamic, and energetic basis of gating in TRPV1 (a founding member of the TRPV subfamily), we performed coarse-grained modeling and all-atom molecular dynamics (MD) simulation based on the recently solved high resolution structures of the open and closed form of TRPV1. Our coarse-grained normal mode analysis captures two key modes of collective motions involved in the TRPV1 gating transition, featuring a quaternary twist motion of the transmembrane domains (TMDs) relative to the intracellular domains (ICDs). Our transition pathway modeling predicts a sequence of structural movements that propagate from the ICDs to the TMDs via key interface domains (including the membrane proximal domain and the C-terminal domain), leading to sequential opening of the selectivity filter followed by the lower gate in the channel pore (confirmed by modeling conformational changes induced by the activation of ICDs). The above findings of coarse-grained modeling are robust to perturbation by lipids. Finally, our MD simulation of the ICD identifies key residues that contribute differently to the nonpolar energy of the open and closed state, and these residues are predicted to control the temperature sensitivity of TRPV1 gating. These computational predictions offer new insights to the mechanism for heat activation of TRPV1 gating, and will guide our future electrophysiology and mutagenesis studies. PMID:25918362
Wambo, Thierry O; Chen, Liao Y; McHardy, Stanton F; Tsin, Andrew T
2016-01-01
Human carbonic anhydrase II (hCAII) represents an ultimate example of the perfectly efficient metalloenzymes, which is capable of catalyzing the hydration of carbon dioxide with a rate approaching the diffusion controlled limit. Extensive experimental studies of this physiologically important metalloprotein have been done to elucidate the fundamentals of its enzymatic actions: what residues anchor the Zn(2+) (or another divalent cation) at the bottom of the binding pocket; how the relevant residues work concertedly with the divalent cation in the reversible conversions between CO2 and HCO3(-); what are the protonation states of the relevant residues and acetazolamide, an inhibitor complexed with hCAII, etc. In this article, we present a detailed computational study on the basis of the all-atom CHARMM force field where Zn(2+) is represented with a simple model of divalent cation using the transferrable parameters available from the current literature. We compute the hydration free energy of Zn(2+), the characteristics of hCAII-Zn(2+) complexation, and the absolute free energy of binding acetazolamide to the hCAII-Zn(2+) complex. In each of these three problems, our computed results agree with the experimental data within the known margin of error without making any case-by-case adjustments to the parameters. The quantitatively accurate insights we gain in this all-atom molecular dynamics study should be helpful in the search and design of more specific inhibitors of this and other carbonic anhydrases. PMID:27232456
NASA Astrophysics Data System (ADS)
Wang, Guan M.; Sandberg, William C.
2007-04-01
In order to gain insight into the mechanical and dynamical behaviour of free and tethered short chains of ss/ds DNA molecules in flow, and in parallel to investigate the properties of long chain molecules in flow fields, we have developed a series of quantum and molecular methods to extend the well developed equilibrium software CHARMM to handle non-equilibrium dynamics. These methods have been applied to cases of DNA molecules in shear flows in nanochannels. Biomolecules, both free and wall-tethered, have been simulated in the all-atom style in solvent-filled nanochannels. The new methods were demonstrated by carrying out NEMD simulations of free single-stranded DNA (ssDNA) molecules of 21 bases as well as double-stranded DNA (dsDNA) molecules of 21 base pairs tethered on gold surfaces in an ionic water shear flow. The tethering of the linker molecule (6-mercapto-1-hexanol) to perfect Au(111) surfaces was parametrized based on density functional theory (DFT) calculations. Force field parameters were incorporated into the CHARMM database. Gold surfaces are simulated in a Lennard-Jones style model that was fitted to the Morse potential model of bulk gold. The bonding force of attachment of the DNA molecules to the gold substrate linker molecule was computed to be up to a few nN when the DNA molecules are fully stretched at high shear rates. For the first time, we calculated the relaxation time of DNA molecules in picoseconds (ps) and the hydrodynamic force up to a few nanoNewtons (nN) per base pair in a nanochannel flow. The velocity profiles in the solvent due to the presence of the tethered DNA molecules were found to be nonlinear only at high shear flow rates. Free ssDNA molecules in a shear flow were observed to behave differently from each other depending upon their initial orientation in the flow field. Both free and tethered DNA molecules are clearly observed to be stretching, rotating and relaxing. Methods developed in this initial work can be incorporated
Li, Xianfeng; Murthy, N Sanjeeva; Becker, Matthew L; Latour, Robert A
2016-06-01
A multiscale modeling approach is presented for the efficient construction of an equilibrated all-atom model of a cross-linked poly(ethylene glycol) (PEG)-based hydrogel using the all-atom polymer consistent force field (PCFF). The final equilibrated all-atom model was built with a systematic simulation toolset consisting of three consecutive parts: (1) building a global cross-linked PEG-chain network at experimentally determined cross-link density using an on-lattice Monte Carlo method based on the bond fluctuation model, (2) recovering the local molecular structure of the network by transitioning from the lattice model to an off-lattice coarse-grained (CG) model parameterized from PCFF, followed by equilibration using high performance molecular dynamics methods, and (3) recovering the atomistic structure of the network by reverse mapping from the equilibrated CG structure, hydrating the structure with explicitly represented water, followed by final equilibration using PCFF parameterization. The developed three-stage modeling approach has application to a wide range of other complex macromolecular hydrogel systems, including the integration of peptide, protein, and/or drug molecules as side-chains within the hydrogel network for the incorporation of bioactivity for tissue engineering, regenerative medicine, and drug delivery applications. PMID:27013229
Assembling a xylanase-lichenase chimera through all-atom molecular dynamics simulations.
Cota, Junio; Oliveira, Leandro C; Damásio, André R L; Citadini, Ana P; Hoffmam, Zaira B; Alvarez, Thabata M; Codima, Carla A; Leite, Vitor B P; Pastore, Glaucia; de Oliveira-Neto, Mario; Murakami, Mario T; Ruller, Roberto; Squina, Fabio M
2013-08-01
Multifunctional enzyme engineering can improve enzyme cocktails for emerging biofuel technology. Molecular dynamics through structure-based models (SB) is an effective tool for assessing the tridimensional arrangement of chimeric enzymes as well as for inferring the functional practicability before experimental validation. This study describes the computational design of a bifunctional xylanase-lichenase chimera (XylLich) using the xynA and bglS genes from Bacillus subtilis. In silico analysis of the average solvent accessible surface area (SAS) and the root mean square fluctuation (RMSF) predicted a fully functional chimera, with minor fluctuations and variations along the polypeptide chains. Afterwards, the chimeric enzyme was built by fusing the xynA and bglS genes. XylLich was evaluated through small-angle X-ray scattering (SAXS) experiments, resulting in scattering curves with a very accurate fit to the theoretical protein model. The chimera preserved the biochemical characteristics of the parental enzymes, with the exception of a slight variation in the temperature of operation and the catalytic efficiency (kcat/Km). The absence of substantial shifts in the catalytic mode of operation was also verified. Furthermore, the production of chimeric enzymes could be more profitable than producing a single enzyme separately, based on comparing the recombinant protein production yield and the hydrolytic activity achieved for XylLich with that of the parental enzymes. PMID:23459129
Elastic properties of dynein motor domain obtained from all-atom molecular dynamics simulations
Kamiya, Narutoshi; Mashimo, Tadaaki; Takano, Yu; Kon, Takahide; Kurisu, Genji; Nakamura, Haruki
2016-01-01
Dyneins are large microtubule motor proteins that convert ATP energy to mechanical power. High-resolution crystal structures of ADP-bound cytoplasmic dynein have revealed the organization of the motor domain, comprising the AAA+ ring, the linker, the stalk/strut and the C sequence. Recently, the ADP.vanadate-bound structure, which is similar to the ATP hydrolysis transition state, revealed how the structure of dynein changes upon ATP binding. Although both the ADP- and ATP-bound state structures have been resolved, the dynamic properties at the atomic level remain unclear. In this work, we built two models named ‘the ADP model’ and ‘the ATP model’, where ADP and ATP are bound to AAA1 in the AAA+ ring, respectively, to observe the initial procedure of the structural change from the unprimed to the primed state. We performed 200-ns molecular dynamics simulations for both models and compared their structures and dynamics. The motions of the stalk, consisting of a long coiled coil with a microtubule-binding domain, significantly differed between the two models. The elastic properties of the stalk were analyzed and compared with the experimental results. PMID:27334455
Elastic properties of dynein motor domain obtained from all-atom molecular dynamics simulations.
Kamiya, Narutoshi; Mashimo, Tadaaki; Takano, Yu; Kon, Takahide; Kurisu, Genji; Nakamura, Haruki
2016-08-01
Dyneins are large microtubule motor proteins that convert ATP energy to mechanical power. High-resolution crystal structures of ADP-bound cytoplasmic dynein have revealed the organization of the motor domain, comprising the AAA(+) ring, the linker, the stalk/strut and the C sequence. Recently, the ADP.vanadate-bound structure, which is similar to the ATP hydrolysis transition state, revealed how the structure of dynein changes upon ATP binding. Although both the ADP- and ATP-bound state structures have been resolved, the dynamic properties at the atomic level remain unclear. In this work, we built two models named 'the ADP model' and 'the ATP model', where ADP and ATP are bound to AAA1 in the AAA(+) ring, respectively, to observe the initial procedure of the structural change from the unprimed to the primed state. We performed 200-ns molecular dynamics simulations for both models and compared their structures and dynamics. The motions of the stalk, consisting of a long coiled coil with a microtubule-binding domain, significantly differed between the two models. The elastic properties of the stalk were analyzed and compared with the experimental results. PMID:27334455
A robust all-atom model for LCAT generated by homology modeling.
Segrest, Jere P; Jones, Martin K; Catte, Andrea; Thirumuruganandham, Saravana P
2015-03-01
LCAT is activated by apoA-I to form cholesteryl ester. We combined two structures, phospholipase A2 (PLA2) that hydrolyzes the ester bond at the sn-2 position of oxidized (short) acyl chains of phospholipid, and bacteriophage tubulin PhuZ, as C- and N-terminal templates, respectively, to create a novel homology model for human LCAT. The juxtaposition of multiple structural motifs matching experimental data is compelling evidence for the general correctness of many features of the model: i) The N-terminal 10 residues of the model, required for LCAT activity, extend the hydrophobic binding trough for the sn-2 chain 15-20 Å relative to PLA2. ii) The topography of the trough places the ester bond of the sn-2 chain less than 5 Å from the hydroxyl of the catalytic nucleophile, S181. iii) A β-hairpin resembling a lipase lid separates S181 from solvent. iv) S181 interacts with three functionally critical residues: E149, that regulates sn-2 chain specificity, and K128 and R147, whose mutations cause LCAT deficiency. Because the model provides a novel explanation for the complicated thermodynamic problem of the transfer of hydrophobic substrates from HDL to the catalytic triad of LCAT, it is an important step toward understanding the antiatherogenic role of HDL in reverse cholesterol transport. PMID:25589508
A robust all-atom model for LCAT generated by homology modeling[S
Segrest, Jere P.; Jones, Martin K.; Catte, Andrea; Thirumuruganandham, Saravana P.
2015-01-01
LCAT is activated by apoA-I to form cholesteryl ester. We combined two structures, phospholipase A2 (PLA2) that hydrolyzes the ester bond at the sn-2 position of oxidized (short) acyl chains of phospholipid, and bacteriophage tubulin PhuZ, as C- and N-terminal templates, respectively, to create a novel homology model for human LCAT. The juxtaposition of multiple structural motifs matching experimental data is compelling evidence for the general correctness of many features of the model: i) The N-terminal 10 residues of the model, required for LCAT activity, extend the hydrophobic binding trough for the sn-2 chain 15–20 Å relative to PLA2. ii) The topography of the trough places the ester bond of the sn-2 chain less than 5 Å from the hydroxyl of the catalytic nucleophile, S181. iii) A β-hairpin resembling a lipase lid separates S181 from solvent. iv) S181 interacts with three functionally critical residues: E149, that regulates sn-2 chain specificity, and K128 and R147, whose mutations cause LCAT deficiency. Because the model provides a novel explanation for the complicated thermodynamic problem of the transfer of hydrophobic substrates from HDL to the catalytic triad of LCAT, it is an important step toward understanding the antiatherogenic role of HDL in reverse cholesterol transport. PMID:25589508
Energy functions for rubber from microscopic potentials
NASA Astrophysics Data System (ADS)
Johal, A. S.; Dunstan, D. J.
2007-04-01
The finite deformation theory of rubber and related materials is based on energy functions that describe the macroscopic response of these materials under deformation. Energy functions and elastic constants are here derived from a simple microscopic (ball-and-spring) model. Exact uniaxial force-extension relationships are given for Hooke's Law and for the thermodynamic entropy-based microscopic model using the Gaussian and the inverse Langevin statistical approximations. Methods are given for finding the energy functions as expansions of tensor invariants of deformation, with exact solutions for functions that can be expressed as expansions in even powers of the extension. Comparison with experiment shows good agreement with the neo-Hookean energy function and we show how this derives directly from the simple Gaussian statistical model with a small modification.
Adiabatic corrections to density functional theory energies and wave functions.
Mohallem, José R; Coura, Thiago de O; Diniz, Leonardo G; de Castro, Gustavo; Assafrão, Denise; Heine, Thomas
2008-09-25
The adiabatic finite-nuclear-mass-correction (FNMC) to the electronic energies and wave functions of atoms and molecules is formulated for density-functional theory and implemented in the deMon code. The approach is tested for a series of local and gradient corrected density functionals, using MP2 results and diagonal-Born-Oppenheimer corrections from the literature for comparison. In the evaluation of absolute energy corrections of nonorganic molecules the LDA PZ81 functional works surprisingly better than the others. For organic molecules the GGA BLYP functional has the best performance. FNMC with GGA functionals, mainly BLYP, show a good performance in the evaluation of relative corrections, except for nonorganic molecules containing H atoms. The PW86 functional stands out with the best evaluation of the barrier of linearity of H2O and the isotopic dipole moment of HDO. In general, DFT functionals display an accuracy superior than the common belief and because the corrections are based on a change of the electronic kinetic energy they are here ranked in a new appropriate way. The approach is applied to obtain the adiabatic correction for full atomization of alcanes C(n)H(2n+2), n = 4-10. The barrier of 1 mHartree is approached for adiabatic corrections, justifying its insertion into DFT. PMID:18537228
All-atom normal-mode analysis reveals an RNA-induced allostery in a bacteriophage coat protein
NASA Astrophysics Data System (ADS)
Dykeman, Eric C.; Twarock, Reidun
2010-03-01
Assembly of the T=3 bacteriophage MS2 is initiated by the binding of a 19 nucleotide RNA stem loop from within the phage genome to a symmetric coat protein dimer. This binding event effects a folding of the FG loop in one of the protein subunits of the dimer and results in the formation of an asymmetric dimer. Since both the symmetric and asymmetric forms of the dimer are needed for the assembly of the protein container, this allosteric switch plays an important role in the life cycle of the phage. We provide here details of an all-atom normal-mode analysis of this allosteric effect. The results suggest that asymmetric contacts between the A -duplex RNA phosphodiester backbone of the stem loop with the EF loop in one coat protein subunit results in an increased dynamic behavior of its FG loop. The four lowest-frequency modes, which encompass motions predominantly on the FG loops, account for over 90% of the increased dynamic behavior due to a localization of the vibrational pattern on a single FG loop. Finally, we show that an analysis of the allosteric effect using an elastic network model fails to predict this localization effect, highlighting the importance of using an all-atom full force field method for this problem.
Universal Nuclear Energy Density Functional
Carlson, Joseph; Furnstahl, Richard; Horoi, Mihai; Lusk, Rusty; Nazarewicz, Witold; Ng, Esmond; Thompson, Ian; Vary, James
2012-12-01
An understanding of the properties of atomic nuclei is crucial for a complete nuclear theory, for element formation, for properties of stars, and for present and future energy and defense applications. During the period of Dec. 1 2006 – Jun. 30, 2012, the UNEDF collaboration carried out a comprehensive study of all nuclei, based on the most accurate knowledge of the strong nuclear interaction, the most reliable theoretical approaches, the most advanced algorithms, and extensive computational resources, with a view towards scaling to the petaflop platforms and beyond. Until recently such an undertaking was hard to imagine, and even at the present time such an ambitious endeavor would be far beyond what a single researcher or a traditional research group could carry out.
Nonlocal kinetic-energy-density functionals
Garcia-Gonzalez, P.; Alvarellos, J.E.; Chacon, E. |
1996-04-01
In this paper we present nonlocal kinetic-energy functionals {ital T}[{ital n}] within the average density approximation (ADA) framework, which do not require any extra input when applied to any electron system and recover the exact kinetic energy and the linear response function of a homogeneous system. In contrast with previous ADA functionals, these present good behavior of the long-range tail of the exact weight function. The averaging procedure for the kinetic functional (averaging the Fermi momentum of the electron gas, instead of averaging the electron density) leads to a functional without numerical difficulties in the calculation of extended systems, and it gives excellent results when applied to atoms and jellium surfaces. {copyright} {ital 1996 The American Physical Society.}
Mohammadiarani, Hossein; Vashisth, Harish
2016-01-01
The receptor tyrosine kinase superfamily comprises many cell-surface receptors including the insulin receptor (IR) and type 1 insulin-like growth factor receptor (IGF1R) that are constitutively homodimeric transmembrane glycoproteins. Therefore, these receptors require ligand-triggered domain rearrangements rather than receptor dimerization for activation. Specifically, binding of peptide ligands to receptor ectodomains transduces signals across the transmembrane domains for trans-autophosphorylation in cytoplasmic kinase domains. The molecular details of these processes are poorly understood in part due to the absence of structures of full-length receptors. Using MD simulations and enhanced conformational sampling algorithms, we present all-atom structural models of peptides containing 51 residues from the transmembrane and juxtamembrane regions of IR and IGF1R. In our models, the transmembrane regions of both receptors adopt helical conformations with kinks at Pro961 (IR) and Pro941 (IGF1R), but the C-terminal residues corresponding to the juxtamembrane region of each receptor adopt unfolded and flexible conformations in IR as opposed to a helix in IGF1R. We also observe that the N-terminal residues in IR form a kinked-helix sitting at the membrane–solvent interface, while homologous residues in IGF1R are unfolded and flexible. These conformational differences result in a larger tilt-angle of the membrane-embedded helix in IGF1R in comparison to IR to compensate for interactions with water molecules at the membrane–solvent interfaces. Our metastable/stable states for the transmembrane domain of IR, observed in a lipid bilayer, are consistent with a known NMR structure of this domain determined in detergent micelles, and similar states in IGF1R are consistent with a previously reported model of the dimerized transmembrane domains of IGF1R. Our all-atom structural models suggest potentially unique structural organization of kinase domains in each receptor. PMID
Date, Atsushi; Ishizuka, Ryosuke; Matubayasi, Nobuyuki
2016-05-21
Energetic analysis was conducted for nonpolar and polar solutes bound in a cationic micelle of dodecyl trimethyl ammonium bromide (DTAB), an anionic micelle of sodium dodecyl sulfate (SDS), and a nonionic micelle of tetraethylene glycol monododecyl ether (Brij30). All-atom molecular dynamics simulation was performed, and the free energies of binding the solutes in the hydrophobic-core and headgroup regions of the micelles were computed using the energy-representation method. It was found in all the micelles examined that aromatic naphthalene is preferably located more outward than aliphatic propane and that the polar solutes are localized at the interface of the hydrophobic and hydrophilic regions. The roles of the surfactant and water were then elucidated by decomposing the free energy into the contributions from the respective species. Water was observed to play a decisive role in determining the binding location of the solute, while the surfactant was found to be more important for the overall stabilization of the solute within the micelle. The effects of attractive and repulsive interactions of the solute with the surfactant and water were further examined, and their competition was analyzed in connection with the preferable location of the solute in the micellar system. PMID:27117093
Nguyen, Trang Truc; Viet, Man Hoang
2014-01-01
The influence of water models SPC, SPC/E, TIP3P, and TIP4P on ligand binding affinity is examined by calculating the binding free energy ΔGbind of oseltamivir carboxylate (Tamiflu) to the wild type of glycoprotein neuraminidase from the pandemic A/H5N1 virus. ΔGbind is estimated by the Molecular Mechanic-Poisson Boltzmann Surface Area method and all-atom simulations with different combinations of these aqueous models and four force fields AMBER99SB, CHARMM27, GROMOS96 43a1, and OPLS-AA/L. It is shown that there is no correlation between the binding free energy and the water density in the binding pocket in CHARMM. However, for three remaining force fields ΔGbind decays with increase of water density. SPC/E provides the lowest binding free energy for any force field, while the water effect is the most pronounced in CHARMM. In agreement with the popular GROMACS recommendation, the binding score obtained by combinations of AMBER-TIP3P, OPLS-TIP4P, and GROMOS-SPC is the most relevant to the experiments. For wild-type neuraminidase we have found that SPC is more suitable for CHARMM than TIP3P recommended by GROMACS for studying ligand binding. However, our study for three of its mutants reveals that TIP3P is presumably the best choice for CHARMM. PMID:24672329
Cable energy function of cortical axons
Ju, Huiwen; Hines, Michael L.; Yu, Yuguo
2016-01-01
Accurate estimation of action potential (AP)-related metabolic cost is essential for understanding energetic constraints on brain connections and signaling processes. Most previous energy estimates of the AP were obtained using the Na+-counting method, which seriously limits accurate assessment of metabolic cost of ionic currents that underlie AP conduction along the axon. Here, we first derive a full cable energy function for cortical axons based on classic Hodgkin-Huxley (HH) neuronal equations and then apply the cable energy function to precisely estimate the energy consumption of AP conduction along axons with different geometric shapes. Our analytical approach predicts an inhomogeneous distribution of metabolic cost along an axon with either uniformly or nonuniformly distributed ion channels. The results show that the Na+-counting method severely underestimates energy cost in the cable model by 20–70%. AP propagation along axons that differ in length may require over 15% more energy per unit of axon area than that required by a point model. However, actual energy cost can vary greatly depending on axonal branching complexity, ion channel density distributions, and AP conduction states. We also infer that the metabolic rate (i.e. energy consumption rate) of cortical axonal branches as a function of spatial volume exhibits a 3/4 power law relationship. PMID:27439954
Cable energy function of cortical axons.
Ju, Huiwen; Hines, Michael L; Yu, Yuguo
2016-01-01
Accurate estimation of action potential (AP)-related metabolic cost is essential for understanding energetic constraints on brain connections and signaling processes. Most previous energy estimates of the AP were obtained using the Na(+)-counting method, which seriously limits accurate assessment of metabolic cost of ionic currents that underlie AP conduction along the axon. Here, we first derive a full cable energy function for cortical axons based on classic Hodgkin-Huxley (HH) neuronal equations and then apply the cable energy function to precisely estimate the energy consumption of AP conduction along axons with different geometric shapes. Our analytical approach predicts an inhomogeneous distribution of metabolic cost along an axon with either uniformly or nonuniformly distributed ion channels. The results show that the Na(+)-counting method severely underestimates energy cost in the cable model by 20-70%. AP propagation along axons that differ in length may require over 15% more energy per unit of axon area than that required by a point model. However, actual energy cost can vary greatly depending on axonal branching complexity, ion channel density distributions, and AP conduction states. We also infer that the metabolic rate (i.e. energy consumption rate) of cortical axonal branches as a function of spatial volume exhibits a 3/4 power law relationship. PMID:27439954
Landscape of an exact energy functional
NASA Astrophysics Data System (ADS)
Cohen, Aron J.; Mori-Sánchez, Paula
2016-04-01
One of the great challenges of electronic structure theory is the quest for the exact functional of density functional theory. Its existence is proven, but it is a complicated multivariable functional that is almost impossible to conceptualize. In this paper the asymmetric two-site Hubbard model is studied, which has a two-dimensional universe of density matrices. The exact functional becomes a simple function of two variables whose three-dimensional energy landscape can be visualized and explored. A walk on this unique landscape, tilted to an angle defined by the one-electron Hamiltonian, gives a valley whose minimum is the exact total energy. This is contrasted with the landscape of some approximate functionals, explaining their failure for electron transfer in the strongly correlated limit. We show concrete examples of pure-state density matrices that are not v representable due to the underlying nonconvex nature of the energy landscape. The exact functional is calculated for all numbers of electrons, including fractional, allowing the derivative discontinuity to be visualized and understood. The fundamental gap for all possible systems is obtained solely from the derivatives of the exact functional.
Solar wind-magnetosphere energy input functions
Bargatze, L.F.; McPherron, R.L.; Baker, D.N.
1985-01-01
A new formula for the solar wind-magnetosphere energy input parameter, P/sub i/, is sought by applying the constraints imposed by dimensional analysis. Applying these constraints yields a general equation for P/sub i/ which is equal to rho V/sup 3/l/sub CF//sup 2/F(M/sub A/,theta) where, rho V/sup 3/ is the solar wind kinetic energy density and l/sub CF//sup 2/ is the scale size of the magnetosphere's effective energy ''collection'' region. The function F which depends on M/sub A/, the Alfven Mach number, and on theta, the interplanetary magnetic field clock angle is included in the general equation for P/sub i/ in order to model the magnetohydrodynamic processes which are responsible for solar wind-magnetosphere energy transfer. By assuming the form of the function F, it is possible to further constrain the formula for P/sub i/. This is accomplished by using solar wind data, geomagnetic activity indices, and simple statistical methods. It is found that P/sub i/ is proportional to (rho V/sup 2/)/sup 1/6/VBG(theta) where, rho V/sup 2/ is the solar wind dynamic pressure and VBG(theta) is a rectified version of the solar wind motional electric field. Furthermore, it is found that G(theta), the gating function which modulates the energy input to the magnetosphere, is well represented by a ''leaky'' rectifier function such as sin/sup 4/(theta/2). This function allows for enhanced energy input when the interplanetary magnetic field is oriented southward. This function also allows for some energy input when the interplanetary magnetic field is oriented northward. 9 refs., 4 figs.
Functional materials for energy-efficient buildings
NASA Astrophysics Data System (ADS)
Ebert, H.-P.
2015-08-01
The substantial improving of the energy efficiency is essential to meet the ambitious energy goals of the EU. About 40% of the European energy consumption belongs to the building sector. Therefore the reduction of the energy demand of the existing building stock is one of the key measures to deliver a substantial contribution to reduce CO2-emissions of our society. Buildings of the future have to be efficient in respect to energy consumption for construction and operation. Current research activities are focused on the development of functional materials with outstanding thermal and optical properties to provide, for example, slim thermally superinsulated facades, highly integrated heat storage systems or adaptive building components. In this context it is important to consider buildings as entities which fulfill energy and comfort claims as well as aesthetic aspects of a sustainable architecture.
Denning, Elizabeth J.; Priyakumar, U. Deva; Nilsson, Lennart; MacKerell, Alexander D.
2011-01-01
Here, we present an update of the CHARMM27 all-atom additive force field for nucleic acids that improves the treatment of RNA molecules. The original CHARMM27 force field parameters exhibit enhanced Watson-Crick (WC) base pair opening which is not consistent with experiment while analysis of MD simulations show the 2′-hydroxyl moiety to almost exclusively sample the O3′ orientation. Quantum mechanical studies of RNA related model compounds indicate the energy minimum associated with the O3′ orientation to be too favorable, consistent with the MD results. Optimization of the dihedral parameters dictating the energy of the 2′-hydroxyl proton targeting the QM data yielded several parameter sets, which sample both the base and O3′ orientations of the 2′-hydroxyl to varying degrees. Selection of the final dihedral parameters was based on reproduction of hydration behavior as related to a survey of crystallographic data and better agreement with experimental NMR J-coupling values. Application of the model, designated CHARMM36, to a collection of canonical and non-canonical RNA molecules reveals overall improved agreement with a range of experimental observables as compared to CHARMM27. The results also indicate the sensitivity of the conformational heterogeneity of RNA to the orientation of the 2′-hydroxyl moiety and support a model whereby the 2′-hydroxyl can enhance the probability of conformational transitions in RNA. PMID:21469161
Energy landscapes and functions of supramolecular systems.
Tantakitti, Faifan; Boekhoven, Job; Wang, Xin; Kazantsev, Roman V; Yu, Tao; Li, Jiahe; Zhuang, Ellen; Zandi, Roya; Ortony, Julia H; Newcomb, Christina J; Palmer, Liam C; Shekhawat, Gajendra S; de la Cruz, Monica Olvera; Schatz, George C; Stupp, Samuel I
2016-04-01
By means of two supramolecular systems-peptide amphiphiles engaged in hydrogen-bonded β-sheets, and chromophore amphiphiles driven to assemble by π-orbital overlaps-we show that the minima in the energy landscapes of supramolecular systems are defined by electrostatic repulsion and the ability of the dominant attractive forces to trap molecules in thermodynamically unfavourable configurations. These competing interactions can be selectively switched on and off, with the order of doing so determining the position of the final product in the energy landscape. Within the same energy landscape, the peptide-amphiphile system forms a thermodynamically favoured product characterized by long bundled fibres that promote biological cell adhesion and survival, and a metastable product characterized by short monodisperse fibres that interfere with adhesion and can lead to cell death. Our findings suggest that, in supramolecular systems, functions and energy landscapes are linked, superseding the more traditional connection between molecular design and function. PMID:26779883
Energy landscapes and functions of supramolecular systems
NASA Astrophysics Data System (ADS)
Tantakitti, Faifan; Boekhoven, Job; Wang, Xin; Kazantsev, Roman V.; Yu, Tao; Li, Jiahe; Zhuang, Ellen; Zandi, Roya; Ortony, Julia H.; Newcomb, Christina J.; Palmer, Liam C.; Shekhawat, Gajendra S.; de La Cruz, Monica Olvera; Schatz, George C.; Stupp, Samuel I.
2016-04-01
By means of two supramolecular systems--peptide amphiphiles engaged in hydrogen-bonded β-sheets, and chromophore amphiphiles driven to assemble by π-orbital overlaps--we show that the minima in the energy landscapes of supramolecular systems are defined by electrostatic repulsion and the ability of the dominant attractive forces to trap molecules in thermodynamically unfavourable configurations. These competing interactions can be selectively switched on and off, with the order of doing so determining the position of the final product in the energy landscape. Within the same energy landscape, the peptide-amphiphile system forms a thermodynamically favoured product characterized by long bundled fibres that promote biological cell adhesion and survival, and a metastable product characterized by short monodisperse fibres that interfere with adhesion and can lead to cell death. Our findings suggest that, in supramolecular systems, functions and energy landscapes are linked, superseding the more traditional connection between molecular design and function.
Energy landscapes and function of supramolecular systems
Tantakitti, Faifan; Boekhoven, Job; Wang, Xin; Kazantsev, Roman; Yu, Tao; Li, Jiahe; Zhuang, Ellen; Zandi, Roya; Ortony, Julia H.; Newcomb, Christina J.; Palmer, Liam C.; Shekhawat, Gajendra S.; de la Cruz, Monica Olvera; Schatz, George C.; Stupp, Samuel I.
2015-01-01
By means of two supramolecular systems - peptide amphiphiles engaged in hydrogen-bonded β-sheets, and chromophore amphiphiles driven to assemble by π-orbital overlaps - we show that the minima in the energy landscapes of supramolecular systems are defined by electrostatic repulsion and the ability of the dominant attractive forces to trap molecules in thermodynamically unfavourable configurations. These competing interactions can be selectively switched on and off, with the order of doing so determining the position of the final product in the energy landscape. Within the same energy landscape, the peptide-amphiphile system forms a thermodynamically favoured product characterized by long bundled fibres that promote biological cell adhesion and survival, and a metastable product characterized by short monodisperse fibres that interfere with adhesion and can lead to cell death. Our findings suggest that, in supramolecular systems, function and energy landscape are linked, superseding the more traditional connection between molecular design and function. PMID:26779883
Harvesting Vibrational Energy Using Material Work Functions
NASA Astrophysics Data System (ADS)
Varpula, Aapo; Laakso, Sampo J.; Havia, Tahvo; Kyynäräinen, Jukka; Prunnila, Mika
2014-10-01
Vibration energy harvesters scavenge energy from mechanical vibrations to energise low power electronic devices. In this work, we report on vibration energy harvesting scheme based on the charging phenomenon occurring naturally between two bodies with different work functions. Such work function energy harvester (WFEH) is similar to electrostatic energy harvester with the fundamental distinction that neither external power supplies nor electrets are needed. A theoretical model and description of different operation modes of WFEHs are presented. The WFEH concept is tested with macroscopic experiments, which agree well with the model. The feasibility of miniaturizing WFEHs is shown by simulating a realistic MEMS device. The WFEH can be operated as a charge pump that pushes charge and energy into an energy storage element. We show that such an operation mode is highly desirable for applications and that it can be realised with either a charge shuttle or with switches. The WFEH is shown to give equal or better output power in comparison to traditional electrostatic harvesters. Our findings indicate that WFEH has great potential in energy harvesting applications.
Harvesting Vibrational Energy Using Material Work Functions
Varpula, Aapo; Laakso, Sampo J.; Havia, Tahvo; Kyynäräinen, Jukka; Prunnila, Mika
2014-01-01
Vibration energy harvesters scavenge energy from mechanical vibrations to energise low power electronic devices. In this work, we report on vibration energy harvesting scheme based on the charging phenomenon occurring naturally between two bodies with different work functions. Such work function energy harvester (WFEH) is similar to electrostatic energy harvester with the fundamental distinction that neither external power supplies nor electrets are needed. A theoretical model and description of different operation modes of WFEHs are presented. The WFEH concept is tested with macroscopic experiments, which agree well with the model. The feasibility of miniaturizing WFEHs is shown by simulating a realistic MEMS device. The WFEH can be operated as a charge pump that pushes charge and energy into an energy storage element. We show that such an operation mode is highly desirable for applications and that it can be realised with either a charge shuttle or with switches. The WFEH is shown to give equal or better output power in comparison to traditional electrostatic harvesters. Our findings indicate that WFEH has great potential in energy harvesting applications. PMID:25348004
Nuclear diffractive structure functions at high energies
Marquet,C.; Kowalski, H.; Lappi, T.; Venugopalan, R.
2008-08-08
A future high-energy electron-ion collider would explore the non-linear weakly-coupled regime of QCD, and test the Color Glass Condensate (CGC) approach to high-energy scattering. Hard diffraction in deep inelastic scattering off nuclei will provide many fundamental measurements. In this work, the nuclear diffractive structure function F{sub 2,A}{sup D} is predicted in the CGC framework, and the features of nuclear enhancement and suppression are discussed.
Density-dependent covariant energy density functionals
Lalazissis, G. A.
2012-10-20
Relativistic nuclear energy density functionals are applied to the description of a variety of nuclear structure phenomena at and away fromstability line. Isoscalar monopole, isovector dipole and isoscalar quadrupole giant resonances are calculated using fully self-consistent relativistic quasiparticle randomphase approximation, based on the relativistic Hartree-Bogoliubovmodel. The impact of pairing correlations on the fission barriers in heavy and superheavy nuclei is examined. The role of pion in constructing desnity functionals is also investigated.
Electron energy-distribution functions in gases
Pitchford, L.C.
1981-01-01
Numerical calculation of the electron energy distribution functions in the regime of drift tube experiments is discussed. The discussion is limited to constant applied fields and values of E/N (ratio of electric field strength to neutral density) low enough that electron growth due to ionization can be neglected. (GHT)
Ulmschneider, Jakob P.; Smith, Jeremy C.; Ulmschneider, Martin B.; Ulrich, Anne S.; Strandberg, Erik
2012-01-01
The membrane-active antimicrobial peptide PGLa from Xenopus laevis is known from solid-state 2H-, 15N-, and 19F-NMR spectroscopy to occupy two distinct α-helical surface adsorbed states in membranes: a surface-bound S-state with a tilt angle of ∼95° at low peptide/lipid molar ratio (P/L = 1:200), and an obliquely tilted T-state with a tilt angle of 127° at higher peptide concentration (P/L = 1:50). Using a rapid molecular-dynamics insertion protocol in combination with microsecond-scale simulation, we have characterized the structure of both states in detail. As expected, the amphiphilic peptide resides horizontally on the membrane surface in a monomeric form at a low P/L, whereas the T-state is seen in the simulations to be a symmetric antiparallel dimer, with close contacts between small glycine and alanine residues at the interface. The computed tilt angles and azimuthal rotations, as well as the quadrupolar splittings predicted from the simulations agree with the experimental NMR data. The simulations reveal many structural details previously inaccessible, such as the immersion depth of the peptide in the membrane and the packing of the dimerization interface. The study highlights the ability and limitations of current state-of-the-art multimicrosecond all-atom simulations of membrane-active peptides to complement experimental data from solid-state NMR. PMID:22947863
SURFACE SYMMETRY ENERGY OF NUCLEAR ENERGY DENSITY FUNCTIONALS
Nikolov, N; Schunck, N; Nazarewicz, W; Bender, M; Pei, J
2010-12-20
We study the bulk deformation properties of the Skyrme nuclear energy density functionals. Following simple arguments based on the leptodermous expansion and liquid drop model, we apply the nuclear density functional theory to assess the role of the surface symmetry energy in nuclei. To this end, we validate the commonly used functional parametrizations against the data on excitation energies of superdeformed band-heads in Hg and Pb isotopes, and fission isomers in actinide nuclei. After subtracting shell effects, the results of our self-consistent calculations are consistent with macroscopic arguments and indicate that experimental data on strongly deformed configurations in neutron-rich nuclei are essential for optimizing future nuclear energy density functionals. The resulting survey provides a useful benchmark for further theoretical improvements. Unlike in nuclei close to the stability valley, whose macroscopic deformability hangs on the balance of surface and Coulomb terms, the deformability of neutron-rich nuclei strongly depends on the surface-symmetry energy; hence, its proper determination is crucial for the stability of deformed phases of the neutron-rich matter and description of fission rates for r-process nucleosynthesis.
Spin constraints on nuclear energy density functionals
NASA Astrophysics Data System (ADS)
Robledo, L. M.; Bernard, R. N.; Bertsch, G. F.
2014-02-01
The Gallagher-Moszkowski rule in the spectroscopy of odd-odd nuclei imposes a new spin constraint on the energy functionals for self-consistent mean field theory. The commonly used parametrization of the effective three-body interaction in the Gogny and Skyrme families of energy functionals is ill suited to satisfy the spin constraint. In particular, the Gogny parametrization of the three-body interaction has the spin dependence opposite to that required by the observed spectra. The two-body part has a correct sign, but in combination the rule is violated as often as not. We conclude that a new functional form is needed for the effective three-body interaction that can take into better account the different spin-isospin channels of the interaction.
Editorial: Functional nanomaterials for energy applications
Devan, Rupesh S.; Ma, Yuan -Ron; Kim, Jin -Hyeok; Bhattacharya, Raghu N.; Ghosh, Kartik C.
2015-02-16
In order to leap forward from the energy crisis issues and improve lifestyle, we all are looking positively toward nanomaterials or nanostructures. Thus, the exploration of new features of both typical and novel materials at the nanoscale level is playing important role in the development of innovative and improved energy technologies that have the capability of conserve/convert energy at large extend. By tailoring the surface morphology of materials in its nanoforms, the functional properties can be significantly adapted and specifically combined to produce highly potent multifunctional materials for conversion, storage, and consumption of energy in various forms. The papers selected for this special issue represent a good panel for addressing various energy applications including solar cell, fuel cells, nanofluid twisters, and gas sensors. Of course, the selected topic and the papers are not an exhaustive representation of the utilization of functional nanomaterials for energy applications. Nevertheless, they represent the rich and many-facet knowledge, which we have the pleasure of sharing with the readers.
Editorial: Functional nanomaterials for energy applications
Devan, Rupesh S.; Ma, Yuan -Ron; Kim, Jin -Hyeok; Bhattacharya, Raghu N.; Ghosh, Kartik C.
2015-02-16
In order to leap forward from the energy crisis issues and improve lifestyle, we all are looking positively toward nanomaterials or nanostructures. Thus, the exploration of new features of both typical and novel materials at the nanoscale level is playing important role in the development of innovative and improved energy technologies that have the capability of conserve/convert energy at large extend. By tailoring the surface morphology of materials in its nanoforms, the functional properties can be significantly adapted and specifically combined to produce highly potent multifunctional materials for conversion, storage, and consumption of energy in various forms. The papers selectedmore » for this special issue represent a good panel for addressing various energy applications including solar cell, fuel cells, nanofluid twisters, and gas sensors. Of course, the selected topic and the papers are not an exhaustive representation of the utilization of functional nanomaterials for energy applications. Nevertheless, they represent the rich and many-facet knowledge, which we have the pleasure of sharing with the readers.« less
Xu, Jiabin; Huang, Lei; Shakhnovich, Eugene I.
2011-01-01
In this work, we apply a detailed all-atom model with a transferable knowledge-based potential to study the folding kinetics of Formin-Binding protein, FBP28, which is a canonical three-stranded β-sheet WW domain. Replica exchange Monte Carlo (REMC) simulations starting from random coils find native-like (C α RMSD of 2.68Å) lowest energy structure. We also study the folding kinetics of FBP28 WW domain by performing a large number of ab initio Monte Carlo folding simulations. Using these trajectories, we examine the order of formation of two β –hairpins, the folding mechanism of each individual β– hairpin, and transition state ensemble (TSE) of FBP28 WW domain and compare our results with experimental data and previous computational studies. To obtain detailed structural information on the folding dynamics viewed as an ensemble process, we perform a clustering analysis procedure based on graph theory. Further, a rigorous Pfold analysis is used to obtain representative samples of the TSEs showing good quantitative agreement between experimental and simulated Φ values. Our analysis shows that the turn structure between first and second β strands is a partially stable structural motif that gets formed before entering the TSE in FBP28 WW domain and there exist two major pathways for the folding of FBP28 WW domain, which differ in the order and mechanism of hairpin formation. PMID:21365688
Vanommeslaeghe, K.; Hatcher, E.; Acharya, C.; Kundu, S.; Zhong, S.; Shim, J.; Darian, E.; Guvench, O.; Lopes, P.; Vorobyov, I.; MacKerell, A. D.
2010-01-01
The widely used CHARMM additive all-atom force field includes parameters for proteins, nucleic acids, lipids and carbohydrates. In the present paper an extension of the CHARMM force field to drug-like molecules is presented. The resulting CHARMM General Force Field (CGenFF) covers a wide range of chemical groups present in biomolecules and drug-like molecules, including a large number of heterocyclic scaffolds. The parametrization philosophy behind the force field focuses on quality at the expense of transferability, with the implementation concentrating on an extensible force field. Statistics related to the quality of the parametrization with a focus on experimental validation are presented. Additionally, the parametrization procedure, described fully in the present paper in the context of the model systems, pyrrolidine, and 3-phenoxymethylpyrrolidine will allow users to readily extend the force field to chemical groups that are not explicitly covered in the force field as well as add functional groups to and link together molecules already available in the force field. CGenFF thus makes it possible to perform “all-CHARMM” simulations on drug-target interactions thereby extending the utility of CHARMM force fields to medicinally relevant systems. PMID:19575467
Gould, Tim; Bučko, Tomáš
2016-08-01
Using time-dependent density functional theory (TDDFT) with exchange kernels, we calculate and test imaginary frequency-dependent dipole polarizabilities for all atoms and many ions in rows 1-6 of the periodic table. These are then integrated over frequency to produce C6 coefficients. Results are presented under different models: straight TDDFT calculations using two different kernels; "benchmark" TDDFT calculations corrected by more accurate quantum chemical and experimental data; and "benchmark" TDDFT with frozen orbital anions. Parametrizations are presented for 411+ atoms and ions, allowing results to be easily used by other researchers. A curious relationship, C6,XY ∝ [αX(0)αY(0)](0.73), is found between C6 coefficients and static polarizabilities α(0). The relationship C6,XY = 2C6,XC6,Y/[(αX/αY)C6,Y + (αY/αX)C6,X] is tested and found to work well (<5% errors) in ∼80% of the cases, but can break down badly (>30% errors) in a small fraction of cases. PMID:27304856
Nonequilibrium self-energy functional theory
NASA Astrophysics Data System (ADS)
Hofmann, Felix; Eckstein, Martin; Arrigoni, Enrico; Potthoff, Michael
2013-10-01
The self-energy functional theory (SFT) is generalized to describe the real-time dynamics of correlated lattice-fermion models far from thermal equilibrium. This is achieved by starting from a reformulation of the original equilibrium theory in terms of double-time Green's functions on the Keldysh-Matsubara contour. With the help of a generalized Luttinger-Ward functional, we construct a functional Ω̂[Σ] which is stationary at the physical (nonequilibrium) self-energy Σ and which yields the grand potential of the initial thermal state Ω at the physical point. Nonperturbative approximations can be defined by specifying a reference system that serves to generate trial self-energies. These self-energies are varied by varying the reference system's one-particle parameters on the Keldysh-Matsubara contour. In the case of thermal equilibrium, this approach reduces to the conventional SFT. Contrary to the equilibrium theory, however, “unphysical” variations, i.e., variations that are different on the upper and the lower branches of the Keldysh contour, must be considered to fix the time dependence of the optimal physical parameters via the variational principle. Functional derivatives in the nonequilibrium SFT Euler equation are carried out analytically to derive conditional equations for the variational parameters that are accessible to a numerical evaluation via a time-propagation scheme. Approximations constructed by means of the nonequilibrium SFT are shown to be inherently causal, internally consistent, and to respect macroscopic conservation laws resulting from gauge symmetries of the Hamiltonian. This comprises the nonequilibrium dynamical mean-field theory but also dynamical-impurity and variational-cluster approximations that are specified by reference systems with a finite number of degrees of freedom. In this way, nonperturbative and consistent approximations can be set up, the numerical evaluation of which is accessible to an exact
Potential energy function for the hydroperoxyl radical
Lemon, W.J.; Hase, W.L.
1987-03-12
A switching function formalism is used to derive an analytic potential energy surface for the O + OH in equilibrium HO/sub 2/ in equilibrium H + O/sub 2/ reactive system. Both experimental and ab initio data are used to derive parameters for the potential energy surface. Trajectory calculations for highly excited HO/sub 2/ are performed on this surface. From these trajectories quasi-periodic eigentrajectories are found for vibrational levels near the HO/sub 2/ dissociation threshold with small amounts of quanta in the OH stretch mode and large amounts of quanta in the OO stretch mode.
Peguin, Robson P S; Kamath, Ganesh; Potoff, Jeffrey J; da Rocha, Sandro R P
2009-01-01
A new all-atom force field capable of accurately predicting the bulk and interfacial properties of 1,1,1,2-tetrafluoroethane (HFA134a) is reported. Parameterization of several force fields with different initial charge configurations from ab initio calculations was performed using the histogram reweighting method and Monte Carlo simulations in the grand canonical ensemble. The 12-6 Lennard-Jones well depth and diameter for the different HFA134a models were determined by fitting the simulation results to pure-component vapor-equilibrium data. Initial screening of the force fields was achieved by comparing the calculated and experimental bulk properties. The surface tension of pure HFA134a served as an additional screening property to help discriminate an optimum model. The proposed model reproduces the experimental saturated liquid and vapor densities, and the vapor pressure for HFA134a within average errors of 0.7%, 4.4%, and 3.1%, respectively. Critical density, temperature, vapor pressure, normal boiling point, and heat of vaporization at 298 K are also in good agreement with experimental data with errors of 0.2%, 0.1%, 6.2%, 0%, 2.2%, respectively. The calculated surface tension is found to be within the experimental range of 7.7-8.1 mN.m(-1). The dipole moment of the different models was found to significantly affect the prediction of the vapor pressure and surface tension. The ability of the HFA134a models in predicting the interfacial tension against water is also discussed. The results presented here are relevant in the development of technologies where the more environmentally friendly HFA134a is utilized as a substitute to the ozone depleting chlorofluorocarbon propellants. PMID:19086791
Bottaro, Sandro; Lindorff-Larsen, Kresten; Best, Robert B
2013-12-10
The development of accurate implicit solvation models with low computational cost is essential for addressing many large-scale biophysical problems. Here, we present an efficient solvation term based on a Gaussian solvent-exclusion model (EEF1) for simulations of proteins in aqueous environment, with the primary aim of having a good overlap with explicit solvent simulations, particularly for unfolded and disordered states - as would be needed for multiscale applications. In order to achieve this, we have used a recently proposed coarse-graining procedure based on minimization of an entropy-related objective function to train the model to reproduce the equilibrium distribution obtained from explicit water simulations. Via this methodology, we have optimized both a charge screening parameter and a backbone torsion term against explicit solvent simulations of an α-helical and a β-stranded peptide. The performance of the resulting effective energy function, termed EEF1-SB, is tested with respect to the properties of folded proteins, the folding of small peptides or fast-folding proteins, and NMR data for intrinsically disordered proteins. The results show that EEF1-SB provides a reasonable description of a wide range of systems, but its key advantage over other methods tested is that it captures very well the structure and dimension of disordered or weakly structured peptides. EEF1-SB is thus a computationally inexpensive (~ 10 times faster than Generalized-Born methods) and transferable approximation for treating solvent effects. PMID:24748852
Functional Carbon Materials for Electrochemical Energy Storage
NASA Astrophysics Data System (ADS)
Zhou, Huihui
The ability to harvest and convert solar energy has been associated with the evolution of human civilization. The increasing consumption of fossil fuels since the industrial revolution, however, has brought to concerns in ecological deterioration and depletion of the fossil fuels. Facing these challenges, humankind is forced to seek for clean, sustainable and renewable energy resources, such as biofuels, hydraulic power, wind power, geothermal energy and other kinds of alternative energies. However, most alternative energy sources, generally in the form of electrical energy, could not be made available on a continuous basis. It is, therefore, essential to store such energy into chemical energy, which are portable and various applications. In this context, electrochemical energy-storage devices hold great promises towards this goal. The most common electrochemical energy-storage devices are electrochemical capacitors (ECs, also called supercapacitors) and batteries. In comparison to batteries, ECs posses high power density, high efficiency, long cycling life and low cost. ECs commonly utilize carbon as both (symmetric) or one of the electrodes (asymmetric), of which their performance is generally limited by the capacitance of the carbon electrodes. Therefore, developing better carbon materials with high energy density has been emerging as one the most essential challenges in the field. The primary objective of this dissertation is to design and synthesize functional carbon materials with high energy density at both aqueous and organic electrolyte systems. The energy density (E) of ECs are governed by E = CV 2/2, where C is the total capacitance and V is the voltage of the devices. Carbon electrodes with high capacitance and high working voltage should lead to high energy density. In the first part of this thesis, a new class of nanoporous carbons were synthesized for symmetric supercapacitors using aqueous Li2SO4 as the electrolyte. A unique precursor was adopted to
Ischemia detection using Isoelectric Energy Function.
Kumar, Amit; Singh, Mandeep
2016-01-01
A novel method has been proposed for the detection of ischemia using an isoelectric energy function (IEEF) resulting from ST segment deviations in ECG signals. The method consists of five stages: pre-processing, delineation, measurement of isoelectric energy, a beat characterization algorithm and detection of ischemia. The isoelectric energy threshold is used to differentiate ischemic beats from normal beats for ischemic episode detection. Then, ischemic episodes are classified as transmural or subendocardial. The method is validated for recordings of the annotated European ST-T database (EDB). The results show 98.12% average sensitivity (SE) and 98.16% average specificity (SP). These results are significantly better than those of existing methods cited in the literature. The advantage of the proposed method includes simplicity, ruggedness and automatic discarding of noisy beats. PMID:26623944
Ou, Shu-Ching; Cui, Di; Wezowicz, Matthew; Taufer, Michela; Patel, Sandeep
2015-06-15
In this study, we examine the temperature dependence of free energetics of nanotube association using graphical processing unit-enabled all-atom molecular dynamics simulations (FEN ZI) with two (10,10) single-walled carbon nanotubes in 3 m NaI aqueous salt solution. Results suggest that the free energy, enthalpy and entropy changes for the association process are all reduced at the high temperature, in agreement with previous investigations using other hydrophobes. Via the decomposition of free energy into individual components, we found that solvent contribution (including water, anion, and cation contributions) is correlated with the spatial distribution of the corresponding species and is influenced distinctly by the temperature. We studied the spatial distribution and the structure of the solvent in different regions: intertube, intratube and the bulk solvent. By calculating the fluctuation of coarse-grained tube-solvent surfaces, we found that tube-water interfacial fluctuation exhibits the strongest temperature dependence. By taking ions to be a solvent-like medium in the absence of water, tube-anion interfacial fluctuation shows similar but weaker dependence on temperature, while tube-cation interfacial fluctuation shows no dependence in general. These characteristics are discussed via the malleability of their corresponding solvation shells relative to the nanotube surface. Hydrogen bonding profiles and tetrahedrality of water arrangement are also computed to compare the structure of solvent in the solvent bulk and intertube region. The hydrophobic confinement induces a relatively lower concentration environment in the intertube region, therefore causing different intertube solvent structures which depend on the tube separation. This study is relevant in the continuing discourse on hydrophobic interactions (as they impact generally a broad class of phenomena in biology, biochemistry, and materials science and soft condensed matter research), and
Ou, Shu-Ching; Cui, Di; Wezowicz, Matthew; Taufer, Michela; Patel, Sandeep
2015-01-01
In this study we examine the temperature dependence of free energetics of nanotube association by using GPU-enabled all-atom molecular dynamics simulations (FEN ZI) with two (10,10) single-walled carbon nanotubes in 3 m NaI aqueous salt solution. Results suggest that the free energy, enthalpy and entropy changes for the association process are all reduced at the high temperature, in agreement with previous investigations using other hydrophobes. Via the decomposition of free energy into individual components, we found that solvent contribution (including water, anion and cation contributions) is correlated with the spatial distribution of the corresponding species and is influenced distinctly by the temperature. We studied the spatial distribution and the structure of the solvent in different regions: intertube, intra-tube and the bulk solvent. By calculating the fluctuation of coarse-grained tube-solvent surfaces, we found that tube-water interfacial fluctuation exhibits the strongest temperature dependence. By taking ions to be a solvent-like medium in the absence of water, tube-anion interfacial fluctuation also shows similar but weaker dependence on temperature, while tube-cation interfacial fluctuation shows no dependence in general. These characteristics are discussed via the malleability of their corresponding solvation shells relative to the nanotube surface. Hydrogen bonding profiles and tetrahedrality of water arrangement are also computed to compare the structure of solvent in the solvent bulk and intertube region. The hydrophobic confinement induces a relatively lower concentration environment in the intertube region, therefore causing different intertube solvent structures which depend on the tube separation. This study is relevant in the continuing discourse on hydrophobic interactions (as they impact generally a broad class of phenomena in biology, biochemistry, and materials science and soft condensed matter research), and interpretations of
Markutsya, Sergiy; Lamm, Monica H
2014-11-07
We report on a new approach for deriving coarse-grained intermolecular forces that retains the frictional contribution that is often discarded by conventional coarse-graining methods. The approach is tested for water and an aqueous glucose solution, and the results from the new implementation for coarse-grained molecular dynamics simulation show remarkable agreement with the dynamics obtained from reference all-atom simulations. The agreement between the structural properties observed in the coarse-grained and all-atom simulations is also preserved. We discuss how this approach may be applied broadly to any existing coarse-graining method where the coarse-grained models are rigorously derived from all-atom reference systems.
Popa, Vlad; Trecroce, Danielle A; McAllister, Robert G; Konermann, Lars
2016-06-16
Electrospray ionization mass spectrometry (ESI-MS) has become an indispensable technique for examining noncovalent protein complexes. Collision-induced dissociation (CID) of these multiply protonated gaseous ions usually culminates in ejection of a single subunit with a disproportionately large amount of charge. Experiments suggest that this process involves subunit unfolding prior to separation from the residual complex, as well as H(+) migration onto the unravelling chain. Molecular dynamics (MD) simulations are a promising avenue for gaining detailed insights into these CID events. Unfortunately, typical MD algorithms do not allow for mobile protons. Here we address this limitation by implementing a strategy that combines atomistic force fields (such as OPLS/AA and CHARMM36) with a proton hopping algorithm, focusing on the tetrameric complexes transthyretin and streptavidin. Protons are redistributed over all acidic and basic sites in 20 ps intervals, subject to an energy function that reflects electrostatic interactions and proton affinities. Our simulations predict that nativelike conformers at the onset of collisional heating contain multiple salt bridges. Collisional heating initially causes subtle structural changes that lead to a gradual decline of these zwitterionic patterns. Many of the MD runs show gradual unfolding of a single subunit in conjunction with H(+) migration, culminating in subunit separation from the complex. However, there are also instances where two or more chains start to unfold simultaneously, giving rise to charge competition. The scission point where the "winning" subunit separates from the complex can be attained for different degrees of unfolding, giving rise to product ions in various charge states. The simulated product ion distributions are in close agreement with experimental CID data. Proton enrichment in the departing subunit is driven by charge-charge repulsion, but the combination of salt bridge depletion, charge migration
Shen, Lin; Yang, Weitao
2016-04-12
We developed a new multiresolution method that spans three levels of resolution with quantum mechanical, atomistic molecular mechanical, and coarse-grained models. The resolution-adapted all-atom and coarse-grained water model, in which an all-atom structural description of the entire system is maintained during the simulations, is combined with the ab initio quantum mechanics and molecular mechanics method. We apply this model to calculate the redox potentials of the aqueous ruthenium and iron complexes by using the fractional number of electrons approach and thermodynamic integration simulations. The redox potentials are recovered in excellent accordance with the experimental data. The speed-up of the hybrid all-atom and coarse-grained water model renders it computationally more attractive. The accuracy depends on the hybrid all-atom and coarse-grained water model used in the combined quantum mechanical and molecular mechanical method. We have used another multiresolution model, in which an atomic-level layer of water molecules around redox center is solvated in supramolecular coarse-grained waters for the redox potential calculations. Compared with the experimental data, this alternative multilayer model leads to less accurate results when used with the coarse-grained polarizable MARTINI water or big multipole water model for the coarse-grained layer. PMID:26930454
Casimir energies of cylinders: Universal function
Abalo, E. K.; Milton, K. A.; Kaplan, L.
2010-12-15
New exact results are given for the interior Casimir energies of infinitely long waveguides of triangular cross section (equilateral, hemiequilateral, and isosceles right triangles). Results for cylinders of rectangular cross section are rederived. In particular, results are obtained for interior modes belonging to Dirichlet and Neumann boundary conditions (TM and TE modes). These results are expressed in rapidly convergent series using the Chowla-Selberg formula, and in fact may be given in closed form, except for general rectangles. The energies are finite because only the first three heat-kernel coefficients can be nonzero for the case of polygonal boundaries. What appears to be a universal behavior of the Casimir energy as a function of the shape of the regular or quasiregular cross-sectional figure is presented. Furthermore, numerical calculations for arbitrary right triangular cross sections suggest that the universal behavior may be extended to waveguides of general polygonal cross sections. The new exact and numerical results are compared with the proximity force approximation (PFA).
Scientific Benchmarks for Guiding Macromolecular Energy Function Improvement
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
Transcription factor binding energy vs. biological function
NASA Astrophysics Data System (ADS)
Djordjevic, M.; Grotewold, E.
2007-03-01
Transcription factors (TFs) are proteins that bind to DNA and regulate expression of genes. Identification of transcription factor binding sites within the regulatory segments of genomic DNA is an important step towards understanding of gene regulatory networks. Recent theoretical advances that we developed [1,2], allow us to infer TF-DNA interaction parameters from in-vitro selection experiments [3]. We use more than 6000 binding sequences [3], assembled under controlled conditions, to obtain protein-DNA interaction parameters for a mammalian TF with up to now unprecedented accuracy. Can one accurately identify biologically functional TF binding sites (i.e. the binding sites that regulate gene expression), even with the best possible protein-DNA interaction parameters? To address this issue we i) compare our prediction of protein binding with gene expression data, ii) use evolutionary comparison between related mammalian genomes. Our results strongly suggest that in a genome there exists a large number of randomly occurring high energy binding sites that are not biologically functional. [1] M Djordjevic, submitted to Biomol. Eng. [2] M. Djordjevic and A. M. Sengupta, Phys. Biol. 3: 13, 2006. [3] E. Roulet et al., Nature Biotech. 20: 831, 2002.
Building a Universal Nuclear Energy Density Functional
Carlson, Joe A.; Furnstahl, Dick; Horoi, Mihai; Lust, Rusty; Nazaewicc, Witek; Ng, Esmond; Thompson, Ian; Vary, James
2012-12-30
During the period of Dec. 1 2006 – Jun. 30, 2012, the UNEDF collaboration carried out a comprehensive study of all nuclei, based on the most accurate knowledge of the strong nuclear interaction, the most reliable theoretical approaches, the most advanced algorithms, and extensive computational resources, with a view towards scaling to the petaflop platforms and beyond. The long-term vision initiated with UNEDF is to arrive at a comprehensive, quantitative, and unified description of nuclei and their reactions, grounded in the fundamental interactions between the constituent nucleons. We seek to replace current phenomenological models of nuclear structure and reactions with a well-founded microscopic theory that delivers maximum predictive power with well-quantified uncertainties. Specifically, the mission of this project has been three-fold: First, to find an optimal energy density functional (EDF) using all our knowledge of the nucleonic Hamiltonian and basic nuclear properties; Second, to apply the EDF theory and its extensions to validate the functional using all the available relevant nuclear structure and reaction data; Third, to apply the validated theory to properties of interest that cannot be measured, in particular the properties needed for reaction theory.
Pillardy, Jarosław; Czaplewski, Cezary; Liwo, Adam; Lee, Jooyoung; Ripoll, Daniel R.; Kaźmierkiewicz, Rajmund; Ołdziej, Stanisław; Wedemeyer, William J.; Gibson, Kenneth D.; Arnautova, Yelena A.; Saunders, Jeff; Ye, Yuan-Jie; Scheraga, Harold A.
2001-01-01
Recent improvements of a hierarchical ab initio or de novo approach for predicting both α and β structures of proteins are described. The united-residue energy function used in this procedure includes multibody interactions from a cumulant expansion of the free energy of polypeptide chains, with their relative weights determined by Z-score optimization. The critical initial stage of the hierarchical procedure involves a search of conformational space by the conformational space annealing (CSA) method, followed by optimization of an all-atom model. The procedure was assessed in a recent blind test of protein structure prediction (CASP4). The resulting lowest-energy structures of the target proteins (ranging in size from 70 to 244 residues) agreed with the experimental structures in many respects. The entire experimental structure of a cyclic α-helical protein of 70 residues was predicted to within 4.3 Å α-carbon (Cα) rms deviation (rmsd) whereas, for other α-helical proteins, fragments of roughly 60 residues were predicted to within 6.0 Å Cα rmsd. Whereas β structures can now be predicted with the new procedure, the success rate for α/β- and β-proteins is lower than that for α-proteins at present. For the β portions of α/β structures, the Cα rmsd's are less than 6.0 Å for contiguous fragments of 30–40 residues; for one target, three fragments (of length 10, 23, and 28 residues, respectively) formed a compact part of the tertiary structure with a Cα rmsd less than 6.0 Å. Overall, these results constitute an important step toward the ab initio prediction of protein structure solely from the amino acid sequence. PMID:11226239
The Nuclear Energy Density Functional Formalism
NASA Astrophysics Data System (ADS)
Duguet, T.
The present document focuses on the theoretical foundations of the nuclear energy density functional (EDF) method. As such, it does not aim at reviewing the status of the field, at covering all possible ramifications of the approach or at presenting recent achievements and applications. The objective is to provide a modern account of the nuclear EDF formalism that is at variance with traditional presentations that rely, at one point or another, on a Hamiltonian-based picture. The latter is not general enough to encompass what the nuclear EDF method represents as of today. Specifically, the traditional Hamiltonian-based picture does not allow one to grasp the difficulties associated with the fact that currently available parametrizations of the energy kernel E[g',g] at play in the method do not derive from a genuine Hamilton operator, would the latter be effective. The method is formulated from the outset through the most general multi-reference, i.e. beyond mean-field, implementation such that the single-reference, i.e. "mean-field", derives as a particular case. As such, a key point of the presentation provided here is to demonstrate that the multi-reference EDF method can indeed be formulated in a mathematically meaningful fashion even if E[g',g] does not derive from a genuine Hamilton operator. In particular, the restoration of symmetries can be entirely formulated without making any reference to a projected state, i.e. within a genuine EDF framework. However, and as is illustrated in the present document, a mathematically meaningful formulation does not guarantee that the formalism is sound from a physical standpoint. The price at which the latter can be enforced as well in the future is eventually alluded to.
Functional Mock-up Unit Export of EnergyPlus
2012-08-01
The Functional Mock-up Unit Export of EnergyPlus is a software package that allows EnergyPlus to be exported as a Functional Mock-up Unit. This allows other software tools to run EnergyPlus as part of a larger simulation. To do so, the outside software needs to implement the Functional Mock-up interface standard (http://www.modelisar.com/), and be able to import Functional Mock-up Units for co-simulation.
Molecular Multipole Potential Energy Functions for Water.
Tan, Ming-Liang; Tran, Kelly N; Pickard, Frank C; Simmonett, Andrew C; Brooks, Bernard R; Ichiye, Toshiko
2016-03-01
Water is the most common liquid on this planet, with many unique properties that make it essential for life as we know it. These properties must arise from features in the charge distribution of a water molecule, so it is essential to capture these features in potential energy functions for water to reproduce its liquid state properties in computer simulations. Recently, models that utilize a multipole expansion located on a single site in the water molecule, or "molecular multipole models", have been shown to rival and even surpass site models with up to five sites in reproducing both the electrostatic potential around a molecule and a variety of liquid state properties in simulations. However, despite decades of work using multipoles, confusion still remains about how to truncate the multipole expansions efficiently and accurately. This is particularly important when using molecular multipole expansions to describe water molecules in the liquid state, where the short-range interactions must be accurate, because the higher order multipoles of a water molecule are large. Here, truncation schemes designed for a recent efficient algorithm for multipoles in molecular dynamics simulations are assessed for how well they reproduce results for a simple three-site model of water when the multipole moments and Lennard-Jones parameters of that model are used. In addition, the multipole analysis indicates that site models that do not account for out-of-plane electron density overestimate the stability of a non-hydrogen-bonded conformation, leading to serious consequences for the simulated liquid. PMID:26562223
Functional derivative of the kinetic energy functional for spherically symmetric systems.
Nagy, Á
2011-07-28
Ensemble non-interacting kinetic energy functional is constructed for spherically symmetric systems. The differential virial theorem is derived for the ensemble. A first-order differential equation for the functional derivative of the ensemble non-interacting kinetic energy functional and the ensemble Pauli potential is presented. This equation can be solved and a special case of the solution provides the original non-interacting kinetic energy of the density functional theory. PMID:21806089
NASA Astrophysics Data System (ADS)
Zheng, Wenjun; Glenn, Paul
2015-01-01
The Bacteriophage T4 Lysozyme (T4L) is a prototype modular protein comprised of an N-terminal and a C-domain domain, which was extensively studied to understand the folding/unfolding mechanism of modular proteins. To offer detailed structural and dynamic insights to the folded-state stability and the mechanical unfolding behaviors of T4L, we have performed extensive equilibrium and steered molecular dynamics simulations of both the wild-type (WT) and a circular permutation (CP) variant of T4L using all-atom and coarse-grained force fields. Our all-atom and coarse-grained simulations of the folded state have consistently found greater stability of the C-domain than the N-domain in isolation, which is in agreement with past thermostatic studies of T4L. While the all-atom simulation cannot fully explain the mechanical unfolding behaviors of the WT and the CP variant observed in an optical tweezers study, the coarse-grained simulations based on the Go model or a modified elastic network model (mENM) are in qualitative agreement with the experimental finding of greater unfolding cooperativity in the WT than the CP variant. Interestingly, the two coarse-grained models predict different structural mechanisms for the observed change in cooperativity between the WT and the CP variant—while the Go model predicts minor modification of the unfolding pathways by circular permutation (i.e., preserving the general order that the N-domain unfolds before the C-domain), the mENM predicts a dramatic change in unfolding pathways (e.g., different order of N/C-domain unfolding in the WT and the CP variant). Based on our simulations, we have analyzed the limitations of and the key differences between these models and offered testable predictions for future experiments to resolve the structural mechanism for cooperative folding/unfolding of T4L.
Zheng, Wenjun Glenn, Paul
2015-01-21
The Bacteriophage T4 Lysozyme (T4L) is a prototype modular protein comprised of an N-terminal and a C-domain domain, which was extensively studied to understand the folding/unfolding mechanism of modular proteins. To offer detailed structural and dynamic insights to the folded-state stability and the mechanical unfolding behaviors of T4L, we have performed extensive equilibrium and steered molecular dynamics simulations of both the wild-type (WT) and a circular permutation (CP) variant of T4L using all-atom and coarse-grained force fields. Our all-atom and coarse-grained simulations of the folded state have consistently found greater stability of the C-domain than the N-domain in isolation, which is in agreement with past thermostatic studies of T4L. While the all-atom simulation cannot fully explain the mechanical unfolding behaviors of the WT and the CP variant observed in an optical tweezers study, the coarse-grained simulations based on the Go model or a modified elastic network model (mENM) are in qualitative agreement with the experimental finding of greater unfolding cooperativity in the WT than the CP variant. Interestingly, the two coarse-grained models predict different structural mechanisms for the observed change in cooperativity between the WT and the CP variant—while the Go model predicts minor modification of the unfolding pathways by circular permutation (i.e., preserving the general order that the N-domain unfolds before the C-domain), the mENM predicts a dramatic change in unfolding pathways (e.g., different order of N/C-domain unfolding in the WT and the CP variant). Based on our simulations, we have analyzed the limitations of and the key differences between these models and offered testable predictions for future experiments to resolve the structural mechanism for cooperative folding/unfolding of T4L.
Risk as a Function of Energy Finance.
ERIC Educational Resources Information Center
Hansen, Shirley J.
1987-01-01
Discusses the risk factors involved in the development of energy efficient projects in schools. Defines the nature of the risks and provides an outline for managing risks through alternative financing. (MD)
NASA Astrophysics Data System (ADS)
Kuang, Zhifeng; Farmer, Barry; Pandey, Ras
2013-03-01
Binding of peptide P2 (EPLQLKM) [1] and its mutations (P2G, P2Q) to a graphene sheet are studied by a coarse-grained computer simulation. Our hierarchical coarse-grained approach involves all-atom MD simulation to assess the binding interaction of each residue with the graphene sheet. Data from all-atom simulations are then used as input to phenomenological interaction in a coarse-grained MC simulation [2]. Binding of each peptide and its residue in corresponding sequence (P2, P2G, P2Q) are evaluated by analyzing the adsorption of each residue, its mobility, and structural profiles. Although it is difficult to identify overall morphological differences in adsorbed peptides by visual inspections, quantitative analysis of the conformational changes of adsorbed peptides shows variations in size among P2E and its mutations. Results on binding of peptide P1 (HSSYWYAFNNKT) may also be presented if data become available. This work is supported by the Air Force Research Laboratory.
Aguayo, Daniel; González-Nilo, Fernando D; Chipot, Christophe
2012-05-01
Simulation of three models of cardiolipin (CL) containing membranes using a new set of parameters for tetramyristoyl and tetraoleoyl CLs has been developed in the framework of the united-atom CHARMM27-UA and the all-atom CHARMM36 force fields with the aim of performing molecular dynamics (MD) simulations of cardiolipin-containing mixed-lipid membranes. The new parameters use a hybrid representation of all-atom head groups in conjunction with implicit-hydrogen united-atom (UA) to describe the oleoyl and myristoyl chains of the CLs, in lieu of the fully atomistic description, thereby allowing longer simulations to be undertaken. The physicochemical properties of the bilayers were determined and compared with previously reported data. Furthermore, using tetramyristoyl CL mixed with POPG and POPE lipids, a mitochondrial membrane was simulated. The results presented here show the different behavior of the bilayers as a result of the lipid composition, where the length of the acyl chain and the conformation of the headgroup can be associated with the mitochondrial membrane properties. The new hybrid CL parameters prove to be well suited for the simulation of the molecular structure of CL-containing bilayers and can be extended to other lipid bilayers composed of CLs with different acyl chains or alternate head groups. PMID:26593668
Impact Energy of Functionally Graded Steels in Crack Arrester Configuration
NASA Astrophysics Data System (ADS)
Nazari, A.; Aghazadeh Mohandesi, J.
2010-10-01
Charpy impact energy of functionally graded steels produced by electroslag remelting composed of graded ferrite and austenite layers together with bainite or martensite intermediate layer in the form of crack arrester configuration has been investigated. The results obtained in the present study indicate that the notch tip position with respect to bainite or martensite layer significantly affects the impact energy. The closer the notch tip to the tougher layer, the higher the impact energy of the composite due to increment of energy absorbed by plastic deformation zone ahead of the notch and vice versa. Empirical relationships have been determined to correlate the impact energy of functionally graded steels to the morphology of layers.
Hierarchy of equations for the energy functional of the density-functional theory
NASA Astrophysics Data System (ADS)
Nagy, Á.
1993-04-01
A hierarchy of equations has been derived for the energy functionals of the density-functional theory using the virial theorem and the Levy-Perdew relation. In the local-density approximation, the solution of the equations of hierarchy for the kinetic and exchange energies provides the well-known Thomas-Fermi expression for the kinetic energy and the Slater-Gáspár-Kohn-Sham expression for the exchange. The truncation of the hierarchies of the kinetic and exchange energies results in rigorous lower bounds to the kinetic energy and upper bounds to the exchange energy in the plane-wave approximation.
Low-energy dynamics and biological function
NASA Astrophysics Data System (ADS)
Lechner, R. E.; Fitter, J.; Dencher, N. A.; Hauß, T.
2006-11-01
Results from QENS experiments using a resolution of 93 μeV on a biological system are reported. The photocycle of the proton pump bacteriorhodopsin (BR) is known to slow down with decreasing temperature and humidity, a behaviour related to the ‘dynamic transition’. We have achieved a separation of the pure thermal activation effect involving the plasticizing action of hydration water, from effects due to the variation of the hydration level on the dynamics of purple membrane (PM) with its integral protein BR, and have correlated this with its ability to function. This demonstrates that the biological function of BR requires molecular dynamics in the ps range.
Energy Transfer and a Recurring Mathematical Function
ERIC Educational Resources Information Center
Atkin, Keith
2013-01-01
This paper extends the interesting work of a previous contributor concerning the analogies between physical phenomena such as mechanical collisions and the transfer of power in an electric circuit. Emphasis is placed on a mathematical function linking these different areas of physics. This unifying principle is seen as an exciting opportunity to…
Garcia-Aldea, David; Alvarellos, J. E.
2008-02-15
We propose a kinetic energy density functional scheme with nonlocal terms based on the von Weizsaecker functional, instead of the more traditional approach where the nonlocal terms have the structure of the Thomas-Fermi functional. The proposed functionals recover the exact kinetic energy and reproduce the linear response function of homogeneous electron systems. In order to assess their quality, we have tested the total kinetic energies as well as the kinetic energy density for atoms. The results show that these nonlocal functionals give as good results as the most sophisticated functionals in the literature. The proposed scheme for constructing the functionals means a step ahead in the field of fully nonlocal kinetic energy functionals, because they are capable of giving better local behavior than the semilocal functionals, yielding at the same time accurate results for total kinetic energies. Moreover, the functionals enjoy the possibility of being evaluated as a single integral in momentum space if an adequate reference density is defined, and then quasilinear scaling for the computational cost can be achieved.
Kinetic-energy matrix elements for atomic Hylleraas-CI wave functions.
Harris, Frank E
2016-05-28
Hylleraas-CI is a superposition-of-configurations method in which each configuration is constructed from a Slater-type orbital (STO) product to which is appended (linearly) at most one interelectron distance rij. Computations of the kinetic energy for atoms by this method have been difficult due to the lack of formulas expressing these matrix elements for general angular momentum in terms of overlap and potential-energy integrals. It is shown here that a strategic application of angular-momentum theory, including the use of vector spherical harmonics, enables the reduction of all atomic kinetic-energy integrals to overlap and potential-energy matrix elements. The new formulas are validated by showing that they yield correct results for a large number of integrals published by other investigators. PMID:27250282
Kinetic-energy matrix elements for atomic Hylleraas-CI wave functions
NASA Astrophysics Data System (ADS)
Harris, Frank E.
2016-05-01
Hylleraas-CI is a superposition-of-configurations method in which each configuration is constructed from a Slater-type orbital (STO) product to which is appended (linearly) at most one interelectron distance rij. Computations of the kinetic energy for atoms by this method have been difficult due to the lack of formulas expressing these matrix elements for general angular momentum in terms of overlap and potential-energy integrals. It is shown here that a strategic application of angular-momentum theory, including the use of vector spherical harmonics, enables the reduction of all atomic kinetic-energy integrals to overlap and potential-energy matrix elements. The new formulas are validated by showing that they yield correct results for a large number of integrals published by other investigators.
Advanced Functional Materials for Energy Related Applications
NASA Astrophysics Data System (ADS)
Sasan, Koroush
The current global heavy dependency on fossil fuels gives rise to two critical problems: I) fossil fuels will be depleted in the near future; II) the release of green house gas CO2 generated by the combustion of fossil fuels contributes to global warming. To potentially address both problems, this dissertation documents three primary areas of investigation related to the development of alternative energy sources: electrocatalysts for fuel cells, photocatalysts for hydrogen generation, and photoreduction catalysts for converting CO2 to CH4. Fuel cells could be a promising source of alternative energy. Decreasing the cost and improving the durability and power density of Pt/C as a catalyst for reducing oxygen are major challenges for developing fuel cells. To address these concerns, we have synthesized a Nitrogen-Sulfur-Iron-doped porous carbon material. Our results indicate that the synthesized catalyst exhibits not only higher current density and stability but also higher tolerance to crossover chemicals than the commercial Pt/C catalyst. More importantly, the synthetic method is simple and inexpensive. Using photocatalysts and solar energy is another potential alternative solution for energy demand. We have synthesized a new biomimetic heterogeneous photocatalyst through the incorporation of homogeneous complex 1 [(i-SCH 2)2NC(O)C5H4N]-Fe2(CO) 6] into the highly robust zirconium-porphyrin based metal-organic framework (ZrPF). As photosensitizer ZrPF absorbs the visible light and produces photoexcited electrons that can be transferred through axial covalent bond to di-nuclear complex 1 for hydrogen generation. Additionally, we have studied the photoreduction of CO2 to CH4 using self-doped TiO2 (Ti+3@TiO 2) as photocatalytic materials. The incorporation of Ti3+ into TiO2 structures narrows the band gap, leading to significantly increased photocatalytic activity for the reduction of CO2 into renewable hydrocarbon fuel in the presence of water vapor under visible
NASA Astrophysics Data System (ADS)
Bunker, Alex
We summarize our recent work, using all atom molecular dynamics simulation to study the role of poly(ethylene glycol) (PEG) in drug delivery. We have simulated the drug delivery liposome membrane, in both the Gel and Liquid crystalline states. The simulations of the PEGylated membrane have been carried out in the presence of a physiological concentration of NaCl, and two other salts encountered in physiological conditions, KCL and CaCl2. We also simulated targeting moieties on the PEGylated membrane, comparing the behavior of two targeting moieties. We also simulated PEG with three drug molecules for which it is used as a delivery aid: paclitaxel, piroxicam, and hematoporphyrin. We found that the specific properties of PEG, its solubility in both polar and non-polar solvents, and its acting as a polymer electrolyte, have a significant e_ect on its behavior when used in drug delivery.
Das, Anuradha; Das, Suman; Biswas, Ranjit
2015-01-21
Temperature dependent relaxation dynamics, particle motion characteristics, and heterogeneity aspects of deep eutectic solvents (DESs) made of acetamide (CH3CONH2) and urea (NH2CONH2) have been investigated by employing time-resolved fluorescence measurements and all-atom molecular dynamics simulations. Three different compositions (f) for the mixture [fCH3CONH2 + (1 - f)NH2CONH2] have been studied in a temperature range of 328-353 K which is ∼120-145 K above the measured glass transition temperatures (∼207 K) of these DESs but much lower than the individual melting temperature of either of the constituents. Steady state fluorescence emission measurements using probe solutes with sharply different lifetimes do not indicate any dependence on excitation wavelength in these metastable molten systems. Time-resolved fluorescence anisotropy measurements reveal near-hydrodynamic coupling between medium viscosity and rotation of a dissolved dipolar solute. Stokes shift dynamics have been found to be too fast to be detected by the time-resolution (∼70 ps) employed, suggesting extremely rapid medium polarization relaxation. All-atom simulations reveal Gaussian distribution for particle displacements and van Hove correlations, and significant overlap between non-Gaussian (α2) and new non-Gaussian (γ) heterogeneity parameters. In addition, no stretched exponential relaxations have been detected in the simulated wavenumber dependent acetamide dynamic structure factors. All these results are in sharp contrast to earlier observations for ionic deep eutectics with acetamide [Guchhait et al., J. Chem. Phys. 140, 104514 (2014)] and suggest a fundamental difference in interaction and dynamics between ionic and non-ionic deep eutectic solvent systems. PMID:25612718
NASA Astrophysics Data System (ADS)
Das, Anuradha; Das, Suman; Biswas, Ranjit
2015-01-01
Temperature dependent relaxation dynamics, particle motion characteristics, and heterogeneity aspects of deep eutectic solvents (DESs) made of acetamide (CH3CONH2) and urea (NH2CONH2) have been investigated by employing time-resolved fluorescence measurements and all-atom molecular dynamics simulations. Three different compositions (f) for the mixture [fCH3CONH2 + (1 - f)NH2CONH2] have been studied in a temperature range of 328-353 K which is ˜120-145 K above the measured glass transition temperatures (˜207 K) of these DESs but much lower than the individual melting temperature of either of the constituents. Steady state fluorescence emission measurements using probe solutes with sharply different lifetimes do not indicate any dependence on excitation wavelength in these metastable molten systems. Time-resolved fluorescence anisotropy measurements reveal near-hydrodynamic coupling between medium viscosity and rotation of a dissolved dipolar solute. Stokes shift dynamics have been found to be too fast to be detected by the time-resolution (˜70 ps) employed, suggesting extremely rapid medium polarization relaxation. All-atom simulations reveal Gaussian distribution for particle displacements and van Hove correlations, and significant overlap between non-Gaussian (α2) and new non-Gaussian (γ) heterogeneity parameters. In addition, no stretched exponential relaxations have been detected in the simulated wavenumber dependent acetamide dynamic structure factors. All these results are in sharp contrast to earlier observations for ionic deep eutectics with acetamide [Guchhait et al., J. Chem. Phys. 140, 104514 (2014)] and suggest a fundamental difference in interaction and dynamics between ionic and non-ionic deep eutectic solvent systems.
Das, Anuradha; Das, Suman; Biswas, Ranjit
2015-01-21
Temperature dependent relaxation dynamics, particle motion characteristics, and heterogeneity aspects of deep eutectic solvents (DESs) made of acetamide (CH{sub 3}CONH{sub 2}) and urea (NH{sub 2}CONH{sub 2}) have been investigated by employing time-resolved fluorescence measurements and all-atom molecular dynamics simulations. Three different compositions (f) for the mixture [fCH{sub 3}CONH{sub 2} + (1 − f)NH{sub 2}CONH{sub 2}] have been studied in a temperature range of 328-353 K which is ∼120-145 K above the measured glass transition temperatures (∼207 K) of these DESs but much lower than the individual melting temperature of either of the constituents. Steady state fluorescence emission measurements using probe solutes with sharply different lifetimes do not indicate any dependence on excitation wavelength in these metastable molten systems. Time-resolved fluorescence anisotropy measurements reveal near-hydrodynamic coupling between medium viscosity and rotation of a dissolved dipolar solute. Stokes shift dynamics have been found to be too fast to be detected by the time-resolution (∼70 ps) employed, suggesting extremely rapid medium polarization relaxation. All-atom simulations reveal Gaussian distribution for particle displacements and van Hove correlations, and significant overlap between non-Gaussian (α{sub 2}) and new non-Gaussian (γ) heterogeneity parameters. In addition, no stretched exponential relaxations have been detected in the simulated wavenumber dependent acetamide dynamic structure factors. All these results are in sharp contrast to earlier observations for ionic deep eutectics with acetamide [Guchhait et al., J. Chem. Phys. 140, 104514 (2014)] and suggest a fundamental difference in interaction and dynamics between ionic and non-ionic deep eutectic solvent systems.
Energy Management and Control System: Desired Capabilities and Functionality
Hatley, Darrel D.; Meador, Richard J.; Katipamula, Srinivas; Brambley, Michael R.; Wouden, Carl
2005-04-29
This document discusses functions and capabilities of a typical building/facility energy management and control systems (EMCS). The overall intent is to provide a building operator, manager or engineer with basic background information and recommended functions, capabilities, and good/best practices that will enable the control systems to be fully utilized/optimized, resulting in improved building occupant quality of life and more reliable, energy efficient facilities.
Kinetic-energy density functional: Atoms and shell structure
Garcia-Gonzalez, P.; Alvarellos, J.E.; Chacon, E. |
1996-09-01
We present a nonlocal kinetic-energy functional which includes an anisotropic average of the density through a symmetrization procedure. This functional allows a better description of the nonlocal effects of the electron system. The main consequence of the symmetrization is the appearance of a clear shell structure in the atomic density profiles, obtained after the minimization of the total energy. Although previous results with some of the nonlocal kinetic functionals have given incipient structures for heavy atoms, only our functional shows a clear shell structure for most of the atoms. The atomic total energies have a good agreement with the exact calculations. Discussion of the chemical potential and the first ionization potential in atoms is included. The functional is also extended to spin-polarized systems. {copyright} {ital 1996 The American Physical Society.}
Dark energy and normalization of the cosmological wave function
NASA Astrophysics Data System (ADS)
Huang, Peng; Huang, Yue; Li, Miao; Li, Nan
2016-08-01
Dark energy is investigated from the perspective of quantum cosmology. It is found that, together with an appropriate normal ordering factor q, only when there is dark energy can the cosmological wave function be normalized. This interesting observation may require further attention.
Occupation-number-based energy functional for nuclear masses
Bertolli, Michael G.; Papenbrock, Thomas F; Wild, S. M.
2012-01-01
We develop an energy functional with shell-model occupations as the relevant degrees of freedom and compute nuclear masses across the nuclear chart. The functional is based on Hohenberg-Kohn theory with phenomenologically motivated terms. A global fit of the 17-parameter functional to 2049 nuclear masses yields a root-mean-square deviation of =1.31 MeV. Nuclear radii are computed within a model that employs the resulting occupation numbers.
Occupation number-based energy functional for nuclear masses.
Bertolli, M.; Papenbrock, T.; Wild, S. M.
2012-01-01
We develop an energy functional with shell-model occupations as the relevant degrees of freedom and compute nuclear masses across the nuclear chart. The functional is based on Hohenberg-Kohn theory with phenomenologically motivated terms. A global fit of the 17-parameter functional to 2049 nuclear masses yields a root-mean-square deviation of {chi} = 1.31 MeV. Nuclear radii are computed within a model that employs the resulting occupation numbers.
An Atomistic Statistically Effective Energy Function for Computational Protein Design.
Topham, Christopher M; Barbe, Sophie; André, Isabelle
2016-08-01
Shortcomings in the definition of effective free-energy surfaces of proteins are recognized to be a major contributory factor responsible for the low success rates of existing automated methods for computational protein design (CPD). The formulation of an atomistic statistically effective energy function (SEEF) suitable for a wide range of CPD applications and its derivation from structural data extracted from protein domains and protein-ligand complexes are described here. The proposed energy function comprises nonlocal atom-based and local residue-based SEEFs, which are coupled using a novel atom connectivity number factor to scale short-range, pairwise, nonbonded atomic interaction energies and a surface-area-dependent cavity energy term. This energy function was used to derive additional SEEFs describing the unfolded-state ensemble of any given residue sequence based on computed average energies for partially or fully solvent-exposed fragments in regions of irregular structure in native proteins. Relative thermal stabilities of 97 T4 bacteriophage lysozyme mutants were predicted from calculated energy differences for folded and unfolded states with an average unsigned error (AUE) of 0.84 kcal mol(-1) when compared to experiment. To demonstrate the utility of the energy function for CPD, further validation was carried out in tests of its capacity to recover cognate protein sequences and to discriminate native and near-native protein folds, loop conformers, and small-molecule ligand binding poses from non-native benchmark decoys. Experimental ligand binding free energies for a diverse set of 80 protein complexes could be predicted with an AUE of 2.4 kcal mol(-1) using an additional energy term to account for the loss in ligand configurational entropy upon binding. The atomistic SEEF is expected to improve the accuracy of residue-based coarse-grained SEEFs currently used in CPD and to extend the range of applications of extant atom-based protein statistical
Total energy equation leading to exchange-correlation functional
NASA Astrophysics Data System (ADS)
Liu, Feng; Wang, Tzu-Chiang
2015-05-01
By solving the total energy equation, we obtain the formula of exchange-correlation functional for the first time. This functional is usually determined by fitting experimental data or the numerical results of models. In the uniform electron gas limit, our exchange-correlation functional can exactly reproduce the results of Perdew-Zunger parameterization from the jellium model. By making use of a particular solution, our exchange-correlation functional could take into account the case of non-uniform electron density, and its validity can be confirmed through comparisons of the band structure, equilibrium lattice constant, and bulk modulus of aluminum and silicon. The absence of mechanical prescriptions for the systematic improvement of exchange-correlation functional hinders further development of density-functional theory (DFT), and the formula of exchange-correlation functional given in this study might provide a new perspective to help DFT out of this awkward situation.
Ghoufi, A; Morineau, D; Lefort, R; Malfreyt, P
2010-10-12
Many interesting physical phenomena occur on length and time scales that are not accessible by atomistic molecular simulations. By introducing a coarse graining of the degrees of freedom, coarse-grained (CG) models allow ther study of larger scale systems for longer times. Coarse-grained force fields have been mostly derived for large molecules, including polymeric materials and proteins. By contrast, there exist no satisfactory CG potentials for mesostructured porous solid materials in the literature. This issue has become critical among a growing number of studies on confinement effects on fluid properties, which require both long time and large scale simulations and the conservation of a sufficient level of atomistic description to account for interfacial phenomena. In this paper, we present a general multiscale procedure to derive a hybrid coarse grained/all atoms force field CG/AA model for mesoporous systems. The method is applied to mesostructured MCM-41 molecular sieves, while the parameters of the mesoscopic interaction potentials are obtained and validated from the computation of the adsorption isotherm of methanol by grand canonical molecular dynamic simulation. PMID:26616783
NASA Astrophysics Data System (ADS)
Sharma, Anirban; Ghorai, Pradip Kr.
2016-03-01
Composition dependent structural and dynamical properties of aqueous hydrophobic 1-butyl-3-methylimidazolium hexafluorophosphate ([BMIM][PF6]) ionic liquid (IL) have been investigated by using all-atom molecular dynamics simulation. We observe that addition of water does not increase significant number of dissociated ions in the solution over the pure state. As a consequence, self-diffusion coefficient of the cation and anion is comparable to each other at all water concentration similar to that is observed for the pure state. Voronoi polyhedra analysis exhibits strong dependence on the local environment of IL concentration. Void and neck distributions in Voronoi tessellation are approximately Gaussian for pure IL but upon subsequent addition of water, we observe deviation from the Gaussian behaviour with an asymmetric broadening with long tail of exponential decay at large void radius, particularly at higher water concentrations. The increase in void space and neck size at higher water concentration facilitates ionic motion, thus, decreasing dynamical heterogeneity and IL reorientation time and increases self-diffusion coefficient significantly.
Core level binding energies of functionalized and defective graphene.
Susi, Toma; Kaukonen, Markus; Havu, Paula; Ljungberg, Mathias P; Ayala, Paola; Kauppinen, Esko I
2014-01-01
X-ray photoelectron spectroscopy (XPS) is a widely used tool for studying the chemical composition of materials and it is a standard technique in surface science and technology. XPS is particularly useful for characterizing nanostructures such as carbon nanomaterials due to their reduced dimensionality. In order to assign the measured binding energies to specific bonding environments, reference energy values need to be known. Experimental measurements of the core level signals of the elements present in novel materials such as graphene have often been compared to values measured for molecules, or calculated for finite clusters. Here we have calculated core level binding energies for variously functionalized or defected graphene by delta Kohn-Sham total energy differences in the real-space grid-based projector-augmented wave density functional theory code (GPAW). To accurately model extended systems, we applied periodic boundary conditions in large unit cells to avoid computational artifacts. In select cases, we compared the results to all-electron calculations using an ab initio molecular simulations (FHI-aims) code. We calculated the carbon and oxygen 1s core level binding energies for oxygen and hydrogen functionalities such as graphane-like hydrogenation, and epoxide, hydroxide and carboxylic functional groups. In all cases, we considered binding energy contributions arising from carbon atoms up to the third nearest neighbor from the functional group, and plotted C 1s line shapes by using experimentally realistic broadenings. Furthermore, we simulated the simplest atomic defects, namely single and double vacancies and the Stone-Thrower-Wales defect. Finally, we studied modifications of a reactive single vacancy with O and H functionalities, and compared the calculated values to data found in the literature. PMID:24605278
Core level binding energies of functionalized and defective graphene
Kaukonen, Markus; Havu, Paula; Ljungberg, Mathias P; Ayala, Paola; Kauppinen, Esko I
2014-01-01
Summary X-ray photoelectron spectroscopy (XPS) is a widely used tool for studying the chemical composition of materials and it is a standard technique in surface science and technology. XPS is particularly useful for characterizing nanostructures such as carbon nanomaterials due to their reduced dimensionality. In order to assign the measured binding energies to specific bonding environments, reference energy values need to be known. Experimental measurements of the core level signals of the elements present in novel materials such as graphene have often been compared to values measured for molecules, or calculated for finite clusters. Here we have calculated core level binding energies for variously functionalized or defected graphene by delta Kohn–Sham total energy differences in the real-space grid-based projector-augmented wave density functional theory code (GPAW). To accurately model extended systems, we applied periodic boundary conditions in large unit cells to avoid computational artifacts. In select cases, we compared the results to all-electron calculations using an ab initio molecular simulations (FHI-aims) code. We calculated the carbon and oxygen 1s core level binding energies for oxygen and hydrogen functionalities such as graphane-like hydrogenation, and epoxide, hydroxide and carboxylic functional groups. In all cases, we considered binding energy contributions arising from carbon atoms up to the third nearest neighbor from the functional group, and plotted C 1s line shapes by using experimentally realistic broadenings. Furthermore, we simulated the simplest atomic defects, namely single and double vacancies and the Stone–Thrower–Wales defect. Finally, we studied modifications of a reactive single vacancy with O and H functionalities, and compared the calculated values to data found in the literature. PMID:24605278
Teaching Potential Energy Functions and Stability with Slap Bracelets
NASA Astrophysics Data System (ADS)
Van Hook, Stephen J.
2005-10-01
The slap bracelet, an inexpensive child's toy, makes it easy to engage students in hands-on exploration of potential energy curves as well as of stable, unstable, and meta-stable states. Rather than just observing the teacher performing a demonstration, the students can manipulate the equipment themselves and make their own observations, which are then pooled to focus a class discussion on potential energy functions and stability.
McKechnie, Scott; Booth, George H.; Cohen, Aron J.; Cole, Jacqueline M.
2015-05-21
The best practice in computational methods for determining vertical ionization energies (VIEs) is assessed, via reference to experimentally determined VIEs that are corroborated by highly accurate coupled-cluster calculations. These reference values are used to benchmark the performance of density functional theory (DFT) and wave function methods: Hartree-Fock theory, second-order Møller-Plesset perturbation theory, and Electron Propagator Theory (EPT). The core test set consists of 147 small molecules. An extended set of six larger molecules, from benzene to hexacene, is also considered to investigate the dependence of the results on molecule size. The closest agreement with experiment is found for ionization energies obtained from total energy difference calculations. In particular, DFT calculations using exchange-correlation functionals with either a large amount of exact exchange or long-range correction perform best. The results from these functionals are also the least sensitive to an increase in molecule size. In general, ionization energies calculated directly from the orbital energies of the neutral species are less accurate and more sensitive to an increase in molecule size. For the single-calculation approach, the EPT calculations are in closest agreement for both sets of molecules. For the orbital energies from DFT functionals, only those with long-range correction give quantitative agreement with dramatic failing for all other functionals considered. The results offer a practical hierarchy of approximations for the calculation of vertical ionization energies. In addition, the experimental and computational reference values can be used as a standardized set of benchmarks, against which other approximate methods can be compared.
McKechnie, Scott; Booth, George H; Cohen, Aron J; Cole, Jacqueline M
2015-05-21
The best practice in computational methods for determining vertical ionization energies (VIEs) is assessed, via reference to experimentally determined VIEs that are corroborated by highly accurate coupled-cluster calculations. These reference values are used to benchmark the performance of density functional theory (DFT) and wave function methods: Hartree-Fock theory, second-order Møller-Plesset perturbation theory, and Electron Propagator Theory (EPT). The core test set consists of 147 small molecules. An extended set of six larger molecules, from benzene to hexacene, is also considered to investigate the dependence of the results on molecule size. The closest agreement with experiment is found for ionization energies obtained from total energy difference calculations. In particular, DFT calculations using exchange-correlation functionals with either a large amount of exact exchange or long-range correction perform best. The results from these functionals are also the least sensitive to an increase in molecule size. In general, ionization energies calculated directly from the orbital energies of the neutral species are less accurate and more sensitive to an increase in molecule size. For the single-calculation approach, the EPT calculations are in closest agreement for both sets of molecules. For the orbital energies from DFT functionals, only those with long-range correction give quantitative agreement with dramatic failing for all other functionals considered. The results offer a practical hierarchy of approximations for the calculation of vertical ionization energies. In addition, the experimental and computational reference values can be used as a standardized set of benchmarks, against which other approximate methods can be compared. PMID:26001454
Ab initio derivation of model energy density functionals
NASA Astrophysics Data System (ADS)
Dobaczewski, Jacek
2016-08-01
I propose a simple and manageable method that allows for deriving coupling constants of model energy density functionals (EDFs) directly from ab initio calculations performed for finite fermion systems. A proof-of-principle application allows for linking properties of finite nuclei, determined by using the nuclear nonlocal Gogny functional, to the coupling constants of the quasilocal Skyrme functional. The method does not rely on properties of infinite fermion systems but on the ab initio calculations in finite systems. It also allows for quantifying merits of different model EDFs in describing the ab initio results.
Self-interaction-free nonlocal correlation energy functional associated with a Jastrow function
NASA Astrophysics Data System (ADS)
Umezawa, Naoto; Austin, Brian; Lester, William A., Jr.
2010-03-01
We propose a self-interaction-free nonlocal correlation energy functional based on the transcorrelated method [1]. An effective Hamiltonian, Heff=1F H F, is derived from a similarity transformation with respect to a `Jastrow' correlation factor, F. The total energy is given by the expectation value of Heff with respect to a single Slater determinant. If a two-body Jastrow function is adopted, the resulting method resembles a Kohn-Sham density functional theory in which the correlation energy functional consists of two- and three-body interactions [2]. To simplify our calculations, we exclude the three-body terms and instead multiply the two-body term by an adjustable parameter that ensures convergence of the correlation energy to the exact limit for the homogeneous electron gas. The computational cost of the proposed method is comparable to the Hartree-Fock method. Moreover, the present correlation functional does not include self-interaction terms. The performance of this functional for various atoms and molecules will be presented. [1]S. F. Boys and N. C. Handy, Proc. Roy. Soc. A, 309, 209; 310, 43; 310, 63; 311, 309 (1969). [2] N. Umezawa and T. Chikyow, Phys. Rev. A 73, 062116 (2006).
Towards the island of stability with relativistic energy density functionals
Prassa, V.; Niksic, T.; Lalazissis, G. A.; Vretenar, D.
2012-10-20
Relativistic energy density functionals (REDF) provide a complete and accurate, global description of nuclear structure phenomena. Modern semi-empirical functionals, adjusted to the nuclear matter equation of state and to empirical masses of deformed nuclei, are applied to studies of shapes of superheavy nuclei. The theoretical framework is tested in a comparison to empirical masses, quadrupole deformations, and energy barriers of actinide nuclei. The model is used in a self-consistent mean-field calculation of spherical, axial and triaxial shapes of superheavy nuclei, alpha-decay energies and lifetimes. The effect of explicit treatment of collective correlations is analyzed in calculations that consistently use a collective Hamiltonian model based on REDFs.
Frembgen-Kesner, Tamara; Andrews, Casey T.; Li, Shuxiang; Ngo, Nguyet Anh; Shubert, Scott A.; Jain, Aakash; Olayiwola, Oluwatoni; Weishaar, Mitch R.; Elcock, Adrian H.
2015-01-01
Recently, we reported the parameterization of a set of coarse-grained (CG) nonbonded potential functions, derived from all-atom explicit-solvent molecular dynamics (MD) simulations of amino acid pairs, and designed for use in (implicit-solvent) Brownian dynamics (BD) simulations of proteins; this force field was named COFFDROP (COarse-grained Force Field for Dynamic Representations Of Proteins). Here, we describe the extension of COFFDROP to include bonded backbone terms derived from fitting to results of explicit-solvent MD simulations of all possible two-residue peptides containing the 20 standard amino acids, with histidine modeled in both its protonated and neutral forms. The iterative Boltzmann inversion (IBI) method was used to optimize new CG potential functions for backbone-related terms by attempting to reproduce angle, dihedral and distance probability distributions generated by the MD simulations. In a simple test of the transferability of the extended force field, the angle, dihedral and distance probability distributions obtained from BD simulations of 56 three-residue peptides were compared to results from corresponding explicit-solvent MD simulations. In a more challenging test of the COFFDROP force field, it was used to simulate eight intrinsically disordered proteins and was shown to quite accurately reproduce the experimental hydrodynamic radii (Rhydro), provided that the favorable nonbonded interactions of the force field were uniformly scaled downwards in magnitude. Overall, the results indicate that the COFFDROP force field is likely to find use in modeling the conformational behavior of intrinsically disordered proteins and multi-domain proteins connected by flexible linkers. PMID:26574429
Optimizing potential energy functions for maximal intrinsic hyperpolarizability
Zhou Juefei; Szafruga, Urszula B.; Kuzyk, Mark G.; Watkins, David S.
2007-11-15
We use numerical optimization to study the properties of (1) the class of one-dimensional potential energy functions and (2) systems of point nuclei in two dimensions that yield the largest intrinsic hyperpolarizabilities, which we find to be within 30% of the fundamental limit. In all cases, we use a one-electron model. It is found that a broad range of optimized potentials, each of very different character, yield the same intrinsic hyperpolarizability ceiling of 0.709. Furthermore, all optimized potential energy functions share common features such as (1) the value of the normalized transition dipole moment to the dominant state, which forces the hyperpolarizability to be dominated by only two excited states and (2) the energy ratio between the two dominant states. All optimized potentials are found to obey the three-level ansatz to within about 1%. Many of these potential energy functions may be implementable in multiple quantum well structures. The subset of potentials with undulations reaffirm that modulation of conjugation may be an approach for making better organic molecules, though there appear to be many others. Additionally, our results suggest that one-dimensional molecules may have larger diagonal intrinsic hyperpolarizability {beta}{sub xxx}{sup int} than higher-dimensional systems.
Förster-Induced Energy Transfer in Functionalized Graphene.
Malic, Ermin; Appel, Heiko; Hofmann, Oliver T; Rubio, Angel
2014-05-01
Carbon nanostructures are ideal substrates for functionalization with molecules since they consist of a single atomic layer giving rise to an extraordinary sensitivity to changes in their surrounding. The functionalization opens a new research field of hybrid nanostructures with tailored properties. Here, we present a microscopic view on the substrate-molecule interaction in the exemplary hybrid material consisting of graphene functionalized with perylene molecules. First experiments on similar systems have been recently realized illustrating an extremely efficient transfer of excitation energy from adsorbed molecules to the carbon substrate, a process with a large application potential for high-efficiency photovoltaic devices and biomedical imaging and sensing. So far, there has been no microscopically founded explanation for the observed energy transfer. Based on first-principle calculations, we have explicitly investigated the different transfer mechanisms revealing the crucial importance of Förster coupling. Due to the efficient Coulomb interaction in graphene, we obtain strong Förster rates in the range of 1/fs. We investigate its dependence on the substrate-molecule distance R and describe the impact of the momentum transfer q for an efficient energy transfer. Furthermore, we find that the Dexter transfer mechanism is negligibly small due to the vanishing overlap between the involved strongly localized orbital functions. The gained insights are applicable to a variety of carbon-based hybrid nanostructures. PMID:24808936
Förster-Induced Energy Transfer in Functionalized Graphene
2014-01-01
Carbon nanostructures are ideal substrates for functionalization with molecules since they consist of a single atomic layer giving rise to an extraordinary sensitivity to changes in their surrounding. The functionalization opens a new research field of hybrid nanostructures with tailored properties. Here, we present a microscopic view on the substrate–molecule interaction in the exemplary hybrid material consisting of graphene functionalized with perylene molecules. First experiments on similar systems have been recently realized illustrating an extremely efficient transfer of excitation energy from adsorbed molecules to the carbon substrate, a process with a large application potential for high-efficiency photovoltaic devices and biomedical imaging and sensing. So far, there has been no microscopically founded explanation for the observed energy transfer. Based on first-principle calculations, we have explicitly investigated the different transfer mechanisms revealing the crucial importance of Förster coupling. Due to the efficient Coulomb interaction in graphene, we obtain strong Förster rates in the range of 1/fs. We investigate its dependence on the substrate–molecule distance R and describe the impact of the momentum transfer q for an efficient energy transfer. Furthermore, we find that the Dexter transfer mechanism is negligibly small due to the vanishing overlap between the involved strongly localized orbital functions. The gained insights are applicable to a variety of carbon-based hybrid nanostructures. PMID:24808936
A density functional for core-valence correlation energy
NASA Astrophysics Data System (ADS)
Ranasinghe, Duminda S.; Frisch, Michael J.; Petersson, George A.
2015-12-01
A density functional, ɛCV-DFT(ρc, ρv), describing the core-valence correlation energy has been constructed as a linear combination of ɛLY Pcorr(ρc), ɛV WN5corr(ρc, ρv), ɛPBEcorr(ρc, ρv), ɛSlaterex(ρc, ρv), ɛHCTHex(ρc, ρv), ɛHFex(ρc, ρv), and F CV -DFT (" separators=" N i , Z i ) , a function of the nuclear charges. This functional, with 6 adjustable parameters, reproduces (±0.27 kcal/mol rms error) a benchmark set of 194 chemical energy changes including 9 electron affinities, 18 ionization potentials, and 167 total atomization energies covering the first- and second-rows of the periodic table. This is almost twice the rms error (±0.16 kcal/mol) obtained with CCSD(T)/MTsmall calculations, but less than half the rms error (±0.65 kcal/mol) obtained with MP2/GTlargeXP calculations, and somewhat smaller than the rms error (±0.39 kcal/mol) obtained with CCSD/MTsmall calculations. The largest positive and negative errors from ɛCV-DFT(ρc, ρv) were 0.88 and -0.75 kcal/mol with the set of 194 core-valence energy changes ranging from +3.76 kcal/mol for the total atomization energy of propyne to -9.05 kcal/mol for the double ionization of Mg. Evaluation of the ɛCV-DFT(ρc, ρv) functional requires less time than a single SCF iteration, and the accuracy is adequate for any model chemistry based on the CCSD(T) level of theory.
A density functional for core-valence correlation energy.
Ranasinghe, Duminda S; Frisch, Michael J; Petersson, George A
2015-12-01
A density functional, εCV-DFT(ρc, ρv), describing the core-valence correlation energy has been constructed as a linear combination of εLY P (corr)(ρc), εV WN5 (corr)(ρc, ρv), εPBE (corr)(ρc, ρv), εSlater (ex)(ρc, ρv), εHCTH (ex)(ρc, ρv), εHF (ex)(ρc, ρv), and FCV-DFTNi,Zi, a function of the nuclear charges. This functional, with 6 adjustable parameters, reproduces (±0.27 kcal/mol rms error) a benchmark set of 194 chemical energy changes including 9 electron affinities, 18 ionization potentials, and 167 total atomization energies covering the first- and second-rows of the periodic table. This is almost twice the rms error (±0.16 kcal/mol) obtained with CCSD(T)/MTsmall calculations, but less than half the rms error (±0.65 kcal/mol) obtained with MP2/GTlargeXP calculations, and somewhat smaller than the rms error (±0.39 kcal/mol) obtained with CCSD/MTsmall calculations. The largest positive and negative errors from εCV-DFT(ρc, ρv) were 0.88 and -0.75 kcal/mol with the set of 194 core-valence energy changes ranging from +3.76 kcal/mol for the total atomization energy of propyne to -9.05 kcal/mol for the double ionization of Mg. Evaluation of the εCV-DFT(ρc, ρv) functional requires less time than a single SCF iteration, and the accuracy is adequate for any model chemistry based on the CCSD(T) level of theory. PMID:26646873
Efficient solution for equilibrium points in transient energy function analysis
Irisarri, G.D.; Ejebe, G.C.; Waight, J.G. ); Tinney, W.F. , Portland, OR )
1994-05-01
A new method for the determination of stable and unstable equilibrium points in the Transient Energy Function method of stability analysis is presented. Computation of the Unstable Equilibrium Point is one of the fundamental steps in determination of the energy margin. The basis of the new method is its formulation as a power flow problem and the use of well known power flow algorithms for its solution. Sparse matrix methods are used to achieve the indicated speedups. The new method has shown robust behavior in all systems tested and performance improvements over previous methods. Results using test systems of up to 161 generators, 901 buses, and 2,000 lines are given.
Curvature and Frontier Orbital Energies in Density Functional Theory
Stein, Tamar; Autschbach, Jochen; Govind, Niranjan; Kronik, Leeor; Baer, Roi
2012-12-20
Perdew et al. [Phys. Rev. Lett 49, 1691 (1982)] discovered and proved two different properties that exact Kohn-Sham density functional theory (DFT) must obey: (i) The exact total energy versus particle number must be a series of linear segments between integer electron points; (ii) Across an integer number of electrons, the exchange-correlation potential may ``jump’’ by a constant, known as the derivative discontinuity (DD). Here, we show analytically that in both the original and the generalized Kohn-Sham formulation of DFT, the two are in fact two sides of the same coin. Absence of a derivative discontinuity necessitates deviation from piecewise linearity, and the latter can be used to correct for the former, thereby restoring the physical meaning of the orbital energies. Using selected small molecules, we show that this results in a simple correction scheme for any underlying functional, including semi-local and hybrid functionals as well as Hartree-Fock theory, suggesting a practical correction for the infamous gap problem of density functional theory. Moreover, we show that optimally-tuned range-separated hybrid functionals can inherently minimize both DD and curvature, thus requiring no correction, and show that this can be used as a sound theoretical basis for novel tuning strategies.
Physiology of leptin: energy homeostasis, neuroendocrine function and metabolism
Park, Hyeong-Kyu; Ahima, Rexford S.
2014-01-01
Leptin is secreted by adipose tissue and regulates energy homeostasis, neuroendocrine function, metabolism, immune function and other systems through its effects on the central nervous system and peripheral tissues. Leptin administration has been shown to restore metabolic and neuroendocrine abnormalities in individuals with leptin-deficient states, including hypothalamic amenorrhea and lipoatrophy. In contrast, obese individuals are resistant to leptin. Recombinant leptin is beneficial in patients with congenital leptin deficiency or generalized lipodystrophy. However, further research on molecular mediators of leptin resistance is needed for the development of targeted leptin sensitizing therapies for obesity and related metabolic diseases. PMID:25199978
Relativistic and binding energy corrections to heavy quark fragmentation functions
Yusuf, M.A.; Bashir, A.
1997-11-01
We calculate the fragmentation function for a charm quark to decay inclusively into S-wave charmonium states, including relativistic and binding energy corrections in powers of the quark relative velocity v. We also use these fragmentation functions to estimate their contribution to the production rate of {eta}{sub c} and J/{psi} in Z{sup 0} decay. These corrections contribute about 38{percent} to the integrated c{r_arrow}J/{psi}+X fragmentation. For {eta}{sub c}, these corrections are found to be small. {copyright} {ital 1997} {ital The American Physical Society}
Energy-loss function of TTF-TCNQ
NASA Astrophysics Data System (ADS)
Lošić, Željana Bonačić
2012-02-01
We investigate the energy-loss function for a previously developed model of quasi-one-dimensional metals with two one-dimensional electron bands per donor and acceptor chains and the three-dimensional long-range Coulomb electron-electron interaction within the random phase approximation. It is essentially influenced by two hybridized collective modes which result from the strong coupling of the intraband plasmon and the interband dipolar modes. Our calculations show that the spectral weights of the renormalized plasmon and the dipolar mode dominate within the long wavelength limit, while for large longitudinal wave vectors the intraband electron-hole quasi-continuumgains some experimentally observable spectral weight as the second mode approaches it. The function obtained is brought into correspondence with the data of the quasi-one-dimensional organic conductor tetrathiafulvalene-tetracyanoquinodimethane (TTF-TCNQ) obtained from electron energy-loss spectroscopy (EELS) measurements.
Controlling the Electron Energy Distribution Function Using an Anode
NASA Astrophysics Data System (ADS)
Baalrud, Scott D.; Barnat, Edward V.; Hopkins, Mathew M.
2014-10-01
Positively biased electrodes inserted into plasmas influence the electron energy distribution function (EEDF) by providing a sink for low energy electrons that would otherwise be trapped by ion sheaths at the chamber walls. We develop a model for the EEDF in a hot filament generated discharge in the presence of positively biased electrodes of various surface areas, and compare the model results with experimental Langmuir probe measurements and particle-in-cell simulations. In the absence of an anode, the EEDF is characterized by a cool trapped population at energies below the sheath energy, and a comparatively warm tail population associated with the filament primaries. Anodes that are small enough to collect a negligible fraction of the electrons exiting the plasma have little affect on the EEDF, but as the anode area approaches √{me /mi }Aw , where Aw is the chamber wall area, the anode collects most of the electrons leaving the plasma. This drastically reduces the density of the otherwise trapped population, causing an effective heating of the electrons and a corresponding density decrease. A global model is developed based on the EEDF model and current balance, which shows the interconnected nature of the electron temperature, density and the plasma potential. This work was supported by the Office of Fusion Energy Science at the U.S. Department of Energy under Contract DE-AC04-94SL85000, and by the University of Iowa Old Gold Program.
Energy functionals for inhomogeneous many-electron systems
Geldart, D.J.W. . Dept. of Physics); Rasolt, M. )
1991-10-01
The primary purpose of these lectures is to provide a pedagogical introduction Density Functional Theory (DF). We begin with the very early picture of Thomas and Fermi for the ground state energy of a neutral atom and proceed to the highly successful method of Kohn and Sham (KS) which focuses attention on the exchange-correlation contribution E{sub XC}(n) to the energy functional. We stress the importance of a systematic approach to the study of the subtle nonlocal structure of E{sub XC}(n) in inhomogeneous systems. The local and global convergence properties of gradient expansions are examined in some detail for detail for both density and low density systems. The structure of E{sub XC}(n) in the low density regime is described. Aspects of energy functionals which are determined by global symmetries and boundary conditions (in contrast to largely local energetics) are illustrated by the examples of the structure factor in bounded geometry and band gap discontinuities in semiconductors. An illustrative application of DFT is made to the problem of instabilities of the strongly correlated low density electron liquid with respect to charge modulated ground states.
Bernardes, Carlos E S; Canongia Lopes, José N; Minas da Piedade, Manuel E
2013-10-31
A previously developed OPLS-based all-atom force field for organometallic compounds was extended to a series of first-, second-, and third-row transition metals based on the study of M(CO)(n) (M = Cr, Fe, Ni, Mo, Ru, or W) complexes. For materials that are solid at ambient temperature and pressure (M = Cr, Mo, W) the validation of the force field was based on reported structural data and on the standard molar enthalpies of sublimation at 298.15 K, experimentally determined by Calvet-drop microcalorimetry using samples corresponding to a specific and well-characterized crystalline phase: Δ(sub)H(m)° = 72.6 ± 0.3 kJ·mol(–1) for Cr(CO)(6), 73.4 ± 0.3 kJ·mol(–1) for Mo(CO)(6), and 77.8 ± 0.3 kJ·mol(–1) for W(CO)(6). For liquids, where problems of polymorphism or phase mixtures are absent, critically analyzed literature data were used. The force field was able to reproduce the volumetric properties of the test set (density and unit cell volume) with an average deviations smaller than 2% and the experimentally determined enthalpies of sublimation and vaporization with an accuracy better than 2.3 kJ·mol(–1). The Lennard-Jones (12-6) potential function parameters used to calculate the repulsive and dispersion contributions of the metals within the framework of the force field were found to be transferable between chromium, iron, and nickel (first row) and between molybdenum and ruthenium (second row). PMID:24079472
Contrastive studies of potential energy functions of some diatomic molecules
NASA Astrophysics Data System (ADS)
Abdallah, Hassan H.; Abdullah, Hewa Y.
2016-03-01
It was proposed that iron hydride, FeH, would be formed only on grains at the clouds through the reaction of the adsorbed H atoms or H2 molecules with the adsorbed Fe atoms on the grains. The importance of FeH in Astrophysics presents an additional motivation to study its energetic, spectroscopic constants and Potential Energy Curves. The structural optimization for ground state of FeH was calculated by different theoretical methods, namely, Hartree-Fock (HF), the density functional theory (DFT), B3LYP, MP2 method and QCISD(T) methods and compared with available data from the literature. The single ionized forms, cation and anion, were also obtained at the same level of calculations. Charges, dipole moment, geometrical parameters, molecular orbital energies and spectroscopic parameters were calculated and reported. In addition, the molecular ionization potential, electron affinity and dissociation energy were investigated.
Antagonistic functions of LMNA isoforms in energy expenditure and lifespan.
Lopez-Mejia, Isabel C; de Toledo, Marion; Chavey, Carine; Lapasset, Laure; Cavelier, Patricia; Lopez-Herrera, Celia; Chebli, Karim; Fort, Philippe; Beranger, Guillaume; Fajas, Lluis; Amri, Ez Z; Casas, Francois; Tazi, Jamal
2014-05-01
Alternative RNA processing of LMNA pre-mRNA produces three main protein isoforms, that is, lamin A, progerin, and lamin C. De novo mutations that favor the expression of progerin over lamin A lead to Hutchinson-Gilford progeria syndrome (HGPS), providing support for the involvement of LMNA processing in pathological aging. Lamin C expression is mutually exclusive with the splicing of lamin A and progerin isoforms and occurs by alternative polyadenylation. Here, we investigate the function of lamin C in aging and metabolism using mice that express only this isoform. Intriguingly, these mice live longer, have decreased energy metabolism, increased weight gain, and reduced respiration. In contrast, progerin-expressing mice show increased energy metabolism and are lipodystrophic. Increased mitochondrial biogenesis is found in adipose tissue from HGPS-like mice, whereas lamin C-only mice have fewer mitochondria. Consistently, transcriptome analyses of adipose tissues from HGPS and lamin C-only mice reveal inversely correlated expression of key regulators of energy expenditure, including Pgc1a and Sfrp5. Our results demonstrate that LMNA encodes functionally distinct isoforms that have opposing effects on energy metabolism and lifespan in mammals. PMID:24639560
Proton-Proton Elastic Scattering Excitation Functions at Intermediate Energies
Bisplinghoff, J.; Daniel, R.; Diehl, O.; Engelhardt, H.; Ernst, J.; Eversheim, P.; Gro-Hardt, R.; Heider, S.; Heine, A.; Hinterberger, F.; Jahn, R.; Jeske, M.; Lahr, U.; Maschuw, R.; Mayer-Kuckuk, T.; Mosel, F.; Rohdje, H.; Rosendaal, D.; Ro, U.; Scheid, H.; Schulz-Rojahn, M.; Schwandt, F.; Schwarz, V.; Trelle, H.; Wiedmann, W.; Ziegler, R.; Albers, D.; Bollmann, R.; Bueer, K.; Dohrmann, F.; Gasthuber, M.; Greiff, J.; Gro, A.; Igelbrink, M.; Langkau, R.; Lindlein, J.; Mueller, M.; Muenstermann, M.; Schirm, N.; Scobel, W.; Wellinghausen, A.; Woller, K.; Cloth, P.; Gebel, R.; Maier, R.; Prasuhn, D.; von Rossen, P.; Sterzenbach, G.
1997-03-01
Excitation functions of proton-proton elastic scattering cross sections have been measured in narrow steps for projectile momenta p{sub p} (energies T{sub p}) from 1100 to 3300MeV/c (500 to 2500MeV) in the angular range 35{degree}{le}{Theta}{sub c.m.}{le}90{degree} with a detector providing {Delta}{Theta}{sub c.m.}{approx}1.4{degree} resolution. Measurements have been performed continuously during projectile acceleration in the cooler synchrotron COSY with an internal CH{sub 2} fiber target, taking particular care to monitor luminosity as a function of T{sub p}. The advantages of this experimental technique are demonstrated, and the excitation functions obtained are compared to existing cross section data. No evidence for narrow structures was found. {copyright} {ital 1997} {ital The American Physical Society}
A solvation-free-energy functional: a reference-modified density functional formulation.
Sumi, Tomonari; Mitsutake, Ayori; Maruyama, Yutaka
2015-07-01
The three-dimensional reference interaction site model (3D-RISM) theory, which is one of the most applicable integral equation theories for molecular liquids, overestimates the absolute values of solvation-free-energy (SFE) for large solute molecules in water. To improve the free-energy density functional for the SFE of solute molecules, we propose a reference-modified density functional theory (RMDFT) that is a general theoretical approach to construct the free-energy density functional systematically. In the RMDFT formulation, hard-sphere (HS) fluids are introduced as the reference system instead of an ideal polyatomic molecular gas, which has been regarded as the appropriate reference system of the interaction-site-model density functional theory for polyatomic molecular fluids. We show that using RMDFT with a reference HS system can significantly improve the absolute values of the SFE for a set of neutral amino acid side-chain analogues as well as for 504 small organic molecules. PMID:26032201
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. PMID:21693886
NASA Astrophysics Data System (ADS)
Domain, C.; Olsson, P.; Becquart, C. S.; Legris, A.; Guillemoles, J. F.
2008-02-01
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.
Potential function and dissociation energy of alkali halide
NASA Astrophysics Data System (ADS)
Srivastava, Abhay P.; Pandey, Anjani K.; Pandey, Brijesh K.
2016-05-01
Dissociation energy of some alkali halides have been calculated by using different interaction potential function such as Born-Mayer, Varshani-Shukla and L5 potential model. The theoretical calculation is compared with experimental values. The Result shows that the values of dissociation energy as calculated by using different potential models have an equal amount of deviation with experimental values. The above said deviation with experimental values can be explained by consideration of rotational-vibrational coupling between the constituents of molecules in the limelight of molecular spectroscopy. Findings of present work suggest that the existing potential model need to be reviewed in view of the correction factors solely depending on the rotational, vibrational and electronic coupling between the constituents of molecules.
Dipole polarizability of 120Sn and nuclear energy density functionals
NASA Astrophysics Data System (ADS)
Hashimoto, T.; Krumbholz, A. M.; Reinhard, P.-G.; Tamii, A.; von Neumann-Cosel, P.; Adachi, T.; Aoi, N.; Bertulani, C. A.; Fujita, H.; Fujita, Y.; GanioÇ§lu, E.; Hatanaka, K.; Ideguchi, E.; Iwamoto, C.; Kawabata, T.; Khai, N. T.; Krugmann, A.; Martin, D.; Matsubara, H.; Miki, K.; Neveling, R.; Okamura, H.; Ong, H. J.; Poltoratska, I.; Ponomarev, V. Yu.; Richter, A.; Sakaguchi, H.; Shimbara, Y.; Shimizu, Y.; Simonis, J.; Smit, F. D.; Süsoy, G.; Suzuki, T.; Thies, J. H.; Yosoi, M.; Zenihiro, J.
2015-09-01
The electric dipole strength distribution in 120Sn between 5 and 22 MeV has been determined at the Research Center for Nuclear Physics, Osaka, from polarization transfer observables measured in proton inelastic scattering at E0=295 MeV and forward angles including 0∘. Combined with photoabsorption data, a highly precise electric dipole polarizability αD(120Sn) =8.93 (36 ) fm3 is extracted. The dipole polarizability as isovector observable par excellence carries direct information on nuclear symmetry energy and its density dependence. The correlation of the new value with the well-established αD(208Pb) serves as a test of its prediction by nuclear energy density functionals. Models based on modern Skyrme interactions describe the data fairly well while most calculations based on relativistic Hamiltonians cannot.
Descriptions of carbon isotopes within the energy density functional theory
Ismail, Atef; Cheong, Lee Yen; Yahya, Noorhana; Tammam, M.
2014-10-24
Within the energy density functional (EDF) theory, the structure properties of Carbon isotopes are systematically studied. The shell model calculations are done for both even-A and odd-A nuclei, to study the structure of rich-neutron Carbon isotopes. The EDF theory indicates the single-neutron halo structures in {sup 15}C, {sup 17}C and {sup 19}C, and the two-neutron halo structures in {sup 16}C and {sup 22}C nuclei. It is also found that close to the neutron drip-line, there exist amazing increase in the neutron radii and decrease on the binding energies BE, which are tightly related with the blocking effect and correspondingly the blocking effect plays a significant role in the shell model configurations.
Density functional theory for protein transfer free energy.
Mills, Eric A; Plotkin, Steven S
2013-10-24
We cast the problem of protein transfer free energy within the formalism of density functional theory (DFT), treating the protein as a source of external potential that acts upon the solvent. Solvent excluded volume, solvent-accessible surface area, and temperature dependence of the transfer free energy all emerge naturally within this formalism, and may be compared with simplified "back of the envelope" models, which are also developed here. Depletion contributions to osmolyte induced stability range from 5 to 10 kBT for typical protein lengths. The general DFT transfer theory developed here may be simplified to reproduce a Langmuir isotherm condensation mechanism on the protein surface in the limits of short-ranged interactions, and dilute solute. Extending the equation of state to higher solute densities results in non-monotonic behavior of the free energy driving protein or polymer collapse. Effective interaction potentials between protein backbone or side chains and TMAO are obtained, assuming a simple backbone/side chain two-bead model for the protein with an effective 6-12 potential with the osmolyte. The transfer free energy δg shows significant entropy: d(δg)/dT ≈ 20 kB for a 100-residue protein. The application of DFT to effective solvent forces for use in implicit-solvent molecular dynamics is also developed. The simplest DFT expressions for implicit-solvent forces contain both depletion interactions and an "impeded-solvation" repulsive force at larger distances. PMID:23944753
Functional Arrays for Light Energy Capture and Charge Separation.
Flamigni, Lucia
2016-06-01
This article draws, with a simplified but rigorous approach, the typical procedure for the design and optimization of functional multicomponent structures for light to chemical energy conversion for two series of multipartite structures based on prototypical chromophores: polypyridyl metal complexes and porphyrinoids. Starting from a photophysical study performed by steady-state and time-resolved spectroscopic methods, the full deactivation dynamics of the light-absorbing chromophore(s) are disclosed. The preferred deactivation step (electron transfer in this case) is then optimized. This can be done by simply operating on the solvent, but also by changing structure/components that can alter electronic and nuclear factors, via continuous feedback with the research groups in charge of the synthesis. With a presentation suitable for a wide audience, it is here discussed how the effective design of functional multicomponent structures for charge separation can be achieved. PMID:27027981
Computational predictions of energy materials using density functional theory
NASA Astrophysics Data System (ADS)
Jain, Anubhav; Shin, Yongwoo; Persson, Kristin A.
2016-01-01
In the search for new functional materials, quantum mechanics is an exciting starting point. The fundamental laws that govern the behaviour of electrons have the possibility, at the other end of the scale, to predict the performance of a material for a targeted application. In some cases, this is achievable using density functional theory (DFT). In this Review, we highlight DFT studies predicting energy-related materials that were subsequently confirmed experimentally. The attributes and limitations of DFT for the computational design of materials for lithium-ion batteries, hydrogen production and storage materials, superconductors, photovoltaics and thermoelectric materials are discussed. In the future, we expect that the accuracy of DFT-based methods will continue to improve and that growth in computing power will enable millions of materials to be virtually screened for specific applications. Thus, these examples represent a first glimpse of what may become a routine and integral step in materials discovery.
BUILDING A UNIVERSAL NUCLEAR ENERGY DENSITY FUNCTIONAL (UNEDF)
Nazarewicz, Witold
2012-07-01
The long-term vision initiated with UNEDF is to arrive at a comprehensive, quantitative, and unified description of nuclei and their reactions, grounded in the fundamental interactions between the constituent nucleons. We seek to replace current phenomenological models of nuclear structure and reactions with a well-founded microscopic theory that delivers maximum predictive power with well-quantified uncertainties. Specifically, the mission of this project has been three-fold: First, to find an optimal energy density functional (EDF) using all our knowledge of the nucleonic Hamiltonian and basic nuclear properties. Second, to apply the EDF theory and its extensions to validate the functional using all the available relevant nuclear structure and reaction data. Third, to apply the validated theory to properties of interest that cannot be measured, in particular the properties needed for reaction theory.
Nuclear clustering in the energy density functional approach
Ebran, J.-P.; Khan, E.; Nikšić, T.; Vretenar, D.
2015-10-15
Nuclear Energy Density Functionals (EDFs) are a microscopic tool of choice extensively used over the whole chart to successfully describe the properties of atomic nuclei ensuing from their quantum liquid nature. In the last decade, they also have proved their ability to deal with the cluster phenomenon, shedding a new light on its fundamental understanding by treating on an equal footing both quantum liquid and cluster aspects of nuclei. Such a unified microscopic description based on nucleonic degrees of freedom enables to tackle the question pertaining to the origin of the cluster phenomenon and emphasizes intrinsic mechanisms leading to the emergence of clusters in nuclei.
Nuclear clustering in the energy density functional approach
NASA Astrophysics Data System (ADS)
Ebran, J.-P.; Khan, E.; Nikšić, T.; Vretenar, D.
2015-10-01
Nuclear Energy Density Functionals (EDFs) are a microscopic tool of choice extensively used over the whole chart to successfully describe the properties of atomic nuclei ensuing from their quantum liquid nature. In the last decade, they also have proved their ability to deal with the cluster phenomenon, shedding a new light on its fundamental understanding by treating on an equal footing both quantum liquid and cluster aspects of nuclei. Such a unified microscopic description based on nucleonic degrees of freedom enables to tackle the question pertaining to the origin of the cluster phenomenon and emphasizes intrinsic mechanisms leading to the emergence of clusters in nuclei.
Tensor part of the Skyrme energy density functional: Spherical nuclei
NASA Astrophysics Data System (ADS)
Lesinski, T.; Bender, M.; Bennaceur, K.; Duguet, T.; Meyer, J.
2007-07-01
We perform a systematic study of the impact of the J2 tensor term in the Skyrme energy functional on properties of spherical nuclei. In the Skyrme energy functional, the tensor terms originate from both zero-range central and tensor forces. We build a set of 36 parametrizations, covering a wide range of the parameter space of the isoscalar and isovector tensor term coupling constants with a fit protocol very similar to that of the successful SLy parametrizations. We analyze the impact of the tensor terms on a large variety of observables in spherical mean-field calculations, such as the spin-orbit splittings and single-particle spectra of doubly-magic nuclei, the evolution of spin-orbit splittings along chains of semi-magic nuclei, mass residuals of spherical nuclei, and known anomalies of radii. The major findings of our study are as follows: (i) Tensor terms should not be added perturbatively to existing parametrizations; a complete refit of the entire parameter set is imperative. (ii) The free variation of the tensor terms does not lower the χ2 within a standard Skyrme energy functional. (iii) For certain regions of the parameter space of their coupling constants, the tensor terms lead to instabilities of the spherical shell structure, or even to the coexistence of two configurations with different spherical shell structures. (iv) The standard spin-orbit interaction does not scale properly with the principal quantum number, such that single-particle states with one or several nodes have too large spin-orbit splittings, whereas those of nodeless intruder levels are tentatively too small. Tensor terms with realistic coupling constants cannot cure this problem. (v) Positive values of the coupling constants of proton-neutron and like-particle tensor terms allow for a qualitative description of the evolution of spin-orbit splittings in chains of Ca, Ni, and Sn isotopes. (vi) For the same values of the tensor term coupling constants, however, the overall agreement of
Relativistic Energy Density Functionals: Exotic modes of excitation
Vretenar, D.; Paar, N.; Marketin, T.
2008-11-11
The framework of relativistic energy density functionals has been applied to the description of a variety of nuclear structure phenomena, not only in spherical and deformed nuclei along the valley of {beta}-stability, but also in exotic systems with extreme isospin values and close to the particle drip-lines. Dynamical aspects of exotic nuclear structure have been investigated with the relativistic quasiparticle random-phase approximation. We present results for the evolution of low-lying dipole (pygmy) strength in neutron-rich nuclei, and charged-current neutrino-nucleus cross sections.
Ion energy distribution functions in a supersonic plasma jet
NASA Astrophysics Data System (ADS)
Caldirola, S.; Roman, H. E.; Riccardi, C.
2014-11-01
Starting from experimental measurements of ion energy distribution functions (IEDFs) in a low pressure supersonic plasma jet, we propose a model to simulate them numerically from first principles calculations. Experimentally we acquired IEDFs with a quadrupole mass spectrometer (QMS) collecting the argon ions produced from a inductively coupled plasma (ICP) and driven into a supersonic free gas expansion. From the discussion of these results and the physics of our system we developed a simulation code. Integrating the equations of motion the code evolves the trajectory of a single ion across the jet. Ar+- Ar collisions are modelled with a 12-4 Lennard-Jones potential which considers induced dipole interactions. IEDFs were simulated at different positions along the jet and compared with the experimental data showing good agreement. We have also implemented a charge transfer mechanism in which the ion releases its charge to a neutral atom which can take place at sufficiently close distances and is a function of the impact energy.
Interfacial properties and design of functional energy materials.
Sumpter, Bobby G; Liang, Liangbo; Nicolaï, Adrien; Meunier, Vincent
2014-11-18
CONSPECTUS: The vital importance of energy to society continues to demand a relentless pursuit of energy responsive materials that can bridge fundamental chemical structures at the molecular level and achieve improved functionality and performance. This demand can potentially be realized by harnessing the power of self-assembly, a spontaneous process where molecules or much larger entities form ordered aggregates as a consequence of predominately noncovalent (weak) interactions. Self-assembly is the key to bottom-up design of molecular devices, because the nearly atomic-level control is very difficult to realize in a top-down, for example, lithographic, approach. However, while function in simple systems such as single crystals can often be evaluated a priori, predicting the function of the great variety of self-assembled molecular architectures is complicated by the lack of understanding and control over nanoscale interactions, mesoscale architectures, and macroscale order. To establish a foundation toward delivering practical solutions, it is critical to develop an understanding of the chemical and physical mechanisms responsible for the self-assembly of molecular and hybrid materials on various support substrates. Typical molecular self-assembly involves noncovalent intermolecular and substrate-molecule interactions. These interactions remain poorly understood, due to the combination of many-body interactions compounded by local or collective influences from the substrate atomic lattice and electronic structure. Progress toward unraveling the underlying physicochemical processes that control the structure and macroscopic physical, chemical, mechanical, electrical, and transport properties of materials increasingly requires tight integration of theory, modeling, and simulation with precision synthesis, advanced experimental characterization, and device measurements. Theory, modeling, and simulation can accelerate the process of materials understanding and design
Horn, Paul R; Head-Gordon, Martin
2016-02-28
In energy decomposition analysis (EDA) of intermolecular interactions calculated via density functional theory, the initial supersystem wavefunction defines the so-called "frozen energy" including contributions such as permanent electrostatics, steric repulsions, and dispersion. This work explores the consequences of the choices that must be made to define the frozen energy. The critical choice is whether the energy should be minimized subject to the constraint of fixed density. Numerical results for Ne2, (H2O)2, BH3-NH3, and ethane dissociation show that there can be a large energy lowering associated with constant density orbital relaxation. By far the most important contribution is constant density inter-fragment relaxation, corresponding to charge transfer (CT). This is unwanted in an EDA that attempts to separate CT effects, but it may be useful in other contexts such as force field development. An algorithm is presented for minimizing single determinant energies at constant density both with and without CT by employing a penalty function that approximately enforces the density constraint. PMID:26931692
NASA Astrophysics Data System (ADS)
Horn, Paul R.; Head-Gordon, Martin
2016-02-01
In energy decomposition analysis (EDA) of intermolecular interactions calculated via density functional theory, the initial supersystem wavefunction defines the so-called "frozen energy" including contributions such as permanent electrostatics, steric repulsions, and dispersion. This work explores the consequences of the choices that must be made to define the frozen energy. The critical choice is whether the energy should be minimized subject to the constraint of fixed density. Numerical results for Ne2, (H2O)2, BH3-NH3, and ethane dissociation show that there can be a large energy lowering associated with constant density orbital relaxation. By far the most important contribution is constant density inter-fragment relaxation, corresponding to charge transfer (CT). This is unwanted in an EDA that attempts to separate CT effects, but it may be useful in other contexts such as force field development. An algorithm is presented for minimizing single determinant energies at constant density both with and without CT by employing a penalty function that approximately enforces the density constraint.
Building A Universal Nuclear Energy Density Functional (UNEDF)
Joe Carlson; Dick Furnstahl; Mihai Horoi; Rusty Lusk; Witek Nazarewicz; Esmond Ng; Ian Thompson; James Vary
2012-09-30
During the period of Dec. 1 2006 - Jun. 30, 2012, the UNEDF collaboration carried out a comprehensive study of all nuclei, based on the most accurate knowledge of the strong nuclear interaction, the most reliable theoretical approaches, the most advanced algorithms, and extensive computational resources, with a view towards scaling to the petaflop platforms and beyond. The long-term vision initiated with UNEDF is to arrive at a comprehensive, quantitative, and unified description of nuclei and their reactions, grounded in the fundamental interactions between the constituent nucleons. We seek to replace current phenomenological models of nuclear structure and reactions with a well-founded microscopic theory that delivers maximum predictive power with well-quantified uncertainties. Specifically, the mission of this project has been three-fold: first, to find an optimal energy density functional (EDF) using all our knowledge of the nucleonic Hamiltonian and basic nuclear properties; second, to apply the EDF theory and its extensions to validate the functional using all the available relevant nuclear structure and reaction data; third, to apply the validated theory to properties of interest that cannot be measured, in particular the properties needed for reaction theory. The main physics areas of UNEDF, defined at the beginning of the project, were: ab initio structure; ab initio functionals; DFT applications; DFT extensions; reactions.
NASA Technical Reports Server (NTRS)
Tschunko, H. F. A.
1983-01-01
Reference is made to a study by Tschunko (1979) in which it was discussed how apodization modifies the modulation transfer function for various central obstruction ratios. It is shown here how apodization, together with the central obstruction ratio, modifies the point spread function, which is the basic element for the comparison of imaging performance and for the derivation of energy integrals and other functions. At high apodization levels and lower central obstruction (less than 0.1), new extended radial zones are formed in the outer part of the central ring groups. These transmutation of the image functions are of more than theoretical interest, especially if the irradiance levels in the outer ring zones are to be compared to the background irradiance levels. Attention is then given to the energy distribution in point images generated by annular apertures apodized by various transmission functions. The total energy functions are derived; partial energy integrals are determined; and background irradiance functions are discussed.
Protein side chain conformation predictions with an MMGBSA energy function.
Gaillard, Thomas; Panel, Nicolas; Simonson, Thomas
2016-06-01
The prediction of protein side chain conformations from backbone coordinates is an important task in structural biology, with applications in structure prediction and protein design. It is a difficult problem due to its combinatorial nature. We study the performance of an "MMGBSA" energy function, implemented in our protein design program Proteus, which combines molecular mechanics terms, a Generalized Born and Surface Area (GBSA) solvent model, with approximations that make the model pairwise additive. Proteus is not a competitor to specialized side chain prediction programs due to its cost, but it allows protein design applications, where side chain prediction is an important step and MMGBSA an effective energy model. We predict the side chain conformations for 18 proteins. The side chains are first predicted individually, with the rest of the protein in its crystallographic conformation. Next, all side chains are predicted together. The contributions of individual energy terms are evaluated and various parameterizations are compared. We find that the GB and SA terms, with an appropriate choice of the dielectric constant and surface energy coefficients, are beneficial for single side chain predictions. For the prediction of all side chains, however, errors due to the pairwise additive approximation overcome the improvement brought by these terms. We also show the crucial contribution of side chain minimization to alleviate the rigid rotamer approximation. Even without GB and SA terms, we obtain accuracies comparable to SCWRL4, a specialized side chain prediction program. In particular, we obtain a better RMSD than SCWRL4 for core residues (at a higher cost), despite our simpler rotamer library. Proteins 2016; 84:803-819. © 2016 Wiley Periodicals, Inc. PMID:26948696
Interfacial Properties and Design of Functional Energy Materials
Sumpter, Bobby G; Liang, Liangbo; Nicolai, Adrien; Meunier, V.
2014-01-01
The vital importance of energy to society continues to demand a relentless pursuit of energy responsive materials that can bridge fundamental chemical structures at the molecular level and achieve improved functionality, such as efficient energy conversion/storage/transmission, over multiple length scales. This demand can potentially be realized by harnessing the power of self-assembly a spontaneous process where molecules or much larger entities form ordered aggregates as a consequence of predominately non-covalent (weak) interactions. Self-assembly is the key to bottom-up design of molecular devices, because the nearly atomic-level control is very difficult to realize in a top-down, e.g., lithographic approach. However, while function (e.g., charge mobility) in simple systems such as single crystals can often be predicted, predicting the function of the great variety of self-assembled molecular architectures is complicated by the lack of understanding and control over nanoscale interactions, mesoscale architectures, and macroscale (long-range) order. To establish a foundation toward delivering practical solutions, it is critical to develop an understanding of the chemical and physical mechanisms responsible for the self-assembly of molecular and hybrid materials on various substrates. Typically molecular self-assembly involves poorly understood non-covalent intermolecular and substrate-molecule interactions compounded by local and/or collective influences from the substrate atomic lattice (symmetry and/or topological features) and electronic structure. Thus, progress towards unraveling the underlying physicochemical processes that control the structure and macroscopic physical, mechanical, electrical, and transport properties of materials increasingly requires tight integration of theory, modeling and simulation with precision synthesis, advanced experimental characterization, and device measurements. In this mode, theory and simulation can greatly accelerate the
Garcia-Aldea, David; Alvarellos, J. E.
2007-11-15
We study two families of approximate nonlocal kinetic-energy functionals that include a full von Weizsaecker functional, and that have nonlocal terms with the mathematical structure of the Thomas-Fermi functional. The functionals recover the exact kinetic energy and the linear response function of a homogeneous electron system. The first family is a generalization of a successful previous nonlocal functional. The second family is proposed in the paper, and is designed to obtain functionals suitable for use in both localized and extended systems. Furthermore, this family has been designed to be evaluated by a single integration in momentum space when a constant reference density is used. The atomic total kinetic energies are in good agreement with the exact calculations. The kinetic-energy density corresponding to each functional has been assessed to control its quality. The results show that, in general, these functionals behave better than both the Thomas-Fermi and all semilocal generalized gradient approximation functionals when describing the kinetic-energy density of atoms, providing a better description of the nonlocal effects of the kinetic energy of electron systems.
Measurement of the nucleon structure function using high energy muons
Meyers, P.D.
1983-12-01
We have measured the inclusive deep inelastic scattering of muons on nucleons in iron using beams of 93 and 215 GeV muons. To perform this measurement, we have built and operated the Multimuon Spectrometer (MMS) in the muon beam at Fermilab. The MMS is a magnetized iron target/spectrometer/calorimeter which provides 5.61 kg/cm/sup 2/ of target, 9% momentum resolution on scattered muons, and a direct measure of total hadronic energy with resolution sigma/sub nu/ = 1.4..sqrt..nu(GeV). In the distributed target, the average beam energies at the interaction are 88.0 and 209 GeV. Using the known form of the radiatively-corrected electromagnetic cross section, we extract the structure function F/sub 2/(x,Q/sup 2/) with a typical precision of 2% over the range 5 < Q/sup 2/ < 200 GeV/sup 2//c/sup 2/. We compare our measurements to the predictions of lowest order quantum chromodynamics (QCD) and find a best fit value of the QCD scale parameter ..lambda../sub LO/ = 230 +- 40/sup stat/ +- 80/sup syst/ MeV/c, assuming R = 0 and without applying Fermi motion corrections. Comparing the cross sections at the two beam energies, we measure R = -0.06 +- 0.06/sup stat/ +- 0.11/sup syst/. Our measurements show qualitative agreement with QCD, but quantitative comparison is hampered by phenomenological uncertainties. The experimental situation is quite good, with substantial agreement between our measurements and those of others. 86 references.
Functions for detecting malposition of transcutaneous energy transmission coils.
Ozeki, Toshinaga; Chinzei, Tsuneo; Abe, Yusuke; Saito, Itsuro; Isoyama, Takashi; Mochizuki, Shuuichi; Ishimaru, Mitsuhiko; Takiura, Koki; Baba, Atsushi; Toyama, Takahiro; Imachi, Kou
2003-01-01
A transcutaneous energy transmission system (TETS) for artificial hearts and ventricular assist devices uses electrical coupling of power between external and implanted coils. If the position of coils changes relative to each other, the TETS cannot feed the required power of the implanted device. During activity or sleep, the coils may move accidentally. TETS users and the people around them have to pay attention to this because the range of the position where the required power can be fed efficiently is not wide. Therefore, we added functions for the position changes of the coils to the TETS. Regular, cautious, and irregular positions were introduced, and the ranges of them were decided upon in our experiments. The cautious position was determined by the area where the change of the relative position of the coils was relatively small. When the coils were in the cautious position, the circuit was tuned by way of changing the resonant point. This modulation could give good power efficiency in the cautious position. When the coils were in the irregular position, an alarm switch was turned on. These functions ease the restriction of the coil position and give better quality of life (QOL) than do the conventional TETS. PMID:12918593
Does shallow geothermal energy use threaten groundwater ecosystem functions?
NASA Astrophysics Data System (ADS)
Brielmann, Heike; Schmidt, Susanne I.; Ferraro, Francesco; Schreglmann, Kathrin; Griebler, Christian; Lueders, Tillmann
2010-05-01
Today, the use of geothermal energy is strongly promoted as an alternative and sustainable source of energy. However, regarding the authorization, regulation and monitoring of such facilities with respect to possible environmental impacts, a severe lack of knowledge has been identified. Aquifers are not only abiotic reservoirs of water and sediment, but they are complex ecosystems harbouring an almost untapped diversity of microorganisms and fauna. Intrinsic groundwater organisms are highly adapted to extremely oligotrophic, but stable conditions including temperature. At the same time, groundwater biota are the key drivers of important ecosystem services, especially functions connected to water quality. So what happens if groundwater biota need to cope with sudden temperature dynamics caused by GSHP use? Potential effects of thermal use on pristine aquifers, and on groundwater systems already facing enhanced loads of nutrients or contamination require urgent scientific attention. Within this project, we have assessed - both in the field and in the laboratory - the impacts of temperature discharge and withdrawal on biotic parameters and functional characteristics of exemplary shallow groundwater systems. In the field, aquifer microbes did not show significant impacts under increased temperatures in terms of total cell numbers, selected enzyme activities and carbon production. However, bacterial diversity clearly increased with temperature, accompanied by the appearance of new bacterial lineages and the disappearance of others. On the contrary, faunal diversity decreased with temperature, highlighting the temperature sensitivity of groundwater invertebrates. These results demonstrate that aquifer thermal energy discharge can affect intrinsic aquifer biotic populations, while at the same time being only one of several drivers contributing to total variability connected to seasonal dynamics and spatial heterogeneity. In laboratory column experiments covering a larger
Towards a Microscopic Reaction Description Based on Energy Density Functionals
Nobre, G A; DIetrich, F S; Escher, J E; Thompson, I J; Dupuis, M; Terasaki, J; Engel, J
2011-09-26
A microscopic calculation of reaction cross sections for nucleon-nucleus scattering has been performed by explicitly coupling the elastic channel to all particle-hole excitations in the target and one-nucleon pickup channels. The particle-hole states may be regarded as doorway states through which the flux flows to more complicated configurations, and subsequently to long-lived compound nucleus resonances. Target excitations for {sup 40,48}Ca, {sup 58}Ni, {sup 90}Zr and {sup 144}Sm were described in a random-phase framework using a Skyrme functional. Reaction cross sections obtained agree very well with experimental data and predictions of a state-of-the-art fitted optical potential. Couplings between inelastic states were found to be negligible, while the pickup channels contribute significantly. The effect of resonances from higher-order channels was assessed. Elastic angular distributions were also calculated within the same method, achieving good agreement with experimental data. For the first time observed absorptions are completely accounted for by explicit channel coupling, for incident energies between 10 and 70 MeV, with consistent angular distribution results.
Energy function-based approaches to graph coloring.
Di Blas, A; Jagota, A; Hughey, R
2002-01-01
We describe an approach to optimization based on a multiple-restart quasi-Hopfield network where the only problem-specific knowledge is embedded in the energy function that the algorithm tries to minimize. We apply this method to three different variants of the graph coloring problem: the minimum coloring problem, the spanning subgraph k-coloring problem, and the induced subgraph k-coloring problem. Though Hopfield networks have been applied in the past to the minimum coloring problem, our encoding is more natural and compact than almost all previous ones. In particular, we use k-state neurons while almost all previous approaches use binary neurons. This reduces the number of connections in the network from (Nk)(2) to N(2) asymptotically and also circumvents a problem in earlier approaches, that of multiple colors being assigned to a single vertex. Experimental results show that our approach compares favorably with other algorithms, even nonneural ones specifically developed for the graph coloring problem. PMID:18244411
Excitation energies of molecules within time-independent density functional theory
Hemanadhan, M. Harbola, Manoj K.
2014-04-24
Recently proposed exchange energy functional for excited-states is tested for obtaining excitation energies of diatomic molecules. The functional is the ground-state counterpart of the local-density approximation, the modified local spin density (MLSD). The MLSD functional is tested for the N{sub 2} and CO diatomic molecules. The excitation energy obtained with the MLSD functional for the N{sub 2} molecule is in close vicinity to that obtained from the exact exchange orbital functional, Krieger, Li and Iafrate (KLI). For the CO molecule, the departure in excitation energy is observed and is due to the overcorrection of self-interaction.
Afanasjev, A. V.
2015-10-15
The assessment of the global performance of the state-of-the-art covariant energy density functionals and related theoretical uncertainties in the description of ground state observables has recently been performed. Based on these results, the correlations between global description of binding energies and nuclear matter properties of covariant energy density functionals have been studied in this contribution.
Is there a low energy enhancement in the photon strength function in molybdenum?
Sheets, S A
2008-01-30
Recent claims of a low energy enhancement in the photon strength function of {sup 96}Mo are investigated. Using the DANCE detector the gamma-ray spectra following resonance neutron capture was measured. The spectrum fitting method was used to indirectly extract a photon strength function from the gamma-ray spectra. No strong low energy enhancement in the photon strength function was found.
Changes in cotton gin energy consumption apportioned by ten functions
Technology Transfer Automated Retrieval System (TEKTRAN)
The public is concerned about air quality and sustainability. Cotton producers, gin owners and plant managers are concerned about rising energy prices. Both have an interest in cotton gin energy consumption trends. Changes in cotton gins’ energy consumption over the past fifty years, a period of ...
Parathyroid function following total thyroidectomy using energy devices.
Ciftci, Fatih; Sakalli, Erdal; Abdurrahman, Ibrahim; Guler, Burak
2016-07-01
LigaSure precise (LP) and harmonic scalpel (HS) are two energy-based devices used in thyroidectomy surgery. We aimed to compare the effect of these two devices in patients who had undergone total thyroidectomy, by highlighting the post-operative parathyroid function. A total of 201 consecutive patients for whom total thyroidectomy had been planned were prospectively classified into two groups. There were 104 patients in LP group and 97 patients in HS group. Hypoparathyroidism was followed up by serially measuring the levels of intact parathyroid hormone (iPTH) and serum calcium. The early iPTH level was 29 (8-50) pg/mL in group LP, and 17 (4-43) pg/mL in group HS. The early iPTH level was significantly lower in the HS group (p < 0.001). However, these levels were within the reference interval in both groups. The early iPTH level was lower than 20 pg/mL in 23 (23.1 %) patients in HS group, and 15 (13.7 %) patients in LP group (p < 0.001). Also, the late iPTH levels were not statistically significance between two groups. The early and late serum calcium levels were not statistically significant between groups. However, the amount of calcium replacement was higher in the HS group than the LP group and the duration of treatment was longer in the HS group than the LP group (p < 0.05). In conclusion, although parathyroid hormone levels impaired in the HS group more than LP group in the early period, these levels were in the normal limits in both groups. These levels were not significant between groups in the long time period. PMID:26141753
Quasar Spectral Energy Distributions As A Function Of Physical Property
NASA Astrophysics Data System (ADS)
Townsend, Shonda; Ganguly, R.; Stark, M. A.; Derseweh, J. A.; Richmond, J. M.
2012-05-01
Galaxy evolution models have shown that quasars are a crucial ingredient in the evolution of massive galaxies. Outflows play a key role in the story of quasars and their host galaxies, by helping regulate the accretion process, the star-formation rate and mass of the host galaxy (i.e., feedback). The prescription for modeling outflows as a contributor to feedback requires knowledge of the outflow velocity, geometry, and column density. In particular, we need to understand how these depend on physical parameters and how much is determined stochastically (and with what distribution). In turn, models of outflows have shown particular sensitivity to the shape of the spectral energy distribution (SED), depending on the UV luminosity to transfer momentum to the gas, the X-ray luminosity to regulate how efficiently that transfer can be, etc. To investigate how SED changes with physical properties, we follow up on Richards et al. (2006), who constructed SEDs with varying luminosity. Here, we construct SEDs as a function of redshift, and physical property (black hole mass, bolometric luminosity, Eddington ratio) for volume limited samples drawn from the Sloan Digital Sky Survey, with photometry supplemented from 2MASS, WISE, GALEX, ROSAT, and Chandra. To estimate black hole masses, we adopt the scaling relations from Greene & Ho (2005) based on the H-alpha emission line FWHM. This requires redshifts less than 0.4. To construct volume-limited subsamples, we begin by adopting g=19.8 as a nominal limiting magnitude over which we are guaranteed to detect z<0.4 quasars. At redshift 0.4, we are complete down to Mg=-21.8, which yields 3300 objects from Data Release 7. At z=0.1, we are complete down to Mg=-18.5. This material is based upon work supported by the National Aeronautics and Space Administration under Grant No. 09-ADP09-0016 issued through the Astrophysics Data Analysis Program.
Recycling Energy to Restore Impaired Ankle Function during Human Walking
Collins, Steven H.; Kuo, Arthur D.
2010-01-01
Background Humans normally dissipate significant energy during walking, largely at the transitions between steps. The ankle then acts to restore energy during push-off, which may be the reason that ankle impairment nearly always leads to poorer walking economy. The replacement of lost energy is necessary for steady gait, in which mechanical energy is constant on average, external dissipation is negligible, and no net work is performed over a stride. However, dissipation and replacement by muscles might not be necessary if energy were instead captured and reused by an assistive device. Methodology/Principal Findings We developed a microprocessor-controlled artificial foot that captures some of the energy that is normally dissipated by the leg and “recycles” it as positive ankle work. In tests on subjects walking with an artificially-impaired ankle, a conventional prosthesis reduced ankle push-off work and increased net metabolic energy expenditure by 23% compared to normal walking. Energy recycling restored ankle push-off to normal and reduced the net metabolic energy penalty to 14%. Conclusions/Significance These results suggest that reduced ankle push-off contributes to the increased metabolic energy expenditure accompanying ankle impairments, and demonstrate that energy recycling can be used to reduce such cost. PMID:20174659
All-atom Simulation of Amyloid Aggregates
NASA Astrophysics Data System (ADS)
Berhanu, Workalemahu M.; Alred, Erik J.; Bernhardt, Nathan A.; Hansmann, Ulrich H. E.
Molecular simulations are now commonly used to complement experiments in the investigation of amyloid formation and their role in human diseases. While various simulations based on enhanced sampling techniques are used in amyloid formation simulations, this article will focus on those using standard atomistic simulations to evaluate the stability of fibril models. Such studies explore the limitations that arise from the choice of force field or polymorphism; and explore the stability of in vivo and in vitro forms of Aβ fibril aggregates, and the role of heterologous seeding as a link between different amyloid diseases.
Symmetry Energy as a Function of Density and Mass
Danielewicz, Pawel; Lee, Jenny
2007-10-26
Energy in nuclear matter is, in practice, completely characterized at different densities and asymmetries, when the density dependencies of symmetry energy and of energy of symmetric matter are specified. The density dependence of the symmetry energy at subnormal densities produces mass dependence of nuclear symmetry coefficient and, thus, can be constrained by that latter dependence. We deduce values of the mass dependent symmetry coefficients, by using excitation energies to isobaric analog states. The coefficient systematic, for intermediate and high masses, is well described in terms of the symmetry coefficient values of a{sub a}{sup V} = (31.5-33.5) MeV for the volume coefficient and a{sub a}{sup S} = (9-12) MeV for the surface coefficient. These two further correspond to the parameter values describing density dependence of symmetry energy, of L{approx}95 MeV and K{sub sym}{approx}25 MeV.
Propagation of spectral functions and dilepton production at SIS energies
Wolf, Gy.; Kaempfer, B.; Zetenyi, M.
2012-06-15
The time evolution of vector meson spectral functions is studied within a BUU-type transport model. Applications focus on {rho} and {omega} mesons being important pieces for the interpretation of the dielectron invariant mass spectrum. Since the evolution of the spectral functions is driven by the local density, the inmedium modifications turn out to compete, in this approach, with the known vacuum contributions.
Low-energy behavior of E 2 strength functions
NASA Astrophysics Data System (ADS)
Schwengner, R.
2014-12-01
Electric quadrupole strength functions have been deduced from averages of a large number of E 2 transition strengths calculated within the shell model for the nuclides 94Mo and 95Mo. These strength functions are at variance with phenomenological approximations as provided by the Reference Input Parameter Library RIPL-3 for calculations of reaction rates on the basis of the statistical model.
Averkiev, Boris B; Zhao, Yan; Truhlar, Donald G
2010-06-01
The structures of Pd(PH₃)₂ and Pt(PH₃)₂ complexes with ethene and conjugated CnH_{n+2} systems (n=4, 6, 8, and 10) were studied. Their binding energies were calculated using both wave function theory (WFT) and density functional theory (DFT). Previously it was reported that the binding energy of the alkene to the transition metal does not depend strongly on the size of the conjugated C_{n}H_{n+2} ligand, but that DFT methods systematically underestimate the binding energy more and more significantly as the size of the conjugated system is increased. Our results show that recently developed density functionals predict the binding energy for these systems much more accurately. New benchmark calculations carried out by the coupled cluster method based on Brueckner orbitals with double excitations and a quasiperturbative treatment of connected triple excitations (BCCD(T)) with a very large basis set agree even better with the DFT predictions than do the previous best estimates. The mean unsigned error in absolute and relative binding energies of the alkene ligands to Pd(PH₃)₂ is 2.5 kcal/mol for the ωB97 and M06 density functionals and 2.9 kcal/mol for the M06-L functional. Adding molecular mechanical damped dispersion yields even smaller mean unsigned errors: 1.3 kcal/mol for the M06-D functional, 1.5 kcal/mol for M06- L-D, and 1.8 kcal/mol for B97-D and ωB97X-D. The new functionals also lead to improved accuracy for the analogous Pt complexes. These results show that recently developed density functionals may be very useful for studying catalytic systems involving Pd d¹º centers and alkenes.
The Association between Energy Cost of Walking and Physical Function in Older Adults
Wert, David M.; Brach, Jennifer S.; Perera, Subashan; VanSwearingen, Jessie
2013-01-01
To assess the association between energy cost of walking and self-report of function, independent of comorbidity and gait speed, in older adults with mobility limitations. This cross-sectional observational study was conducted within an ambulatory clinical research training center. Forty-two older adults, age 65 and older, with slow and variable gait participated. Function was assessed using the Late Life Function and Disability Index- Basic Lower Extremity subscale, while energy cost of walking was derived by standardizing the mean oxygen consumption recorded during physiological steady state by gait speed. Comorbidity and gait speed were collected as co-variates. Pearson’s r correlation coefficient and regression analyses were used to assess the relationship between energy cost and function. Energy cost of walking was significantly correlated with self-reported function (Pearson’s r= −.50, p <.001); furthermore, energy cost of walking explained an additional 17% (p=.002) of the variance in self-reported function above and beyond the variance explained by comorbidity and gait speed combined. Energy cost of walking is emerging as another significant factor related to functional performance among older adults, even after controlling for comorbidity and gait speed- robust variables known for their strong contributions to function. Knowledge of and attention to the efficiency of how one moves (high energy cost of walking) may enhance rehabilitation efforts to further reduce “functional burden” in older adults. PMID:23680536
The association between energy cost of walking and physical function in older adults.
Wert, David M; Brach, Jennifer S; Perera, Subashan; VanSwearingen, Jessie
2013-01-01
To assess the association between energy cost of walking and self-report of function, independent of comorbidity and gait speed, in older adults with mobility limitations. This cross-sectional observational study was conducted within an ambulatory clinical research training center. Forty-two older adults, age 65 and older, with slow and variable gait participated. Function was assessed using the Late Life Function and Disability Index-Basic Lower Extremity Subscale, while energy cost of walking was derived by standardizing the mean oxygen consumption recorded during physiological steady state by gait speed. Comorbidity and gait speed were collected as co-variates. Pearson's r correlation coefficient and regression analyses were used to assess the relationship between energy cost and function. Energy cost of walking was significantly correlated with self-reported function (Pearson's r=-0.50, p<0.001); furthermore, energy cost of walking explained an additional 17% (p=0.002) of the variance in self-reported function above and beyond the variance explained by comorbidity and gait speed combined. Energy cost of walking is emerging as another significant factor related to functional performance among older adults, even after controlling for comorbidity and gait speed - robust variables known for their strong contributions to function. Knowledge of and attention to the efficiency of how one moves (high energy cost of walking) may enhance rehabilitation efforts to further reduce "functional burden" in older adults. PMID:23680536
Ponizovskiy, Michail R
2016-01-01
Interactions between nucleus and mitochondria functions induce the mechanism of maintenance stability of cellular internal energy according to the first law of thermodynamics in able-bodied cells and changes the mechanisms of maintenance stability of cellular internal energy creating a transition stationary state of ablebodied cells into quasi-stationary pathologic states of acute inflammation transiting then into chronic inflammation and then transmuting into cancer metabolism. The mechanisms' influences of intruding etiologic pathologic agents (microbe, virus, etc.) lead to these changes of energy interactions between nucleus and mitochondria functions causing general acute inflammation, then passing into local chronic inflammation, and reversing into cancer metabolism transmutation. Interactions between biochemical processes and biophysical processes of cellular capacitors' operations create a supplementary mechanism of maintenance stability of cellular internal energy in the norm and in pathology. Discussion of some scientific works eliminates doubts of the authors of these works. PMID:27480780
Energy functions for knots: Beginning to predict physical behavior
Simon, J.
1996-12-31
Several definitions have been proposed for the {open_quotes}energy{close_quotes} of a knot. The intuitive goal is to define a number u(K) that somehow measures how {open_quotes}tangled{close_quotes} or {open_quotes}crumpled{close_quotes} a knot K is. Typically, one starts with the idea that a small piece of the knot somehow repels other pieces, and then adds up the contributions from all the pieces. From a purely mathematical standpoint, one may hope to define new knot-type invariants, e.g by considering the minimum of u(K) as K ranges over all the knots of a given knot-type. We also are motivated by the desire to understand and predict how knot-type affects the behavior of physically real knots, in particular DNA loops in gel electrophoresis or random knotting experiments. Despite the physical naivete of recently studied knot energies, there now is enough laboratory data on relative gel velocity, along with computer calculations of idealized knot energies, to justify the assertion that knot energies can predict relative knot behavior in physical systems. The relationships between random knot frequencies and either gel velocities or knot energies is less clear at this time. 50 refs., 8 figs., 2 tabs.
Jin, Chengjun; Markussen, Troels; Thygesen, Kristian S.; Strange, Mikkel; Solomon, Gemma C.
2013-11-14
We study the effect of functional groups (CH{sub 3}*4, OCH{sub 3}, CH{sub 3}, Cl, CN, F*4) on the electronic transport properties of 1,4-benzenediamine molecular junctions using the non-equilibrium Green function method. Exchange and correlation effects are included at various levels of theory, namely density functional theory (DFT), energy level-corrected DFT (DFT+Σ), Hartree-Fock and the many-body GW approximation. All methods reproduce the expected trends for the energy of the frontier orbitals according to the electron donating or withdrawing character of the substituent group. However, only the GW method predicts the correct ordering of the conductance amongst the molecules. The absolute GW (DFT) conductance is within a factor of two (three) of the experimental values. Correcting the DFT orbital energies by a simple physically motivated scissors operator, Σ, can bring the DFT conductances close to experiments, but does not improve on the relative ordering. We ascribe this to a too strong pinning of the molecular energy levels to the metal Fermi level by DFT which suppresses the variation in orbital energy with functional group.
NASA Astrophysics Data System (ADS)
Nymmik, Rikho; Pervaia, Taisia
2016-07-01
Experimental data on the fluxes of protons of solar energetic particles (SEP) are analyzed. It is known that above energies of 2-45 MeV (averaging 27-30 MeV), the proton spectra are a power-law function of the energy (at relativistic energies - from the momentum) of the particles. At lower energies, the spectra become harder, with the high-energy part of the spectra forming the "knee". This report is devoted to the determination of the parameters of the SEP spectra, having the form of a "double power-law shape", to ascertain the reliability of the parameters of the approximations of the experimental data.
Energy and temperature relaxation described by nonequilibrium green's functions
NASA Astrophysics Data System (ADS)
Vorberger, J.; Gericke, D. O.; Bornath, Th; Schlanges, M.
2010-04-01
A quantum kinetic approach is presented to investigate the energy relaxation of dense strongly coupled two-temperature plasmas. We derive a balance equation for the mean total energy of a plasma species including a quite general expression for the transfer rate. An approximation scheme is used leading to an expression of the transfer rates for systems with coupled modes relevant for the warm dense matter regime. The theory is then applied to dense beryllium plasmas under conditions such as realized in recent experiments. Special attention is paid to the influence of correlation and quantum effects on the relaxation process.
Is there a low-energy enhancement in the photon strength function in molybdenum?
Sheets, S. A.
2008-04-17
Recent claims of a low-energy enhancement in the photon strength function of {sup 96}Mo are investigated. Using the DANCE detector the gamma-ray spectra following resonance neutron capture was measured. The spectrum fitting method was used to indirectly extract a photon strength function from the gamma-ray spectra. No strong low energy enhancement in the photon strength function was found.
Expanded explorations into the optimization of an energy function for protein design
Huang, Yao-ming; Bystroff, Christopher
2014-01-01
Nature possesses a secret formula for the energy as a function of the structure of a protein. In protein design, approximations are made to both the structural representation of the molecule and to the form of the energy equation, such that the existence of a general energy function for proteins is by no means guaranteed. Here we present new insights towards the application of machine learning to the problem of finding a general energy function for protein design. Machine learning requires the definition of an objective function, which carries with it the implied definition of success in protein design. We explored four functions, consisting of two functional forms, each with two criteria for success. Optimization was carried out by a Monte Carlo search through the space of all variable parameters. Cross-validation of the optimized energy function against a test set gave significantly different results depending on the choice of objective function, pointing to relative correctness of the built-in assumptions. Novel energy cross-terms correct for the observed non-additivity of energy terms and an imbalance in the distribution of predicted amino acids. This paper expands on the work presented at ACM-BCB, Orlando FL , October 2012. PMID:24384706
Expanded explorations into the optimization of an energy function for protein design.
Huang, Yao-Ming; Bystroff, Christopher
2013-01-01
Nature possesses a secret formula for the energy as a function of the structure of a protein. In protein design, approximations are made to both the structural representation of the molecule and to the form of the energy equation, such that the existence of a general energy function for proteins is by no means guaranteed. Here, we present new insights toward the application of machine learning to the problem of finding a general energy function for protein design. Machine learning requires the definition of an objective function, which carries with it the implied definition of success in protein design. We explored four functions, consisting of two functional forms, each with two criteria for success. Optimization was carried out by a Monte Carlo search through the space of all variable parameters. Cross-validation of the optimized energy function against a test set gave significantly different results depending on the choice of objective function, pointing to relative correctness of the built-in assumptions. Novel energy cross terms correct for the observed nonadditivity of energy terms and an imbalance in the distribution of predicted amino acids. This paper expands on the work presented at the 2012 ACM-BCB. PMID:24384706
The effect of bond functions on dissociation energies
NASA Technical Reports Server (NTRS)
Bauschlicher, C. W., Jr.
1985-01-01
The procedure employing bond functions recently suggested by Wright and Buenker has been applied to the N2 X 1 Sigma g + potential curve within the CAS SCF + MRSD CI treatment of electron correlation. The basis set used herein is identical to that employed by these authors in their SCF + CI calculations. The De and and the shape of the resulting potential curve, as judged by the computed vibrational levels, is not so accurate as would be expected from the results reported by Wright and Buenker (1984). The results indicate that using the CI superposition errors associated with bond functions to cancel basis set incompleteness depends on the treatment of the electron correlation.
Functional zinc oxide nanostructures for electronic and energy applications
NASA Astrophysics Data System (ADS)
Prasad, Abhishek
ZnO has proven to be a multifunctional material with important nanotechnological applications. ZnO nanostructures can be grown in various forms such as nanowires, nanorods, nanobelts, nanocombs etc. In this work, ZnO nanostructures are grown in a double quartz tube configuration thermal Chemical Vapor Deposition (CVD) system. We focus on functionalized ZnO Nanostructures by controlling their structures and tuning their properties for various applications. The following topics have been investigated: (1) We have fabricated various ZnO nanostructures using a thermal CVD technique. The growth parameters were optimized and studied for different nanostructures. (2) We have studied the application of ZnO nanowires (ZnONWs) for field effect transistors (FETs). Unintentional n-type conductivity was observed in our FETs based on as-grown ZnO NWs. We have then shown for the first time that controlled incorporation of hydrogen into ZnO NWs can introduce p-type characters to the nanowires. We further found that the n-type behaviors remained, leading to the ambipolar behaviors of hydrogen incorporated ZnO NWs. Importantly, the detected p- and n- type behaviors are stable for longer than two years when devices were kept in ambient conditions. All these can be explained by an ab initio model of Zn vacancy-Hydrogen complexes, which can serve as the donor, acceptors, or green photoluminescence quencher, depend on the number of hydrogen atoms involved. (3) Next ZnONWs were tested for electron field emission. We focus on reducing the threshold field (Eth) of field emission from non-aligned ZnO NWs. As encouraged by our results on enhancing the conductivity of ZnO NWs by hydrogen annealing described in Chapter 3, we have studied the effect of hydrogen annealing for improving field emission behavior of our ZnO NWs. We found that optimally annealed ZnO NWs offered much lower threshold electric field and improved emission stability. We also studied field emission from ZnO NWs at moderate
Visualization of Potential Energy Function Using an Isoenergy Approach and 3D Prototyping
ERIC Educational Resources Information Center
Teplukhin, Alexander; Babikov, Dmitri
2015-01-01
In our three-dimensional world, one can plot, see, and comprehend a function of two variables at most, V(x,y). One cannot plot a function of three or more variables. For this reason, visualization of the potential energy function in its full dimensionality is impossible even for the smallest polyatomic molecules, such as triatomics. This creates…
NASA Astrophysics Data System (ADS)
Abate, Bayileyegn A.; Peralta, Juan E.
2013-12-01
The structural parameters and relative energies of the minimum-energy crossing points (MECPs) of eight small molecules are calculated using five different representative density functional theory approximations as well as MP2, MP4, and CCSD(T) as a reference. Compared to high-level wavefunction methods, the main structural features of the MECPs of the systems included in this Letter are reproduced reasonably well by density functional approximations, in agreement with previous works. Our results show that when high-level wavefunction methods are computationally prohibitive, density functional approximations offer a good alternative for locating and characterizing the MECP in spin-forbidden chemical reactions.
Standard thermodynamic functions and Gibbs energy of holmium tungstenates
Nadiradze, A.A.; Gvelesiani, G.G.; Abashidze, T.D.; Makharadze, I.A.
1986-12-01
The Gibbs free energy of meta- and normal holmium tungstenates was studied by the emf method with the solid oxygen-ion electrolyte. The standard values of the entropy and enthalpy of formation of holmium tungstenates Ho/sub 6/WO/sub 12/, Ho/sub 10/W/sub 2/O/sub 21/, Ho/sub 14/W/sub 4/O/sub 33/, Ho/sub 2/WO/sub 6/, and Ho/sub 2/(WO/sub 4/)/sub 3/ were calculated. Three-term equations for the Gibbs energy of formation of the indicated tungstenates from the oxides for a wide temperature range were constructed. It was shown that the values of the standard atomic entropies and enthalpies of formation of these compounds decrease as their WO/sub 3/ content increases.
AMPK: a master energy regulator for gonadal function
Bertoldo, Michael J.; Faure, Melanie; Dupont, Joëlle; Froment, Pascal
2015-01-01
From C. elegans to mammals (including humans), nutrition and energy metabolism significantly influence reproduction. At the cellular level, some detectors of energy status indicate whether energy reserves are abundant (obesity), or poor (diet restriction). One of these detectors is AMPK (5′ AMP-activated protein kinase), a protein kinase activated by ATP deficiency but also by several natural substances such as polyphenols or synthetic molecules like metformin, used in the treatment of insulin resistance. AMPK is expressed in muscle and liver, but also in the ovary and testis. This review focuses on the main effects of AMPK identified in gonadal cells. We describe the role of AMPK in gonadal steroidogenesis, in proliferation and survival of somatic gonadal cells and in the maturation of oocytes or spermatozoa. We discuss also the role of AMPK in germ and somatic cell interactions within the cumulus-oocyte complex and in the blood testis barrier. Finally, the interface in the gonad between AMPK and modification of metabolism is reported and discussion about the role of AMPK on fertility, in regards to the treatment of infertility associated with insulin resistance (male obesity, polycystic ovary syndrome). PMID:26236179
AMPK: a master energy regulator for gonadal function.
Bertoldo, Michael J; Faure, Melanie; Dupont, Joëlle; Froment, Pascal
2015-01-01
From C. elegans to mammals (including humans), nutrition and energy metabolism significantly influence reproduction. At the cellular level, some detectors of energy status indicate whether energy reserves are abundant (obesity), or poor (diet restriction). One of these detectors is AMPK (5' AMP-activated protein kinase), a protein kinase activated by ATP deficiency but also by several natural substances such as polyphenols or synthetic molecules like metformin, used in the treatment of insulin resistance. AMPK is expressed in muscle and liver, but also in the ovary and testis. This review focuses on the main effects of AMPK identified in gonadal cells. We describe the role of AMPK in gonadal steroidogenesis, in proliferation and survival of somatic gonadal cells and in the maturation of oocytes or spermatozoa. We discuss also the role of AMPK in germ and somatic cell interactions within the cumulus-oocyte complex and in the blood testis barrier. Finally, the interface in the gonad between AMPK and modification of metabolism is reported and discussion about the role of AMPK on fertility, in regards to the treatment of infertility associated with insulin resistance (male obesity, polycystic ovary syndrome). PMID:26236179
Accuracy of exchange-correlation functionals and effect of solvation on the surface energy of copper
NASA Astrophysics Data System (ADS)
Fishman, Matthew; Zhuang, Houlong L.; Mathew, Kiran; Dirschka, William; Hennig, Richard G.
2013-06-01
Surface energies are important for predicting the shapes of nanocrystals and describing the faceting and roughening of surfaces. Copper surfaces are of particular interest in recent years since they are the preferred surfaces for growing graphene using chemical vapor deposition. In this study we calculate the surface energies of copper for the three low-index facets (111), (100), and (110) and one high-index facet, (210), using density-functional theory with both the local-density approximation and various parametrizations of the generalized-gradient approximation to the exchange-correlation functional. To assess the accuracy of the different functionals, we obtain the average surface energies of an isotropic crystal using a broken-bond model. We use this method, which can be generalized to other crystal structures, to compare calculated surface energies to experimental surface energies for fcc crystals. We find that the recent exchange-correlation functionals AM05 and PBEsol are the most accurate functionals for calculating the surface energies of copper. To determine how solvents affect the surface energies of copper, we perform calculations using a continuum solvation model. We find that aqueous solvation changes the overall magnitude of the surface energies only slightly but leads to more isotropic surface energies.
Evaluation of the Effects of Different Energy Drinks and Coffee on Endothelial Function.
Molnar, Janos; Somberg, John C
2015-11-01
Endothelial function plays an important role in circulatory physiology. There has been differing reports on the effect of energy drink on endothelial function. We set out to evaluate the effect of 3 energy drinks and coffee on endothelial function. Endothelial function was evaluated in healthy volunteers using a device that uses digital peripheral arterial tonometry measuring endothelial function as the reactive hyperemia index (RHI). Six volunteers (25 ± 7 years) received energy drink in a random order at least 2 days apart. Drinks studied were 250 ml "Red Bull" containing 80 mg caffeine, 57 ml "5-hour Energy" containing 230 mg caffeine, and a can of 355 ml "NOS" energy drink containing 120 mg caffeine. Sixteen volunteers (25 ± 5 years) received a cup of 473 ml coffee containing 240 mg caffeine. Studies were performed before drink (baseline) at 1.5 and 4 hours after drink. Two of the energy drinks (Red Bull and 5-hour Energy) significantly improved endothelial function at 4 hours after drink, whereas 1 energy drink (NOS) and coffee did not change endothelial function significantly. RHI increased by 82 ± 129% (p = 0.028) and 63 ± 37% (p = 0.027) after 5-hour Energy and Red Bull, respectively. The RHI changed after NOS by 2 ± 30% (p = 1.000) and by 7 ± 30% (p = 1.000) after coffee. In conclusion, some energy drinks appear to significantly improve endothelial function. Caffeine does not appear to be the component responsible for these differences. PMID:26341184
NASA Astrophysics Data System (ADS)
Fucci, Guglielmo; Kirsten, Klaus
2016-07-01
In this paper we analyze the spectral zeta function associated with a Laplace operator acting on scalar functions on an N-dimensional Euclidean space in the presence of a spherically symmetric background potential. The obtained analytic continuation of the spectral zeta function is then used to derive very simple results for the functional determinant of the operator and the Casimir energy of the scalar field.
Nanoscale friction as a function of activation energies
NASA Astrophysics Data System (ADS)
Chong, W. W. F.; Rahnejat, H.
2015-12-01
Understanding the scale-dependence of friction is increasingly viewed as a critical quest. With progressively thinner films, mixed and boundary regimes of lubrication have become commonplace. Therefore, at the micro-scale a greater need for mitigating friction is desired in order to improve operational efficiency of many machines and mechanisms. Furthermore, there is a growing tendency to use low friction hard wear-resistant advanced coatings to guard against wear. In parallel, there has been much attention paid to lubricant rheology and formulation. However, only in recent times there has been an emerging view of lubricant-surface combination as a system. In this perspective it is essential to relate the observed and measured friction at component level to the underlying interactions in micro/nano-scales. This is the approach in this paper. Observed phenomenon at micro-scale are related back to the activation energies of lubricant-surface system, providing in particular results for surface modified Ni-SiC coated specimen in combination with formulated lubricants, the combination of which represent the lubricant-surface system of choice in cylinders of high performance race engine. The nano-scale conjunction of an AFM tip with lubricated surface-engineered specimen, subjected to various conjunctional loading and sliding kinematics is investigated. It is shown that the measured frictional characteristics can be adequately described in terms of activation energies in line with the Eyring’s thermal activation model for cases of fairly smooth asperity tip contact conjunctions.
Bubin, Sergiy; Adamowicz, Ludwik
2008-03-21
In this work we consider explicitly correlated complex Gaussian basis functions for expanding the wave function of an N-particle system with the L=1 total orbital angular momentum. We derive analytical expressions for various matrix elements with these basis functions including the overlap, kinetic energy, and potential energy (Coulomb interaction) matrix elements, as well as matrix elements of other quantities. The derivatives of the overlap, kinetic, and potential energy integrals with respect to the Gaussian exponential parameters are also derived and used to calculate the energy gradient. All the derivations are performed using the formalism of the matrix differential calculus that facilitates a way of expressing the integrals in an elegant matrix form, which is convenient for the theoretical analysis and the computer implementation. The new method is tested in calculations of two systems: the lowest P state of the beryllium atom and the bound P state of the positronium molecule (with the negative parity). Both calculations yielded new, lowest-to-date, variational upper bounds, while the number of basis functions used was significantly smaller than in previous studies. It was possible to accomplish this due to the use of the analytic energy gradient in the minimization of the variational energy. PMID:18361554
Model Etch Profiles for Ion Energy Distribution Functions in an Inductively Coupled Plasma Reactor
Abraham-Shrauner, B.; Chen, W.; Woodworth, J.R.
1998-12-14
Rectangular trench profiles are modeled with analytic etch rates determined from measured ion distribution functions. The pattern transfer step for this plasma etch is for trilayer lithography. Argon and chlorine angular ion energy distribution functions measured by a spherical collector ring analyzer are fit to a sum of drifting Maxwellian velocity distribution functions with anisotropic temperatures. The fit of the model ion distribution functions by a simulated annealing optimization procedure converges adequately for only two drifting Maxwellians. The etch rates are proportional to analytic expressions for the ion energy flux. Numerical computation of the etch profiles by integration of the characteristic equations for profile points and connection of the profiles points is efficient.
Koretke, K. K.; Luthey-Schulten, Z.; Wolynes, P. G.
1996-01-01
A quantitative form of the principle of minimal frustration is used to obtain from a database analysis statistical mechanical energy functions and gap parameters for aligning sequences to three-dimensional structures. The analysis that partially takes into account correlations in the energy landscape improves upon the previous approximations of Goldstein et al. (1994, 1995) (Goldstein R, Luthey-Schulten Z, Wolynes P, 1994, Proceedings of the 27th Hawaii International Conference on System Sciences. Los Alamitos, California: IEEE Computer Society Press. pp 306-315; Goldstein R, Luthey-Schulten Z, Wolynes P, 1995, In: Elber R, ed. New developments in theoretical studies of proteins. Singapore: World Scientific). The energy function allows for ordering of alignments based on the compatibility of a sequence to be in a given structure (i.e., lowest energy) and therefore removes the necessity of using percent identity or similarity as scoring parameters. The alignments produced by the energy function on distant homologues with low percent identity (less than 21%) are generally better than those generated with evolutionary information. The lowest energy alignment generated with the energy function for sequences containing prosite signatures but unknown structures is a structure containing the same prosite signature, providing a check on the robustness of the algorithm. Finally, the energy function can make use of known experimental evidence as constraints within the alignment algorithm to aid in finding the correct structural alignment. PMID:8762136
NASA Astrophysics Data System (ADS)
Schunck, N.; Duke, D.; Carr, H.
2015-03-01
Understanding the mechanisms of induced nuclear fission for a broad range of neutron energies could help resolve fundamental science issues, such as the formation of elements in the universe, but could have also a large impact on societal applications in energy production or nuclear waste management. The goal of this paper is to set up the foundations of a microscopic theory to study the static aspects of induced fission as a function of the excitation energy of the incident neutron, from thermal to fast neutrons. To account for the high excitation energy of the compound nucleus, we employ a statistical approach based on finite temperature nuclear density functional theory with Skyrme energy densities, which we benchmark on the 239Pu(n ,f ) reaction. We compute the evolution of the least-energy fission pathway across multidimensional potential energy surfaces with up to five collective variables as a function of the nuclear temperature and predict the evolution of both the inner and the outer fission barriers as a function of the excitation energy of the compound nucleus. We show that the coupling to the continuum induced by the finite temperature is negligible in the range of neutron energies relevant for many applications of neutron-induced fission. We prove that the concept of quantum localization introduced recently can be extended to T >0 , and we apply the method to study the interaction energy and total kinetic energy of fission fragments as a function of the temperature for the most probable fission. While large uncertainties in theoretical modeling remain, we conclude that a finite temperature nuclear density functional may provide a useful framework to obtain accurate predictions of fission fragment properties.
Spectroscopic properties of nuclear skyrme energy density functionals.
Tarpanov, D; Dobaczewski, J; Toivanen, J; Carlsson, B G
2014-12-19
We address the question of how to improve the agreement between theoretical nuclear single-particle energies (SPEs) and observations. Empirically, in doubly magic nuclei, the SPEs can be deduced from spectroscopic properties of odd nuclei that have one more or one less neutron or proton. Theoretically, bare SPEs, before being confronted with observations, must be corrected for the effects of the particle vibration coupling (PVC). In the present work, we determine the PVC corrections in a fully self-consistent way. Then, we adjust the SPEs, with PVC corrections included, to empirical data. In this way, the agreement with observations, on average, improves; nevertheless, large discrepancies still remain. We conclude that the main source of disagreement is still in the underlying mean fields, and not in including or neglecting the PVC corrections. PMID:25554877
The curvature elastic-energy function of the lipid-water cubic mesophase
NASA Astrophysics Data System (ADS)
Chung, Hesson; Caffrey, Martin
1994-03-01
CELL and lipid membranes are able to bend, as manifested during membrane fusion and the formation of non-lamellar lyotropic mesopbases in water. But there is an energy cost to bending of lipid layers, called the curvature elastic energy. Although the functional form of this energy is known1, a complete quantitative knowledge of the curvature elastic energy, which is central to predicting the relative stability of the large number of phases that lipid membranes can adopt, has been lacking. Here we use X-ray synchrotron diffraction measurements of the variation of lattice parameter with pressure and temperature for the periodic Ia3d (Q230) cubic phase of hydrated monoolein to calculate the complete curvature elastic-energy function for the lipid cubic mesophase. This allows us to predict the stabilities of different cubic and lamellar phases for this system as a function of composition.
Potential energy function information from quantum phase shift using the variable phase method.
Lemes, Nelson H T; Braga, João P; Alves, Márcio O; Costa, Éderson D'M
2014-07-01
The present work discusses quantum phase shift sensitivity analysis with respect to the potential energy function. A set of differential equations for the functional derivative of the quantum phase shift with respect to the potential energy function was established and coupled with the variable phase equation. This set of differential equations provides a simple, exact and straightforward way to establish the sensitivity matrix. The present procedure is easier to use than the finite difference approach, in which several direct problems have to be addressed. Furthermore, integration of the established equations can be used to demonstrate how the sensitivity phase shift is accumulated as a function of the interatomic distance. The potential energy function was refined to produce a better quality function. The average error on the phase shift decreased from 9.8% in the original potential function to 0.13% in the recovered potential. The present procedure is an important initial step for further work towards recovering potential energy functions in upper dimensions or to recovering this function from cross sections. PMID:24935112
Towards improved local hybrid functionals by calibration of exchange-energy densities
Arbuznikov, Alexei V. E-mail: martin.kaupp@tu-berlin.de; Kaupp, Martin E-mail: martin.kaupp@tu-berlin.de
2014-11-28
A new approach for the calibration of (semi-)local and exact exchange-energy densities in the context of local hybrid functionals is reported. The calibration functions are derived from only the electron density and its spatial derivatives, avoiding spatial derivatives of the exact-exchange energy density or other computationally unfavorable contributions. The calibration functions fulfill the seven more important out of nine known exact constraints. It is shown that calibration improves substantially the definition of a non-dynamical correlation energy term for generalized gradient approximation (GGA)-based local hybrids. Moreover, gauge artifacts in the potential-energy curves of noble-gas dimers may be corrected by calibration. The developed calibration functions are then evaluated for a large range of energy-related properties (atomization energies, reaction barriers, ionization potentials, electron affinities, and total atomic energies) of three sets of local hybrids, using a simple one-parameter local-mixing. The functionals are based on (a) local spin-density approximation (LSDA) or (b) Perdew-Burke-Ernzerhof (PBE) exchange and correlation, and on (c) Becke-88 (B88) exchange and Lee-Yang-Parr (LYP) correlation. While the uncalibrated GGA-based functionals usually provide very poor thermochemical data, calibration allows a dramatic improvement, accompanied by only a small deterioration of reaction barriers. In particular, an optimized BLYP-based local-hybrid functional has been found that is a substantial improvement over the underlying global hybrids, as well as over previously reported LSDA-based local hybrids. It is expected that the present calibration approach will pave the way towards new generations of more accurate hyper-GGA functionals based on a local mixing of exchange-energy densities.
Towards improved local hybrid functionals by calibration of exchange-energy densities
NASA Astrophysics Data System (ADS)
Arbuznikov, Alexei V.; Kaupp, Martin
2014-11-01
A new approach for the calibration of (semi-)local and exact exchange-energy densities in the context of local hybrid functionals is reported. The calibration functions are derived from only the electron density and its spatial derivatives, avoiding spatial derivatives of the exact-exchange energy density or other computationally unfavorable contributions. The calibration functions fulfill the seven more important out of nine known exact constraints. It is shown that calibration improves substantially the definition of a non-dynamical correlation energy term for generalized gradient approximation (GGA)-based local hybrids. Moreover, gauge artifacts in the potential-energy curves of noble-gas dimers may be corrected by calibration. The developed calibration functions are then evaluated for a large range of energy-related properties (atomization energies, reaction barriers, ionization potentials, electron affinities, and total atomic energies) of three sets of local hybrids, using a simple one-parameter local-mixing. The functionals are based on (a) local spin-density approximation (LSDA) or (b) Perdew-Burke-Ernzerhof (PBE) exchange and correlation, and on (c) Becke-88 (B88) exchange and Lee-Yang-Parr (LYP) correlation. While the uncalibrated GGA-based functionals usually provide very poor thermochemical data, calibration allows a dramatic improvement, accompanied by only a small deterioration of reaction barriers. In particular, an optimized BLYP-based local-hybrid functional has been found that is a substantial improvement over the underlying global hybrids, as well as over previously reported LSDA-based local hybrids. It is expected that the present calibration approach will pave the way towards new generations of more accurate hyper-GGA functionals based on a local mixing of exchange-energy densities.
NASA Technical Reports Server (NTRS)
King, H. F.; Komornicki, A.
1986-01-01
Formulas are presented relating Taylor series expansion coefficients of three functions of several variables, the energy of the trial wave function (W), the energy computed using the optimized variational wave function (E), and the response function (lambda), under certain conditions. Partial derivatives of lambda are obtained through solution of a recursive system of linear equations, and solution through order n yields derivatives of E through order 2n + 1, extending Puley's application of Wigner's 2n + 1 rule to partial derivatives in couple perturbation theory. An examination of numerical accuracy shows that the usual two-term second derivative formula is less stable than an alternative four-term formula, and that previous claims that energy derivatives are stationary properties of the wave function are fallacious. The results have application to quantum theoretical methods for the computation of derivative properties such as infrared frequencies and intensities.
Modeling the Transfer Function for the Dark Energy Survey
Chang, C.
2015-03-04
We present a forward-modeling simulation framework designed to model the data products from the Dark Energy Survey (DES). This forward-model process can be thought of as a transfer function—a mapping from cosmological/astronomical signals to the final data products used by the scientists. Using output from the cosmological simulations (the Blind Cosmology Challenge), we generate simulated images (the Ultra Fast Image Simulator) and catalogs representative of the DES data. In this work we demonstrate the framework by simulating the 244 deg2 coadd images and catalogs in five bands for the DES Science Verification data. The simulation output is compared with themore » corresponding data to show that major characteristics of the images and catalogs can be captured. We also point out several directions of future improvements. Two practical examples—star-galaxy classification and proximity effects on object detection—are then used to illustrate how one can use the simulations to address systematics issues in data analysis. With clear understanding of the simplifications in our model, we show that one can use the simulations side-by-side with data products to interpret the measurements. This forward modeling approach is generally applicable for other upcoming and future surveys. It provides a powerful tool for systematics studies that is sufficiently realistic and highly controllable.« less
Modeling the Transfer Function for the Dark Energy Survey
NASA Astrophysics Data System (ADS)
Chang, C.; Busha, M. T.; Wechsler, R. H.; Refregier, A.; Amara, A.; Rykoff, E.; Becker, M. R.; Bruderer, C.; Gamper, L.; Leistedt, B.; Peiris, H.; Abbott, T.; Abdalla, F. B.; Balbinot, E.; Banerji, M.; Bernstein, R. A.; Bertin, E.; Brooks, D.; Carnero, A.; Desai, S.; da Costa, L. N.; Cunha, C. E.; Eifler, T.; Evrard, A. E.; Fausti Neto, A.; Gerdes, D.; Gruen, D.; James, D.; Kuehn, K.; Maia, M. A. G.; Makler, M.; Ogando, R.; Plazas, A.; Sanchez, E.; Santiago, B.; Schubnell, M.; Sevilla-Noarbe, I.; Smith, C.; Soares-Santos, M.; Suchyta, E.; Swanson, M. E. C.; Tarle, G.; Zuntz, J.
2015-03-01
We present a forward-modeling simulation framework designed to model the data products from the Dark Energy Survey (DES). This forward-model process can be thought of as a transfer function—a mapping from cosmological/astronomical signals to the final data products used by the scientists. Using output from the cosmological simulations (the Blind Cosmology Challenge), we generate simulated images (the Ultra Fast Image Simulator) and catalogs representative of the DES data. In this work we demonstrate the framework by simulating the 244 deg2 coadd images and catalogs in five bands for the DES Science Verification data. The simulation output is compared with the corresponding data to show that major characteristics of the images and catalogs can be captured. We also point out several directions of future improvements. Two practical examples—star-galaxy classification and proximity effects on object detection—are then used to illustrate how one can use the simulations to address systematics issues in data analysis. With clear understanding of the simplifications in our model, we show that one can use the simulations side-by-side with data products to interpret the measurements. This forward modeling approach is generally applicable for other upcoming and future surveys. It provides a powerful tool for systematics studies that is sufficiently realistic and highly controllable.
Modeling the Transfer Function for the Dark Energy Survey
Chang, C.
2015-03-04
We present a forward-modeling simulation framework designed to model the data products from the Dark Energy Survey (DES). This forward-model process can be thought of as a transfer function—a mapping from cosmological/astronomical signals to the final data products used by the scientists. Using output from the cosmological simulations (the Blind Cosmology Challenge), we generate simulated images (the Ultra Fast Image Simulator) and catalogs representative of the DES data. In this work we demonstrate the framework by simulating the 244 deg^{2} coadd images and catalogs in five bands for the DES Science Verification data. The simulation output is compared with the corresponding data to show that major characteristics of the images and catalogs can be captured. We also point out several directions of future improvements. Two practical examples—star-galaxy classification and proximity effects on object detection—are then used to illustrate how one can use the simulations to address systematics issues in data analysis. With clear understanding of the simplifications in our model, we show that one can use the simulations side-by-side with data products to interpret the measurements. This forward modeling approach is generally applicable for other upcoming and future surveys. It provides a powerful tool for systematics studies that is sufficiently realistic and highly controllable.
Long-range correlation energy calculated from coupled atomic response functions
Ambrosetti, Alberto; Reilly, Anthony M.; Tkatchenko, Alexandre; DiStasio, Robert A.
2014-05-14
An accurate determination of the electron correlation energy is an essential prerequisite for describing the structure, stability, and function in a wide variety of systems. Therefore, the development of efficient approaches for the calculation of the correlation energy (and hence the dispersion energy as well) is essential and such methods can be coupled with many density-functional approximations, local methods for the electron correlation energy, and even interatomic force fields. In this work, we build upon the previously developed many-body dispersion (MBD) framework, which is intimately linked to the random-phase approximation for the correlation energy. We separate the correlation energy into short-range contributions that are modeled by semi-local functionals and long-range contributions that are calculated by mapping the complex all-electron problem onto a set of atomic response functions coupled in the dipole approximation. We propose an effective range-separation of the coupling between the atomic response functions that extends the already broad applicability of the MBD method to non-metallic materials with highly anisotropic responses, such as layered nanostructures. Application to a variety of high-quality benchmark datasets illustrates the accuracy and applicability of the improved MBD approach, which offers the prospect of first-principles modeling of large structurally complex systems with an accurate description of the long-range correlation energy.
Solar wind-magnetosphere energy coupling function fitting: Results from a global MHD simulation
NASA Astrophysics Data System (ADS)
Wang, C.; Han, J. P.; Li, H.; Peng, Z.; Richardson, J. D.
2014-08-01
Quantitatively estimating the energy input from the solar wind into the magnetosphere on a global scale is still an observational challenge. We perform three-dimensional magnetohydrodynamic (MHD) simulations to derive the energy coupling function. Based on 240 numerical test runs, the energy coupling function is given by Ein=3.78×107nsw0.24Vsw1.47BT0.86[sin2.70(θ/2)+0.25]. We study the correlations between the energy coupling function and a wide variety of magnetospheric activity, such as the indices of Dst, Kp, ap, AE, AU, AL, the polar cap index, and the hemispheric auroral power. The results indicate that this energy coupling function gives better correlations than the ɛ function. This result is also applied to a storm event under northward interplanetary magnetic field conditions. About 13% of the solar wind kinetic energy is transferred into the magnetosphere and about 35% of the input energy is dissipated in the ionosphere, consistent with previous studies.
[Effect of exogenously administered ATP on heart function and energy status].
Chernikov, V S; Darbinian, T M; Bakuleva, N P
1993-01-01
It has been shown that ATP (24.10(-6) M) administered once into the circulating solution improved strength and speed characteristics of aerobically perfused hearts. The increasing demands of the hearts in oxygen and energy substrates were satisfied due to coronary vessels dilatation without harming the energy status of the myocardium. When the functional parameters of the hearts in the test and control groups did not differ, an exogenously administered ATP was included into the energy metabolism and increased considerably ATP and CP tissue levels, the sum of high-energy phosphates and ATP/ADP ratio. Artificial supplementation of tissue energy resources was accompanied by a decrease in energy-dependent end-diastolic pressure and diastolic left ventricular elasticity and by increased extensibility of the heart muscle, which may improve functional parameters. PMID:8185075
Energy distribution functions of kilovolt ions in a modified Penning discharge
NASA Technical Reports Server (NTRS)
Roth, J. R.
1972-01-01
The distribution function of ion energy parallel to the magnetic field of a Penning discharge was measured with a retarding potential energy analyzer. Simultaneous measurements of the ion energy distribution function perpendicular to the magnetic field were made with a charge-exchange neutral detector. The ion energy distribution functions are approximately Maxwellian, and their kinetic temperatures are equal within experimental error. This suggests that turbulent processes previously observed Maxwellianize the velocity distribution along a radius in velocity space, and result in an isotropic energy distribution. The kinetic temperatures are on the order of kilovolts, and the tails of the ion energy distribution functions are Maxwellian up to a factor of 7 e-folds in energy. When the distributions depart from Maxwellian, they are enhanced above the Maxwellian tail. Above densities of about 10 to the 10th power particles/cc, this enhancement appears to be the result of a second, higher temperature Maxwellian distribution. At these high particle energies, only the ions perpendicular to the magnetic field lines were investigated.
NASA Astrophysics Data System (ADS)
Buchowiecki, Marcin
2016-05-01
The ratios of partition functions at different temperatures are calculated and its dependence on potential energy shape is analyzed. The role of anharmonicity and non-rigidity of rotations is discussed in the context of the angular frequency and the shape of potential energy curve. A role of inflection point of potential energy curve for the quality of rigid rotor harmonic oscillator and rigid rotor Morse oscillator is elucidated.
A simple parameterization for quality factor as a function of linear energy transfer
NASA Technical Reports Server (NTRS)
Townsend, Lawrence W.; Wilson, John; Cucinotta, Francis A.
1987-01-01
The paper presents a simple analytic approximation of the radiation quality factor (Q) as a function of linear energy transfer for use in radiation protection calculations. The paper also presents estimated quality factors in water for protons over a broad range of incident energies. It is shown that the quality factors are less than unity for all proton energies greater than 13 MeV.
Functional Metal Oxide Nanostructures: Their Synthesis, Characterization, and Energy Applications
NASA Astrophysics Data System (ADS)
Iyer, Aparna
This research focuses on studying metal oxides (MnO 2, Co3O4, MgO, Y2O3) for various applications including water oxidation and photocatalytic oxidation, developing different synthesis methodologies, and presenting detailed characterization studies of these metal oxides. This research consists of three major parts. The first part is studying novel applications and developing a synthesis method for manganese oxide nanomaterials. Manganese oxide materials were studied for renewable energy applications by using them as catalysts for water oxidation reactions. In this study, various crystallographic forms of manganese oxides (amorphous, 2D layered, 1D 2 x 2 tunnel structures) were evaluated for water oxidation catalysis. Amorphous manganese oxides (AMO) were found to be catalytically active for chemical and photochemical water oxidation compared to cryptomelane type tunnel manganese oxides (2 x 2 tunnels; OMS2) or layered birnessite (OL-1) materials. Detailed characterization was done to establish a correlation between the properties of the manganese oxide materials and their catalytic activities in water oxidation. The gas phase photocatalytic oxidation of 2-propanol under visible light was studied using manganese oxide 2 x 2 tunnel structures (OMS-2) as catalysts (Chapter 3). The reaction is 100% selective to acetone. As suggested by the photocatalytic and characterization data, important factors for the design of active OMS-2 photocatalysts are synthesis methodology, morphology, mixed valency and the release of oxygen from the OMS-2 structure. Manganese oxide octahedral molecular sieves (2 x 2 tunnels; OMS-2) with self-assembled dense or hollow sphere morphologies were fabricated via a room temperature ultrasonic atomization assisted synthesis (Chapter 4). The properties and catalytic activities of these newly developed materials were compared with that of OMS-2 synthesized by conventional reflux route. These materials exhibit exceptionally high catalytic activities
Bond Functions and Core Correlation Energy Contributions To HeBe Potential
NASA Astrophysics Data System (ADS)
Shalabi, A. S.; Nour, E. M.; Abdel Halim, W. S.
An empirical scheme for implementation of bond functions in heteronuclear diatomics is suggested and applied to HeBe using universal even-tempered functions. The effects of bond functions and core-correlation energy on the interaction potential of HeBe calculated at the uncorrelated (SCF) and correlated (MBPT and CC) levels are examined. The results confirm that an accuracy of sub μ Hartree level can be obtained using even-tempered functions with s-, p-, and d- symmetry and that bond functions of size {4s2p} for He and {6s3p} for Be recovers 100% of energy lowering obtained from the addition of 10d atom-centered functions to He and 13d atom centred functions to Be. The various treatments of the electron correlation, conclude that the system is interacting weakly with a well depth from 14.5-24.7 μEh at a separation near 9.1a0 compared with 20.7-25.5 μEh previously reported with a rather limited basis set. The most reliable well depth corrected for BSSE (19.0 μEh) was obtained at the CC-SD(T)level at separation of 8.71a0 taking into account the effects of bond functions and core correlation energy. Potential energy curves at the CC-SD(T) valence and CC-SD(T) valence + core correlation levels are analyzed in analytical forms in terms of exchange repulsion, induction and dispersion components.
NEUTROPHIL FUNCTION AND ENERGY STATUS IN HOLSTEIN COWS WITH UTERINE HEALTH DISORDERS
Technology Transfer Automated Retrieval System (TEKTRAN)
The objectives of this study were to investigate the associations between peripheral blood neutrophil (PMN) function, energy status, and uterine health in periparturient dairy cows. Data were collected from 83 multiparous Holstein cows. Blood samples for PMN function determination were collected w...
Level densities of iron isotopes and low-energy enhancement of {gamma}-strength function
Voinov, A. V.; Grimes, S. M.; Brune, C. R.; Hornish, M. J.; Massey, T. N.; Agvaanluvsan, U.; Algin, E.; Belgya, T.; Guttormsen, M.; Rekstad, J.; Siem, S.; Mitchell, G. E.; Schiller, A.
2006-03-13
The neutron spectrum from the 55Mn(d, n)56Fe reaction has been measured at Ed = 7 MeV. The level density of 56Fe obtained from neutron evaporation spectrum has been compared to the level density obtained from Oslo-type 57Fe(3He, {alpha}{gamma})56Fe experiment. The good agreement supports the recent results including the low-energy enhancement in the {gamma}-strength function for iron isotopes. The new level density function allowed us to investigate an excitation energy dependence of this enhancement, which is shown to increase with increasing excitation energy.
NASA Astrophysics Data System (ADS)
Sergeev, Alexey; Jovanovic, Raka; Kais, Sabre; Alharbi, Fahhad H.
2016-07-01
We consider the density of a fermionic system as a functional of the potential, in one-dimensional case, where it is approximated by the Thomas–Fermi term plus semiclassical corrections through the gradient expansion. We compare this asymptotic series with the exact answer for the case of the harmonic oscillator and the Morse potential. It is found that the leading (Thomas–Fermi) term is in agreement with the exact density, but the subdominant term does not agree in terms of the asymptotic behavior because of the presence of oscillations in the exact density, but their absence in the gradient expansion. However, after regularization of the density by convolution with a Gaussian, the agreement can be established even in the subdominant term. Moreover, it is found that the expansion is always divergent, and its terms grow proportionally to the factorial function of the order, similar to the well-known divergence of perturbation series in field theory and the quantum anharmonic oscillator. Padé–Hermite approximants allow summation of the series, and one of the branches of the approximants agrees with the density.
Xiang, Zhonghua; Dai, Quanbin; Chen, Jian-Feng; Dai, Liming
2016-08-01
Edge functionalization by selectively attaching chemical moieties at the edge of graphene sheets with minimal damage of the carbon basal plane can impart solubility, film-forming capability, and electrocatalytic activity, while largely retaining the physicochemical properties of the pristine graphene. The resultant edge-functionalized graphene materials (EFGs) are attractive for various potential applications. Here, a focused, concise review on the synthesis of EFGs is presented, along with their 2D covalent organic polymer (2D COP) analogues, as energy materials. The versatility of edge-functionalization is revealed for producing tailor-made graphene and COP materials for efficient energy conversion and storage. PMID:27038041
Correlation functions of the energy-momentum tensor in SU(2) gauge theory at finite temperature
Huebner, K.; Pica, C.; Karsch, F.
2008-11-01
We calculate correlation functions of the energy-momentum tensor in the vicinity of the deconfinement phase transition of (3+1)-dimensional SU(2) gauge theory and discuss their critical behavior in the vicinity of the second order deconfinement transition. We show that correlation functions of the trace of the energy-momentum tensor diverge uniformly at the critical point in proportion to the specific heat singularity. Correlation functions of the pressure, on the other hand, stay finite at the critical point. We discuss the consequences of these findings for the analysis of transport coefficients, in particular, the bulk viscosity, in the vicinity of a second order phase transition point.
Surface energy fluctuation effects in single crystals of DNA-functionalized nanoparticles
NASA Astrophysics Data System (ADS)
Li, Ting I. N. G.; Olvera de la Cruz, Monica
2015-12-01
Surface energy is a fundamental material property that determines important functions such as catalytic, sensing, and imaging properties. Over the past century, various experimental studies and models including the broken bond theory and Wulff construction have been developed to analyze surface free energies. However, it remains a challenge to measure or predict thermal fluctuation effects on surface energies. In particular, crystals of functionalized building blocks, such as self-assembling proteins and DNA-functionalized nanoparticles, assembled via the specific surface interactions of the building blocks, are highly sensitive to thermal fluctuations. In the case of DNA-functionalized nanoparticles, it has been shown that the crystals are formed as a result of thermally active hybridizations. We show here that the surface energy along different planes can be obtained from the ratio of hybridization events. The surface energy fluctuations in these systems are shown to bear a nearly linear correlation with the fluctuations in DNA hybridization events in the bulk. We further demonstrate that short DNA chains and high DNA loading increase the volume density of the DNA sticky ends. The relationship between thermally active hybridizations and surface energy found here can be used to aid the design of single crystals of functionalized colloids with active surface groups.
Effects of the Electron Energy Distribution Function on Modeled X-ray Spectra
Shlyaptseva, A S; Hansen, S B
2004-02-19
This paper presents the results of a broad investigation into the effects of the electron energy distribution function on the predictions of non-LTE collisional-radiative atomic kinetics models. The effects of non-Maxwellian and suprathermal (''hot'') electron distributions on collisional rates (including three-body recombination) are studied. It is shown that most collisional rates are fairly insensitive to the functional form and characteristic energy of the electron distribution function as long as the characteristic energy is larger than the threshold energy for the collisional process. Collisional excitation and ionization rates, however, are highly sensitive to the fraction of hot electrons. This permits the development of robust spectroscopic diagnostics that can be used to characterize the electron density, bulk electron temperature, and hot electron fraction of plasmas with non-equilibrium electron distribution functions (EDFs). Hot electrons are shown to increase and spread out plasma charge state distributions, amplify the intensities of emission lines fed by direct collisional excitation and radiative cascades, and alter the structure of satellite features in both K- and L-shell spectra. The characteristic energy, functional form, and spatial properties of hot electron distributions in plasmas are open to characterization through their effects on high-energy continuum and line emission and on the polarization of spectral lines.
NASA Astrophysics Data System (ADS)
Sotiropoulou, P.; Koukou, V.; Martini, N.; Michail, C.; Kounadi, E.; Kandarakis, I.; Nikiforidis, G.; Fountos, G.
2015-09-01
In this study an analytical approximation of dual-energy inverse functions is presented for the estimation of the calcium-to-phosphorous (Ca/P) mass ratio, which is a crucial parameter in bone health. Bone quality could be examined by the X-ray dual-energy method (XDEM), in terms of bone tissue material properties. Low- and high-energy, log- intensity measurements were combined by using a nonlinear function, to cancel out the soft tissue structures and generate the dual energy bone Ca/P mass ratio. The dual-energy simulated data were obtained using variable Ca and PO4 thicknesses on a fixed total tissue thickness. The XDEM simulations were based on a bone phantom. Inverse fitting functions with least-squares estimation were used to obtain the fitting coefficients and to calculate the thickness of each material. The examined inverse mapping functions were linear, quadratic, and cubic. For every thickness, the nonlinear quadratic function provided the optimal fitting accuracy while requiring relative few terms. The dual-energy method, simulated in this work could be used to quantify bone Ca/P mass ratio with photon-counting detectors.
Oferkin, Igor V.; Katkova, Ekaterina V.; Sulimov, Alexey V.; Kutov, Danil C.; Sobolev, Sergey I.; Voevodin, Vladimir V.; Sulimov, Vladimir B.
2015-01-01
The adequate choice of the docking target function impacts the accuracy of the ligand positioning as well as the accuracy of the protein-ligand binding energy calculation. To evaluate a docking target function we compared positions of its minima with the experimentally known pose of the ligand in the protein active site. We evaluated five docking target functions based on either the MMFF94 force field or the PM7 quantum-chemical method with or without implicit solvent models: PCM, COSMO, and SGB. Each function was tested on the same set of 16 protein-ligand complexes. For exhaustive low-energy minima search the novel MPI parallelized docking program FLM and large supercomputer resources were used. Protein-ligand binding energies calculated using low-energy minima were compared with experimental values. It was demonstrated that the docking target function on the base of the MMFF94 force field in vacuo can be used for discovery of native or near native ligand positions by finding the low-energy local minima spectrum of the target function. The importance of solute-solvent interaction for the correct ligand positioning is demonstrated. It is shown that docking accuracy can be improved by replacement of the MMFF94 force field by the new semiempirical quantum-chemical PM7 method. PMID:26693223
Sun, Yu; Welsh, William J; Latour, Robert A
2005-06-01
When simulating protein adsorption behavior, decisions must first be made regarding how the protein should be oriented on the surface. To address this problem, we have developed a molecular simulation program that combines an empirical adsorption free energy function with an efficient configurational search method to calculate orientation-dependent adsorption free energies between proteins and functionalized surfaces. The configuration space is searched systematically using a quaternion rotation technique, and the adsorption free energy is evaluated using an empirical energy function with an efficient grid-based calculational method. In this paper, the developed method is applied to analyze the preferred orientations of a model protein, lysozyme, on various functionalized alkanethiol self-assembled monolayer (SAM) surfaces by the generation of contour graphs that relate adsorption free energy to adsorbed orientation, and the results are compared with experimental observations. As anticipated, the adsorbed orientation of lysozyme is predicted to be dependent on the discrete organization of the functional groups presented by the surface. Lysozyme, which is a positively charged protein, is predicted to adsorb on its 'side' on both hydrophobic and negatively charged surfaces. On surfaces with discrete positively charged sites, attractive interaction energies can also be obtained due to the presence of discrete local negative charges present on the lysozyme surface. In this case, 'end-on' orientations are preferred. Additionally, SAM surface models with mixed functionality suggest that the interactions between lysozyme and surfaces could be greatly enhanced if individual surface functional groups are able to access the catalytic cleft region of lysozyme, similar to ligand-receptor interactions. The contour graphs generated by this method can be used to identify low-energy orientations that can then be used as starting points for further simulations to investigate
Detailed first-principles studies on surface energy and work function of hexagonal metals
NASA Astrophysics Data System (ADS)
Ji, De-Peng; Zhu, Quanxi; Wang, Shao-Qing
2016-09-01
The surface energies and work functions for ten kinds of Miller-indices surfaces of hexagonal metals, Be, Mg, Tc, Re, Ru, and Os are calculated by means of the density functional theory (DFT) method. The results show that the metals belonging to the same group have a very similar rule in work functions and surface energies. The work functions of (0001), (01 1 - 1)" separators=",, and (10 1 - 0)" separators=", surfaces are generally larger than the work functions of (11 2 - 1)" separators=",, (11 2 - 2)" separators=",, (11 2 - 3)" separators=",, and (31 4 - 0)" separators=", surfaces. In contrast to work functions, there is more regularity in the crystallographic orientation dependence of surface energies. However, for the metals belonging to different groups, there are always some differences in the exact order of orientation dependence. It is also shown that the work functions and surface energies of the main group metals decrease as they go from top to the bottom in the same group of periodic table, while for the transition metals, they do not always obey this rule.
New approaches for the calibration of exchange-energy densities in local hybrid functionals.
Maier, Toni M; Haasler, Matthias; Arbuznikov, Alexei V; Kaupp, Martin
2016-08-21
The ambiguity of exchange-energy densities is a fundamental challenge for the development of local hybrid functionals, or of other functionals based on a local mixing of exchange-energy densities. In this work, a systematic construction of semi-local calibration functions (CFs) for adjusting the exchange-energy densities in local hybrid functionals is provided, which directly links a given CF to an underlying semi-local exchange functional, as well as to the second-order gradient expansion of the exchange hole. Using successive steps of integration by parts allows the derivation of correction terms of increasing order, resulting in more and more complicated but also more flexible CFs. We derive explicit first- and second-order CFs (pig1 and pig2) based on B88 generalized-gradient approximation (GGA) exchange, and a first-order CF (tpig1) based on τ-dependent B98 meta-GGA exchange. We combine these CFs with different long-range damping functions and evaluate them for calibration of LDA, B88 GGA, and TPSS meta-GGA exchange-energy densities. Based on a minimization of unphysical nondynamical correlation contributions in three noble-gas dimer potential-energy curves, free parameters in the CFs are optimized, and performance of various approaches in the calibration of different exchange-energy densities is compared. Most notably, the second-order pig2 CF provides the largest flexibility with respect to the diffuseness of the damping function. This suggests that higher-order CFs based on the present integration-by-parts scheme may be particularly suitable for the flexible construction of local hybrid functionals. PMID:27080804
Glycolytic Enzymes Localize to Synapses under Energy Stress to Support Synaptic Function.
Jang, SoRi; Nelson, Jessica C; Bend, Eric G; Rodríguez-Laureano, Lucelenie; Tueros, Felipe G; Cartagenova, Luis; Underwood, Katherine; Jorgensen, Erik M; Colón-Ramos, Daniel A
2016-04-20
Changes in neuronal activity create local and transient changes in energy demands at synapses. Here we discover a metabolic compartment that forms in vivo near synapses to meet local energy demands and support synaptic function in Caenorhabditis elegans neurons. Under conditions of energy stress, glycolytic enzymes redistribute from a diffuse localization in the cytoplasm to a punctate localization adjacent to synapses. Glycolytic enzymes colocalize, suggesting the ad hoc formation of a glycolysis compartment, or a "glycolytic metabolon," that can maintain local levels of ATP. Local formation of the glycolytic metabolon is dependent on presynaptic scaffolding proteins, and disruption of the glycolytic metabolon blocks the synaptic vesicle cycle, impairs synaptic recovery, and affects locomotion. Our studies indicate that under energy stress conditions, energy demands in C. elegans synapses are met locally through the assembly of a glycolytic metabolon to sustain synaptic function and behavior. VIDEO ABSTRACT. PMID:27068791
Golubev, S. V.; Izotov, I. V.; Mansfeld, D. A.; Semenov, V. E.
2012-02-15
Experimental investigation is undertaken to study formation of electron energy distribution function (EEDF) at the initial stage of electron cyclotron resonance (ECR) discharge inside magnetic mirror trap. In experiment, where discharge was initiated by high power radiation of gyrotron operated in the mm-wavelength range, electrons were revealed to leave the trap having EEDF be quite different from Maxwellian one. Specifically, the EEDF was found to decrease slowly with energy up to 400-500 keV and drops abruptly further. The possible physical mechanisms are discussed to explain losses of high energy electrons from the trap and a limitation of their energy.
Golubev, S V; Izotov, I V; Mansfeld, D A; Semenov, V E
2012-02-01
Experimental investigation is undertaken to study formation of electron energy distribution function (EEDF) at the initial stage of electron cyclotron resonance (ECR) discharge inside magnetic mirror trap. In experiment, where discharge was initiated by high power radiation of gyrotron operated in the mm-wavelength range, electrons were revealed to leave the trap having EEDF be quite different from Maxwellian one. Specifically, the EEDF was found to decrease slowly with energy up to 400-500 keV and drops abruptly further. The possible physical mechanisms are discussed to explain losses of high energy electrons from the trap and a limitation of their energy. PMID:22380303
Degenerate RS perturbation theory. [Rayleigh-Schroedinger energies and wave functions
NASA Technical Reports Server (NTRS)
Hirschfelder, J. O.; Certain, P. R.
1974-01-01
A concise, systematic procedure is given for determining the Rayleigh-Schroedinger energies and wave functions of degenerate states to arbitrarily high orders even when the degeneracies of the various states are resolved in arbitrary orders. The procedure is expressed in terms of an iterative cycle in which the energy through the (2n + 1)-th order is expressed in terms of the partially determined wave function through the n-th order. Both a direct and an operator derivation are given. The two approaches are equivalent and can be transcribed into each other. The direct approach deals with the wave functions (without the use of formal operators) and has the advantage that it resembles the usual treatment of nondegenerate perturbations and maintains close contact with the basic physics. In the operator approach, the wave functions are expressed in terms of infinite-order operators which are determined by the successive resolution of the space of the zeroth-order functions.
Carmona-Espíndola, Javier; Gázquez, José L.; Vela, Alberto; Trickey, S. B.
2015-02-07
A new non-empirical exchange energy functional of the generalized gradient approximation (GGA) type, which gives an exchange potential with the correct asymptotic behavior, is developed and explored. In combination with the Perdew-Burke-Ernzerhof (PBE) correlation energy functional, the new CAP-PBE (CAP stands for correct asymptotic potential) exchange-correlation functional gives heats of formation, ionization potentials, electron affinities, proton affinities, binding energies of weakly interacting systems, barrier heights for hydrogen and non-hydrogen transfer reactions, bond distances, and harmonic frequencies on standard test sets that are fully competitive with those obtained from other GGA-type functionals that do not have the correct asymptotic exchange potential behavior. Distinct from them, the new functional provides important improvements in quantities dependent upon response functions, e.g., static and dynamic polarizabilities and hyperpolarizabilities. CAP combined with the Lee-Yang-Parr correlation functional gives roughly equivalent results. Consideration of the computed dynamical polarizabilities in the context of the broad spectrum of other properties considered tips the balance to the non-empirical CAP-PBE combination. Intriguingly, these improvements arise primarily from improvements in the highest occupied and lowest unoccupied molecular orbitals, and not from shifts in the associated eigenvalues. Those eigenvalues do not change dramatically with respect to eigenvalues from other GGA-type functionals that do not provide the correct asymptotic behavior of the potential. Unexpected behavior of the potential at intermediate distances from the nucleus explains this unexpected result and indicates a clear route for improvement.
Toward an energy function for the contact map representation of proteins.
Park, K; Vendruscolo, M; Domany, E
2000-08-01
We analyzed several energy functions for predicting the native state of proteins from an energy minimization procedure. We derived the parameters of a given energy function by imposing the basic requirement that the energy of the native conformation of a protein is lower than that of any conformation chosen from a set of decoys. Our work is motivated by a recent result which proved that the simple pairwise contact approximation of the energy is insufficient to satisfy simultaneously such a basic requirement for all the proteins in a database. Here, we investigate the reasons of such negative results and show how to improve the predictive power of methods based on energy minimization. We generated decoys by gapless threading, and we derive energy parameters by perceptron learning. We first considered hydrophobic contributions to the energy, defined in several ways, and showed that the additional hydrophobic terms enlarge slightly the number of proteins that can be stabilized together. Next, we performed various modifications of the pairwise energy term. We introduced (1) a distinction between inter-residue contacts on the surface and in the core of a protein and (2) a simple distance-dependent pairwise interaction in which a two-tier definition of contact replaces the original (single-tier) one. Our results suggest that a detailed treatment of the pairwise potential is likely to be more relevant than the consideration of other forces. PMID:10842339
Do, Hainam; Wheatley, Richard J
2016-08-28
A robust and model free Monte Carlo simulation method is proposed to address the challenge in computing the classical density of states and partition function of solids. Starting from the minimum configurational energy, the algorithm partitions the entire energy range in the increasing energy direction ("upward") into subdivisions whose integrated density of states is known. When combined with the density of states computed from the "downward" energy partitioning approach [H. Do, J. D. Hirst, and R. J. Wheatley, J. Chem. Phys. 135, 174105 (2011)], the equilibrium thermodynamic properties can be evaluated at any temperature and in any phase. The method is illustrated in the context of the Lennard-Jones system and can readily be extended to other molecular systems and clusters for which the structures are known. PMID:27586913
Validation of local hybrid functionals for TDDFT calculations of electronic excitation energies
NASA Astrophysics Data System (ADS)
Maier, Toni M.; Bahmann, Hilke; Arbuznikov, Alexei V.; Kaupp, Martin
2016-02-01
The first systematic evaluation of local hybrid functionals for the calculation of electronic excitation energies within linear-response time-dependent density functional theory (TDDFT) is reported. Using our recent efficient semi-numerical TDDFT implementation [T. M. Maier et al., J. Chem. Theory Comput. 11, 4226 (2015)], four simple, thermochemically optimized one-parameter local hybrid functionals based on local spin-density exchange are evaluated against a database of singlet and triplet valence excitations of organic molecules, and against a mixed database including also Rydberg, intramolecular charge-transfer (CT) and core excitations. The four local hybrids exhibit comparable performance to standard global or range-separated hybrid functionals for common singlet valence excitations, but several local hybrids outperform all other functionals tested for the triplet excitations of the first test set, as well as for relative energies of excited states. Evaluation for the combined second test set shows that local hybrids can also provide excellent Rydberg and core excitations, in the latter case rivaling specialized functionals optimized specifically for such excitations. This good performance of local hybrids for different excitation types could be traced to relatively large exact-exchange (EXX) admixtures in a spatial region intermediate between valence and asymptotics, as well as close to the nucleus, and lower EXX admixtures in the valence region. In contrast, the tested local hybrids cannot compete with the best range-separated hybrids for intra- and intermolecular CT excitation energies. Possible directions for improvement in the latter category are discussed. As the used efficient TDDFT implementation requires essentially the same computational effort for global and local hybrids, applications of local hybrid functionals to excited-state problems appear promising in a wide range of fields. Influences of current-density dependence of local kinetic-energy
Molecular tests of the random phase approximation to the exchange-correlation energy functional
NASA Astrophysics Data System (ADS)
Furche, Filipp
2001-11-01
The exchange-correlation energy functional within the random phase approximation (RPA) is recast into an explicitly orbital-dependent form. A method to evaluate the functional in finite basis sets is introduced. The basis set dependence of the RPA correlation energy is analyzed. Extrapolation using large, correlation-consistent basis sets is essential for accurate estimates of RPA correlation energies. The potential energy curve of N2 is discussed. The RPA is found to recover most of the strong static correlation at large bond distance. Atomization energies of main-group molecules are rather uniformly underestimated by the RPA. The method performs better than generalized-gradient-type approximations (GGA's) only for some electron-rich systems. However, the RPA functional is free of error cancellation between exchange and correlation, and behaves qualitatively correct in the high-density limit, as is demonstrated by the coupling strength decomposition of the atomization energy of F2. The GGA short-range correlation correction to the RPA by Yan, Perdew, and Kurth [Phys. Rev. B 61, 16 430 (2000)] does not seem to improve atomization energies consistently.
Atomic electron energies including relativistic effects and quantum electrodynamic corrections
NASA Technical Reports Server (NTRS)
Aoyagi, M.; Chen, M. H.; Crasemann, B.; Huang, K. N.; Mark, H.
1977-01-01
Atomic electron energies have been calculated relativistically. Hartree-Fock-Slater wave functions served as zeroth-order eigenfunctions to compute the expectation of the total Hamiltonian. A first order correction to the local approximation was thus included. Quantum-electrodynamic corrections were made. For all orbitals in all atoms with 2 less than or equal to Z less than or equal to 106, the following quantities are listed: total energies, electron kinetic energies, electron-nucleus potential energies, electron-electron potential energies consisting of electrostatic and Breit interaction (magnetic and retardation) terms, and vacuum polarization energies. These results will serve for detailed comparison of calculations based on other approaches. The magnitude of quantum electrodynamic corrections is exhibited quantitatively for each state.
Kumakura, Sho Kurisu, Yosuke; Kimura, Daiju; Yano, Keisuke; Imai, Youta; Sato, Fuminobu; Kato, Yushi; Iida, Toshiyuki
2014-02-15
We are constructing a tandem type electron cyclotron resonance (ECR) ion source (ECRIS). High-energy electrons in ECRIS plasma affect electron energy distribution and generate multicharged ion. In this study, we measure electron energy distribution function (EEDF) of low energy region (≦100 eV) in ECRIS plasma at extremely low pressures (10{sup −3}–10{sup −5} Pa) by using cylindrical Langmuir probe. From the result, it is found that the EEDF correlates with the electron density and the temperature from the conventional probe analysis. In addition, we confirm that the tail of EEDF spreads to high energy region as the pressure rises and that there are electrons with high energy in ECR multicharged ion source plasma. The effective temperature estimated from the experimentally obtained EEDF is larger than the electron temperature obtained from the conventional method.
Stafford, L.; Margot, J.; Moisan, M.; Khare, R.; Donnelly, V. M.
2009-01-12
Electron energy distribution functions (EEDFs) were measured in a 50 mTorr oxygen plasma column sustained by propagating surface waves. Trace-rare-gas-optical-emission spectroscopy was used to derive EEDFs by selecting lines to extract ''electron temperature''(T{sub e}) corresponding to either lower energy electrons that excite high-lying levels through stepwise excitation via metastable states or higher energy electrons that excite emission directly from the ground state. Lower energy T{sub e}'s decreased from 8 to 5.5 eV with distance from the wave launcher, while T{sub e}{approx_equal}6 eV for higher energy electrons and T{sub e}>20 eV for a high-energy tail. Mechanisms for such EEDFs are discussed.
NASA Astrophysics Data System (ADS)
Mi, Bin-Zhou; Zhai, Liang-Jun; Hua, Ling-Ling
2016-01-01
The effect of magnetic spin correlation on the thermodynamic properties of Heisenberg ferromagnetic single-walled nanotubes are comprehensively investigated by use of the double-time Green's function method. The influence of temperature, spin quantum number, diameter of the tube, anisotropy strength and external magnetic field to internal energy, free energy, and magnon specific heat are carefully calculated. Compared to the mean field approximation, the consideration of the magnetic correlation effect significantly improves the internal energy values at finite temperature, while it does not so near zero temperature, and this effect is related to the diameter of the tube, anisotropy strength, and spin quantum number. The magnetic correlation effect lowers the internal energy at finite temperature. As a natural consequence of the reduction of the internal energy, the specific heat is reduced, and the free energy is elevated.
A Cavity Corrected 3D-RISM Functional for Accurate Solvation Free Energies
2014-01-01
We show that an Ng bridge function modified version of the three-dimensional reference interaction site model (3D-RISM-NgB) solvation free energy method can accurately predict the hydration free energy (HFE) of a set of 504 organic molecules. To achieve this, a single unique constant parameter was adjusted to the computed HFE of single atom Lennard-Jones solutes. It is shown that 3D-RISM is relatively accurate at predicting the electrostatic component of the HFE without correction but requires a modification of the nonpolar contribution that originates in the formation of the cavity created by the solute in water. We use a free energy functional with the Ng scaling of the direct correlation function [Ng, K. C. J. Chem. Phys.1974, 61, 2680]. This produces a rapid, reliable small molecule HFE calculation for applications in drug design. PMID:24634616
A Cavity Corrected 3D-RISM Functional for Accurate Solvation Free Energies.
Truchon, Jean-François; Pettitt, B Montgomery; Labute, Paul
2014-03-11
We show that an Ng bridge function modified version of the three-dimensional reference interaction site model (3D-RISM-NgB) solvation free energy method can accurately predict the hydration free energy (HFE) of a set of 504 organic molecules. To achieve this, a single unique constant parameter was adjusted to the computed HFE of single atom Lennard-Jones solutes. It is shown that 3D-RISM is relatively accurate at predicting the electrostatic component of the HFE without correction but requires a modification of the nonpolar contribution that originates in the formation of the cavity created by the solute in water. We use a free energy functional with the Ng scaling of the direct correlation function [Ng, K. C. J. Chem. Phys. 1974, 61, 2680]. This produces a rapid, reliable small molecule HFE calculation for applications in drug design. PMID:24634616
Using Density Functional Theory (DFT) for the Calculation of Atomization Energies
NASA Technical Reports Server (NTRS)
Bauschlicher, Charles W., Jr.; Partridge, Harry; Langhoff, Stephen R. (Technical Monitor)
1995-01-01
The calculation of atomization energies using density functional theory (DFT), using the B3LYP hybrid functional, is reported. The sensitivity of the atomization energy to basis set is studied and compared with the coupled cluster singles and doubles approach with a perturbational estimate of the triples (CCSD(T)). Merging the B3LYP results with the G2(MP2) approach is also considered. It is found that replacing the geometry optimization and calculation of the zero-point energy by the analogous quantities computed using the B3LYP approach reduces the maximum error in the G2(MP2) approach. In addition to the 55 G2 atomization energies, some results for transition metal containing systems will also be presented.
Fargali, Samira; Sadahiro, Masato; Jiang, Cheng; Frick, Amy L.; Indall, Tricia; Cogliani, Valeria; Welagen, Jelle; Lin, Wei-jye; Salton, Stephen R.
2012-01-01
Members of the neurotrophin family, including nerve growth factor (NGF), brain-derived neurotrophic factor (BDNF), neurotrophin-3 (NT-3), and neurotrophin-4/5 (NT-4/5), and other neurotrophic growth factors such as ciliary neurotrophic factor (CNTF) and artemin, regulate peripheral and central nervous system development and function. A subset of the neurotrophin-dependent pathways in the hypothalamus, brainstem, and spinal cord, and those that project via the sympathetic nervous system to peripheral metabolic tissues including brown and white adipose tissue (BAT and WAT), muscle and liver, regulate feeding, energy storage, and energy expenditure. We briefly review the role that neurotrophic growth factors play in energy balance, as regulators of neuronal survival and differentiation, neurogenesis, and circuit formation and function, and as inducers of critical gene products that control energy homeostasis. PMID:22581449
Svinarenko, A. A.; Loboda, A. V.; Sukharev, D. E.; Dubrovskaya, Yu. V.; Mudraya, N. V.; Serga, I. N.; Glushkov, A. V.
2010-05-04
We report the further development of an effective approach to construction of the electron Green's function (GF) for the Dirac equation with a complex energy and non-singular central nuclear potential. The nuclear charge distribution and the corresponding nuclear potential are received within the relativistic mean field (RMF) model. The Green's function is usually represented as a combination of two fundamental solutions of the Dirac equation. In the numerical procedure we use the Ivanov-Ivanova effective numerical algorithm and reduce a definition of the Dirac equation fundamental solutions to solving the system of differential equations, which includes the differential equations for the RMF nuclear potential too. As an application, we estimate the self-energy shift correction to atomic levels energies within the Mohr covariant procedure and presented GF approach and calculate the transitions energies for some heavy Li-like multi-charged ions within the QED many-body perturbation theory formalism.
Modern energy density functional for nuclei and the nuclear matter equation of state
Shlomo, S.
2010-08-15
We discuss a method of determining a modern energy density functional (EDF) in nuclei. We adopt a Skyrme type EDF and fit the Skyrme parameters to an extensive set of experimental data on the ground-state binding energies, radii, and the breathing mode energies of a wide range of nuclei. We further constrain the values of the Skyrme parameters by requiring positive values for the slope of the symmetry energy S, the enhancement factor {kappa}, associated with the isovector giant dipole resonance, and the Landau parameter G{sub 0}{sup '}. This is done within the approaches of Hartree-Fock (HF) and HF with the inclusion of correlation effects, using a simulated-annealing based algorithm forminimizing {chi}{sup 2}.We also present results of HF based random phase approximation for the excitation strength function of the breathing mode and discuss the current status of the nuclear matter incompressibility coefficient.
Low-energy ion distribution functions on a magnetically quiet day at geostationary altitude /L = 7/
NASA Technical Reports Server (NTRS)
Singh, N.; Raitt, W. J.; Yasuhara, F.
1982-01-01
Ion energy and pitch angle distribution functions are examined for a magnetically quiet day using averaged data from ATS 6. For both field-aligned and perpendicular fluxes, the populations have a mixture of characteristic energies, and the distribution functions can be fairly well approximated by Maxwellian distributions over three different energy bands in the range 3-600 eV. Pitch angle distributions varying with local time, and energy distributions are used to compute total ion density. Pitch angle scattering mechanisms responsible for the observed transformation of pitch angle distribution are examined, and it is found that a magnetic noise of a certain power spectral density belonging to the electromagnetic ion cyclotron mode near the ion cyclotron frequency can be effective in trapping the field aligned fluxes by pitch angle scattering.
NASA Astrophysics Data System (ADS)
Raza, Nauman; Sial, Sultan; Siddiqi, Shahid S.
2009-04-01
The Sobolev gradient technique has been discussed previously in this journal as an efficient method for finding energy minima of certain Ginzburg-Landau type functionals [S. Sial, J. Neuberger, T. Lookman, A. Saxena, Energy minimization using Sobolev gradients: application to phase separation and ordering, J. Comput. Phys. 189 (2003) 88-97]. In this article a Sobolev gradient method for the related time evolution is discussed.
A high time resolution study of the solar wind-magnetosphere energy coupling function
NASA Technical Reports Server (NTRS)
Akasofu, S.-I.; Carbary, J. F.; Meng, C.-I.; Sullivan, J. P.; Lepping, R. P.
1982-01-01
A high time resolution study of the relationships between the solar wind-magnetosphere energy coupling function and the total energy dissipation rate of the magnetosphere is made using 5-min average values of solar wind data and of the geomagnetic indices AE and Dst. All the results are essentially the same as those obtained by the earlier studies which were based on the hourly average data set. Therefore, it is confirmed that the magnetosphere is primarily a driven system
Tait, E W; Ratcliff, L E; Payne, M C; Haynes, P D; Hine, N D M
2016-05-18
Experimental techniques for electron energy loss spectroscopy (EELS) combine high energy resolution with high spatial resolution. They are therefore powerful tools for investigating the local electronic structure of complex systems such as nanostructures, interfaces and even individual defects. Interpretation of experimental electron energy loss spectra is often challenging and can require theoretical modelling of candidate structures, which themselves may be large and complex, beyond the capabilities of traditional cubic-scaling density functional theory. In this work, we present functionality to compute electron energy loss spectra within the onetep linear-scaling density functional theory code. We first demonstrate that simulated spectra agree with those computed using conventional plane wave pseudopotential methods to a high degree of precision. The ability of onetep to tackle large problems is then exploited to investigate convergence of spectra with respect to supercell size. Finally, we apply the novel functionality to a study of the electron energy loss spectra of defects on the (1 0 1) surface of an anatase slab and determine concentrations of defects which might be experimentally detectable. PMID:27094207
NASA Astrophysics Data System (ADS)
Tait, E. W.; Ratcliff, L. E.; Payne, M. C.; Haynes, P. D.; Hine, N. D. M.
2016-05-01
Experimental techniques for electron energy loss spectroscopy (EELS) combine high energy resolution with high spatial resolution. They are therefore powerful tools for investigating the local electronic structure of complex systems such as nanostructures, interfaces and even individual defects. Interpretation of experimental electron energy loss spectra is often challenging and can require theoretical modelling of candidate structures, which themselves may be large and complex, beyond the capabilities of traditional cubic-scaling density functional theory. In this work, we present functionality to compute electron energy loss spectra within the onetep linear-scaling density functional theory code. We first demonstrate that simulated spectra agree with those computed using conventional plane wave pseudopotential methods to a high degree of precision. The ability of onetep to tackle large problems is then exploited to investigate convergence of spectra with respect to supercell size. Finally, we apply the novel functionality to a study of the electron energy loss spectra of defects on the (1 0 1) surface of an anatase slab and determine concentrations of defects which might be experimentally detectable.
Statistical Measurement of the Gamma-Ray Source-count Distribution as a Function of Energy
NASA Astrophysics Data System (ADS)
Zechlin, Hannes-S.; Cuoco, Alessandro; Donato, Fiorenza; Fornengo, Nicolao; Regis, Marco
2016-08-01
Statistical properties of photon count maps have recently been proven as a new tool to study the composition of the gamma-ray sky with high precision. We employ the 1-point probability distribution function of six years of Fermi-LAT data to measure the source-count distribution dN/dS and the diffuse components of the high-latitude gamma-ray sky as a function of energy. To that aim, we analyze the gamma-ray emission in five adjacent energy bands between 1 and 171 GeV. It is demonstrated that the source-count distribution as a function of flux is compatible with a broken power law up to energies of ˜50 GeV. The index below the break is between 1.95 and 2.0. For higher energies, a simple power-law fits the data, with an index of {2.2}-0.3+0.7 in the energy band between 50 and 171 GeV. Upper limits on further possible breaks as well as the angular power of unresolved sources are derived. We find that point-source populations probed by this method can explain {83}-13+7% ({81}-19+52%) of the extragalactic gamma-ray background between 1.04 and 1.99 GeV (50 and 171 GeV). The method has excellent capabilities for constraining the gamma-ray luminosity function and the spectra of unresolved blazars.
Supersymmetric QCD and high energy cosmic rays: Fragmentation functions of supersymmetric QCD
NASA Astrophysics Data System (ADS)
Corianò, Claudio; Faraggi, Alon E.
2002-04-01
The supersymmetric evolution of the fragmentation functions (or timelike evolution) within N=1 QCD is discussed and predictions for the fragmentation functions of the theory (into final protons) are given. We use a backward running of the supersymmetric DGLAP equations, using a method developed in previous works. We start from the usual QCD parametrizations at low energy and run the DGLAP back, up to an intermediate scale-assumed to be supersymmetric-where we switch-on supersymmetry. From there on we assume the applicability of an N=1 supersymmetric evolution (ESAP). We elaborate on the possible application of these results to high energy cosmic rays near the GZK cutoff.
Energy Densities in the Strong-Interaction Limit of Density Functional Theory.
Mirtschink, André; Seidl, Michael; Gori-Giorgi, Paola
2012-09-11
We discuss energy densities in the strong-interaction limit of density functional theory, deriving an exact expression within the definition (gauge) of the electrostatic potential of the exchange-correlation hole. Exact results for small atoms and small model quantum dots (Hooke's atoms) are compared with available approximations defined in the same gauge. The idea of a local interpolation along the adiabatic connection is discussed, comparing the energy densities of the Kohn-Sham, the physical, and the strong-interacting systems. We also use our results to analyze the local version of the Lieb-Oxford bound, widely used in the construction of approximate exchange-correlation functionals. PMID:26605721
Relativistic Energy Density Functionals: beyond mean-field description of exotic structures
Vretenar, D.; Niksic, T.; Ring, P.; Lalazissis, G. A.
2009-01-28
The framework of relativistic energy density functionals is extended to include correlations related to the restoration of broken symmetries and to fluctuations of collective variables. The generator coordinate method is used to perform configuration mixing of angular-momentum and particle-number projected relativistic wave functions. This approach enables a quantitative description of the evolution of shell-structure, deformation and shape coexistence phenomena in nuclei with soft potential energy surfaces, and singular properties of excitation spectra and transition rates at critical points of quantum shape phase transitions.
The energy coupling function and the power generated by the solar wind-magnetosphere dynamo
NASA Technical Reports Server (NTRS)
Kan, J. R.; Lee, L. C.; Akasofu, S.-I.
1980-01-01
A solar wind parameter epsilon, known as the energy coupling function, has been shown to correlate with the power consumption in the magnetosphere. It is shown in the present paper that the parameter epsilon can be identified semi-quantitatively as the dynamo power delivered from the solar wind to an open magnetosphere. This identification not only provides a theoretical basis for the energy coupling function, but also constitutes an observational verification of the solar wind-magnetosphere dynamo along the magnetotail. Moreover, one can now conclude that a substorm results when the dynamo power exceeds 10 to the 18th erg/s.
Liu, Siyu; Zhao, Ning; Cheng, Zhen; Liu, Hongguang
2015-04-21
Amino-functionalized fluorescent carbon dots have been prepared by hydrothermal treatment of glucosamine with excess pyrophosphate. The produced carbon dots showed stabilized green emission fluorescence at various excitation wavelengths and pH environments. Herein, we demonstrate the surface energy transfer between the amino-functionalized carbon dots and negatively charged hyaluronate stabilized gold nanoparticles. Hyaluronidase can degrade hyaluronate and break down the hyaluronate stabilized gold nanoparticles to inhibit the surface energy transfer. The developed fluorescent carbon dot/gold nanoparticle system can be utilized as a biosensor for sensitive and selective detection of hyaluronidase by two modes which include fluorescence measurements and colorimetric analysis. PMID:25807038
End User Functional and Performance Requirements for HTGR Energy Supply to Industrial Processes
L.E. Demick
2010-09-01
This document specifies end user functional and performance requirements to be used in the development of the design of a high temperature gas-cooled reactor (HTGR) based plant supplying energy to industrial processes. These requirements were developed from collaboration with industry and HTGR suppliers and from detailed evaluation of integration of the HTGR technology in industrial processes. The functional and performance requirements specified herein are an effective representation of the industrial sector energy needs and an effective basis for developing a plant design that will serve the broadest range of industrial applications.
Arrigoni, Enrico; Knap, Michael; Linden, Wolfgang von der
2011-07-01
Among the various numerical techniques to study the physics of strongly correlated quantum many-body systems, the self-energy functional approach (SFA) has become increasingly important. In its previous form, however, SFA is not applicable to Bose-Einstein condensation or superfluidity. In this paper, we show how to overcome this shortcoming. To this end, we identify an appropriate quantity, which we term D, that represents the correlation correction of the condensate order parameter, as it does the self-energy for Green's function. An appropriate functional is derived, which is stationary at the exact physical realization of D and of the self-energy. Its derivation is based on a functional-integral representation of the grand potential followed by an appropriate sequence of Legendre transformations. The approach is not perturbative and, therefore, applicable to a wide range of models with local interactions. We show that the variational cluster approach based on the extended self-energy functional is equivalent to the ''pseudoparticle'' approach proposed in Phys. Rev. B 83, 134507 (2011). We present results for the superfluid density in the two-dimensional Bose-Hubbard model, which shows a remarkable agreement with those of quantum-Monte-Carlo calculations.
Covariant energy density functionals: Nuclear matter constraints and global ground state properties
NASA Astrophysics Data System (ADS)
Afanasjev, A. V.; Agbemava, S. E.
2016-05-01
The correlations between global description of the ground state properties (binding energies, charge radii) and nuclear matter properties of the state-of-the-art covariant energy density functionals have been studied. It was concluded that the strict enforcement of the constraints on the nuclear matter properties (NMP) defined in Dutra et al. [Phys. Rev. C 90, 055203 (2014), 10.1103/PhysRevC.90.055203] will not necessarily lead to the functionals with good description of the binding energies and other ground and excited state properties. In addition, it will not substantially reduce the uncertainties in the predictions of the binding energies in neutron-rich systems. It turns out that the functionals, which come close to satisfying these NMP constraints, have some problems in the description of existing data. On the other hand, these problems are either absent or much smaller in the functionals which are carefully fitted to finite nuclei but which violate some NMP constraints. This is a consequence of the fact that the properties of finite nuclei are defined not only by nuclear matter properties but also by underlying shell effects. The mismatch of phenomenological content, existing in all modern functionals, related to nuclear matter physics and the physics of finite nuclei could also be responsible.
Guidez, Emilie B; Gordon, Mark S
2015-03-12
The modeling of dispersion interactions in density functional theory (DFT) is commonly performed using an energy correction that involves empirically fitted parameters for all atom pairs of the system investigated. In this study, the first-principles-derived dispersion energy from the effective fragment potential (EFP) method is implemented for the density functional theory (DFT-D(EFP)) and Hartree-Fock (HF-D(EFP)) energies. Overall, DFT-D(EFP) performs similarly to the semiempirical DFT-D corrections for the test cases investigated in this work. HF-D(EFP) tends to underestimate binding energies and overestimate intermolecular equilibrium distances, relative to coupled cluster theory, most likely due to incomplete accounting for electron correlation. Overall, this first-principles dispersion correction yields results that are in good agreement with coupled-cluster calculations at a low computational cost. PMID:25651435
Neutron-star matter within the energy-density functional theory and neutron-star structure
Fantina, A. F.; Chamel, N.; Goriely, S.; Pearson, J. M.
2015-02-24
In this lecture, we will present some nucleonic equations of state of neutron-star matter calculated within the nuclear energy-density functional theory using generalized Skyrme functionals developed by the Brussels-Montreal collaboration. These equations of state provide a consistent description of all regions of a neutron star. The global structure of neutron stars predicted by these equations of state will be discussed in connection with recent astrophysical observations.
Towards an Optimal Gradient-dependent Energy Functional of the PZ-SIC Form
Jónsson, Elvar Örn; Lehtola, Susi; Jónsson, Hannes
2015-06-01
Results of Perdew–Zunger self-interaction corrected (PZ-SIC) density functional theory calculations of the atomization energy of 35 molecules are compared to those of high-level quantum chemistry calculations. While the PBE functional, which is commonly used in calculations of condensed matter, is known to predict on average too high atomization energy (overbinding of the molecules), the application of PZ-SIC gives a large overcorrection and leads to significant underestimation of the atomization energy. The exchange enhancement factor that is optimal for the generalized gradient approximation within the Kohn-Sham (KS) approach may not be optimal for the self-interaction corrected functional. The PBEsol functional, wheremore » the exchange enhancement factor was optimized for solids, gives poor results for molecules in KS but turns out to work better than PBE in PZ-SIC calculations. The exchange enhancement is weaker in PBEsol and the functional is closer to the local density approximation. Furthermore, the drop in the exchange enhancement factor for increasing reduced gradient in the PW91 functional gives more accurate results than the plateaued enhancement in the PBE functional. A step towards an optimal exchange enhancement factor for a gradient dependent functional of the PZ-SIC form is taken by constructing an exchange enhancement factor that mimics PBEsol for small values of the reduced gradient, and PW91 for large values. The average atomization energy is then in closer agreement with the high-level quantum chemistry calculations, but the variance is still large, the F2 molecule being a notable outlier.« less
Towards an Optimal Gradient-dependent Energy Functional of the PZ-SIC Form
Jónsson, Elvar Örn; Lehtola, Susi; Jónsson, Hannes
2015-06-01
Results of Perdew–Zunger self-interaction corrected (PZ-SIC) density functional theory calculations of the atomization energy of 35 molecules are compared to those of high-level quantum chemistry calculations. While the PBE functional, which is commonly used in calculations of condensed matter, is known to predict on average too high atomization energy (overbinding of the molecules), the application of PZ-SIC gives a large overcorrection and leads to significant underestimation of the atomization energy. The exchange enhancement factor that is optimal for the generalized gradient approximation within the Kohn-Sham (KS) approach may not be optimal for the self-interaction corrected functional. The PBEsol functional, where the exchange enhancement factor was optimized for solids, gives poor results for molecules in KS but turns out to work better than PBE in PZ-SIC calculations. The exchange enhancement is weaker in PBEsol and the functional is closer to the local density approximation. Furthermore, the drop in the exchange enhancement factor for increasing reduced gradient in the PW91 functional gives more accurate results than the plateaued enhancement in the PBE functional. A step towards an optimal exchange enhancement factor for a gradient dependent functional of the PZ-SIC form is taken by constructing an exchange enhancement factor that mimics PBEsol for small values of the reduced gradient, and PW91 for large values. The average atomization energy is then in closer agreement with the high-level quantum chemistry calculations, but the variance is still large, the F_{2} molecule being a notable outlier.
On the ground state energy of the δ-function Bose gas
NASA Astrophysics Data System (ADS)
Tracy, Craig A.; Widom, Harold
2016-07-01
The weak coupling asymptotics, to order {(c/ρ )}2, of the ground state energy of the delta-function Bose gas is derived. Here 2c≥slant 0 is the delta-function potential amplitude and ρ the density of the gas in the thermodynamic limit. The analysis uses the electrostatic interpretation of the Lieb–Liniger integral equation. Dedicated to Professor Tony Guttmann on the occasion of his 70th birthday.
NASA Astrophysics Data System (ADS)
Öberg, S.; Adjizian, J.-J.; Erbahar, D.; Rio, J.; Humbert, B.; Dossot, M.; Soldatov, A.; Lefrant, S.; Mevellec, J.-Y.; Briddon, P.; Rayson, M. J.; Ewels, C. P.
2016-01-01
While changes in resonant Raman scattering measurements are commonly used to measure the effect of chemical functionalization on single-walled carbon nanotubes, the precise effects of functionalization on these spectra have yet to be clearly identified. In this density functional theory study, we explore the effects of functionalization on both the nanotube resonance energy and frequency shifts in radial breathing mode. Charge transfer effects cause a shift in the first Van Hove singularity spacings, and hence resonance excitation energy, and lead to a decrease in the radial breathing mode frequency, notably when the Fermi level decreases. By varying stochastically the effective mass of carbon atoms in the tube, we simulate the mass effect of functionalization on breathing mode frequency. Finally, full density functional calculations are performed for different nanotubes with varying functional group distribution and concentration using fluorination and hydrogenation, allowing us to determine overall effect on radial breathing mode and charge transfer. The results concur well with experiment, and we discuss the importance when using Raman spectroscopy to interpret experimental functionalization treatments.
Energy of Cohesion, Compressibility, and the Potential Energy Functions of the Graphite System
NASA Technical Reports Server (NTRS)
Girifalco, L. A.; Lad, R. A.
1956-01-01
The lattice summations of the potential energy of importance in the graphite system have been computed by direct summation assuming a Lennard-Jones 6-12 potential between carbon atoms. From these summations, potential energy curves were constructed for interactions between a carbon atom and a graphite monolayer, between a carbon atom and a graphite surface, between a graphite monolayer and a semi-infinite graphite crystal and between two graphite semi-infinite crystals. Using these curves, the equilibrium distance between two isolated physically interacting carbon atoms was found to be 2.70 a, where a is the carbon-carbon distance in a graphite sheet. The distance between a surface plane and the rest of the crystal was found to be 1.7% greater than the interlayer spacing. Theoretical values of the energy of cohesion and the compressibility were calculated from the potential curve for the interaction between two semi-infinite crystals. They were (delta)E(sub c) = -330 ergs/sq cm and beta =3.18x10(exp -12)sq cm/dyne, respectively. These compared favorably with the experimental values of (delta)E(sub c) = -260 ergs/sq cm and beta = 2.97 X 10(exp -2) sq cm/dyne.
Yang, W.; Wu, H.; Cao, L.
2012-07-01
More and more MOX fuels are used in all over the world in the past several decades. Compared with UO{sub 2} fuel, it contains some new features. For example, the neutron spectrum is harder and more resonance interference effects within the resonance energy range are introduced because of more resonant nuclides contained in the MOX fuel. In this paper, the wavelets scaling function expansion method is applied to study the resonance behavior of plutonium isotopes within MOX fuel. Wavelets scaling function expansion continuous-energy self-shielding method is developed recently. It has been validated and verified by comparison to Monte Carlo calculations. In this method, the continuous-energy cross-sections are utilized within resonance energy, which means that it's capable to solve problems with serious resonance interference effects without iteration calculations. Therefore, this method adapts to treat the MOX fuel resonance calculation problem natively. Furthermore, plutonium isotopes have fierce oscillations of total cross-section within thermal energy range, especially for {sup 240}Pu and {sup 242}Pu. To take thermal resonance effect of plutonium isotopes into consideration the wavelet scaling function expansion continuous-energy resonance calculation code WAVERESON is enhanced by applying the free gas scattering kernel to obtain the continuous-energy scattering source within thermal energy range (2.1 eV to 4.0 eV) contrasting against the resonance energy range in which the elastic scattering kernel is utilized. Finally, all of the calculation results of WAVERESON are compared with MCNP calculation. (authors)
NASA Astrophysics Data System (ADS)
Xia, Junchao; Carter, Emily A.
2015-01-01
We present a comprehensive study of single-point kinetic energy density functionals (KEDFs) to be used in orbital-free density functional theory (DFT) calculations. We first propose a form of KEDFs based on a pointwise Kohn-Sham (KS) kinetic energy density (KED) and electron localization function (ELF) analysis. We find that the ELF and modified enhancement factor have a very strong and transferable correlation with the reduced density in various bulk metals. The non-self-consistent kinetic energy errors predicted by our KEDF models are decreased greatly compared to previously reported generalized gradient approximation (GGA) KEDFs. Second, we perform self-consistent calculations with various single-point KEDFs and investigate their numerical convergence behavior. We find striking numerical instabilities for previous GGA KEDFs; most of the GGA KEDFs fail to converge and show unphysical densities during the optimization. In contrast, our KEDFs demonstrate stable convergence, and their self-consistent results of various bulk properties agree reasonably well with KSDFT. A further detailed KED analysis reveals an interesting bifurcation phenomenon in defective metals and alloys, which may shed light on directions for future KEDF development.
NASA Astrophysics Data System (ADS)
Sadigh, Babak; Erhart, Paul; Ã berg, Daniel
2015-08-01
We conduct a detailed investigation of the polaron self-interaction (pSI) error in standard approximations to the exchange-correlation (XC) functional within density-functional theory (DFT). The pSI leads to delocalization error in the polaron wave function and energy, as calculated from the Kohn-Sham (KS) potential in the native charge state of the polaron. This constitutes the origin of the systematic failure of DFT to describe the polaron formation in band insulators. It is shown that the delocalization error in these systems is, however, largely absent in the KS potential of the closed-shell neutral charge state. This leads to a modification of the DFT total-energy functional that corrects the pSI in the XC functional. The resulting pSIC-DFT method constitutes an accurate parameter-free ab initio methodology for calculating polaron properties in insulators at a computational cost that is orders of magnitude smaller than hybrid XC functionals. Unlike approaches that rely on parametrized localized potentials such as DFT+U , the pSIC-DFT method properly captures both site and bond-centered polaron configurations. This is demonstrated by studying formation and migration of self-trapped holes in alkali halides (bond-centered) as well as self-trapped electrons in an elpasolite compound (site-centered). The pSIC-DFT approach consistently reproduces the results obtained by hybrid XC functionals parametrized by DFT+G0W0 calculations. Finally, we generalize the pSIC approach to hybrid functionals, and show that in stark contrast to conventional hybrid calculations of polaron energies, the pSIC-hybrid method is insensitive to the parametrization of the hybrid XC functional. On this basis, we further rationalize the success of the pSIC-DFT approach.
N-dimensional switch function for energy conservation in multiprocess reaction dynamics.
Mogo, César; Brandão, João
2016-06-15
The MReaDy program was designed for studying Multiprocess Reactive Dynamic systems, that is, complex chemical systems involving different and concurrent reactions. It builds a global potential energy surface integrating a variety of potential energy surfaces, each one of them representing an elementary reaction expected to play a role in the chemical process. For each elementary reaction, energy continuity problems may happen in the transition between potential energy surfaces due to differences in the functional form for each of the fragments, especially if built by different authors. A N-dimensional switch function is introduced in MReaDy in order to overcome such a problem. As an example, results of a collision trajectory calculation for H2 + OH → H3 O are presented, showing smooth transition in the potential energy, leading to conservation in the total energy. Calculations for a hydrogen combustion system from 1000 K up to 4000 K shows a variation of 0.012% when compared to the total energy of the system. © 2016 Wiley Periodicals, Inc. PMID:26992438
Lin, Bin; Wong, Ka-Yiu; Hu, Char; Kokubo, Hironori; Pettitt, B. Montgomery
2011-01-01
Although detailed atomic models may be applied for a full description of solvation, simpler phenomenological models are particularly useful to interpret the results for scanning many, large, complex systems where a full atomic model is too computationally expensive to use. Among the most costly are solvation free energy evaluations by simulation. Here we develop a fast way to calculate electrostatic solvation free energy while retaining much of the accuracy of explicit solvent free energy simulation. The basis of our method is to treat the solvent not as a structureless dielectric continuum, but as a structured medium by making use of universal proximal radial distribution functions. Using a deca-alanine peptide as a test case, we compare the use of our theory with free energy simulations and traditional continuum estimates of the electrostatic solvation free energy. PMID:21765968
Lin, Bin; Wong, Ka-Yiu; Hu, Char Y.; Kokubo, Hironori; Pettitt, Bernard M.
2011-07-07
Although detailed atomic models may be applied for a full description of solvation, simpler phenomenologicalmodels are particularly useful to interpret the results for scanning many large, complex systems, where a full atomic model is too computationally expensive to use. Among the most costly are solvation free-energy evaluations by simulation. Here we develop a fast way to calculate electrostatic solvation free energy while retaining much of the accuracy of explicit solvent free-energy simulation. The basis of our method is to treat the solvent not as a structureless dielectric continuum but as a structured medium by making use of universal proximal radial distribution functions. Using a deca-alanine peptide as a test case, we compare the use of our theory with free-energy simulations and traditional continuum estimates of the electrostatic solvation free energy.
NASA Technical Reports Server (NTRS)
Jensen, Per; Li, Yan; Hirsch, Gerhard; Buenker, Robert J.; Lee, Timothy J.; Arnold, James O. (Technical Monitor)
1994-01-01
We report an ab initio investigation of the cluster effect (i.e., the formation of nearly degenerate, four member groups of rotation-vibration energy levels at higher J and K(sub a). values) in the H2Te molecule. The potential energy function has been calculated ab initio at a total of 334 molecular geometries by means of the CCSD(T) method where the (1s-4f) core electrons of Te were described by an effective core potential. The values of the potential energy function obtained cover the region up to around 10,000/cm above the equilibrium energy. On the basis of the ab initio potential, the rotation-vibration energy spectra of H2Te-130 and its deuterated isotopomers have been calculated with the MORBID (Morse Oscillator Rigid Bender Internal Dynamics) Hamiltonian and computer program. In particular, we have calculated the rotational energy manifolds for J less than or = 40 in the vibrational ground state, the upsilon(sub 2) state, the "first triad" (the upsilon(sub l)/upsilon(sub 3)/2upsilon(sub 2) interacting vibrational states), and the "second triad" (the upsilon(sub 1) + upsilon(sub 2/upsilon(sub 2) + upsilon(sub 3)/3upsilon(sub 2) states) of H2Te-130. We find that the cluster formation in H2Te is very similar to those of of H2Se and H2S, which we have studied previously. However, contrary to semiclassical predictions, we do not determine any significant displacement of the clusters towards lower J values relative to H2Se. Hence the experimental observation of the cluster states in H2Te will be at least as difficult as in H2Se.
New method for evaluation of finite-energy few-electron spectral function expressions
NASA Astrophysics Data System (ADS)
Carmelo, J. M. P.; Penc, K.; Sacramento, P. D.; Claessen, R.
2004-04-01
We present a method for the calculation of few-electron spectral functions of the one-dimen- sional Hubbard model which relies on a pseudofermion description introduced recently in Ref. [6]. The spectral functions are expressed as a convolution of pseudofermion dynamical correlation functions. Our general method involves the direct evaluation of the matrix elements of pseudofermion operators between the ground state and the excited states. We briefly discuss the application of our general method to the study of the unusual finite-energy spectral properties observed in the quasi-one-dimensional organic conductor TTF-TCNQ. Key words. correlation effects spectral properties organic conductors
Schmidt, Markus H
2014-11-01
The energy allocation (EA) model defines behavioral strategies that optimize the temporal utilization of energy to maximize reproductive success. This model proposes that all species of the animal kingdom share a universal sleep function that shunts waking energy utilization toward sleep-dependent biological investment. For endotherms, REM sleep evolved to enhance energy appropriation for somatic and CNS-related processes by eliminating thermoregulatory defenses and skeletal muscle tone. Alternating REM with NREM sleep conserves energy by decreasing the need for core body temperature defense. Three EA phenotypes are proposed: sleep-wake cycling, torpor, and continuous (or predominant) wakefulness. Each phenotype carries inherent costs and benefits. Sleep-wake cycling downregulates specific biological processes in waking and upregulates them in sleep, thereby decreasing energy demands imposed by wakefulness, reducing cellular infrastructure requirements, and resulting in overall energy conservation. Torpor achieves the greatest energy savings, but critical biological operations are compromised. Continuous wakefulness maximizes niche exploitation, but endures the greatest energy demands. The EA model advances a new construct for understanding sleep-wake organization in ontogenetic and phylogenetic domains. PMID:25117535
Ion energy distribution functions of low energy beams formed by wire extraction electrodes
Tokumura, S.; Kasuya, T.; Vasquez, M. Jr.; Maeno, S.; Wada, M.
2012-02-15
The two-electrode extractor system made of 0.1 mm diameter tungsten wires separated by 0.7 mm has formed an argon ion beam with 50 V extraction potential. Energy spreads of the extracted beams were typically less than 2 eV when the beam current density was low. The beam intensity rapidly decreased as the distance between the extractor and the beam detector increased, indicating space charge limited transport of the beam. Problems associated with the emittance measurements are also discussed.
Ab initio design of low work function complex oxides for thermionic energy conversion
NASA Astrophysics Data System (ADS)
Mack, Stephanie; Li, Guo; Neaton, Jeffrey
Understanding and controlling work functions, or band edge energies, is of interest for a variety of applications in optoelectronics and energy conversion. In particular, while recent advances in device design have improved the feasibility of thermionic generators, new low work function materials are needed to enable their widespread use. Perovskite-based oxides (ABO3) are a diverse class of materials that, depending on the transition metal atoms on the A and B sites, can give rise to myriad emergent and collective phenomena. Here, we use density functional theory calculations to examine how the work function of one such oxide, SrRuO3 (SRO), can be tuned by monolayers of SrTiO3 (STO) and other polar or near-polar oxides. We find that SRO work functions can be tuned by over 1 eV with one layer of STO, although the calculated reduction in work function is an order of magnitude less than would be expected from the bulk polarization. We understand the variation in work function via a detailed analysis of Born effective charges at the surface, which are as small as 10% of their bulk values, and charge rearrangement at the STO surface and SRO/STO interface.
NASA Astrophysics Data System (ADS)
Chamel, N.; Fantina, A. F.; Pearson, J. M.; Goriely, S.
2016-01-01
We study the constraints imposed by nuclear mass measurements and neutron-star observations on the symmetry energy. For this purpose, we use a family of unified equations of state of neutron-star interiors, based on generalised Skyrme functionals that were fitted to essentially all the experimental nuclear mass data while ensuring a realistic neutron-matter equation of state.
NASA Astrophysics Data System (ADS)
Liu, Siyu; Zhao, Ning; Cheng, Zhen; Liu, Hongguang
2015-04-01
Amino-functionalized fluorescent carbon dots have been prepared by hydrothermal treatment of glucosamine with excess pyrophosphate. The produced carbon dots showed stabilized green emission fluorescence at various excitation wavelengths and pH environments. Herein, we demonstrate the surface energy transfer between the amino-functionalized carbon dots and negatively charged hyaluronate stabilized gold nanoparticles. Hyaluronidase can degrade hyaluronate and break down the hyaluronate stabilized gold nanoparticles to inhibit the surface energy transfer. The developed fluorescent carbon dot/gold nanoparticle system can be utilized as a biosensor for sensitive and selective detection of hyaluronidase by two modes which include fluorescence measurements and colorimetric analysis.Amino-functionalized fluorescent carbon dots have been prepared by hydrothermal treatment of glucosamine with excess pyrophosphate. The produced carbon dots showed stabilized green emission fluorescence at various excitation wavelengths and pH environments. Herein, we demonstrate the surface energy transfer between the amino-functionalized carbon dots and negatively charged hyaluronate stabilized gold nanoparticles. Hyaluronidase can degrade hyaluronate and break down the hyaluronate stabilized gold nanoparticles to inhibit the surface energy transfer. The developed fluorescent carbon dot/gold nanoparticle system can be utilized as a biosensor for sensitive and selective detection of hyaluronidase by two modes which include fluorescence measurements and colorimetric analysis. Electronic supplementary information (ESI) available. See DOI: 10.1039/c5nr00070j
Farrel, Alvin; Murphy, Jonathan; Guo, Jun-tao
2016-01-01
Transcription factors (TFs) regulate gene expression through binding to specific target DNA sites. Accurate annotation of transcription factor binding sites (TFBSs) at genome scale represents an essential step toward our understanding of gene regulation networks. In this article, we present a structure-based method for computational prediction of TFBSs using a novel, integrative energy (IE) function. The new energy function combines a multibody (MB) knowledge-based potential and two atomic energy terms (hydrogen bond and π interaction) that might not be accurately captured by the knowledge-based potential owing to the mean force nature and low count problem. We applied the new energy function to the TFBS prediction using a non-redundant dataset that consists of TFs from 12 different families. Our results show that the new IE function improves the prediction accuracy over the knowledge-based, statistical potentials, especially for homeodomain TFs, the second largest TF family in mammals. Contact: jguo4@uncc.edu Supplementary information: Supplementary data are available at Bioinformatics online. PMID:27307632
Low-energy enhancement in the γ -ray strength functions of Ge,7473
NASA Astrophysics Data System (ADS)
Renstrøm, T.; Nyhus, H.-T.; Utsunomiya, H.; Schwengner, R.; Goriely, S.; Larsen, A. C.; Filipescu, D. M.; Gheorghe, I.; Bernstein, L. A.; Bleuel, D. L.; Glodariu, T.; Görgen, A.; Guttormsen, M.; Hagen, T. W.; Kheswa, B. V.; Lui, Y.-W.; Negi, D.; Ruud, I. E.; Shima, T.; Siem, S.; Takahisa, K.; Tesileanu, O.; Tornyi, T. G.; Tveten, G. M.; Wiedeking, M.
2016-06-01
The γ -ray strength functions and level densities of Ge,7473 have been extracted up to the neutron-separation energy Sn from particle-γ coincidence data using the Oslo method. Moreover, the γ -ray strength function of 74Ge above Sn has been determined from photoneutron measurements; hence these two experiments cover the range of Eγ≈1 -13 MeV for 74Ge. The obtained data show that both Ge,7473 display an increase in strength at low γ energies. The experimental γ -ray strength functions are compared with M 1 strength functions deduced from average B (M 1 ) values calculated within the shell model for a large number of transitions. The observed low-energy enhancements in Ge,7473 are adopted in the calculations of the Ge,7372(n ,γ ) cross sections, where there are no direct experimental data. Calculated reaction rates for more neutron-rich germanium isotopes are shown to be strongly dependent on the presence of the low-energy enhancement.
NASA Astrophysics Data System (ADS)
Ahmad, Farooq; Malik, Manzoor A.; Mir, Hameeda
2014-02-01
We evaluate a distribution function for the system of galaxies clustering gravitationally in an expanding universe on the basis of statistical mechanics. We extend our previous work to incorporate the effect of any ratio of gravitational potential to kinetic energies. We determine the cosmological many-body partition function inclusive of higher order terms and calculate all thermodynamic quantities and the distribution function from it. We find that our new results are consistent with the previous ones, particularly in the large bar{N} (average number of galaxies) limit. We also investigate the effect on clustering parameter b and find our new results in very good agreement with the previous ones in the small b limit. We find that for large b, the departure from the original distribution function is greater. We also observe that the effect of softening on the distribution function is consistent with our previous work.
Measurement of the electron structure function F2e at LEP energies
NASA Astrophysics Data System (ADS)
Abdallah, J.; Abreu, P.; Adam, W.; Adzic, P.; Albrecht, T.; Alemany-Fernandez, R.; Allmendinger, T.; Allport, P. P.; Amaldi, U.; Amapane, N.; Amato, S.; Anashkin, E.; Andreazza, A.; Andringa, S.; Anjos, N.; Antilogus, P.; Apel, W.-D.; Arnoud, Y.; Ask, S.; Asman, B.; Augustin, J. E.; Augustinus, A.; Baillon, P.; Ballestrero, A.; Bambade, P.; Barbier, R.; Bardin, D.; Barker, G. J.; Baroncelli, A.; Battaglia, M.; Baubillier, M.; Becks, K.-H.; Begalli, M.; Behrmann, A.; Belous, K.; Ben-Haim, E.; Benekos, N.; Benvenuti, A.; Berat, C.; Berggren, M.; Bertrand, D.; Besancon, M.; Besson, N.; Bloch, D.; Blom, M.; Bluj, M.; Bonesini, M.; Boonekamp, M.; Booth, P. S. L.; Borisov, G.; Botner, O.; Bouquet, B.; Bowcock, T. J. V.; Boyko, I.; Bracko, M.; Brenner, R.; Brodet, E.; Bruckman, P.; Brunet, J. M.; Buschbeck, B.; Buschmann, P.; Calvi, M.; Camporesi, T.; Canale, V.; Carena, F.; Castro, N.; Cavallo, F.; Chapkin, M.; Charpentier, Ph.; Checchia, P.; Chierici, R.; Chliapnikov, P.; Chudoba, J.; Chung, S. U.; Cieslik, K.; Collins, P.; Contri, R.; Cosme, G.; Cossutti, F.; Costa, M. J.; Crennell, D.; Cuevas, J.; D'Hondt, J.; da Silva, T.; Da Silva, W.; Della Ricca, G.; De Angelis, A.; De Boer, W.; De Clercq, C.; De Lotto, B.; De Maria, N.; De Min, A.; de Paula, L.; Di Ciaccio, L.; Di Simone, A.; Doroba, K.; Drees, J.; Eigen, G.; Ekelof, T.; Ellert, M.; Elsing, M.; Espirito Santo, M. C.; Fanourakis, G.; Fassouliotis, D.; Feindt, M.; Fernandez, J.; Ferrer, A.; Ferro, F.; Flagmeyer, U.; Foeth, H.; Fokitis, E.; Fulda-Quenzer, F.; Fuster, J.; Gandelman, M.; Garcia, C.; Gavillet, Ph.; Gazis, E.; Gokieli, R.; Golob, B.; Gomez-Ceballos, G.; Gonçalves, P.; Graziani, E.; Grosdidier, G.; Grzelak, K.; Guy, J.; Haag, C.; Hallgren, A.; Hamacher, K.; Hamilton, K.; Haug, S.; Hauler, F.; Hedberg, V.; Hennecke, M.; Hoffman, J.; Holmgren, S.-O.; Holt, P. J.; Houlden, M. A.; Jackson, J. N.; Jarlskog, G.; Jarry, P.; Jeans, D.; Johansson, E. K.; Jonsson, P.; Joram, C.; Jungermann, L.; Kapusta, F.; Katsanevas, S.; Katsoufis, E.; Kernel, G.; Kersevan, B. P.; Kerzel, U.; King, B. T.; Kjaer, N. J.; Kluit, P.; Kokkinias, P.; Kourkoumelis, C.; Kouznetsov, O.; Krumstein, Z.; Kucharczyk, M.; Lamsa, J.; Leder, G.; Ledroit, F.; Leinonen, L.; Leitner, R.; Lemonne, J.; Lepeltier, V.; Lesiak, T.; Liebig, W.; Liko, D.; Lipniacka, A.; Lopes, J. H.; Lopez, J. M.; Loukas, D.; Lutz, P.; Lyons, L.; MacNaughton, J.; Malek, A.; Maltezos, S.; Mandl, F.; Marco, J.; Marco, R.; Marechal, B.; Margoni, M.; Marin, J.-C.; Mariotti, C.; Markou, A.; Martinez-Rivero, C.; Masik, J.; Mastroyiannopoulos, N.; Matorras, F.; Matteuzzi, C.; Mazzucato, F.; Mazzucato, M.; Mc Nulty, R.; Meroni, C.; Migliore, E.; Mitaroff, W.; Mjoernmark, U.; Moa, T.; Moch, M.; Moenig, K.; Monge, R.; Montenegro, J.; Moraes, D.; Moreno, S.; Morettini, P.; Mueller, U.; Muenich, K.; Mulders, M.; Mundim, L.; Murray, W.; Muryn, B.; Myatt, G.; Myklebust, T.; Nassiakou, M.; Navarria, F.; Nawrocki, K.; Nemecek, S.; Nicolaidou, R.; Nikolenko, M.; Oblakowska-Mucha, A.; Obraztsov, V.; Olshevski, A.; Onofre, A.; Orava, R.; Osterberg, K.; Ouraou, A.; Oyanguren, A.; Paganoni, M.; Paiano, S.; Palacios, J. P.; Palka, H.; Papadopoulou, Th. D.; Pape, L.; Parkes, C.; Parodi, F.; Parzefall, U.; Passeri, A.; Passon, O.; Peralta, L.; Perepelitsa, V.; Perrotta, A.; Petrolini, A.; Piedra, J.; Pieri, L.; Pierre, F.; Pimenta, M.; Piotto, E.; Podobnik, T.; Poireau, V.; Pol, M. E.; Polok, G.; Pozdniakov, V.; Pukhaeva, N.; Pullia, A.; Radojicic, D.; Rebecchi, P.; Rehn, J.; Reid, D.; Reinhardt, R.; Renton, P.; Richard, F.; Ridky, J.; Rivero, M.; Rodriguez, D.; Romero, A.; Ronchese, P.; Roudeau, P.; Rovelli, T.; Ruhlmann-Kleider, V.; Ryabtchikov, D.; Sadovsky, A.; Salmi, L.; Salt, J.; Sander, C.; Savoy-Navarro, A.; Schwickerath, U.; Sekulin, R.; Siebel, M.; Sisakian, A.; Slominski, W.; Smadja, G.; Smirnova, O.; Sokolov, A.; Sopczak, A.; Sosnowski, R.; Spassov, T.; Stanitzki, M.; Stocchi, A.; Strauss, J.; Stugu, B.; Szczekowski, M.; Szeptycka, M.; Szumlak, T.; Szwed, J.; Tabarelli, T.; Tegenfeldt, F.; Timmermans, J.; Tkatchev, L.; Tobin, M.; Todorovova, S.; Tomé, B.; Tonazzo, A.; Tortosa, P.; Travnicek, P.; Treille, D.; Tristram, G.; Trochimczuk, M.; Troncon, C.; Turluer, M.-L.; Tyapkin, I. A.; Tyapkin, P.; Tzamarias, S.; Uvarov, V.; Valenti, G.; Van Dam, P.; Van Eldik, J.; van Remortel, N.; Van Vulpen, I.; Vegni, G.; Veloso, F.; Venus, W.; Verdier, P.; Verzi, V.; Vilanova, D.; Vitale, L.; Vrba, V.; Wahlen, H.; Washbrook, A. J.; Weiser, C.; Wicke, D.; Wickens, J.; Wilkinson, G.; Winter, M.; Witek, M.; Yushchenko, O.; Zalewska, A.; Zalewski, P.; Zavrtanik, D.; Zhuravlov, V.; Zimin, N. I.; Zintchenko, A.; Zupan, M.
2014-10-01
The hadronic part of the electron structure function F2e has been measured for the first time, using e+e- data collected by the DELPHI experiment at LEP, at centre-of-mass energies of √{ s} = 91.2- 209.5 GeV. The data analysis is simpler than that of the measurement of the photon structure function. The electron structure function F2e data are compared to predictions of phenomenological models based on the photon structure function. It is shown that the contribution of large target photon virtualities is significant. The data presented can serve as a cross-check of the photon structure function F2γ analyses and help in refining existing parameterisations.
NASA Astrophysics Data System (ADS)
Balabin, Roman M.; Lomakina, Ekaterina I.
2009-08-01
Artificial neural network (ANN) approach has been applied to estimate the density functional theory (DFT) energy with large basis set using lower-level energy values and molecular descriptors. A total of 208 different molecules were used for the ANN training, cross validation, and testing by applying BLYP, B3LYP, and BMK density functionals. Hartree-Fock results were reported for comparison. Furthermore, constitutional molecular descriptor (CD) and quantum-chemical molecular descriptor (QD) were used for building the calibration model. The neural network structure optimization, leading to four to five hidden neurons, was also carried out. The usage of several low-level energy values was found to greatly reduce the prediction error. An expected error, mean absolute deviation, for ANN approximation to DFT energies was 0.6±0.2 kcal mol-1. In addition, the comparison of the different density functionals with the basis sets and the comparison of multiple linear regression results were also provided. The CDs were found to overcome limitation of the QD. Furthermore, the effective ANN model for DFT/6-311G(3df,3pd) and DFT/6-311G(2df,2pd) energy estimation was developed, and the benchmark results were provided.
Energy-efficient specialization of functional units in a Coarse-Grained Reconfigurable Array
Van Essen, B; Panda, R; Wood, A; Ebeling, C; Hauck, S
2010-12-01
Functional units provide the backbone of any spatial accelerator by providing the computing resources. The desire for having rich and expensive functional units is in tension with producing a regular and energy-efficient computing fabric. This paper explores the design trade-off between complex, universal functional units and simpler, limited functional units. We show that a modest amount of specialization reduces the area-delay-energy product of an optimized architecture to 0.86x a baseline architecture. Furthermore, we provide a design guideline that allows an architect to customize the contents of the computing fabric just by examining the profile of benchmarks within the application domains. Functional units are the core of compute-intensive spatial accelerators. They perform the computation of interest with support from local storage and communication structures. Ideally, the functional units will provide rich functionality, supporting operations ranging from simple addition, to fused multiply-adds, to advanced transcendental functions and domain specific operations like add-compare-select. However, the total opportunity cost to support the more complex operations is a function of the cost of the hardware, the rate of occurrence of the operation in the application domain, and the inefficiency of emulating the operation with simpler operators. Examples of operations that are typically emulated in spatial accelerators are division and trigonometric functions, which can be solved using table-lookup based algorithms and the CORDIC algorithm. One reason to avoid having direct hardware support for complex operations in a tiled architecture like a Coarse-Grained Reconfigurable Array (CGRA) is that the expensive hardware will typically need to be replicated in some or all of the architecture's tiles. Tiled architecture are designed such that their tiles are either homogeneous or heterogeneous. Homogeneous architectures are simpler to design but heterogeneous
NASA Astrophysics Data System (ADS)
Parashar, Prachi; Milton, Kimball A.; Shajesh, K. V.; Schaden, M.
2012-10-01
We derive boundary conditions for electromagnetic fields on a δ-function plate. The optical properties of such a plate are shown to necessarily be anisotropic in that they only depend on the transverse properties of the plate. We unambiguously obtain the boundary conditions for a perfectly conducting δ-function plate in the limit of infinite dielectric response. We show that a material does not “optically vanish” in the thin-plate limit. The thin-plate limit of a plasma slab of thickness d with plasma frequency ωp2=ζp/d reduces to a δ-function plate for frequencies (ω=iζ) satisfying ζd≪ζpd≪1. We show that the Casimir interaction energy between two parallel perfectly conducting δ-function plates is the same as that for parallel perfectly conducting slabs. Similarly, we show that the interaction energy between an atom and a perfect electrically conducting δ-function plate is the usual Casimir-Polder energy, which is verified by considering the thin-plate limit of dielectric slabs. The “thick” and “thin” boundary conditions considered by Bordag are found to be identical in the sense that they lead to the same electromagnetic fields.
Moustakidis, Ch. C.; Lalazissis, G. A.; Niksic, T.; Vretenar, D.; Ring, P.
2010-06-15
The transition density n{sub t} and pressure P{sub t} at the inner edge between the liquid core and the solid crust of a neutron star are analyzed using the thermodynamical method and the framework of relativistic nuclear energy density functionals. Starting from a functional that has been carefully adjusted to experimental binding energies of finite nuclei, and varying the density dependence of the corresponding symmetry energy within the limits determined by isovector properties of finite nuclei, we estimate the constraints on the core-crust transition density and pressure of neutron stars: 0.086 fm{sup -3}<=n{sub t}<0.090 fm{sup -3} and 0.3 MeV fm{sup -3}
Level densities of iron isotopes and lower-energy enhancement of y-strength function
Voinov, A V; Grimes, S M; Agvaanluvsan, U; Algin, E; Belgya, T; Brune, C R; Guttormsen, M; Hornish, M J; Massey, T N; Mitchell, G; Rekstad, J; Schiller, A; Siem, S
2005-08-30
The neutron spectrum from the {sup 55}Mn(d,n){sup 56}Fe reaction has been measured at E{sub d} = 7 MeV. The level density of {sup 56}Fe obtained from neutron evaporation spectrum has been compared to the level density from Oslo-type {sup 57}Fe({sup 3}He, a{gamma}){sup 56}Fe experiment [1]. The good agreement supports the recent results [1, 8] including an availability of a low-energy enhancement in the {gamma}-strength function for iron isotopes. The new level density function allowed us to investigate an excitation energy dependence of this enhancement, which is shown to increase with increasing excitation energy.
Variational calculations with explicit energy functionals for fermion systems at zero temperature
NASA Astrophysics Data System (ADS)
Takano, M.; Suzuki, T.; Sakumichi, N.
2016-03-01
The variational method with explicit energy functionals (EEFs) is applied to infinite neutron matter. Starting from the Argonne v8’ two-body potential and the repulsive part of the Urbana IX three-body potential, the energy per neutron is expressed explicitly with the spin-dependent central, tensor, and spin-orbit distribution functions. This EEF is constructed as an extension of the previously proposed one for the Argonne v6’ potential, including central and tensor forces. The Euler-Lagrange equations derived from this EEF are solved numerically. The obtained fully minimized energy with this EEF is in good agreement with that obtained from the auxiliary field diffusion Monte Carlo calculation.
NASA Astrophysics Data System (ADS)
Lim, Youbong; Kim, Holak; Park, Jaesun; Seon, Jongho; Choe, Wonho
2014-10-01
Ion energy distribution functions (IEDFs) of individual ion species having different charge states (i.e. Xe+, Xe2+, Xe3+, etc.) in the Hall thruster plasma are obtained from the measured E × B probe spectrum by a novel inversion technique using the iterative Tikhonov regularization method. The obtained IEDFs show the existence of a high-energy tail in the cylindrical Hall thruster plasmas that is mainly due to Xe+ ions despite the presence of Xe2+ and Xe3+ ions with a large fraction. Ion dynamics inside the plasma was numerically investigated to demonstrate that the high-energy tail is due to nonlinear ion acceleration in the plasma oscillating at typically 100 to 500 kHz. We found that this oscillation driven by transit-time instability is responsible for the shift of the IEDF of the Xe+ ions toward the high-energy side, showing the formation of high-energy tail in the overall IEDF. It was also found that the Xe flow rate raised from 4 to 10 sccm increases the oscillation strength at the same frequency of 360 kHz, which can be applied to control of the shape of the IEDF.
Effects of high-energy ultrasound on the functional properties of proteins.
Higuera-Barraza, O A; Del Toro-Sanchez, C L; Ruiz-Cruz, S; Márquez-Ríos, E
2016-07-01
In recent years, high-energy ultrasound has been used as an alternative to improve the functional properties of various proteins, such as from milk, eggs, soy and poultry. The benefits of implementing this technology depend on the inherent characteristics of the protein source and the intensity and amplitude of the ultrasound, as well as on the pH, temperature, ionic strength, time, and all of the variables that have an effect on the physicochemical properties of proteins. Therefore, it is necessary to establish the optimal conditions for each type of food. The use of ultrasound is a promising technique in food technology with a low impact on the environment, and it has thus become known as a green technology. Therefore, this review focuses on the application of high-energy ultrasound to food; its effects on the functional properties of proteins; and how different conditions such as the frequency, time, amplitude, temperature, and protein concentration affect the functional properties. PMID:26964983
Chakraborty, Arindam; Truhlar, Donald G; Bowman, Joel M; Carter, Stuart
2004-08-01
The rovibration partition function of CH4 was calculated in the temperature range of 100-1000 K using well-converged energy levels that were calculated by vibrational-rotational configuration interaction using the Watson Hamiltonian for total angular momenta J = 0-50 and the MULTIMODE computer program. The configuration state functions are products of ground-state occupied and virtual modals obtained using the vibrational self-consistent field method. The Gilbert and Jordan potential energy surface was used for the calculations. The resulting partition function was used to test the harmonic oscillator approximation and the separable-rotation approximation. The harmonic oscillator, rigid-rotator approximation is in error by a factor of 2.3 at 300 K, but we also propose a separable-rotation approximation that is accurate within 2% from 100 to 1000 K. PMID:15260761
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
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
Complex-energy approach to sum rules within nuclear density functional theory
Hinohara, Nobuo; Kortelainen, Markus; Nazarewicz, Witold; Olsen, Erik
2015-04-27
The linear response of the nucleus to an external field contains unique information about the effective interaction, correlations governing the behavior of the many-body system, and properties of its excited states. To characterize the response, it is useful to use its energy-weighted moments, or sum rules. By comparing computed sum rules with experimental values, the information content of the response can be utilized in the optimization process of the nuclear Hamiltonian or nuclear energy density functional (EDF). But the additional information comes at a price: compared to the ground state, computation of excited states is more demanding. To establish anmore » efficient framework to compute energy-weighted sum rules of the response that is adaptable to the optimization of the nuclear EDF and large-scale surveys of collective strength, we have developed a new technique within the complex-energy finite-amplitude method (FAM) based on the quasiparticle random- phase approximation. The proposed sum-rule technique based on the complex-energy FAM is a tool of choice when optimizing effective interactions or energy functionals. The method is very efficient and well-adaptable to parallel computing. As a result, the FAM formulation is especially useful when standard theorems based on commutation relations involving the nuclear Hamiltonian and external field cannot be used.« less
Time evolution of the electron energy distribution function in pulsed microwave magnetoplasma in H2
NASA Astrophysics Data System (ADS)
Jauberteau, J. L.; Jauberteau, I.; Cortázar, O. D.; Megía-Macías, A.
2016-03-01
Time evolution of the Electron Energy Distribution Function (EEDF) is measured in pulsed hydrogen microwave magnetoplasma working at 2.45 GHz. Analysis is performed both in resonance (B = 0.087 T) and off-resonance conditions (B = 0.120 T), at two pressures (0.38 Pa and 0.62 Pa), respectively, and for different incident microwave powers. The important effect of the magnetic field on the electron kinetic is discussed, and a critical analysis of Langmuir probe measurements is given. The Electron Energy Distribution Function is calculated using the Druyvesteyn theory (EEDF) and is corrected using the theory developed by Arslanbekov in the case of magnetized plasma. Three different components are observed in the EEDF, whatever the theory used. They are: (a) a low electron energy component at energy lower than 10 eV, which is ascribed to the electron having inelastic collisions with heavy species (H2, H, ions), (b) a high energy component with a mean energy ranging from 10 to 20 eV, which is generally ascribed to the heating of the plasma by the incident microwave power, and (c) a third component observed between the two other ones, mainly at low pressure and in resonance conditions, has been correlated to the electron rotation in the magnetic field.
Complex-energy approach to sum rules within nuclear density functional theory
Hinohara, Nobuo; Kortelainen, Markus; Nazarewicz, Witold; Olsen, Erik
2015-04-27
The linear response of the nucleus to an external field contains unique information about the effective interaction, correlations governing the behavior of the many-body system, and properties of its excited states. To characterize the response, it is useful to use its energy-weighted moments, or sum rules. By comparing computed sum rules with experimental values, the information content of the response can be utilized in the optimization process of the nuclear Hamiltonian or nuclear energy density functional (EDF). But the additional information comes at a price: compared to the ground state, computation of excited states is more demanding. To establish an efficient framework to compute energy-weighted sum rules of the response that is adaptable to the optimization of the nuclear EDF and large-scale surveys of collective strength, we have developed a new technique within the complex-energy finite-amplitude method (FAM) based on the quasiparticle random- phase approximation. The proposed sum-rule technique based on the complex-energy FAM is a tool of choice when optimizing effective interactions or energy functionals. The method is very efficient and well-adaptable to parallel computing. As a result, the FAM formulation is especially useful when standard theorems based on commutation relations involving the nuclear Hamiltonian and external field cannot be used.
Development of an Enhanced Payback Function for the Superior Energy Performance Program
Therkelsen, Peter; Rao, Prakash; McKane, Aimee; Sabouni, Ridah; Sheihing, Paul
2015-08-03
The U.S. DOE Superior Energy Performance (SEP) program provides recognition to industrial and commercial facilities that achieve certification to the ISO 50001 energy management system standard and third party verification of energy performance improvements. Over 50 industrial facilities are participating and 28 facilities have been certified in the SEP program. These facilities find value in the robust, data driven energy performance improvement result that the SEP program delivers. Previous analysis of SEP certified facility data demonstrated the cost effectiveness of SEP and identified internal staff time to be the largest cost component related to SEP implementation and certification. This paper analyzes previously reported and newly collected data of costs and benefits associated with the implementation of an ISO 50001 and SEP certification. By disaggregating “sunk energy management system (EnMS) labor costs”, this analysis results in a more accurate and detailed understanding of the costs and benefits of SEP participation. SEP is shown to significantly improve and sustain energy performance and energy cost savings, resulting in a highly attractive return on investment. To illustrate these results, a payback function has been developed and is presented. On average facilities with annual energy spend greater than $2M can expect to implement SEP with a payback of less than 1.5 years. Finally, this paper also observes and details decreasing facility costs associated with implementing ISO 50001 and certifying to the SEP program, as the program has improved from pilot, to demonstration, to full launch.
Molecular density functional theory for water with liquid-gas coexistence and correct pressure
Jeanmairet, Guillaume Levesque, Maximilien; Sergiievskyi, Volodymyr; Borgis, Daniel
2015-04-21
The solvation of hydrophobic solutes in water is special because liquid and gas are almost at coexistence. In the common hypernetted chain approximation to integral equations, or equivalently in the homogenous reference fluid of molecular density functional theory, coexistence is not taken into account. Hydration structures and energies of nanometer-scale hydrophobic solutes are thus incorrect. In this article, we propose a bridge functional that corrects this thermodynamic inconsistency by introducing a metastable gas phase for the homogeneous solvent. We show how this can be done by a third order expansion of the functional around the bulk liquid density that imposes the right pressure and the correct second order derivatives. Although this theory is not limited to water, we apply it to study hydrophobic solvation in water at room temperature and pressure and compare the results to all-atom simulations. The solvation free energy of small molecular solutes like n-alkanes and hard sphere solutes whose radii range from angstroms to nanometers is now in quantitative agreement with reference all atom simulations. The macroscopic liquid-gas surface tension predicted by the theory is comparable to experiments. This theory gives an alternative to the empirical hard sphere bridge correction used so far by several authors.
Verma, Anurag; Ford, David M
2011-05-01
The free-energy difference between coexisting solid and liquid phases is studied in the context of classical density functional theory (DFT). A bridge function is used to represent the higher-order (n>2) terms in the perturbative expansion of the excess Helmholtz free energy, and the values of this bridge function within the solid lattice are determined by inversion using literature Monte Carlo simulation results. Four potential models, specifically hard-sphere and inverse twelfth-, sixth-, and fourth-power repulsive, are studied. The face-centered cubic (fcc) solid is considered for the hard-sphere and inverse twelfth- and sixth-power potentials, while the body-centered cubic (bcc) solid is considered for the inverse sixth- and fourth-power potentials. For a given solid structure there is a remarkable similarity among the bridge functions for different potentials that is analogous to the universality in the sum of elementary diagrams, or bridge functions, of liquid-state theory as originally observed by Rosenfeld and Ashcroft [Phys. Rev. A 20, 1208 (1979)]. In further analogy with liquid-state theory, the bridge functions in the present problem are plotted as functionals of the second-order convolution term in the perturbative expansion. In each case, the plot indicates a unique functionality in the dense regions of the solid near the lattice sites but a scattered and nonunique behavior in the void regions. Interestingly, knowledge of the functional relationship in the unique region near the lattice sites seems to be sufficient to quantitatively model the solid-fluid phase transition. These qualitative observations are true for both fcc and bcc solid phases, although there are some quantitative differences between them. The findings suggest that pursuit of a closure-based DFT of solid-fluid transitions may be profitable. PMID:21728493
Rabanal-León, Walter A; Murillo-López, Juliana A; Páez-Hernández, Dayán; Arratia-Pérez, Ramiro
2015-09-24
The high interest in lanthanide chemistry, and particularly in their luminescence, has been encouraged by the need of understanding the lanthanide chemical coordination and how the design of new luminescent materials can be affected by this. This work is focused on the understanding of the electronic structure, bonding nature, and optical properties of a set of lanthanide hexaaza macrocyclic complexes, which can lead to potential optical applications. Here we found that the DFT ground state of the open-shell complexes are mainly characterized by the manifold of low lying f states, having small HOMO-LUMO energy gaps. The results obtained from the wave function theory calculations (SO-RASSI) put on evidence the multiconfigurational character of their ground state and it is observed that the large spin-orbit coupling and the weak crystal field produce a strong mix of the ground and the excited states. The electron localization function (ELF) and the energy decomposition analysis (EDA) support the idea of a dative interaction between the macrocyclic ligand and the lanthanide center for all the studied systems; noting that, this interaction has a covalent character, where the d-orbital participation is evidenced from NBO analysis, leaving the f shell completely noninteracting in the chemical bonding. From the optical part we observed in all cases the characteristic intraligand (IL) (π-π*) and ligand to metal charge-transfer (LMCT) bands that are present in the ultraviolet and visible regions, and for the open-shell complexes we found the inherent f-f electronic transitions on the visible and near-infrared region. PMID:26325624
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.
Tung, Wei-Cheng; Adamowicz, Ludwik
2014-03-28
Very accurate calculations of the ground-state potential energy curve (PEC) of the LiH(+) ion performed with all-electron explicitly correlated Gaussian functions with shifted centers are presented. The variational method is employed. The calculations involve optimization of nonlinear exponential parameters of the Gaussians performed with the aid of the analytical first derivatives of the energy determined with respect to the parameters. The diagonal adiabatic correction is also calculated for each PEC point. The PEC is then used to calculate the vibrational energies of the system. In that calculation, the non-adiabatic effects are accounted for by using an effective vibrational mass obtained by the minimization of the difference between the vibrational energies obtained from the calculations where the Born-Oppenheimer approximation was not assumed and the results of the present calculations. PMID:24697449
NASA Astrophysics Data System (ADS)
Tung, Wei-Cheng; Adamowicz, Ludwik
2014-03-01
Very accurate calculations of the ground-state potential energy curve (PEC) of the LiH+ ion performed with all-electron explicitly correlated Gaussian functions with shifted centers are presented. The variational method is employed. The calculations involve optimization of nonlinear exponential parameters of the Gaussians performed with the aid of the analytical first derivatives of the energy determined with respect to the parameters. The diagonal adiabatic correction is also calculated for each PEC point. The PEC is then used to calculate the vibrational energies of the system. In that calculation, the non-adiabatic effects are accounted for by using an effective vibrational mass obtained by the minimization of the difference between the vibrational energies obtained from the calculations where the Born-Oppenheimer approximation was not assumed and the results of the present calculations.
Modeling Molecular Interactions in Water: From Pairwise to Many-Body Potential Energy Functions.
Cisneros, Gerardo Andrés; Wikfeldt, Kjartan Thor; Ojamäe, Lars; Lu, Jibao; Xu, Yao; Torabifard, Hedieh; Bartók, Albert P; Csányi, Gábor; Molinero, Valeria; Paesani, Francesco
2016-07-13
Almost 50 years have passed from the first computer simulations of water, and a large number of molecular models have been proposed since then to elucidate the unique behavior of water across different phases. In this article, we review the recent progress in the development of analytical potential energy functions that aim at correctly representing many-body effects. Starting from the many-body expansion of the interaction energy, specific focus is on different classes of potential energy functions built upon a hierarchy of approximations and on their ability to accurately reproduce reference data obtained from state-of-the-art electronic structure calculations and experimental measurements. We show that most recent potential energy functions, which include explicit short-range representations of two-body and three-body effects along with a physically correct description of many-body effects at all distances, predict the properties of water from the gas to the condensed phase with unprecedented accuracy, thus opening the door to the long-sought "universal model" capable of describing the behavior of water under different conditions and in different environments. PMID:27186804
Observations of the directional distribution of the wind energy input function over swell waves
NASA Astrophysics Data System (ADS)
Shabani, Behnam; Babanin, Alex V.; Baldock, Tom E.
2016-02-01
Field measurements of wind stress over shallow water swell traveling in different directions relative to the wind are presented. The directional distribution of the measured stresses is used to confirm the previously proposed but unverified directional distribution of the wind energy input function. The observed wind energy input function is found to follow a much narrower distribution (β∝cos3.6θ) than the Plant (1982) cosine distribution. The observation of negative stress angles at large wind-wave angles, however, indicates that the onset of negative wind shearing occurs at about θ≈ 50°, and supports the use of the Snyder et al. (1981) directional distribution. Taking into account the reverse momentum transfer from swell to the wind, Snyder's proposed parameterization is found to perform exceptionally well in explaining the observed narrow directional distribution of the wind energy input function, and predicting the wind drag coefficients. The empirical coefficient (ɛ) in Snyder's parameterization is hypothesised to be a function of the wave shape parameter, with ɛ value increasing as the wave shape changes between sinusoidal, sawtooth, and sharp-crested shoaling waves.
An Energy-Based Limit State Function for Estimation of Structural Reliability in Shock Environments
Guthrie, Michael A.
2013-01-01
limit state function is developed for the estimation of structural reliability in shock environments. This limit state function uses peak modal strain energies to characterize environmental severity and modal strain energies at failure to characterize the structural capacity. The Hasofer-Lind reliability index is briefly reviewed and its computation for the energy-based limit state function is discussed. Applications to two degree of freedom mass-spring systems and to a simple finite element model are considered. For these examples, computation of the reliability index requires little effort beyond a modal analysis, but still accounts for relevant uncertainties in both the structure and environment.more » For both examples, the reliability index is observed to agree well with the results of Monte Carlo analysis. In situations where fast, qualitative comparison of several candidate designs is required, the reliability index based on the proposed limit state function provides an attractive metric which can be used to compare and control reliability.« less
Inferring modules of functionally interacting proteins using the Bond Energy Algorithm
Watanabe, Ryosuke LA; Morett, Enrique; Vallejo, Edgar E
2008-01-01
Background Non-homology based methods such as phylogenetic profiles are effective for predicting functional relationships between proteins with no considerable sequence or structure similarity. Those methods rely heavily on traditional similarity metrics defined on pairs of phylogenetic patterns. Proteins do not exclusively interact in pairs as the final biological function of a protein in the cellular context is often hold by a group of proteins. In order to accurately infer modules of functionally interacting proteins, the consideration of not only direct but also indirect relationships is required. In this paper, we used the Bond Energy Algorithm (BEA) to predict functionally related groups of proteins. With BEA we create clusters of phylogenetic profiles based on the associations of the surrounding elements of the analyzed data using a metric that considers linked relationships among elements in the data set. Results Using phylogenetic profiles obtained from the Cluster of Orthologous Groups of Proteins (COG) database, we conducted a series of clustering experiments using BEA to predict (upper level) relationships between profiles. We evaluated our results by comparing with COG's functional categories, And even more, with the experimentally determined functional relationships between proteins provided by the DIP and ECOCYC databases. Our results demonstrate that BEA is capable of predicting meaningful modules of functionally related proteins. BEA outperforms traditionally used clustering methods, such as k-means and hierarchical clustering by predicting functional relationships between proteins with higher accuracy. Conclusion This study shows that the linked relationships of phylogenetic profiles obtained by BEA is useful for detecting functional associations between profiles and extending functional modules not found by traditional methods. BEA is capable of detecting relationship among phylogenetic patterns by linking them through a common element shared in
NASA Astrophysics Data System (ADS)
Osamu Nishikawa; Haruhiko Koyama; Masahiko Tomitori
1991-04-01
The variation of work functions and electronic structures of Mo surfaces with Si coverages was studied using the atom-probe with a field emission electron spectrometer (AP/FEES). The field emission microscope images of a Si/Mo surface indicate that the deposited Si atoms form micro-clusters, the work function of which is found to be more than 10% larger than the Mo substrate. The FEES spectrum of the clusters implies that the Si/Mo surface is semiconductive even if the Si coverage is reduced to a fraction of a monolayer. The work functions of the Mo silicides formed by heating the Si/Mo tips are about 10% smaller than that of a clean Mo surface and the FEES analysis indicates that the silicide surface is metallic. At the Si-Mo and silicide-Mo interfaces, energy spectra, work functions and compositions vary abruptly in the range of one to a few atomic layers.
Terry, Rebecca C.; Rowe, Rebecca J.
2015-01-01
Research on the ecological impacts of environmental change has primarily focused at the species level, leaving the responses of ecosystem-level properties like energy flow poorly understood. This is especially so over millennial timescales inaccessible to direct observation. Here we examine how energy flow within a Great Basin small mammal community responded to climate-driven environmental change during the past 12,800 y, and use this baseline to evaluate responses observed during the past century. Our analyses reveal marked stability in energy flow during rapid climatic warming at the terminal Pleistocene despite dramatic turnover in the distribution of mammalian body sizes and habitat-associated functional groups. Functional group turnover was strongly correlated with climate-driven changes in regional vegetation, with climate and vegetation change preceding energetic shifts in the small mammal community. In contrast, the past century has witnessed a substantial reduction in energy flow caused by an increase in energetic dominance of small-bodied species with an affinity for closed grass habitats. This suggests that modern changes in land cover caused by anthropogenic activities—particularly the spread of nonnative annual grasslands—has led to a breakdown in the compensatory dynamics of energy flow. Human activities are thus modifying the small mammal community in ways that differ from climate-driven expectations, resulting in an energetically novel ecosystem. Our study illustrates the need to integrate across ecological and temporal scales to provide robust insights for long-term conservation and management. PMID:26170294
Hoque, Md Tamjidul; Yang, Yuedong; Mishra, Avdesh; Zhou, Yaoqi
2016-05-01
An important unsolved problem in molecular and structural biology is the protein folding and structure prediction problem. One major bottleneck for solving this is the lack of an accurate energy to discriminate near-native conformations against other possible conformations. Here we have developed sDFIRE energy function, which is an optimized linear combination of DFIRE (the Distance-scaled Finite Ideal gas Reference state based Energy), the orientation dependent (polar-polar and polar-nonpolar) statistical potentials, and the matching scores between predicted and model structural properties including predicted main-chain torsion angles and solvent accessible surface area. The weights for these scoring terms are optimized by three widely used decoy sets consisting of a total of 134 proteins. Independent tests on CASP8 and CASP9 decoy sets indicate that sDFIRE outperforms other state-of-the-art energy functions in selecting near native structures and in the Pearson's correlation coefficient between the energy score and structural accuracy of the model (measured by TM-score). © 2016 Wiley Periodicals, Inc. PMID:26849026
NASA Astrophysics Data System (ADS)
Trickey, S. B.; Karasiev, Valentin V.; Chakraborty, Debajit
2015-09-01
We suggest a more nuanced view of the merit and utility of generalized gradient approximations (GGAs) for the noninteracting kinetic energy (KE) than the critique of Xia and Carter (XC) [Phys. Rev. B 91, 045124 (2015), 10.1103/PhysRevB.91.045124]. Specifically, the multiple valuedness of the Pauli term enhancement factor (denoted G [n ] by XC) with respect to the inhomogeneity variable s can be excluded by enforcement of a bound on the Kohn-Sham KE to achieve universality of the functional along with enforcement of proper large-s behavior. This is physically sensible in that the excluded G values occur for s values that correspond to low densities. The behavior is exacerbated by peculiarities of pseudodensities. The VT84F KE GGA, constructed with these constraints, does not have the numerical instability in our older PBE2 functional analyzed by XC.
Functions of a new photoreceptor membrane. [energy conversion via halobacteria rhodopsin changes
NASA Technical Reports Server (NTRS)
Oesterhelt, D.; Stoeckenius, W.
1973-01-01
In the investigation of light responses on halobacteria phototaxis; ATP synthesis; and changes in O2 consumption, purple membrane biosynthesis, and proton translocation were found. The last three effects are discussed, which suggest that the purple membrane may function as an energy-coupling membrane for light. It is also suggested that purple membrane, through cyclic light-induced conformational changes of its bacteriorhodopsin, directly converts absorbed light energy into a proton gradient and presumably also an electric potential difference across the membrane analogous to observations in other prokaryotic cells, mitochondria, and chloroplasts.
Employing homogeneity properties of density functionals to determine the total electronic energy
NASA Astrophysics Data System (ADS)
Morrison, Robert C.; Parr, Robert G.
1996-05-01
The exchange-correlation energy is calculated from expressions for (Exc+Tc)/2 and (Exc-Tc)/2. The expression for Exc+Tc is known exactly. The expression for Exc-Tc is not known exactly and we approximate Gxc-Tc, where Gxc=Exc+J/N, by assuming that it is a functional that is homogeneous of degree 1 in the electron density and that Tc is homogeneous of degree 0 in the electron density. The resulting formula for the total energy reduces the average of the errors in the Parr and Ghosh
Interacting boson model from energy density functionals: {gamma}-softness and the related topics
Nomura, K.
2012-10-20
A comprehensive way of deriving the Hamiltonian of the interacting boson model (IBM) is described. Based on the fact that the multi-nucleon induced surface deformation in finite nucleus is simulated by effective boson degrees of freedom, the potential energy surface calculated with self-consistent mean-field method employing a given energy density functional (EDF) is mapped onto the IBM analog, and thereby the excitation spectra and transition rates with good symmetry quantum numbers are calculated. Recent applications of the proposed approach are reported: (i) an alternative robust interpretation of the {gamma}-soft nuclei and (ii) shape coexistence in lead isotopes.
Modern energy density functional and the current status of the equation of state of nuclear matter
Shlomo, S.
2012-11-20
We first describe a method, based on the simulated annealing approach, for determining a modern energy density functional within the Skyrme Hartree-Fock (HF) theory by carrying out a fit to extensive set of experimental data with additional constraints on the Skyrme parameters. Next, we review the HF-based random phase approximation (RPA) approach for calculating properties of giant resonances. We then present results of calculations for the centroid energies of giant resonances within the HF-based RPA and discuss the current status of the equation of state of nuclear matter.
Golisz, Suzanne R.; Gunnoe, T. Brent; Goddard, William A.; Groves, John T.; Periana, Roy A.
2010-12-02
Selective catalysts that activate small molecules such as hydrocarbons, dioxygen, water, carbon dioxide and dihydrogen are central to new technologies for the use of alternative energy sources. For example, controlled hydrocarbon functionalization can lead to high impact technologies, but such catalysts require a level of molecular control beyond current means. The Center for Catalytic Hydrocarbon Functionalization facilitates collaborations among research groups in catalysis, materials, electrochemistry, bioinorganic chemistry and quantum mechanics to develop, validate and optimize new methods to rearrange the bonds of hydrocarbons, activate and transform water and carbon dioxide, implement enzymatic strategies into synthetic systems and design optimal environments for catalysis.
Prociuk, Alexander; Van Kuiken, Ben; Dunietz, Barry D
2006-11-28
Electronic transmission through a metal-molecule-metal system is calculated by employing a Green's function formalism in the scattering based scheme. Self-energy models representing the bulk and the potential bias are used to describe electron transport through the molecular system. Different self-energies can be defined by varying the partition between device and bulk regions of the metal-molecule-metal model system. In addition, the self-energies are calculated with different representations of the bulk through its Green's function. In this work, the dependence of the calculated transmission on varying the self-energy subspaces is benchmarked. The calculated transmission is monitored with respect to the different choices defining the self-energy model. In this report, we focus on one-dimensional model systems with electronic structures calculated at the density functional level of theory. PMID:17144733
Experimental Energy Levels and Partition Function of the 12C2 Molecule
NASA Astrophysics Data System (ADS)
Furtenbacher, Tibor; Szabó, István; Császár, Attila G.; Bernath, Peter F.; Yurchenko, Sergei N.; Tennyson, Jonathan
2016-06-01
The carbon dimer, the 12C2 molecule, is ubiquitous in astronomical environments. Experimental-quality rovibronic energy levels are reported for 12C2, based on rovibronic transitions measured for and among its singlet, triplet, and quintet electronic states, reported in 42 publications. The determination utilizes the Measured Active Rotational-Vibrational Energy Levels (MARVEL) technique. The 23,343 transitions measured experimentally and validated within this study determine 5699 rovibronic energy levels, 1325, 4309, and 65 levels for the singlet, triplet, and quintet states investigated, respectively. The MARVEL analysis provides rovibronic energies for six singlet, six triplet, and two quintet electronic states. For example, the lowest measurable energy level of the {{a}}{}3{{{\\Pi }}}{{u}} state, corresponding to the J = 2 total angular momentum quantum number and the F 1 spin-multiplet component, is 603.817(5) cm‑1. This well-determined energy difference should facilitate observations of singlet–triplet intercombination lines, which are thought to occur in the interstellar medium and comets. The large number of highly accurate and clearly labeled transitions that can be derived by combining MARVEL energy levels with computed temperature-dependent intensities should help a number of astrophysical observations as well as corresponding laboratory measurements. The experimental rovibronic energy levels, augmented, where needed, with ab initio variational ones based on empirically adjusted and spin–orbit coupled potential energy curves obtained using the Duo code, are used to obtain a highly accurate partition function, and related thermodynamic data, for 12C2 up to 4000 K.
Evolution of the electron energy distribution function during genesis of breakdown plasma
Bhattacharjee, Sudeep; Paul, Samit; Ghosh, Sayandip
2014-08-15
During the process of plasma initiation by an electromagnetic wave, it is found that the electron energy distribution function (EEDF) that is initially Maxwellian with the most probable energy at room temperature, evolves with time and tends toward a Bi-Maxwellian – indicating attainment of thermodynamic equilibrium in the individual electron populations prior to breakdown, with a significant increase in hot electron density. In the intermediate states during the evolution, however, non-equilibrium processes are prevalent under fast pulse excitation and the EEDF initially exhibits substantial deviation from a Maxwellian. An analysis of the deviation has been carried out by optimizing the residual sum of squares of the probabilities obtained from the simulation and a fitted Maxwellian curve. The equilibrium regain time defined as the time required to attain thermodynamic equilibrium again, is investigated as a function of neutral pressure, wave electric, and external magnetostatic fields.
The time-varying electron energy distribution function in the plume of a Hall thruster
NASA Astrophysics Data System (ADS)
Dannenmayer, K.; Mazouffre, S.; Kudrna, P.; Tichý, M.
2014-12-01
Time-resolved Langmuir probe measurements have been performed in the plume of the 1.5 kW class PPS®1350-ML Hall thruster. The time-dependent electron energy distribution function (EEDF) has been inferred from the probe current-voltage characteristic curves obtained after active stabilization of the discharge. The distribution function changes in the course of time at the breathing oscillation frequency (13.8 kHz). The EEDF is Maxwellian with a depleted tail above the xenon ionization energy whatever the location and the time. The electron density and temperature computed from the EEDF also oscillate at the breathing mode frequency. Experimental outcomes indicate the existence of a low-frequency plasma wave that propagates axially. The wave front speed (2700 m s-1) was found to be compatible with the ion acoustic speed (2300 m s-1).
Accelerating self-consistent field convergence with the augmented Roothaan–Hall energy function
Hu, Xiangqian; Yang, Weitao
2010-01-01
Based on Pulay’s direct inversion iterative subspace (DIIS) approach, we present a method to accelerate self-consistent field (SCF) convergence. In this method, the quadratic augmented Roothaan–Hall (ARH) energy function, proposed recently by Høst and co-workers [J. Chem. Phys. 129, 124106 (2008)], is used as the object of minimization for obtaining the linear coefficients of Fock matrices within DIIS. This differs from the traditional DIIS of Pulay, which uses an object function derived from the commutator of the density and Fock matrices. Our results show that the present algorithm, abbreviated ADIIS, is more robust and efficient than the energy-DIIS (EDIIS) approach. In particular, several examples demonstrate that the combination of ADIIS and DIIS (“ADIIS+DIIS”) is highly reliable and efficient in accelerating SCF convergence. PMID:20136307
Functional integration of vertical flight path and speed control using energy principles
NASA Technical Reports Server (NTRS)
Lambregts, A. A.
1984-01-01
A generalized automatic flight control system was developed which integrates all longitudinal flight path and speed control functions previously provided by a pitch autopilot and autothrottle. In this design, a net thrust command is computed based on total energy demand arising from both flight path and speed targets. The elevator command is computed based on the energy distribution error between flight path and speed. The engine control is configured to produce the commanded net thrust. The design incorporates control strategies and hierarchy to deal systematically and effectively with all aircraft operational requirements, control nonlinearities, and performance limits. Consistent decoupled maneuver control is achieved for all modes and flight conditions without outer loop gain schedules, control law submodes, or control function duplication.
NASA Astrophysics Data System (ADS)
Nelson, Florence
For more than 60 years, semiconductor research has been advancing up the periodic table. The first transistor was made from germanium. This later gave way to silicon-based devices due to the latter's ability to form an excellent interface with thermally-grown oxide. Now for the last ˜8 years, the focus has moved up one more row to carbon for post-CMOS devices in order to comply with the scaling limitations of Moore's law. However, for each of these, the measurements of film properties and dimensions have always been required for technological applications. These measurement methods often incorporate the use of light or electrons in order to take advantage of a wavelength that is on the order of, or smaller than, the feature sizes of interest. This thesis compares the dielectric function of graphene measured by an optical method to that obtained from an electron energy loss method in order to observe the effect of contamination and substrate on the optical properties of graphene exposed to the environment. Whether viewed in terms of how light affects a material (dielectric function) or how a material affects light (refractive index), the optical response is a quantity that may be used to obtain information about a film's thickness, energy structure, and the types of excitations that are responsible for energy loss. The three main experimental methods used in this thesis work are spectroscopic ellipsometry (SE), scanning transmission electron microscopy (STEM), and electron energy loss spectroscopy (EELS). SE is commonly used in clean-room environments for optical measurement over the energy range of ˜0-5 eV. This method is used to study graphene's dielectric function from the ultraviolet (UV) through infrared (IR) regions through use of an oscillator dispersion model. A nearly constant absorbance over the IR and into the visible region is observed due to vertical transitions between graphene's linearly dispersed pi-bands at the Dirac points. An exciton
Mathematical representation of the incident solar energy as a function of latitude and time
Simmons, P.A.
1988-07-01
A simple mathematical representation of the incoming solar radiation as a function of latitude and time is introduced. The expression approximates the total zonally and daily averaged solar energy incident on the earth's surface before any is absorbed. It includes dependence on both the obliquity and the precession of the equinoxes and, with its accuracy limits, the representation is convenient for use in long-term climate modelling. 7 references.
Drallos, P.J.; Wadehra, J.M.
1988-06-01
We are presenting a novel numerical technique for obtaining the time evolution of the electron velocity and electron energy distribution functions in the presence of a uniform electric field. Using this technique, the various swarm parameters can be evolved for sufficiently long times so that equilibrium can be reached without incurring any numerical instabilities. Results are presented for electron swarms in gaseous neon for various values of E/N.
Nuclear energy density functionals: What we can learn about/from their global performance?
Afanasjev, A. V.; Agbemava, S. E.; Ray, D.; Ring, P.
2014-10-15
A short review of recent results on the global performance of covariant energy density functionals is presented. It is focused on an analysis of the accuracy of the description of physical observables of ground and excited states as well as to related theoretical uncertainties. In addition, a global analysis of pairing properties is presented and the impact of pairing on the position of two-neutron drip line is discussed.
Validating a Coarse-Grained Potential Energy Function through Protein Loop Modelling
MacDonald, James T.; Kelley, Lawrence A.; Freemont, Paul S.
2013-01-01
Coarse-grained (CG) methods for sampling protein conformational space have the potential to increase computational efficiency by reducing the degrees of freedom. The gain in computational efficiency of CG methods often comes at the expense of non-protein like local conformational features. This could cause problems when transitioning to full atom models in a hierarchical framework. Here, a CG potential energy function was validated by applying it to the problem of loop prediction. A novel method to sample the conformational space of backbone atoms was benchmarked using a standard test set consisting of 351 distinct loops. This method used a sequence-independent CG potential energy function representing the protein using -carbon positions only and sampling conformations with a Monte Carlo simulated annealing based protocol. Backbone atoms were added using a method previously described and then gradient minimised in the Rosetta force field. Despite the CG potential energy function being sequence-independent, the method performed similarly to methods that explicitly use either fragments of known protein backbones with similar sequences or residue-specific /-maps to restrict the search space. The method was also able to predict with sub-Angstrom accuracy two out of seven loops from recently solved crystal structures of proteins with low sequence and structure similarity to previously deposited structures in the PDB. The ability to sample realistic loop conformations directly from a potential energy function enables the incorporation of additional geometric restraints and the use of more advanced sampling methods in a way that is not possible to do easily with fragment replacement methods and also enable multi-scale simulations for protein design and protein structure prediction. These restraints could be derived from experimental data or could be design restraints in the case of computational protein design. C++ source code is available for download from http
Wang Ning; Scheid, Werner; Wu Xizhen; Liu Min; Li Zhuxia
2006-10-15
The Skyrme energy-density functional approach has been extended to study massive heavy-ion fusion reactions. Based on the potential barrier obtained and the parametrized barrier distribution the fusion (capture) excitation functions of a lot of heavy-ion fusion reactions are studied systematically. The average deviations of fusion cross sections at energies near and above the barriers from experimental data are less than 0.05 for 92% of 76 fusion reactions with Z{sub 1}Z{sub 2}<1200. For the massive fusion reactions, for example, the {sup 238}U-induced reactions and {sup 48}Ca+{sup 208}Pb, the capture excitation functions have been reproduced remarkably well. The influence of structure effects in the reaction partners on the capture cross sections is studied with our parametrized barrier distribution. By comparing the reactions induced by double-magic nucleus {sup 48}Ca and by {sup 32}S and {sup 35}Cl, the ''threshold-like'' behavior in the capture excitation function for {sup 48}Ca-induced reactions is explored and an optimal balance between the capture cross section and the excitation energy of the compound nucleus is studied. Finally, the fusion reactions with {sup 36}S, {sup 37}Cl, {sup 48}Ca, and {sup 50}Ti bombarding {sup 248}Cm, {sup 247,249}Bk, {sup 250,252,254}Cf, and {sup 252,254}Es, as well as the reactions leading to the same compound nucleus with Z=120 and N=182, are studied further. The calculation results for these reactions are useful for searching for the optimal fusion configuration and suitable incident energy in the synthesis of superheavy nuclei.
Dielectric function for doped graphene layer with barium titanate
NASA Astrophysics Data System (ADS)
Martinez Ramos, Manuel; Garces Garcia, Eric; Magana, Fernado; Vazquez Fonseca, Gerardo Jorge
2015-03-01
The aim of our study is to calculate the dielectric function for a system formed with a graphene layer doped with barium titanate. Density functional theory, within the local density approximation, plane-waves and pseudopotentials scheme as implemented in Quantum Espresso suite of programs was used. We considered 128 carbon atoms with a barium titanate cluster of 11 molecules as unit cell with periodic conditions. The geometry optimization is achieved. Optimization of structural configuration is performed by relaxation of all atomic positions to minimize their total energies. Band structure, density of states and linear optical response (the imaginary part of dielectric tensor) were calculated. We thank Dirección General de Asuntos del Personal Académico de la Universidad Nacional Autónoma de México, partial financial support by Grant IN-106514 and we also thank Miztli Super-Computing center the technical assistance.
NASA Astrophysics Data System (ADS)
Kim, June Young; Cho, Won-Hwi; Dang, Jeong-Jeung; Chung, Kyoung-Jae; Hwang, Y. S.
2016-02-01
Electron kinetics regime is characterized with the evolution of electron energy probability functions (EEPFs) in inductively coupled hydrogen plasmas. Measurements on EEPFs are carried out with a radio-frequency-compensated single Langmuir probe at the center of a planar-type hydrogen plasma driven by 13.56 MHz wave frequency. Measured EEPFs deviate considerably from the Maxwellian distribution only at relatively high pressures (15-40 mTorr), and the effective electron temperature steeply decreases as the gas pressure increases. Such evolution of the EEPF shapes with pressures is discussed in the consideration of the electron energy relaxation length and various characteristic frequencies. It is found that the EEPFs show locally depleted electron energy distribution where the electron-molecule vibrational collision frequency exceeds the electron-electron collision frequency at the local kinetics regime, while the measured EEPF is not dependent on the vibrational collision frequency at the non-local kinetics regime. Variation of the EEPF shape with distance from the heating region at the local kinetics regime is also well explained in the context of the energy relaxation length and electron-molecule collision frequencies. This study indicates that the control of electron energy distribution should be carried out in the consideration of electron kinetic regime depending on the energy relaxation length for various hydrogen plasma sources.
Nonlinear vibration energy harvesting based on variable double well potential function
NASA Astrophysics Data System (ADS)
Yang, Wei; Towfighian, Shahrzad
2016-04-01
Converting ambient mechanical energy to electricity, vibration energy harvesting, enables powering of the low-power remote sensors. Nonlinear energy harvesters have the advantage of a wider frequency spectrum compared to linear resonators making them more efficient in scavenging the broadband frequency of ambient vibrations. To increase the output power of the nonlinear resonators, we propose an energy harvester composed of a cantilever piezoelectric beam carrying a movable magnet facing a fixed magnet at a distance. The movable magnet on the beam is attached to a spring at the base of the beam. The spring-magnet system on the cantilever beam creates the variable double well potential function. The spring attached to the magnet is in its compressed position when the beam is not deflected, as the beam oscillates, the spring energy gradually releases and further increases the amplitude of vibration. To describe the motion of the cantilever beam, we obtained two coupled partial differential equations by assuming the cantilever beam as Euler-Bernoulli beam considering the effect of the moving magnet. Method of multiple scales is used to solve the coupled equations. The cantilever beam with the two magnets is a bi-stable system. Making one magnet movable can create internal resonance that is explored as a mechanism to increase the frequency bandwidth. The effect of system parameters on the frequency bandwidth of the resonator is investigated through numerical solutions. This study benefits vibration energy harvesting to achieve a higher performance when excited by the wideband ambient vibrations.
Sanders, C R; Schwonek, J P
1993-01-01
An empirical model of a liquid crystalline (L alpha phase) phosphatidylcholine (PC) bilayer interface is presented along with a function which calculates the position-dependent energy of associated solutes. The model approximates the interface as a gradual two-step transition, the first step being from an aqueous phase to a phase of reduced polarity, but which maintains a high enough concentration of water and/or polar head group moieties to satisfy the hydrogen bond-forming potential of the solute. The second transition is from the hydrogen bonding/low polarity region to an effectively anhydrous hydrocarbon phase. The "interfacial energies" of solutes within this variable medium are calculated based upon atomic positions and atomic parameters describing general polarity and hydrogen bond donor/acceptor propensities. This function was tested for its ability to reproduce experimental water-solvent partitioning energies and water-bilayer partitioning data. In both cases, the experimental data was reproduced fairly well. Energy minimizations carried out on beta-hexyl glucopyranoside led to identification of a global minimum for the interface-associated glycolipid which exhibited glycosidic torsion angles in agreement with prior results (Hare, B.J., K.P. Howard, and J.H. Prestegard. 1993. Biophys. J. 64:392-398). Molecular dynamics simulations carried out upon this same molecule within the simulated interface led to results which were consistent with a number of experimentally based conclusions from previous work, but failed to quantitatively reproduce an available NMR quadrupolar/dipolar coupling data set (Sanders, C.R., and J.H. Prestegard. 1991. J. Am. Chem. Soc. 113:1987-1996). The proposed model and functions are readily incorporated into computational energy modeling algorithms and may prove useful in future studies of membrane-associated molecules. PMID:8241401
NASA Technical Reports Server (NTRS)
Huang, K.-N.; Aoyagi, M.; Mark, H.; Chen, M. H.; Crasemann, B.
1976-01-01
Electron binding energies in neutral atoms have been calculated relativistically, with the requirement of complete relaxation. Hartree-Fock-Slater wave functions served as zeroth-order eigenfunctions to compute the expectation of the total Hamiltonian. A first-order correction to the local approximation was thus included. Quantum-electrodynamic corrections were made. For all elements with atomic numbers ranging from 2 to 106, the following quantities are listed: total energies, electron kinetic energies, electron-nucleus potential energies, electron-electron potential energies consisting of electrostatic and Breit interaction (magnetic and retardation) terms, and vacuum polarization energies. Binding energies including relaxation are listed for all electrons in all atoms over the indicated range of atomic numbers. A self-energy correction is included for the 1s, 2s, and 2p(1/2) levels. Results for selected atoms are compared with energies calculated by other methods and with experimental values.
Do Bond Functions Help for the Calculation of Accurate Bond Energies?
NASA Technical Reports Server (NTRS)
Bauschlicher, Charles W., Jr.; Arnold, James (Technical Monitor)
1998-01-01
The bond energies of 8 chemically bound diatomics are computed using several basis sets with and without bond functions (BF). The bond energies obtained using the aug-pVnZ+BF basis sets (with a correction for basis set superposition error, BSSE) tend to be slightly smaller that the results obtained using the aug-pV(n+I)Z basis sets, but slightly larger than the BSSE corrected aug-pV(n+I)Z results. The aug-cc-pVDZ+BF and aug-cc-pVTZ+BF basis sets yield reasonable estimates of bond energies, but, in most cases, these results cannot be considered highly accurate. Extrapolation of the results obtained with basis sets including bond functions appears to be inferior to the results obtained by extrapolation using atom-centered basis sets. Therefore bond functions do not appear to offer a path for obtaining highly accurate results for chemically bound systems at a lower computational cost than atom centered basis sets.
Smart Polyacrylonitrile (PAN) Nanofibers with Thermal Energy Storage and Retrieval Functionality
NASA Astrophysics Data System (ADS)
Cherry, De'Andre James
Phase change materials (PCMs) are generally substances with a high heat of fusion in the process of solid to liquid phase change. The nature of PCMs make them efficient materials to store and retrieve large amounts of thermal energy. Presently, high efficiency thermal energy storage/retrieval in applications where flexibility and space saving are required, such as smart textiles, still remains as a challenge. In this study, lauric acid (LA) and myristic acid (MA) were combined to prepare a specific binary fatty acid eutectic (LA-MA) with a melting point near the operating body temperature of a human being and then encapsulated in polyacrylonitrile (PAN) nanofibers through the electrospinning technique. Functionalized PCM-enhanced PAN nanofibers containing LA-MA at 30%, 50%, 70% and 100% of the weight of the PAN were successfully synthesized. The morphological structures and thermal energy storage capacity of the PCM-enhanced PAN nanofibers were characterized by electron microscopy (EM) and differential scanning calorimetry (DSC). The novel PCM-enhanced PAN nanofibers maintained their cylindrical fiber morphology after multiple heating-cooling cycles and retained their latent heat storage functionality. Thus, it is envisioned that the prepared PCM-enhanced PAN nanofibers will find use in applications such as smart textiles where temperature regulation functionality is required.
NASA Astrophysics Data System (ADS)
Chevrier, V. L.; Ong, S. P.; Armiento, R.; Chan, M. K. Y.; Ceder, G.
2010-08-01
We compare the accuracy of conventional semilocal density functional theory (DFT), the DFT+U method, and the Heyd-Scuseria-Ernzerhof (HSE06) hybrid functional for structural parameters, redox reaction energies, and formation energies of transition metal compounds. Conventional DFT functionals significantly underestimate redox potentials for these compounds. Zhou [Phys. Rev. B 70, 235121 (2004)]10.1103/PhysRevB.70.235121 addressed this issue with DFT+U and a linear-response scheme for calculating U values. We show that the Li intercalation potentials of prominent Li-ion intercalation battery materials, such as the layered LixMO2 ( M=Co and Ni), LixTiS2 ; olivine LixMPO4 ( M=Mn , Fe, Co, and Ni); and spinel-like LixMn2O4 , LixTi2O4 , are also well reproduced by HSE06, due to the self-interaction error correction from the partial inclusion of Hartree-Fock exchange. For formation energies, HSE06 performs well for transition metal compounds, which typically are not well reproduced by conventional DFT functionals but does not significantly improve the results of nontransition metal oxides. Hence, we find that hybrid functionals provide a good alternative to DFT+U for transition metal applications when the large extra computational effort is compensated by the benefits of (i) avoiding species-specific adjustable parameters and (ii) a more universal treatment of the self-interaction error that is not exclusive to specific atomic orbital projections on selected ions.
Nonuniqueness of magnetic fields and energy derivatives in spin-polarized density functional theory
NASA Astrophysics Data System (ADS)
Gál, T.; Ayers, P. W.; De Proft, F.; Geerlings, P.
2009-10-01
The effect of the recently uncovered nonuniqueness of the external magnetic field B(r⃑) corresponding to a given pair of density n(r⃑) and spin density ns(r⃑) on the derivative of the energy functional of spin-polarized density functional theory, and its implications for the definition of chemical reactivity descriptors, is examined. For ground states, the nonuniqueness of B(r⃑) implies the nondifferentiability of the energy functional Ev,B[n,ns] with respect to ns(r⃑). It is shown, on the other hand, that this nonuniqueness allows the existence of the one-sided derivatives of Ev,B[n,ns] with respect to ns(r⃑). Although the N-electron ground state can always be obtained from the minimization of Ev,B[n,ns] without any constraint on the spin number Ns=∫ns(r⃑)dr⃑, the Lagrange multiplier μs associated with the fixation of Ns does not vanish even for ground states. μs is identified as the left- or right-side derivative of the total energy with respect to Ns, which justifies the interpretation of μs as a (spin) chemical potential. This is relevant not only for the spin-polarized generalization of conceptual density functional theory, the spin chemical potential being one of the elementary reactivity descriptors, but also for the extension of the thermodynamical analogy of density functional theory for the spin-polarized case. For higher-order reactivity indices, B(r⃑)'s nonuniqueness has similar implications as for μs, leading to a split of the indices with respect to Ns into one-sided reactivity descriptors.
On the form of the strain energy function for a family of SBR materials. [Styrene-Butadiene Rubber
NASA Technical Reports Server (NTRS)
Arenz, R. J.
1977-01-01
Styrene-butadiene materials with varying crosslink densities are analyzed through use of a strain energy function of the type introduced by Valanis and Landel (1967). A form of the strain energy function derived from strip biaxial tests proves to be accurate when checked against uniaxial and other biaxial test results.
Ayouz, Mehdi; Babikov, Dmitri
2012-01-01
New global potential energy surface for the ground electronic state of ozone is constructed at the complete basis set level of the multireference configuration interaction theory. A method of fitting the data points by analytical permutationally invariant polynomial function is adopted. A small set of 500 points is preoptimized using the old surface of ozone. In this procedure the positions of points in the configuration space are chosen such that the RMS deviation of the fit is minimized. New ab initio calculations are carried out at these points and are used to build new surface. Additional points are addedmore » to the vicinity of the minimum energy path in order to improve accuracy of the fit, particularly in the region where the surface of ozone exhibits a shallow van der Waals well. New surface can be used to study formation of ozone at thermal energies and its spectroscopy near the dissociation threshold.« less
Nanocluster ionization energies and work function of aluminum, and their temperature dependence.
Halder, Avik; Kresin, Vitaly V
2015-10-28
Ionization threshold energies of Al(n) (n = 32-95) nanoclusters are determined by laser ionization of free neutral metal clusters thermalized to several temperatures in the range from 65 K to 230 K. The photoion yield curves of cold clusters follow a quadratic energy dependence above threshold, in agreement with the Fowler law of surface photoemission. Accurate data collection and analysis procedures make it possible to resolve very small (few parts in a thousand) temperature-induced shifts in the ionization energies. Extrapolation of the data to the bulk limit enables a determination of the thermal shift of the polycrystalline metal work function, found to be in excellent agreement with theoretical prediction based on the influence of thermal expansion. Small clusters display somewhat larger thermal shifts, reflecting their greater susceptibility to thermal expansion. Ionization studies of free size-resolved nanoclusters facilitate understanding of the interplay of surface, electronic, and lattice properties under contamination-free conditions. PMID:26520519
Nanocluster ionization energies and work function of aluminum, and their temperature dependence
NASA Astrophysics Data System (ADS)
Halder, Avik; Kresin, Vitaly V.
2015-10-01
Ionization threshold energies of Aln (n = 32-95) nanoclusters are determined by laser ionization of free neutral metal clusters thermalized to several temperatures in the range from 65 K to 230 K. The photoion yield curves of cold clusters follow a quadratic energy dependence above threshold, in agreement with the Fowler law of surface photoemission. Accurate data collection and analysis procedures make it possible to resolve very small (few parts in a thousand) temperature-induced shifts in the ionization energies. Extrapolation of the data to the bulk limit enables a determination of the thermal shift of the polycrystalline metal work function, found to be in excellent agreement with theoretical prediction based on the influence of thermal expansion. Small clusters display somewhat larger thermal shifts, reflecting their greater susceptibility to thermal expansion. Ionization studies of free size-resolved nanoclusters facilitate understanding of the interplay of surface, electronic, and lattice properties under contamination-free conditions.
Analysis of electron energy distribution function in the Linac4 H⁻ source.
Mochizuki, S; Mattei, S; Nishida, K; Hatayama, A; Lettry, J
2016-02-01
To understand the Electron Energy Distribution Function (EEDF) in the Radio Frequency Inductively Coupled Plasmas (RF-ICPs) in hydrogen negative ion sources, the detailed analysis of the EEDFs using numerical simulation and the theoretical approach based on Boltzmann equation has been performed. It is shown that the EEDF of RF-ICPs consists of two parts, one is the low energy part which obeys Maxwellian distribution and the other is high energy part deviated from Maxwellian distribution. These simulation results have been confirmed to be reasonable by the analytical approach. The results suggest that it is possible to enhance the dissociation of molecules and the resultant H(-) negative ion production by reducing the gas pressure. PMID:26931990
Kalinin, Sergei V; Balke, Nina
2010-09-15
Energy storage and conversion systems are an integral component of emerging green technologies, including mobile electronic devices, automotive, and storage components of solar and wind energy economics. Despite the rapidly expanding manufacturing capabilities and wealth of phenomenological information on the macroscopic device behaviors, the microscopic mechanisms underpinning battery and fuel cell operations in the nanometer-micrometer range are virtually unknown. This lack of information is due to the dearth of experimental techniques capable of addressing elementary mechanisms involved in battery operation, including electronic and ion transport, vacancy injection, and interfacial reactions, on the nanometer scale. In this article, a brief overview of scanning probe microscopy (SPM) methods addressing nanoscale electrochemical functionalities is provided and compared with macroscopic electrochemical methods. Future applications of emergent SPM methods, including near field optical, electromechanical, microwave, and thermal probes and combined SPM-(S)TEM (scanning transmission electron microscopy) methods in energy storage and conversion materials are discussed. PMID:20730814
Bang, Jin-Young; Chung, Chin-Wook
2010-12-15
Electron energy distribution functions (EEDFs) were determined from probe characteristics using a numerical ac superimposed method with a distortion correction of high derivative terms by varying amplitude of a sinusoidal perturbation voltage superimposed onto the dc sweep voltage, depending on the related electron energy. Low amplitude perturbation applied around the plasma potential represented the low energy peak of the EEDF exactly, and high amplitude perturbation applied around the floating potential was effective to suppress noise or distortion of the probe characteristic, which is fatal to the tail electron distribution. When a small random noise was imposed over the stabilized prove characteristic, the numerical differentiation method was not suitable to determine the EEDF, while the numerical ac superimposed method was able to obtain a highly precise EEDF.
Nanocluster ionization energies and work function of aluminum, and their temperature dependence
Halder, Avik; Kresin, Vitaly V.
2015-10-28
Ionization threshold energies of Al{sub n} (n = 32-95) nanoclusters are determined by laser ionization of free neutral metal clusters thermalized to several temperatures in the range from 65 K to 230 K. The photoion yield curves of cold clusters follow a quadratic energy dependence above threshold, in agreement with the Fowler law of surface photoemission. Accurate data collection and analysis procedures make it possible to resolve very small (few parts in a thousand) temperature-induced shifts in the ionization energies. Extrapolation of the data to the bulk limit enables a determination of the thermal shift of the polycrystalline metal work function, found to be in excellent agreement with theoretical prediction based on the influence of thermal expansion. Small clusters display somewhat larger thermal shifts, reflecting their greater susceptibility to thermal expansion. Ionization studies of free size-resolved nanoclusters facilitate understanding of the interplay of surface, electronic, and lattice properties under contamination-free conditions.
Enhanced von Weizsäcker Wang-Govind-Carter kinetic energy density functional for semiconductors
Shin, Ilgyou; Carter, Emily A.
2014-05-14
We propose a new form of orbital-free (OF) kinetic energy density functional (KEDF) for semiconductors that is based on the Wang-Govind-Carter (WGC99) nonlocal KEDF. We enhance within the latter the semi-local von Weizsäcker KEDF term, which is exact for a single orbital. The enhancement factor we introduce is related to the extent to which the electron density is localized. The accuracy of the new KEDF is benchmarked against Kohn-Sham density functional theory (KSDFT) by comparing predicted energy differences between phases, equilibrium volumes, and bulk moduli for various semiconductors, along with metal-insulator phase transition pressures. We also compare point defect and (100) surface energies in silicon for a broad test of its applicability. This new KEDF accurately reproduces the exact non-interacting kinetic energy of KSDFT with only one additional adjustable parameter beyond the three parameters in the WGC99 KEDF; it exhibits good transferability between semiconducting to metallic silicon phases and between various III-V semiconductors without parameter adjustment. Overall, this KEDF is more accurate than previously proposed OF KEDFs (e.g., the Huang-Carter (HC) KEDF) for semiconductors, while the computational efficiency remains at the level of the WGC99 KEDF (several hundred times faster than the HC KEDF). This accurate, fast, and transferable new KEDF holds considerable promise for large-scale OFDFT simulations of metallic through semiconducting materials.
Enhanced von Weizsäcker Wang-Govind-Carter kinetic energy density functional for semiconductors
NASA Astrophysics Data System (ADS)
Shin, Ilgyou; Carter, Emily A.
2014-05-01
We propose a new form of orbital-free (OF) kinetic energy density functional (KEDF) for semiconductors that is based on the Wang-Govind-Carter (WGC99) nonlocal KEDF. We enhance within the latter the semi-local von Weizsäcker KEDF term, which is exact for a single orbital. The enhancement factor we introduce is related to the extent to which the electron density is localized. The accuracy of the new KEDF is benchmarked against Kohn-Sham density functional theory (KSDFT) by comparing predicted energy differences between phases, equilibrium volumes, and bulk moduli for various semiconductors, along with metal-insulator phase transition pressures. We also compare point defect and (100) surface energies in silicon for a broad test of its applicability. This new KEDF accurately reproduces the exact non-interacting kinetic energy of KSDFT with only one additional adjustable parameter beyond the three parameters in the WGC99 KEDF; it exhibits good transferability between semiconducting to metallic silicon phases and between various III-V semiconductors without parameter adjustment. Overall, this KEDF is more accurate than previously proposed OF KEDFs (e.g., the Huang-Carter (HC) KEDF) for semiconductors, while the computational efficiency remains at the level of the WGC99 KEDF (several hundred times faster than the HC KEDF). This accurate, fast, and transferable new KEDF holds considerable promise for large-scale OFDFT simulations of metallic through semiconducting materials.
NASA Astrophysics Data System (ADS)
Modine, N. A.; Wright, A. F.; Lee, S. R.
The rate of defect-induced carrier recombination is determined by both defect levels and carrier capture cross-sections. Density functional theory (DFT) has been widely and successfully used to predict defect levels, but only recently has work begun to focus on using DFT to determine carrier capture cross-sections. Lang and Henry developed the theory of carrier-capture by multiphonon emission in the 1970s and showed that carrier-capture cross-sections differ between defects primarily due to differences in their carrier capture activation energies. We present an approach to using DFT to calculate carrier capture activation energies that does not depend on an assumed configuration coordinate and that fully accounts for anharmonic effects, which can substantially modify carrier activation energies. We demonstrate our approach for intrinisic defects in GaAs and GaN and discuss how our results depend on the choice of exchange-correlation functional and the treatment of spin polarization. Sandia National Laboratories is a multi-program laboratory managed and operated by Sandia Corporation, a wholly owned subsidiary of Lockheed Martin Corporation, for the U.S. Department of Energy's National Nuclear Security Administration under Contract DE-AC04-94AL85000.
Stochastic averaging based on generalized harmonic functions for energy harvesting systems
NASA Astrophysics Data System (ADS)
Jiang, Wen-An; Chen, Li-Qun
2016-09-01
A stochastic averaging method is proposed for nonlinear vibration energy harvesters subject to Gaussian white noise excitation. The generalized harmonic transformation scheme is applied to decouple the electromechanical equations, and then obtained an equivalent nonlinear system which is uncoupled to an electric circuit. The frequency function is given through the equivalent potential energy which is independent of the total energy. The stochastic averaging method is developed by using the generalized harmonic functions. The averaged Itô equations are derived via the proposed procedure, and the Fokker-Planck-Kolmogorov (FPK) equations of the decoupled system are established. The exact stationary solution of the averaged FPK equation is used to determine the probability densities of the amplitude and the power of the stationary response. The procedure is applied to three different type Duffing vibration energy harvesters under Gaussian white excitations. The effects of the system parameters on the mean-square voltage and the output power are examined. It is demonstrated that quadratic nonlinearity only and quadratic combined with properly cubic nonlinearities can increase the mean-square voltage and the output power, respectively. The approximate analytical outcomes are qualitatively and quantitatively supported by the Monte Carlo simulations.
Tensor polarization dependent fragmentation functions and e+e-→V π X at high energies
NASA Astrophysics Data System (ADS)
Chen, Kai-bao; Yang, Wei-hua; Wei, Shu-yi; Liang, Zuo-tang
2016-08-01
We present the systematic results for three-dimensional fragmentation functions of spin-1 hadrons defined via the quark-quark correlator. There are totally 72 such fragmentation functions, among them 18 are twist-2, 36 are twist-3 and 18 are twist-4. We also present the relationships between the twist-3 parts and those defined via the quark-gluon-quark correlator obtained from the QCD equation of motion. We show that the two particle semi-inclusive hadron production process e+e-→V π X at high energies is one of the best places to study the three-dimensional tensor polarization dependent fragmentation functions. We present the general kinematic analysis of this process and show that the cross section should be expressed in terms of 81 independent structure functions. After that we present parton model results for the hadronic tensor, the structure functions, and the azimuthal and spin asymmetries in terms of these gauge invariant fragmentation functions at the leading order perturbative quantum chromodynamics up to twist-3.
An Energy-Independent Pro-longevity Function of Triacylglycerol in Yeast.
Handee, Witawas; Li, Xiaobo; Hall, Kevin W; Deng, Xiexiong; Li, Pan; Benning, Christoph; Williams, Barry L; Kuo, Min-Hao
2016-02-01
Intracellular triacylglycerol (TAG) is a ubiquitous energy storage lipid also involved in lipid homeostasis and signaling. Comparatively, little is known about TAG's role in other cellular functions. Here we show a pro-longevity function of TAG in the budding yeast Saccharomyces cerevisiae. In yeast strains derived from natural and laboratory environments a correlation between high levels of TAG and longer chronological lifespan was observed. Increased TAG abundance through the deletion of TAG lipases prolonged chronological lifespan of laboratory strains, while diminishing TAG biosynthesis shortened lifespan without apparently affecting vegetative growth. TAG-mediated lifespan extension was independent of several other known stress response factors involved in chronological aging. Because both lifespan regulation and TAG metabolism are conserved, this cellular pro-longevity function of TAG may extend to other organisms. PMID:26907989
Li, Z.; Pan, Y.K.; Tao, F.M.
1996-01-15
Bond function basis sets combined with the counterpoise procedure are used to calculate the molecular dissociation energies D{sub e} of 24 diatomic molecules and ions. The calculated values of D{sub e} are compared to those without bond functions and/or counterpoise corrections. The equilibrium bond lengths r{sub e}, and harmonic frequencies w{sub e} are also calculated for a few selected molecules. The calculations at the fourth-order-Moller-Plesset approximation (MP4) have consistently recovered about 95-99% of the experimental values for D{sub e}, compared to as low as 75% without use of bond functions. The calculated values of r{sub 3} are typically 0.01 {Angstrom} larger than the experimental values, and the calculated values of w{sub e} are over 95% of the experimental values. 37 refs., 2 tabs.
Optical function spectra and bandgap energy of Cu{sub 2}SnSe{sub 3}
Choi, S. G. Kang, J.; Beall, C.; Wei, S.-H.; Christensen, S. T.; Repins, I. L.; Li, J.; Haneef, H.; Podraza, N. J.
2015-01-26
We present the optical function spectra of Cu{sub 2}SnSe{sub 3} determined from 0.30 to 6.45 eV by spectroscopic ellipsometry (SE) at room temperature. We analyze the SE data using the Tauc-Lorentz model and obtain the direct-bandgap energy of 0.49 ± 0.02 eV, which is much smaller than the previously known value of 0.84 eV for the monoclinic-phase Cu{sub 2}SnSe{sub 3}. We also perform density-functional theory calculations to obtain the complex dielectric function data, and the results show good agreement with the experimental spectrum. Finally, we discuss the electronic origin of the main optical structures.
An Energy-Independent Pro-longevity Function of Triacylglycerol in Yeast
Hall, Kevin W.; Deng, Xiexiong; Li, Pan; Benning, Christoph; Williams, Barry L.; Kuo, Min-Hao
2016-01-01
Intracellular triacylglycerol (TAG) is a ubiquitous energy storage lipid also involved in lipid homeostasis and signaling. Comparatively, little is known about TAG’s role in other cellular functions. Here we show a pro-longevity function of TAG in the budding yeast Saccharomyces cerevisiae. In yeast strains derived from natural and laboratory environments a correlation between high levels of TAG and longer chronological lifespan was observed. Increased TAG abundance through the deletion of TAG lipases prolonged chronological lifespan of laboratory strains, while diminishing TAG biosynthesis shortened lifespan without apparently affecting vegetative growth. TAG-mediated lifespan extension was independent of several other known stress response factors involved in chronological aging. Because both lifespan regulation and TAG metabolism are conserved, this cellular pro-longevity function of TAG may extend to other organisms. PMID:26907989
Lee, Kyungtae; Gu, Geun Ho; Mullen, Charles A; Boateng, Akwasi A; Vlachos, Dionisios G
2015-01-01
Density functional theory is used to study the adsorption of guaiacol and its initial hydrodeoxygenation (HDO) reactions on Pt(111). Previous Brønsted-Evans-Polanyi (BEP) correlations for small open-chain molecules are inadequate in estimating the reaction barriers of phenolic compounds except for the side group (methoxy) carbon-dehydrogenation. New BEP relations are established using a select group of phenolic compounds. These relations are applied to construct a potential-energy surface of guaiacol-HDO to catechol. Analysis shows that catechol is mainly produced via dehydrogenation of the methoxy functional group followed by the CHx (x<3) removal of the functional group and hydrogenation of the ring carbon, in contrast to a hypothesis of a direct demethylation path. Dehydroxylation and demethoxylation are slow, implying that phenol is likely produced from catechol but not through its direct dehydroxylation followed by aromatic carbon-ring hydrogenation. PMID:25470789
NASA Astrophysics Data System (ADS)
Kotiuga, Michele; Egger, David; Kronik, Leeor; Neaton, Jeffrey B.
2015-03-01
Accurate calculations of energy level alignment at complex interfaces are imperative for understanding a variety of transport and spectroscopy measurements, as well as for elucidating new interfacial electronic structure phenomena. However, standard approaches to such calculations, based on density functional theory (DFT), are well known to be deficient. In prior work on molecular junctions and physisorbed molecules on surfaces, an approximate GW approach, DFT+ Σ, has been successful in describing the conductance and level alignment of amine and pyridine terminated molecules on gold surfaces and in junctions. Here, via the use of hybrid functionals, we preform quantitative studies of the level alignment of thiol- and carbon-terminated phenyls on gold, where the formation of a strong chemical bond and presence of gateway states limit the validity of the DFT+ Σ approximation as currently formulated. We contrast these systems to prior work on weakly-coupled molecules, including bipyridine or phenyl-diamines. Additionally, we compute transmission functions using both DFT-PBE and DFT-HSE starting points and predict conductance and thermopower with these methods, comparing to experiments where possible. We acknowledge DOE, DOD, NERSC, ERC, ISF, and FWF.
Assessment of Solvated Interaction Energy Function for Ranking Antibody-Antigen Binding Affinities.
Sulea, Traian; Vivcharuk, Victor; Corbeil, Christopher R; Deprez, Christophe; Purisima, Enrico O
2016-07-25
Affinity modulation of antibodies and antibody fragments of therapeutic value is often required in order to improve their clinical efficacies. Virtual affinity maturation has the potential to quickly focus on the critical hotspot residues without the combinatorial explosion problem of conventional display and library approaches. However, this requires a binding affinity scoring function that is capable of ranking single-point mutations of a starting antibody. We focus here on assessing the solvated interaction energy (SIE) function that was originally developed for and is widely applied to scoring of protein-ligand binding affinities. To this end, we assembled a structure-function data set called Single-Point Mutant Antibody Binding (SiPMAB) comprising several antibody-antigen systems suitable for this assessment, i.e., based on high-resolution crystal structures for the parent antibodies and coupled with high-quality binding affinity measurements for sets of single-point antibody mutants in each system. Using this data set, we tested the SIE function with several mutation protocols based on the popular methods SCWRL, Rosetta, and FoldX. We found that the SIE function coupled with a protocol limited to sampling only the mutated side chain can reasonably predict relative binding affinities with a Spearman rank-order correlation coefficient of about 0.6, outperforming more aggressive sampling protocols. Importantly, this performance is maintained for each of the seven system-specific component subsets as well as for other relevant subsets including non-alanine and charge-altering mutations. The transferability and enrichment in affinity-improving mutants can be further enhanced using consensus ranking over multiple methods, including the SIE, Talaris, and FOLDEF energy functions. The knowledge gained from this study can lead to successful prospective applications of virtual affinity maturation. PMID:27367467
Hyder, Fahmeed; Fulbright, Robert K; Shulman, Robert G; Rothman, Douglas L
2013-01-01
Rodent 13C magnetic resonance spectroscopy studies show that glutamatergic signaling requires high oxidative energy in the awake resting state and allowed calibration of functional magnetic resonance imaging (fMRI) signal in terms of energy relative to the resting energy. Here, we derived energy used for glutamatergic signaling in the awake resting human. We analyzed human data of electroencephalography (EEG), positron emission tomography (PET) maps of oxygen (CMRO2) and glucose (CMRglc) utilization, and calibrated fMRI from a variety of experimental conditions. CMRglc and EEG in the visual cortex were tightly coupled over several conditions, showing that the oxidative demand for signaling was four times greater than the demand for nonsignaling events in the awake state. Variations of CMRO2 and CMRglc from gray-matter regions and networks were within ±10% of means, suggesting that most areas required similar energy for ubiquitously high resting activity. Human calibrated fMRI results suggest that changes of fMRI signal in cognitive studies contribute at most ±10% CMRO2 changes from rest. The PET data of sleep, vegetative state, and anesthesia show metabolic reductions from rest, uniformly >20% across, indicating no region is selectively reduced when consciousness is lost. Future clinical investigations will benefit from using quantitative metabolic measures. PMID:23299240
Analytic model of energy-absorption response functions in compound X-ray detector materials.
Yun, Seungman; Kim, Ho Kyung; Youn, Hanbean; Tanguay, Jesse; Cunningham, Ian A
2013-10-01
The absorbed energy distribution (AED) in X-ray imaging detectors is an important factor that affects both energy resolution and image quality through the Swank factor and detective quantum efficiency. In the diagnostic energy range (20-140 keV), escape of characteristic photons following photoelectric absorption and Compton scatter photons are primary sources of absorbed-energy dispersion in X-ray detectors. In this paper, we describe the development of an analytic model of the AED in compound X-ray detector materials, based on the cascaded-systems approach, that includes the effects of escape and reabsorption of characteristic and Compton-scatter photons. We derive analytic expressions for both semi-infinite slab and pixel geometries and validate our approach by Monte Carlo simulations. The analytic model provides the energy-dependent X-ray response function of arbitrary compound materials without time-consuming Monte Carlo simulations. We believe this model will be useful for correcting spectral distortion artifacts commonly observed in photon-counting applications and optimal design and development of novel X-ray detectors. PMID:23744671
Modern money theory and ecological tax reform: A functional finance approach to energy conservation
NASA Astrophysics Data System (ADS)
McConnell, Scott L. B.
This dissertation contributes to heterodox economics by developing a theoretical and policy-relevant link that will promote the conservation of energy while driving the value of the domestic currency. The analysis relies upon the theoretical foundation of modern money theory and functional finance, which states that "taxes-drive-money" where the value of a sovereign nation's currency is imputed through the acceptance by the sovereign nation of the currency in payment of taxation. This theoretical perspective lends itself to various public policy prescriptions, such as government employment policies or the employer of last resort (ELR), which has been discussed at length elsewhere (Wray 1998; Tcherneva 2007, Forstater 2003). This research contributes to this overall program by arguing that the basis for taxation under modern money theory allows public policy makers various alternatives regarding the make-up of the tax system in place. In particular, following functional finance, taxes do not have the sole purpose of paying for government spending, but rather drive the value of the currency and may be designed to perform other functions as well, such as penalizing socially undesirable behavior. The focus in this dissertation is on the amelioration of pollution and increasing energy conservation. The research question for this dissertation is this: what federally implemented tax would best serve the multiple criteria of 1) driving the value of the currency, 2) promoting energy conservation and 3) ameliorating income and wealth disparities inherent in a monetary production economy? This dissertation provides a suggestion for such a tax that would be part of a much larger overall policy program based upon the tenets of modern money theory and functional finance. Additionally, this research seeks to provide an important theoretical contribution to the emerging Post Keynesian and ecological economics dialog.
NASA Astrophysics Data System (ADS)
Betzinger, Markus; Friedrich, Christoph; Görling, Andreas; Blügel, Stefan
2015-12-01
We present a methodology to calculate frequency and momentum dependent all-electron response functions determined within Kohn-Sham density functional theory. It overcomes the main obstacle in calculating response functions in practice, which is the slow convergence with respect to the number of unoccupied states and the basis-set size. In this approach, the usual sum-over-states expression of perturbation theory is complemented by the response of the orbital basis functions, explicitly constructed by radial integrations of frequency-dependent Sternheimer equations. To an essential extent an infinite number of unoccupied states are included in this way. Furthermore, the response of the core electrons is treated virtually exactly, which is out of reach otherwise. The method is an extension of the recently introduced incomplete-basis-set correction (IBC) [Betzinger et al., Phys. Rev. B 85, 245124 (2012), 10.1103/PhysRevB.85.245124; Phys. Rev. B 88, 075130 (2013), 10.1103/PhysRevB.88.075130] to the frequency and momentum domain. We have implemented the generalized IBC within the all-electron full-potential linearized augmented-plane-wave method and demonstrate for rocksalt BaO the improved convergence of the dynamical Kohn-Sham polarizability. We apply this technique to compute (a) quasiparticle energies employing the COHSEX approximation for the self-energy of many-body perturbation theory and (b) all-electron RPA correlation energies. It is shown that the favorable convergence of the polarizability is passed over to the COHSEX and RPA calculation.
Free Energy Calculations of Crystalline Hard Sphere Complexes Using Density Functional Theory
Gunawardana, K. G.S.H.; Song, Xueyu
2014-12-22
Recently developed fundamental measure density functional theory (FMT) is used to study binary hard sphere (HS) complexes in crystalline phases. By comparing the excess free energy, pressure and phase diagram, we show that the fundamental measure functional yields good agreements to the available simulation results of AB, AB_{2} and AB_{13} crystals. Additionally, we use this functional to study the HS models of five binary crystals, Cu_{5}Zr(C15_{b}), Cu_{51}Zr_{14}(β), Cu_{10}Zr_{7}(φ), CuZr(B2) and CuZr_{2} (C11_{b}), which are observed in the Cu-Zr system. The FMT functional gives well behaved minimum for most of the hard sphere crystal complexes in the two dimensional Gaussian space, namely a crystalline phase. However, the current version of FMT functional (white Bear) fails to give a stable minimum for the structure Cu_{10}Zr_{7}(φ). We argue that the observed solid phases for the HS models of the Cu-Zr system are true thermodynamic stable phases and can be used as a reference system in perturbation calculations.
Free Energy Calculations of Crystalline Hard Sphere Complexes Using Density Functional Theory
Gunawardana, K. G.S.H.; Song, Xueyu
2014-12-22
Recently developed fundamental measure density functional theory (FMT) is used to study binary hard sphere (HS) complexes in crystalline phases. By comparing the excess free energy, pressure and phase diagram, we show that the fundamental measure functional yields good agreements to the available simulation results of AB, AB2 and AB13 crystals. Additionally, we use this functional to study the HS models of five binary crystals, Cu5Zr(C15b), Cu51Zr14(β), Cu10Zr7(φ), CuZr(B2) and CuZr2 (C11b), which are observed in the Cu-Zr system. The FMT functional gives well behaved minimum for most of the hard sphere crystal complexes in the two dimensional Gaussian space,more » namely a crystalline phase. However, the current version of FMT functional (white Bear) fails to give a stable minimum for the structure Cu10Zr7(φ). We argue that the observed solid phases for the HS models of the Cu-Zr system are true thermodynamic stable phases and can be used as a reference system in perturbation calculations.« less
NASA Astrophysics Data System (ADS)
Rodrıguez-Guzmán, R.; Robledo, L. M.
2016-01-01
Mean-field calculations, based on the D1S, D1N and D1M parametrizations of the Gogny energy density functional, have been carried out to obtain the potential energy surfaces relevant to fission in several Ra isotopes with the neutron number 144≤ N≤ 176. Inner and outer barrier heights as well as first and second isomer excitation energies are given. The existence of a well-developed third minimum along the fission paths of Ra nuclei is analyzed in terms of the energetics of the "fragments" defining such elongated configuration. The masses and charges of the fission fragments are studied as functions of the neutron number in the parent Ra isotope. The comparison between fission and α -decay half-lives, reveals that the former becomes faster for increasing neutron numbers. Though there exists a strong variance of the results with respect to the parameters used in the computation of the spontaneous fission rate, a change in tendency is observed at N=164 with a steady increase that makes heavier neutron-rich Ra isotopes stable against fission, diminishing the importance of fission recycling in the r-process.
NASA Astrophysics Data System (ADS)
Oates, William S.; Miles, Paul; Leon, Lider; Smith, Ralph
2016-04-01
Density functional theory (DFT) provides exceptional predictions of material properties of ideal crystal structures such as elastic modulus and dielectric constants. This includes ferroelectric crystals where excellent predictions of spontaneous polarization, lattice strain, and elastic moduli have been predicted using DFT. Less analysis has focused on quantifying uncertainty of the energy landscape over a broad range of polarization states in ferroelectric materials. This is non-trivial because the degrees of freedom contained within a unit cell are reduced to a single vector order parameter which is normally polarization. For example, lead titanate contains five atoms and 15 degrees of freedom of atomic nuclei motion which contribute to the overall unit cell polarization. Bayesian statistics is used to identify the uncertainty and propagation of error of a continuum scale, Landau energy function for lead titanate. Uncertainty in different parameters is quantified and this uncertainty is propagated through the model to illustrate error propagation over the energy surface. Such results are shown to have an impact in integration of quantum simulations within a ferroelectric phase field continuum modeling framework.
NASA Astrophysics Data System (ADS)
Tran, Fabien; Blaha, Peter; Schwarz, Karlheinz; Novák, Pavel
2006-10-01
For the treatment of strongly correlated electrons, the corresponding Hartree-Fock exchange energy is used instead of the local density approximation (LDA) or generalized gradient approximation (GGA) functional, as suggested recently [P. Novák , Phys. Status Solidi B 243, 563 (2006)]. If this is done only inside the atomic spheres, using an augmented plane wave scheme, a significant simplification and reduction of computational cost is achieved with respect to the usual but costly implementation of the Hartree-Fock formalism in solids. Starting from this, we construct exchange-correlation energy functionals of the hybrid form like B3PW91, PBE0, etc. These functionals are tested on the transition-metal monoxides MnO, FeO, CoO, and NiO, and the results are compared with the LDA, GGA, LDA+U , and experimental ones. The results show that the proposed method, which does not contain any system-dependent input parameter, gives results comparable or superior to the ones obtained with LDA+U which is designed to improve significantly over the LDA and GGA results for systems containing strongly correlated electrons. The computational efficiency, similar to the LDA+U one, and accuracy of the proposed method show that it represents a very good alternative to LDA+U .
SirT1 gain-of-function increases energy efficiency and prevents diabetes in mice
Banks, Alexander S.; Kon, Ning; Knight, Colette; Matsumoto, Michihiro; Gutiérrez-Juárez, Roger; Rossetti, Luciano; Gu, Wei; Accili, Domenico
2011-01-01
Summary In yeast, worms and flies, an extra copy of the gene encoding the Sirtuin Sir2 increases metabolic efficiency, as does administration of polyphenols like resveratrol, thought to act through Sirtuins. But evidence that Sirtuin gain-of-function results in increased metabolic efficiency in mammals is limited. We generated transgenic mice with moderate overexpression of SirT1, designed to mimic the Sirtuin gain-of-function that improves metabolism in C.elegans. These mice exhibit normal insulin sensitivity, but decreased food intake and locomotor activity, resulting in decreased energy expenditure. However, in various models of insulin resistance and diabetes, SirT1 transgenics display improved glucose tolerance due to decreased hepatic glucose production and increased adiponectin levels, without changes in body weight or composition. We conclude that SirT1 gain-of-function primes the organism for metabolic adaptation to insulin resistance, increasing hepatic insulin sensitivity and decreasing whole-body energy requirements. These findings have important implications for Sirtuin-based therapies in humans. PMID:18840364
Bao, Peng
2013-01-01
An interaction energy decomposition analysis method based on the block-localized wavefunction (BLW-ED) approach is described. The first main feature of the BLW-ED method is that it combines concepts of valence bond and molecular orbital theories such that the intermediate and physically intuitive electron-localized states are variationally optimized by self-consistent field calculations. Furthermore, the block-localization scheme can be used both in wave function theory and in density functional theory, providing a useful tool to gain insights on intermolecular interactions that would otherwise be difficult to obtain using the delocalized Kohn–Sham DFT. These features allow broad applications of the BLW method to energy decomposition (BLW-ED) analysis for intermolecular interactions. In this perspective, we outline theoretical aspects of the BLW-ED method, and illustrate its applications in hydrogen-bonding and π–cation intermolecular interactions as well as metal–carbonyl complexes. Future prospects on the development of a multistate density functional theory (MSDFT) are presented, making use of block-localized electronic states as the basis configurations. PMID:21369567
NASA Astrophysics Data System (ADS)
Feng, Yue
Plasma is currently a hot topic and it has many significant applications due to its composition of both positively and negatively charged particles. The energy distribution function is important in plasma science since it characterizes the ability of the plasma to affect chemical reactions, affect physical outcomes, and drive various applications. The Boltzmann Transport Equation is an important kinetic equation that provides an accurate basis for characterizing the distribution function---both in energy and space. This dissertation research proposes a multi-term approximation to solve the Boltzmann Transport Equation by treating the relaxation process using an expansion of the electron distribution function in Legendre polynomials. The elastic and 29 inelastic cross sections for electron collisions with nitrogen molecules (N2) and singly ionized nitrogen molecules ( N+2 ) have been used in this application of the Boltzmann Transport Equation. Different numerical methods have been considered to compare the results. The numerical methods discussed in this thesis are the implicit time-independent method, the time-dependent Euler method, the time-dependent Runge-Kutta method, and finally the implicit time-dependent relaxation method by generating the 4-way grid with a matrix solver. The results show that the implicit time-dependent relaxation method is the most accurate and stable method for obtaining reliable results. The results were observed to match with the published experimental data rather well.
Enhanced cardiovascular function and energy level by a novel chromium (III)-supplement.
Thirunavukkarasu, Mahesh; Penumathsa, Sureshvarma; Juhasz, Bela; Zhan, Lijun; Bagchi, Manashi; Yasmin, Taharat; Shara, Michael A; Thatte, Hemant S; Bagchi, Debasis; Maulik, Nilanjana
2006-01-01
The impetus for the novel Energy Formula (EF) which combines the niacin-bound chromium (III) (0.45%) (NBC), standardized extract of Withania somnifera extracts (10.71%), caffeine (22.76%), D-ribose (10.71%) and selected amino acids such as phenylalanine, taurine and glutamine (55.37%) was based on the knowledge of the cardioprotective potentials of the Withania somnifera extract, caffeine and D-ribose as well as their abilities to increase energy levels and the abilities of amino acids to increase the muscle mass and energy levels. The effect of oral supplementation of EF on the safety, myocardial energy levels and cardioprotective ability were investigated in an ischemic-reperfused myocardium model in both male and female Sprague-Dawley rats over 90 days trial period. At the completion of 90 days, the EF-treated male and female rats gained 9.4% and 3.1% less body weights, respectively, as compared to their corresponding control groups. No significant difference was found in the levels of lipid peroxidation and activities of hepatic Aspartate transaminase, Alanine transaminase and Alkaline phosphatase in EF treatment when compared with control animals. The male and female rat hearts were subjected to 30 min of global ischemia followed by 2 h of reperfusion at 30 and 90 days of EF treatment. Cardiovascular functions including heart rate, coronary flow, aortic flow, dp/dt(max), left ventricular developed pressure (LVDP) and infarct size were monitored. The levels of myocardial adenosine triphosphate (ATP), creatine phosphate (CP), phospho-adenosine monophosphate kinase (p-AMPK) levels, were analyzed at the end of 30 and 90 days of treatment. Significant improvement was observed in all parameters in the EF treatment groups as compared to their corresponding controls. Thus the niacin-bound chromium (III) based energy formula is safe and effective supplement to boost energy levels and cardioprotection. PMID:17012764
Wang, F-F; Jenness, G; Al-Saidi, W A; Jordan, K D
2010-04-01
Localized molecular orbital energy decomposition analysis and symmetry-adapted perturbation theory (SAPT) calculations are used to analyze the two- and three-body interaction energies of four low-energy isomers of (H(2)O)(6) in order to gain insight into the performance of several popular density functionals for describing the electrostatic, exchange-repulsion, induction, and short-range dispersion interactions between water molecules. The energy decomposition analyses indicate that all density functionals considered significantly overestimate the contributions of charge transfer to the interaction energies. Moreover, in contrast to some studies that state that density functional theory (DFT) does not include dispersion interactions, we adopt a broader definition and conclude that for (H(2)O)(6) the short-range dispersion interactions recovered in the DFT calculations account about 75% or more of the net (short-range plus long-range) dispersion energies obtained from the SAPT calculations. PMID:20387929
NASA Astrophysics Data System (ADS)
Wang, F.-F.; Jenness, G.; Al-Saidi, W. A.; Jordan, K. D.
2010-04-01
Localized molecular orbital energy decomposition analysis and symmetry-adapted perturbation theory (SAPT) calculations are used to analyze the two- and three-body interaction energies of four low-energy isomers of (H2O)6 in order to gain insight into the performance of several popular density functionals for describing the electrostatic, exchange-repulsion, induction, and short-range dispersion interactions between water molecules. The energy decomposition analyses indicate that all density functionals considered significantly overestimate the contributions of charge transfer to the interaction energies. Moreover, in contrast to some studies that state that density functional theory (DFT) does not include dispersion interactions, we adopt a broader definition and conclude that for (H2O)6 the short-range dispersion interactions recovered in the DFT calculations account about 75% or more of the net (short-range plus long-range) dispersion energies obtained from the SAPT calculations.
Hussain, Tanveer; Ahuja, Rajeev; Chakraborty, Sudip; De Sarkar, Abir; Johansson, Börje
2014-09-22
The electronic structure, stability, and hydrogen storage capacity of strain induced Mg functionalized silicene (SiMg) and silicane (SiHMg) monolayers have been studied by means of van der Waals induced first principles calculations. A drastic increase in the binding energy of Mg adatoms on both the monolayers under the biaxial symmetric strain of 10% ensures the uniform distribution of dopants over the substrates. A significant positive charge on each Mg accumulates a maximum of six H{sub 2} molecules with H{sub 2} storage capacity of 8.10% and 7.95% in case of SiMg and SiHMg, respectively. The average adsorption energy for H{sub 2} molecules has been found ideal for practical H{sub 2} storage materials.
LDRD final report : energy conversion using chromophore-functionalized carbon nanotubes.
Vance, Andrew L.; Zifer, Thomas; Zhou, Xinjian; Leonard, Francois Leonard; Wong, Bryan Matthew; Kane, Alexander; Katzenmeyer, Aaron Michael; Krafcik, Karen Lee
2010-09-01
With the goal of studying the conversion of optical energy to electrical energy at the nanoscale, we developed and tested devices based on single-walled carbon nanotubes functionalized with azobenzene chromophores, where the chromophores serve as photoabsorbers and the nanotube as the electronic read-out. By synthesizing chromophores with specific absorption windows in the visible spectrum and anchoring them to the nanotube surface, we demonstrated the controlled detection of visible light of low intensity in narrow ranges of wavelengths. Our measurements suggested that upon photoabsorption, the chromophores isomerize to give a large change in dipole moment, changing the electrostatic environment of the nanotube. All-electron ab initio calculations were used to study the chromophore-nanotube hybrids, and show that the chromophores bind strongly to the nanotubes without disturbing the electronic structure of either species. Calculated values of the dipole moments supported the notion of dipole changes as the optical detection mechanism.
Jaworski, M A; Gray, T K; Kaita, R; Kallman, J; Kugel, H; LeBlanc, B; McLean, A; Sabbagh, S A; Soukanovskii, V; Stotler, D P
2011-06-03
The National Spherical Torus Experiment (NSTX) has recently studied the use of a liquid lithium divertor (LLD). Divertor Langmuir probes have also been installed for making measurements of the local plasma conditions. A non-local probe interpretation method is used to supplement the classical probe interpretation and obtain measurements of the electron energy distribution function (EEDF) which show the occurrence of a hot-electron component. Analysis is made of two discharges within a sequence that exhibited changes in plasma fueling efficiency. It is found that the local electron temperature increases and that this increase is most strongly correlated with the energy contained within the hot-electron population. Preliminary interpretative modeling indicates that kinetic effects are likely in the NSTX.
Orbital relaxation effects on Kohn–Sham frontier orbital energies in density functional theory
Zhang, DaDi; Zheng, Xiao; Li, Chen; Yang, Weitao
2015-04-21
We explore effects of orbital relaxation on Kohn–Sham frontier orbital energies in density functional theory by using a nonempirical scaling correction approach developed in Zheng et al. [J. Chem. Phys. 138, 174105 (2013)]. Relaxation of Kohn–Sham orbitals upon addition/removal of a fractional number of electrons to/from a finite system is determined by a systematic perturbative treatment. The information of orbital relaxation is then used to improve the accuracy of predicted Kohn–Sham frontier orbital energies by Hartree–Fock, local density approximation, and generalized gradient approximation methods. The results clearly highlight the significance of capturing the orbital relaxation effects. Moreover, the proposed scaling correction approach provides a useful way of computing derivative gaps and Fukui quantities of N-electron finite systems (N is an integer), without the need to perform self-consistent-field calculations for (N ± 1)-electron systems.
Photoemission and density functional theory study of Ir(111); energy band gap mapping
NASA Astrophysics Data System (ADS)
Pletikosić, I.; Kralj, M.; Šokčević, D.; Brako, R.; Lazić, P.; Pervan, P.
2010-04-01
We have performed combined angle-resolved photoemission spectroscopy (ARPES) experiments and density functional theory (DFT) calculations of the electronic structure of the Ir(111) surface, with the focus on the existence of energy band gaps. The investigation was motivated by the experimental results suggesting Ir(111) as an ideal support for the growth of weakly bonded graphene. Therefore, our prime interest was electronic structure around the \\bar {\\mathrm {K}} symmetry point. In accordance with DFT calculations, ARPES has shown a wide energy band gap with the shape of a parallelogram centred around the \\bar {\\mathrm {K}} point. Within the gap three surface states were identified; one just below the Fermi level and two spin-orbit split surface states at the bottom of the gap.
NASA Astrophysics Data System (ADS)
Endo, Kazunaka
2016-02-01
In the Auger electron spectra (AES) simulations, we define theoretical modified kinetic energies of AES in the density functional theory (DFT) calculations. The modified kinetic energies correspond to two final-state holes at the ground state and at the transition-state in DFT calculations, respectively. This method is applied to simulate Auger electron spectra (AES) of 2nd periodic atom (Li, Be, B, C, N, O, F)-involving substances (LiF, beryllium, boron, graphite, GaN, SiO2, PTFE) by deMon DFT calculations using the model molecules of the unit cell. Experimental KVV (valence band electrons can fill K-shell core holes or be emitted during KVV-type transitions) AES of the (Li, O) atoms in the substances agree considerably well with simulation of AES obtained with the maximum kinetic energies of the atoms, while, for AES of LiF, and PTFE substance, the experimental F KVV AES is almost in accordance with the spectra from the transitionstate kinetic energy calculations.
2015-01-01
A key quantity for molecule–metal interfaces is the energy level alignment of molecular electronic states with the metallic Fermi level. We develop and apply an efficient theoretical method, based on density functional theory (DFT) that can yield quantitatively accurate energy level alignment information for physisorbed metal–molecule interfaces. The method builds on the “DFT+Σ” approach, grounded in many-body perturbation theory, which introduces an approximate electron self-energy that corrects the level alignment obtained from conventional DFT for missing exchange and correlation effects associated with the gas-phase molecule and substrate polarization. Here, we extend the DFT+Σ approach in two important ways: first, we employ optimally tuned range-separated hybrid functionals to compute the gas-phase term, rather than rely on GW or total energy differences as in prior work; second, we use a nonclassical DFT-determined image-charge plane of the metallic surface to compute the substrate polarization term, rather than the classical DFT-derived image plane used previously. We validate this new approach by a detailed comparison with experimental and theoretical reference data for several prototypical molecule–metal interfaces, where excellent agreement with experiment is achieved: benzene on graphite (0001), and 1,4-benzenediamine, Cu-phthalocyanine, and 3,4,9,10-perylene-tetracarboxylic-dianhydride on Au(111). In particular, we show that the method correctly captures level alignment trends across chemical systems and that it retains its accuracy even for molecules for which conventional DFT suffers from severe self-interaction errors. PMID:25741626
Effective Ginzburg-Landau free energy functional for multi-band isotropic superconductors
NASA Astrophysics Data System (ADS)
Grigorishin, Konstantin V.
2016-04-01
It has been shown that interband mixing of gradients of two order parameters (drag effect) in an isotropic bulk two-band superconductor plays important role - such a quantity of the intergradients coupling exists that the two-band superconductor is characterized with a single coherence length and a single Ginzburg-Landau (GL) parameter. Other quantities or neglecting of the drag effect lead to existence of two coherence lengths and dynamical instability due to violation of the phase relations between the order parameters. Thus so-called type-1.5 superconductors are impossible. An approximate method for solving of set of GL equations for a multi-band superconductor has been developed: using the result about the drag effect it has been shown that the free-energy functional for a multi-band superconductor can be reduced to the GL functional for an effective single-band superconductor.
Quasi-particle energy spectra in local reduced density matrix functional theory.
Lathiotakis, Nektarios N; Helbig, Nicole; Rubio, Angel; Gidopoulos, Nikitas I
2014-10-28
Recently, we introduced [N. N. Lathiotakis, N. Helbig, A. Rubio, and N. I. Gidopoulos, Phys. Rev. A 90, 032511 (2014)] local reduced density matrix functional theory (local RDMFT), a theoretical scheme capable of incorporating static correlation effects in Kohn-Sham equations. Here, we apply local RDMFT to molecular systems of relatively large size, as a demonstration of its computational efficiency and its accuracy in predicting single-electron properties from the eigenvalue spectrum of the single-particle Hamiltonian with a local effective potential. We present encouraging results on the photoelectron spectrum of molecular systems and the relative stability of C20 isotopes. In addition, we propose a modelling of the fractional occupancies as functions of the orbital energies that further improves the efficiency of the method useful in applications to large systems and solids. PMID:25362285
Quasi-particle energy spectra in local reduced density matrix functional theory
Lathiotakis, Nektarios N.; Helbig, Nicole; Rubio, Angel
2014-10-28
Recently, we introduced [N. N. Lathiotakis, N. Helbig, A. Rubio, and N. I. Gidopoulos, Phys. Rev. A 90, 032511 (2014)] local reduced density matrix functional theory (local RDMFT), a theoretical scheme capable of incorporating static correlation effects in Kohn-Sham equations. Here, we apply local RDMFT to molecular systems of relatively large size, as a demonstration of its computational efficiency and its accuracy in predicting single-electron properties from the eigenvalue spectrum of the single-particle Hamiltonian with a local effective potential. We present encouraging results on the photoelectron spectrum of molecular systems and the relative stability of C{sub 20} isotopes. In addition, we propose a modelling of the fractional occupancies as functions of the orbital energies that further improves the efficiency of the method useful in applications to large systems and solids.
Brandenburg, Jan Gerit; Caldeweyher, Eike; Grimme, Stefan
2016-06-21
We extend the recently introduced PBEh-3c global hybrid density functional [S. Grimme et al., J. Chem. Phys., 2015, 143, 054107] by a screened Fock exchange variant based on the Henderson-Janesko-Scuseria exchange hole model. While the excellent performance of the global hybrid is maintained for small covalently bound molecules, its performance for computed condensed phase mass densities is further improved. Most importantly, a speed up of 30 to 50% can be achieved and especially for small orbital energy gap cases, the method is numerically much more robust. The latter point is important for many applications, e.g., for metal-organic frameworks, organic semiconductors, or protein structures. This enables an accurate density functional based electronic structure calculation of a full DNA helix structure on a single core desktop computer which is presented as an example in addition to comprehensive benchmark results. PMID:27240749
Stored energy function and compressibility of compressible rubberlike materials under large strain
NASA Technical Reports Server (NTRS)
Peng, S. T. J.; Landel, R. F.
1975-01-01
By using new invariants in the theory of finite elasticity an expression is obtained for the stored energy function of slightly compressible materials in which the effects of the distortional change (change of shape) and of the volume change are clearly separated. The volume-related terms are expressed as a function of the third invariant, the classical compressibility, and an induced anisotropy of the effective compressibility which is due to the large deformations. After evaluating the terms, using data on pressure, volume, uniaxial strain, and fractional volume change vs strain data on natural rubber from the literature, it is shown that the volume change contribution to the total stress observed in a simple tensile experiment can be clearly separated from the distortional contribution, even at finite strains.
Georgakilas, Vasilios; Tiwari, Jitendra N; Kemp, K Christian; Perman, Jason A; Bourlinos, Athanasios B; Kim, Kwang S; Zboril, Radek
2016-05-11
This Review focuses on noncovalent functionalization of graphene and graphene oxide with various species involving biomolecules, polymers, drugs, metals and metal oxide-based nanoparticles, quantum dots, magnetic nanostructures, other carbon allotropes (fullerenes, nanodiamonds, and carbon nanotubes), and graphene analogues (MoS2, WS2). A brief description of π-π interactions, van der Waals forces, ionic interactions, and hydrogen bonding allowing noncovalent modification of graphene and graphene oxide is first given. The main part of this Review is devoted to tailored functionalization for applications in drug delivery, energy materials, solar cells, water splitting, biosensing, bioimaging, environmental, catalytic, photocatalytic, and biomedical technologies. A significant part of this Review explores the possibilities of graphene/graphene oxide-based 3D superstructures and their use in lithium-ion batteries. This Review ends with a look at challenges and future prospects of noncovalently modified graphene and graphene oxide. PMID:27033639
High-resolution Rotational Spectrum, Dunham Coefficients, and Potential Energy Function of NaCl
NASA Astrophysics Data System (ADS)
Cabezas, C.; Cernicharo, J.; Quintana-Lacaci, G.; Peña, I.; Agundez, M.; Velilla Prieto, L.; Castro-Carrizo, A.; Zuñiga, J.; Bastida, A.; Alonso, J. L.; Requena, A.
2016-07-01
We report laboratory spectroscopy for the first time of the J = 1–0 and J = 2–1 lines of Na35Cl and Na37Cl in several vibrational states. The hyperfine structure has been resolved in both transitions for all vibrational levels, which permit us to predict with high accuracy the hyperfine splitting of the rotational transitions of the two isotopologues at higher frequencies. The new data have been merged with all previous works at microwave, millimeter, and infrared wavelengths and fitted to a series of mass-independent Dunham parameters and to a potential energy function. The obtained parameters have been used to compute a new dipole moment function, from which the dipole moment for infrared transitions up to Δv = 8 has been derived. Frequency and intensity predictions are provided for all rovibrational transitions up to J = 150 and v = 8, from which the ALMA data of evolved stars can be modeled and interpreted.
The diene isomerization energies dataset: A difficult test for double-hybrid density functionals?
NASA Astrophysics Data System (ADS)
Wykes, M.; Pérez-Jiménez, A. J.; Adamo, C.; Sancho-García, J. C.
2015-06-01
We have systematically analyzed the performance of some representative double-hybrid density functionals (including PBE0-DH, PBE-QIDH, PBE0-2, XYG3, XYGJ-OS, and xDH-PBE0) for a recently introduced database of diene isomerization energies. Double-hybrid models outperform their corresponding hybrid forms (for example, PBE0-DH, PBE0-2, and PBE-QIDH are more accurate than PBE0) and the XYG3, XYGJ-OS, and xDH-PBE0 functionals perform excellently, providing root mean square deviation values within "calibration accuracy." XYGJ-OS and xDH-PBE0 also rival the best performing post-Hartree-Fock methods at a substantially lower cost.
NASA Astrophysics Data System (ADS)
Kang, Hyun-Ju; Choi, Hyeok; Kim, Jae-Hyun; Lee, Se-Hun; Yoo, Tae-Ho; Chung, Chin-Wook
2016-06-01
A modified central difference method (MCDM) is proposed to obtain the electron energy distribution functions (EEDFs) in single Langmuir probes. Numerical calculation of the EEDF with MCDM is simple and has less noise. This method provides the second derivatives at a given point as the weighted average of second order central difference derivatives calculated at different voltage intervals, weighting each by the square of the interval. In this paper, the EEDFs obtained from MCDM are compared to those calculated via the averaged central difference method. It is found that MCDM effectively suppresses the noises in the EEDF, while the same number of points are used to calculate of the second derivative.
Ulrich-Lai, Yvonne M.; Ryan, Karen K.
2014-01-01
Significant co-morbidities between obesity-related metabolic disease and stress-related psychological disorders suggest important functional interactions between energy balance and brain stress integration. Largely overlapping neural circuits control these systems, and this anatomical arrangement optimizes opportunities for mutual influence. Here we first review the current literature identifying effects of metabolic neuroendocrine signals on stress regulation, and vice versa. Next, the contributions of reward driven food intake to these metabolic and stress interactions are discussed. Lastly, we consider the inter-relationships among metabolism, stress and reward in light of their important implications in the development of therapies for metabolism- or stress-related disease. PMID:24630812
Constitutive Modeling of Skeletal Muscle Tissue with an Explicit Strain-Energy Function
Odegard, G.M.; Donahue, T.L. Haut; Morrow, D.A.; Kaufman, K.R.
2010-01-01
While much work has previously been done in the modeling of skeletal muscle, no model has, to date, been developed that describes the mechanical behavior with an explicit strain-energy function associated with the active response of skeletal muscle tissue. A model is presented herein that has been developed to accommodate this design consideration using a robust dynamical approach. The model shows excellent agreement with a previously published model of both the active and passive length-tension properties of skeletal muscle. PMID:19045546
Nam, Sang Ki; Verboncoeur, John P.
2008-10-13
Global models (GMs) have proven a key modeling tool for the plasma processing field due to simplicity and speed. However, a GM requires specification of the electron energy distribution function (EEDF). The assumption of a Maxwellian EEDF leads to inaccurate reaction rate coefficients and results in error in plasma parameter prediction in high power microwave (HPM) driven discharges. Recently, a GM was developed with a pressure-independent enhanced EEDF to improve fidelity for modeling HPM breakdown. In this work, the GM is extended to 2 decades in frequency, and the frequency effect on HPM breakdown and the EEDF is investigated.
Klein, A.; Körber, C.; Wachau, A.; Säuberlich, F.; Gassenbauer, Y.; Harvey, S.P.; Proffit, Diana E.; Mason, Thomas O.
2010-11-02
Doping limits, band gaps, work functions and energy band alignments of undoped and donor-doped transparent conducting oxides ZnO, In{sub 2}O{sub 3}, and SnO{sub 2} as accessed by X-ray and ultraviolet photoelectron spectroscopy (XPS/UPS) are summarized and compared. The presented collection provides an extensive data set of technologically relevant electronic properties of photovoltaic transparent electrode materials and illustrates how these relate to the underlying defect chemistry, the dependence of surface dipoles on crystallographic orientation and/or surface termination, and Fermi level pinning.
Skeleton series and multivaluedness of the self-energy functional in zero space-time dimensions
NASA Astrophysics Data System (ADS)
Rossi, Riccardo; Werner, Félix
2015-12-01
Recently, Kozik, Ferrero and Georges discovered numerically that for a family of fundamental models of interacting fermions, the self-energy {{Σ }}[G] is a multi-valued functional of the fully dressed single-particle propagator G, and that the skeleton diagrammatic series {{{Σ }}}{{bold}}[G] converges to the wrong branch above a critical interaction strength. We consider the zero space-time dimensional case, where the same mathematical phenomena appear from elementary algebra. We also find a similar phenomenology for the fully bold formalism built on the fully dressed single-particle propagator and pair propagator.
Characterization of detection efficiency as function of energy for soft x-ray detectorsa)
NASA Astrophysics Data System (ADS)
Pacella, D.; Mazon, D.; Romano, A.; Malard, P.; Pizzicaroli, G.
2008-10-01
A new technique has been especially developed for determining the detection efficiency of the silicon surface barrier diodes used for tomography reconstructions at Tore Supra, as function of the energy of the x-ray photons, in the range of 4-25keV. The response of these diodes has been studied for different bias voltages (0-120V), with a portable x-ray electronic tube and a cooled Si-p-i-n diode, working in photon counting mode, for the absolute calibration.
Brown, James Carrington, Tucker
2015-07-28
Although phase-space localized Gaussians are themselves poor basis functions, they can be used to effectively contract a discrete variable representation basis [A. Shimshovitz and D. J. Tannor, Phys. Rev. Lett. 109, 070402 (2012)]. This works despite the fact that elements of the Hamiltonian and overlap matrices labelled by discarded Gaussians are not small. By formulating the matrix problem as a regular (i.e., not a generalized) matrix eigenvalue problem, we show that it is possible to use an iterative eigensolver to compute vibrational energy levels in the Gaussian basis.
Matrix coefficient identification in an elliptic equation with the convex energy functional method
NASA Astrophysics Data System (ADS)
Hinze, Michael; Nhan Tam Quyen, Tran
2016-08-01
In this paper we study the inverse problem of identifying the diffusion matrix in an elliptic PDE from measurements. The convex energy functional method with Tikhonov regularization is applied to tackle this problem. For the discretization we use the variational discretization concept, where the PDE is discretized with piecewise linear, continuous finite elements. We show the convergence of approximations. Using a suitable source condition, we prove an error bound for discrete solutions. For the numerical solution we propose a gradient-projection algorithm and prove the strong convergence of its iterates to a solution of the identification problem. Finally, we present a numerical experiment which illustrates our theoretical results.
Brown, James; Carrington, Tucker
2015-07-28
Although phase-space localized Gaussians are themselves poor basis functions, they can be used to effectively contract a discrete variable representation basis [A. Shimshovitz and D. J. Tannor, Phys. Rev. Lett. 109, 070402 (2012)]. This works despite the fact that elements of the Hamiltonian and overlap matrices labelled by discarded Gaussians are not small. By formulating the matrix problem as a regular (i.e., not a generalized) matrix eigenvalue problem, we show that it is possible to use an iterative eigensolver to compute vibrational energy levels in the Gaussian basis. PMID:26233104
NASA Astrophysics Data System (ADS)
Brown, James; Carrington, Tucker
2015-07-01
Although phase-space localized Gaussians are themselves poor basis functions, they can be used to effectively contract a discrete variable representation basis [A. Shimshovitz and D. J. Tannor, Phys. Rev. Lett. 109, 070402 (2012)]. This works despite the fact that elements of the Hamiltonian and overlap matrices labelled by discarded Gaussians are not small. By formulating the matrix problem as a regular (i.e., not a generalized) matrix eigenvalue problem, we show that it is possible to use an iterative eigensolver to compute vibrational energy levels in the Gaussian basis.
NASA Astrophysics Data System (ADS)
Morris, Nicholas J.
During the previous decade, the development of energy harvesting devices based on piezoelectric materials has garnered great interest. The ability to capture ambient mechanical energy and convert it to useable electricity is a potential solution to the ever-growing energy crisis. One of the most attractive functional materials used in these devices is zinc oxide (ZnO). This material's relative low cost and ease of large-area processing has spurred numerous device designs based around it. The ability to grow ZnO nanostructures of various geometries with low-temperature chemical methods makes this material even more attractive for flexible devices. Although numerous device architectures have been developed, the long-term mechanical reliability has not been addressed. This work focuses on the fabrication and mechanical failure analysis of the flexible components typically used in piezoelectric energy harvesting devices. A three-phase iterative design process was used to fabricate prototypical piezoelectric nanogenerators, based on ZnO nanowires. An output of several millivolts was achieved under normal contact and microtensile loading, but device failure occurred after only a few loading cycles, in all cases. Ex situ failure analysis confirmed the primary sources of failure, which became the focus of further, component-level studies. Failure was primarily seen in the flexible electrodes of the nanogenerating devices, but was also observed in the functional piezoelectric layer itself. Flexible electrodes comprised of polyester substrates with transparent conductive oxide (TCO) coatings were extensively investigated under various loading scenarios to mimic tribo-mechanical stresses applied during fabrication and use in flexible contact-based devices. The durability of these films was explored using microtensile testing, spherical nanoindentation, controlled mechanical buckling, stress corrosion cracking, and shear-contact reciprocating wear. The electro
Efficient calculation of potential energy surfaces for the generation of vibrational wave functions
NASA Astrophysics Data System (ADS)
Rauhut, Guntram
2004-11-01
An automatic procedure for the generation of potential energy surfaces based on high level ab initio calculations is described. It allows us to determine the vibrational wave functions for molecules of up to ten atoms. Speedups in computer time of about four orders of magnitude in comparison to standard implementations were achieved. Effects due to introduced approximations—within the computation of the potential—on fundamental modes obtained from vibrational self-consistent field and vibrational configuration interaction calculations are discussed. Benchmark calculations are provided for formaldehyde and 1,2,5-oxadiazole (furazan).
Efficient calculation of potential energy surfaces for the generation of vibrational wave functions.
Rauhut, Guntram
2004-11-15
An automatic procedure for the generation of potential energy surfaces based on high level ab initio calculations is described. It allows us to determine the vibrational wave functions for molecules of up to ten atoms. Speedups in computer time of about four orders of magnitude in comparison to standard implementations were achieved. Effects due to introduced approximations--within the computation of the potential--on fundamental modes obtained from vibrational self-consistent field and vibrational configuration interaction calculations are discussed. Benchmark calculations are provided for formaldehyde and 1,2,5-oxadiazole (furazan). PMID:15538851
Tunable fluorescence in chromophore-functionalized nanodiamond induced by energy transfer
NASA Astrophysics Data System (ADS)
Maitra, Urmimala; Jain, Ankit; George, Subi J.; Rao, C. N. R.
2011-08-01
Hybrid materials comprising diamond nanoparticles (ND) and oligo(phenylenevinylenes) (OPVs) have been synthesized by the covalent linking of acid-functionalized ND and OPV-amine. Chromophore-functionalized ND particles with long alkyl and π-conjugated groups are readily dispersed in various organic solvents without any precipitation after several hours. A careful study of the properties of the hybrid materials revealed an aggregation-induced energy transfer from the blue fluorescent nanodiamonds to green emitting OPVs. At very low concentrations the hybrid emits in the blue region, but as the concentration is increased a gradual transition from blue to green emission occurs. Competitive processes such as aggregation-induced enhanced emission and self-absorption have been ruled out and a molecular picture of the phenomenon is proposed. This strategy can open a plethora of new avenues for fluorescent nanodiamonds in optoelectronics and light harvesting apart from bio-imaging.Hybrid materials comprising diamond nanoparticles (ND) and oligo(phenylenevinylenes) (OPVs) have been synthesized by the covalent linking of acid-functionalized ND and OPV-amine. Chromophore-functionalized ND particles with long alkyl and π-conjugated groups are readily dispersed in various organic solvents without any precipitation after several hours. A careful study of the properties of the hybrid materials revealed an aggregation-induced energy transfer from the blue fluorescent nanodiamonds to green emitting OPVs. At very low concentrations the hybrid emits in the blue region, but as the concentration is increased a gradual transition from blue to green emission occurs. Competitive processes such as aggregation-induced enhanced emission and self-absorption have been ruled out and a molecular picture of the phenomenon is proposed. This strategy can open a plethora of new avenues for fluorescent nanodiamonds in optoelectronics and light harvesting apart from bio-imaging. Electronic
Density functional theory for low-energy electron-molecule scattering
NASA Astrophysics Data System (ADS)
Burke, Kieron; Wasserman, Adam
2004-09-01
Time-dependent density functional theory (TDDFT) is becoming popular as an approach to time-dependent electronic problems[1]. In the weak field regime, TDDFT predicts electronic transition frequencies and optical spectra of atoms, molecules, clusters, and solids, with an accuracy comparable to high-level wavefunction calculations at a fraction of the computational cost[2]. For large systems, TDDFT is the method of choice. Given the importance of correlation effects in low-energy electron-molecule scattering, extracting scattering amplitudes from TDDFT appears desirable. I will review this background, and outline how this can be done[3]. Detailed results will be shown by Wasserman in another talk. [1] Time-Dependent Density Functional Theory, M.A.L. Marques and E.K.U. Gross, Annu. Rev. Phys. Chem. 55, 427 (2004). [2] Time-dependent density functional theory in quantum chemistry, F. Furche and K. Burke, to appear in 1st vol. of Annu. Rev. of Computational Chemistry (2004) [3] Electron-molecule scattering from time-dependent density functional theory A. Wasserman, N.T. Maitra, and K. Burke, submitted (see http:dft.rutgers.edu/pubs/publist.html).
NASA Astrophysics Data System (ADS)
Atalla, Viktor; Zhang, Igor Ying; Hofmann, Oliver T.; Ren, Xinguo; Rinke, Patrick; Scheffler, Matthias
2016-07-01
We obtain the exchange parameter of hybrid functionals by imposing the fundamental condition of a piecewise linear total energy with respect to electron number. For the Perdew-Burke-Ernzerhof (PBE) hybrid family of exchange-correlation functionals (i.e., for an approximate generalized Kohn-Sham theory) this implies that (i) the highest occupied molecular orbital corresponds to the ionization potential (I ), (ii) the energy of the lowest unoccupied molecular orbital corresponds to the electron affinity (A ), and (iii) the energies of the frontier orbitals are constant as a function of their occupation. In agreement with a previous study [N. Sai et al., Phys. Rev. Lett. 106, 226403 (2011), 10.1103/PhysRevLett.106.226403], we find that these conditions are met for high values of the exact exchange admixture α and illustrate their importance for the tetrathiafulvalene-tetracyanoquinodimethane complex for which standard density functional theory functionals predict artificial electron transfer. We further assess the performance for atomization energies and weak interaction energies. We find that atomization energies are significantly underestimated compared to PBE or PBE0, whereas the description of weak interaction energies improves significantly if a 1 /R6 van der Waals correction scheme is employed.
Extra-galactic high-energy transients: event rate density and luminosity function
NASA Astrophysics Data System (ADS)
Sun, Hui; Zhang, Bing; Li, Zhuo
2015-08-01
Several types of extra-galactic high-energy transients have been discovered, which include high-luminosity and low-luminosity long-duration gamma-ray bursts (GRBs), short-duration GRBs, supernova shock breakouts (SBOs), and tidal disruption events (TDEs) without or with a relativistic jet. In this paper, we apply a unified method to systematically study the reshift-dependent event rate densities and luminosity functions of these extra-galactic high-energy transients. We consider star formation history as the tracer of the redshift distribution for long GRBs and SBOs. For short GRBs, we consider the compact star merger model to introduce several possible merger delay time distribution models. For TDEs, we consider the mass distribution of supermassive black holes as a function of redshift. We derive some empirical formulae for the redshift-dependent event rate density for different types of transients. Based on the observed events, we derive the local specific event rate density, ρ0,L ∝ dρ0/dL for each type of transient, which represents its luminosity function. All the transients are consistent with having a single power law luminosity function, except the high luminosity long GRBs (HL-lGRBs), whose luminosity function can be well described by a broken power law. The total event rate density for a particular transient depends on the luminosity threshold, and we obtain the following values in units of Gpc-3 yr-1: 2.82^{+0.41}_{-0.36} for HL-lGRBs above 4×1049 erg s-1 218^{+130}_{-86} for low luminosity long GRBs above 6×1046 erg s-1 3.18^{+0.88}_{-0.70}, 2.87^{+0.80}_{-0.64}, and 6.25^{+1.73}_{-1.38} above 5×1049 erg s-1 for short GRBs with three different merger delay models (Gaussian, log-normal, and power law); 2.0^{+2.6}_{-1.3}×104 above 9×1043 erg s-1 for SBOs, 3.0^{+1.0}_{-0.8}×105 for normal TDEs above 1042 erg s-1 and 6.2^{+8.2}_{-4.0} above 3×1047 erg s-1for TDE jets as discovered by Swift. Intriguingly, the global specific event rate densities
Peterson, K.A. ); Dunning, T.H. Jr. )
1995-02-01
The hydrogen bond energy and geometry of the HF dimer have been investigated using the series of correlation consistent basis sets from aug-cc-pVDZ to aug-cc-pVQZ and several theoretical methods including Moller--Plesset perturbation and coupled cluster theories. Estimates of the complete basis set (CBS) limit have been derived for the binding energy of (HF)[sub 2] at each level of theory by utilizing the regular convergence characteristics of the correlation consistent basis sets. CBS limit hydrogen bond energies of 3.72, 4.53, 4.55, and 4.60 kcal/mol are estimated at the SCF, MP2, MP4, and CCSD(T) levels of theory, respectively. CBS limits for the intermolecular F--F distance are estimated to be 2.82, 2.74, 2.73, and 2.73 A, respectively, for the same correlation methods. The effects of basis set superposition error (BSSE) on both the binding energies and structures have also been investigated for each basis set using the standard function counterpoise (CP) method. While BSSE has a negligible effect on the intramolecular geometries, the CP-corrected F--F distance and binding energy differ significantly from the uncorrected values for the aug-cc-pVDZ basis set; these differences decrease regularly with increasing basis set size, yielding the same limits in the CBS limit. Best estimates for the equilibrium properties of the HF dimer from CCSD(T) calculations are [ital D][sub [ital e
Radiated Energy of Great Earthquakes from Teleseismic Empirical Green's Function Deconvolution
NASA Astrophysics Data System (ADS)
Baltay, Annemarie S.; Beroza, Gregory C.; Ide, Satoshi
2014-10-01
We expand on the empirical Green's function deconvolution method of Ide et al. (2011) to estimate radiated energy for the six largest earthquakes worldwide over the last 10 years: 2011 M w 9.0 Tohoku-Oki, 2004 M w 9.1 Sumatra, 2010 M w 8.8 Maule, 2005 M w 8.7 Nias, 2007 M w 8.5 Bengkulu, and 2012 M w 8.6 off-Sumatra. Deconvolution of P, SV and SH components gives consistent energy results that are comparable to estimates found independently by other researchers. Apparent stress for the five great thrust earthquakes is between 0.4 and 0.8 MPa, while the 2012 off-Sumatra strike-slip earthquake has a higher apparent stress of 3 MPa, which is consistent with other studies that find a tendency for strike-slip events to be more energetic. Our results are within the spread of apparent stress from the wider global earthquake population over a large magnitude range. The azimuthal distribution of energy in each case shows signs of directivity, and in some cases, shows less energy radiated in the trench-ward direction, which may suggest enhanced tsunami potential. We find that eGfs as small as ~M 6.5 can be used for teleseismic deconvolution, and that an eGf-mainshock magnitude difference of 1.5 units yields stable results. This implies that M 8 is the minimum mainshock size for which teleseismic eGf deconvolution will work well. We propose that a database of eGf events could be used to calculate radiated energy and apparent stress of great, hazardous events in near real time, i.e., promptly enough that it could contribute to rapid response measures.
Convexity of Energy-Like Functions: Theoretical Results and Applications to Power System Operations
Dvijotham, Krishnamurthy; Chertkov, Michael; Low, Steven
2015-01-22
Power systems are undergoing unprecedented transformations with increased adoption of renewables and distributed generation, as well as the adoption of demand response programs. All of these changes, while making the grid more responsive and potentially more efficient, pose significant challenges for power systems operators. Conventional operational paradigms are no longer sufficient as the power system may no longer have big dispatchable generators with sufficient positive and negative reserves. This increases the need for tools and algorithms that can efficiently predict safe regions of operation of the power system. In this paper, we study energy functions as a tool to design algorithms for various operational problems in power systems. These have a long history in power systems and have been primarily applied to transient stability problems. In this paper, we take a new look at power systems, focusing on an aspect that has previously received little attention: Convexity. We characterize the domain of voltage magnitudes and phases within which the energy function is convex in these variables. We show that this corresponds naturally with standard operational constraints imposed in power systems. We show that power of equations can be solved using this approach, as long as the solution lies within the convexity domain. We outline various desirable properties of solutions in the convexity domain and present simple numerical illustrations supporting our results.
Octupole deformation properties of the Barcelona-Catania-Paris energy density functionals
Robledo, L. M.; Baldo, M.; Schuck, P.; Vinas, X.
2010-03-15
We discuss the octupole deformation properties of the recently proposed Barcelona-Catania-Paris (BCP) energy density functionals for two sets of isotopes, those of radium and barium, in which it is believed that octupole deformation plays a role in the description of the ground state. The analysis is carried out in the mean field framework (Hartree-Fock-Bogoliubov approximation) by using the axially symmetric octupole moment as a constraint. The main ingredients entering the octupole collective Hamiltonian are evaluated and the lowest-lying octupole eigenstates are obtained. In this way we restore, in an approximate way, the parity symmetry spontaneously broken by the mean field and also incorporate octupole fluctuations around the ground-state solution. For each isotope the energy of the lowest lying 1{sup -} state and the B(E1) and B(E3) transition probabilities have been computed and compared to both the experimental data and the results obtained in the same framework with the Gogny D1S interaction, which are used here as a well-established benchmark. Finally, the octupolarity of the configurations involved in the way down to fission of {sup 240}Pu, which is strongly connected to the asymmetric fragment mass distribution, is studied. We confirm with this thorough study the suitability of the BCP functionals to describe octupole-related phenomena.
Complex carbohydrates as a possible source of high energy to formulate functional feeds.
Ochoa, Leonel; Paniagua Michel, José de Jesús; Olmos-Soto, Jorge
2014-01-01
Carbohydrates (CHOs) are the most abundant organic compounds found in living organisms and are a great source of metabolic energy, both for plants and animals. Besides of CHOs great potential to solve animal's energy requirements and diminishing high feed cost, we first must to understand its digestibility and assimilation to avoid several inconvenients. Today, CHOs feed animal inclusions are of great concern about cost-benefits, animal's health status, and environmental pollution. In this chapter, we make a brief description about sugars (DP1-2), oligosaccharides (DP3-9), polysaccharides (DP ≥10), and their essential characteristics to understand the role of marine and terrestrial CHOs in animal nutrition. Subsequently, we talk about basic concepts, CHOs functional benefits, suggestions about their application and successful cases. This information will contribute to produce a new generation of high-quality and energetic functional feed formulations for livestock and aquaculture farms; which must be of low cost, healthy, and environmentally friendly, with the inclusion of prebiotics and probiotics. PMID:25300550
Building a Universal Nuclear Energy Density Functional (UNEDF): SciDAC-2 Project
Carlson, Joe; Furnstahl, Dick; Lusk, Rusty; Nazarewicz, Witek; Ng, Esmond; Thompson, Ian; Vary, James
2012-06-30
An understanding of the properties of atomic nuclei is crucial for a complete nuclear theory, for element formation, for properties of stars, and for present and future energy and defense applications. During the period of Dec. 1, 2006 - Jun. 30, 2012, the UNEDF collaboration carried out a comprehensive study of all nuclei based on the most accurate knowledge of the strong nuclear interaction, the most reliable theoretical approaches, the most advanced algorithms, and extensive computational resources, with a view towards scaling to the petaflop platforms and beyond. The long-term vision initiated with UNEDF is to arrive at a comprehensive, quantitative, and unified description of nuclei and their reactions, grounded in the fundamental interactions between the constituent nucleons. We seek to replace current phenomenological models of nuclear structure and reactions with a well-founded microscopic theory that delivers maximum predictive power with well-quantified uncertainties. Specifically, the mission of this project has been three-fold: first, to find an optimal energy density functional (EDF) using all our knowledge of the nucleonic Hamiltonian and basic nuclear properties; second, to apply the EDF theory and its extensions to validate the functional using all the available relevant nuclear structure and reaction data; and third, to apply the validated theory to properties of interest that cannot be measured, in particular the properties needed for reaction theory.
Bufalo, Gennaro; Ambrosone, Luigi
2016-01-14
A method for studying the kinetics of thermal degradation of complex compounds is suggested. Although the method is applicable to any matrix whose grain size can be measured, herein we focus our investigation on thermogravimetric analysis, under a nitrogen atmosphere, of ground soft wheat and ground maize. The thermogravimetric curves reveal that there are two well-distinct jumps of mass loss. They correspond to volatilization, which is in the temperature range 298-433 K, and decomposition regions go from 450 to 1073 K. Thermal degradation is schematized as a reaction in the solid state whose kinetics is analyzed separately in each of the two regions. By means of a sieving analysis different size fractions of the material are separated and studied. A quasi-Newton fitting algorithm is used to obtain the grain size distribution as best fit to experimental data. The individual fractions are thermogravimetrically analyzed for deriving the functional relationship between activation energy of the degradation reactions and the particle size. Such functional relationship turns out to be crucial to evaluate the moments of the activation energy distribution, which is unknown in terms of the distribution calculated by sieve analysis. From the knowledge of moments one can reconstruct the reaction conversion. The method is applied first to the volatilization region, then to the decomposition region. The comparison with the experimental data reveals that the method reproduces the experimental conversion with an accuracy of 5-10% in the volatilization region and of 3-5% in the decomposition region. PMID:26671287
On the evaluation of the non-interacting kinetic energy in density functional theory.
Peach, Michael J G; Griffiths, David G J; Tozer, David J
2012-04-14
The utility of both an orbital-free and a single-orbital expression for computing the non-interacting kinetic energy in density functional theory is investigated for simple atomic systems. The accuracy of both expressions is governed by the extent to which the Kohn-Sham equation is solved for the given exchange-correlation functional and so special attention is paid to the influence of finite Gaussian basis sets. The orbital-free expression is a statement of the virial theorem and its accuracy is quantified. The accuracy of the single-orbital expression is sensitive to the choice of Kohn-Sham orbital. The use of particularly compact orbitals is problematic because the failure to solve the Kohn-Sham equation exactly in regions where the orbital has decayed to near-zero leads to unphysical behaviour in regions that contribute to the kinetic energy, rendering it inaccurate. This problem is particularly severe for core orbitals, which would otherwise appear attractive due to their formally nodeless nature. The most accurate results from the single-orbital expression are obtained using the relatively diffuse, highest occupied orbitals, although special care is required at orbital nodes. PMID:22502495
NASA Astrophysics Data System (ADS)
Molz, F. J.; Guan, J.
2004-12-01
To improve understanding of property measurements in heterogeneous media, an energy-based weighting function concept was developed [Molz et al., WRR, 39(4), DAN-1, 2003]. In (assumed) homogeneous media, the instrument spatial weighting function (ISWF) depends only on the energy dissipation distribution set up by the measurement procedure, and it reduces to simply inverse sample volume (uniform weighting) for the 1-D parallel flow case (ideal permeameter). For 1-D transient flow in homogeneous media, such as with slug tests, the ISWF varies with position and time, with 95% of the total weighting contained within 115 well radii, even late in the test [Molz et al., Ground Water, in press, 2004]. The present talk deals with the heterogeneous case, which is what one deals with in natural systems. Thus, in actual measurements, the identification of the ISWF is connected to the problem of determining an "equivalent" hydraulic conductivity (Ke), and it would be ideal if the criterion for "equivalence" based on energy-dissipation- rate-weighting would produce the same Ke as that based on the common permeameter test. It can be shown that for 1-D linear and radial flow in heterogeneous porous media, the energy-dissipation based Ke and the usual Ke calculated using assumed homogeneity and Darcy's law are identical. We will explore whether this same equivalence holds in general for 2-D and 3-D heterogeneity. The results to date imply that as one makes K measurements in heterogeneous media at different locations or on different cores of heterogeneous materials, the ISWF will be heterogeneity-dependent, implying that the averaging process resulting in the "equivalent" K value also varies with position. If the testing procedure is transient, then the averaging process varies also with time. This suggests a fundamental ambiguity in the interpretation of hydraulic conductivity measurements in heterogeneous media that may impact how we approach modeling and prediction in a practical
Dai, Sheng
2009-01-01
Self-Assembly Synthesis and Functionalization of Mesoporous Carbon Materials for Energy-Related Applications Sheng Dai Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831-6201 Porous carbon materials are ubiquitous in separation, catalysis, and energy storage/conversion. Well-defined mesoporous carbon materials are essential for a number of the aforementioned applications. Ordered porous carbon materials have previously been synthesized using colloidal crystals and presynthesized mesoporous silicas as hard templates. The mesostructures of these carbon materials are connected via ultrathin carbon filaments and can readily collapse under high-temperature conditions. Furthermore, these hard-template methodologies are extremely difficult to adapt to the fabrication of large-scale ordered nanoporous films or monoliths with controlled pore orientations. More recently, my research group at the Oak Ridge National Laboratory and several others around the world have developed alternative methods for synthesis of highly ordered mesoporous carbons via self-assembly. Unlike the mesoporous carbons synthesized via hard-template methods, these mesoporous carbons are highly stable and can be graphitized at high temperature (>2800ᵒC) without significant loss of mesopores. The surface properties of these materials can be further tailored via surface functionalization. This seminar will provide an overview and perspective of the mesoporous carbon materials derived from soft-template synthesis and surface functionalization and their fascinating applications in catalysis, separation, and energy storage devices. Dr. Sheng Dai got his B.S. and M.S. degrees from Zhejiang University in 1984 and 1986, respectively. He subsequently obtained a PhD degree from the University of Tennessee, Knoxville in 1990. He is currently a Senior Staff Scientist and Group Leader of Nanomaterials Group and Center for Nanophase Materials Science of Oak Ridge National Laboratory and
NASA Technical Reports Server (NTRS)
Roth, R. J.
1973-01-01
The distribution function of ion energy parallel to the magnetic field of a modified Penning discharge has been measured with a retarding potential energy analyzer. These ions escaped through one of the throats of the magnetic mirror geometry. Simultaneous measurements of the ion energy distribution function perpendicular to the magnetic field have been made with a charge exchange neutral detector. The ion energy distribution functions are approximately Maxwellian, and the parallel and perpendicular kinetic temperatures are equal within experimental error. These results suggest that turbulent processes previously observed in this discharge Maxwellianize the velocity distribution along a radius in velocity space and cause an isotropic energy distribution. When the distributions depart from Maxwellian, they are enhanced above the Maxwellian tail.
Effects of Functional Oils on Coccidiosis and Apparent Metabolizable Energy in Broiler Chickens
Murakami, A. E.; Eyng, C.; Torrent, J.
2014-01-01
The objective of the present study was to investigate the effects of a mixture of functional oils (Essential, Oligo Basics Agroind. Ltda) on performance response of chickens challenged with coccidiosis and the determination of apparent metabolizable energy (AME), nitrogen-corrected apparent metabolizable energy (AMEn), the coefficients of protein and ether extract digestibility and intestinal morphology of broilers fed with diets containing Essential. In Exp. 1, a completely randomized design (CRD) was used, with one control diet without Essential inclusion with coccidiosis (Eimeria acervulina, Eimeria maxima, and Eimeria tenella) challenged birds and two different inclusion rates of Essential (1.5 kg/ton and 2 kg/ton) with coccidiosis-challenged and non-challenged birds for each inclusion rate, using 10 replicates and 50 birds per experimental unit. After 7 d of coccidiosis challenge, the livability was approximately 10% lower (p<0.05) for the control group. Intestinal lesion scores were lower (p<0.05) in the anterior intestine and the cecum for the chickens supplemented. Feed efficiency and growth rate were improved in birds supplemented with Essential (p<0.05) before the coccidiosis challenge and during the first 7 d post infection. In Exp. 2, a CRD was used, with one control diet without Essential inclusion and one diet with inclusion of Essential (1.5 kg/ton), using nine replications and 33 chicks per pen. The diets with Essential yielded approximately 4% higher AME (p = 0.003) and AMEn (p = 0.001). Essential supplementation increased villus height in the jejunum on d 14 (p<0.05). Villus height:crypt depth ratio for the supplemented birds was larger (p<0.05) in the jejunum on d 7, larger (p<0.05) in the jejunum and ileum on d 14. In conclusion, these functional oils improved the energy utilization and the livability and decreased lesions caused by coccidiosis in supplemented birds. PMID:25050040
Resolution and sensitivity as a function of energy and incident geometry for germanium detectors
NASA Astrophysics Data System (ADS)
Keyser, Ronald M.
2004-01-01
The use of modeling programs such as MCNP to predict the response of HPGe detectors is increasing in importance. Accurate simulation of germanium detectors to incident gamma rays relies on knowledge of the performance of the detector in different detector-source geometries. Two important performance parameters are the resolution and sensitivity. The resolution is the FWHM and FW.1M/FWHM ratio. The IEEE 325-1996 standard only specifies the FWHM measurement at one geometry and two energies. Nearly all measurements are made in a different geometry and at other energies. Other investigators [Specifications for Today's Coaxial HPGe Detectors, 2001 ANS Annual Meeting, Milwaukee, WI; Metzger, private communication, see also: Radionuclide Depth Distribution by Collimated Spectroscopy, 2002 ANS Topical Meeting, Santa Fe, NM], have shown that the sensitivity and resolution change with position of the incident gamma ray on the front of the detector. Such variability has possible implications for the accuracy of peak shape and area determination, since the calibration is potentially a function of angle of incidence. To quantify the sensitivity and resolution variation as a function of energy and point of incidence, measurements have been made on several coaxial detectors of various crystal types and sizes in different source-detector geometries. The full-energy peaks from 59 keV to 2.6 MeV were used. The detectors were placed in a low-background shield to reduce any contribution from external sources. None of the detectors tested was a low-background type. The sources used were an 241Am source, 60Co source and a natural thorium oxide sample. The 241Am 59 keV gamma rays were collimated by a 2 cm thick, 1 mm diameter lead collimator. Several gamma rays from the thorium source were used and collimated by a 10 cm thick and 2 mm diameter tungsten collimator. These collimated sources were used to collect spectra for the incident beam on the front and sides of the detectors. The peak
Electron energy distribution function in the divertor region of the COMPASS tokamak
NASA Astrophysics Data System (ADS)
Dimitrova, M.; Hasan, E.; Ivanova, P.; Vasileva, E.; Popov, Tsv; Dejarnac, R.; Stöckel, J.; Panek, R.
2016-03-01
The plasma parameters during an L-mode hydrogen discharge in the COMPASS tokamak with a toroidal magnetic field BT =1.15 T, line-averaged electron density ne = 6×1019 m-3 and a plasma current variation from 209 kA to 100 kA were studied in the divertor region. The electron energy distribution function for 209 kA at the high-field side and the private region is Maxwellian with a temperature in the range of 5 -- 9 eV, while around the outer strike point and the low-field side it is bi-Maxwellian with a low-energy electron group (4 -- 5 eV) and higher energy electrons (10 -- 20 eV). As the plasma current decreases, the appearance of the bi-Maxwellian EEDF is shifted towards the low-field side; at plasma current of 100 kA, the EEDF is Maxwellian in the whole divertor region.
NASA Astrophysics Data System (ADS)
Gherghel-Lascu, A.; Apel, W. D.; Arteaga-Velázquez, J. C.; Bekk, K.; Bertaina, M.; Blümer, J.; Bozdog, H.; Brancus, I. M.; Cantoni, E.; Chiavassa, A.; Cossavella, F.; Daumiller, K.; de Souza, V.; Di Pierro, F.; Doll, P.; Engel, R.; Engler, J.; Fuchs, B.; Fuhrmann, D.; Gils, H. J.; Glasstetter, R.; Grupen, C.; Haungs, A.; Heck, D.; Hörandel, J. R.; Huber, D.; Huege, T.; Kampert, K.-H.; Kang, D.; Klages, H. O.; Link, K.; Łuczak, P.; Mathes, H. J.; Mayer, H. J.; Milke, J.; Mitrica, B.; Morello, C.; Oehlschläger, J.; Ostapchenko, S.; Palmieri, N.; Petcu, M.; Pierog, T.; Rebel, H.; Roth, M.; Schieler, H.; Schoo, S.; Schröder, F. G.; Sima, O.; Toma, G.; Trinchero, G. C.; Ulrich, H.; Weindl, A.; Wochele, J.; Zabierowski, J.
2015-02-01
In previous studies of KASCADE-Grande data, a Monte Carlo simulation code based on the GEANT3 program has been developed to describe the energy deposited by EAS particles in the detector stations. In an attempt to decrease the simulation time and ensure compatibility with the geometry description in standard KASCADE-Grande analysis software, several structural elements have been neglected in the implementation of the Grande station geometry. To improve the agreement between experimental and simulated data, a more accurate simulation of the response of the KASCADE-Grande detector is necessary. A new simulation code has been developed based on the GEANT4 program, including a realistic geometry of the detector station with structural elements that have not been considered in previous studies. The new code is used to study the influence of a realistic detector geometry on the energy deposited in the Grande detector stations by particles from EAS events simulated by CORSIKA. Lateral Energy Correction Functions are determined and compared with previous results based on GEANT3.
Zuo, Lei; Cui, Wen
2013-10-01
This paper proposes a novel retrofittable approach for dual-functional energy-harvesting and robust vibration control by integrating the tuned mass damper (TMD) and electromagnetic shunted resonant damping. The viscous dissipative element between the TMD and primary system is replaced by an electromagnetic transducer shunted with a resonant RLC circuit. An efficient gradient based numeric method is presented for the parameter optimization in the control framework for vibration suppression and energy harvesting. A case study is performed based on the Taipei 101 TMD. It is found that by tuning the TMD resonance and circuit resonance close to that of the primary structure, the electromagnetic resonant-shunt TMD achieves the enhanced effectiveness and robustness of double-mass series TMDs, without suffering from the significantly amplified motion stroke. It is also observed that the parameters and performances optimized for vibration suppression are close to those optimized for energy harvesting, and the performance is not sensitive to the resistance of the charging circuit or electrical load. PMID:23918165
Sub-barrier fusion excitation function data and energy dependent Woods-Saxon potential
NASA Astrophysics Data System (ADS)
Gautam, Manjeet Singh
2016-07-01
This paper analyzed the role of intrinsic degrees of freedom of colliding nuclei in the enhancement of sub-barrier fusion cross-section data of various heavy ion fusion reactions. The influences of inelastic surface vibrations of colliding pairs are found to be dominant and their couplings result in the significantly larger fusion enhancement over the predictions of the one dimensional barrier penetration model at sub-barrier energies. The theoretical calculations are performed by using energy dependent Woods-Saxon potential model (EDWSP model) in conjunction with the one dimensional Wong formula. The effects of dominant intrinsic channels are entertained within framework of the coupled channel calculations obtained by using the code CCFULL. It is quite interesting to note that the energy dependence in Woods-Saxon potential simulates the effects of inelastic surface vibrational states of reactants wherein significantly larger value of diffuseness parameter ranging from a = 0.85 fm to a = 0.95 fm is required to address the observed fusion excitation function data of the various heavy ion fusion reactions.
The influence of alcoholic intoxication on the short-time energy function of speech.
Heinrich, Christian; Schiel, Florian
2014-05-01
This study investigates rhythmic features based on the short-time energy function of speech signals with the aim of finding robust, speaker-independent features that indicate speaker intoxication. Data from the German Alcohol Language Corpus, which comprises read, spontaneous, and command&control speech uttered by 162 speakers of both genders and various age groups when sober and intoxicated, were analyzed. Energy contours are compared directly (Root Mean Squared Error, statistical correlation, or the Euclidean distance in the spectral space of the contour) and by parameterization of the contour using the Discrete Cosine Transform (DCT) and the first and second moments of the lower DCT spectrum. Contours are also analyzed by Principal Components Analysis aiming at fundamental "eigen contour" changes that might encode intoxication. Energy contours differ significantly with intoxication in terms of distance measures, the second and fourth DCT coefficients, and the first and second moments of the lower DCT spectrum. Principal Components Analysis did not yield interpretable "eigen contours" that could be used in distinguishing intoxicated from sober contours. PMID:24815274
Peng, Shengjie; Jin, Guorui; Li, Linlin; Li, Kai; Srinivasan, Madhavi; Ramakrishna, Seeram; Chen, Jun
2016-03-01
Tissue regeneration, energy conversion & storage, and water treatment are some of the most critical challenges facing humanity in the 21st century. In order to address such challenges, one-dimensional (1D) materials are projected to play a key role in developing emerging solutions for the increasingly complex problems. Eletrospinning technology has been demonstrated to be a simple, versatile, and cost-effective method in fabricating a rich variety of materials with 1D nanostructures. These include polymers, composites, and inorganic materials with unique chemical and physical properties. In this tutorial review, we first give a brief introduction to electrospun materials with a special emphasis on the design, fabrication, and modification of 1D functional materials. Adopting the perspective of chemists and materials scientists, we then focus on the recent significant progress made in the domains of tissue regeneration (e.g., skin, nerve, heart and bone) and conversion & storage of clean energy (e.g., solar cells, fuel cells, batteries, and supercapacitors), where nanofibres have been used as active nanomaterials. Furthermore, this review's scope also includes the advances in the use of electrospun materials for the removal of heavy metal ions, organic pollutants, gas and bacteria in water treatment applications. Finally a conclusion and perspective is provided, in which we discuss the remaining challenges for 1D electrospun nanomaterials in tissue regeneration, energy conversion & storage, and water treatment. PMID:26727278
NASA Astrophysics Data System (ADS)
Tantakitti, Faifan
Supramolecular chemistry is a powerful tool to create a material of a defined structure with tunable properties. This strategy has led to catalytically active, bioactive, and environment-responsive materials, among others, that are valuable in applications ranging from sensor technology to energy and medicine. Supramolecular polymers formed by peptide amphiphiles (PAs) have been especially relevant in tissue regeneration due to their ability to form biocompatible structures and mimic many important signaling molecules in biology. These supramolecular polymers can form nanofibers that create networks which mimic natural extracellular matrices. PA materials have been shown to induce growth of blood vessels, bone, cartilage, and nervous tissue, among others. The work described in this thesis not only studied the relationship between molecular structure and functions of PA assemblies, but also uncovered a powerful link between the energy landscape of their supramolecular self-assembly and the ability of PA materials to interact with cells. In chapter 2, it is argued that fabricating fibrous nanostructures with defined mechanical properties and decoration with bioactive molecules is not sufficient to create a material that can effectively communicate with cells. By systemically placing the fibronectin-derived RGDS epitope at increasing distances from the surface of PA nanofibers through a linker of one to five glycine residues, integrin-mediated RGDS signaling was enhanced. The results suggested that the spatial presentation of an epitope on PA nanofibers strongly influences the bioactivity of the PA substrates. In further improving functionality of a PA-based scaffold to effectively direct cell growth and differentiation, chapter 3 explored the use of a cell microcarrier to compartmentalize and simultaneously tune insoluble and soluble signals in a single matrix. PA nanofibers were incorporated at the surface of the microcarrier in order to promote cell adhesion, while
NASA Astrophysics Data System (ADS)
Brambilla, M.; Giovannini, A.; Ugoccioni, R.
2006-06-01
Theorems on zeros of the truncated generating function in the complex plane are reviewed. When examined in the framework of a statistical model of high energy collisions based on the negative binomial (Pascal) multiplicity distribution, these results lead to maps of zeros of the grand canonical partition function which allow us to interpret in a novel way different classes of events in pp collisions at LHC c.m. energies.
Cheong, Seokjung; Clomburg, James M; Gonzalez, Ramon
2016-05-01
Anabolic metabolism can produce an array of small molecules, but yields and productivities are low owing to carbon and energy inefficiencies and slow kinetics. Catabolic and fermentative pathways, on the other hand, are carbon and energy efficient but support only a limited product range. We used carbon- and energy-efficient non-decarboxylative Claisen condensation reactions and subsequent β-reduction reactions, which can accept a variety of functionalized primers and functionalized extender units and operate in an iterative manner, to synthesize functionalized small molecules. Using different ω- and ω-1-functionalized primers and α-functionalized extender units in combination with various termination pathways, we demonstrate the synthesis of 18 products from 10 classes, including ω-phenylalkanoic, α,ω-dicarboxylic, ω-hydroxy, ω-1-oxo, ω-1-methyl, 2-methyl, 2-methyl-2-enolic and 2,3-dihydroxy acids, β-hydroxy-ω-lactones, and ω-1-methyl alcohols. PMID:27088721
Liu, Wei; Schuler, Bruno; Xu, Yong; Moll, Nikolaj; Meyer, Gerhard; Gross, Leo; Tkatchenko, Alexandre
2016-03-17
Reliability is one of the major concerns and challenges in designing organic/inorganic interfaces for (opto)electronic applications. Even small structural differences for molecules on substrates can result in a significant variation in the interface functionality, due to the strong correlation between geometry, stability, and electronic structure. Here, we employed state-of-the-art first-principles calculations with van der Waals interactions, in combination with atomic force microscopy experiments, to explore the interaction mechanism for three structurally related olympicene molecules adsorbed on the Cu(111) surface. The substitution of a single atom in the olympicene molecule switches the nature of adsorption from predominantly physisorptive character [olympicene on Cu(111)], to an intermediate state [olympicene-derived ketone on Cu(111)], then to chemisorptive character [olympicene radical on Cu(111)]. Despite the remarkable difference in adsorption structures (by up to 0.9 Å in adsorption height) and different nature of bonding, the olympicene, its ketone, and its radical derivatives have essentially identical binding energies and work functions upon interaction with the metal substrate. Our findings suggest that the stability and work functions of molecular adsorbates could be rendered insensitive to their adsorption structures, which could be a useful property for (opto)electronic applications. PMID:26928143
Tamamoto, Lauren C; Schmidt, Shelly J; Lee, Soo-Yeun
2010-08-01
Energy drinks have increased in popularity in recent years due to the claimed energy boost provided by functional ingredients. A multitude of functional ingredients have been utilized; however, there is limited research on their sensory effects in energy drink formulations. A 13-member descriptive analysis panel was conducted to investigate the effects on the sensory and rheological properties of 3 common functional ingredients-caffeine, ginseng, and taurine-in a noncarbonated model energy drink solution. Combinations of these functional ingredients at 3 levels (low, medium, high) were added to create a total of 27 different solutions (3 x 3 x 3 factorial design). Analysis of variance was performed to evaluate the sensory effects of the varying concentrations of functional ingredients in solution. Principal component analysis (PCA) was performed to summarize the relationship among the attributes and solutions. In general, high levels of caffeine in solution resulted in low ratings of fruity attributes and high ratings of bitter tea and fruit bitter attributes. The high level of ginseng in solution was characterized by high ratings of bitter attributes. A horns effect was observed as the sweet, artificial lemon-lime, pear, mango, and pineapple attributes were rated lower in intensity with increased ginseng levels. Taurine levels of up to 416 mg/100 mL had no significant effect on the sensory attribute ratings of the model energy drink solutions. These findings can be utilized to predict the changes in sensory characteristics when formulating energy drinks containing these popular functional ingredients. PMID:20722948
Tian, Ye; Huang, Xiaoqiang; Zhu, Yushan
2015-08-01
Enzyme amino-acid sequences at ligand-binding interfaces are evolutionarily optimized for reactions, and the natural conformation of an enzyme-ligand complex must have a low free energy relative to alternative conformations in native-like or non-native sequences. Based on this assumption, a combined energy function was developed for enzyme design and then evaluated by recapitulating native enzyme sequences at ligand-binding interfaces for 10 enzyme-ligand complexes. In this energy function, the electrostatic interaction between polar or charged atoms at buried interfaces is described by an explicitly orientation-dependent hydrogen-bonding potential and a pairwise-decomposable generalized Born model based on the general side chain in the protein design framework. The energy function is augmented with a pairwise surface-area based hydrophobic contribution for nonpolar atom burial. Using this function, on average, 78% of the amino acids at ligand-binding sites were predicted correctly in the minimum-energy sequences, whereas 84% were predicted correctly in the most-similar sequences, which were selected from the top 20 sequences for each enzyme-ligand complex. Hydrogen bonds at the enzyme-ligand binding interfaces in the 10 complexes were usually recovered with the correct geometries. The binding energies calculated using the combined energy function helped to discriminate the active sequences from a pool of alternative sequences that were generated by repeatedly solving a series of mixed-integer linear programming problems for sequence selection with increasing integer cuts. PMID:26162695
Kamph, Jerome Henri; Robinson, Darren; Wetter, Michael
2009-09-01
There is an increasing interest in the use of computer algorithms to identify combinations of parameters which optimise the energy performance of buildings. For such problems, the objective function can be multi-modal and needs to be approximated numerically using building energy simulation programs. As these programs contain iterative solution algorithms, they introduce discontinuities in the numerical approximation to the objective function. Metaheuristics often work well for such problems, but their convergence to a global optimum cannot be established formally. Moreover, different algorithms tend to be suited to particular classes of optimization problems. To shed light on this issue we compared the performance of two metaheuristics, the hybrid CMA-ES/HDE and the hybrid PSO/HJ, in minimizing standard benchmark functions and real-world building energy optimization problems of varying complexity. From this we find that the CMA-ES/HDE performs well on more complex objective functions, but that the PSO/HJ more consistently identifies the global minimum for simpler objective functions. Both identified similar values in the objective functions arising from energy simulations, but with different combinations of model parameters. This may suggest that the objective function is multi-modal. The algorithms also correctly identified some non-intuitive parameter combinations that were caused by a simplified control sequence of the building energy system that does not represent actual practice, further reinforcing their utility.
NASA Astrophysics Data System (ADS)
Loveridge, A. J.; van der Sluys, M. V.; Kalogera, V.
2011-12-01
The common-envelope (CE) phase is an important stage in the evolution of binary stellar populations. The most common way to compute the change in orbital period during a CE is to relate the binding energy of the envelope of the Roche-lobe filling giant to the change in orbital energy. Especially in population-synthesis codes, where the evolution of millions of stars must be computed and detailed evolutionary models are too expensive computationally, simple approximations are made for the envelope binding energy. In this study, we present accurate analytic prescriptions based on detailed stellar-evolution models that provide the envelope binding energy for giants with metallicities between Z = 10-4 and Z = 0.03 and masses between 0.8 M ⊙ and 100 M ⊙, as a function of the metallicity, mass, radius, and evolutionary phase of the star. Our results are also presented in the form of electronic data tables and Fortran routines that use them. We find that the accuracy of our fits is better than 15% for 90% of our model data points in all cases, and better than 10% for 90% of our data points in all cases except the asymptotic giant branches for three of the six metallicities we consider. For very massive stars (M >~ 50 M ⊙), when stars lose more than ~20% of their initial mass due to stellar winds, our fits do not describe the models as accurately. Our results are more widely applicable—covering wider ranges of metallicity and mass—and are of higher accuracy than those of previous studies.
Loveridge, A. J.; Van der Sluys, M. V.; Kalogera, V.
2011-12-10
The common-envelope (CE) phase is an important stage in the evolution of binary stellar populations. The most common way to compute the change in orbital period during a CE is to relate the binding energy of the envelope of the Roche-lobe filling giant to the change in orbital energy. Especially in population-synthesis codes, where the evolution of millions of stars must be computed and detailed evolutionary models are too expensive computationally, simple approximations are made for the envelope binding energy. In this study, we present accurate analytic prescriptions based on detailed stellar-evolution models that provide the envelope binding energy for giants with metallicities between Z = 10{sup -4} and Z = 0.03 and masses between 0.8 M{sub Sun} and 100 M{sub Sun }, as a function of the metallicity, mass, radius, and evolutionary phase of the star. Our results are also presented in the form of electronic data tables and Fortran routines that use them. We find that the accuracy of our fits is better than 15% for 90% of our model data points in all cases, and better than 10% for 90% of our data points in all cases except the asymptotic giant branches for three of the six metallicities we consider. For very massive stars (M {approx}> 50 M{sub Sun }), when stars lose more than {approx}20% of their initial mass due to stellar winds, our fits do not describe the models as accurately. Our results are more widely applicable-covering wider ranges of metallicity and mass-and are of higher accuracy than those of previous studies.
Description of superheavy nuclei on the basis of a modified version of the DF3 energy functional
Tolokonnikov, S. V.; Saperstein, E. E.
2010-10-15
The possibility of describing nuclei of the uranium and transuranium region within the generalized method of the energy functional proposed by Fayans and his coauthors is studied. It turned out that, in the functional DF3, it is necessary, for this purpose, to modify the spin-orbit terms whose parameters were chosen in such a way as to describe the binding energies and charge radii of spherical nuclei from calcium to lead. The modified functional (DF3-a) describes well the energy features and charged radii for isotopic chains of uranium and neighboring elements. For deformed nuclei, the deformation was taken into account approximately. The nucleon-drip-line position obtained for these chains proved to be close to the predictions of one of the most successful calculations by the Skyrme-Hartree-Fock method with the HFB-17 functional. It is verified that the use of the functional DF3-a does not impair the description of the properties of lighter nuclei, for which the functional DF3 was devised. Moreover, the modified functional describes better, than the original one, new data on spin-orbit splitting in magic and semimagic nuclei. The calculation with the functional DF3-a confirms the doubly magic nature of the superheavy nuclide {sub 114}{sup 298}X{sub 184}. As for the neutron-separation energies S{sub n} along the isotopic chain of this element, our results are close to the predictions of the so-called micro-macro method.
Song, Tao; Sun, Baoquan
2013-03-01
Wearable power supplies: Photo-rechargeable devices integrating power conversion and energy storage functions are useful for supplying power to portable electronics. A recent report introduces a facile method to fabricate flexible dual-functional devices on a single metal wire which paves the way for wearable fabric power supplies. PMID:23345079
Code of Federal Regulations, 2010 CFR
2010-04-01
... 23 Highways 1 2010-04-01 2010-04-01 false National Reference Energy Mean Emission Levels as a Function of Speed A Appendix A to Part 772 Highways FEDERAL HIGHWAY ADMINISTRATION, DEPARTMENT OF... Function of Speed EC14OC91.013...
NASA Astrophysics Data System (ADS)
Lee, Ha-Woon; Kim, Jeong-Woo; Kim, Cheol S.; Kim, Soo-Joong
1995-04-01
The optical wavelet circular harmonic function minimum average correlation energy (WCHF- MACE) filter is proposed. The proposed WCHF-MACE filter uses the wavelet transformed image by Mexican-hat wavelet function for circular harmonic function and the multiple harmonic components of circular harmonic function are used for MACE filter synthesis. The proposed filter has good discrimination compared with the conventional circular harmonic function filter and conventional circular harmonic MACE filter about the limited rotated images. And the filter is made of the type of optical wavelet matched filter (WMF), so that the proposed filter can use the conventional 4f correlator.
Bi-functional Mo-doped WO3 nanowire array electrochromism-plus electrochemical energy storage.
Zhou, D; Shi, F; Xie, D; Wang, D H; Xia, X H; Wang, X L; Gu, C D; Tu, J P
2016-03-01
Metal-doping is considered to be an effective way for construction of advanced semiconducting metal oxides with tailored physicochemical properties. Herein, Mo-doped WO3 nanowire arrays are rationally fabricated by a sulfate-assisted hydrothermal method. Compared to the pure WO3, the optimized Mo-doped WO3 nanowire arrays exhibit improved electrochromic properties with fast switching speed (3.2s and 2.6s for coloration and bleaching, respectively), significant optical modulation (56.7% at 750nm, 83.0% at 1600nm and 48.5% at 10μm), high coloration efficiency (123.5cm(2)C(-1)) and excellent cycling stability. In addition, as a proof of concept, the Mo-doped WO3 nanowire arrays are demonstrated with electrochemical energy storage monitored by the electrochromism. This electrode design protocol can provide an alternative way for developing high-performance active materials for bi-functional electrochromic batteries. PMID:26669497
NASA Astrophysics Data System (ADS)
Zhou, Shan-Gui
2016-06-01
The intrinsic nuclear shapes deviating from a sphere not only manifest themselves in nuclear collective states but also play important roles in determining nuclear potential energy surfaces (PES’s) and fission barriers. In order to describe microscopically and self-consistently nuclear shapes and PES’s with as many shape degrees of freedom as possible included, we developed multidimensionally constrained covariant density functional theories (MDC-CDFTs). In MDC-CDFTs, the axial symmetry and the reflection symmetry are both broken and all deformations characterized by {β }λ μ with even μ are considered. We have used the MDC-CDFTs to study PES’s and fission barriers of actinides, the non-axial octupole Y 32 correlations in N = 150 isotones and shapes of hypernuclei. In this Review we will give briefly the formalism of MDC-CDFTs and present the applications to normal nuclei.
Equation satisfied by the energy-density functional for electron-electron mutual Coulomb repulsion
Joubert, Daniel P.
2011-10-15
It is shown that the electron-electron mutual Coulomb repulsion energy-density functional V{sub ee}{sup {gamma}}[{rho}] satisfies the equationV{sub ee}{sup {gamma}}[{rho}{sub N}{sup 1}]-V{sub ee}{sup {gamma}}[{rho}{sub N-1}{sup {gamma}}]={integral}d{sup 3}r({delta}V{sub ee}{sup {gamma}}[{rho}{sub N}{sup 1}]/{delta}{rho}{sub N}{sup 1}(r))[{rho}{sub N}{sup 1}(r)-{rho}{sub N-1}{sup {gamma}}(r)], where {rho}{sub N}{sup 1}(r) and {rho}{sub N-1}{sup {gamma}}(r) are N-electron and (N-1)-electron densities determined from the same adiabatic scaled external potential of the N-electron system at coupling strength {gamma}.
Density functional theory calculations of magnetocrystalline anisotropy energies for (Fe1-xCox)2B
Daene, Markus; Kim, Soo Kyung; Surh, Michael P.; Aberg, Daniel; Benedict, Lorin X.
2015-06-15
We present and discuss density functional theory calculations of magnetic properties of the family of ferromagnetic compounds, (Fe1-xCox)2B, focusing specifically on the magnetocrystalline anisotropy energy (MAE). Using periodic supercells of various sizes (up to 96 atoms), it is shown that the general qualitative features of the composition dependence of the MAE is in agreement with experimental findings, while our predicted magnitudes are larger than those of experiment. We find that the use of small supercells (6 and 12-atom) favors larger MAE values relative to a statistical sample of configurations constructed with 96-atom supercells. As a result, the effect of latticemore » relaxations is shown to be small. Calculations of the Curie temperature for this alloy are also presented.« less
NASA Astrophysics Data System (ADS)
Zenkour, Ashraf M.; Abbas, Ibrahim A.
2015-12-01
The electro-magneto-thermo-elastic analysis problem of an infinite functionally graded (FG) hollow cylinder is studied in the context of Green-Naghdi's (G-N) generalized thermoelasticity theory (without energy dissipation). Material properties are assumed to be graded in the radial direction according to a novel power-law distribution in terms of the volume fractions of the metal and ceramic constituents. The inner surface of the FG cylinder is pure metal whereas the outer surface is pure ceramic. The equations of motion and the heat-conduction equation are used to derive the governing second-order differential equations. A finite element scheme is presented for the numerical purpose. The system of differential equations is solved numerically and some plots for displacement, radial and electromagnetic stresses, and temperature are presented. The radial displacement, mechanical stresses and temperature as well as the electromagnetic stress are all investigated along the radial direction of the infinite cylinder.
NASA Astrophysics Data System (ADS)
Grzybowski, Przemysław R.; Czekaj, Łukasz; Nogala, Mariusz; Ścibior, Adam; Chhajlany, Ravindra W.
2016-06-01
Models of noninteracting fermions coupled to auxiliary classical fields are relevant to the understanding of a wide variety of problems in many-body physics, e.g., the description of manganites, diluted magnetic semiconductors, or strongly interacting electrons on lattices. We present a flat-histogram Monte Carlo algorithm that simulates a statistical ensemble that allows one to directly acquire the partition function at all temperatures for such systems. The defining feature of the algorithm is that it utilizes the complete thermodynamic information from the full energy spectrum of noninteracting fermions available during sampling of the configuration space of the classical fields. We benchmark the method for the classical Ising and Potts models in two dimensions, as well as the Falicov-Kimball model describing itinerant electrons interacting with heavy ions.
NASA Astrophysics Data System (ADS)
Marschalkó, G.; Petrovay, K.; Petrovay, K.
2013-11-01
A simple analytical relation of form α=2κ-1 between the magnetic energy spectral exponent α of the turbulent magnetic field in the solar photosphere and its magnetic flux cancellation exponent κ, valid under certain restrictive assumptions, is tested and extended outside its range of validity in a series of Monte Carlo simulations. In these numerical tests artificial ``magnetograms'' are constructed in 1D and 2D by superposing a discrete set of Fourier modes of the magnetic field distribution with amplitudes following a power law spectrum and measuring the cancellation function on these simulated magnetograms. Our results confirm the validity of the analytical relation and extend it to the domain α<-1 where κ-> 0 as α-> -∞. The observationally derived upper limit of 0.38 on κ implies α<-0.24 in the granular size range, apparently at odds with a small scale dynamo driven in the inertial range.
Liwo, Adam; Arłukowicz, Piotr; Czaplewski, Cezary; Ołdziej, Stanisław; Pillardy, Jarosław; Scheraga, Harold A.
2002-01-01
A method for optimizing potential-energy functions of proteins is proposed. The method assumes a hierarchical structure of the energy landscape, which means that the energy decreases as the number of native-like elements in a structure increases, being lowest for structures from the native family and highest for structures with no native-like element. A level of the hierarchy is defined as a family of structures with the same number of native-like elements (or degree of native likeness). Optimization of a potential-energy function is aimed at achieving such a hierarchical structure of the energy landscape by forcing appropriate free-energy gaps between hierarchy levels to place their energies in ascending order. This procedure is different from methods developed thus far, in which the energy gap and/or the Z score between the native structure and all non-native structures are maximized, regardless of the degree of native likeness of the non-native structures. The advantage of this approach lies in reducing the number of structures with decreasing energy, which should ensure the searchability of the potential. The method was tested on two proteins, PDB ID codes 1FSD and 1IGD, with an off-lattice united-residue force field. For 1FSD, the search of the conformational space with the use of the conformational space annealing method and the newly optimized potential-energy function found the native structure very quickly, as opposed to the potential-energy functions obtained by former optimization methods. After even incomplete optimization, the force field obtained by using 1IGD located the native-like structures of two peptides, 1FSD and betanova (a designed three-stranded β-sheet peptide), as the lowest-energy conformations, whereas for the 46-residue N-terminal fragment of staphylococcal protein A, the native-like conformation was the second-lowest-energy conformation and had an energy 2 kcal/mol above that of the lowest-energy structure. PMID:11854494
First-principles study of the surface energy and work function of III-V semiconductor compounds
NASA Astrophysics Data System (ADS)
Liu, W.; Zheng, W. T.; Jiang, Q.
2007-06-01
Surface energy and work function of 12 III-V semiconductors, AlP, AlAs, AlSb, AlBi, GaP, GaAs, GaSb, GaBi, InP, InAs, InSb, and InBi, on (110) surfaces are calculated using ab initio density functional theory. The obtained values are proportional to the corresponding cohesive energy and are in good agreement with available experimental data and theoretical models. The linear relationship among cohesive energy, surface energy, and work function is interpreted by analyzing their electronic properties where four (110) surfaces of Al series semiconductors, AlP, AlAs, AlSb, and AlBi, are taken as examples.
NASA Astrophysics Data System (ADS)
Shi, De-Heng; Liu, Yu-Fang; Sun, Jin-Feng; Zhu, Zun-Lue; Yang, Xiang-Dong
2006-12-01
The reasonable dissociation limit of the second excited singlet state B1Π of 7LiH molecule is obtained. The accurate dissociation energy and equilibrium geometry of the B1Π state are calculated using a symmetry-adapted-cluster configuration-interaction method in full active space. The whole potential energy curve for the B1Π state is obtained over the internuclear distance ranging from about 0.10 nm to 0.54 nm, and has a least-square fit to the analytic Murrell-Sorbie function form. The vertical excitation energy is calculated from the ground state to the B1Π state and compared with previous theoretical results. The equilibrium internuclear distance obtained by geometry optimization is found to be quite different from that obtained by single-point energy scanning under the same calculation condition. Based on the analytic potential energy function, the harmonic frequency value of the B1Π state is estimated. A comparison of the theoretical calculations of dissociation energies, equilibrium interatomic distances and the analytic potential energy function with those obtained by previous theoretical results clearly shows that the present work is more comprehensive and in better agreement with experiments than previous theories, thus it is an improvement on previous theories.
The 14th Ile residue is essential for Leptin function in regulating energy homeostasis in rat
Xu, Shuyang; Zhu, Xianmin; Li, Hong; Hu, Youtian; Zhou, Jinping; He, Di; Feng, Yun; Lu, Lina; Du, Guizhen; Hu, Youjin; Liu, Tiancheng; Wang, Zhen; Ding, Guohui; Chen, Jiayu; Gao, Shaorong; Wu, Fang; Xue, Zhigang; Li, Yixue; Fan, Guoping
2016-01-01
LEPTIN (LEP) is a circulating hormone released primarily from white adipocytes and is crucial for regulating satiety and energy homeostasis in humans and animals. Using the CRISPR technology, we created a set of Lep mutant rats that carry either null mutations or a deletion of the 14th Ile (LEP∆I14) in the mature LEP protein. We examined the potential off-target sites (OTS) by whole-genome high-throughput sequencing and/or Sanger-sequencing analysis and found no OTS in mutant rats. Mature LEP∆I14 is incessantly produced and released to blood at a much elevated level due to the feedback loop. Structure modeling of binding conformation between mutant LEP∆I14 and LEPTIN receptor (LEPR) suggests that the conformation of LEP∆I14 impairs its binding with LEPR, consistent with its inability to activate STAT3-binding element in the luciferase reporter assay. Phenotypic study demonstrated that Lep∆I14 rats recapitulate phenotypes of Lep-null mutant rats including obesity, hyperinsulinemia, hepatic steatosis, nephropathy, and infertility. Compared to the existing ob/ob mouse models, this Lep∆I14/∆I14 rat strain provides a robust tool for further dissecting the roles of LEP in the diabetes related kidney disease and reproduction problem, beyond its well established function in regulating energy homeostasis. PMID:27378381
A new Skyrme energy density functional for a better description of spin-isospin resonances
NASA Astrophysics Data System (ADS)
Roca-Maza, X.; Colò, G.; Cao, Li-Gang; Sagawa, H.
2015-10-01
A correct determination of the isospin and spin-isospin properties of the nuclear effective interaction should lead to an accurate description of the Gamow-Teller resonance (GT), the Spin Dipole Resonance (SDR), the Giant Dipole Resonance (GDR) or the Antianalog Giant Dipole Resonance (AGDR), among others. A new Skyrme energy density functional named SAMi is introduced with the aim of going a step forward in setting the bases for a more precise description of spin-isospin resonances [1, 2]. In addition, we will discuss some new features of our analysis on the AGDR in 208Pb [3] as compared with available experimental data on this resonance [4, 5, 6], and on the GDR [7]. Such study, guided by a simple yet physical pocket formula, has been developed by employing the so called SAMi-J family of systematically varied interactions. This set of interactions is compatible with experimental data for values of the symmetry energy at saturation J and slope parameter L falling in the ranges 31-33 MeV and 75-95 MeV, respectively.
Accurate hydrogen bond energies within the density functional tight binding method.
Domínguez, A; Niehaus, T A; Frauenheim, T
2015-04-01
The density-functional-based tight-binding (DFTB) approach has been recently extended by incorporating one-center exchange-like terms in the expansion of the multicenter integrals. This goes beyond the Mulliken approximation and leads to a scheme which treats in a self-consistent way the fluctuations of the whole dual density matrix and not only its diagonal elements (Mulliken charges). To date, only the performance of this new formalism to reproduce excited-state properties has been assessed (Domínguez et al. J. Chem. Theory Comput., 2013, 9, 4901-4914). Here we study the effect of our corrections on the computation of hydrogen bond energies for water clusters and water-containing systems. The limitations of traditional DFTB to reproduce hydrogen bonds has been acknowledged often. We compare our results for a set of 22 small water clusters and water-containing systems as well as for five water hexadecamers to those obtained with the DFTB3 method. Additionally, we combine our extension with a third-order energy expansion in the charge fluctuations. Our results show that the new formalisms significantly improve upon original DFTB. PMID:25763597