Combinatorial treatments enhance recovery following facial nerve crush.

PubMed

Sharma, Nijee; Moeller, Carl W; Marzo, Sam J; Jones, Kathryn J; Foecking, Eileen M

2010-08-01

To investigate the effects of various combinatorial treatments, consisting of a tapering dose of prednisone (P), a brief period of nerve electrical stimulation (ES), and systemic testosterone propionate (TP) on improving functional recovery following an intratemporal facial nerve crush injury. Prospective, controlled animal study. After a right intratemporal facial nerve crush, adult male Sprague-Dawley rats were divided into the following eight treatment groups: 1) no treatment, 2) P only, 3) ES only, 4) ES + P, 5) TP only, 6) TP + P, 7) ES + TP, and 8) ES + TP + P. For each group n = 4-8. Recovery of the eyeblink reflex and vibrissae orientation and movement were assessed. Changes in peak amplitude and latency of evoked response, in response to facial nerve stimulation, was also recorded weekly. : Brief ES of the proximal nerve stump most effectively accelerated the initiation of functional recovery. Also, ES or TP treatments enhanced recovery of some functional parameters more than P treatment. When administered alone, none of the three treatments improved recovery of complete facial function. Only the combinatorial treatment of ES + TP, regardless of the presence of P, accelerated complete functional recovery and return of normal motor nerve conduction. Our findings suggest that a combinatorial treatment strategy of using brief ES and TP together promises to be an effective therapeutic intervention for promoting regeneration following facial nerve injury. Administration of P neither augments nor hinders recovery.

Nonparametric Combinatorial Sequence Models

NASA Astrophysics Data System (ADS)

Wauthier, Fabian L.; Jordan, Michael I.; Jojic, Nebojsa

This work considers biological sequences that exhibit combinatorial structures in their composition: groups of positions of the aligned sequences are "linked" and covary as one unit across sequences. If multiple such groups exist, complex interactions can emerge between them. Sequences of this kind arise frequently in biology but methodologies for analyzing them are still being developed. This paper presents a nonparametric prior on sequences which allows combinatorial structures to emerge and which induces a posterior distribution over factorized sequence representations. We carry out experiments on three sequence datasets which indicate that combinatorial structures are indeed present and that combinatorial sequence models can more succinctly describe them than simpler mixture models. We conclude with an application to MHC binding prediction which highlights the utility of the posterior distribution induced by the prior. By integrating out the posterior our method compares favorably to leading binding predictors.

Multiconfiguration Pair-Density Functional Theory.

PubMed

Li Manni, Giovanni; Carlson, Rebecca K; Luo, Sijie; Ma, Dongxia; Olsen, Jeppe; Truhlar, Donald G; Gagliardi, Laura

2014-09-09

We present a new theoretical framework, called Multiconfiguration Pair-Density Functional Theory (MC-PDFT), which combines multiconfigurational wave functions with a generalization of density functional theory (DFT). A multiconfigurational self-consistent-field (MCSCF) wave function with correct spin and space symmetry is used to compute the total electronic density, its gradient, the on-top pair density, and the kinetic and Coulomb contributions to the total electronic energy. We then use a functional of the total density, its gradient, and the on-top pair density to calculate the remaining part of the energy, which we call the on-top-density-functional energy in contrast to the exchange-correlation energy of Kohn-Sham DFT. Because the on-top pair density is an element of the two-particle density matrix, this goes beyond the Hohenberg-Kohn theorem that refers only to the one-particle density. To illustrate the theory, we obtain first approximations to the required new type of density functionals by translating conventional density functionals of the spin densities using a simple prescription, and we perform post-SCF density functional calculations using the total density, density gradient, and on-top pair density from the MCSCF calculations. Double counting of dynamic correlation or exchange does not occur because the MCSCF energy is not used. The theory is illustrated by applications to the bond energies and potential energy curves of H2, N2, F2, CaO, Cr2, and NiCl and the electronic excitation energies of Be, C, N, N(+), O, O(+), Sc(+), Mn, Co, Mo, Ru, N2, HCHO, C4H6, c-C5H6, and pyrazine. The method presented has a computational cost and scaling similar to MCSCF, but a quantitative accuracy, even with the present first approximations to the new types of density functionals, that is comparable to much more expensive multireference perturbation theory methods.

A methodology to find the elementary landscape decomposition of combinatorial optimization problems.

PubMed

Chicano, Francisco; Whitley, L Darrell; Alba, Enrique

2011-01-01

A small number of combinatorial optimization problems have search spaces that correspond to elementary landscapes, where the objective function f is an eigenfunction of the Laplacian that describes the neighborhood structure of the search space. Many problems are not elementary; however, the objective function of a combinatorial optimization problem can always be expressed as a superposition of multiple elementary landscapes if the underlying neighborhood used is symmetric. This paper presents theoretical results that provide the foundation for algebraic methods that can be used to decompose the objective function of an arbitrary combinatorial optimization problem into a sum of subfunctions, where each subfunction is an elementary landscape. Many steps of this process can be automated, and indeed a software tool could be developed that assists the researcher in finding a landscape decomposition. This methodology is then used to show that the subset sum problem is a superposition of two elementary landscapes, and to show that the quadratic assignment problem is a superposition of three elementary landscapes.

Combinatorial study of Ni-Ti-Pt ternary metal gate electrodes on HfO{sub 2} for the advanced gate stack

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

Chang, K.-S.; Green, M. L.; Suehle, J.

2006-10-02

The authors have fabricated combinatorial Ni-Ti-Pt ternary metal gate thin film libraries on HfO{sub 2} using magnetron co-sputtering to investigate flatband voltage shift ({delta}V{sub fb}), work function ({phi}{sub m}), and leakage current density (J{sub L}) variations. A more negative {delta}V{sub fb} is observed close to the Ti-rich corner than at the Ni- and Pt-rich corners, implying smaller {phi}{sub m} near the Ti-rich corners and higher {phi}{sub m} near the Ni- and Pt-rich corners. In addition, measured J{sub L} values can be explained consistently with the observed {phi}{sub m} variations. Combinatorial methodologies prove to be useful in surveying the large compositionalmore » space of ternary alloy metal gate electrode systems.« less

Combinatorial Optimization in Project Selection Using Genetic Algorithm

NASA Astrophysics Data System (ADS)

Dewi, Sari; Sawaluddin

2018-01-01

This paper discusses the problem of project selection in the presence of two objective functions that maximize profit and minimize cost and the existence of some limitations is limited resources availability and time available so that there is need allocation of resources in each project. These resources are human resources, machine resources, raw material resources. This is treated as a consideration to not exceed the budget that has been determined. So that can be formulated mathematics for objective function (multi-objective) with boundaries that fulfilled. To assist the project selection process, a multi-objective combinatorial optimization approach is used to obtain an optimal solution for the selection of the right project. It then described a multi-objective method of genetic algorithm as one method of multi-objective combinatorial optimization approach to simplify the project selection process in a large scope.

Insights into Hox protein function from a large scale combinatorial analysis of protein domains.

PubMed

Merabet, Samir; Litim-Mecheri, Isma; Karlsson, Daniel; Dixit, Richa; Saadaoui, Mehdi; Monier, Bruno; Brun, Christine; Thor, Stefan; Vijayraghavan, K; Perrin, Laurent; Pradel, Jacques; Graba, Yacine

2011-10-01

Protein function is encoded within protein sequence and protein domains. However, how protein domains cooperate within a protein to modulate overall activity and how this impacts functional diversification at the molecular and organism levels remains largely unaddressed. Focusing on three domains of the central class Drosophila Hox transcription factor AbdominalA (AbdA), we used combinatorial domain mutations and most known AbdA developmental functions as biological readouts to investigate how protein domains collectively shape protein activity. The results uncover redundancy, interactivity, and multifunctionality of protein domains as salient features underlying overall AbdA protein activity, providing means to apprehend functional diversity and accounting for the robustness of Hox-controlled developmental programs. Importantly, the results highlight context-dependency in protein domain usage and interaction, allowing major modifications in domains to be tolerated without general functional loss. The non-pleoitropic effect of domain mutation suggests that protein modification may contribute more broadly to molecular changes underlying morphological diversification during evolution, so far thought to rely largely on modification in gene cis-regulatory sequences.

Insights into Hox Protein Function from a Large Scale Combinatorial Analysis of Protein Domains

PubMed Central

Karlsson, Daniel; Dixit, Richa; Saadaoui, Mehdi; Monier, Bruno; Brun, Christine; Thor, Stefan; Vijayraghavan, K.; Perrin, Laurent; Pradel, Jacques; Graba, Yacine

2011-01-01

Protein function is encoded within protein sequence and protein domains. However, how protein domains cooperate within a protein to modulate overall activity and how this impacts functional diversification at the molecular and organism levels remains largely unaddressed. Focusing on three domains of the central class Drosophila Hox transcription factor AbdominalA (AbdA), we used combinatorial domain mutations and most known AbdA developmental functions as biological readouts to investigate how protein domains collectively shape protein activity. The results uncover redundancy, interactivity, and multifunctionality of protein domains as salient features underlying overall AbdA protein activity, providing means to apprehend functional diversity and accounting for the robustness of Hox-controlled developmental programs. Importantly, the results highlight context-dependency in protein domain usage and interaction, allowing major modifications in domains to be tolerated without general functional loss. The non-pleoitropic effect of domain mutation suggests that protein modification may contribute more broadly to molecular changes underlying morphological diversification during evolution, so far thought to rely largely on modification in gene cis-regulatory sequences. PMID:22046139

Building synthetic gene circuits from combinatorial libraries: screening and selection strategies.

PubMed

Schaerli, Yolanda; Isalan, Mark

2013-07-01

The promise of wide-ranging biotechnology applications inspires synthetic biologists to design novel genetic circuits. However, building such circuits rationally is still not straightforward and often involves painstaking trial-and-error. Mimicking the process of natural selection can help us to bridge the gap between our incomplete understanding of nature's design rules and our desire to build functional networks. By adopting the powerful method of directed evolution, which is usually applied to protein engineering, functional networks can be obtained through screening or selecting from randomised combinatorial libraries. This review first highlights the practical options to introduce combinatorial diversity into gene circuits and then examines strategies for identifying the potentially rare library members with desired functions, either by screening or selection.

Comprehensive human transcription factor binding site map for combinatory binding motifs discovery.

PubMed

Müller-Molina, Arnoldo J; Schöler, Hans R; Araúzo-Bravo, Marcos J

2012-01-01

To know the map between transcription factors (TFs) and their binding sites is essential to reverse engineer the regulation process. Only about 10%-20% of the transcription factor binding motifs (TFBMs) have been reported. This lack of data hinders understanding gene regulation. To address this drawback, we propose a computational method that exploits never used TF properties to discover the missing TFBMs and their sites in all human gene promoters. The method starts by predicting a dictionary of regulatory "DNA words." From this dictionary, it distills 4098 novel predictions. To disclose the crosstalk between motifs, an additional algorithm extracts TF combinatorial binding patterns creating a collection of TF regulatory syntactic rules. Using these rules, we narrowed down a list of 504 novel motifs that appear frequently in syntax patterns. We tested the predictions against 509 known motifs confirming that our system can reliably predict ab initio motifs with an accuracy of 81%-far higher than previous approaches. We found that on average, 90% of the discovered combinatorial binding patterns target at least 10 genes, suggesting that to control in an independent manner smaller gene sets, supplementary regulatory mechanisms are required. Additionally, we discovered that the new TFBMs and their combinatorial patterns convey biological meaning, targeting TFs and genes related to developmental functions. Thus, among all the possible available targets in the genome, the TFs tend to regulate other TFs and genes involved in developmental functions. We provide a comprehensive resource for regulation analysis that includes a dictionary of "DNA words," newly predicted motifs and their corresponding combinatorial patterns. Combinatorial patterns are a useful filter to discover TFBMs that play a major role in orchestrating other factors and thus, are likely to lock/unlock cellular functional clusters.

Comprehensive Human Transcription Factor Binding Site Map for Combinatory Binding Motifs Discovery

PubMed Central

Müller-Molina, Arnoldo J.; Schöler, Hans R.; Araúzo-Bravo, Marcos J.

2012-01-01

To know the map between transcription factors (TFs) and their binding sites is essential to reverse engineer the regulation process. Only about 10%–20% of the transcription factor binding motifs (TFBMs) have been reported. This lack of data hinders understanding gene regulation. To address this drawback, we propose a computational method that exploits never used TF properties to discover the missing TFBMs and their sites in all human gene promoters. The method starts by predicting a dictionary of regulatory “DNA words.” From this dictionary, it distills 4098 novel predictions. To disclose the crosstalk between motifs, an additional algorithm extracts TF combinatorial binding patterns creating a collection of TF regulatory syntactic rules. Using these rules, we narrowed down a list of 504 novel motifs that appear frequently in syntax patterns. We tested the predictions against 509 known motifs confirming that our system can reliably predict ab initio motifs with an accuracy of 81%—far higher than previous approaches. We found that on average, 90% of the discovered combinatorial binding patterns target at least 10 genes, suggesting that to control in an independent manner smaller gene sets, supplementary regulatory mechanisms are required. Additionally, we discovered that the new TFBMs and their combinatorial patterns convey biological meaning, targeting TFs and genes related to developmental functions. Thus, among all the possible available targets in the genome, the TFs tend to regulate other TFs and genes involved in developmental functions. We provide a comprehensive resource for regulation analysis that includes a dictionary of “DNA words,” newly predicted motifs and their corresponding combinatorial patterns. Combinatorial patterns are a useful filter to discover TFBMs that play a major role in orchestrating other factors and thus, are likely to lock/unlock cellular functional clusters. PMID:23209563

Combinatorial Methods for Exploring Complex Materials

NASA Astrophysics Data System (ADS)

Amis, Eric J.

2004-03-01

Combinatorial and high-throughput methods have changed the paradigm of pharmaceutical synthesis and have begun to have a similar impact on materials science research. Already there are examples of combinatorial methods used for inorganic materials, catalysts, and polymer synthesis. For many investigations the primary goal has been discovery of new material compositions that optimize properties such as phosphorescence or catalytic activity. In the midst of the excitement generated to "make things", another opportunity arises for materials science to "understand things" by using the efficiency of combinatorial methods. We have shown that combinatorial methods hold potential for rapid and systematic generation of experimental data over the multi-parameter space typical of investigations in polymer physics. We have applied the combinatorial approach to studies of polymer thin films, biomaterials, polymer blends, filled polymers, and semicrystalline polymers. By combining library fabrication, high-throughput measurements, informatics, and modeling we can demonstrate validation of the methodology, new observations, and developments toward predictive models. This talk will present some of our latest work with applications to coating stability, multi-component formulations, and nanostructure assembly.

Why is combinatorial communication rare in the natural world, and why is language an exception to this trend?

PubMed

Scott-Phillips, Thomas C; Blythe, Richard A

2013-11-06

In a combinatorial communication system, some signals consist of the combinations of other signals. Such systems are more efficient than equivalent, non-combinatorial systems, yet despite this they are rare in nature. Why? Previous explanations have focused on the adaptive limits of combinatorial communication, or on its purported cognitive difficulties, but neither of these explains the full distribution of combinatorial communication in the natural world. Here, we present a nonlinear dynamical model of the emergence of combinatorial communication that, unlike previous models, considers how initially non-communicative behaviour evolves to take on a communicative function. We derive three basic principles about the emergence of combinatorial communication. We hence show that the interdependence of signals and responses places significant constraints on the historical pathways by which combinatorial signals might emerge, to the extent that anything other than the most simple form of combinatorial communication is extremely unlikely. We also argue that these constraints can be bypassed if individuals have the socio-cognitive capacity to engage in ostensive communication. Humans, but probably no other species, have this ability. This may explain why language, which is massively combinatorial, is such an extreme exception to nature's general trend for non-combinatorial communication.

Combinatorial structures to modeling simple games and applications

NASA Astrophysics Data System (ADS)

Molinero, Xavier

2017-09-01

We connect three different topics: combinatorial structures, game theory and chemistry. In particular, we establish the bases to represent some simple games, defined as influence games, and molecules, defined from atoms, by using combinatorial structures. First, we characterize simple games as influence games using influence graphs. It let us to modeling simple games as combinatorial structures (from the viewpoint of structures or graphs). Second, we formally define molecules as combinations of atoms. It let us to modeling molecules as combinatorial structures (from the viewpoint of combinations). It is open to generate such combinatorial structures using some specific techniques as genetic algorithms, (meta-)heuristics algorithms and parallel programming, among others.

Combinatorial complexity of pathway analysis in metabolic networks.

PubMed

Klamt, Steffen; Stelling, Jörg

2002-01-01

Elementary flux mode analysis is a promising approach for a pathway-oriented perspective of metabolic networks. However, in larger networks it is hampered by the combinatorial explosion of possible routes. In this work we give some estimations on the combinatorial complexity including theoretical upper bounds for the number of elementary flux modes in a network of a given size. In a case study, we computed the elementary modes in the central metabolism of Escherichia coli while utilizing four different substrates. Interestingly, although the number of modes occurring in this complex network can exceed half a million, it is still far below the upper bound. Hence, to a certain extent, pathway analysis of central catabolism is feasible to assess network properties such as flexibility and functionality.

Metaheuristics-Assisted Combinatorial Screening of Eu2+-Doped Ca-Sr-Ba-Li-Mg-Al-Si-Ge-N Compositional Space in Search of a Narrow-Band Green Emitting Phosphor and Density Functional Theory Calculations.

PubMed

Lee, Jin-Woong; Singh, Satendra Pal; Kim, Minseuk; Hong, Sung Un; Park, Woon Bae; Sohn, Kee-Sun

2017-08-21

A metaheuristics-based design would be of great help in relieving the enormous experimental burdens faced during the combinatorial screening of a huge, multidimensional search space, while providing the same effect as total enumeration. In order to tackle the high-throughput powder processing complications and to secure practical phosphors, metaheuristics, an elitism-reinforced nondominated sorting genetic algorithm (NSGA-II), was employed in this study. The NSGA-II iteration targeted two objective functions. The first was to search for a higher emission efficacy. The second was to search for narrow-band green color emissions. The NSGA-II iteration finally converged on BaLi 2 Al 2 Si 2 N 6 :Eu 2+ phosphors in the Eu 2+ -doped Ca-Sr-Ba-Li-Mg-Al-Si-Ge-N compositional search space. The BaLi 2 Al 2 Si 2 N 6 :Eu 2+ phosphor, which was synthesized with no human intervention via the assistance of NSGA-II, was a clear single phase and gave an acceptable luminescence. The BaLi 2 Al 2 Si 2 N 6 :Eu 2+ phosphor as well as all other phosphors that appeared during the NSGA-II iterations were examined in detail by employing powder X-ray diffraction-based Rietveld refinement, X-ray absorption near edge structure, density functional theory calculation, and time-resolved photoluminescence. The thermodynamic stability and the band structure plausibility were confirmed, and more importantly a novel approach to the energy transfer analysis was also introduced for BaLi 2 Al 2 Si 2 N 6 :Eu 2+ phosphors.

Hypergraph-Based Combinatorial Optimization of Matrix-Vector Multiplication

ERIC Educational Resources Information Center

Wolf, Michael Maclean

2009-01-01

Combinatorial scientific computing plays an important enabling role in computational science, particularly in high performance scientific computing. In this thesis, we will describe our work on optimizing matrix-vector multiplication using combinatorial techniques. Our research has focused on two different problems in combinatorial scientific…

Dynamic combinatorial libraries: new opportunities in systems chemistry.

PubMed

Hunt, Rosemary A R; Otto, Sijbren

2011-01-21

Combinatorial chemistry is a tool for selecting molecules with special properties. Dynamic combinatorial chemistry started off aiming to be just that. However, unlike ordinary combinatorial chemistry, the interconnectedness of dynamic libraries gives them an extra dimension. An understanding of these molecular networks at systems level is essential for their use as a selection tool and creates exciting new opportunities in systems chemistry. In this feature article we discuss selected examples and considerations related to the advanced exploitation of dynamic combinatorial libraries for their originally conceived purpose of identifying strong binding interactions. Also reviewed are examples illustrating a trend towards increasing complexity in terms of network behaviour and reversible chemistry. Finally, new applications of dynamic combinatorial chemistry in self-assembly, transport and self-replication are discussed.

Integrated microfluidic devices for combinatorial cell-based assays.

PubMed

Yu, Zeta Tak For; Kamei, Ken-ichiro; Takahashi, Hiroko; Shu, Chengyi Jenny; Wang, Xiaopu; He, George Wenfu; Silverman, Robert; Radu, Caius G; Witte, Owen N; Lee, Ki-Bum; Tseng, Hsian-Rong

2009-06-01

The development of miniaturized cell culture platforms for performing parallel cultures and combinatorial assays is important in cell biology from the single-cell level to the system level. In this paper we developed an integrated microfluidic cell-culture platform, Cell-microChip (Cell-microChip), for parallel analyses of the effects of microenvironmental cues (i.e., culture scaffolds) on different mammalian cells and their cellular responses to external stimuli. As a model study, we demonstrated the ability of culturing and assaying several mammalian cells, such as NIH 3T3 fibroblast, B16 melanoma and HeLa cell lines, in a parallel way. For functional assays, first we tested drug-induced apoptotic responses from different cell lines. As a second functional assay, we performed "on-chip" transfection of a reporter gene encoding an enhanced green fluorescent protein (EGFP) followed by live-cell imaging of transcriptional activation of cyclooxygenase 2 (Cox-2) expression. Collectively, our Cell-microChip approach demonstrated the capability to carry out parallel operations and the potential to further integrate advanced functions and applications in the broader space of combinatorial chemistry and biology.

Integrated microfluidic devices for combinatorial cell-based assays

PubMed Central

Yu, Zeta Tak For; Kamei, Ken-ichiro; Takahashi, Hiroko; Shu, Chengyi Jenny; Wang, Xiaopu; He, George Wenfu; Silverman, Robert

2010-01-01

The development of miniaturized cell culture platforms for performing parallel cultures and combinatorial assays is important in cell biology from the single-cell level to the system level. In this paper we developed an integrated microfluidic cell-culture platform, Cell-microChip (Cell-μChip), for parallel analyses of the effects of microenvir-onmental cues (i.e., culture scaffolds) on different mammalian cells and their cellular responses to external stimuli. As a model study, we demonstrated the ability of culturing and assaying several mammalian cells, such as NIH 3T3 fibro-blast, B16 melanoma and HeLa cell lines, in a parallel way. For functional assays, first we tested drug-induced apoptotic responses from different cell lines. As a second functional assay, we performed "on-chip" transfection of a reporter gene encoding an enhanced green fluorescent protein (EGFP) followed by live-cell imaging of transcriptional activation of cyclooxygenase 2 (Cox-2) expression. Collectively, our Cell-μChip approach demonstrated the capability to carry out parallel operations and the potential to further integrate advanced functions and applications in the broader space of combinatorial chemistry and biology. PMID:19130244

Tumor-targeting peptides from combinatorial libraries*

PubMed Central

Liu, Ruiwu; Li, Xiaocen; Xiao, Wenwu; Lam, Kit S.

2018-01-01

Cancer is one of the major and leading causes of death worldwide. Two of the greatest challenges infighting cancer are early detection and effective treatments with no or minimum side effects. Widespread use of targeted therapies and molecular imaging in clinics requires high affinity, tumor-specific agents as effective targeting vehicles to deliver therapeutics and imaging probes to the primary or metastatic tumor sites. Combinatorial libraries such as phage-display and one-bead one-compound (OBOC) peptide libraries are powerful approaches in discovering tumor-targeting peptides. This review gives an overview of different combinatorial library technologies that have been used for the discovery of tumor-targeting peptides. Examples of tumor-targeting peptides identified from each combinatorial library method will be discussed. Published tumor-targeting peptide ligands and their applications will also be summarized by the combinatorial library methods and their corresponding binding receptors. PMID:27210583

Combinatorial Characterization of TiO2 Chemical Vapor Deposition Utilizing Titanium Isopropoxide.

PubMed

Reinke, Michael; Ponomarev, Evgeniy; Kuzminykh, Yury; Hoffmann, Patrik

2015-07-13

The combinatorial characterization of the growth kinetics in chemical vapor deposition processes is challenging because precise information about the local precursor flow is usually difficult to access. In consequence, combinatorial chemical vapor deposition techniques are utilized more to study functional properties of thin films as a function of chemical composition, growth rate or crystallinity than to study the growth process itself. We present an experimental procedure which allows the combinatorial study of precursor surface kinetics during the film growth using high vacuum chemical vapor deposition. As consequence of the high vacuum environment, the precursor transport takes place in the molecular flow regime, which allows predicting and modifying precursor impinging rates on the substrate with comparatively little experimental effort. In this contribution, we study the surface kinetics of titanium dioxide formation using titanium tetraisopropoxide as precursor molecule over a large parameter range. We discuss precursor flux and temperature dependent morphology, crystallinity, growth rates, and precursor deposition efficiency. We conclude that the surface reaction of the adsorbed precursor molecules comprises a higher order reaction component with respect to precursor surface coverage.

Density functional theory and an experimentally-designed energy functional of electron density.

PubMed

Miranda, David A; Bueno, Paulo R

2016-09-21

We herein demonstrate that capacitance spectroscopy (CS) experimentally allows access to the energy associated with the quantum mechanical ground state of many-electron systems. Priorly, electrochemical capacitance, C [small mu, Greek, macron] [ρ], was previously understood from conceptual and computational density functional theory (DFT) calculations. Thus, we herein propose a quantum mechanical experiment-based variational method for electron charging processes based on an experimentally-designed functional of the ground state electron density. In this methodology, the electron state density, ρ, and an energy functional of the electron density, E [small mu, Greek, macron] [ρ], can be obtained from CS data. CS allows the derivative of the electrochemical potential with respect to the electron density, (δ[small mu, Greek, macron][ρ]/δρ), to be obtained as a unique functional of the energetically minimised system, i.e., β/C [small mu, Greek, macron] [ρ], where β is a constant (associated with the size of the system) and C [small mu, Greek, macron] [ρ] is an experimentally observable quantity. Thus the ground state energy (at a given fixed external potential) can be obtained simply as E [small mu, Greek, macron] [ρ], from the experimental measurement of C [small mu, Greek, macron] [ρ]. An experimental data-set was interpreted to demonstrate the potential of this quantum mechanical experiment-based variational principle.

Density Functionals of Chemical Bonding

PubMed Central

Putz, Mihai V.

2008-01-01

The behavior of electrons in general many-electronic systems throughout the density functionals of energy is reviewed. The basic physico-chemical concepts of density functional theory are employed to highlight the energy role in chemical structure while its extended influence in electronic localization function helps in chemical bonding understanding. In this context the energy functionals accompanied by electronic localization functions may provide a comprehensive description of the global-local levels electronic structures in general and of chemical bonds in special. Becke-Edgecombe and author’s Markovian electronic localization functions are discussed at atomic, molecular and solid state levels. Then, the analytical survey of the main workable kinetic, exchange, and correlation density functionals within local and gradient density approximations is undertaken. The hierarchy of various energy functionals is formulated by employing both the parabolic and statistical correlation degree of them with the electronegativity and chemical hardness indices by means of quantitative structure-property relationship (QSPR) analysis for basic atomic and molecular systems. PMID:19325846

Neural Meta-Memes Framework for Combinatorial Optimization

NASA Astrophysics Data System (ADS)

Song, Li Qin; Lim, Meng Hiot; Ong, Yew Soon

In this paper, we present a Neural Meta-Memes Framework (NMMF) for combinatorial optimization. NMMF is a framework which models basic optimization algorithms as memes and manages them dynamically when solving combinatorial problems. NMMF encompasses neural networks which serve as the overall planner/coordinator to balance the workload between memes. We show the efficacy of the proposed NMMF through empirical study on a class of combinatorial problem, the quadratic assignment problem (QAP).

Tumor-targeting peptides from combinatorial libraries.

PubMed

Liu, Ruiwu; Li, Xiaocen; Xiao, Wenwu; Lam, Kit S

2017-02-01

Cancer is one of the major and leading causes of death worldwide. Two of the greatest challenges in fighting cancer are early detection and effective treatments with no or minimum side effects. Widespread use of targeted therapies and molecular imaging in clinics requires high affinity, tumor-specific agents as effective targeting vehicles to deliver therapeutics and imaging probes to the primary or metastatic tumor sites. Combinatorial libraries such as phage-display and one-bead one-compound (OBOC) peptide libraries are powerful approaches in discovering tumor-targeting peptides. This review gives an overview of different combinatorial library technologies that have been used for the discovery of tumor-targeting peptides. Examples of tumor-targeting peptides identified from each combinatorial library method will be discussed. Published tumor-targeting peptide ligands and their applications will also be summarized by the combinatorial library methods and their corresponding binding receptors. Copyright © 2017. Published by Elsevier B.V.

Combinatorial chemical bath deposition of CdS contacts for chalcogenide photovoltaics

DOE PAGES

Mokurala, Krishnaiah; Baranowski, Lauryn L.; de Souza Lucas, Francisco W.; ...

2016-08-01

Contact layers play an important role in thin film solar cells, but new material development and optimization of its thickness is usually a long and tedious process. A high-throughput experimental approach has been used to accelerate the rate of research in photovoltaic (PV) light absorbers and transparent conductive electrodes, however the combinatorial research on contact layers is less common. Here, we report on the chemical bath deposition (CBD) of CdS thin films by combinatorial dip coating technique and apply these contact layers to Cu(In,Ga)Se 2 (CIGSe) and Cu 2ZnSnSe 4 (CZTSe) light absorbers in PV devices. Combinatorial thickness steps ofmore » CdS thin films were achieved by removal of the substrate from the chemical bath, at regular intervals of time, and in equal distance increments. The trends in the photoconversion efficiency and in the spectral response of the PV devices as a function of thickness of CdS contacts were explained with the help of optical and morphological characterization of the CdS thin films. The maximum PV efficiency achieved for the combinatorial dip-coating CBD was similar to that for the PV devices processed using conventional CBD. Finally, the results of this study lead to the conclusion that combinatorial dip-coating can be used to accelerate the optimization of PV device performance of CdS and other candidate contact layers for a wide range of emerging absorbers.« less

Use of combinatorial chemistry to speed drug discovery.

PubMed

Rádl, S

1998-10-01

IBC's International Conference on Integrating Combinatorial Chemistry into the Discovery Pipeline was held September 14-15, 1998. The program started with a pre-conference workshop on High-Throughput Compound Characterization and Purification. The agenda of the main conference was divided into sessions of Synthesis, Automation and Unique Chemistries; Integrating Combinatorial Chemistry, Medicinal Chemistry and Screening; Combinatorial Chemistry Applications for Drug Discovery; and Information and Data Management. This meeting was an excellent opportunity to see how big pharma, biotech and service companies are addressing the current bottlenecks in combinatorial chemistry to speed drug discovery. (c) 1998 Prous Science. All rights reserved.

Asessing for Structural Understanding in Childrens' Combinatorial Problem Solving.

ERIC Educational Resources Information Center

English, Lyn

1999-01-01

Assesses children's structural understanding of combinatorial problems when presented in a variety of task situations. Provides an explanatory model of students' combinatorial understandings that informs teaching and assessment. Addresses several components of children's structural understanding of elementary combinatorial problems. (Contains 50…

Multicomponent density functional theory embedding formulation.

PubMed

Culpitt, Tanner; Brorsen, Kurt R; Pak, Michael V; Hammes-Schiffer, Sharon

2016-07-28

Multicomponent density functional theory (DFT) methods have been developed to treat two types of particles, such as electrons and nuclei, quantum mechanically at the same level. In the nuclear-electronic orbital (NEO) approach, all electrons and select nuclei, typically key protons, are treated quantum mechanically. For multicomponent DFT methods developed within the NEO framework, electron-proton correlation functionals based on explicitly correlated wavefunctions have been designed and used in conjunction with well-established electronic exchange-correlation functionals. Herein a general theory for multicomponent embedded DFT is developed to enable the accurate treatment of larger systems. In the general theory, the total electronic density is separated into two subsystem densities, denoted as regular and special, and different electron-proton correlation functionals are used for these two electronic densities. In the specific implementation, the special electron density is defined in terms of spatially localized Kohn-Sham electronic orbitals, and electron-proton correlation is included only for the special electron density. The electron-proton correlation functional depends on only the special electron density and the proton density, whereas the electronic exchange-correlation functional depends on the total electronic density. This scheme includes the essential electron-proton correlation, which is a relatively local effect, as well as the electronic exchange-correlation for the entire system. This multicomponent DFT-in-DFT embedding theory is applied to the HCN and FHF(-) molecules in conjunction with two different electron-proton correlation functionals and three different electronic exchange-correlation functionals. The results illustrate that this approach provides qualitatively accurate nuclear densities in a computationally tractable manner. The general theory is also easily extended to other types of partitioning schemes for multicomponent systems.

Survival of the most transferable at the top of Jacob's ladder: Defining and testing the ωB97M(2) double hybrid density functional

NASA Astrophysics Data System (ADS)

Mardirossian, Narbe; Head-Gordon, Martin

2018-06-01

A meta-generalized gradient approximation, range-separated double hybrid (DH) density functional with VV10 non-local correlation is presented. The final 14-parameter functional form is determined by screening trillions of candidate fits through a combination of best subset selection, forward stepwise selection, and random sample consensus (RANSAC) outlier detection. The MGCDB84 database of 4986 data points is employed in this work, containing a training set of 870 data points, a validation set of 2964 data points, and a test set of 1152 data points. Following an xDH approach, orbitals from the ωB97M-V density functional are used to compute the second-order perturbation theory correction. The resulting functional, ωB97M(2), is benchmarked against a variety of leading double hybrid density functionals, including B2PLYP-D3(BJ), B2GPPLYP-D3(BJ), ωB97X-2(TQZ), XYG3, PTPSS-D3(0), XYGJ-OS, DSD-PBEP86-D3(BJ), and DSD-PBEPBE-D3(BJ). Encouragingly, the overall performance of ωB97M(2) on nearly 5000 data points clearly surpasses that of all of the tested density functionals. As a Rung 5 density functional, ωB97M(2) completes our family of combinatorially optimized functionals, complementing B97M-V on Rung 3, and ωB97X-V and ωB97M-V on Rung 4. The results suggest that ωB97M(2) has the potential to serve as a powerful predictive tool for accurate and efficient electronic structure calculations of main-group chemistry.

Multicomponent density functional theory embedding formulation

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

Culpitt, Tanner; Brorsen, Kurt R.; Pak, Michael V.

Multicomponent density functional theory (DFT) methods have been developed to treat two types of particles, such as electrons and nuclei, quantum mechanically at the same level. In the nuclear-electronic orbital (NEO) approach, all electrons and select nuclei, typically key protons, are treated quantum mechanically. For multicomponent DFT methods developed within the NEO framework, electron-proton correlation functionals based on explicitly correlated wavefunctions have been designed and used in conjunction with well-established electronic exchange-correlation functionals. Herein a general theory for multicomponent embedded DFT is developed to enable the accurate treatment of larger systems. In the general theory, the total electronic density ismore » separated into two subsystem densities, denoted as regular and special, and different electron-proton correlation functionals are used for these two electronic densities. In the specific implementation, the special electron density is defined in terms of spatially localized Kohn-Sham electronic orbitals, and electron-proton correlation is included only for the special electron density. The electron-proton correlation functional depends on only the special electron density and the proton density, whereas the electronic exchange-correlation functional depends on the total electronic density. This scheme includes the essential electron-proton correlation, which is a relatively local effect, as well as the electronic exchange-correlation for the entire system. This multicomponent DFT-in-DFT embedding theory is applied to the HCN and FHF{sup −} molecules in conjunction with two different electron-proton correlation functionals and three different electronic exchange-correlation functionals. The results illustrate that this approach provides qualitatively accurate nuclear densities in a computationally tractable manner. The general theory is also easily extended to other types of partitioning schemes for multicomponent

Analytical gradients for subsystem density functional theory within the slater-function-based amsterdam density functional program.

PubMed

Schlüns, Danny; Franchini, Mirko; Götz, Andreas W; Neugebauer, Johannes; Jacob, Christoph R; Visscher, Lucas

2017-02-05

We present a new implementation of analytical gradients for subsystem density-functional theory (sDFT) and frozen-density embedding (FDE) into the Amsterdam Density Functional program (ADF). The underlying theory and necessary expressions for the implementation are derived and discussed in detail for various FDE and sDFT setups. The parallel implementation is numerically verified and geometry optimizations with different functional combinations (LDA/TF and PW91/PW91K) are conducted and compared to reference data. Our results confirm that sDFT-LDA/TF yields good equilibrium distances for the systems studied here (mean absolute deviation: 0.09 Å) compared to reference wave-function theory results. However, sDFT-PW91/PW91k quite consistently yields smaller equilibrium distances (mean absolute deviation: 0.23 Å). The flexibility of our new implementation is demonstrated for an HCN-trimer test system, for which several different setups are applied. © 2016 Wiley Periodicals, Inc. © 2016 Wiley Periodicals, Inc.

MIFT: GIFT Combinatorial Geometry Input to VCS Code

DTIC Science & Technology

1977-03-01

r-w w-^ H ^ß0318is CQ BRL °RCUMr REPORT NO. 1967 —-S: ... MIFT: GIFT COMBINATORIAL GEOMETRY INPUT TO VCS CODE Albert E...TITLE (and Subtitle) MIFT: GIFT Combinatorial Geometry Input to VCS Code S. TYPE OF REPORT & PERIOD COVERED FINAL 6. PERFORMING ORG. REPORT NUMBER...Vehicle Code System (VCS) called MORSE was modified to accept the GIFT combinatorial geometry package. GIFT , as opposed to the geometry package

The combinatorial control of alternative splicing in C. elegans

PubMed Central

2017-01-01

Normal development requires the right splice variants to be made in the right tissues at the right time. The core splicing machinery is engaged in all splicing events, but which precise splice variant is made requires the choice between alternative splice sites—for this to occur, a set of splicing factors (SFs) must recognize and bind to short RNA motifs in the pre-mRNA. In C. elegans, there is known to be extensive variation in splicing patterns across development, but little is known about the targets of each SF or how multiple SFs combine to regulate splicing. Here we combine RNA-seq with in vitro binding assays to study how 4 different C. elegans SFs, ASD-1, FOX-1, MEC-8, and EXC-7, regulate splicing. The 4 SFs chosen all have well-characterised biology and well-studied loss-of-function genetic alleles, and all contain RRM domains. Intriguingly, while the SFs we examined have varied roles in C. elegans development, they show an unexpectedly high overlap in their targets. We also find that binding sites for these SFs occur on the same pre-mRNAs more frequently than expected suggesting extensive combinatorial control of splicing. We confirm that regulation of splicing by multiple SFs is often combinatorial and show that this is functionally significant. We also find that SFs appear to combine to affect splicing in two modes—they either bind in close proximity within the same intron or they appear to bind to separate regions of the intron in a conserved order. Finally, we find that the genes whose splicing are regulated by multiple SFs are highly enriched for genes involved in the cytoskeleton and in ion channels that are key for neurotransmission. Together, this shows that specific classes of genes have complex combinatorial regulation of splicing and that this combinatorial regulation is critical for normal development to occur. PMID:29121637

Combinatorial stresses kill pathogenic Candida species

PubMed Central

Kaloriti, Despoina; Tillmann, Anna; Cook, Emily; Jacobsen, Mette; You, Tao; Lenardon, Megan; Ames, Lauren; Barahona, Mauricio; Chandrasekaran, Komelapriya; Coghill, George; Goodman, Daniel; Gow, Neil A. R.; Grebogi, Celso; Ho, Hsueh-Lui; Ingram, Piers; McDonagh, Andrew; De Moura, Alessandro P. S.; Pang, Wei; Puttnam, Melanie; Radmaneshfar, Elahe; Romano, Maria Carmen; Silk, Daniel; Stark, Jaroslav; Stumpf, Michael; Thiel, Marco; Thorne, Thomas; Usher, Jane; Yin, Zhikang; Haynes, Ken; Brown, Alistair J. P.

2012-01-01

Pathogenic microbes exist in dynamic niches and have evolved robust adaptive responses to promote survival in their hosts. The major fungal pathogens of humans, Candida albicans and Candida glabrata, are exposed to a range of environmental stresses in their hosts including osmotic, oxidative and nitrosative stresses. Significant efforts have been devoted to the characterization of the adaptive responses to each of these stresses. In the wild, cells are frequently exposed simultaneously to combinations of these stresses and yet the effects of such combinatorial stresses have not been explored. We have developed a common experimental platform to facilitate the comparison of combinatorial stress responses in C. glabrata and C. albicans. This platform is based on the growth of cells in buffered rich medium at 30°C, and was used to define relatively low, medium and high doses of osmotic (NaCl), oxidative (H 2O2) and nitrosative stresses (e.g., dipropylenetriamine (DPTA)-NONOate). The effects of combinatorial stresses were compared with the corresponding individual stresses under these growth conditions. We show for the first time that certain combinations of combinatorial stress are especially potent in terms of their ability to kill C. albicans and C. glabrata and/or inhibit their growth. This was the case for combinations of osmotic plus oxidative stress and for oxidative plus nitrosative stress. We predict that combinatorial stresses may be highly signif cant in host defences against these pathogenic yeasts. PMID:22463109

A New Approach for Proving or Generating Combinatorial Identities

ERIC Educational Resources Information Center

Gonzalez, Luis

2010-01-01

A new method for proving, in an immediate way, many combinatorial identities is presented. The method is based on a simple recursive combinatorial formula involving n + 1 arbitrary real parameters. Moreover, this formula enables one not only to prove, but also generate many different combinatorial identities (not being required to know them "a…

Density dependence of the nuclear energy-density functional

NASA Astrophysics Data System (ADS)

Papakonstantinou, Panagiota; Park, Tae-Sun; Lim, Yeunhwan; Hyun, Chang Ho

2018-01-01

Background: The explicit density dependence in the coupling coefficients entering the nonrelativistic nuclear energy-density functional (EDF) is understood to encode effects of three-nucleon forces and dynamical correlations. The necessity for the density-dependent coupling coefficients to assume the form of a preferably small fractional power of the density ρ is empirical and the power is often chosen arbitrarily. Consequently, precision-oriented parametrizations risk overfitting in the regime of saturation and extrapolations in dilute or dense matter may lose predictive power. Purpose: Beginning with the observation that the Fermi momentum kF, i.e., the cubic root of the density, is a key variable in the description of Fermi systems, we first wish to examine if a power hierarchy in a kF expansion can be inferred from the properties of homogeneous matter in a domain of densities, which is relevant for nuclear structure and neutron stars. For subsequent applications we want to determine a functional that is of good quality but not overtrained. Method: For the EDF, we fit systematically polynomial and other functions of ρ1 /3 to existing microscopic, variational calculations of the energy of symmetric and pure neutron matter (pseudodata) and analyze the behavior of the fits. We select a form and a set of parameters, which we found robust, and examine the parameters' naturalness and the quality of resulting extrapolations. Results: A statistical analysis confirms that low-order terms such as ρ1 /3 and ρ2 /3 are the most relevant ones in the nuclear EDF beyond lowest order. It also hints at a different power hierarchy for symmetric vs. pure neutron matter, supporting the need for more than one density-dependent term in nonrelativistic EDFs. The functional we propose easily accommodates known or adopted properties of nuclear matter near saturation. More importantly, upon extrapolation to dilute or asymmetric matter, it reproduces a range of existing microscopic

On the suitability of different representations of solid catalysts for combinatorial library design by genetic algorithms.

PubMed

Gobin, Oliver C; Schüth, Ferdi

2008-01-01

Genetic algorithms are widely used to solve and optimize combinatorial problems and are more often applied for library design in combinatorial chemistry. Because of their flexibility, however, their implementation can be challenging. In this study, the influence of the representation of solid catalysts on the performance of genetic algorithms was systematically investigated on the basis of a new, constrained, multiobjective, combinatorial test problem with properties common to problems in combinatorial materials science. Constraints were satisfied by penalty functions, repair algorithms, or special representations. The tests were performed using three state-of-the-art evolutionary multiobjective algorithms by performing 100 optimization runs for each algorithm and test case. Experimental data obtained during the optimization of a noble metal-free solid catalyst system active in the selective catalytic reduction of nitric oxide with propene was used to build up a predictive model to validate the results of the theoretical test problem. A significant influence of the representation on the optimization performance was observed. Binary encodings were found to be the preferred encoding in most of the cases, and depending on the experimental test unit, repair algorithms or penalty functions performed best.

Density-functional theory for internal magnetic fields

NASA Astrophysics Data System (ADS)

Tellgren, Erik I.

2018-01-01

A density-functional theory is developed based on the Maxwell-Schrödinger equation with an internal magnetic field in addition to the external electromagnetic potentials. The basic variables of this theory are the electron density and the total magnetic field, which can equivalently be represented as a physical current density. Hence, the theory can be regarded as a physical current density-functional theory and an alternative to the paramagnetic current density-functional theory due to Vignale and Rasolt. The energy functional has strong enough convexity properties to allow a formulation that generalizes Lieb's convex analysis formulation of standard density-functional theory. Several variational principles as well as a Hohenberg-Kohn-like mapping between potentials and ground-state densities follow from the underlying convex structure. Moreover, the energy functional can be regarded as the result of a standard approximation technique (Moreau-Yosida regularization) applied to the conventional Schrödinger ground-state energy, which imposes limits on the maximum curvature of the energy (with respect to the magnetic field) and enables construction of a (Fréchet) differentiable universal density functional.

Microbatteries for Combinatorial Studies of Conventional Lithium-Ion Batteries

NASA Technical Reports Server (NTRS)

West, William; Whitacre, Jay; Bugga, Ratnakumar

2003-01-01

Integrated arrays of microscopic solid-state batteries have been demonstrated in a continuing effort to develop microscopic sources of power and of voltage reference circuits to be incorporated into low-power integrated circuits. Perhaps even more importantly, arrays of microscopic batteries can be fabricated and tested in combinatorial experiments directed toward optimization and discovery of battery materials. The value of the combinatorial approach to optimization and discovery has been proven in the optoelectronic, pharmaceutical, and bioengineering industries. Depending on the specific application, the combinatorial approach can involve the investigation of hundreds or even thousands of different combinations; hence, it is time-consuming and expensive to attempt to implement the combinatorial approach by building and testing full-size, discrete cells and batteries. The conception of microbattery arrays makes it practical to bring the advantages of the combinatorial approach to the development of batteries.

Spectral function from Reduced Density Matrix Functional Theory

NASA Astrophysics Data System (ADS)

Romaniello, Pina; di Sabatino, Stefano; Berger, Jan A.; Reining, Lucia

2015-03-01

In this work we focus on the calculation of the spectral function, which determines, for example, photoemission spectra, from reduced density matrix functional theory. Starting from its definition in terms of the one-body Green's function we derive an expression for the spectral function that depends on the natural occupation numbers and on an effective energy which accounts for all the charged excitations. This effective energy depends on the two-body as well as higher-order density matrices. Various approximations to this expression are explored by using the exactly solvable Hubbard chains.

Device for preparing combinatorial libraries in powder metallurgy.

PubMed

Yang, Shoufeng; Evans, Julian R G

2004-01-01

This paper describes a powder-metering, -mixing, and -dispensing mechanism that can be used as a method for producing large numbers of samples for metallurgical evaluation or electrical or mechanical testing from multicomponent metal and cermet powder systems. It is designed to make use of the same commercial powders that are used in powder metallurgy and, therefore, to produce samples that are faithful to the microstructure of finished products. The particle assemblies produced by the device could be consolidated by die pressing, isostatic pressing, laser sintering, or direct melting. The powder metering valve provides both on/off and flow rate control of dry powders in open capillaries using acoustic vibration. The valve is simple and involves no relative movement, avoiding seizure with fine powders. An orchestra of such valves can be arranged on a building platform to prepare multicomponent combinatorial libraries. As with many combinatorial devices, identification and evaluation of sources of mixing error as a function of sample size is mandatory. Such an analysis is presented.

Ground-state densities from the Rayleigh-Ritz variation principle and from density-functional theory.

PubMed

Kvaal, Simen; Helgaker, Trygve

2015-11-14

The relationship between the densities of ground-state wave functions (i.e., the minimizers of the Rayleigh-Ritz variation principle) and the ground-state densities in density-functional theory (i.e., the minimizers of the Hohenberg-Kohn variation principle) is studied within the framework of convex conjugation, in a generic setting covering molecular systems, solid-state systems, and more. Having introduced admissible density functionals as functionals that produce the exact ground-state energy for a given external potential by minimizing over densities in the Hohenberg-Kohn variation principle, necessary and sufficient conditions on such functionals are established to ensure that the Rayleigh-Ritz ground-state densities and the Hohenberg-Kohn ground-state densities are identical. We apply the results to molecular systems in the Born-Oppenheimer approximation. For any given potential v ∈ L(3/2)(ℝ(3)) + L(∞)(ℝ(3)), we establish a one-to-one correspondence between the mixed ground-state densities of the Rayleigh-Ritz variation principle and the mixed ground-state densities of the Hohenberg-Kohn variation principle when the Lieb density-matrix constrained-search universal density functional is taken as the admissible functional. A similar one-to-one correspondence is established between the pure ground-state densities of the Rayleigh-Ritz variation principle and the pure ground-state densities obtained using the Hohenberg-Kohn variation principle with the Levy-Lieb pure-state constrained-search functional. In other words, all physical ground-state densities (pure or mixed) are recovered with these functionals and no false densities (i.e., minimizing densities that are not physical) exist. The importance of topology (i.e., choice of Banach space of densities and potentials) is emphasized and illustrated. The relevance of these results for current-density-functional theory is examined.

Morphological Constraints on Cerebellar Granule Cell Combinatorial Diversity.

PubMed

Gilmer, Jesse I; Person, Abigail L

2017-12-13

Combinatorial expansion by the cerebellar granule cell layer (GCL) is fundamental to theories of cerebellar contributions to motor control and learning. Granule cells (GrCs) sample approximately four mossy fiber inputs and are thought to form a combinatorial code useful for pattern separation and learning. We constructed a spatially realistic model of the cerebellar GCL and examined how GCL architecture contributes to GrC combinatorial diversity. We found that GrC combinatorial diversity saturates quickly as mossy fiber input diversity increases, and that this saturation is in part a consequence of short dendrites, which limit access to diverse inputs and favor dense sampling of local inputs. This local sampling also produced GrCs that were combinatorially redundant, even when input diversity was extremely high. In addition, we found that mossy fiber clustering, which is a common anatomical pattern, also led to increased redundancy of GrC input combinations. We related this redundancy to hypothesized roles of temporal expansion of GrC information encoding in service of learned timing, and we show that GCL architecture produces GrC populations that support both temporal and combinatorial expansion. Finally, we used novel anatomical measurements from mice of either sex to inform modeling of sparse and filopodia-bearing mossy fibers, finding that these circuit features uniquely contribute to enhancing GrC diversification and redundancy. Our results complement information theoretic studies of granule layer structure and provide insight into the contributions of granule layer anatomical features to afferent mixing. SIGNIFICANCE STATEMENT Cerebellar granule cells are among the simplest neurons, with tiny somata and, on average, just four dendrites. These characteristics, along with their dense organization, inspired influential theoretical work on the granule cell layer as a combinatorial expander, where each granule cell represents a unique combination of inputs

Signal dimensionality and the emergence of combinatorial structure.

PubMed

Little, Hannah; Eryılmaz, Kerem; de Boer, Bart

2017-11-01

In language, a small number of meaningless building blocks can be combined into an unlimited set of meaningful utterances. This is known as combinatorial structure. One hypothesis for the initial emergence of combinatorial structure in language is that recombining elements of signals solves the problem of overcrowding in a signal space. Another hypothesis is that iconicity may impede the emergence of combinatorial structure. However, how these two hypotheses relate to each other is not often discussed. In this paper, we explore how signal space dimensionality relates to both overcrowding in the signal space and iconicity. We use an artificial signalling experiment to test whether a signal space and a meaning space having similar topologies will generate an iconic system and whether, when the topologies differ, the emergence of combinatorially structured signals is facilitated. In our experiments, signals are created from participants' hand movements, which are measured using an infrared sensor. We found that participants take advantage of iconic signal-meaning mappings where possible. Further, we use trajectory predictability, measures of variance, and Hidden Markov Models to measure the use of structure within the signals produced and found that when topologies do not match, then there is more evidence of combinatorial structure. The results from these experiments are interpreted in the context of the differences between the emergence of combinatorial structure in different linguistic modalities (speech and sign). Copyright © 2017 Elsevier B.V. All rights reserved.

Single-particle energies and density of states in density functional theory

NASA Astrophysics Data System (ADS)

van Aggelen, H.; Chan, G. K.-L.

2015-07-01

Time-dependent density functional theory (TD-DFT) is commonly used as the foundation to obtain neutral excited states and transition weights in DFT, but does not allow direct access to density of states and single-particle energies, i.e. ionisation energies and electron affinities. Here we show that by extending TD-DFT to a superfluid formulation, which involves operators that break particle-number symmetry, we can obtain the density of states and single-particle energies from the poles of an appropriate superfluid response function. The standard Kohn- Sham eigenvalues emerge as the adiabatic limit of the superfluid response under the assumption that the exchange- correlation functional has no dependence on the superfluid density. The Kohn- Sham eigenvalues can thus be interpreted as approximations to the ionisation energies and electron affinities. Beyond this approximation, the formalism provides an incentive for creating a new class of density functionals specifically targeted at accurate single-particle eigenvalues and bandgaps.

Density-dependent covariant energy density functionals

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

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.

Exchange-correlation energies of atoms from efficient density functionals: influence of the electron density

NASA Astrophysics Data System (ADS)

Tao, Jianmin; Ye, Lin-Hui; Duan, Yuhua

2017-12-01

The primary goal of Kohn-Sham density functional theory is to evaluate the exchange-correlation contribution to electronic properties. However, the accuracy of a density functional can be affected by the electron density. Here we apply the nonempirical Tao-Mo (TM) semilocal functional to study the influence of the electron density on the exchange and correlation energies of atoms and ions, and compare the results with the commonly used nonempirical semilocal functionals local spin-density approximation (LSDA), Perdew-Burke-Ernzerhof (PBE), Tao-Perdew-Staroverov-Scuseria (TPSS), and hybrid functional PBE0. We find that the spin-restricted Hartree-Fock density yields the exchange and correlation energies in good agreement with the Optimized Effective Potential method, particularly for spherical atoms and ions. However, the errors of these semilocal and hybrid functionals become larger for self-consistent densities. We further find that the quality of the electron density have greater effect on the exchange-correlation energies of kinetic energy density-dependent meta-GGA functionals TPSS and TM than on those of the LSDA and GGA, and therefore, should have greater influence on the performance of meta-GGA functionals. Finally, we show that the influence of the density quality on PBE0 is slightly reduced, compared to that of PBE, due to the exact mixing.

A Combinatorial Platform for the Optimization of Peptidomimetic Methyl-Lysine Reader Antagonists

NASA Astrophysics Data System (ADS)

Barnash, Kimberly D.

Post-translational modification of histone N-terminal tails mediates chromatin compaction and, consequently, DNA replication, transcription, and repair. While numerous post-translational modifications decorate histone tails, lysine methylation is an abundant mark important for both gene activation and repression. Methyl-lysine (Kme) readers function through binding mono-, di-, or trimethyl-lysine. Chemical intervention of Kme readers faces numerous challenges due to the broad surface-groove interactions between readers and their cognate histone peptides; yet, the increasing interest in understanding chromatin-modifying complexes suggests tractable lead compounds for Kme readers are critical for elucidating the mechanisms of chromatin dysregulation in disease states and validating the druggability of these domains and complexes. The successful discovery of a peptide-derived chemical probe, UNC3866, for the Polycomb repressive complex 1 (PRC1) chromodomain Kme readers has proven the potential for selective peptidomimetic inhibition of reader function. Unfortunately, the systematic modification of peptides-to-peptidomimetics is a costly and inefficient strategy for target-class hit discovery against Kme readers. Through the exploration of biased chemical space via combinatorial on-bead libraries, we have developed two concurrent methodologies for Kme reader chemical probe discovery. We employ biased peptide combinatorial libraries as a hit discovery strategy with subsequent optimization via iterative targeted libraries. Peptide-to-peptidomimetic optimization through targeted library design was applied based on structure-guided library design around the interaction of the endogenous peptide ligand with three target Kme readers. Efforts targeting the WD40 reader EED led to the discovery of the 3-mer peptidomimetic ligand UNC5115 while combinatorial repurposing of UNC3866 for off-target chromodomains resulted in the discovery of UNC4991, a CDYL/2-selective ligand, and

Integrative Analysis of Transcription Factor Combinatorial Interactions Using a Bayesian Tensor Factorization Approach

PubMed Central

Ye, Yusen; Gao, Lin; Zhang, Shihua

2017-01-01

Transcription factors play a key role in transcriptional regulation of genes and determination of cellular identity through combinatorial interactions. However, current studies about combinatorial regulation is deficient due to lack of experimental data in the same cellular environment and extensive existence of data noise. Here, we adopt a Bayesian CANDECOMP/PARAFAC (CP) factorization approach (BCPF) to integrate multiple datasets in a network paradigm for determining precise TF interaction landscapes. In our first application, we apply BCPF to integrate three networks built based on diverse datasets of multiple cell lines from ENCODE respectively to predict a global and precise TF interaction network. This network gives 38 novel TF interactions with distinct biological functions. In our second application, we apply BCPF to seven types of cell type TF regulatory networks and predict seven cell lineage TF interaction networks, respectively. By further exploring the dynamics and modularity of them, we find cell lineage-specific hub TFs participate in cell type or lineage-specific regulation by interacting with non-specific TFs. Furthermore, we illustrate the biological function of hub TFs by taking those of cancer lineage and blood lineage as examples. Taken together, our integrative analysis can reveal more precise and extensive description about human TF combinatorial interactions. PMID:29033978

Integrative Analysis of Transcription Factor Combinatorial Interactions Using a Bayesian Tensor Factorization Approach.

PubMed

Ye, Yusen; Gao, Lin; Zhang, Shihua

2017-01-01

Transcription factors play a key role in transcriptional regulation of genes and determination of cellular identity through combinatorial interactions. However, current studies about combinatorial regulation is deficient due to lack of experimental data in the same cellular environment and extensive existence of data noise. Here, we adopt a Bayesian CANDECOMP/PARAFAC (CP) factorization approach (BCPF) to integrate multiple datasets in a network paradigm for determining precise TF interaction landscapes. In our first application, we apply BCPF to integrate three networks built based on diverse datasets of multiple cell lines from ENCODE respectively to predict a global and precise TF interaction network. This network gives 38 novel TF interactions with distinct biological functions. In our second application, we apply BCPF to seven types of cell type TF regulatory networks and predict seven cell lineage TF interaction networks, respectively. By further exploring the dynamics and modularity of them, we find cell lineage-specific hub TFs participate in cell type or lineage-specific regulation by interacting with non-specific TFs. Furthermore, we illustrate the biological function of hub TFs by taking those of cancer lineage and blood lineage as examples. Taken together, our integrative analysis can reveal more precise and extensive description about human TF combinatorial interactions.

Manipulating Combinatorial Structures.

ERIC Educational Resources Information Center

Labelle, Gilbert

This set of transparencies shows how the manipulation of combinatorial structures in the context of modern combinatorics can easily lead to interesting teaching and learning activities at every level of education from elementary school to university. The transparencies describe: (1) the importance and relations of combinatorics to science and…

Combinatorial structure of genome rearrangements scenarios.

PubMed

Ouangraoua, Aïda; Bergeron, Anne

2010-09-01

In genome rearrangement theory, one of the elusive questions raised in recent years is the enumeration of rearrangement scenarios between two genomes. This problem is related to the uniform generation of rearrangement scenarios and the derivation of tests of statistical significance of the properties of these scenarios. Here we give an exact formula for the number of double-cut-and-join (DCJ) rearrangement scenarios between two genomes. We also construct effective bijections between the set of scenarios that sort a component as well studied combinatorial objects such as parking functions, labeled trees, and prüfer codes.

Exchange-correlation energies of atoms from efficient density functionals: influence of the electron density

DOE PAGES

Tao, Jianmin; Ye, Lin -Hui; Duan, Yuhua

2017-11-20

The primary goal of Kohn–Sham density functional theory is to evaluate the exchange-correlation contribution to electronic properties. However, the accuracy of a density functional can be affected by the electron density. Here we apply the nonempirical Tao–Mo (TM) semilocal functional to study the influence of the electron density on the exchange and correlation energies of atoms and ions, and compare the results with the commonly used nonempirical semilocal functionals local spin-density approximation (LSDA), Perdew–Burke–Ernzerhof (PBE), Tao–Perdew–Staroverov–Scuseria (TPSS), and hybrid functional PBE0. We find that the spin-restricted Hartree–Fock density yields the exchange and correlation energies in good agreement with the Optimizedmore » Effective Potential method, particularly for spherical atoms and ions. However, the errors of these semilocal and hybrid functionals become larger for self-consistent densities. We further find that the quality of the electron density have greater effect on the exchange-correlation energies of kinetic energy density-dependent meta-GGA functionals TPSS and TM than on those of the LSDA and GGA, and therefore, should have greater influence on the performance of meta-GGA functionals. Lastly, we show that the influence of the density quality on PBE0 is slightly reduced, compared to that of PBE, due to the exact mixing.« less

Exchange-correlation energies of atoms from efficient density functionals: influence of the electron density

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

Tao, Jianmin; Ye, Lin -Hui; Duan, Yuhua

The primary goal of Kohn–Sham density functional theory is to evaluate the exchange-correlation contribution to electronic properties. However, the accuracy of a density functional can be affected by the electron density. Here we apply the nonempirical Tao–Mo (TM) semilocal functional to study the influence of the electron density on the exchange and correlation energies of atoms and ions, and compare the results with the commonly used nonempirical semilocal functionals local spin-density approximation (LSDA), Perdew–Burke–Ernzerhof (PBE), Tao–Perdew–Staroverov–Scuseria (TPSS), and hybrid functional PBE0. We find that the spin-restricted Hartree–Fock density yields the exchange and correlation energies in good agreement with the Optimizedmore » Effective Potential method, particularly for spherical atoms and ions. However, the errors of these semilocal and hybrid functionals become larger for self-consistent densities. We further find that the quality of the electron density have greater effect on the exchange-correlation energies of kinetic energy density-dependent meta-GGA functionals TPSS and TM than on those of the LSDA and GGA, and therefore, should have greater influence on the performance of meta-GGA functionals. Lastly, we show that the influence of the density quality on PBE0 is slightly reduced, compared to that of PBE, due to the exact mixing.« less

Combinatorial Interdependence in Lottery

ERIC Educational Resources Information Center

Helman, Danny

2005-01-01

This paper examines a real life question of gamble facing lottery players. Combinatorial dependence plays a central role in shaping the game probabilistic structure, but might not carry the merited weight in punters' considerations.

Combinatorial Partial Hydrogenation Reactions of 4-Nitroacetophenone: An Undergraduate Organic Laboratory

ERIC Educational Resources Information Center

Kittredge, Kevin W.; Marine, Susan S.; Taylor, Richard T.

2004-01-01

A molecule possessing other functional groups that could be hydrogenerated is examined, where a variety of metal catalysts are evaluated under similar reaction conditions. Optimizing organic reactions is both time and labor intensive, and the use of a combinatorial parallel synthesis reactor was great time saving device, as per summary.

Structure-based design of combinatorial mutagenesis libraries

PubMed Central

Verma, Deeptak; Grigoryan, Gevorg; Bailey-Kellogg, Chris

2015-01-01

The development of protein variants with improved properties (thermostability, binding affinity, catalytic activity, etc.) has greatly benefited from the application of high-throughput screens evaluating large, diverse combinatorial libraries. At the same time, since only a very limited portion of sequence space can be experimentally constructed and tested, an attractive possibility is to use computational protein design to focus libraries on a productive portion of the space. We present a general-purpose method, called “Structure-based Optimization of Combinatorial Mutagenesis” (SOCoM), which can optimize arbitrarily large combinatorial mutagenesis libraries directly based on structural energies of their constituents. SOCoM chooses both positions and substitutions, employing a combinatorial optimization framework based on library-averaged energy potentials in order to avoid explicitly modeling every variant in every possible library. In case study applications to green fluorescent protein, β-lactamase, and lipase A, SOCoM optimizes relatively small, focused libraries whose variants achieve energies comparable to or better than previous library design efforts, as well as larger libraries (previously not designable by structure-based methods) whose variants cover greater diversity while still maintaining substantially better energies than would be achieved by representative random library approaches. By allowing the creation of large-scale combinatorial libraries based on structural calculations, SOCoM promises to increase the scope of applicability of computational protein design and improve the hit rate of discovering beneficial variants. While designs presented here focus on variant stability (predicted by total energy), SOCoM can readily incorporate other structure-based assessments, such as the energy gap between alternative conformational or bound states. PMID:25611189

Locality of correlation in density functional theory.

PubMed

Burke, Kieron; Cancio, Antonio; Gould, Tim; Pittalis, Stefano

2016-08-07

The Hohenberg-Kohn density functional was long ago shown to reduce to the Thomas-Fermi (TF) approximation in the non-relativistic semiclassical (or large-Z) limit for all matter, i.e., the kinetic energy becomes local. Exchange also becomes local in this limit. Numerical data on the correlation energy of atoms support the conjecture that this is also true for correlation, but much less relevant to atoms. We illustrate how expansions around a large particle number are equivalent to local density approximations and their strong relevance to density functional approximations. Analyzing highly accurate atomic correlation energies, we show that EC → -AC ZlnZ + BCZ as Z → ∞, where Z is the atomic number, AC is known, and we estimate BC to be about 37 mhartree. The local density approximation yields AC exactly, but a very incorrect value for BC, showing that the local approximation is less relevant for the correlation alone. This limit is a benchmark for the non-empirical construction of density functional approximations. We conjecture that, beyond atoms, the leading correction to the local density approximation in the large-Z limit generally takes this form, but with BC a functional of the TF density for the system. The implications for the construction of approximate density functionals are discussed.

Steam explosion and its combinatorial pretreatment refining technology of plant biomass to bio-based products.

PubMed

Chen, Hong-Zhang; Liu, Zhi-Hua

2015-06-01

Pretreatment is a key unit operation affecting the refinery efficiency of plant biomass. However, the poor efficiency of pretreatment and the lack of basic theory are the main challenges to the industrial implementation of the plant biomass refinery. The purpose of this work is to review steam explosion and its combinatorial pretreatment as a means of overcoming the intrinsic characteristics of plant biomass, including recalcitrance, heterogeneity, multi-composition, and diversity. The main advantages of the selective use of steam explosion and other combinatorial pretreatments across the diversity of raw materials are introduced. Combinatorial pretreatment integrated with other unit operations is proposed as a means to exploit the high-efficiency production of bio-based products from plant biomass. Finally, several pilot- and demonstration-scale operations of the plant biomass refinery are described. Based on the principle of selective function and structure fractionation, and multi-level and directional composition conversion, an integrated process with the combinatorial pretreatments of steam explosion and other pretreatments as the core should be feasible and conform to the plant biomass refinery concept. Combinatorial pretreatments of steam explosion and other pretreatments should be further exploited based on the type and intrinsic characteristics of the plant biomass used, the bio-based products to be made, and the complementarity of the processes. Copyright © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Combinatorial effects on clumped isotopes and their significance in biogeochemistry

NASA Astrophysics Data System (ADS)

Yeung, Laurence Y.

2016-01-01

The arrangement of isotopes within a collection of molecules records their physical and chemical histories. Clumped-isotope analysis interrogates these arrangements, i.e., how often rare isotopes are bound together, which in many cases can be explained by equilibrium and/or kinetic isotope fractionation. However, purely combinatorial effects, rooted in the statistics of pairing atoms in a closed system, are also relevant, and not well understood. Here, I show that combinatorial isotope effects are most important when two identical atoms are neighbors on the same molecule (e.g., O2, N2, and D-D clumping in CH4). When the two halves of an atom pair are either assembled with different isotopic preferences or drawn from different reservoirs, combinatorial effects cause depletions in clumped-isotope abundance that are most likely between zero and -1‰, although they could potentially be -10‰ or larger for D-D pairs. These depletions are of similar magnitude, but of opposite sign, to low-temperature equilibrium clumped-isotope effects for many small molecules. Enzymatic isotope-pairing reactions, which can have site-specific isotopic fractionation factors and atom reservoirs, should express this class of combinatorial isotope effect, although it is not limited to biological reactions. Chemical-kinetic isotope effects, which are related to a bond-forming transition state, arise independently and express second-order combinatorial effects related to the abundance of the rare isotope. Heteronuclear moeties (e.g., Csbnd O and Csbnd H), are insensitive to direct combinatorial influences, but secondary combinatorial influences are evident. In general, both combinatorial and chemical-kinetic factors are important for calculating and interpreting clumped-isotope signatures of kinetically controlled reactions. I apply this analytical framework to isotope-pairing reactions relevant to geochemical oxygen, carbon, and nitrogen cycling that may be influenced by combinatorial

Multiobjective optimization of combinatorial libraries.

PubMed

Agrafiotis, D K

2002-01-01

Combinatorial chemistry and high-throughput screening have caused a fundamental shift in the way chemists contemplate experiments. Designing a combinatorial library is a controversial art that involves a heterogeneous mix of chemistry, mathematics, economics, experience, and intuition. Although there seems to be little agreement as to what constitutes an ideal library, one thing is certain: only one property or measure seldom defines the quality of the design. In most real-world applications, a good experiment requires the simultaneous optimization of several, often conflicting, design objectives, some of which may be vague and uncertain. In this paper, we discuss a class of algorithms for subset selection rooted in the principles of multiobjective optimization. Our approach is to employ an objective function that encodes all of the desired selection criteria, and then use a simulated annealing or evolutionary approach to identify the optimal (or a nearly optimal) subset from among the vast number of possibilities. Many design criteria can be accommodated, including diversity, similarity to known actives, predicted activity and/or selectivity determined by quantitative structure-activity relationship (QSAR) models or receptor binding models, enforcement of certain property distributions, reagent cost and availability, and many others. The method is robust, convergent, and extensible, offers the user full control over the relative significance of the various objectives in the final design, and permits the simultaneous selection of compounds from multiple libraries in full- or sparse-array format.

An Integrated Microfluidic Processor for DNA-Encoded Combinatorial Library Functional Screening

PubMed Central

2017-01-01

DNA-encoded synthesis is rekindling interest in combinatorial compound libraries for drug discovery and in technology for automated and quantitative library screening. Here, we disclose a microfluidic circuit that enables functional screens of DNA-encoded compound beads. The device carries out library bead distribution into picoliter-scale assay reagent droplets, photochemical cleavage of compound from the bead, assay incubation, laser-induced fluorescence-based assay detection, and fluorescence-activated droplet sorting to isolate hits. DNA-encoded compound beads (10-μm diameter) displaying a photocleavable positive control inhibitor pepstatin A were mixed (1920 beads, 729 encoding sequences) with negative control beads (58 000 beads, 1728 encoding sequences) and screened for cathepsin D inhibition using a biochemical enzyme activity assay. The circuit sorted 1518 hit droplets for collection following 18 min incubation over a 240 min analysis. Visual inspection of a subset of droplets (1188 droplets) yielded a 24% false discovery rate (1166 pepstatin A beads; 366 negative control beads). Using template barcoding strategies, it was possible to count hit collection beads (1863) using next-generation sequencing data. Bead-specific barcodes enabled replicate counting, and the false discovery rate was reduced to 2.6% by only considering hit-encoding sequences that were observed on >2 beads. This work represents a complete distributable small molecule discovery platform, from microfluidic miniaturized automation to ultrahigh-throughput hit deconvolution by sequencing. PMID:28199790

An Integrated Microfluidic Processor for DNA-Encoded Combinatorial Library Functional Screening.

PubMed

MacConnell, Andrew B; Price, Alexander K; Paegel, Brian M

2017-03-13

DNA-encoded synthesis is rekindling interest in combinatorial compound libraries for drug discovery and in technology for automated and quantitative library screening. Here, we disclose a microfluidic circuit that enables functional screens of DNA-encoded compound beads. The device carries out library bead distribution into picoliter-scale assay reagent droplets, photochemical cleavage of compound from the bead, assay incubation, laser-induced fluorescence-based assay detection, and fluorescence-activated droplet sorting to isolate hits. DNA-encoded compound beads (10-μm diameter) displaying a photocleavable positive control inhibitor pepstatin A were mixed (1920 beads, 729 encoding sequences) with negative control beads (58 000 beads, 1728 encoding sequences) and screened for cathepsin D inhibition using a biochemical enzyme activity assay. The circuit sorted 1518 hit droplets for collection following 18 min incubation over a 240 min analysis. Visual inspection of a subset of droplets (1188 droplets) yielded a 24% false discovery rate (1166 pepstatin A beads; 366 negative control beads). Using template barcoding strategies, it was possible to count hit collection beads (1863) using next-generation sequencing data. Bead-specific barcodes enabled replicate counting, and the false discovery rate was reduced to 2.6% by only considering hit-encoding sequences that were observed on >2 beads. This work represents a complete distributable small molecule discovery platform, from microfluidic miniaturized automation to ultrahigh-throughput hit deconvolution by sequencing.

Preparation of cherry-picked combinatorial libraries by string synthesis.

PubMed

Furka, Arpád; Dibó, Gábor; Gombosuren, Naran

2005-03-01

String synthesis [1-3] is an efficient and cheap manual method for preparation of combinatorial libraries by using macroscopic solid support units. Sorting the units between two synthetic steps is an important operation of the procedure. The software developed to guide sorting can be used only when complete combinatorial libraries are prepared. Since very often only selected components of the full libraries are needed, new software was constructed that guides sorting in preparation of non-complete combinatorial libraries. Application of the software is described in details.

Synthesis of Chemiluminescent Esters: A Combinatorial Synthesis Experiment for Organic Chemistry Students

ERIC Educational Resources Information Center

Duarte, Robert; Nielson, Janne T.; Dragojlovic, Veljko

2004-01-01

A group of techniques aimed at synthesizing a large number of structurally diverse compounds is called combinatorial synthesis. Synthesis of chemiluminescence esters using parallel combinatorial synthesis and mix-and-split combinatorial synthesis is experimented.

Quantum mechanical energy-based screening of combinatorially generated library of tautomers. TauTGen: a tautomer generator program.

PubMed

Harańczyk, Maciej; Gutowski, Maciej

2007-01-01

We describe a procedure of finding low-energy tautomers of a molecule. The procedure consists of (i) combinatorial generation of a library of tautomers, (ii) screening based on the results of geometry optimization of initial structures performed at the density functional level of theory, and (iii) final refinement of geometry for the top hits at the second-order Möller-Plesset level of theory followed by single-point energy calculations at the coupled cluster level of theory with single, double, and perturbative triple excitations. The library of initial structures of various tautomers is generated with TauTGen, a tautomer generator program. The procedure proved to be successful for these molecular systems for which common chemical knowledge had not been sufficient to predict the most stable structures.

Invention as a combinatorial process: evidence from US patents

PubMed Central

Youn, Hyejin; Strumsky, Deborah; Bettencourt, Luis M. A.; Lobo, José

2015-01-01

Invention has been commonly conceptualized as a search over a space of combinatorial possibilities. Despite the existence of a rich literature, spanning a variety of disciplines, elaborating on the recombinant nature of invention, we lack a formal and quantitative characterization of the combinatorial process underpinning inventive activity. Here, we use US patent records dating from 1790 to 2010 to formally characterize invention as a combinatorial process. To do this, we treat patented inventions as carriers of technologies and avail ourselves of the elaborate system of technology codes used by the United States Patent and Trademark Office to classify the technologies responsible for an invention's novelty. We find that the combinatorial inventive process exhibits an invariant rate of ‘exploitation’ (refinements of existing combinations of technologies) and ‘exploration’ (the development of new technological combinations). This combinatorial dynamic contrasts sharply with the creation of new technological capabilities—the building blocks to be combined—that has significantly slowed down. We also find that, notwithstanding the very reduced rate at which new technologies are introduced, the generation of novel technological combinations engenders a practically infinite space of technological configurations. PMID:25904530

Structure-based design of combinatorial mutagenesis libraries.

PubMed

Verma, Deeptak; Grigoryan, Gevorg; Bailey-Kellogg, Chris

2015-05-01

The development of protein variants with improved properties (thermostability, binding affinity, catalytic activity, etc.) has greatly benefited from the application of high-throughput screens evaluating large, diverse combinatorial libraries. At the same time, since only a very limited portion of sequence space can be experimentally constructed and tested, an attractive possibility is to use computational protein design to focus libraries on a productive portion of the space. We present a general-purpose method, called "Structure-based Optimization of Combinatorial Mutagenesis" (SOCoM), which can optimize arbitrarily large combinatorial mutagenesis libraries directly based on structural energies of their constituents. SOCoM chooses both positions and substitutions, employing a combinatorial optimization framework based on library-averaged energy potentials in order to avoid explicitly modeling every variant in every possible library. In case study applications to green fluorescent protein, β-lactamase, and lipase A, SOCoM optimizes relatively small, focused libraries whose variants achieve energies comparable to or better than previous library design efforts, as well as larger libraries (previously not designable by structure-based methods) whose variants cover greater diversity while still maintaining substantially better energies than would be achieved by representative random library approaches. By allowing the creation of large-scale combinatorial libraries based on structural calculations, SOCoM promises to increase the scope of applicability of computational protein design and improve the hit rate of discovering beneficial variants. While designs presented here focus on variant stability (predicted by total energy), SOCoM can readily incorporate other structure-based assessments, such as the energy gap between alternative conformational or bound states. © 2015 The Protein Society.

Molecular density functional theory of water including density-polarization coupling.

PubMed

Jeanmairet, Guillaume; Levy, Nicolas; Levesque, Maximilien; Borgis, Daniel

2016-06-22

We present a three-dimensional molecular density functional theory of water derived from first-principles that relies on the particle's density and multipolar polarization density and includes the density-polarization coupling. This brings two main benefits: (i) scalar density and vectorial multipolar polarization density fields are much more tractable and give more physical insight than the full position and orientation densities, and (ii) it includes the full density-polarization coupling of water, that is known to be non-vanishing but has never been taken into account. Furthermore, the theory requires only the partial charge distribution of a water molecule and three measurable bulk properties, namely the structure factor and the Fourier components of the longitudinal and transverse dielectric susceptibilities.

Sequence-independent construction of ordered combinatorial libraries with predefined crossover points.

PubMed

Jézéquel, Laetitia; Loeper, Jacqueline; Pompon, Denis

2008-11-01

Combinatorial libraries coding for mosaic enzymes with predefined crossover points constitute useful tools to address and model structure-function relationships and for functional optimization of enzymes based on multivariate statistics. The presented method, called sequence-independent generation of a chimera-ordered library (SIGNAL), allows easy shuffling of any predefined amino acid segment between two or more proteins. This method is particularly well adapted to the exchange of protein structural modules. The procedure could also be well suited to generate ordered combinatorial libraries independent of sequence similarities in a robotized manner. Sequence segments to be recombined are first extracted by PCR from a single-stranded template coding for an enzyme of interest using a biotin-avidin-based method. This technique allows the reduction of parental template contamination in the final library. Specific PCR primers allow amplification of two complementary mosaic DNA fragments, overlapping in the region to be exchanged. Fragments are finally reassembled using a fusion PCR. The process is illustrated via the construction of a set of mosaic CYP2B enzymes using this highly modular approach.

Smooth Constrained Heuristic Optimization of a Combinatorial Chemical Space

DTIC Science & Technology

2015-05-01

ARL-TR-7294•MAY 2015 US Army Research Laboratory Smooth ConstrainedHeuristic Optimization of a Combinatorial Chemical Space by Berend Christopher...7294•MAY 2015 US Army Research Laboratory Smooth ConstrainedHeuristic Optimization of a Combinatorial Chemical Space by Berend Christopher...

Locality of correlation in density functional theory

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

Burke, Kieron; Cancio, Antonio; Gould, Tim

The Hohenberg-Kohn density functional was long ago shown to reduce to the Thomas-Fermi (TF) approximation in the non-relativistic semiclassical (or large-Z) limit for all matter, i.e., the kinetic energy becomes local. Exchange also becomes local in this limit. Numerical data on the correlation energy of atoms support the conjecture that this is also true for correlation, but much less relevant to atoms. We illustrate how expansions around a large particle number are equivalent to local density approximations and their strong relevance to density functional approximations. Analyzing highly accurate atomic correlation energies, we show that E{sub C} → −A{sub C} ZlnZ +more » B{sub C}Z as Z → ∞, where Z is the atomic number, A{sub C} is known, and we estimate B{sub C} to be about 37 mhartree. The local density approximation yields A{sub C} exactly, but a very incorrect value for B{sub C}, showing that the local approximation is less relevant for the correlation alone. This limit is a benchmark for the non-empirical construction of density functional approximations. We conjecture that, beyond atoms, the leading correction to the local density approximation in the large-Z limit generally takes this form, but with B{sub C} a functional of the TF density for the system. The implications for the construction of approximate density functionals are discussed.« less

A combinatorial filtering method for magnetotelluric time-series based on Hilbert-Huang transform

NASA Astrophysics Data System (ADS)

Cai, Jianhua

2014-11-01

Magnetotelluric (MT) time-series are often contaminated with noise from natural or man-made processes. A substantial improvement is possible when the time-series are presented as clean as possible for further processing. A combinatorial method is described for filtering of MT time-series based on the Hilbert-Huang transform that requires a minimum of human intervention and leaves good data sections unchanged. Good data sections are preserved because after empirical mode decomposition the data are analysed through hierarchies, morphological filtering, adaptive threshold and multi-point smoothing, allowing separation of noise from signals. The combinatorial method can be carried out without any assumption about the data distribution. Simulated data and the real measured MT time-series from three different regions, with noise caused by baseline drift, high frequency noise and power-line contribution, are processed to demonstrate the application of the proposed method. Results highlight the ability of the combinatorial method to pick out useful signals, and the noise is suppressed greatly so that their deleterious influence is eliminated for the MT transfer function estimation.

Density-functional expansion methods: Grand challenges.

PubMed

Giese, Timothy J; York, Darrin M

2012-03-01

We discuss the source of errors in semiempirical density functional expansion (VE) methods. In particular, we show that VE methods are capable of well-reproducing their standard Kohn-Sham density functional method counterparts, but suffer from large errors upon using one or more of these approximations: the limited size of the atomic orbital basis, the Slater monopole auxiliary basis description of the response density, and the one- and two-body treatment of the core-Hamiltonian matrix elements. In the process of discussing these approximations and highlighting their symptoms, we introduce a new model that supplements the second-order density-functional tight-binding model with a self-consistent charge-dependent chemical potential equalization correction; we review our recently reported method for generalizing the auxiliary basis description of the atomic orbital response density; and we decompose the first-order potential into a summation of additive atomic components and many-body corrections, and from this examination, we provide new insights and preliminary results that motivate and inspire new approximate treatments of the core-Hamiltonian.

Periodic subsystem density-functional theory

NASA Astrophysics Data System (ADS)

Genova, Alessandro; Ceresoli, Davide; Pavanello, Michele

2014-11-01

By partitioning the electron density into subsystem contributions, the Frozen Density Embedding (FDE) formulation of subsystem Density Functional Theory (DFT) has recently emerged as a powerful tool for reducing the computational scaling of Kohn-Sham DFT. To date, however, FDE has been employed to molecular systems only. Periodic systems, such as metals, semiconductors, and other crystalline solids have been outside the applicability of FDE, mostly because of the lack of a periodic FDE implementation. To fill this gap, in this work we aim at extending FDE to treat subsystems of molecular and periodic character. This goal is achieved by a dual approach. On one side, the development of a theoretical framework for periodic subsystem DFT. On the other, the realization of the method into a parallel computer code. We find that periodic FDE is capable of reproducing total electron densities and (to a lesser extent) also interaction energies of molecular systems weakly interacting with metallic surfaces. In the pilot calculations considered, we find that FDE fails in those cases where there is appreciable density overlap between the subsystems. Conversely, we find FDE to be in semiquantitative agreement with Kohn-Sham DFT when the inter-subsystem density overlap is low. We also conclude that to make FDE a suitable method for describing molecular adsorption at surfaces, kinetic energy density functionals that go beyond the GGA level must be employed.

Periodic subsystem density-functional theory.

PubMed

Genova, Alessandro; Ceresoli, Davide; Pavanello, Michele

2014-11-07

By partitioning the electron density into subsystem contributions, the Frozen Density Embedding (FDE) formulation of subsystem Density Functional Theory (DFT) has recently emerged as a powerful tool for reducing the computational scaling of Kohn-Sham DFT. To date, however, FDE has been employed to molecular systems only. Periodic systems, such as metals, semiconductors, and other crystalline solids have been outside the applicability of FDE, mostly because of the lack of a periodic FDE implementation. To fill this gap, in this work we aim at extending FDE to treat subsystems of molecular and periodic character. This goal is achieved by a dual approach. On one side, the development of a theoretical framework for periodic subsystem DFT. On the other, the realization of the method into a parallel computer code. We find that periodic FDE is capable of reproducing total electron densities and (to a lesser extent) also interaction energies of molecular systems weakly interacting with metallic surfaces. In the pilot calculations considered, we find that FDE fails in those cases where there is appreciable density overlap between the subsystems. Conversely, we find FDE to be in semiquantitative agreement with Kohn-Sham DFT when the inter-subsystem density overlap is low. We also conclude that to make FDE a suitable method for describing molecular adsorption at surfaces, kinetic energy density functionals that go beyond the GGA level must be employed.

The role of seniority-zero states in nuclear level densities

DOE PAGES

Åberg, S.; Carlsson, B. G.; Døssing, Th.; ...

2015-06-01

At low excitation energies seniority-zero states dominate the level density of K=0 bands in deformed even–even nuclei, while they play no role at higher excitation energies. We describe the level densities in a Fermi-gas model as well as in a combinatorial level-density model and compare to detailed experimental data for some rare-earth nuclei.

Raman Optical Activity Spectra from Density Functional Perturbation Theory and Density-Functional-Theory-Based Molecular Dynamics.

PubMed

Luber, Sandra

2017-03-14

We describe the calculation of Raman optical activity (ROA) tensors from density functional perturbation theory, which has been implemented into the CP2K software package. Using the mixed Gaussian and plane waves method, ROA spectra are evaluated in the double-harmonic approximation. Moreover, an approach for the calculation of ROA spectra by means of density functional theory-based molecular dynamics is derived and used to obtain an ROA spectrum via time correlation functions, which paves the way for the calculation of ROA spectra taking into account anharmonicities and dynamic effects at ambient conditions.

Fast Combinatorial Algorithm for the Solution of Linearly Constrained Least Squares Problems

DOEpatents

Van Benthem, Mark H.; Keenan, Michael R.

2008-11-11

A fast combinatorial algorithm can significantly reduce the computational burden when solving general equality and inequality constrained least squares problems with large numbers of observation vectors. The combinatorial algorithm provides a mathematically rigorous solution and operates at great speed by reorganizing the calculations to take advantage of the combinatorial nature of the problems to be solved. The combinatorial algorithm exploits the structure that exists in large-scale problems in order to minimize the number of arithmetic operations required to obtain a solution.

Gedanken densities and exact constraints in density functional theory.

PubMed

Perdew, John P; Ruzsinszky, Adrienn; Sun, Jianwei; Burke, Kieron

2014-05-14

Approximations to the exact density functional for the exchange-correlation energy of a many-electron ground state can be constructed by satisfying constraints that are universal, i.e., valid for all electron densities. Gedanken densities are designed for the purpose of this construction, but need not be realistic. The uniform electron gas is an old gedanken density. Here, we propose a spherical two-electron gedanken density in which the dimensionless density gradient can be an arbitrary positive constant wherever the density is non-zero. The Lieb-Oxford lower bound on the exchange energy can be satisfied within a generalized gradient approximation (GGA) by bounding its enhancement factor or simplest GGA exchange-energy density. This enhancement-factor bound is well known to be sufficient, but our gedanken density shows that it is also necessary. The conventional exact exchange-energy density satisfies no such local bound, but energy densities are not unique, and the simplest GGA exchange-energy density is not an approximation to it. We further derive a strongly and optimally tightened bound on the exchange enhancement factor of a two-electron density, which is satisfied by the local density approximation but is violated by all published GGA's or meta-GGA's. Finally, some consequences of the non-uniform density-scaling behavior for the asymptotics of the exchange enhancement factor of a GGA or meta-GGA are given.

A real-space stochastic density matrix approach for density functional electronic structure.

PubMed

Beck, Thomas L

2015-12-21

The recent development of real-space grid methods has led to more efficient, accurate, and adaptable approaches for large-scale electrostatics and density functional electronic structure modeling. With the incorporation of multiscale techniques, linear-scaling real-space solvers are possible for density functional problems if localized orbitals are used to represent the Kohn-Sham energy functional. These methods still suffer from high computational and storage overheads, however, due to extensive matrix operations related to the underlying wave function grid representation. In this paper, an alternative stochastic method is outlined that aims to solve directly for the one-electron density matrix in real space. In order to illustrate aspects of the method, model calculations are performed for simple one-dimensional problems that display some features of the more general problem, such as spatial nodes in the density matrix. This orbital-free approach may prove helpful considering a future involving increasingly parallel computing architectures. Its primary advantage is the near-locality of the random walks, allowing for simultaneous updates of the density matrix in different regions of space partitioned across the processors. In addition, it allows for testing and enforcement of the particle number and idempotency constraints through stabilization of a Feynman-Kac functional integral as opposed to the extensive matrix operations in traditional approaches.

Beyond Kohn-Sham Approximation: Hybrid Multistate Wave Function and Density Functional Theory.

PubMed

Gao, Jiali; Grofe, Adam; Ren, Haisheng; Bao, Peng

2016-12-15

A multistate density functional theory (MSDFT) is presented in which the energies and densities for the ground and excited states are treated on the same footing using multiconfigurational approaches. The method can be applied to systems with strong correlation and to correctly describe the dimensionality of the conical intersections between strongly coupled dissociative potential energy surfaces. A dynamic-then-static framework for treating electron correlation is developed to first incorporate dynamic correlation into contracted state functions through block-localized Kohn-Sham density functional theory (KSDFT), followed by diagonalization of the effective Hamiltonian to include static correlation. MSDFT can be regarded as a hybrid of wave function and density functional theory. The method is built on and makes use of the current approximate density functional developed in KSDFT, yet it retains its computational efficiency to treat strongly correlated systems that are problematic for KSDFT but too large for accurate WFT. The results presented in this work show that MSDFT can be applied to photochemical processes involving conical intersections.

Combinatorial control of messenger RNAs by Pumilio, Nanos and Brain Tumor Proteins

PubMed Central

Arvola, René M.

2017-01-01

ABSTRACT Eukaryotes possess a vast array of RNA-binding proteins (RBPs) that affect mRNAs in diverse ways to control protein expression. Combinatorial regulation of mRNAs by RBPs is emerging as the rule. No example illustrates this as vividly as the partnership of 3 Drosophila RBPs, Pumilio, Nanos and Brain Tumor, which have overlapping functions in development, stem cell maintenance and differentiation, fertility and neurologic processes. Here we synthesize 30 y of research with new insights into their molecular functions and mechanisms of action. First, we provide an overview of the key properties of each RBP. Next, we present a detailed analysis of their collaborative regulatory mechanism using a classic example of the developmental morphogen, hunchback, which is spatially and temporally regulated by the trio during embryogenesis. New biochemical, structural and functional analyses provide insights into RNA recognition, cooperativity, and regulatory mechanisms. We integrate these data into a model of combinatorial RNA binding and regulation of translation and mRNA decay. We then use this information, transcriptome wide analyses and bioinformatics predictions to assess the global impact of Pumilio, Nanos and Brain Tumor on gene regulation. Together, the results support pervasive, dynamic post-transcriptional control. PMID:28318367

Combinatorial control of messenger RNAs by Pumilio, Nanos and Brain Tumor Proteins.

PubMed

Arvola, René M; Weidmann, Chase A; Tanaka Hall, Traci M; Goldstrohm, Aaron C

2017-11-02

Eukaryotes possess a vast array of RNA-binding proteins (RBPs) that affect mRNAs in diverse ways to control protein expression. Combinatorial regulation of mRNAs by RBPs is emerging as the rule. No example illustrates this as vividly as the partnership of 3 Drosophila RBPs, Pumilio, Nanos and Brain Tumor, which have overlapping functions in development, stem cell maintenance and differentiation, fertility and neurologic processes. Here we synthesize 30 y of research with new insights into their molecular functions and mechanisms of action. First, we provide an overview of the key properties of each RBP. Next, we present a detailed analysis of their collaborative regulatory mechanism using a classic example of the developmental morphogen, hunchback, which is spatially and temporally regulated by the trio during embryogenesis. New biochemical, structural and functional analyses provide insights into RNA recognition, cooperativity, and regulatory mechanisms. We integrate these data into a model of combinatorial RNA binding and regulation of translation and mRNA decay. We then use this information, transcriptome wide analyses and bioinformatics predictions to assess the global impact of Pumilio, Nanos and Brain Tumor on gene regulation. Together, the results support pervasive, dynamic post-transcriptional control.

Periodic subsystem density-functional theory

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

Genova, Alessandro; Pavanello, Michele, E-mail: m.pavanello@rutgers.edu; Ceresoli, Davide

2014-11-07

By partitioning the electron density into subsystem contributions, the Frozen Density Embedding (FDE) formulation of subsystem Density Functional Theory (DFT) has recently emerged as a powerful tool for reducing the computational scaling of Kohn–Sham DFT. To date, however, FDE has been employed to molecular systems only. Periodic systems, such as metals, semiconductors, and other crystalline solids have been outside the applicability of FDE, mostly because of the lack of a periodic FDE implementation. To fill this gap, in this work we aim at extending FDE to treat subsystems of molecular and periodic character. This goal is achieved by a dualmore » approach. On one side, the development of a theoretical framework for periodic subsystem DFT. On the other, the realization of the method into a parallel computer code. We find that periodic FDE is capable of reproducing total electron densities and (to a lesser extent) also interaction energies of molecular systems weakly interacting with metallic surfaces. In the pilot calculations considered, we find that FDE fails in those cases where there is appreciable density overlap between the subsystems. Conversely, we find FDE to be in semiquantitative agreement with Kohn–Sham DFT when the inter-subsystem density overlap is low. We also conclude that to make FDE a suitable method for describing molecular adsorption at surfaces, kinetic energy density functionals that go beyond the GGA level must be employed.« less

Self-Interaction Error in Density Functional Theory: An Appraisal.

PubMed

Bao, Junwei Lucas; Gagliardi, Laura; Truhlar, Donald G

2018-05-03

Self-interaction error (SIE) is considered to be one of the major sources of error in most approximate exchange-correlation functionals for Kohn-Sham density-functional theory (KS-DFT), and it is large with all local exchange-correlation functionals and with some hybrid functionals. In this work, we consider systems conventionally considered to be dominated by SIE. For these systems, we demonstrate that by using multiconfiguration pair-density functional theory (MC-PDFT), the error of a translated local density-functional approximation is significantly reduced (by a factor of 3) when using an MCSCF density and on-top density, as compared to using KS-DFT with the parent functional; the error in MC-PDFT with local on-top functionals is even lower than the error in some popular KS-DFT hybrid functionals. Density-functional theory, either in MC-PDFT form with local on-top functionals or in KS-DFT form with some functionals having 50% or more nonlocal exchange, has smaller errors for SIE-prone systems than does CASSCF, which has no SIE.

Rational Density Functional Selection Using Game Theory.

PubMed

McAnanama-Brereton, Suzanne; Waller, Mark P

2018-01-22

Theoretical chemistry has a paradox of choice due to the availability of a myriad of density functionals and basis sets. Traditionally, a particular density functional is chosen on the basis of the level of user expertise (i.e., subjective experiences). Herein we circumvent the user-centric selection procedure by describing a novel approach for objectively selecting a particular functional for a given application. We achieve this by employing game theory to identify optimal functional/basis set combinations. A three-player (accuracy, complexity, and similarity) game is devised, through which Nash equilibrium solutions can be obtained. This approach has the advantage that results can be systematically improved by enlarging the underlying knowledge base, and the deterministic selection procedure mathematically justifies the density functional and basis set selections.

Density Functional Calculations for the Neutron Star Matter at Subnormal Density

NASA Astrophysics Data System (ADS)

Kashiwaba, Yu; Nakatsukasa, Takashi

The pasta phases of nuclear matter, whose existence is suggested at low density, may influence observable properties of neutron stars. In order to investigate properties of the neutron star matter, we calculate self-consistent solutions for the ground states of slab-like phase using the microscopic density functional theory with Bloch wave functions. The calculations are performed at each point of fixed average density and proton fraction (\\bar{ρ },Yp), varying the lattice constant of the unit cell. For small Yp values, the dripped neutrons emerge in the ground state, while the protons constitute the slab (crystallized) structure. The shell effect of protons affects the thickness of the slab nuclei.

Subsystem density functional theory with meta-generalized gradient approximation exchange-correlation functionals.

PubMed

Śmiga, Szymon; Fabiano, Eduardo; Laricchia, Savio; Constantin, Lucian A; Della Sala, Fabio

2015-04-21

We analyze the methodology and the performance of subsystem density functional theory (DFT) with meta-generalized gradient approximation (meta-GGA) exchange-correlation functionals for non-bonded molecular systems. Meta-GGA functionals depend on the Kohn-Sham kinetic energy density (KED), which is not known as an explicit functional of the density. Therefore, they cannot be directly applied in subsystem DFT calculations. We propose a Laplacian-level approximation to the KED which overcomes this limitation and provides a simple and accurate way to apply meta-GGA exchange-correlation functionals in subsystem DFT calculations. The so obtained density and energy errors, with respect to the corresponding supermolecular calculations, are comparable with conventional approaches, depending almost exclusively on the approximations in the non-additive kinetic embedding term. An embedding energy error decomposition explains the accuracy of our method.

Combinatorial Mathematics: Research into Practice

ERIC Educational Resources Information Center

Sriraman, Bharath; English, Lyn D.

2004-01-01

Implications and suggestions for using combinatorial mathematics in the classroom through a survey and synthesis of numerous research studies are presented. The implications revolve around five major themes that emerge from analysis of these studies.

Excitation energies from range-separated time-dependent density and density matrix functional theory.

PubMed

Pernal, Katarzyna

2012-05-14

Time-dependent density functional theory (TD-DFT) in the adiabatic formulation exhibits known failures when applied to predicting excitation energies. One of them is the lack of the doubly excited configurations. On the other hand, the time-dependent theory based on a one-electron reduced density matrix functional (time-dependent density matrix functional theory, TD-DMFT) has proven accurate in determining single and double excitations of H(2) molecule if the exact functional is employed in the adiabatic approximation. We propose a new approach for computing excited state energies that relies on functionals of electron density and one-electron reduced density matrix, where the latter is applied in the long-range region of electron-electron interactions. A similar approach has been recently successfully employed in predicting ground state potential energy curves of diatomic molecules even in the dissociation limit, where static correlation effects are dominating. In the paper, a time-dependent functional theory based on the range-separation of electronic interaction operator is rigorously formulated. To turn the approach into a practical scheme the adiabatic approximation is proposed for the short- and long-range components of the coupling matrix present in the linear response equations. In the end, the problem of finding excitation energies is turned into an eigenproblem for a symmetric matrix. Assignment of obtained excitations is discussed and it is shown how to identify double excitations from the analysis of approximate transition density matrix elements. The proposed method used with the short-range local density approximation (srLDA) and the long-range Buijse-Baerends density matrix functional (lrBB) is applied to H(2) molecule (at equilibrium geometry and in the dissociation limit) and to Be atom. The method accounts for double excitations in the investigated systems but, unfortunately, the accuracy of some of them is poor. The quality of the other

Combinatorial techniques to efficiently investigate and optimize organic thin film processing and properties.

PubMed

Wieberger, Florian; Kolb, Tristan; Neuber, Christian; Ober, Christopher K; Schmidt, Hans-Werner

2013-04-08

In this article we present several developed and improved combinatorial techniques to optimize processing conditions and material properties of organic thin films. The combinatorial approach allows investigations of multi-variable dependencies and is the perfect tool to investigate organic thin films regarding their high performance purposes. In this context we develop and establish the reliable preparation of gradients of material composition, temperature, exposure, and immersion time. Furthermore we demonstrate the smart application of combinations of composition and processing gradients to create combinatorial libraries. First a binary combinatorial library is created by applying two gradients perpendicular to each other. A third gradient is carried out in very small areas and arranged matrix-like over the entire binary combinatorial library resulting in a ternary combinatorial library. Ternary combinatorial libraries allow identifying precise trends for the optimization of multi-variable dependent processes which is demonstrated on the lithographic patterning process. Here we verify conclusively the strong interaction and thus the interdependency of variables in the preparation and properties of complex organic thin film systems. The established gradient preparation techniques are not limited to lithographic patterning. It is possible to utilize and transfer the reported combinatorial techniques to other multi-variable dependent processes and to investigate and optimize thin film layers and devices for optical, electro-optical, and electronic applications.

Uniform magnetic fields in density-functional theory

NASA Astrophysics Data System (ADS)

Tellgren, Erik I.; Laestadius, Andre; Helgaker, Trygve; Kvaal, Simen; Teale, Andrew M.

2018-01-01

We construct a density-functional formalism adapted to uniform external magnetic fields that is intermediate between conventional density functional theory and Current-Density Functional Theory (CDFT). In the intermediate theory, which we term linear vector potential-DFT (LDFT), the basic variables are the density, the canonical momentum, and the paramagnetic contribution to the magnetic moment. Both a constrained-search formulation and a convex formulation in terms of Legendre-Fenchel transformations are constructed. Many theoretical issues in CDFT find simplified analogs in LDFT. We prove results concerning N-representability, Hohenberg-Kohn-like mappings, existence of minimizers in the constrained-search expression, and a restricted analog to gauge invariance. The issue of additivity of the energy over non-interacting subsystems, which is qualitatively different in LDFT and CDFT, is also discussed.

Uniform magnetic fields in density-functional theory.

PubMed

Tellgren, Erik I; Laestadius, Andre; Helgaker, Trygve; Kvaal, Simen; Teale, Andrew M

2018-01-14

We construct a density-functional formalism adapted to uniform external magnetic fields that is intermediate between conventional density functional theory and Current-Density Functional Theory (CDFT). In the intermediate theory, which we term linear vector potential-DFT (LDFT), the basic variables are the density, the canonical momentum, and the paramagnetic contribution to the magnetic moment. Both a constrained-search formulation and a convex formulation in terms of Legendre-Fenchel transformations are constructed. Many theoretical issues in CDFT find simplified analogs in LDFT. We prove results concerning N-representability, Hohenberg-Kohn-like mappings, existence of minimizers in the constrained-search expression, and a restricted analog to gauge invariance. The issue of additivity of the energy over non-interacting subsystems, which is qualitatively different in LDFT and CDFT, is also discussed.

Long-range corrected density functional through the density matrix expansion based semilocal exchange hole.

PubMed

Patra, Bikash; Jana, Subrata; Samal, Prasanjit

2018-03-28

The exchange hole, which is one of the principal constituents of the density functional formalism, can be used to design accurate range-separated hybrid functionals in association with appropriate correlation. In this regard, the exchange hole derived from the density matrix expansion has gained attention due to its fulfillment of some of the desired exact constraints. Thus, the new long-range corrected density functional proposed here combines the meta generalized gradient approximation level exchange functional designed from the density matrix expansion based exchange hole coupled with the ab initio Hartree-Fock exchange through the range separation of the Coulomb interaction operator using the standard error function technique. Then, in association with the Lee-Yang-Parr correlation functional, the assessment and benchmarking of the above newly constructed range-separated functional with various well-known test sets shows its reasonable performance for a broad range of molecular properties, such as thermochemistry, non-covalent interaction and barrier heights of the chemical reactions.

Combinatorial Strategies for Improving Multiple-Stress Resistance in Industrially Relevant Escherichia coli Strains

PubMed Central

Herrgård, Markus J.

2014-01-01

High-cell-density fermentation for industrial production of chemicals can impose numerous stresses on cells due to high substrate, product, and by-product concentrations; high osmolarity; reactive oxygen species; and elevated temperatures. There is a need to develop platform strains of industrial microorganisms that are more tolerant toward these typical processing conditions. In this study, the growth of six industrially relevant strains of Escherichia coli was characterized under eight stress conditions representative of fed-batch fermentation, and strains W and BL21(DE3) were selected as platforms for transposon (Tn) mutagenesis due to favorable resistance characteristics. Selection experiments, followed by either targeted or genome-wide next-generation-sequencing-based Tn insertion site determination, were performed to identify mutants with improved growth properties under a subset of three stress conditions and two combinations of individual stresses. A subset of the identified loss-of-function mutants were selected for a combinatorial approach, where strains with combinations of two and three gene deletions were systematically constructed and tested for single and multistress resistance. These approaches allowed identification of (i) strain-background-specific stress resistance phenotypes, (ii) novel gene deletion mutants in E. coli that confer single and multistress resistance in a strain-background-dependent manner, and (iii) synergistic effects of multiple gene deletions that confer improved resistance over single deletions. The results of this study underscore the suboptimality and strain-specific variability of the genetic network regulating growth under stressful conditions and suggest that further exploration of the combinatorial gene deletion space in multiple strain backgrounds is needed for optimizing strains for microbial bioprocessing applications. PMID:25085490

Equilibrium problems for Raney densities

NASA Astrophysics Data System (ADS)

Forrester, Peter J.; Liu, Dang-Zheng; Zinn-Justin, Paul

2015-07-01

The Raney numbers are a class of combinatorial numbers generalising the Fuss-Catalan numbers. They are indexed by a pair of positive real numbers (p, r) with p > 1 and 0 < r ⩽ p, and form the moments of a probability density function. For certain (p, r) the latter has the interpretation as the density of squared singular values for certain random matrix ensembles, and in this context equilibrium problems characterising the Raney densities for (p, r) = (θ + 1, 1) and (θ/2 + 1, 1/2) have recently been proposed. Using two different techniques—one based on the Wiener-Hopf method for the solution of integral equations and the other on an analysis of the algebraic equation satisfied by the Green's function—we establish the validity of the equilibrium problems for general θ > 0 and similarly use both methods to identify the equilibrium problem for (p, r) = (θ/q + 1, 1/q), θ > 0 and q \\in Z+ . The Wiener-Hopf method is used to extend the latter to parameters (p, r) = (θ/q + 1, m + 1/q) for m a non-negative integer, and also to identify the equilibrium problem for a family of densities with moments given by certain binomial coefficients.

Density functional study of double ionization energies

NASA Astrophysics Data System (ADS)

Chong, D. P.

2008-02-01

In this paper, double ionization energies (DIEs) of gas-phase atoms and molecules are calculated by energy difference method with density functional theory. To determine the best functional for double ionization energies, we first study 24 main group atoms in the second, third, and fourth periods. An approximation is used in which the electron density is first obtained from a density functional computation with the exchange-correlation potential Vxc known as statistical average of orbital potentials, after which the energy is computed from that density with 59 different exchange-correlation energy functionals Exc. For the 24 atoms, the two best Exc functional providing DIEs with average absolute deviation (AAD) of only 0.25eV are the Perdew-Burke-Ernzerhof functional modified by Hammer et al. [Phys. Rev. B 59, 6413 (1999)] and one known as the Krieger-Chen-Iafrate-Savin functional modified by Krieger et al. (unpublished). Surprisingly, none of the 20 available hybrid functionals is among the top 15 functionals for the DIEs of the 24 atoms. A similar procedure is then applied to molecules, with opposite results: Only hybrid functionals are among the top 15 functionals for a selection of 29molecules. The best Exc functional for the 29molecules is found to be the Becke 1997 functional modified by Wilson et al. [J. Chem. Phys. 115, 9233 (2001)]. With that functional, the AAD from experiment for DIEs of 29molecules is just under 0.5eV. If the two suspected values for C2H2 and Fe(CO)5 are excluded, the AAD improves to 0.32eV. Many other hybrid functionals perform almost as well.

High-flexibility combinatorial peptide synthesis with laser-based transfer of monomers in solid matrix material.

PubMed

Loeffler, Felix F; Foertsch, Tobias C; Popov, Roman; Mattes, Daniela S; Schlageter, Martin; Sedlmayr, Martyna; Ridder, Barbara; Dang, Florian-Xuan; von Bojničić-Kninski, Clemens; Weber, Laura K; Fischer, Andrea; Greifenstein, Juliane; Bykovskaya, Valentina; Buliev, Ivan; Bischoff, F Ralf; Hahn, Lothar; Meier, Michael A R; Bräse, Stefan; Powell, Annie K; Balaban, Teodor Silviu; Breitling, Frank; Nesterov-Mueller, Alexander

2016-06-14

Laser writing is used to structure surfaces in many different ways in materials and life sciences. However, combinatorial patterning applications are still limited. Here we present a method for cost-efficient combinatorial synthesis of very-high-density peptide arrays with natural and synthetic monomers. A laser automatically transfers nanometre-thin solid material spots from different donor slides to an acceptor. Each donor bears a thin polymer film, embedding one type of monomer. Coupling occurs in a separate heating step, where the matrix becomes viscous and building blocks diffuse and couple to the acceptor surface. Furthermore, we can consecutively deposit two material layers of activation reagents and amino acids. Subsequent heat-induced mixing facilitates an in situ activation and coupling of the monomers. This allows us to incorporate building blocks with click chemistry compatibility or a large variety of commercially available non-activated, for example, posttranslationally modified building blocks into the array's peptides with >17,000 spots per cm(2).

Energy density functional on a microscopic basis

NASA Astrophysics Data System (ADS)

Baldo, M.; Robledo, L.; Schuck, P.; Viñas, X.

2010-06-01

In recent years impressive progress has been made in the development of highly accurate energy density functionals, which allow us to treat medium-heavy nuclei. In this approach one tries to describe not only the ground state but also the first relevant excited states. In general, higher accuracy requires a larger set of parameters, which must be carefully chosen to avoid redundancy. Following this line of development, it is unavoidable that the connection of the functional with the bare nucleon-nucleon interaction becomes more and more elusive. In principle, the construction of a density functional from a density matrix expansion based on the effective nucleon-nucleon interaction is possible, and indeed the approach has been followed by few authors. However, to what extent a density functional based on such a microscopic approach can reach the accuracy of the fully phenomenological ones remains an open question. A related question is to establish which part of a functional can be actually derived by a microscopic approach and which part, in contrast, must be left as purely phenomenological. In this paper we discuss the main problems that are encountered when the microscopic approach is followed. To this purpose we will use the method we have recently introduced to illustrate the different aspects of these problems. In particular we will discuss the possible connection of the density functional with the nuclear matter equation of state and the distinct features of finite-size effect typical of nuclei.

Multiconfiguration Pair-Density Functional Theory Outperforms Kohn-Sham Density Functional Theory and Multireference Perturbation Theory for Ground-State and Excited-State Charge Transfer.

PubMed

Ghosh, Soumen; Sonnenberger, Andrew L; Hoyer, Chad E; Truhlar, Donald G; Gagliardi, Laura

2015-08-11

The correct description of charge transfer in ground and excited states is very important for molecular interactions, photochemistry, electrochemistry, and charge transport, but it is very challenging for Kohn-Sham (KS) density functional theory (DFT). KS-DFT exchange-correlation functionals without nonlocal exchange fail to describe both ground- and excited-state charge transfer properly. We have recently proposed a theory called multiconfiguration pair-density functional theory (MC-PDFT), which is based on a combination of multiconfiguration wave function theory with a new type of density functional called an on-top density functional. Here we have used MC-PDFT to study challenging ground- and excited-state charge-transfer processes by using on-top density functionals obtained by translating KS exchange-correlation functionals. For ground-state charge transfer, MC-PDFT performs better than either the PBE exchange-correlation functional or CASPT2 wave function theory. For excited-state charge transfer, MC-PDFT (unlike KS-DFT) shows qualitatively correct behavior at long-range with great improvement in predicted excitation energies.

Functional renormalization group and Kohn-Sham scheme in density functional theory

NASA Astrophysics Data System (ADS)

Liang, Haozhao; Niu, Yifei; Hatsuda, Tetsuo

2018-04-01

Deriving accurate energy density functional is one of the central problems in condensed matter physics, nuclear physics, and quantum chemistry. We propose a novel method to deduce the energy density functional by combining the idea of the functional renormalization group and the Kohn-Sham scheme in density functional theory. The key idea is to solve the renormalization group flow for the effective action decomposed into the mean-field part and the correlation part. Also, we propose a simple practical method to quantify the uncertainty associated with the truncation of the correlation part. By taking the φ4 theory in zero dimension as a benchmark, we demonstrate that our method shows extremely fast convergence to the exact result even for the highly strong coupling regime.

Density functional theory: Foundations reviewed

NASA Astrophysics Data System (ADS)

Kryachko, Eugene S.; Ludeña, Eduardo V.

2014-11-01

Guided by the above motto (quotation), we review a broad range of issues lying at the foundations of Density Functional Theory, DFT, a theory which is currently omnipresent in our everyday computational study of atoms and molecules, solids and nano-materials, and which lies at the heart of modern many-body computational technologies. The key goal is to demonstrate that there are definitely the ways to improve DFT. We start by considering DFT in the larger context provided by reduced density matrix theory (RDMT) and natural orbital functional theory (NOFT), and examine the implications that N-representability conditions on the second-order reduced density matrix (2-RDM) have not only on RDMT and NOFT but, also, by extension, on the functionals of DFT. This examination is timely in view of the fact that necessary and sufficient N-representability conditions on the 2-RDM have recently been attained. In the second place, we review some problems appearing in the original formulation of the first Hohenberg-Kohn theorem which is still a subject of some controversy. In this vein we recall Lieb's comment on this proof and the extension to this proof given by Pino et al. (2009), and in this context examine the conditions that must be met in order that the one-to-one correspondence between ground-state densities and external potentials remains valid for finite subspaces (namely, the subspaces where all Kohn-Sham solutions are obtained in practical applications). We also consider the issue of whether the Kohn-Sham equations can be derived from basic principles or whether they are postulated. We examine this problem in relation to ab initio DFT. The possibility of postulating arbitrary Kohn-Sham-type equations, where the effective potential is by definition some arbitrary mixture of local and non-local terms, is discussed. We also deal with the issue of whether there exists a universal functional, or whether one should advocate instead the construction of problem

Basis convergence of range-separated density-functional theory

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

Franck, Odile, E-mail: odile.franck@etu.upmc.fr; Mussard, Bastien, E-mail: bastien.mussard@upmc.fr; CNRS, UMR 7616, Laboratoire de Chimie Théorique, F-75005 Paris

2015-02-21

Range-separated density-functional theory (DFT) is an alternative approach to Kohn-Sham density-functional theory. The strategy of range-separated density-functional theory consists in separating the Coulomb electron-electron interaction into long-range and short-range components and treating the long-range part by an explicit many-body wave-function method and the short-range part by a density-functional approximation. Among the advantages of using many-body methods for the long-range part of the electron-electron interaction is that they are much less sensitive to the one-electron atomic basis compared to the case of the standard Coulomb interaction. Here, we provide a detailed study of the basis convergence of range-separated density-functional theory. Wemore » study the convergence of the partial-wave expansion of the long-range wave function near the electron-electron coalescence. We show that the rate of convergence is exponential with respect to the maximal angular momentum L for the long-range wave function, whereas it is polynomial for the case of the Coulomb interaction. We also study the convergence of the long-range second-order Møller-Plesset correlation energy of four systems (He, Ne, N{sub 2}, and H{sub 2}O) with cardinal number X of the Dunning basis sets cc − p(C)V XZ and find that the error in the correlation energy is best fitted by an exponential in X. This leads us to propose a three-point complete-basis-set extrapolation scheme for range-separated density-functional theory based on an exponential formula.« less

Basis convergence of range-separated density-functional theory.

PubMed

Franck, Odile; Mussard, Bastien; Luppi, Eleonora; Toulouse, Julien

2015-02-21

Range-separated density-functional theory (DFT) is an alternative approach to Kohn-Sham density-functional theory. The strategy of range-separated density-functional theory consists in separating the Coulomb electron-electron interaction into long-range and short-range components and treating the long-range part by an explicit many-body wave-function method and the short-range part by a density-functional approximation. Among the advantages of using many-body methods for the long-range part of the electron-electron interaction is that they are much less sensitive to the one-electron atomic basis compared to the case of the standard Coulomb interaction. Here, we provide a detailed study of the basis convergence of range-separated density-functional theory. We study the convergence of the partial-wave expansion of the long-range wave function near the electron-electron coalescence. We show that the rate of convergence is exponential with respect to the maximal angular momentum L for the long-range wave function, whereas it is polynomial for the case of the Coulomb interaction. We also study the convergence of the long-range second-order Møller-Plesset correlation energy of four systems (He, Ne, N2, and H2O) with cardinal number X of the Dunning basis sets cc - p(C)V XZ and find that the error in the correlation energy is best fitted by an exponential in X. This leads us to propose a three-point complete-basis-set extrapolation scheme for range-separated density-functional theory based on an exponential formula.

Combinatorial quantisation of the Euclidean torus universe

NASA Astrophysics Data System (ADS)

Meusburger, C.; Noui, K.

2010-12-01

We quantise the Euclidean torus universe via a combinatorial quantisation formalism based on its formulation as a Chern-Simons gauge theory and on the representation theory of the Drinfel'd double DSU(2). The resulting quantum algebra of observables is given by two commuting copies of the Heisenberg algebra, and the associated Hilbert space can be identified with the space of square integrable functions on the torus. We show that this Hilbert space carries a unitary representation of the modular group and discuss the role of modular invariance in the theory. We derive the classical limit of the theory and relate the quantum observables to the geometry of the torus universe.

The force distribution probability function for simple fluids by density functional theory.

PubMed

Rickayzen, G; Heyes, D M

2013-02-28

Classical density functional theory (DFT) is used to derive a formula for the probability density distribution function, P(F), and probability distribution function, W(F), for simple fluids, where F is the net force on a particle. The final formula for P(F) ∝ exp(-AF(2)), where A depends on the fluid density, the temperature, and the Fourier transform of the pair potential. The form of the DFT theory used is only applicable to bounded potential fluids. When combined with the hypernetted chain closure of the Ornstein-Zernike equation, the DFT theory for W(F) agrees with molecular dynamics computer simulations for the Gaussian and bounded soft sphere at high density. The Gaussian form for P(F) is still accurate at lower densities (but not too low density) for the two potentials, but with a smaller value for the constant, A, than that predicted by the DFT theory.

Combinatorial Dyson-Schwinger equations and inductive data types

NASA Astrophysics Data System (ADS)

Kock, Joachim

2016-06-01

The goal of this contribution is to explain the analogy between combinatorial Dyson-Schwinger equations and inductive data types to a readership of mathematical physicists. The connection relies on an interpretation of combinatorial Dyson-Schwinger equations as fixpoint equations for polynomial functors (established elsewhere by the author, and summarised here), combined with the now-classical fact that polynomial functors provide semantics for inductive types. The paper is expository, and comprises also a brief introduction to type theory.

Local and linear chemical reactivity response functions at finite temperature in density functional theory

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

Franco-Pérez, Marco, E-mail: francopj@mcmaster.ca, E-mail: ayers@mcmaster.ca, E-mail: jlgm@xanum.uam.mx, E-mail: avela@cinvestav.mx; Departamento de Química, Universidad Autónoma Metropolitana-Iztapalapa, Av. San Rafael Atlixco 186, México, D.F. 09340; Ayers, Paul W., E-mail: francopj@mcmaster.ca, E-mail: ayers@mcmaster.ca, E-mail: jlgm@xanum.uam.mx, E-mail: avela@cinvestav.mx

2015-12-28

We explore the local and nonlocal response functions of the grand canonical potential density functional at nonzero temperature. In analogy to the zero-temperature treatment, local (e.g., the average electron density and the local softness) and nonlocal (e.g., the softness kernel) intrinsic response functions are defined as partial derivatives of the grand canonical potential with respect to its thermodynamic variables (i.e., the chemical potential of the electron reservoir and the external potential generated by the atomic nuclei). To define the local and nonlocal response functions of the electron density (e.g., the Fukui function, the linear density response function, and the dualmore » descriptor), we differentiate with respect to the average electron number and the external potential. The well-known mathematical relationships between the intrinsic response functions and the electron-density responses are generalized to nonzero temperature, and we prove that in the zero-temperature limit, our results recover well-known identities from the density functional theory of chemical reactivity. Specific working equations and numerical results are provided for the 3-state ensemble model.« less

Local and linear chemical reactivity response functions at finite temperature in density functional theory.

PubMed

Franco-Pérez, Marco; Ayers, Paul W; Gázquez, José L; Vela, Alberto

2015-12-28

We explore the local and nonlocal response functions of the grand canonical potential density functional at nonzero temperature. In analogy to the zero-temperature treatment, local (e.g., the average electron density and the local softness) and nonlocal (e.g., the softness kernel) intrinsic response functions are defined as partial derivatives of the grand canonical potential with respect to its thermodynamic variables (i.e., the chemical potential of the electron reservoir and the external potential generated by the atomic nuclei). To define the local and nonlocal response functions of the electron density (e.g., the Fukui function, the linear density response function, and the dual descriptor), we differentiate with respect to the average electron number and the external potential. The well-known mathematical relationships between the intrinsic response functions and the electron-density responses are generalized to nonzero temperature, and we prove that in the zero-temperature limit, our results recover well-known identities from the density functional theory of chemical reactivity. Specific working equations and numerical results are provided for the 3-state ensemble model.

Combinatorial enzyme technology: Conversion of pectin to oligo species and its effect on microbial growth

USDA-ARS?s Scientific Manuscript database

Plant cell wall polysaccharides, which consist of polymeric backbones with various types of substitution, were studied using the concept of combinatorial enzyme technology for conversion of agricultural fibers to functional products. Using citrus pectin as the starting substrate, an active oligo spe...

Reformulation of Density Functional Theory for N-Representable Densities and the Resolution of the v-Representability Problem

DOE PAGES

Gonis, A.; Zhang, X. G.; Stocks, G. M.; ...

2015-10-23

Density functional theory for the case of general, N-representable densities is reformulated in terms of density functional derivatives of expectation values of operators evaluated with wave functions leading to a density, making no reference to the concept of potential. The developments provide a complete solution of the v-representability problem by establishing a mathematical procedure that determines whether a density is v-representable and in the case of an affirmative answer determines the potential (within an additive constant) as a derivative with respect to the density of a constrained search functional. It also establishes the existence of an energy functional of themore » density that, for v-representable densities, assumes its minimum value at the density describing the ground state of an interacting many-particle system. The theorems of Hohenberg and Kohn emerge as special cases of the formalism.« less

On the calculation of charge transfer transitions with standard density functionals using constrained variational density functional theory.

PubMed

Ziegler, Tom; Krykunov, Mykhaylo

2010-08-21

It is well known that time-dependent density functional theory (TD-DFT) based on standard gradient corrected functionals affords both a quantitative and qualitative incorrect picture of charge transfer transitions between two spatially separated regions. It is shown here that the well known failure can be traced back to the use of linear response theory. Further, it is demonstrated that the inclusion of higher order terms readily affords a qualitatively correct picture even for simple functionals based on the local density approximation. The inclusion of these terms is done within the framework of a newly developed variational approach to excitation energies called constrained variational density functional theory (CV-DFT). To second order [CV(2)-DFT] this theory is identical to adiabatic TD-DFT within the Tamm-Dancoff approximation. With inclusion of fourth order corrections [CV(4)-DFT] it affords a qualitative correct description of charge transfer transitions. It is finally demonstrated that the relaxation of the ground state Kohn-Sham orbitals to first order in response to the change in density on excitation together with CV(4)-DFT affords charge transfer excitations in good agreement with experiment. The new relaxed theory is termed R-CV(4)-DFT. The relaxed scheme represents an effective way in which to introduce double replacements into the description of single electron excitations, something that would otherwise require a frequency dependent kernel.

Nonlinear functional for solvation in Density Functional Theory

NASA Astrophysics Data System (ADS)

Gunceler, Deniz; Sundararaman, Ravishankar; Schwarz, Kathleen; Letchworth-Weaver, Kendra; Arias, T. A.

2013-03-01

Density functional calculations of molecules and surfaces in a liquid can accelerate the development of many technologies ranging from solar energy harvesting to lithium batteries. Such studies require the development of robust functionals describing the liquid. Polarizable continuum models (PCM's) have been applied to some solvated systems; but they do not sufficiently capture solvation effects to describe highly polar systems like surfaces of ionic solids. In this work, we present a nonlinear fluid functional within the framework of Joint Density Functional Theory. The fluid is treated not as a linear dielectric, but as a distribution of dipoles that responds to the solute, which we describe starting from the exact free energy functional for point dipoles. We also show PCM's can be recovered as the linear limit of our functional. Our description is of similar computational cost to PCM's, and captures complex solvation effects like dielectric saturation without requiring new fit parameters. For polar and nonpolar molecules, it achieves millihartree level agreement with experimental solvation energies. Furthermore, our functional now makes it possible to investigate chemistry on the surface of lithium battery materials, which PCM's predict to be unstable. Supported as part of the Energy Materials Center at Cornell, an Energy Frontier Research Center funded by the U.S. Department of Energy, Office of Science, Office of Basic Energy Sciences under Award Number DE-SC0001086

Combining Density Functional Theory and Green's Function Theory: Range-Separated, Nonlocal, Dynamic, and Orbital-Dependent Hybrid Functional.

PubMed

Kananenka, Alexei A; Zgid, Dominika

2017-11-14

We present a rigorous framework which combines single-particle Green's function theory with density functional theory based on a separation of electron-electron interactions into short- and long-range components. Short-range contribution to the total energy and exchange-correlation potential is provided by a density functional approximation, while the long-range contribution is calculated using an explicit many-body Green's function method. Such a hybrid results in a nonlocal, dynamic, and orbital-dependent exchange-correlation functional of a single-particle Green's function. In particular, we present a range-separated hybrid functional called srSVWN5-lrGF2 which combines the local-density approximation and the second-order Green's function theory. We illustrate that similarly to density functional approximations, the new functional is weakly basis-set dependent. Furthermore, it offers an improved description of the short-range dynamic correlation. The many-body contribution to the functional mitigates the many-electron self-interaction error present in many density functional approximations and provides a better description of molecular properties. Additionally, we illustrate that the new functional can be used to scale down the self-energy and, therefore, introduce an additional sparsity to the self-energy matrix that in the future can be exploited in calculations for large molecules or periodic systems.

A Safari Through Density Functional Theory

NASA Astrophysics Data System (ADS)

Dreizler, Reiner M.; Lüdde, Cora S.

Density functional theory is widely used to treat quantum many body problems in many areas of physics and related fields. A brief survey of this method covering foundations, functionals and applications is presented here.

The construction of combinatorial manifolds with prescribed sets of links of vertices

NASA Astrophysics Data System (ADS)

Gaifullin, A. A.

2008-10-01

To every oriented closed combinatorial manifold we assign the set (with repetitions) of isomorphism classes of links of its vertices. The resulting transformation \\mathcal{L} is the main object of study in this paper. We pose an inversion problem for \\mathcal{L} and show that this problem is closely related to Steenrod's problem on the realization of cycles and to the Rokhlin-Schwartz-Thom construction of combinatorial Pontryagin classes. We obtain a necessary condition for a set of isomorphism classes of combinatorial spheres to belong to the image of \\mathcal{L}. (Sets satisfying this condition are said to be balanced.) We give an explicit construction showing that every balanced set of isomorphism classes of combinatorial spheres falls into the image of \\mathcal{L} after passing to a multiple set and adding several pairs of the form (Z,-Z), where -Z is the sphere Z with the orientation reversed. Given any singular simplicial cycle \\xi of a space X, this construction enables us to find explicitly a combinatorial manifold M and a map \\varphi\\colon M\\to X such that \\varphi_* \\lbrack M \\rbrack =r[\\xi] for some positive integer r. The construction is based on resolving singularities of \\xi. We give applications of the main construction to cobordisms of manifolds with singularities and cobordisms of simple cells. In particular, we prove that every rational additive invariant of cobordisms of manifolds with singularities admits a local formula. Another application is the construction of explicit (though inefficient) local combinatorial formulae for polynomials in the rational Pontryagin classes of combinatorial manifolds.

Comparing ab initio density-functional and wave function theories: the impact of correlation on the electronic density and the role of the correlation potential.

PubMed

Grabowski, Ireneusz; Teale, Andrew M; Śmiga, Szymon; Bartlett, Rodney J

2011-09-21

The framework of ab initio density-functional theory (DFT) has been introduced as a way to provide a seamless connection between the Kohn-Sham (KS) formulation of DFT and wave-function based ab initio approaches [R. J. Bartlett, I. Grabowski, S. Hirata, and S. Ivanov, J. Chem. Phys. 122, 034104 (2005)]. Recently, an analysis of the impact of dynamical correlation effects on the density of the neon atom was presented [K. Jankowski, K. Nowakowski, I. Grabowski, and J. Wasilewski, J. Chem. Phys. 130, 164102 (2009)], contrasting the behaviour for a variety of standard density functionals with that of ab initio approaches based on second-order Møller-Plesset (MP2) and coupled cluster theories at the singles-doubles (CCSD) and singles-doubles perturbative triples [CCSD(T)] levels. In the present work, we consider ab initio density functionals based on second-order many-body perturbation theory and coupled cluster perturbation theory in a similar manner, for a range of small atomic and molecular systems. For comparison, we also consider results obtained from MP2, CCSD, and CCSD(T) calculations. In addition to this density based analysis, we determine the KS correlation potentials corresponding to these densities and compare them with those obtained for a range of ab initio density functionals via the optimized effective potential method. The correlation energies, densities, and potentials calculated using ab initio DFT display a similar systematic behaviour to those derived from electronic densities calculated using ab initio wave function theories. In contrast, typical explicit density functionals for the correlation energy, such as VWN5 and LYP, do not show behaviour consistent with this picture of dynamical correlation, although they may provide some degree of correction for already erroneous explicitly density-dependent exchange-only functionals. The results presented here using orbital dependent ab initio density functionals show that they provide a treatment of

"One-sample concept" micro-combinatory for high throughput TEM of binary films.

PubMed

Sáfrán, György

2018-04-01

Phases of thin films may remarkably differ from that of bulk. Unlike to the comprehensive data files of Binary Phase Diagrams [1] available for bulk, complete phase maps for thin binary layers do not exist. This is due to both the diverse metastable, non-equilibrium or instable phases feasible in thin films and the required volume of characterization work with analytical techniques like TEM, SAED and EDS. The aim of the present work was to develop a method that remarkably facilitates the TEM study of the diverse binary phases of thin films, or the creation of phase maps. A micro-combinatorial method was worked out that enables both preparation and study of a gradient two-component film within a single TEM specimen. For a demonstration of the technique thin Mn x Al 1- x binary samples with evolving concentration from x = 0 to x = 1 have been prepared so that the transition from pure Mn to pure Al covers a 1.5 mm long track within the 3 mm diameter TEM grid. The proposed method enables the preparation and study of thin combinatorial samples including all feasible phases as a function of composition or other deposition parameters. Contrary to known "combinatorial chemistry", in which a series of different samples are deposited in one run, and investigated, one at a time, the present micro-combinatorial method produces a single specimen condensing a complete library of a binary system that can be studied, efficiently, within a single TEM session. That provides extremely high throughput for TEM characterization of composition-dependent phases, exploration of new materials, or the construction of phase diagrams of binary films. Copyright © 2018 Elsevier B.V. All rights reserved.

Spin-Multiplet Components and Energy Splittings by Multistate Density Functional Theory.

PubMed

Grofe, Adam; Chen, Xin; Liu, Wenjian; Gao, Jiali

2017-10-05

Kohn-Sham density functional theory has been tremendously successful in chemistry and physics. Yet, it is unable to describe the energy degeneracy of spin-multiplet components with any approximate functional. This work features two contributions. (1) We present a multistate density functional theory (MSDFT) to represent spin-multiplet components and to determine multiplet energies. MSDFT is a hybrid approach, taking advantage of both wave function theory and density functional theory. Thus, the wave functions, electron densities and energy density-functionals for ground and excited states and for different components are treated on the same footing. The method is illustrated on valence excitations of atoms and molecules. (2) Importantly, a key result is that for cases in which the high-spin components can be determined separately by Kohn-Sham density functional theory, the transition density functional in MSDFT (which describes electronic coupling) can be defined rigorously. The numerical results may be explored to design and optimize transition density functionals for configuration coupling in multiconfigurational DFT.

Active Space Dependence in Multiconfiguration Pair-Density Functional Theory.

PubMed

Sharma, Prachi; Truhlar, Donald G; Gagliardi, Laura

2018-02-13

In multiconfiguration pair-density functional theory (MC-PDFT), multiconfiguration self-consistent-field calculations and on-top density functionals are combined to describe both static and dynamic correlation. Here, we investigate how the MC-PDFT total energy and its components depend on the active space choice in the case of the H 2 and N 2 molecules. The active space dependence of the on-top pair density, the total density, the ratio of on-top pair density to half the square of the electron density, and the satisfaction of the virial theorem are also explored. We find that the density and on-top pair density do not change significantly with changes in the active space. However, the on-top ratio does change significantly with respect to active space change, and this affects the on-top energy. This study provides a foundation for designing on-top density functionals and automatizing the active space choice in MC-PDFT.

Extended screened exchange functional derived from transcorrelated density functional theory.

PubMed

Umezawa, Naoto

2017-09-14

We propose a new formulation of the correlation energy functional derived from the transcorrelated method in use in density functional theory (TC-DFT). An effective Hamiltonian, H TC , is introduced by a similarity transformation of a many-body Hamiltonian, H, with respect to a complex function F: H TC =1FHF. It is proved that an expectation value of H TC for a normalized single Slater determinant, D n , corresponds to the total energy: E[n] = ⟨Ψ n |H|Ψ n ⟩/⟨Ψ n |Ψ n ⟩ = ⟨D n |H TC |D n ⟩ under the two assumptions: (1) The electron density nr associated with a trial wave function Ψ n = D n F is v-representable and (2) Ψ n and D n give rise to the same electron density nr. This formulation, therefore, provides an alternative expression of the total energy that is useful for the development of novel correlation energy functionals. By substituting a specific function for F, we successfully derived a model correlation energy functional, which resembles the functional form of the screened exchange method. The proposed functional, named the extended screened exchange (ESX) functional, is described within two-body integrals and is parametrized for a numerically exact correlation energy of the homogeneous electron gas. The ESX functional does not contain any ingredients of (semi-)local functionals and thus is totally free from self-interactions. The computational cost for solving the self-consistent-field equation is comparable to that of the Hartree-Fock method. We apply the ESX functional to electronic structure calculations for a solid silicon, H - ion, and small atoms. The results demonstrate that the TC-DFT formulation is promising for the systematic improvement of the correlation energy functional.

Running Clubs--A Combinatorial Investigation.

ERIC Educational Resources Information Center

Nissen, Phillip; Taylor, John

1991-01-01

Presented is a combinatorial problem based on the Hash House Harriers rule which states that the route of the run should not have previously been traversed by the club. Discovered is how many weeks the club can meet before the rule has to be broken. (KR)

Exact conditions on the temperature dependence of density functionals

DOE PAGES

Burke, K.; Smith, J. C.; Grabowski, P. E.; ...

2016-05-15

Universal exact conditions guided the construction of most ground-state density functional approximations in use today. Here, we derive the relation between the entropy and Mermin free energy density functionals for thermal density functional theory. Both the entropy and sum of kinetic and electron-electron repulsion functionals are shown to be monotonically increasing with temperature, while the Mermin functional is concave downwards. Analogous relations are found for both exchange and correlation. The importance of these conditions is illustrated in two extremes: the Hubbard dimer and the uniform gas.

Combinatorial invariants and covariants as tools for conical intersections.

PubMed

Ryb, Itai; Baer, Roi

2004-12-01

The combinatorial invariant and covariant are introduced as practical tools for analysis of conical intersections in molecules. The combinatorial invariant is a quantity depending on adiabatic electronic states taken at discrete nuclear configuration points. It is invariant to the phase choice (gauge) of these states. In the limit that the points trace a loop in nuclear configuration space, the value of the invariant approaches the corresponding Berry phase factor. The Berry phase indicates the presence of an odd or even number of conical intersections on surfaces bounded by these loops. Based on the combinatorial invariant, we develop a computationally simple and efficient method for locating conical intersections. The method is robust due to its use of gauge invariant nature. It does not rely on the landscape of intersecting potential energy surfaces nor does it require the computation of nonadiabatic couplings. We generalize the concept to open paths and combinatorial covariants for higher dimensions obtaining a technique for the construction of the gauge-covariant adiabatic-diabatic transformation matrix. This too does not make use of nonadiabatic couplings. The importance of using gauge-covariant expressions is underlined throughout. These techniques can be readily implemented by standard quantum chemistry codes. (c) 2004 American Institute of Physics.

Ranked solutions to a class of combinatorial optimizations - with applications in mass spectrometry based peptide sequencing

NASA Astrophysics Data System (ADS)

Doerr, Timothy; Alves, Gelio; Yu, Yi-Kuo

2006-03-01

Typical combinatorial optimizations are NP-hard; however, for a particular class of cost functions the corresponding combinatorial optimizations can be solved in polynomial time. This suggests a way to efficiently find approximate solutions - - find a transformation that makes the cost function as similar as possible to that of the solvable class. After keeping many high-ranking solutions using the approximate cost function, one may then re-assess these solutions with the full cost function to find the best approximate solution. Under this approach, it is important to be able to assess the quality of the solutions obtained, e.g., by finding the true ranking of kth best approximate solution when all possible solutions are considered exhaustively. To tackle this statistical issue, we provide a systematic method starting with a scaling function generated from the fininte number of high- ranking solutions followed by a convergent iterative mapping. This method, useful in a variant of the directed paths in random media problem proposed here, can also provide a statistical significance assessment for one of the most important proteomic tasks - - peptide sequencing using tandem mass spectrometry data.

Quantum Crystallography: Density Matrix-Density Functional Theory and the X-Ray Diffraction Experiment

NASA Astrophysics Data System (ADS)

Soirat, Arnaud J. A.

Density Matrix Theory is a Quantum Mechanical formalism in which the wavefunction is eliminated and its role taken over by reduced density matrices. The interest of this is that, it allows one, in principle, to calculate any electronic property of a physical system, without having to solve the Schrodinger equation, using only two entities much simpler than an N-body wavefunction: first and second -order reduced density matrices. In practice, though, this very promising possibility faces the tremendous theoretical problem of N-representability, which has been solved for the former, but, until now, voids any hope of theoretically determining the latter. However, it has been shown that single determinant reduced density matrices of any order may be recovered from coherent X-ray diffraction data, if one provides a proper Quantum Mechanical description of the Crystallography experiment. A deeper investigation of this method is the purpose of this work, where we, first, further study the calculation of X-ray reduced density matrices N-representable by a single Slater determinant. In this context, we independently derive necessary and sufficient conditions for the uniqueness of the method. We then show how to account for electron correlation in this model. For the first time, indeed, we derive highly accurate, yet practical, density matrices approximately N-representable by correlated-determinant wavefunctions. The interest of such a result lies in the Quantum Mechanical validity of these density matrices, their property of being entirely obtainable from X-ray coherent diffraction data, their very high accuracy conferred by this known property of the N-representing wavefunction, as well as their definition as explicit functionals of the density. All of these properties are finally used in both a theoretical and a numerical application: in the former, we show that these density matrices may be used in the context of Density Functional Theory to highly accurately determine

Learning to Predict Combinatorial Structures

NASA Astrophysics Data System (ADS)

Vembu, Shankar

2009-12-01

The major challenge in designing a discriminative learning algorithm for predicting structured data is to address the computational issues arising from the exponential size of the output space. Existing algorithms make different assumptions to ensure efficient, polynomial time estimation of model parameters. For several combinatorial structures, including cycles, partially ordered sets, permutations and other graph classes, these assumptions do not hold. In this thesis, we address the problem of designing learning algorithms for predicting combinatorial structures by introducing two new assumptions: (i) The first assumption is that a particular counting problem can be solved efficiently. The consequence is a generalisation of the classical ridge regression for structured prediction. (ii) The second assumption is that a particular sampling problem can be solved efficiently. The consequence is a new technique for designing and analysing probabilistic structured prediction models. These results can be applied to solve several complex learning problems including but not limited to multi-label classification, multi-category hierarchical classification, and label ranking.

Measuring and Specifying Combinatorial Coverage of Test Input Configurations

PubMed Central

Kuhn, D. Richard; Kacker, Raghu N.; Lei, Yu

2015-01-01

A key issue in testing is how many tests are needed for a required level of coverage or fault detection. Estimates are often based on error rates in initial testing, or on code coverage. For example, tests may be run until a desired level of statement or branch coverage is achieved. Combinatorial methods present an opportunity for a different approach to estimating required test set size, using characteristics of the test set. This paper describes methods for estimating the coverage of, and ability to detect, t-way interaction faults of a test set based on a covering array. We also develop a connection between (static) combinatorial coverage and (dynamic) code coverage, such that if a specific condition is satisfied, 100% branch coverage is assured. Using these results, we propose practical recommendations for using combinatorial coverage in specifying test requirements. PMID:28133442

Functional thermo-dynamics: a generalization of dynamic density functional theory to non-isothermal situations.

PubMed

Anero, Jesús G; Español, Pep; Tarazona, Pedro

2013-07-21

We present a generalization of Density Functional Theory (DFT) to non-equilibrium non-isothermal situations. By using the original approach set forth by Gibbs in his consideration of Macroscopic Thermodynamics (MT), we consider a Functional Thermo-Dynamics (FTD) description based on the density field and the energy density field. A crucial ingredient of the theory is an entropy functional, which is a concave functional. Therefore, there is a one to one connection between the density and energy fields with the conjugate thermodynamic fields. The connection between the three levels of description (MT, DFT, FTD) is clarified through a bridge theorem that relates the entropy of different levels of description and that constitutes a generalization of Mermin's theorem to arbitrary levels of description whose relevant variables are connected linearly. Although the FTD level of description does not provide any new information about averages and correlations at equilibrium, it is a crucial ingredient for the dynamics in non-equilibrium states. We obtain with the technique of projection operators the set of dynamic equations that describe the evolution of the density and energy density fields from an initial non-equilibrium state towards equilibrium. These equations generalize time dependent density functional theory to non-isothermal situations. We also present an explicit model for the entropy functional for hard spheres.

Identification of combinatorial drug regimens for treatment of Huntington's disease using Drosophila

NASA Astrophysics Data System (ADS)

Agrawal, Namita; Pallos, Judit; Slepko, Natalia; Apostol, Barbara L.; Bodai, Laszlo; Chang, Ling-Wen; Chiang, Ann-Shyn; Michels Thompson, Leslie; Marsh, J. Lawrence

2005-03-01

We explore the hypothesis that pathology of Huntington's disease involves multiple cellular mechanisms whose contributions to disease are incrementally additive or synergistic. We provide evidence that the photoreceptor neuron degeneration seen in flies expressing mutant human huntingtin correlates with widespread degenerative events in the Drosophila CNS. We use a Drosophila Huntington's disease model to establish dose regimens and protocols to assess the effectiveness of drug combinations used at low threshold concentrations. These proof of principle studies identify at least two potential combinatorial treatment options and illustrate a rapid and cost-effective paradigm for testing and optimizing combinatorial drug therapies while reducing side effects for patients with neurodegenerative disease. The potential for using prescreening in Drosophila to inform combinatorial therapies that are most likely to be effective for testing in mammals is discussed. combinatorial treatments | neurodegeneration

An Investigation into Post-Secondary Students' Understanding of Combinatorial Questions

ERIC Educational Resources Information Center

Bulone, Vincent William

2017-01-01

The purpose of this dissertation was to study aspects of how post-secondary students understand combinatorial problems. Within this dissertation, I considered understanding through two different lenses: i) student connections to previous problems; and ii) common combinatorial distinctions such as ordered versus unordered and repetitive versus…

Combinatorial materials approach to accelerate materials discovery for transportation (Conference Presentation)

NASA Astrophysics Data System (ADS)

Tong, Wei

2017-04-01

Combinatorial material research offers fast and efficient solutions to identify promising and advanced materials. It has revolutionized the pharmaceutical industry and now is being applied to accelerate the discovery of other new compounds, e.g. superconductors, luminescent materials, catalysts etc. Differing from the traditional trial-and-error process, this approach allows for the synthesis of a large number of compositionally diverse compounds by varying the combinations of the components and adjusting the ratios. It largely reduces the cost of single-sample synthesis/characterization, along with the turnaround time in the material discovery process, therefore, could dramatically change the existing paradigm for discovering and commercializing new materials. This talk outlines the use of combinatorial materials approach in the material discovery in transportation sector. It covers the general introduction to the combinatorial material concept, state of art for its application in energy-related research. At the end, LBNL capabilities in combinatorial materials synthesis and high throughput characterization that are applicable for material discovery research will be highlighted.

Thermal density functional theory, ensemble density functional theory, and potential functional theory for warm dense matter

NASA Astrophysics Data System (ADS)

Pribram-Jones, Aurora

Warm dense matter (WDM) is a high energy phase between solids and plasmas, with characteristics of both. It is present in the centers of giant planets, within the earth's core, and on the path to ignition of inertial confinement fusion. The high temperatures and pressures of warm dense matter lead to complications in its simulation, as both classical and quantum effects must be included. One of the most successful simulation methods is density functional theory-molecular dynamics (DFT-MD). Despite great success in a diverse array of applications, DFT-MD remains computationally expensive and it neglects the explicit temperature dependence of electron-electron interactions known to exist within exact DFT. Finite-temperature density functional theory (FT DFT) is an extension of the wildly successful ground-state DFT formalism via thermal ensembles, broadening its quantum mechanical treatment of electrons to include systems at non-zero temperatures. Exact mathematical conditions have been used to predict the behavior of approximations in limiting conditions and to connect FT DFT to the ground-state theory. An introduction to FT DFT is given within the context of ensemble DFT and the larger field of DFT is discussed for context. Ensemble DFT is used to describe ensembles of ground-state and excited systems. Exact conditions in ensemble DFT and the performance of approximations depend on ensemble weights. Using an inversion method, exact Kohn-Sham ensemble potentials are found and compared to approximations. The symmetry eigenstate Hartree-exchange approximation is in good agreement with exact calculations because of its inclusion of an ensemble derivative discontinuity. Since ensemble weights in FT DFT are temperature-dependent Fermi weights, this insight may help develop approximations well-suited to both ground-state and FT DFT. A novel, highly efficient approach to free energy calculations, finite-temperature potential functional theory, is derived, which has the

Current Density Functional Theory Using Meta-Generalized Gradient Exchange-Correlation Functionals.

PubMed

Furness, James W; Verbeke, Joachim; Tellgren, Erik I; Stopkowicz, Stella; Ekström, Ulf; Helgaker, Trygve; Teale, Andrew M

2015-09-08

We present the self-consistent implementation of current-dependent (hybrid) meta-generalized gradient approximation (mGGA) density functionals using London atomic orbitals. A previously proposed generalized kinetic energy density is utilized to implement mGGAs in the framework of Kohn-Sham current density functional theory (KS-CDFT). A unique feature of the nonperturbative implementation of these functionals is the ability to seamlessly explore a wide range of magnetic fields up to 1 au (∼235 kT) in strength. CDFT functionals based on the TPSS and B98 forms are investigated, and their performance is assessed by comparison with accurate coupled-cluster singles, doubles, and perturbative triples (CCSD(T)) data. In the weak field regime, magnetic properties such as magnetizabilities and nuclear magnetic resonance shielding constants show modest but systematic improvements over generalized gradient approximations (GGA). However, in the strong field regime, the mGGA-based forms lead to a significantly improved description of the recently proposed perpendicular paramagnetic bonding mechanism, comparing well with CCSD(T) data. In contrast to functionals based on the vorticity, these forms are found to be numerically stable, and their accuracy at high field suggests that the extension of mGGAs to CDFT via the generalized kinetic energy density should provide a useful starting point for further development of CDFT approximations.

Combinatorial Motor Training Results in Functional Reorganization of Remaining Motor Cortex after Controlled Cortical Impact in Rats

PubMed Central

Combs, Hannah L.; Jones, Theresa A.; Kozlowski, Dorothy A.

2016-01-01

Abstract Cortical reorganization subsequent to post-stroke motor rehabilitative training (RT) has been extensively examined in animal models and humans. However, similar studies focused on the effects of motor training after traumatic brain injury (TBI) are lacking. We previously reported that after a moderate/severe TBI in adult male rats, functional improvements in forelimb use were accomplished only with a combination of skilled forelimb reach training and aerobic exercise, with or without nonimpaired forelimb constraint. Thus, the current study was designed to examine the relationship between functional motor cortical map reorganization after experimental TBI and the behavioral improvements resulting from this combinatorial rehabilitative regime. Adult male rats were trained to proficiency on a skilled reaching task, received a unilateral controlled cortical impact (CCI) over the forelimb area of the caudal motor cortex (CMC). Three days post-CCI, animals began RT (n = 13) or no rehabilitative training (NoRT) control procedures (n = 13). The RT group participated in daily skilled reach training, voluntary aerobic exercise, and nonimpaired forelimb constraint. This RT regimen significantly improved impaired forelimb reaching success and normalized reaching strategies, consistent with previous findings. RT also enlarged the area of motor cortical wrist representation, derived by intracortical microstimulation, compared to NoRT. These findings indicate that sufficient RT can greatly improve motor function and improve the functional integrity of remaining motor cortex after a moderate/severe CCI. When compared with findings from stroke models, these findings also suggest that more intense RT may be needed to improve motor function and remodel the injured cortex after TBI. PMID:26421759

Combinatorial Motor Training Results in Functional Reorganization of Remaining Motor Cortex after Controlled Cortical Impact in Rats.

PubMed

Combs, Hannah L; Jones, Theresa A; Kozlowski, Dorothy A; Adkins, DeAnna L

2016-04-15

Cortical reorganization subsequent to post-stroke motor rehabilitative training (RT) has been extensively examined in animal models and humans. However, similar studies focused on the effects of motor training after traumatic brain injury (TBI) are lacking. We previously reported that after a moderate/severe TBI in adult male rats, functional improvements in forelimb use were accomplished only with a combination of skilled forelimb reach training and aerobic exercise, with or without nonimpaired forelimb constraint. Thus, the current study was designed to examine the relationship between functional motor cortical map reorganization after experimental TBI and the behavioral improvements resulting from this combinatorial rehabilitative regime. Adult male rats were trained to proficiency on a skilled reaching task, received a unilateral controlled cortical impact (CCI) over the forelimb area of the caudal motor cortex (CMC). Three days post-CCI, animals began RT (n = 13) or no rehabilitative training (NoRT) control procedures (n = 13). The RT group participated in daily skilled reach training, voluntary aerobic exercise, and nonimpaired forelimb constraint. This RT regimen significantly improved impaired forelimb reaching success and normalized reaching strategies, consistent with previous findings. RT also enlarged the area of motor cortical wrist representation, derived by intracortical microstimulation, compared to NoRT. These findings indicate that sufficient RT can greatly improve motor function and improve the functional integrity of remaining motor cortex after a moderate/severe CCI. When compared with findings from stroke models, these findings also suggest that more intense RT may be needed to improve motor function and remodel the injured cortex after TBI.

Multifunctional combinatorial-designed nanoparticles for nucleic acid therapy

NASA Astrophysics Data System (ADS)

Amiji, Mansoor M.

2016-05-01

Recent advances in biomedical sciences, especially in the field of human genetics, is increasingly considered to facilitate a new frontier in development of novel disease-modifying therapeutics. One of major challenges in the development of nucleic acid therapeutics is efficient and specific delivery of the molecules to the target tissue and cell upon systemic administration. In this report, I discuss our strategy to develop combinatorial-designed multifunctional nanoparticle assemblies based on natural biocompatible and biodegradable polymers for nucleic acid delivery in: (1) overcoming tumor drug resistance and (2) genetic modulation of macrophage functional phenotype from M1 to M2 in treatment of inflammatory diseases.

A brief histone in time: understanding the combinatorial functions of histone PTMs in the nucleosome context.

PubMed

Ng, Marlee K; Cheung, Peter

2016-02-01

It has been over 50 years since Allfrey et al. proposed that histone acetylation regulates RNA synthesis, and the study of histone modifications has progressed at an extraordinary pace for the past two decades. In this review, we provide a perspective on some key events and advances in our understanding of histone modifications. We also highlight reagents and tools from past to present that facilitated progress in this research field. Using histone H3 phosphorylation as an underlying thread, we review the rationale that led to the proposal of the histone code hypothesis, as well as examples that illustrate the concepts of combinatorial histone modifications and cross-talk pathways. We further highlight the importance of investigating these mechanisms in the context of nucleosomes rather than just at the histone level and present current and developing approaches for such studies. Overall, research on histone modifications has yielded great mechanistic insights into the regulation of genomic functions, and extending these studies using nucleosomes will further elucidate the complexity of these pathways in a more physiologically relevant context.

Trivial constraints on orbital-free kinetic energy density functionals

NASA Astrophysics Data System (ADS)

Luo, Kai; Trickey, S. B.

2018-03-01

Approximate kinetic energy density functionals (KEDFs) are central to orbital-free density functional theory. Limitations on the spatial derivative dependencies of KEDFs have been claimed from differential virial theorems. We identify a central defect in the argument: the relationships are not true for an arbitrary density but hold only for the minimizing density and corresponding chemical potential. Contrary to the claims therefore, the relationships are not constraints and provide no independent information about the spatial derivative dependencies of approximate KEDFs. A simple argument also shows that validity for arbitrary v-representable densities is not restored by appeal to the density-potential bijection.

Combinatorial genetic perturbation to refine metabolic circuits for producing biofuels and biochemicals.

PubMed

Kim, Hyo Jin; Turner, Timothy Lee; Jin, Yong-Su

2013-11-01

Recent advances in metabolic engineering have enabled microbial factories to compete with conventional processes for producing fuels and chemicals. Both rational and combinatorial approaches coupled with synthetic and systematic tools play central roles in metabolic engineering to create and improve a selected microbial phenotype. Compared to knowledge-based rational approaches, combinatorial approaches exploiting biological diversity and high-throughput screening have been demonstrated as more effective tools for improving various phenotypes of interest. In particular, identification of unprecedented targets to rewire metabolic circuits for maximizing yield and productivity of a target chemical has been made possible. This review highlights general principles and the features of the combinatorial approaches using various libraries to implement desired phenotypes for strain improvement. In addition, recent applications that harnessed the combinatorial approaches to produce biofuels and biochemicals will be discussed. Copyright © 2013 Elsevier Inc. All rights reserved.

Stretched hydrogen molecule from a constrained-search density-functional perspective

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

Valone, Steven M; Levy, Mel

2009-01-01

Constrained-search density functional theory gives valuable insights into the fundamentals of density functional theory. It provides exact results and bounds on the ground- and excited-state density functionals. An important advantage of the theory is that it gives guidance in the construction of functionals. Here they engage constrained search theory to explore issues associated with the functional behavior of 'stretched bonds' in molecular hydrogen. A constrained search is performed with familiar valence bond wavefunctions ordinarily used to describe molecular hydrogen. The effective, one-electron hamiltonian is computed and compared to the corresponding uncorrelated, Hartree-Fock effective hamiltonian. Analysis of the functional suggests themore » need to construct different functionals for the same density and to allow a competition among these functions. As a result the correlation energy functional is composed explicitly of energy gaps from the different functionals.« less

Combinatorial vector fields and the valley structure of fitness landscapes.

PubMed

Stadler, Bärbel M R; Stadler, Peter F

2010-12-01

Adaptive (downhill) walks are a computationally convenient way of analyzing the geometric structure of fitness landscapes. Their inherently stochastic nature has limited their mathematical analysis, however. Here we develop a framework that interprets adaptive walks as deterministic trajectories in combinatorial vector fields and in return associate these combinatorial vector fields with weights that measure their steepness across the landscape. We show that the combinatorial vector fields and their weights have a product structure that is governed by the neutrality of the landscape. This product structure makes practical computations feasible. The framework presented here also provides an alternative, and mathematically more convenient, way of defining notions of valleys, saddle points, and barriers in landscape. As an application, we propose a refined approximation for transition rates between macrostates that are associated with the valleys of the landscape.

Balancing focused combinatorial libraries based on multiple GPCR ligands

NASA Astrophysics Data System (ADS)

Soltanshahi, Farhad; Mansley, Tamsin E.; Choi, Sun; Clark, Robert D.

2006-08-01

G-Protein coupled receptors (GPCRs) are important targets for drug discovery, and combinatorial chemistry is an important tool for pharmaceutical development. The absence of detailed structural information, however, limits the kinds of combinatorial design techniques that can be applied to GPCR targets. This is particularly problematic given the current emphasis on focused combinatorial libraries. By linking an incremental construction method (OptDesign) to the very fast shape-matching capability of ChemSpace, we have created an efficient method for designing targeted sublibraries that are topomerically similar to known actives. Multi-objective scoring allows consideration of multiple queries (actives) simultaneously. This can lead to a distribution of products skewed towards one particular query structure, however, particularly when the ligands of interest are quite dissimilar to one another. A novel pivoting technique is described which makes it possible to generate promising designs even under those circumstances. The approach is illustrated by application to some serotonergic agonists and chemokine antagonists.

Combinatorial games with a pass: a dynamical systems approach.

PubMed

Morrison, Rebecca E; Friedman, Eric J; Landsberg, Adam S

2011-12-01

By treating combinatorial games as dynamical systems, we are able to address a longstanding open question in combinatorial game theory, namely, how the introduction of a "pass" move into a game affects its behavior. We consider two well known combinatorial games, 3-pile Nim and 3-row Chomp. In the case of Nim, we observe that the introduction of the pass dramatically alters the game's underlying structure, rendering it considerably more complex, while for Chomp, the pass move is found to have relatively minimal impact. We show how these results can be understood by recasting these games as dynamical systems describable by dynamical recursion relations. From these recursion relations, we are able to identify underlying structural connections between these "games with passes" and a recently introduced class of "generic (perturbed) games." This connection, together with a (non-rigorous) numerical stability analysis, allows one to understand and predict the effect of a pass on a game.

Systematic Identification of Combinatorial Drivers and Targets in Cancer Cell Lines

PubMed Central

Tabchy, Adel; Eltonsy, Nevine; Housman, David E.; Mills, Gordon B.

2013-01-01

There is an urgent need to elicit and validate highly efficacious targets for combinatorial intervention from large scale ongoing molecular characterization efforts of tumors. We established an in silico bioinformatic platform in concert with a high throughput screening platform evaluating 37 novel targeted agents in 669 extensively characterized cancer cell lines reflecting the genomic and tissue-type diversity of human cancers, to systematically identify combinatorial biomarkers of response and co-actionable targets in cancer. Genomic biomarkers discovered in a 141 cell line training set were validated in an independent 359 cell line test set. We identified co-occurring and mutually exclusive genomic events that represent potential drivers and combinatorial targets in cancer. We demonstrate multiple cooperating genomic events that predict sensitivity to drug intervention independent of tumor lineage. The coupling of scalable in silico and biologic high throughput cancer cell line platforms for the identification of co-events in cancer delivers rational combinatorial targets for synthetic lethal approaches with a high potential to pre-empt the emergence of resistance. PMID:23577104

Systematic identification of combinatorial drivers and targets in cancer cell lines.

PubMed

Tabchy, Adel; Eltonsy, Nevine; Housman, David E; Mills, Gordon B

2013-01-01

There is an urgent need to elicit and validate highly efficacious targets for combinatorial intervention from large scale ongoing molecular characterization efforts of tumors. We established an in silico bioinformatic platform in concert with a high throughput screening platform evaluating 37 novel targeted agents in 669 extensively characterized cancer cell lines reflecting the genomic and tissue-type diversity of human cancers, to systematically identify combinatorial biomarkers of response and co-actionable targets in cancer. Genomic biomarkers discovered in a 141 cell line training set were validated in an independent 359 cell line test set. We identified co-occurring and mutually exclusive genomic events that represent potential drivers and combinatorial targets in cancer. We demonstrate multiple cooperating genomic events that predict sensitivity to drug intervention independent of tumor lineage. The coupling of scalable in silico and biologic high throughput cancer cell line platforms for the identification of co-events in cancer delivers rational combinatorial targets for synthetic lethal approaches with a high potential to pre-empt the emergence of resistance.

Time-dependent density-functional tight-binding method with the third-order expansion of electron density

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

Nishimoto, Yoshio, E-mail: nishimoto.yoshio@fukui.kyoto-u.ac.jp

2015-09-07

We develop a formalism for the calculation of excitation energies and excited state gradients for the self-consistent-charge density-functional tight-binding method with the third-order contributions of a Taylor series of the density functional theory energy with respect to the fluctuation of electron density (time-dependent density-functional tight-binding (TD-DFTB3)). The formulation of the excitation energy is based on the existing time-dependent density functional theory and the older TD-DFTB2 formulae. The analytical gradient is computed by solving Z-vector equations, and it requires one to calculate the third-order derivative of the total energy with respect to density matrix elements due to the inclusion of themore » third-order contributions. The comparison of adiabatic excitation energies for selected small and medium-size molecules using the TD-DFTB2 and TD-DFTB3 methods shows that the inclusion of the third-order contributions does not affect excitation energies significantly. A different set of parameters, which are optimized for DFTB3, slightly improves the prediction of adiabatic excitation energies statistically. The application of TD-DFTB for the prediction of absorption and fluorescence energies of cresyl violet demonstrates that TD-DFTB3 reproduced the experimental fluorescence energy quite well.« less

Time-dependent density-functional tight-binding method with the third-order expansion of electron density.

PubMed

Nishimoto, Yoshio

2015-09-07

We develop a formalism for the calculation of excitation energies and excited state gradients for the self-consistent-charge density-functional tight-binding method with the third-order contributions of a Taylor series of the density functional theory energy with respect to the fluctuation of electron density (time-dependent density-functional tight-binding (TD-DFTB3)). The formulation of the excitation energy is based on the existing time-dependent density functional theory and the older TD-DFTB2 formulae. The analytical gradient is computed by solving Z-vector equations, and it requires one to calculate the third-order derivative of the total energy with respect to density matrix elements due to the inclusion of the third-order contributions. The comparison of adiabatic excitation energies for selected small and medium-size molecules using the TD-DFTB2 and TD-DFTB3 methods shows that the inclusion of the third-order contributions does not affect excitation energies significantly. A different set of parameters, which are optimized for DFTB3, slightly improves the prediction of adiabatic excitation energies statistically. The application of TD-DFTB for the prediction of absorption and fluorescence energies of cresyl violet demonstrates that TD-DFTB3 reproduced the experimental fluorescence energy quite well.

DNA-Encoded Dynamic Combinatorial Chemical Libraries.

PubMed

Reddavide, Francesco V; Lin, Weilin; Lehnert, Sarah; Zhang, Yixin

2015-06-26

Dynamic combinatorial chemistry (DCC) explores the thermodynamic equilibrium of reversible reactions. Its application in the discovery of protein binders is largely limited by difficulties in the analysis of complex reaction mixtures. DNA-encoded chemical library (DECL) technology allows the selection of binders from a mixture of up to billions of different compounds; however, experimental results often show low a signal-to-noise ratio and poor correlation between enrichment factor and binding affinity. Herein we describe the design and application of DNA-encoded dynamic combinatorial chemical libraries (EDCCLs). Our experiments have shown that the EDCCL approach can be used not only to convert monovalent binders into high-affinity bivalent binders, but also to cause remarkably enhanced enrichment of potent bivalent binders by driving their in situ synthesis. We also demonstrate the application of EDCCLs in DNA-templated chemical reactions. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Force Density Function Relationships in 2-D Granular Media

NASA Technical Reports Server (NTRS)

Youngquist, Robert C.; Metzger, Philip T.; Kilts, Kelly N.

2004-01-01

An integral transform relationship is developed to convert between two important probability density functions (distributions) used in the study of contact forces in granular physics. Developing this transform has now made it possible to compare and relate various theoretical approaches with one another and with the experimental data despite the fact that one may predict the Cartesian probability density and another the force magnitude probability density. Also, the transforms identify which functional forms are relevant to describe the probability density observed in nature, and so the modified Bessel function of the second kind has been identified as the relevant form for the Cartesian probability density corresponding to exponential forms in the force magnitude distribution. Furthermore, it is shown that this transform pair supplies a sufficient mathematical framework to describe the evolution of the force magnitude distribution under shearing. Apart from the choice of several coefficients, whose evolution of values must be explained in the physics, this framework successfully reproduces the features of the distribution that are taken to be an indicator of jamming and unjamming in a granular packing. Key words. Granular Physics, Probability Density Functions, Fourier Transforms

Combinatorial Optimization of Heterogeneous Catalysts Used in the Growth of Carbon Nanotubes

NASA Technical Reports Server (NTRS)

Cassell, Alan M.; Verma, Sunita; Delzeit, Lance; Meyyappan, M.; Han, Jie

2000-01-01

Libraries of liquid-phase catalyst precursor solutions were printed onto iridium-coated silicon substrates and evaluated for their effectiveness in catalyzing the growth of multi-walled carbon nanotubes (MWNTs) by chemical vapor deposition (CVD). The catalyst precursor solutions were composed of inorganic salts and a removable tri-block copolymer (EO)20(PO)70(EO)20 (EO = ethylene oxide, PO = propylene oxide) structure-directing agent (SDA), dissolved in ethanol/methanol mixtures. Sample libraries were quickly assayed using scanning electron microscopy after CVD growth to identify active catalysts and CVD conditions. Composition libraries and focus libraries were then constructed around the active spots identified in the discovery libraries to understand how catalyst precursor composition affects the yield, density, and quality of the nanotubes. Successful implementation of combinatorial optimization methods in the development of highly active, carbon nanotube catalysts is demonstrated, as well as the identification of catalyst formulations that lead to varying densities and shapes of aligned nanotube towers.

Quest for a universal density functional: the accuracy of density functionals across a broad spectrum of databases in chemistry and physics.

PubMed

Peverati, Roberto; Truhlar, Donald G

2014-03-13

Kohn-Sham density functional theory is in principle an exact formulation of quantum mechanical electronic structure theory, but in practice we have to rely on approximate exchange-correlation (xc) functionals. The objective of our work has been to design an xc functional with broad accuracy across as wide an expanse of chemistry and physics as possible, leading--as a long-range goal--to a functional with good accuracy for all problems, i.e. a universal functional. To guide our path towards that goal and to measure our progress, we have developed-building on earlier work of our group-a set of databases of reference data for a variety of energetic and structural properties in chemistry and physics. These databases include energies of molecular processes, such as atomization, complexation, proton addition and ionization; they also include molecular geometries and solid-state lattice constants, chemical reaction barrier heights, and cohesive energies and band gaps of solids. For this paper, we gather many of these databases into four comprehensive databases, two with 384 energetic data for chemistry and solid-state physics and another two with 68 structural data for chemistry and solid-state physics, and we test two wave function methods and 77 density functionals (12 Minnesota meta functionals and 65 others) in a consistent way across this same broad set of data. We especially highlight the Minnesota density functionals, but the results have broader implications in that one may see the successes and failures of many kinds of density functionals when they are all applied to the same data. Therefore, the results provide a status report on the quest for a universal functional.

Combinatorial synthesis of ceramic materials

DOEpatents

Lauf, Robert J [Oak Ridge, TN; Walls, Claudia A [Oak Ridge, TN; Boatner, Lynn A [Oak Ridge, TN

2010-02-23

A combinatorial library includes a gelcast substrate defining a plurality of cavities in at least one surface thereof; and a plurality of gelcast test materials in the cavities, at least two of the test materials differing from the substrate in at least one compositional characteristic, the two test materials differing from each other in at least one compositional characteristic.

Combinatorial synthesis of ceramic materials

DOEpatents

Lauf, Robert J.; Walls, Claudia A.; Boatner, Lynn A.

2006-11-14

A combinatorial library includes a gelcast substrate defining a plurality of cavities in at least one surface thereof; and a plurality of gelcast test materials in the cavities, at least two of the test materials differing from the substrate in at least one compositional characteristic, the two test materials differing from each other in at least one compositional characteristic.

cGRNB: a web server for building combinatorial gene regulatory networks through integrated engineering of seed-matching sequence information and gene expression datasets.

PubMed

Xu, Huayong; Yu, Hui; Tu, Kang; Shi, Qianqian; Wei, Chaochun; Li, Yuan-Yuan; Li, Yi-Xue

2013-01-01

We are witnessing rapid progress in the development of methodologies for building the combinatorial gene regulatory networks involving both TFs (Transcription Factors) and miRNAs (microRNAs). There are a few tools available to do these jobs but most of them are not easy to use and not accessible online. A web server is especially needed in order to allow users to upload experimental expression datasets and build combinatorial regulatory networks corresponding to their particular contexts. In this work, we compiled putative TF-gene, miRNA-gene and TF-miRNA regulatory relationships from forward-engineering pipelines and curated them as built-in data libraries. We streamlined the R codes of our two separate forward-and-reverse engineering algorithms for combinatorial gene regulatory network construction and formalized them as two major functional modules. As a result, we released the cGRNB (combinatorial Gene Regulatory Networks Builder): a web server for constructing combinatorial gene regulatory networks through integrated engineering of seed-matching sequence information and gene expression datasets. The cGRNB enables two major network-building modules, one for MPGE (miRNA-perturbed gene expression) datasets and the other for parallel miRNA/mRNA expression datasets. A miRNA-centered two-layer combinatorial regulatory cascade is the output of the first module and a comprehensive genome-wide network involving all three types of combinatorial regulations (TF-gene, TF-miRNA, and miRNA-gene) are the output of the second module. In this article we propose cGRNB, a web server for building combinatorial gene regulatory networks through integrated engineering of seed-matching sequence information and gene expression datasets. Since parallel miRNA/mRNA expression datasets are rapidly accumulated by the advance of next-generation sequencing techniques, cGRNB will be very useful tool for researchers to build combinatorial gene regulatory networks based on expression datasets

Investigation of estimators of probability density functions

NASA Technical Reports Server (NTRS)

Speed, F. M.

1972-01-01

Four research projects are summarized which include: (1) the generation of random numbers on the IBM 360/44, (2) statistical tests used to check out random number generators, (3) Specht density estimators, and (4) use of estimators of probability density functions in analyzing large amounts of data.

Microscopically based energy density functionals for nuclei using the density matrix expansion: Implementation and pre-optimization

NASA Astrophysics Data System (ADS)

Stoitsov, M.; Kortelainen, M.; Bogner, S. K.; Duguet, T.; Furnstahl, R. J.; Gebremariam, B.; Schunck, N.

2010-11-01

In a recent series of articles, Gebremariam, Bogner, and Duguet derived a microscopically based nuclear energy density functional by applying the density matrix expansion (DME) to the Hartree-Fock energy obtained from chiral effective field theory two- and three-nucleon interactions. Owing to the structure of the chiral interactions, each coupling in the DME functional is given as the sum of a coupling constant arising from zero-range contact interactions and a coupling function of the density arising from the finite-range pion exchanges. Because the contact contributions have essentially the same structure as those entering empirical Skyrme functionals, a microscopically guided Skyrme phenomenology has been suggested in which the contact terms in the DME functional are released for optimization to finite-density observables to capture short-range correlation energy contributions from beyond Hartree-Fock. The present article is the first attempt to assess the ability of the newly suggested DME functional, which has a much richer set of density dependencies than traditional Skyrme functionals, to generate sensible and stable results for nuclear applications. The results of the first proof-of-principle calculations are given, and numerous practical issues related to the implementation of the new functional in existing Skyrme codes are discussed. Using a restricted singular value decomposition optimization procedure, it is found that the new DME functional gives numerically stable results and exhibits a small but systematic reduction of our test χ2 function compared to standard Skyrme functionals, thus justifying its suitability for future global optimizations and large-scale calculations.

π-π stacking tackled with density functional theory

PubMed Central

Swart, Marcel; van der Wijst, Tushar; Fonseca Guerra, Célia

2007-01-01

Through comparison with ab initio reference data, we have evaluated the performance of various density functionals for describing π-π interactions as a function of the geometry between two stacked benzenes or benzene analogs, between two stacked DNA bases, and between two stacked Watson–Crick pairs. Our main purpose is to find a robust and computationally efficient density functional to be used specifically and only for describing π-π stacking interactions in DNA and other biological molecules in the framework of our recently developed QM/QM approach "QUILD". In line with previous studies, most standard density functionals recover, at best, only part of the favorable stacking interactions. An exception is the new KT1 functional, which correctly yields bound π-stacked structures. Surprisingly, a similarly good performance is achieved with the computationally very robust and efficient local density approximation (LDA). Furthermore, we show that classical electrostatic interactions determine the shape and depth of the π-π stacking potential energy surface. Figure Additivity approximation for the π-π interaction between two stacked Watson–Crick base pairs in terms of pairwise interactions between individual bases Electronic supplementary material The online version of this article (doi:10.1007/s00894-007-0239-y) contains supplementary material, which is available to authorized users. PMID:17874150

General dynamical density functional theory for classical fluids.

PubMed

Goddard, Benjamin D; Nold, Andreas; Savva, Nikos; Pavliotis, Grigorios A; Kalliadasis, Serafim

2012-09-21

We study the dynamics of a colloidal fluid including inertia and hydrodynamic interactions, two effects which strongly influence the nonequilibrium properties of the system. We derive a general dynamical density functional theory which shows very good agreement with full Langevin dynamics. In suitable limits, we recover existing dynamical density functional theories and a Navier-Stokes-like equation with additional nonlocal terms.

High-Density IgE Recognition of the Major Grass Pollen Allergen Phl p 1 Revealed with Single-Chain IgE Antibody Fragments Obtained by Combinatorial Cloning

PubMed Central

Madritsch, Christoph; Gadermaier, Elisabeth; Roder, Uwe W.; Lupinek, Christian; Valenta, Rudolf; Flicker, Sabine

2015-01-01

The timothy grass pollen allergen Phl p 1 belongs to the group 1 of highly cross-reactive grass pollen allergens with a molecular mass of ~25–30 kDa. Group 1 allergens are recognized by >95% of grass pollen allergic patients. We investigated the IgE recognition of Phl p 1 using allergen-specific IgE-derived single-chain variable Ab fragments (IgE-ScFvs) isolated from a combinatorial library constructed from PBMCs of a grass pollen–allergic patient. IgE-ScFvs reacted with recombinant Phl p 1 and natural group 1 grass pollen allergens. Using synthetic Phl p 1–derived peptides, the binding sites of two ScFvs were mapped to the N terminus of the allergen. In surface plasmon resonance experiments they showed comparable high-affinity binding to Phl p 1 as a complete human IgE-derived Ab recognizing the allergens’ C terminus. In a set of surface plasmon resonance experiments simultaneous allergen recognition of all three binders was demonstrated. Even in the presence of the three binders, allergic patients’ polyclonal IgE reacted with Phl p 1, indicating high-density IgE recognition of the Phl p 1 allergen. Our results show that multiple IgE Abs can bind with high density to Phl p 1, which may explain the high allergenic activity and sensitizing capacity of this allergen. PMID:25637023

A density functional approach to ferrogels

NASA Astrophysics Data System (ADS)

Cremer, P.; Heinen, M.; Menzel, A. M.; Löwen, H.

2017-07-01

Ferrogels consist of magnetic colloidal particles embedded in an elastic polymer matrix. As a consequence, their structural and rheological properties are governed by a competition between magnetic particle-particle interactions and mechanical matrix elasticity. Typically, the particles are permanently fixed within the matrix, which makes them distinguishable by their positions. Over time, particle neighbors do not change due to the fixation by the matrix. Here we present a classical density functional approach for such ferrogels. We map the elastic matrix-induced interactions between neighboring colloidal particles distinguishable by their positions onto effective pairwise interactions between indistinguishable particles similar to a ‘pairwise pseudopotential’. Using Monte-Carlo computer simulations, we demonstrate for one-dimensional dipole-spring models of ferrogels that this mapping is justified. We then use the pseudopotential as an input into classical density functional theory of inhomogeneous fluids and predict the bulk elastic modulus of the ferrogel under various conditions. In addition, we propose the use of an ‘external pseudopotential’ when one switches from the viewpoint of a one-dimensional dipole-spring object to a one-dimensional chain embedded in an infinitely extended bulk matrix. Our mapping approach paves the way to describe various inhomogeneous situations of ferrogels using classical density functional concepts of inhomogeneous fluids.

Experimental Design for Combinatorial and High Throughput Materials Development

NASA Astrophysics Data System (ADS)

Cawse, James N.

2002-12-01

In the past decade, combinatorial and high throughput experimental methods have revolutionized the pharmaceutical industry, allowing researchers to conduct more experiments in a week than was previously possible in a year. Now high throughput experimentation is rapidly spreading from its origins in the pharmaceutical world to larger industrial research establishments such as GE and DuPont, and even to smaller companies and universities. Consequently, researchers need to know the kinds of problems, desired outcomes, and appropriate patterns for these new strategies. Editor James Cawse's far-reaching study identifies and applies, with specific examples, these important new principles and techniques. Experimental Design for Combinatorial and High Throughput Materials Development progresses from methods that are now standard, such as gradient arrays, to mathematical developments that are breaking new ground. The former will be particularly useful to researchers entering the field, while the latter should inspire and challenge advanced practitioners. The book's contents are contributed by leading researchers in their respective fields. Chapters include: -High Throughput Synthetic Approaches for the Investigation of Inorganic Phase Space -Combinatorial Mapping of Polymer Blends Phase Behavior -Split-Plot Designs -Artificial Neural Networks in Catalyst Development -The Monte Carlo Approach to Library Design and Redesign This book also contains over 200 useful charts and drawings. Industrial chemists, chemical engineers, materials scientists, and physicists working in combinatorial and high throughput chemistry will find James Cawse's study to be an invaluable resource.

Recent developments in LIBXC - A comprehensive library of functionals for density functional theory

NASA Astrophysics Data System (ADS)

Lehtola, Susi; Steigemann, Conrad; Oliveira, Micael J. T.; Marques, Miguel A. L.

2018-01-01

LIBXC is a library of exchange-correlation functionals for density-functional theory. We are concerned with semi-local functionals (or the semi-local part of hybrid functionals), namely local-density approximations, generalized-gradient approximations, and meta-generalized-gradient approximations. Currently we include around 400 functionals for the exchange, correlation, and the kinetic energy, spanning more than 50 years of research. Moreover, LIBXC is by now used by more than 20 codes, not only from the atomic, molecular, and solid-state physics, but also from the quantum chemistry communities.

Quantum Resonance Approach to Combinatorial Optimization

NASA Technical Reports Server (NTRS)

Zak, Michail

1997-01-01

It is shown that quantum resonance can be used for combinatorial optimization. The advantage of the approach is in independence of the computing time upon the dimensionality of the problem. As an example, the solution to a constraint satisfaction problem of exponential complexity is demonstrated.

Combinatorial pretreatment and fermentation optimization enabled a record yield on lignin bioconversion.

PubMed

Liu, Zhi-Hua; Xie, Shangxian; Lin, Furong; Jin, Mingjie; Yuan, Joshua S

2018-01-01

Lignin valorization has recently been considered to be an essential process for sustainable and cost-effective biorefineries. Lignin represents a potential new feedstock for value-added products. Oleaginous bacteria such as Rhodococcus opacus can produce intracellular lipids from biodegradation of aromatic substrates. These lipids can be used for biofuel production, which can potentially replace petroleum-derived chemicals. However, the low reactivity of lignin produced from pretreatment and the underdeveloped fermentation technology hindered lignin bioconversion to lipids. In this study, combinatorial pretreatment with an optimized fermentation strategy was evaluated to improve lignin valorization into lipids using R. opacus PD630. As opposed to single pretreatment, combinatorial pretreatment produced a 12.8-75.6% higher lipid concentration in fermentation using lignin as the carbon source. Gas chromatography-mass spectrometry analysis showed that combinatorial pretreatment released more aromatic monomers, which could be more readily utilized by lignin-degrading strains. Three detoxification strategies were used to remove potential inhibitors produced from pretreatment. After heating detoxification of the lignin stream, the lipid concentration further increased by 2.9-9.7%. Different fermentation strategies were evaluated in scale-up lipid fermentation using a 2.0-l fermenter. With laccase treatment of the lignin stream produced from combinatorial pretreatment, the highest cell dry weight and lipid concentration were 10.1 and 1.83 g/l, respectively, in fed-batch fermentation, with a total soluble substrate concentration of 40 g/l. The improvement of the lipid fermentation performance may have resulted from lignin depolymerization by the combinatorial pretreatment and laccase treatment, reduced inhibition effects by fed-batch fermentation, adequate oxygen supply, and an accurate pH control in the fermenter. Overall, these results demonstrate that combinatorial

Double-hybrid density-functional theory with meta-generalized-gradient approximations

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

Souvi, Sidi M. O., E-mail: sidi.souvi@irsn.fr; Sharkas, Kamal; Toulouse, Julien, E-mail: julien.toulouse@upmc.fr

2014-02-28

We extend the previously proposed one-parameter double-hybrid density-functional theory [K. Sharkas, J. Toulouse, and A. Savin, J. Chem. Phys. 134, 064113 (2011)] to meta-generalized-gradient-approximation (meta-GGA) exchange-correlation density functionals. We construct several variants of one-parameter double-hybrid approximations using the Tao-Perdew-Staroverov-Scuseria (TPSS) meta-GGA functional and test them on test sets of atomization energies and reaction barrier heights. The most accurate variant uses the uniform coordinate scaling of the density and of the kinetic energy density in the correlation functional, and improves over both standard Kohn-Sham TPSS and second-order Møller-Plesset calculations.

Adiabatic corrections to density functional theory energies and wave functions.

PubMed

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.

Subsystem functional and the missing ingredient of confinement physics in density functionals.

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

Armiento, Rickard Roberto; Mattsson, Ann Elisabet; Hao, Feng

2010-08-01

The subsystem functional scheme is a promising approach recently proposed for constructing exchange-correlation density functionals. In this scheme, the physics in each part of real materials is described by mapping to a characteristic model system. The 'confinement physics,' an essential physical ingredient that has been left out in present functionals, is studied by employing the harmonic-oscillator (HO) gas model. By performing the potential {yields} density and the density {yields} exchange energy per particle mappings based on two model systems characterizing the physics in the interior (uniform electron-gas model) and surface regions (Airy gas model) of materials for the HO gases,more » we show that the confinement physics emerges when only the lowest subband of the HO gas is occupied by electrons. We examine the approximations of the exchange energy by several state-of-the-art functionals for the HO gas, and none of them produces adequate accuracy in the confinement dominated cases. A generic functional that incorporates the description of the confinement physics is needed.« less

Self-contained filtered density function

NASA Astrophysics Data System (ADS)

Nouri, A. G.; Nik, M. B.; Givi, P.; Livescu, D.; Pope, S. B.

2017-09-01

The filtered density function (FDF) closure is extended to a "self-contained" format to include the subgrid-scale (SGS) statistics of all of the hydro-thermo-chemical variables in turbulent flows. These are the thermodynamic pressure, the specific internal energy, the velocity vector, and the composition field. In this format, the model is comprehensive and facilitates large-eddy simulation (LES) of flows at both low and high compressibility levels. A transport equation is developed for the joint pressure-energy-velocity-composition filtered mass density function (PEVC-FMDF). In this equation, the effect of convection appears in closed form. The coupling of the hydrodynamics and thermochemistry is modeled via a set of stochastic differential equation for each of the transport variables. This yields a self-contained SGS closure. For demonstration, LES is conducted of a turbulent shear flow with transport of a passive scalar. The consistency of the PEVC-FMDF formulation is established, and its overall predictive capability is appraised via comparison with direct numerical simulation (DNS) data.

Connection formulas for thermal density functional theory

DOE PAGES

Pribram-Jones, A.; Burke, K.

2016-05-23

We show that the adiabatic connection formula of ground-state density functional theory relates the correlation energy to a coupling-constant integral over a purely potential contribution, and is widely used to understand and improve approximations. The corresponding formula for thermal density functional theory is cast as an integral over temperatures instead, ranging upward from the system's physical temperature. We also show how to relate different correlation components to each other, either in terms of temperature or coupling-constant integrations. Lastly, we illustrate our results on the uniform electron gas.

A Systematic Study of Simple Combinatorial Configurations.

ERIC Educational Resources Information Center

Dubois, Jean-Guy

1984-01-01

A classification of the simple combinatorial configurations which correspond to various cases of distribution and ordering of objects into boxes is given (in French). Concrete descriptions, structured relations, translations, and formalizations are discussed. (MNS)

Application of computer assisted combinatorial chemistry in antivirial, antimalarial and anticancer agents design

NASA Astrophysics Data System (ADS)

Burello, E.; Bologa, C.; Frecer, V.; Miertus, S.

Combinatorial chemistry and technologies have been developed to a stage where synthetic schemes are available for generation of a large variety of organic molecules. The innovative concept of combinatorial design assumes that screening of a large and diverse library of compounds will increase the probability of finding an active analogue among the compounds tested. Since the rate at which libraries are screened for activity currently constitutes a limitation to the use of combinatorial technologies, it is important to be selective about the number of compounds to be synthesized. Early experience with combinatorial chemistry indicated that chemical diversity alone did not result in a significant increase in the number of generated lead compounds. Emphasis has therefore been increasingly put on the use of computer assisted combinatorial chemical techniques. Computational methods are valuable in the design of virtual libraries of molecular models. Selection strategies based on computed physicochemical properties of the models or of a target compound are introduced to reduce the time and costs of library synthesis and screening. In addition, computational structure-based library focusing methods can be used to perform in silico screening of the activity of compounds against a target receptor by docking the ligands into the receptor model. Three case studies are discussed dealing with the design of targeted combinatorial libraries of inhibitors of HIV-1 protease, P. falciparum plasmepsin and human urokinase as potential antivirial, antimalarial and anticancer drugs. These illustrate library focusing strategies.

Gian-Carlos Rota and Combinatorial Math.

ERIC Educational Resources Information Center

Kolata, Gina Bari

1979-01-01

Presents the first of a series of occasional articles about mathematics as seen through the eyes of its prominent scholars. In an interview with Gian-Carlos Rota of the Massachusetts Institute of Technology he discusses how combinatorial mathematics began as a field and its future. (HM)

A Model of Students' Combinatorial Thinking

ERIC Educational Resources Information Center

Lockwood, Elise

2013-01-01

Combinatorial topics have become increasingly prevalent in K-12 and undergraduate curricula, yet research on combinatorics education indicates that students face difficulties when solving counting problems. The research community has not yet addressed students' ways of thinking at a level that facilitates deeper understanding of how students…

Iterative optimization of xylose catabolism in Saccharomyces cerevisiae using combinatorial expression tuning.

PubMed

Latimer, Luke N; Dueber, John E

2017-06-01

A common challenge in metabolic engineering is rapidly identifying rate-controlling enzymes in heterologous pathways for subsequent production improvement. We demonstrate a workflow to address this challenge and apply it to improving xylose utilization in Saccharomyces cerevisiae. For eight reactions required for conversion of xylose to ethanol, we screened enzymes for functional expression in S. cerevisiae, followed by a combinatorial expression analysis to achieve pathway flux balancing and identification of limiting enzymatic activities. In the next round of strain engineering, we increased the copy number of these limiting enzymes and again tested the eight-enzyme combinatorial expression library in this new background. This workflow yielded a strain that has a ∼70% increase in biomass yield and ∼240% increase in xylose utilization. Finally, we chromosomally integrated the expression library. This library enriched for strains with multiple integrations of the pathway, which likely were the result of tandem integrations mediated by promoter homology. Biotechnol. Bioeng. 2017;114: 1301-1309. © 2017 Wiley Periodicals, Inc. © 2017 Wiley Periodicals, Inc.

Microscopically based energy density functionals for nuclei using the density matrix expansion. II. Full optimization and validation

NASA Astrophysics Data System (ADS)

Navarro Pérez, R.; Schunck, N.; Dyhdalo, A.; Furnstahl, R. J.; Bogner, S. K.

2018-05-01

Background: Energy density functional methods provide a generic framework to compute properties of atomic nuclei starting from models of nuclear potentials and the rules of quantum mechanics. Until now, the overwhelming majority of functionals have been constructed either from empirical nuclear potentials such as the Skyrme or Gogny forces, or from systematic gradient-like expansions in the spirit of the density functional theory for atoms. Purpose: We seek to obtain a usable form of the nuclear energy density functional that is rooted in the modern theory of nuclear forces. We thus consider a functional obtained from the density matrix expansion of local nuclear potentials from chiral effective field theory. We propose a parametrization of this functional carefully calibrated and validated on selected ground-state properties that is suitable for large-scale calculations of nuclear properties. Methods: Our energy functional comprises two main components. The first component is a non-local functional of the density and corresponds to the direct part (Hartree term) of the expectation value of local chiral potentials on a Slater determinant. Contributions to the mean field and the energy of this term are computed by expanding the spatial, finite-range components of the chiral potential onto Gaussian functions. The second component is a local functional of the density and is obtained by applying the density matrix expansion to the exchange part (Fock term) of the expectation value of the local chiral potential. We apply the UNEDF2 optimization protocol to determine the coupling constants of this energy functional. Results: We obtain a set of microscopically constrained functionals for local chiral potentials from leading order up to next-to-next-to-leading order with and without three-body forces and contributions from Δ excitations. These functionals are validated on the calculation of nuclear and neutron matter, nuclear mass tables, single-particle shell structure

Combinatorial fabrication and screening of organic light-emitting device arrays

NASA Astrophysics Data System (ADS)

Shinar, Joseph; Shinar, Ruth; Zhou, Zhaoqun

2007-11-01

The combinatorial fabrication and screening of 2-dimensional (2-d) small molecular UV-violet organic light-emitting device (OLED) arrays, 1-d blue-to-red arrays, 1-d intense white OLED libraries, 1-d arrays to study Förster energy transfer in guest-host OLEDs, and 2-d arrays to study exciplex emission from OLEDs is described. The results demonstrate the power of combinatorial approaches for screening OLED materials and configurations, and for studying their basic properties.

Dynamic Hierarchical Energy-Efficient Method Based on Combinatorial Optimization for Wireless Sensor Networks

PubMed Central

Tang, Hongying; Cheng, Yongbo; Zhao, Qin; Li, Baoqing; Yuan, Xiaobing

2017-01-01

Routing protocols based on topology control are significantly important for improving network longevity in wireless sensor networks (WSNs). Traditionally, some WSN routing protocols distribute uneven network traffic load to sensor nodes, which is not optimal for improving network longevity. Differently to conventional WSN routing protocols, we propose a dynamic hierarchical protocol based on combinatorial optimization (DHCO) to balance energy consumption of sensor nodes and to improve WSN longevity. For each sensor node, the DHCO algorithm obtains the optimal route by establishing a feasible routing set instead of selecting the cluster head or the next hop node. The process of obtaining the optimal route can be formulated as a combinatorial optimization problem. Specifically, the DHCO algorithm is carried out by the following procedures. It employs a hierarchy-based connection mechanism to construct a hierarchical network structure in which each sensor node is assigned to a special hierarchical subset; it utilizes the combinatorial optimization theory to establish the feasible routing set for each sensor node, and takes advantage of the maximum–minimum criterion to obtain their optimal routes to the base station. Various results of simulation experiments show effectiveness and superiority of the DHCO algorithm in comparison with state-of-the-art WSN routing algorithms, including low-energy adaptive clustering hierarchy (LEACH), hybrid energy-efficient distributed clustering (HEED), genetic protocol-based self-organizing network clustering (GASONeC), and double cost function-based routing (DCFR) algorithms. PMID:28753962

Dynamic Hierarchical Energy-Efficient Method Based on Combinatorial Optimization for Wireless Sensor Networks.

PubMed

Chang, Yuchao; Tang, Hongying; Cheng, Yongbo; Zhao, Qin; Yuan, Baoqing Li andXiaobing

2017-07-19

Routing protocols based on topology control are significantly important for improving network longevity in wireless sensor networks (WSNs). Traditionally, some WSN routing protocols distribute uneven network traffic load to sensor nodes, which is not optimal for improving network longevity. Differently to conventional WSN routing protocols, we propose a dynamic hierarchical protocol based on combinatorial optimization (DHCO) to balance energy consumption of sensor nodes and to improve WSN longevity. For each sensor node, the DHCO algorithm obtains the optimal route by establishing a feasible routing set instead of selecting the cluster head or the next hop node. The process of obtaining the optimal route can be formulated as a combinatorial optimization problem. Specifically, the DHCO algorithm is carried out by the following procedures. It employs a hierarchy-based connection mechanism to construct a hierarchical network structure in which each sensor node is assigned to a special hierarchical subset; it utilizes the combinatorial optimization theory to establish the feasible routing set for each sensor node, and takes advantage of the maximum-minimum criterion to obtain their optimal routes to the base station. Various results of simulation experiments show effectiveness and superiority of the DHCO algorithm in comparison with state-of-the-art WSN routing algorithms, including low-energy adaptive clustering hierarchy (LEACH), hybrid energy-efficient distributed clustering (HEED), genetic protocol-based self-organizing network clustering (GASONeC), and double cost function-based routing (DCFR) algorithms.

What Diagrams Argue in Late Imperial Chinese Combinatorial Texts.

PubMed

Bréard, Andrea

2015-01-01

Attitudes towards diagrammatic reasoning and visualization in mathematics were seldom spelled out in texts from pre-modern China, although illustrations figure prominently in mathematical literature since the eleventh century. Taking the sums of finite series and their combinatorial interpretation as a case study, this article investigates the epistemological function of illustrations from the eleventh to the nineteenth century that encode either the mathematical objects themselves or represent their related algorithms. It particularly focuses on the two illustrations given in Wang Lai's (1768-1813) Mathematical Principles of Sequential Combinations, arguing that they reflect a specific mode of nineteenth-century mathematical argumentative practice and served as a heuristic model for later authors.

Validation of an Instrument and Testing Protocol for Measuring the Combinatorial Analysis Schema.

ERIC Educational Resources Information Center

Staver, John R.; Harty, Harold

1979-01-01

Designs a testing situation to examine the presence of combinatorial analysis, to establish construct validity in the use of an instrument, Combinatorial Analysis Behavior Observation Scheme (CABOS), and to investigate the presence of the schema in young adolescents. (Author/GA)

Magnetic-Field Density-Functional Theory (BDFT): Lessons from the Adiabatic Connection.

PubMed

Reimann, Sarah; Borgoo, Alex; Tellgren, Erik I; Teale, Andrew M; Helgaker, Trygve

2017-09-12

We study the effects of magnetic fields in the context of magnetic field density-functional theory (BDFT), where the energy is a functional of the electron density ρ and the magnetic field B. We show that this approach is a worthwhile alternative to current-density functional theory (CDFT) and may provide a viable route to the study of many magnetic phenomena using density-functional theory (DFT). The relationship between BDFT and CDFT is developed and clarified within the framework of the four-way correspondence of saddle functions and their convex and concave parents in convex analysis. By decomposing the energy into its Kohn-Sham components, we demonstrate that the magnetizability is mainly determined by those energy components that are related to the density. For existing density functional approximations, this implies that, for the magnetizability, improvements of the density will be more beneficial than introducing a magnetic-field dependence in the correlation functional. However, once a good charge density is achieved, we show that high accuracy is likely only obtainable by including magnetic-field dependence. We demonstrate that adiabatic-connection (AC) curves at different field strengths resemble one another closely provided each curve is calculated at the equilibrium geometry of that field strength. In contrast, if all AC curves are calculated at the equilibrium geometry of the field-free system, then the curves change strongly with increasing field strength due to the increasing importance of static correlation. This holds also for density functional approximations, for which we demonstrate that the main error encountered in the presence of a field is already present at zero field strength, indicating that density-functional approximations may be applied to systems in strong fields, without the need to treat additional static correlation.

MARCC (Matrix-Assisted Reader Chromatin Capture): an antibody-free method to enrich and analyze combinatorial nucleosome modifications

PubMed Central

Su, Zhangli

2016-01-01

Combinatorial patterns of histone modifications are key indicators of different chromatin states. Most of the current approaches rely on the usage of antibodies to analyze combinatorial histone modifications. Here we detail an antibody-free method named MARCC (Matrix-Assisted Reader Chromatin Capture) to enrich combinatorial histone modifications. The combinatorial patterns are enriched on native nucleosomes extracted from cultured mammalian cells and prepared by micrococcal nuclease digestion. Such enrichment is achieved by recombinant chromatin-interacting protein modules, or so-called reader domains, which can bind in a combinatorial modification-dependent manner. The enriched chromatin can be quantified by western blotting or mass spectrometry for the co-existence of histone modifications, while the associated DNA content can be analyzed by qPCR or next-generation sequencing. Altogether, MARCC provides a reproducible, efficient and customizable solution to enrich and analyze combinatorial histone modifications. PMID:26131849

Probability density function learning by unsupervised neurons.

PubMed

Fiori, S

2001-10-01

In a recent work, we introduced the concept of pseudo-polynomial adaptive activation function neuron (FAN) and presented an unsupervised information-theoretic learning theory for such structure. The learning model is based on entropy optimization and provides a way of learning probability distributions from incomplete data. The aim of the present paper is to illustrate some theoretical features of the FAN neuron, to extend its learning theory to asymmetrical density function approximation, and to provide an analytical and numerical comparison with other known density function estimation methods, with special emphasis to the universal approximation ability. The paper also provides a survey of PDF learning from incomplete data, as well as results of several experiments performed on real-world problems and signals.

Combinatorial application of two aldehyde oxidoreductases on isobutanol production in the presence of furfural.

PubMed

Seo, Hyung-Min; Jeon, Jong-Min; Lee, Ju Hee; Song, Hun-Suk; Joo, Han-Byul; Park, Sung-Hee; Choi, Kwon-Young; Kim, Yong Hyun; Park, Kyungmoon; Ahn, Jungoh; Lee, Hongweon; Yang, Yung-Hun

2016-01-01

Furfural is a toxic by-product formulated from pretreatment processes of lignocellulosic biomass. In order to utilize the lignocellulosic biomass on isobutanol production, inhibitory effect of the furfural on isobutanol production was investigated and combinatorial application of two oxidoreductases, FucO and YqhD, was suggested as an alternative strategy. Furfural decreased cell growth and isobutanol production when only YqhD or FucO was employed as an isobutyraldehyde oxidoreductase. However, combinatorial overexpression of FucO and YqhD could overcome the inhibitory effect of furfural giving higher isobutanol production by 110% compared with overexpression of YqhD. The combinatorial oxidoreductases increased furfural detoxification rate 2.1-fold and also accelerated glucose consumption 1.4-fold. When it compares to another known system increasing furfural tolerance, membrane-bound transhydrogenase (pntAB), the combinatorial aldehyde oxidoreductases were better on cell growth and production. Thus, to control oxidoreductases is important to produce isobutanol using furfural-containing biomass and the combinatorial overexpression of FucO and YqhD can be an alternative strategy.

Multi-Objectivising Combinatorial Optimisation Problems by Means of Elementary Landscape Decompositions.

PubMed

Ceberio, Josu; Calvo, Borja; Mendiburu, Alexander; Lozano, Jose A

2018-02-15

In the last decade, many works in combinatorial optimisation have shown that, due to the advances in multi-objective optimisation, the algorithms from this field could be used for solving single-objective problems as well. In this sense, a number of papers have proposed multi-objectivising single-objective problems in order to use multi-objective algorithms in their optimisation. In this article, we follow up this idea by presenting a methodology for multi-objectivising combinatorial optimisation problems based on elementary landscape decompositions of their objective function. Under this framework, each of the elementary landscapes obtained from the decomposition is considered as an independent objective function to optimise. In order to illustrate this general methodology, we consider four problems from different domains: the quadratic assignment problem and the linear ordering problem (permutation domain), the 0-1 unconstrained quadratic optimisation problem (binary domain), and the frequency assignment problem (integer domain). We implemented two widely known multi-objective algorithms, NSGA-II and SPEA2, and compared their performance with that of a single-objective GA. The experiments conducted on a large benchmark of instances of the four problems show that the multi-objective algorithms clearly outperform the single-objective approaches. Furthermore, a discussion on the results suggests that the multi-objective space generated by this decomposition enhances the exploration ability, thus permitting NSGA-II and SPEA2 to obtain better results in the majority of the tested instances.

Density-Decomposed Orbital-Free Density Functional Theory for Covalent Systems and Application to Li-Si alloys

NASA Astrophysics Data System (ADS)

Xia, Junchao; Carter, Emily

2014-03-01

We propose a density decomposition scheme using a Wang-Govind-Carter (WGC)-based kinetic energy density functional (KEDF) to accurately and efficiently simulate covalent systems within orbital-free (OF) density functional theory (DFT). By using a local, density-dependent scale function, the total density is decomposed into a localized density within covalent bond regions and a flattened delocalized density, with the former described by semilocal KEDFs and the latter treated by the WGC KEDF. The new model predicts reasonable equilibrium volumes, bulk moduli, and phase ordering energies for various semiconductors compared to Kohn-Sham (KS) DFT benchmarks. The surface energy of Si(100) also agrees well with KSDFT. We further apply the model to study mechanical properties of Li-Si alloys, which have been recently recognized as a promising candidate for next-generation anodes of Li-ion batteries with outstanding capacity. We study multiple crystalline Li-Si alloys. The WGCD KEDF predicts accurate cell lattice vectors, equilibrium volumes, elastic moduli, electron densities, alloy formation and Li adsorption energies. Because of its quasilinear scaling, coupled with the level of accuracy shown here, OFDFT appears quite promising for large-scale simulation of such materials phenomena. Office of Naval Research, National Science Foundation, Tigress High Performance Computing Center.

Combinatorial study of zinc tin oxide thin-film transistors

NASA Astrophysics Data System (ADS)

McDowell, M. G.; Sanderson, R. J.; Hill, I. G.

2008-01-01

Groups of thin-film transistors using a zinc tin oxide semiconductor layer have been fabricated via a combinatorial rf sputtering technique. The ZnO :SnO2 ratio of the film varies as a function of position on the sample, from pure ZnO to SnO2, allowing for a study of zinc tin oxide transistor performance as a function of channel stoichiometry. The devices were found to have mobilities ranging from 2to12cm2/Vs, with two peaks in mobility in devices at ZnO fractions of 0.80±0.03 and 0.25±0.05, and on/off ratios as high as 107. Transistors composed predominantly of SnO2 were found to exhibit light sensitivity which affected both the on/off ratios and threshold voltages of these devices.

Course 4: Density Functional Theory, Methods, Techniques, and Applications

NASA Astrophysics Data System (ADS)

Chrétien, S.; Salahub, D. R.

Contents 1 Introduction 2 Density functional theory 2.1 Hohenberg and Kohn theorems 2.2 Levy's constrained search 2.3 Kohn-Sham method 3 Density matrices and pair correlation functions 4 Adiabatic connection or coupling strength integration 5 Comparing and constrasting KS-DFT and HF-CI 6 Preparing new functionals 7 Approximate exchange and correlation functionals 7.1 The Local Spin Density Approximation (LSDA) 7.2 Gradient Expansion Approximation (GEA) 7.3 Generalized Gradient Approximation (GGA) 7.4 meta-Generalized Gradient Approximation (meta-GGA) 7.5 Hybrid functionals 7.6 The Optimized Effective Potential method (OEP) 7.7 Comparison between various approximate functionals 8 LAP correlation functional 9 Solving the Kohn-Sham equations 9.1 The Kohn-Sham orbitals 9.2 Coulomb potential 9.3 Exchange-correlation potential 9.4 Core potential 9.5 Other choices and sources of error 9.6 Functionality 10 Applications 10.1 Ab initio molecular dynamics for an alanine dipeptide model 10.2 Transition metal clusters: The ecstasy, and the agony... 10.3 The conversion of acetylene to benzene on Fe clusters 11 Conclusions

A classical density functional theory of ionic liquids.

PubMed

Forsman, Jan; Woodward, Clifford E; Trulsson, Martin

2011-04-28

We present a simple, classical density functional approach to the study of simple models of room temperature ionic liquids. Dispersion attractions as well as ion correlation effects and excluded volume packing are taken into account. The oligomeric structure, common to many ionic liquid molecules, is handled by a polymer density functional treatment. The theory is evaluated by comparisons with simulations, with an emphasis on the differential capacitance, an experimentally measurable quantity of significant practical interest.

Simulating the component counts of combinatorial structures.

PubMed

Arratia, Richard; Barbour, A D; Ewens, W J; Tavaré, Simon

2018-02-09

This article describes and compares methods for simulating the component counts of random logarithmic combinatorial structures such as permutations and mappings. We exploit the Feller coupling for simulating permutations to provide a very fast method for simulating logarithmic assemblies more generally. For logarithmic multisets and selections, this approach is replaced by an acceptance/rejection method based on a particular conditioning relationship that represents the distribution of the combinatorial structure as that of independent random variables conditioned on a weighted sum. We show how to improve its acceptance rate. We illustrate the method by estimating the probability that a random mapping has no repeated component sizes, and establish the asymptotic distribution of the difference between the number of components and the number of distinct component sizes for a very general class of logarithmic structures. Copyright © 2018. Published by Elsevier Inc.

Generation of Synthetic Copolymer Libraries by Combinatorial Assembly on Nucleic Acid Templates.

PubMed

Kong, Dehui; Yeung, Wayland; Hili, Ryan

2016-07-11

Recent advances in nucleic acid-templated copolymerization have expanded the scope of sequence-controlled synthetic copolymers beyond the molecular architectures witnessed in nature. This has enabled the power of molecular evolution to be applied to synthetic copolymer libraries to evolve molecular function ranging from molecular recognition to catalysis. This Review seeks to summarize different approaches available to generate sequence-defined monodispersed synthetic copolymer libraries using nucleic acid-templated polymerization. Key concepts and principles governing nucleic acid-templated polymerization, as well as the fidelity of various copolymerization technologies, will be described. The Review will focus on methods that enable the combinatorial generation of copolymer libraries and their molecular evolution for desired function.

Self-contained filtered density function

DOE PAGES

Nouri, Arash G.; Nik, Mehdi B.; Givi, Pope; ...

2017-09-18

The filtered density function (FDF) closure is extended to a “self-contained” format to include the subgrid-scale (SGS) statistics of all of the hydro-thermo-chemical variables in turbulent flows. These are the thermodynamic pressure, the specific internal energy, the velocity vector, and the composition field. In this format, the model is comprehensive and facilitates large-eddy simulation (LES) of flows at both low and high compressibility levels. A transport equation is developed for the joint pressure-energy-velocity-composition filtered mass density function (PEVC-FMDF). In this equation, the effect of convection appears in closed form. The coupling of the hydrodynamics and thermochemistry is modeled via amore » set of stochastic differential equation for each of the transport variables. This yields a self-contained SGS closure. We demonstrated how LES is conducted of a turbulent shear flow with transport of a passive scalar. Finally, the consistency of the PEVC-FMDF formulation is established, and its overall predictive capability is appraised via comparison with direct numerical simulation (DNS) data.« less

Self-contained filtered density function

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

Nouri, Arash G.; Nik, Mehdi B.; Givi, Pope

The filtered density function (FDF) closure is extended to a “self-contained” format to include the subgrid-scale (SGS) statistics of all of the hydro-thermo-chemical variables in turbulent flows. These are the thermodynamic pressure, the specific internal energy, the velocity vector, and the composition field. In this format, the model is comprehensive and facilitates large-eddy simulation (LES) of flows at both low and high compressibility levels. A transport equation is developed for the joint pressure-energy-velocity-composition filtered mass density function (PEVC-FMDF). In this equation, the effect of convection appears in closed form. The coupling of the hydrodynamics and thermochemistry is modeled via amore » set of stochastic differential equation for each of the transport variables. This yields a self-contained SGS closure. We demonstrated how LES is conducted of a turbulent shear flow with transport of a passive scalar. Finally, the consistency of the PEVC-FMDF formulation is established, and its overall predictive capability is appraised via comparison with direct numerical simulation (DNS) data.« less

Evaluating the Effect of Peptoid Lipophilicity on Antimicrobial Potency, Cytotoxicity, and Combinatorial Library Design.

PubMed

Turkett, Jeremy A; Bicker, Kevin L

2017-04-10

Growing prevalence of antibiotic resistant bacterial infections necessitates novel antimicrobials, which could be rapidly identified from combinatorial libraries. We report the use of the peptoid library agar diffusion (PLAD) assay to screen peptoid libraries against the ESKAPE pathogens, including the optimization of assay conditions for each pathogen. Work presented here focuses on the tailoring of combinatorial peptoid library design through a detailed study of how peptoid lipophilicity relates to antibacterial potency and mammalian cell toxicity. The information gleaned from this optimization was then applied using the aforementioned screening method to examine the relative potency of peptoid libraries against Staphylococcus aureus, Acinetobacter baumannii, and Enterococcus faecalis prior to and following functionalization with long alkyl tails. The data indicate that overall peptoid hydrophobicity and not simply alkyl tail length is strongly correlated with mammalian cell toxicity. Furthermore, this work demonstrates the utility of the PLAD assay in rapidly evaluating the effect of molecular property changes in similar libraries.

Combinatorial delivery of small interfering RNAs reduces RNAi efficacy by selective incorporation into RISC

PubMed Central

Castanotto, Daniela; Sakurai, Kumi; Lingeman, Robert; Li, Haitang; Shively, Louise; Aagaard, Lars; Soifer, Harris; Gatignol, Anne; Riggs, Arthur; Rossi, John J.

2007-01-01

Despite the great potential of RNAi, ectopic expression of shRNA or siRNAs holds the inherent risk of competition for critical RNAi components, thus altering the regulatory functions of some cellular microRNAs. In addition, specific siRNA sequences can potentially hinder incorporation of other siRNAs when used in a combinatorial approach. We show that both synthetic siRNAs and expressed shRNAs compete against each other and with the endogenous microRNAs for transport and for incorporation into the RNA induced silencing complex (RISC). The same siRNA sequences do not display competition when expressed from a microRNA backbone. We also show that TAR RNA binding protein (TRBP) is one of the sensors for selection and incorporation of the guide sequence of interfering RNAs. These findings reveal that combinatorial siRNA approaches can be problematic and have important implications for the methodology of expression and use of therapeutic interfering RNAs. PMID:17660190

Multiconfiguration Pair-Density Functional Theory Is Free From Delocalization Error.

PubMed

Bao, Junwei Lucas; Wang, Ying; He, Xiao; Gagliardi, Laura; Truhlar, Donald G

2017-11-16

Delocalization error has been singled out by Yang and co-workers as the dominant error in Kohn-Sham density functional theory (KS-DFT) with conventional approximate functionals. In this Letter, by computing the vertical first ionization energy for well separated He clusters, we show that multiconfiguration pair-density functional theory (MC-PDFT) is free from delocalization error. To put MC-PDFT in perspective, we also compare it with some Kohn-Sham density functionals, including both traditional and modern functionals. Whereas large delocalization errors are almost universal in KS-DFT (the only exception being the very recent corrected functionals of Yang and co-workers), delocalization error is removed by MC-PDFT, which bodes well for its future as a step forward from KS-DFT.

Ensemble density variational methods with self- and ghost-interaction-corrected functionals

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

Pastorczak, Ewa; Pernal, Katarzyna, E-mail: pernalk@gmail.com

2014-05-14

Ensemble density functional theory (DFT) offers a way of predicting excited-states energies of atomic and molecular systems without referring to a density response function. Despite a significant theoretical work, practical applications of the proposed approximations have been scarce and they do not allow for a fair judgement of the potential usefulness of ensemble DFT with available functionals. In the paper, we investigate two forms of ensemble density functionals formulated within ensemble DFT framework: the Gross, Oliveira, and Kohn (GOK) functional proposed by Gross et al. [Phys. Rev. A 37, 2809 (1988)] alongside the orbital-dependent eDFT form of the functional introducedmore » by Nagy [J. Phys. B 34, 2363 (2001)] (the acronym eDFT proposed in analogy to eHF – ensemble Hartree-Fock method). Local and semi-local ground-state density functionals are employed in both approaches. Approximate ensemble density functionals contain not only spurious self-interaction but also the so-called ghost-interaction which has no counterpart in the ground-state DFT. We propose how to correct the GOK functional for both kinds of interactions in approximations that go beyond the exact-exchange functional. Numerical applications lead to a conclusion that functionals free of the ghost-interaction by construction, i.e., eDFT, yield much more reliable results than approximate self- and ghost-interaction-corrected GOK functional. Additionally, local density functional corrected for self-interaction employed in the eDFT framework yields excitations energies of the accuracy comparable to that of the uncorrected semi-local eDFT functional.« less

Students' Verification Strategies for Combinatorial Problems

ERIC Educational Resources Information Center

Mashiach Eizenberg, Michal; Zaslavsky, Orit

2004-01-01

We focus on a major difficulty in solving combinatorial problems, namely, on the verification of a solution. Our study aimed at identifying undergraduate students' tendencies to verify their solutions, and the verification strategies that they employ when solving these problems. In addition, an attempt was made to evaluate the level of efficiency…

Counting Pizza Pieces and Other Combinatorial Problems.

ERIC Educational Resources Information Center

Maier, Eugene

1988-01-01

The general combinatorial problem of counting the number of regions into which the interior of a circle is divided by a family of lines is considered. A general formula is developed and its use is illustrated in two situations. (PK)

Density-functional energy gaps of solids demystified

NASA Astrophysics Data System (ADS)

Perdew, John P.; Ruzsinszky, Adrienn

2018-06-01

The fundamental energy gap of a solid is a ground-state second energy difference. Can one find the fundamental gap from the gap in the band structure of Kohn-Sham density functional theory? An argument of Williams and von Barth (WB), 1983, suggests that one can. In fact, self-consistent band-structure calculations within the local density approximation or the generalized gradient approximation (GGA) yield the fundamental gap within the same approximation for the energy. Such a calculation with the exact density functional would yield a band gap that also underestimates the fundamental gap, because the exact Kohn-Sham potential in a solid jumps up by an additive constant when one electron is added, and the WB argument does not take this effect into account. The WB argument has been extended recently to generalized Kohn-Sham theory, the simplest way to implement meta-GGAs and hybrid functionals self-consistently, with an exchange-correlation potential that is a non-multiplication operator. Since this operator is continuous, the band gap is again the fundamental gap within the same approximation, but, because the approximations are more realistic, so is the band gap. What approximations might be even more realistic?

Recent progress in density functional theory

NASA Astrophysics Data System (ADS)

Truhlar, Donald

2014-03-01

Ongoing work involves several areas of density functional theory: new methods for computing electronic excitation energies, including a new way to remove spin contamination in the spin-flip Tamm-Dancoff approximation and a configuration-interaction-corrected Tamm-Dancoff Approximation for treating conical intersections; new ways to treat open-shell states, including a reinterpreted broken-symmetry method and multi-configuration Kohn-Sham theory; a new exchange-correlation functional; new tests of density functional theory against databases for electronic transition energies and molecules and solids containing metal atoms; and applications. A selection of results will be presented. I am grateful to the following collaborators for contributions to the ongoing work: Boris Averkiev, Rebecca Carlson, Laura Fernandez, Laura Gagliardi, Chad Hoyer, Francesc Illas, Miho Isegawa, Shaohong Li, Giovanni Li Manni, Sijie Luo, Dongxia Ma, Remi Maurice, Rubén Means-Pañeda, Roberto Peverati, Nora Planas, Prasenjit Seal, Pragya Verma, Bo Wang, Xuefei Xu, Ke R. Yang, Haoyu Yu, Wenjing Zhang, and Jingjing Zheng. Supported in part by the AFOSR and U.S. DOE.

Optimization of constrained density functional theory

NASA Astrophysics Data System (ADS)

O'Regan, David D.; Teobaldi, Gilberto

2016-07-01

Constrained density functional theory (cDFT) is a versatile electronic structure method that enables ground-state calculations to be performed subject to physical constraints. It thereby broadens their applicability and utility. Automated Lagrange multiplier optimization is necessary for multiple constraints to be applied efficiently in cDFT, for it to be used in tandem with geometry optimization, or with molecular dynamics. In order to facilitate this, we comprehensively develop the connection between cDFT energy derivatives and response functions, providing a rigorous assessment of the uniqueness and character of cDFT stationary points while accounting for electronic interactions and screening. In particular, we provide a nonperturbative proof that stable stationary points of linear density constraints occur only at energy maxima with respect to their Lagrange multipliers. We show that multiple solutions, hysteresis, and energy discontinuities may occur in cDFT. Expressions are derived, in terms of convenient by-products of cDFT optimization, for quantities such as the dielectric function and a condition number quantifying ill definition in multiple constraint cDFT.

An Indexed Combinatorial Library: The Synthesis and Testing of Insect Repellents

NASA Astrophysics Data System (ADS)

Miles, William H.; Gelato, Kathy A.; Pompizzi, Kristen M.; Scarbinsky, Aislinn M.; Albrecht, Brian K.; Reynolds, Elaine R.

2001-04-01

An indexed combinatorial library of amides was prepared by the reaction of amines and acid chlorides. A simple test for insect repellency using fruit flies (Drosophila melanogaster) allowed the determination of the most repellent sublibraries. The student-generated data were collected and analyzed to determine the most active amide(s) in the library. This experiment illustrates the fundamentals of combinatorial chemistry, a field that has undergone explosive growth in the last decade.

Linear-response time-dependent density-functional theory with pairing fields.

PubMed

Peng, Degao; van Aggelen, Helen; Yang, Yang; Yang, Weitao

2014-05-14

Recent development in particle-particle random phase approximation (pp-RPA) broadens the perspective on ground state correlation energies [H. van Aggelen, Y. Yang, and W. Yang, Phys. Rev. A 88, 030501 (2013), Y. Yang, H. van Aggelen, S. N. Steinmann, D. Peng, and W. Yang, J. Chem. Phys. 139, 174110 (2013); D. Peng, S. N. Steinmann, H. van Aggelen, and W. Yang, J. Chem. Phys. 139, 104112 (2013)] and N ± 2 excitation energies [Y. Yang, H. van Aggelen, and W. Yang, J. Chem. Phys. 139, 224105 (2013)]. So far Hartree-Fock and approximated density-functional orbitals have been utilized to evaluate the pp-RPA equation. In this paper, to further explore the fundamentals and the potential use of pairing matrix dependent functionals, we present the linear-response time-dependent density-functional theory with pairing fields with both adiabatic and frequency-dependent kernels. This theory is related to the density-functional theory and time-dependent density-functional theory for superconductors, but is applied to normal non-superconducting systems for our purpose. Due to the lack of the proof of the one-to-one mapping between the pairing matrix and the pairing field for time-dependent systems, the linear-response theory is established based on the representability assumption of the pairing matrix. The linear response theory justifies the use of approximated density-functionals in the pp-RPA equation. This work sets the fundamentals for future density-functional development to enhance the description of ground state correlation energies and N ± 2 excitation energies.

More Combinatorial Proofs via Flagpole Arrangements

ERIC Educational Resources Information Center

DeTemple, Duane; Reynolds, H. David, II

2006-01-01

Combinatorial identities are proved by counting the number of arrangements of a flagpole and guy wires on a row of blocks that satisfy a set of conditions. An identity is proved by first deriving and then equating two expressions that each count the number of permissible arrangements. Identities for binomial coefficients and recursion relations…

Assessing Density Functionals Using Many Body Theory for Hybrid Perovskites

NASA Astrophysics Data System (ADS)

Bokdam, Menno; Lahnsteiner, Jonathan; Ramberger, Benjamin; Schäfer, Tobias; Kresse, Georg

2017-10-01

Which density functional is the "best" for structure simulations of a particular material? A concise, first principles, approach to answer this question is presented. The random phase approximation (RPA)—an accurate many body theory—is used to evaluate various density functionals. To demonstrate and verify the method, we apply it to the hybrid perovskite MAPbI3 , a promising new solar cell material. The evaluation is done by first creating finite temperature ensembles for small supercells using RPA molecular dynamics, and then evaluating the variance between the RPA and various approximate density functionals for these ensembles. We find that, contrary to recent suggestions, van der Waals functionals do not improve the description of the material, whereas hybrid functionals and the strongly constrained appropriately normed (SCAN) density functional yield very good agreement with the RPA. Finally, our study shows that in the room temperature tetragonal phase of MAPbI3 , the molecules are preferentially parallel to the shorter lattice vectors but reorientation on ps time scales is still possible.

Cryptographic Combinatorial Securities Exchanges

NASA Astrophysics Data System (ADS)

Thorpe, Christopher; Parkes, David C.

We present a useful new mechanism that facilitates the atomic exchange of many large baskets of securities in a combinatorial exchange. Cryptography prevents information about the securities in the baskets from being exploited, enhancing trust. Our exchange offers institutions who wish to trade large positions a new alternative to existing methods of block trading: they can reduce transaction costs by taking advantage of other institutions’ available liquidity, while third party liquidity providers guarantee execution—preserving their desired portfolio composition at all times. In our exchange, institutions submit encrypted orders which are crossed, leaving a “remainder”. The exchange proves facts about the portfolio risk of this remainder to third party liquidity providers without revealing the securities in the remainder, the knowledge of which could also be exploited. The third parties learn either (depending on the setting) the portfolio risk parameters of the remainder itself, or how their own portfolio risk would change if they were to incorporate the remainder into a portfolio they submit. In one setting, these third parties submit bids on the commission, and the winner supplies necessary liquidity for the entire exchange to clear. This guaranteed clearing, coupled with external price discovery from the primary markets for the securities, sidesteps difficult combinatorial optimization problems. This latter method of proving how taking on the remainder would change risk parameters of one’s own portfolio, without revealing the remainder’s contents or its own risk parameters, is a useful protocol of independent interest.

Accelerating large scale Kohn-Sham density functional theory calculations with semi-local functionals and hybrid functionals

NASA Astrophysics Data System (ADS)

Lin, Lin

The computational cost of standard Kohn-Sham density functional theory (KSDFT) calculations scale cubically with respect to the system size, which limits its use in large scale applications. In recent years, we have developed an alternative procedure called the pole expansion and selected inversion (PEXSI) method. The PEXSI method solves KSDFT without solving any eigenvalue and eigenvector, and directly evaluates physical quantities including electron density, energy, atomic force, density of states, and local density of states. The overall algorithm scales as at most quadratically for all materials including insulators, semiconductors and the difficult metallic systems. The PEXSI method can be efficiently parallelized over 10,000 - 100,000 processors on high performance machines. The PEXSI method has been integrated into a number of community electronic structure software packages such as ATK, BigDFT, CP2K, DGDFT, FHI-aims and SIESTA, and has been used in a number of applications with 2D materials beyond 10,000 atoms. The PEXSI method works for LDA, GGA and meta-GGA functionals. The mathematical structure for hybrid functional KSDFT calculations is significantly different. I will also discuss recent progress on using adaptive compressed exchange method for accelerating hybrid functional calculations. DOE SciDAC Program, DOE CAMERA Program, LBNL LDRD, Sloan Fellowship.

Postfragmentation density function for bacterial aggregates in laminar flow.

PubMed

Byrne, Erin; Dzul, Steve; Solomon, Michael; Younger, John; Bortz, David M

2011-04-01

The postfragmentation probability density of daughter flocs is one of the least well-understood aspects of modeling flocculation. We use three-dimensional positional data of Klebsiella pneumoniae bacterial flocs in suspension and the knowledge of hydrodynamic properties of a laminar flow field to construct a probability density function of floc volumes after a fragmentation event. We provide computational results which predict that the primary fragmentation mechanism for large flocs is erosion. The postfragmentation probability density function has a strong dependence on the size of the original floc and indicates that most fragmentation events result in clumps of one to three bacteria eroding from the original floc. We also provide numerical evidence that exhaustive fragmentation yields a limiting density inconsistent with the log-normal density predicted in the literature, most likely due to the heterogeneous nature of K. pneumoniae flocs. To support our conclusions, artificial flocs were generated and display similar postfragmentation density and exhaustive fragmentation. ©2011 American Physical Society

Postfragmentation density function for bacterial aggregates in laminar flow

PubMed Central

Byrne, Erin; Dzul, Steve; Solomon, Michael; Younger, John

2014-01-01

The postfragmentation probability density of daughter flocs is one of the least well-understood aspects of modeling flocculation. We use three-dimensional positional data of Klebsiella pneumoniae bacterial flocs in suspension and the knowledge of hydrodynamic properties of a laminar flow field to construct a probability density function of floc volumes after a fragmentation event. We provide computational results which predict that the primary fragmentation mechanism for large flocs is erosion. The postfragmentation probability density function has a strong dependence on the size of the original floc and indicates that most fragmentation events result in clumps of one to three bacteria eroding from the original floc. We also provide numerical evidence that exhaustive fragmentation yields a limiting density inconsistent with the log-normal density predicted in the literature, most likely due to the heterogeneous nature of K. pneumoniae flocs. To support our conclusions, artificial flocs were generated and display similar postfragmentation density and exhaustive fragmentation. PMID:21599205

A combinatorial perspective of the protein inference problem.

PubMed

Yang, Chao; He, Zengyou; Yu, Weichuan

2013-01-01

In a shotgun proteomics experiment, proteins are the most biologically meaningful output. The success of proteomics studies depends on the ability to accurately and efficiently identify proteins. Many methods have been proposed to facilitate the identification of proteins from peptide identification results. However, the relationship between protein identification and peptide identification has not been thoroughly explained before. In this paper, we devote ourselves to a combinatorial perspective of the protein inference problem. We employ combinatorial mathematics to calculate the conditional protein probabilities (protein probability means the probability that a protein is correctly identified) under three assumptions, which lead to a lower bound, an upper bound, and an empirical estimation of protein probabilities, respectively. The combinatorial perspective enables us to obtain an analytical expression for protein inference. Our method achieves comparable results with ProteinProphet in a more efficient manner in experiments on two data sets of standard protein mixtures and two data sets of real samples. Based on our model, we study the impact of unique peptides and degenerate peptides (degenerate peptides are peptides shared by at least two proteins) on protein probabilities. Meanwhile, we also study the relationship between our model and ProteinProphet. We name our program ProteinInfer. Its Java source code, our supplementary document and experimental results are available at: >http://bioinformatics.ust.hk/proteininfer.

Estimating meme fitness in adaptive memetic algorithms for combinatorial problems.

PubMed

Smith, J E

2012-01-01

Among the most promising and active research areas in heuristic optimisation is the field of adaptive memetic algorithms (AMAs). These gain much of their reported robustness by adapting the probability with which each of a set of local improvement operators is applied, according to an estimate of their current value to the search process. This paper addresses the issue of how the current value should be estimated. Assuming the estimate occurs over several applications of a meme, we consider whether the extreme or mean improvements should be used, and whether this aggregation should be global, or local to some part of the solution space. To investigate these issues, we use the well-established COMA framework that coevolves the specification of a population of memes (representing different local search algorithms) alongside a population of candidate solutions to the problem at hand. Two very different memetic algorithms are considered: the first using adaptive operator pursuit to adjust the probabilities of applying a fixed set of memes, and a second which applies genetic operators to dynamically adapt and create memes and their functional definitions. For the latter, especially on combinatorial problems, credit assignment mechanisms based on historical records, or on notions of landscape locality, will have limited application, and it is necessary to estimate the value of a meme via some form of sampling. The results on a set of binary encoded combinatorial problems show that both methods are very effective, and that for some problems it is necessary to use thousands of variables in order to tease apart the differences between different reward schemes. However, for both memetic algorithms, a significant pattern emerges that reward based on mean improvement is better than that based on extreme improvement. This contradicts recent findings from adapting the parameters of operators involved in global evolutionary search. The results also show that local reward schemes

Linking density functional and mode coupling models for supercooled liquids

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

Premkumar, Leishangthem; Bidhoodi, Neeta; Das, Shankar P.

2016-03-28

We compare predictions from two familiar models of the metastable supercooled liquid, respectively, constructed with thermodynamic and dynamic approaches. In the so called density functional theory the free energy F[ρ] of the liquid is a functional of the inhomogeneous density ρ(r). The metastable state is identified as a local minimum of F[ρ]. The sharp density profile characterizing ρ(r) is identified as a single particle oscillator, whose frequency is obtained from the parameters of the optimum density function. On the other hand, a dynamic approach to supercooled liquids is taken in the mode coupling theory (MCT) which predict a sharp ergodicity-non-ergodicitymore » transition at a critical density. The single particle dynamics in the non-ergodic state, treated approximately, represents a propagating mode whose characteristic frequency is computed from the corresponding memory function of the MCT. The mass localization parameters in the above two models (treated in their simplest forms) are obtained, respectively, in terms of the corresponding natural frequencies depicted and are shown to have comparable magnitudes.« less

Multifunctionalized biocatalytic P22 nanoreactor for combinatory treatment of ER+ breast cancer.

PubMed

Chauhan, Kanchan; Hernandez-Meza, Juan M; Rodríguez-Hernández, Ana G; Juarez-Moreno, Karla; Sengar, Prakhar; Vazquez-Duhalt, Rafael

2018-02-20

Tamoxifen is the standard endocrine therapy for breast cancers, which require metabolic activation by cytochrome P450 enzymes (CYP). However, the lower and variable concentrations of CYP activity at the tumor remain major bottlenecks for the efficient treatment, causing severe side-effects. Combination nanotherapy has gained much recent attention for cancer treatment as it reduces the drug-associated toxicity without affecting the therapeutic response. Here we show the modular design of P22 bacteriophage virus-like particles for nanoscale integration of virus-driven enzyme prodrug therapy and photodynamic therapy. These virus capsids carrying CYP activity at the core are decorated with photosensitizer and targeting moiety at the surface for effective combinatory treatment. The estradiol-functionalized nanoparticles are recognized and internalized into ER+ breast tumor cells increasing the intracellular CYP activity and showing the ability to produce reactive oxygen species (ROS) upon UV 365 nm irradiation. The generated ROS in synergy with enzymatic activity drastically enhanced the tamoxifen sensitivity in vitro, strongly inhibiting tumor cells. This work clearly demonstrated that the targeted combinatory treatment using multifunctional biocatalytic P22 represents the effective nanotherapeutics for ER+ breast cancer.

Developing Thermal Density Functional Theory Using the Asymmetric Hubbard Dimer

NASA Astrophysics Data System (ADS)

Smith, Justin Clifford

In this dissertation, I introduce both ground-state and thermal density functional theory. Throughout I use the asymmetric two-site Hubbard model, called the Hubbard dimer for short, to better understand and/or develop these theories. This model is used because it can be solved analytically and it contains all the necessary physics while still being conceptually simple enough to tease apart the various aspects of density functional theory. Ground-state density functional theory has seen broad use in many disciplines including physics, chemistry, geology, and material science and has led to a number of important physical and technological successes. In the first two chapters I elucidate the behavior of the ground-state theory using the Hubbard dimer. The simplicity of the model allows me to showcase aspects of the theory that are common points of confusion within the electronic structure community, e.g. the fundamental gap problem. The next two chapters focus on thermal density functional theory which has been coming to prominence as the study of warm dense matter has become a growing interest at the national laboratories and in the astronomical body community. The Hubbard dimer allows me to do the first ever exact thermal density functional theory calculation. In this work I am better able to understand the approximations used in thermal density functional theory and can point to why they succeed and fail. This also allows me to illustrate old conditions and derive new ones. I conclude with an overview of the work and a few different directions in which the asymmetric Hubbard dimer could be used further.

"Anticlumping" and Other Combinatorial Effects on Clumped Isotopes: Implications for Tracing Biogeochemical Cycling

NASA Astrophysics Data System (ADS)

Yeung, L.

2015-12-01

I present a mode of isotopic ordering that has purely combinatorial origins. It can be important when identical rare isotopes are paired by coincidence (e.g., they are neighbors on the same molecule), or when extrinsic factors govern the isotopic composition of the two atoms that share a chemical bond. By itself, combinatorial isotope pairing yields products with isotopes either randomly distributed or with a deficit relative to a random distribution of isotopes. These systematics arise because of an unconventional coupling between the formation of singly- and multiply-substituted isotopic moieties. In a random distribution, rare isotopes are symmetrically distributed: Single isotopic substitutions (e.g., H‒D and D‒H in H2) occur with equal probability, and double isotopic substitutions (e.g., D2) occur according to random chance. The absence of symmetry in a bond-making complex can yield unequal numbers of singly-substituted molecules (e.g., more H‒D than D‒H in H2), which is recorded in the product molecule as a deficit in doubly-substituted moieties and an "anticlumped" isotope distribution (i.e., Δn < 0). Enzymatic isotope pairing reactions, which can have site-specific isotopic fractionation factors and atom reservoirs, should express this class of combinatorial isotope effect. Chemical-kinetic isotope effects, which are related to the bond-forming transition state, arise independently and express second-order combinatorial effects. In general, both combinatorial and chemical factors are important for calculating and interpreting clumped-isotope signatures of individual reactions. In many reactions relevant to geochemical oxygen, carbon, and nitrogen cycling, combinatorial isotope pairing likely plays a strong role in the clumped isotope distribution of the products. These isotopic signatures, manifest as either directly bound isotope clumps or as features of a molecule's isotopic anatomy, could be exploited as tracers of biogeochemistry that can

Source-Free Exchange-Correlation Magnetic Fields in Density Functional Theory.

PubMed

Sharma, S; Gross, E K U; Sanna, A; Dewhurst, J K

2018-03-13

Spin-dependent exchange-correlation energy functionals in use today depend on the charge density and the magnetization density: E xc [ρ, m]. However, it is also correct to define the functional in terms of the curl of m for physical external fields: E xc [ρ,∇ × m]. The exchange-correlation magnetic field, B xc , then becomes source-free. We study this variation of the theory by uniquely removing the source term from local and generalized gradient approximations to the functional. By doing so, the total Kohn-Sham moments are improved for a wide range of materials for both functionals. Significantly, the moments for the pnictides are now in good agreement with experiment. This source-free method is simple to implement in all existing density functional theory codes.

Exploiting Quantum Resonance to Solve Combinatorial Problems

NASA Technical Reports Server (NTRS)

Zak, Michail; Fijany, Amir

2006-01-01

Quantum resonance would be exploited in a proposed quantum-computing approach to the solution of combinatorial optimization problems. In quantum computing in general, one takes advantage of the fact that an algorithm cannot be decoupled from the physical effects available to implement it. Prior approaches to quantum computing have involved exploitation of only a subset of known quantum physical effects, notably including parallelism and entanglement, but not including resonance. In the proposed approach, one would utilize the combinatorial properties of tensor-product decomposability of unitary evolution of many-particle quantum systems for physically simulating solutions to NP-complete problems (a class of problems that are intractable with respect to classical methods of computation). In this approach, reinforcement and selection of a desired solution would be executed by means of quantum resonance. Classes of NP-complete problems that are important in practice and could be solved by the proposed approach include planning, scheduling, search, and optimal design.

Density functional theory studies of etoricoxib

NASA Astrophysics Data System (ADS)

Sachdeva, Ritika; Kaur, Prabhjot; Singh, V. P.; Saini, G. S. S.

2016-05-01

Etoricoxib is a COX-2 selective inhibitor drug with molecular formula C18H15ClN2O2S. It is primarily used for the treatment of arthritis(rheumatoid, psoriatic, osteoarthritis), ankylosing spondylitis, gout and chronic low back pain. Theoretical studies of the molecule including geometry optimization and vibrational frequency calculations were carried out with the help of density functional theory calculations using 6-311++ g (d, p) basis set and B3LYP functional.

Multiconfiguration Pair-Density Functional Theory Spectral Calculations Are Stable to Adding Diffuse Basis Functions.

PubMed

Hoyer, Chad E; Gagliardi, Laura; Truhlar, Donald G

2015-11-05

Time-dependent Kohn-Sham density functional theory (TD-KS-DFT) is useful for calculating electronic excitation spectra of large systems, but the low-energy spectra are often complicated by artificially lowered higher-energy states. This affects even the lowest energy excited states. Here, by calculating the lowest energy spin-conserving excited state for atoms from H to K and for formaldehyde, we show that this problem does not occur in multiconfiguration pair-density functional theory (MC-PDFT). We use the tPBE on-top density functional, which is a translation of the PBE exchange-correlation functional. We compare to a robust multireference method, namely, complete active space second-order perturbation theory (CASPT2), and to TD-KS-DFT with two popular exchange-correlation functionals, PBE and PBE0. We find for atoms that the mean unsigned error (MUE) of MC-PDFT with the tPBE functional improves from 0.42 to 0.40 eV with a double set of diffuse functions, whereas the MUEs for PBE and PBE0 drastically increase from 0.74 to 2.49 eV and from 0.45 to 1.47 eV, respectively.

DNA Assembly Techniques for Next Generation Combinatorial Biosynthesis of Natural Products

PubMed Central

Cobb, Ryan E.; Ning, Jonathan C.; Zhao, Huimin

2013-01-01

Natural product scaffolds remain important leads for pharmaceutical development. However, transforming a natural product into a drug entity often requires derivatization to enhance the compound’s therapeutic properties. A powerful method by which to perform this derivatization is combinatorial biosynthesis, the manipulation of the genes in the corresponding pathway to divert synthesis towards novel derivatives. While these manipulations have traditionally been carried out via restriction digestion/ligation-based cloning, the shortcomings of such techniques limit their throughput and thus the scope of corresponding combinatorial biosynthesis experiments. In the burgeoning field of synthetic biology, the demand for facile DNA assembly techniques has promoted the development of a host of novel DNA assembly strategies. Here we describe the advantages of these recently-developed tools for rapid, efficient synthesis of large DNA constructs. We also discuss their potential to facilitate the simultaneous assembly of complete libraries of natural product biosynthetic pathways, ushering in the next generation of combinatorial biosynthesis. PMID:24127070

Combinatorial chemistry on solid support in the search for central nervous system agents.

PubMed

Zajdel, Paweł; Pawłowski, Maciej; Martinez, Jean; Subra, Gilles

2009-08-01

The advent of combinatorial chemistry was one of the most important developments, that has significantly contributed to the drug discovery process. Within just a few years, its initial concept aimed at production of libraries containing huge number of compounds (thousands to millions), so called screening libraries, has shifted towards preparation of small and medium-sized rationally designed libraries. When applicable, the use of solid supports for the generation of libraries has been a real breakthrough in enhancing productivity. With a limited amount of resin and simple manual workups, the split/mix procedure may generate thousands of bead-tethered compounds. Beads can be chemically or physically encoded to facilitate the identification of a hit after the biological assay. Compartmentalization of solid supports using small reactors like teabags, kans or pellicular discrete supports like Lanterns resulted in powerful sort and combine technologies, relying on codes 'written' on the reactor, and thus reducing the need for automation and improving the number of compounds synthesized. These methods of solid-phase combinatorial chemistry have been recently supported by introduction of solid-supported reagents and scavenger resins. The first part of this review discusses the general premises of combinatorial chemistry and some methods used in the design of primary and focused combinatorial libraries. The aim of the second part is to present combinatorial chemistry methodologies aimed at discovering bioactive compounds acting on diverse GPCR involved in central nervous system disorders.

Relativistic density functional theory with picture-change corrected electron density based on infinite-order Douglas-Kroll-Hess method

NASA Astrophysics Data System (ADS)

Oyama, Takuro; Ikabata, Yasuhiro; Seino, Junji; Nakai, Hiromi

2017-07-01

This Letter proposes a density functional treatment based on the two-component relativistic scheme at the infinite-order Douglas-Kroll-Hess (IODKH) level. The exchange-correlation energy and potential are calculated using the electron density based on the picture-change corrected density operator transformed by the IODKH method. Numerical assessments indicated that the picture-change uncorrected density functional terms generate significant errors, on the order of hartree for heavy atoms. The present scheme was found to reproduce the energetics in the four-component treatment with high accuracy.

Orbital-dependent density functionals: Theory and applications

NASA Astrophysics Data System (ADS)

Kümmel, Stephan; Kronik, Leeor

2008-01-01

This review provides a perspective on the use of orbital-dependent functionals, which is currently considered one of the most promising avenues in modern density-functional theory. The focus here is on four major themes: the motivation for orbital-dependent functionals in terms of limitations of semilocal functionals; the optimized effective potential as a rigorous approach to incorporating orbital-dependent functionals within the Kohn-Sham framework; the rationale behind and advantages and limitations of four popular classes of orbital-dependent functionals; and the use of orbital-dependent functionals for predicting excited-state properties. For each of these issues, both formal and practical aspects are assessed.

Density functional theory for polymeric systems in 2D.

PubMed

Słyk, Edyta; Roth, Roland; Bryk, Paweł

2016-06-22

We propose density functional theory for polymeric fluids in two dimensions. The approach is based on Wertheim's first order thermodynamic perturbation theory (TPT) and closely follows density functional theory for polymers proposed by Yu and Wu (2002 J. Chem. Phys. 117 2368). As a simple application we evaluate the density profiles of tangent hard-disk polymers at hard walls. The theoretical predictions are compared against the results of the Monte Carlo simulations. We find that for short chain lengths the theoretical density profiles are in an excellent agreement with the Monte Carlo data. The agreement is less satisfactory for longer chains. The performance of the theory can be improved by recasting the approach using the self-consistent field theory formalism. When the self-avoiding chain statistics is used, the theory yields a marked improvement in the low density limit. Further improvements for long chains could be reached by going beyond the first order of TPT.

Criticism of EFSA's scientific opinion on combinatorial effects of 'stacked' GM plants.

PubMed

Bøhn, Thomas

2018-01-01

Recent genetically modified plants tend to include both insect resistance and herbicide tolerance traits. Some of these 'stacked' GM plants have multiple Cry-toxins expressed as well as tolerance to several herbicides. This means that non-target organisms in the environment (biodiversity) will be co-exposed to multiple stressors simultaneously. A similar co-exposure may happen to consumers through chemical residues in the food chain. EFSA, the responsible unit for minimizing risk of harm in European food chains, has expressed its scientific interest in combinatorial effects. However, when new data showed how two Cry-toxins acted in combination (added toxicity), and that the same Cry-toxins showed combinatorial effects when co-exposed with Roundup (Bøhn et al., 2016), EFSA dismissed these new peer-reviewed results. In effect, EFSA claimed that combinatorial effects are not relevant for itself. EFSA was justifying this by referring to a policy question, and by making invalid assumptions, which could have been checked directly with the lead-author. With such approach, EFSA may miss the opportunity to improve its environmental and health risk assessment of toxins and pesticides in the food chain. Failure to follow its own published requests for combinatorial effects research, may also risk jeopardizing EFSA's scientific and public reputation. Copyright © 2017. Published by Elsevier Ltd.

DC-Analyzer-facilitated combinatorial strategy for rapid directed evolution of functional enzymes with multiple mutagenesis sites.

PubMed

Wang, Xiong; Zheng, Kai; Zheng, Huayu; Nie, Hongli; Yang, Zujun; Tang, Lixia

2014-12-20

Iterative saturation mutagenesis (ISM) has been shown to be a powerful method for directed evolution. In this study, the approach was modified (termed M-ISM) by combining the single-site saturation mutagenesis method with a DC-Analyzer-facilitated combinatorial strategy, aiming to evolve novel biocatalysts efficiently in the case where multiple sites are targeted simultaneously. Initially, all target sites were explored individually by constructing single-site saturation mutagenesis libraries. Next, the top two to four variants in each library were selected and combined using the DC-Analyzer-facilitated combinatorial strategy. In addition to site-saturation mutagenesis, iterative saturation mutagenesis also needed to be performed. The advantages of M-ISM over ISM were that the screening effort is greatly reduced, and the entire M-ISM procedure was less time-consuming. The M-ISM strategy was successfully applied to the randomization of halohydrin dehalogenase from Agrobacterium radiobacter AD1 (HheC) when five interesting sites were targeted simultaneously. After screening 900 clones in total, six positive mutants were obtained. These mutants exhibited 4.0- to 9.3-fold higher k(cat) values than did the wild-type HheC toward 1,3-dichloro-2-propanol. However, with the ISM strategy, the best hit showed a 5.9-fold higher k(cat) value toward 1,3-DCP than the wild-type HheC, which was obtained after screening 4000 clones from four rounds of mutagenesis. Therefore, M-ISM could serve as a simple and efficient version of ISM for the randomization of target genes with multiple positions of interest.

Combinatorial quantization of the Hamiltonian Chern-Simons theory II

NASA Astrophysics Data System (ADS)

Alekseev, Anton Yu.; Grosse, Harald; Schomerus, Volker

1996-01-01

This paper further develops the combinatorial approach to quantization of the Hamiltonian Chern Simons theory advertised in [1]. Using the theory of quantum Wilson lines, we show how the Verlinde algebra appears within the context of quantum group gauge theory. This allows to discuss flatness of quantum connections so that we can give a mathematically rigorous definition of the algebra of observables A CS of the Chern Simons model. It is a *-algebra of “functions on the quantum moduli space of flat connections” and comes equipped with a positive functional ω (“integration”). We prove that this data does not depend on the particular choices which have been made in the construction. Following ideas of Fock and Rosly [2], the algebra A CS provides a deformation quantization of the algebra of functions on the moduli space along the natural Poisson bracket induced by the Chern Simons action. We evaluate a volume of the quantized moduli space and prove that it coincides with the Verlinde number. This answer is also interpreted as a partition partition function of the lattice Yang-Mills theory corresponding to a quantum gauge group.

Central depression in nucleonic densities: Trend analysis in the nuclear density functional theory approach

NASA Astrophysics Data System (ADS)

Schuetrumpf, B.; Nazarewicz, W.; Reinhard, P.-G.

2017-08-01

Background: The central depression of nucleonic density, i.e., a reduction of density in the nuclear interior, has been attributed to many factors. For instance, bubble structures in superheavy nuclei are believed to be due to the electrostatic repulsion. In light nuclei, the mechanism behind the density reduction in the interior has been discussed in terms of shell effects associated with occupations of s orbits. Purpose: The main objective of this work is to reveal mechanisms behind the formation of central depression in nucleonic densities in light and heavy nuclei. To this end, we introduce several measures of the internal nucleonic density. Through the statistical analysis, we study the information content of these measures with respect to nuclear matter properties. Method: We apply nuclear density functional theory with Skyrme functionals. Using the statistical tools of linear least square regression, we inspect correlations between various measures of central depression and model parameters, including nuclear matter properties. We study bivariate correlations with selected quantities as well as multiple correlations with groups of parameters. Detailed correlation analysis is carried out for 34Si for which a bubble structure has been reported recently, 48Ca, and N =82 , 126, and 184 isotonic chains. Results: We show that the central depression in medium-mass nuclei is very sensitive to shell effects, whereas for superheavy systems it is firmly driven by the electrostatic repulsion. An appreciable semibubble structure in proton density is predicted for 294Og, which is currently the heaviest nucleus known experimentally. Conclusion: Our correlation analysis reveals that the central density indicators in nuclei below 208Pb carry little information on parameters of nuclear matter; they are predominantly driven by shell structure. On the other hand, in the superheavy nuclei there exists a clear relationship between the central nucleonic density and symmetry energy.

Combinatorial Color Space Models for Skin Detection in Sub-continental Human Images

NASA Astrophysics Data System (ADS)

Khaled, Shah Mostafa; Saiful Islam, Md.; Rabbani, Md. Golam; Tabassum, Mirza Rehenuma; Gias, Alim Ul; Kamal, Md. Mostafa; Muctadir, Hossain Muhammad; Shakir, Asif Khan; Imran, Asif; Islam, Saiful

Among different color models HSV, HLS, YIQ, YCbCr, YUV, etc. have been most popular for skin detection. Most of the research done in the field of skin detection has been trained and tested on human images of African, Mongolian and Anglo-Saxon ethnic origins, skin colors of Indian sub-continentals have not been focused separately. Combinatorial algorithms, without affecting asymptotic complexity can be developed using the skin detection concepts of these color models for boosting detection performance. In this paper a comparative study of different combinatorial skin detection algorithms have been made. For training and testing 200 images (skin and non skin) containing pictures of sub-continental male and females have been used to measure the performance of the combinatorial approaches, and considerable development in success rate with True Positive of 99.5% and True Negative of 93.3% have been observed.

Density Functional Methods for Shock Physics and High Energy Density Science

NASA Astrophysics Data System (ADS)

Desjarlais, Michael

2017-06-01

Molecular dynamics with density functional theory has emerged over the last two decades as a powerful and accurate framework for calculating thermodynamic and transport properties with broad application to dynamic compression, high energy density science, and warm dense matter. These calculations have been extensively validated against shock and ramp wave experiments, are a principal component of high-fidelity equation of state generation, and are having wide-ranging impacts on inertial confinement fusion, planetary science, and shock physics research. In addition to thermodynamic properties, phase boundaries, and the equation of state, one also has access to electrical conductivity, thermal conductivity, and lower energy optical properties. Importantly, all these properties are obtained within the same theoretical framework and are manifestly consistent. In this talk I will give a brief history and overview of molecular dynamics with density functional theory and its use in calculating a wide variety of thermodynamic and transport properties for materials ranging from ambient to extreme conditions and with comparisons to experimental data. I will also discuss some of the limitations and difficulties, as well as active research areas. Sandia 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.

The maximal-density mass function for primordial black hole dark matter

NASA Astrophysics Data System (ADS)

Lehmann, Benjamin V.; Profumo, Stefano; Yant, Jackson

2018-04-01

The advent of gravitational wave astronomy has rekindled interest in primordial black holes (PBH) as a dark matter candidate. As there are many different observational probes of the PBH density across different masses, constraints on PBH models are dependent on the functional form of the PBH mass function. This complicates general statements about the mass functions allowed by current data, and, in particular, about the maximum total density of PBH. Numerical studies suggest that some forms of extended mass functions face tighter constraints than monochromatic mass functions, but they do not preclude the existence of a functional form for which constraints are relaxed. We use analytical arguments to show that the mass function which maximizes the fraction of the matter density in PBH subject to all constraints is a finite linear combination of monochromatic mass functions. We explicitly compute the maximum fraction of dark matter in PBH for different combinations of current constraints, allowing for total freedom of the mass function. Our framework elucidates the dependence of the maximum PBH density on the form of observational constraints, and we discuss the implications of current and future constraints for the viability of the PBH dark matter paradigm.

Exchange Energy Density Functionals that reproduce the Linear Response Function of the Free Electron Gas

NASA Astrophysics Data System (ADS)

García-Aldea, David; Alvarellos, J. E.

2009-03-01

We present several nonlocal exchange energy density functionals that reproduce the linear response function of the free electron gas. These nonlocal functionals are constructed following a similar procedure used previously for nonlocal kinetic energy density functionals by Chac'on-Alvarellos-Tarazona, Garc'ia-Gonz'alez et al., Wang-Govind-Carter and Garc'ia-Aldea-Alvarellos. The exchange response function is not known but we have used the approximate response function developed by Utsumi and Ichimaru, even we must remark that the same ansatz can be used to reproduce any other response function with the same scaling properties. We have developed two families of new nonlocal functionals: one is constructed with a mathematical structure based on the LDA approximation -- the Dirac functional for the exchange - and for the second one the structure of the second order gradient expansion approximation is took as a model. The functionals are constructed is such a way that they can be used in localized systems (using real space calculations) and in extended systems (using the momentum space, and achieving a quasilinear scaling with the system size if a constant reference electron density is defined).

Evaluation of the Optimum Composition of Low-Temperature Fuel Cell Electrocatalysts for Methanol Oxidation by Combinatorial Screening.

PubMed

Antolini, Ermete

2017-02-13

Combinatorial chemistry and high-throughput screening represent an innovative and rapid tool to prepare and evaluate a large number of new materials, saving time and expense for research and development. Considering that the activity and selectivity of catalysts depend on complex kinetic phenomena, making their development largely empirical in practice, they are prime candidates for combinatorial discovery and optimization. This review presents an overview of recent results of combinatorial screening of low-temperature fuel cell electrocatalysts for methanol oxidation. Optimum catalyst compositions obtained by combinatorial screening were compared with those of bulk catalysts, and the effect of the library geometry on the screening of catalyst composition is highlighted.

The Combinatorial Trace Method in Action

ERIC Educational Resources Information Center

Krebs, Mike; Martinez, Natalie C.

2013-01-01

On any finite graph, the number of closed walks of length k is equal to the sum of the kth powers of the eigenvalues of any adjacency matrix. This simple observation is the basis for the combinatorial trace method, wherein we attempt to count (or bound) the number of closed walks of a given length so as to obtain information about the graph's…

What correlation effects are covered by density functional theory?

NASA Astrophysics Data System (ADS)

He, Yuan; Grafenstein, Jurgen; Kraka, Elfi; Cremer, Dieter

The electron density distribution rho(r) generated by a DFT calculation was systematically studied by comparison with a series of reference densities obtained by wavefunction theory (WFT) methods that cover typical electron correlation effects. As a sensitive indicator for correlation effects the dipole moment of the CO molecule was used. The analysis reveals that typical LDA and GGA exchange functionals already simulate effects that are actually reminiscent of pair and three-electron correlation effects covered by MP2, MP4, and CCSD(T) in WFT. Correlation functionals contract the density towards the bond and the valence region thus taking negative charge out of the van der Waals region. It is shown that these improvements are relevant for the description of van der Waals interactions. Similar to certain correlated single-determinant WFT methods, BLYP and other GGA functionals underestimate ionic terms needed for a correct description of polar bonds. This is compensated for in hybrid functionals by mixing in HF exchange. The balanced mixing of local and non-local exchange and correlation effects leads to the correct description of polar bonds as in the B3LYP description of the CO molecule. The density obtained with B3LYP is closer to CCSD and CCSD(T) than to MP2 or MP4, which indicates that the B3LYP hybrid functional mimics those pair and three-electron correlation effects, which in WFT are only covered by coupled cluster methods.

Natural products and combinatorial chemistry: back to the future.

PubMed

Ortholand, Jean-Yves; Ganesan, A

2004-06-01

The introduction of high-throughput synthesis and combinatorial chemistry has precipitated a global decline in the screening of natural products by the pharmaceutical industry. Some companies terminated their natural products program, despite the unproven success of the new technologies. This was a premature decision, as natural products have a long history of providing important medicinal agents. Furthermore, they occupy a complementary region of chemical space compared with the typical synthetic compound library. For these reasons, the interest in natural products has been rekindled. Various approaches have evolved that combine the power of natural products and organic chemistry, ranging from the combinatorial total synthesis of analogues to the exploration of natural product scaffolds and the design of completely unnatural molecules that resemble natural products in their molecular characteristics.

Combinatorial atmospheric pressure chemical vapor deposition of graded TiO₂-VO₂ mixed-phase composites and their dual functional property as self-cleaning and photochromic window coatings.

PubMed

Wilkinson, Mia; Kafizas, Andreas; Bawaked, Salem M; Obaid, Abdullah Y; Al-Thabaiti, Shaeel A; Basahel, Sulaiman N; Carmalt, Claire J; Parkin, Ivan P

2013-06-10

A combinatorial film with a phase gradient from V:TiO₂ (V: Ti ≥ 0.08), through a range of TiO₂-VO₂ composites, to a vanadium-rich composite (V: Ti = 1.81) was grown by combinatorial atmospheric pressure chemical vapor deposition (cAPCVD). The film was grown from the reaction of TiCl₄, VCl₄, ethyl acetate (EtAc), and H₂O at 550 °C on glass. The gradient in gas mixtures across the reactor induced compositional film growth, producing a single film with numerous phases and compositions at different positions. Seventeen unique positions distributed evenly along a central horizontal strip were investigated. The physical properties were characterized by wavelength dispersive X-ray (WDX) analysis, X-ray diffraction (XRD), Raman spectroscopy, scanning electron microscopy (SEM), and UV-visible spectroscopy. The functional properties examined included the degree of photoinduced hydrophilicity (PIH), UVC-photocatalysis, and thermochromism. Superhydrophilic contact angles could be achieved at all positions, even within a highly VO₂-rich composite (V: Ti = 1.81). A maximum level of UVC photocatalysis was observed at a position bordering the solubility limit of V:TiO₂ (V: Ti ≈ 0.21) and fragmentation into a mixed-phase composite. Within the mixed-phase TiO₂: VO₂ composition region (V: Ti = 1.09 to 1.81) a decrease in the semiconductor-to-metal transition temperature of VO₂ from 68 to 51 °C was observed.

Excitation energies of molecules within time-independent density functional theory

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

Hemanadhan, M., E-mail: hemanadh@iitk.ac.in; Harbola, Manoj K., E-mail: hemanadh@iitk.ac.in

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.

Excitation energies of molecules within time-independent density functional theory

NASA Astrophysics Data System (ADS)

Hemanadhan, M.; Harbola, Manoj K.

2014-04-01

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 N2 and CO diatomic molecules. The excitation energy obtained with the MLSD functional for the N2 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.

Joint density-functional theory and its application to systems in solution

NASA Astrophysics Data System (ADS)

Petrosyan, Sahak A.

The physics of solvation, the interaction of water with solutes, plays a central role in chemistry and biochemistry, and it is essential for the very existence of life. Despite the central importance of water and the advent of the quantum theory early in the twentieth century, the link between the fundamental laws of physics and the observable properties of water remain poorly understood to this day. The central goal of this thesis is to develop a new formalism and framework to make the study of systems (solutes or surfaces) in contact with liquid water as practical and accurate as standard electronic structure calculations without the need for explicit averaging over large ensembles of configurations of water molecules. The thesis introduces a new form of density functional theory for the ab initio description of electronic systems in contact with a molecular liquid environment. This theory rigorously joins an electron density-functional for the electrons of a solute with a classical density-functional theory for the liquid into a single variational principle for the free energy of the combined system. Using the new form of density-functional theory for the ab initio description of electronic systems in contact with a molecular liquid environment, the thesis then presents the first detailed study of the impact of a solvent on the surface chemistry of Cr2O3, the passivating layer of stainless steel alloys. In comparison to a vacuum, we predict that the presence of water has little impact on the adsorption of chloride ions to the oxygen-terminated surface but has a dramatic effect on the binding of hydrogen to that surface. A key ingredient of a successful joint density functional theory is a good approximate functional for describing the solvent. We explore how the simplest examples of the best known class of approximate forms for the classical density functional fail when applied directly to water. The thesis then presents a computationally efficient density-functional

Optimization of an exchange-correlation density functional for water

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

Fritz, Michelle; Fernández-Serra, Marivi; Institute for Advanced Computational Science, Stony Brook University, Stony Brook, New York 11794-3800

2016-06-14

We describe a method, that we call data projection onto parameter space (DPPS), to optimize an energy functional of the electron density, so that it reproduces a dataset of experimental magnitudes. Our scheme, based on Bayes theorem, constrains the optimized functional not to depart unphysically from existing ab initio functionals. The resulting functional maximizes the probability of being the “correct” parameterization of a given functional form, in the sense of Bayes theory. The application of DPPS to water sheds new light on why density functional theory has performed rather poorly for liquid water, on what improvements are needed, and onmore » the intrinsic limitations of the generalized gradient approximation to electron exchange and correlation. Finally, we present tests of our water-optimized functional, that we call vdW-DF-w, showing that it performs very well for a variety of condensed water systems.« less

Co-LncRNA: investigating the lncRNA combinatorial effects in GO annotations and KEGG pathways based on human RNA-Seq data.

PubMed

Zhao, Zheng; Bai, Jing; Wu, Aiwei; Wang, Yuan; Zhang, Jinwen; Wang, Zishan; Li, Yongsheng; Xu, Juan; Li, Xia

2015-01-01

Long non-coding RNAs (lncRNAs) are emerging as key regulators of diverse biological processes and diseases. However, the combinatorial effects of these molecules in a specific biological function are poorly understood. Identifying co-expressed protein-coding genes of lncRNAs would provide ample insight into lncRNA functions. To facilitate such an effort, we have developed Co-LncRNA, which is a web-based computational tool that allows users to identify GO annotations and KEGG pathways that may be affected by co-expressed protein-coding genes of a single or multiple lncRNAs. LncRNA co-expressed protein-coding genes were first identified in publicly available human RNA-Seq datasets, including 241 datasets across 6560 total individuals representing 28 tissue types/cell lines. Then, the lncRNA combinatorial effects in a given GO annotations or KEGG pathways are taken into account by the simultaneous analysis of multiple lncRNAs in user-selected individual or multiple datasets, which is realized by enrichment analysis. In addition, this software provides a graphical overview of pathways that are modulated by lncRNAs, as well as a specific tool to display the relevant networks between lncRNAs and their co-expressed protein-coding genes. Co-LncRNA also supports users in uploading their own lncRNA and protein-coding gene expression profiles to investigate the lncRNA combinatorial effects. It will be continuously updated with more human RNA-Seq datasets on an annual basis. Taken together, Co-LncRNA provides a web-based application for investigating lncRNA combinatorial effects, which could shed light on their biological roles and could be a valuable resource for this community. Database URL: http://www.bio-bigdata.com/Co-LncRNA/. © The Author(s) 2015. Published by Oxford University Press.

Co-LncRNA: investigating the lncRNA combinatorial effects in GO annotations and KEGG pathways based on human RNA-Seq data

PubMed Central

Zhao, Zheng; Bai, Jing; Wu, Aiwei; Wang, Yuan; Zhang, Jinwen; Wang, Zishan; Li, Yongsheng; Xu, Juan; Li, Xia

2015-01-01

Long non-coding RNAs (lncRNAs) are emerging as key regulators of diverse biological processes and diseases. However, the combinatorial effects of these molecules in a specific biological function are poorly understood. Identifying co-expressed protein-coding genes of lncRNAs would provide ample insight into lncRNA functions. To facilitate such an effort, we have developed Co-LncRNA, which is a web-based computational tool that allows users to identify GO annotations and KEGG pathways that may be affected by co-expressed protein-coding genes of a single or multiple lncRNAs. LncRNA co-expressed protein-coding genes were first identified in publicly available human RNA-Seq datasets, including 241 datasets across 6560 total individuals representing 28 tissue types/cell lines. Then, the lncRNA combinatorial effects in a given GO annotations or KEGG pathways are taken into account by the simultaneous analysis of multiple lncRNAs in user-selected individual or multiple datasets, which is realized by enrichment analysis. In addition, this software provides a graphical overview of pathways that are modulated by lncRNAs, as well as a specific tool to display the relevant networks between lncRNAs and their co-expressed protein-coding genes. Co-LncRNA also supports users in uploading their own lncRNA and protein-coding gene expression profiles to investigate the lncRNA combinatorial effects. It will be continuously updated with more human RNA-Seq datasets on an annual basis. Taken together, Co-LncRNA provides a web-based application for investigating lncRNA combinatorial effects, which could shed light on their biological roles and could be a valuable resource for this community. Database URL: http://www.bio-bigdata.com/Co-LncRNA/ PMID:26363020

Orbital nodal surfaces: Topological challenges for density functionals

NASA Astrophysics Data System (ADS)

Aschebrock, Thilo; Armiento, Rickard; Kümmel, Stephan

2017-06-01

Nodal surfaces of orbitals, in particular of the highest occupied one, play a special role in Kohn-Sham density-functional theory. The exact Kohn-Sham exchange potential, for example, shows a protruding ridge along such nodal surfaces, leading to the counterintuitive feature of a potential that goes to different asymptotic limits in different directions. We show here that nodal surfaces can heavily affect the potential of semilocal density-functional approximations. For the functional derivatives of the Armiento-Kümmel (AK13) [Phys. Rev. Lett. 111, 036402 (2013), 10.1103/PhysRevLett.111.036402] and Becke88 [Phys. Rev. A 38, 3098 (1988), 10.1103/PhysRevA.38.3098] energy functionals, i.e., the corresponding semilocal exchange potentials, as well as the Becke-Johnson [J. Chem. Phys. 124, 221101 (2006), 10.1063/1.2213970] and van Leeuwen-Baerends (LB94) [Phys. Rev. A 49, 2421 (1994), 10.1103/PhysRevA.49.2421] model potentials, we explicitly demonstrate exponential divergences in the vicinity of nodal surfaces. We further point out that many other semilocal potentials have similar features. Such divergences pose a challenge for the convergence of numerical solutions of the Kohn-Sham equations. We prove that for exchange functionals of the generalized gradient approximation (GGA) form, enforcing correct asymptotic behavior of the potential or energy density necessarily leads to irregular behavior on or near orbital nodal surfaces. We formulate constraints on the GGA exchange enhancement factor for avoiding such divergences.

Introduction to Classical Density Functional Theory by a Computational Experiment

ERIC Educational Resources Information Center

Jeanmairet, Guillaume; Levy, Nicolas; Levesque, Maximilien; Borgis, Daniel

2014-01-01

We propose an in silico experiment to introduce the classical density functional theory (cDFT). Density functional theories, whether quantum or classical, rely on abstract concepts that are nonintuitive; however, they are at the heart of powerful tools and active fields of research in both physics and chemistry. They led to the 1998 Nobel Prize in…

Electron correlation and the self-interaction error of density functional theory

NASA Astrophysics Data System (ADS)

Polo, Victor; Kraka, Elfi; Cremer, Dieter

The self-interaction error (SIE) of commonly used DFT functionals has been systematically investigated by comparing the electron density distribution ρ( r ) generated by self-interaction corrected DFT (SIC-DFT) with a series of reference densities obtained by DFT or wavefunction theory (WFT) methods that cover typical electron correlation effects. Although the SIE of GGA functionals is considerably smaller than that of LDA functionals, it has significant consequences for the coverage of electron correlation effects at the DFT level of theory. The exchange SIE mimics long range (non-dynamic) pair correlation effects, and is responsible for the fact that the electron density of DFT exchange-only calculations resembles often that of MP4, MP2 or even CCSD(T) calculations. Changes in the electron density caused by SICDFT exchange are comparable with those that are associated with HF exchange. Correlation functionals contract the density towards the bond and the valence region, thus taking negative charge out of the van der Waals region where these effects are exaggerated by the influence of the SIE of the correlation functional. Hence, SIC-DFT leads in total to a relatively strong redistribution of negative charge from van der Waals, non-bonding, and valence regions of heavy atoms to the bond regions. These changes, although much stronger, resemble those obtained when comparing the densities of hybrid functionals such as B3LYP with the corresponding GGA functional BLYP. Hence, the balanced mixing of local and non-local exchange and correlation effects as it is achieved by hybrid functionals mimics SIC-DFT and can be considered as an economic way to include some SIC into standard DFT. However, the investigation shows also that the SIC-DFT description of molecules is unreliable because the standard functionals used were optimized for DFT including the SIE.

Applications of Density Functional Theory in Soft Condensed Matter

NASA Astrophysics Data System (ADS)

Löwen, Hartmut

Applications of classical density functional theory (DFT) to soft matter systems like colloids, liquid crystals and polymer solutions are discussed with a focus on the freezing transition and on nonequilibrium Brownian dynamics. First, after a brief reminder of equilibrium density functional theory, DFT is applied to the freezing transition of liquids into crystalline lattices. In particular, spherical particles with radially symmetric pair potentials will be treated (like hard spheres, the classical one-component plasma or Gaussian-core particles). Second, the DFT will be generalized towards Brownian dynamics in order to tackle nonequilibrium problems. After a general introduction to Brownian dynamics using the complementary Smoluchowski and Langevin pictures appropriate for the dynamics of colloidal suspensions, the dynamical density functional theory (DDFT) will be derived from the Smoluchowski equation. This will be done first for spherical particles (e.g. hard spheres or Gaussian-cores) without hydrodynamic interactions. Then we show how to incorporate hydrodynamic interactions between the colloidal particles into the DDFT framework and compare to Brownian dynamics computer simulations. Third orientational degrees of freedom (rod-like particles) will be considered as well. In the latter case, the stability of intermediate liquid crystalline phases (isotropic, nematic, smectic-A, plastic crystals etc) can be predicted. Finally, the corresponding dynamical extension of density functional theory towards orientational degrees of freedom is proposed and the collective behaviour of "active" (self-propelled) Brownian particles is briefly discussed.

Dendritic Cytoskeletal Architecture Is Modulated by Combinatorial Transcriptional Regulation in Drosophila melanogaster.

PubMed

Das, Ravi; Bhattacharjee, Shatabdi; Patel, Atit A; Harris, Jenna M; Bhattacharya, Surajit; Letcher, Jamin M; Clark, Sarah G; Nanda, Sumit; Iyer, Eswar Prasad R; Ascoli, Giorgio A; Cox, Daniel N

2017-12-01

Transcription factors (TFs) have emerged as essential cell autonomous mediators of subtype specific dendritogenesis; however, the downstream effectors of these TFs remain largely unknown, as are the cellular events that TFs control to direct morphological change. As dendritic morphology is largely dictated by the organization of the actin and microtubule (MT) cytoskeletons, elucidating TF-mediated cytoskeletal regulatory programs is key to understanding molecular control of diverse dendritic morphologies. Previous studies in Drosophila melanogaster have demonstrated that the conserved TFs Cut and Knot exert combinatorial control over aspects of dendritic cytoskeleton development, promoting actin and MT-based arbor morphology, respectively. To investigate transcriptional targets of Cut and/or Knot regulation, we conducted systematic neurogenomic studies, coupled with in vivo genetic screens utilizing multi-fluor cytoskeletal and membrane marker reporters. These analyses identified a host of putative Cut and/or Knot effector molecules, and a subset of these putative TF targets converge on modulating dendritic cytoskeletal architecture, which are grouped into three major phenotypic categories, based upon neuromorphometric analyses: complexity enhancer, complexity shifter, and complexity suppressor. Complexity enhancer genes normally function to promote higher order dendritic growth and branching with variable effects on MT stabilization and F-actin organization, whereas complexity shifter and complexity suppressor genes normally function in regulating proximal-distal branching distribution or in restricting higher order branching complexity, respectively, with spatially restricted impacts on the dendritic cytoskeleton. Collectively, we implicate novel genes and cellular programs by which TFs distinctly and combinatorially govern dendritogenesis via cytoskeletal modulation. Copyright © 2017 by the Genetics Society of America.

Plato: A localised orbital based density functional theory code

NASA Astrophysics Data System (ADS)

Kenny, S. D.; Horsfield, A. P.

2009-12-01

The Plato package allows both orthogonal and non-orthogonal tight-binding as well as density functional theory (DFT) calculations to be performed within a single framework. The package also provides extensive tools for analysing the results of simulations as well as a number of tools for creating input files. The code is based upon the ideas first discussed in Sankey and Niklewski (1989) [1] with extensions to allow high-quality DFT calculations to be performed. DFT calculations can utilise either the local density approximation or the generalised gradient approximation. Basis sets from minimal basis through to ones containing multiple radial functions per angular momenta and polarisation functions can be used. Illustrations of how the package has been employed are given along with instructions for its utilisation. Program summaryProgram title: Plato Catalogue identifier: AEFC_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEFC_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: Standard CPC licence, http://cpc.cs.qub.ac.uk/licence/licence.html No. of lines in distributed program, including test data, etc.: 219 974 No. of bytes in distributed program, including test data, etc.: 1 821 493 Distribution format: tar.gz Programming language: C/MPI and PERL Computer: Apple Macintosh, PC, Unix machines Operating system: Unix, Linux and Mac OS X Has the code been vectorised or parallelised?: Yes, up to 256 processors tested RAM: Up to 2 Gbytes per processor Classification: 7.3 External routines: LAPACK, BLAS and optionally ScaLAPACK, BLACS, PBLAS, FFTW Nature of problem: Density functional theory study of electronic structure and total energies of molecules, crystals and surfaces. Solution method: Localised orbital based density functional theory. Restrictions: Tight-binding and density functional theory only, no exact exchange. Unusual features: Both atom centred and uniform meshes available

General framework for fluctuating dynamic density functional theory

NASA Astrophysics Data System (ADS)

Durán-Olivencia, Miguel A.; Yatsyshin, Peter; Goddard, Benjamin D.; Kalliadasis, Serafim

2017-12-01

We introduce a versatile bottom-up derivation of a formal theoretical framework to describe (passive) soft-matter systems out of equilibrium subject to fluctuations. We provide a unique connection between the constituent-particle dynamics of real systems and the time evolution equation of their measurable (coarse-grained) quantities, such as local density and velocity. The starting point is the full Hamiltonian description of a system of colloidal particles immersed in a fluid of identical bath particles. Then, we average out the bath via Zwanzig’s projection-operator techniques and obtain the stochastic Langevin equations governing the colloidal-particle dynamics. Introducing the appropriate definition of the local number and momentum density fields yields a generalisation of the Dean-Kawasaki (DK) model, which resembles the stochastic Navier-Stokes description of a fluid. Nevertheless, the DK equation still contains all the microscopic information and, for that reason, does not represent the dynamical law of observable quantities. We address this controversial feature of the DK description by carrying out a nonequilibrium ensemble average. Adopting a natural decomposition into local-equilibrium and nonequilibrium contribution, where the former is related to a generalised version of the canonical distribution, we finally obtain the fluctuating-hydrodynamic equation governing the time-evolution of the mesoscopic density and momentum fields. Along the way, we outline the connection between the ad hoc energy functional introduced in previous DK derivations and the free-energy functional from classical density-functional theory. The resultant equation has the structure of a dynamical density-functional theory (DDFT) with an additional fluctuating force coming from the random interactions with the bath. We show that our fluctuating DDFT formalism corresponds to a particular version of the fluctuating Navier-Stokes equations, originally derived by Landau and Lifshitz

Neural correlates of implicit and explicit combinatorial semantic processing

PubMed Central

Graves, William W.; Binder, Jeffrey R.; Desai, Rutvik H.; Conant, Lisa L.; Seidenberg, Mark S.

2010-01-01

Language consists of sequences of words, but comprehending phrases involves more than concatenating meanings: A boat house is a shelter for boats, whereas a summer house is a house used during summer, and a ghost house is typically uninhabited. Little is known about the brain bases of combinatorial semantic processes. We performed two fMRI experiments using familiar, highly meaningful phrases (LAKE HOUSE) and unfamiliar phrases with minimal meaning created by reversing the word order of the familiar items (HOUSE LAKE). The first experiment used a 1-back matching task to assess implicit semantic processing, and the second used a classification task to engage explicit semantic processing. These conditions required processing of the same words, but with more effective combinatorial processing in the meaningful condition. The contrast of meaningful versus reversed phrases revealed activation primarily during the classification task, to a greater extent in the right hemisphere, including right angular gyrus, dorsomedial prefrontal cortex, and bilateral posterior cingulate/precuneus, areas previously implicated in semantic processing. Positive correlations of fMRI signal with lexical (word-level) frequency occurred exclusively with the 1-back task and to a greater spatial extent on the left, including left posterior middle temporal gyrus and bilateral parahippocampus. These results reveal strong effects of task demands on engagement of lexical versus combinatorial processing and suggest a hemispheric dissociation between these levels of semantic representation. PMID:20600969

Iconicity and the Emergence of Combinatorial Structure in Language.

PubMed

Verhoef, Tessa; Kirby, Simon; de Boer, Bart

2016-11-01

In language, recombination of a discrete set of meaningless building blocks forms an unlimited set of possible utterances. How such combinatorial structure emerged in the evolution of human language is increasingly being studied. It has been shown that it can emerge when languages culturally evolve and adapt to human cognitive biases. How the emergence of combinatorial structure interacts with the existence of holistic iconic form-meaning mappings in a language is still unknown. The experiment presented in this paper studies the role of iconicity and human cognitive learning biases in the emergence of combinatorial structure in artificial whistled languages. Participants learned and reproduced whistled words for novel objects with the use of a slide whistle. Their reproductions were used as input for the next participant, to create transmission chains and simulate cultural transmission. Two conditions were studied: one in which the persistence of iconic form-meaning mappings was possible and one in which this was experimentally made impossible. In both conditions, cultural transmission caused the whistled languages to become more learnable and more structured, but this process was slightly delayed in the first condition. Our findings help to gain insight into when and how words may lose their iconic origins when they become part of an organized linguistic system. Copyright © 2015 Cognitive Science Society, Inc.

What Density Functional Theory could do for Quantum Information

NASA Astrophysics Data System (ADS)

Mattsson, Ann

2015-03-01

The Hohenberg-Kohn theorem of Density Functional Theory (DFT), and extensions thereof, tells us that all properties of a system of electrons can be determined through their density, which uniquely determines the many-body wave-function. Given access to the appropriate, universal, functionals of the density we would, in theory, be able to determine all observables of any electronic system, without explicit reference to the wave-function. On the other hand, the wave-function is at the core of Quantum Information (QI), with the wave-function of a set of qubits being the central computational resource in a quantum computer. While there is seemingly little overlap between DFT and QI, reliance upon observables form a key connection. Though the time-evolution of the wave-function and associated phase information is fundamental to quantum computation, the initial and final states of a quantum computer are characterized by observables of the system. While observables can be extracted directly from a system's wave-function, DFT tells us that we may be able to intuit a method for extracting them from its density. In this talk, I will review the fundamentals of DFT and how these principles connect to the world of QI. This will range from DFT's utility in the engineering of physical qubits, to the possibility of using it to efficiently (but approximately) simulate Hamiltonians at the logical level. The apparent paradox of describing algorithms based on the quantum mechanical many-body wave-function with a DFT-like theory based on observables will remain a focus throughout. The ultimate goal of this talk is to initiate a dialog about what DFT could do for QI, in theory and in practice. 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.

Exact model reduction of combinatorial reaction networks

PubMed Central

Conzelmann, Holger; Fey, Dirk; Gilles, Ernst D

2008-01-01

Background Receptors and scaffold proteins usually possess a high number of distinct binding domains inducing the formation of large multiprotein signaling complexes. Due to combinatorial reasons the number of distinguishable species grows exponentially with the number of binding domains and can easily reach several millions. Even by including only a limited number of components and binding domains the resulting models are very large and hardly manageable. A novel model reduction technique allows the significant reduction and modularization of these models. Results We introduce methods that extend and complete the already introduced approach. For instance, we provide techniques to handle the formation of multi-scaffold complexes as well as receptor dimerization. Furthermore, we discuss a new modeling approach that allows the direct generation of exactly reduced model structures. The developed methods are used to reduce a model of EGF and insulin receptor crosstalk comprising 5,182 ordinary differential equations (ODEs) to a model with 87 ODEs. Conclusion The methods, presented in this contribution, significantly enhance the available methods to exactly reduce models of combinatorial reaction networks. PMID:18755034

A Scalable Implementation of Van der Waals Density Functionals

NASA Astrophysics Data System (ADS)

Wu, Jun; Gygi, Francois

2010-03-01

Recently developed Van der Waals density functionals[1] offer the promise to account for weak intermolecular interactions that are not described accurately by local exchange-correlation density functionals. In spite of recent progress [2], the computational cost of such calculations remains high. We present a scalable parallel implementation of the functional proposed by Dion et al.[1]. The method is implemented in the Qbox first-principles simulation code (http://eslab.ucdavis.edu/software/qbox). Application to large molecular systems will be presented. [4pt] [1] M. Dion et al. Phys. Rev. Lett. 92, 246401 (2004).[0pt] [2] G. Roman-Perez and J. M. Soler, Phys. Rev. Lett. 103, 096102 (2009).

Statistical Mechanics of Combinatorial Auctions

NASA Astrophysics Data System (ADS)

Galla, Tobias; Leone, Michele; Marsili, Matteo; Sellitto, Mauro; Weigt, Martin; Zecchina, Riccardo

2006-09-01

Combinatorial auctions are formulated as frustrated lattice gases on sparse random graphs, allowing the determination of the optimal revenue by methods of statistical physics. Transitions between computationally easy and hard regimes are found and interpreted in terms of the geometric structure of the space of solutions. We introduce an iterative algorithm to solve intermediate and large instances, and discuss competing states of optimal revenue and maximal number of satisfied bidders. The algorithm can be generalized to the hard phase and to more sophisticated auction protocols.

An evaluation of methods for estimating the number of local optima in combinatorial optimization problems.

PubMed

Hernando, Leticia; Mendiburu, Alexander; Lozano, Jose A

2013-01-01

The solution of many combinatorial optimization problems is carried out by metaheuristics, which generally make use of local search algorithms. These algorithms use some kind of neighborhood structure over the search space. The performance of the algorithms strongly depends on the properties that the neighborhood imposes on the search space. One of these properties is the number of local optima. Given an instance of a combinatorial optimization problem and a neighborhood, the estimation of the number of local optima can help not only to measure the complexity of the instance, but also to choose the most convenient neighborhood to solve it. In this paper we review and evaluate several methods to estimate the number of local optima in combinatorial optimization problems. The methods reviewed not only come from the combinatorial optimization literature, but also from the statistical literature. A thorough evaluation in synthetic as well as real problems is given. We conclude by providing recommendations of methods for several scenarios.

Effective model hierarchies for dynamic and static classical density functional theories

NASA Astrophysics Data System (ADS)

Majaniemi, S.; Provatas, N.; Nonomura, M.

2010-09-01

The origin and methodology of deriving effective model hierarchies are presented with applications to solidification of crystalline solids. In particular, it is discussed how the form of the equations of motion and the effective parameters on larger scales can be obtained from the more microscopic models. It will be shown that tying together the dynamic structure of the projection operator formalism with static classical density functional theories can lead to incomplete (mass) transport properties even though the linearized hydrodynamics on large scales is correctly reproduced. To facilitate a more natural way of binding together the dynamics of the macrovariables and classical density functional theory, a dynamic generalization of density functional theory based on the nonequilibrium generating functional is suggested.

Subsystem real-time time dependent density functional theory.

PubMed

Krishtal, Alisa; Ceresoli, Davide; Pavanello, Michele

2015-04-21

We present the extension of Frozen Density Embedding (FDE) formulation of subsystem Density Functional Theory (DFT) to real-time Time Dependent Density Functional Theory (rt-TDDFT). FDE is a DFT-in-DFT embedding method that allows to partition a larger Kohn-Sham system into a set of smaller, coupled Kohn-Sham systems. Additional to the computational advantage, FDE provides physical insight into the properties of embedded systems and the coupling interactions between them. The extension to rt-TDDFT is done straightforwardly by evolving the Kohn-Sham subsystems in time simultaneously, while updating the embedding potential between the systems at every time step. Two main applications are presented: the explicit excitation energy transfer in real time between subsystems is demonstrated for the case of the Na4 cluster and the effect of the embedding on optical spectra of coupled chromophores. In particular, the importance of including the full dynamic response in the embedding potential is demonstrated.

Accuracy of electron densities obtained via Koopmans-compliant hybrid functionals

NASA Astrophysics Data System (ADS)

Elmaslmane, A. R.; Wetherell, J.; Hodgson, M. J. P.; McKenna, K. P.; Godby, R. W.

2018-04-01

We evaluate the accuracy of electron densities and quasiparticle energy gaps given by hybrid functionals by directly comparing these to the exact quantities obtained from solving the many-electron Schrödinger equation. We determine the admixture of Hartree-Fock exchange to approximate exchange-correlation in our hybrid functional via one of several physically justified constraints, including the generalized Koopmans' theorem. We find that hybrid functionals yield strikingly accurate electron densities and gaps in both exchange-dominated and correlated systems. We also discuss the role of the screened Fock operator in the success of hybrid functionals.

Training and Transfer in Combinatorial Problem Solving: The Development of Formal Reasoning During Early Adolescence

ERIC Educational Resources Information Center

Barratt, Barnaby B.

1975-01-01

This study investigated the emergence of combinatorial competence in early adolescence and the effectiveness of a programmed discovery training procedure. Significant increases in combinatorial skill with age were shown; it was found that the expression of this skill was significantly facilitated if problems involved concrete material of low…

Optimized Reaction Conditions for Amide Bond Formation in DNA-Encoded Combinatorial Libraries.

PubMed

Li, Yizhou; Gabriele, Elena; Samain, Florent; Favalli, Nicholas; Sladojevich, Filippo; Scheuermann, Jörg; Neri, Dario

2016-08-08

DNA-encoded combinatorial libraries are increasingly being used as tools for the discovery of small organic binding molecules to proteins of biological or pharmaceutical interest. In the majority of cases, synthetic procedures for the formation of DNA-encoded combinatorial libraries incorporate at least one step of amide bond formation between amino-modified DNA and a carboxylic acid. We investigated reaction conditions and established a methodology by using 1-ethyl-3-(3-(dimethylamino)propyl)carbodiimide, 1-hydroxy-7-azabenzotriazole and N,N'-diisopropylethylamine (EDC/HOAt/DIPEA) in combination, which provided conversions greater than 75% for 423/543 (78%) of the carboxylic acids tested. These reaction conditions were efficient with a variety of primary and secondary amines, as well as with various types of amino-modified oligonucleotides. The reaction conditions, which also worked efficiently over a broad range of DNA concentrations and reaction scales, should facilitate the synthesis of novel DNA-encoded combinatorial libraries.

Differentiability of energy functionals in spin-density-functional theory

NASA Astrophysics Data System (ADS)

Gál, Tamás

2007-06-01

Recently, nonuniqueness of external electrostatic and magnetic fields yielding a given many-electron ground state has been pointed out [K. Capelle and G. Vignale, Phys. Rev. Lett. 86, 5546 (2001); H. Eschrig and W. E. Pickett, Solid State Commun. 118, 123 (2001)], implying the nondifferentiability of the ground-state energy functional of spin-density-functional theory (SDFT), on the basis of which the applicability of widely used DFT methods in SDFT has been put into question and the need for a critical reexamination of those applications has been concluded. Here it is shown, for collinear magnetic fields, that the nonuniqueness of the external potentials in SDFT does not imply the nonexistence of number-conserving functional derivatives as well, with the use of which therefore problems arising from the nondifferentiability are avoided.

Random vs. Combinatorial Methods for Discrete Event Simulation of a Grid Computer Network

NASA Technical Reports Server (NTRS)

Kuhn, D. Richard; Kacker, Raghu; Lei, Yu

2010-01-01

This study compared random and t-way combinatorial inputs of a network simulator, to determine if these two approaches produce significantly different deadlock detection for varying network configurations. Modeling deadlock detection is important for analyzing configuration changes that could inadvertently degrade network operations, or to determine modifications that could be made by attackers to deliberately induce deadlock. Discrete event simulation of a network may be conducted using random generation, of inputs. In this study, we compare random with combinatorial generation of inputs. Combinatorial (or t-way) testing requires every combination of any t parameter values to be covered by at least one test. Combinatorial methods can be highly effective because empirical data suggest that nearly all failures involve the interaction of a small number of parameters (1 to 6). Thus, for example, if all deadlocks involve at most 5-way interactions between n parameters, then exhaustive testing of all n-way interactions adds no additional information that would not be obtained by testing all 5-way interactions. While the maximum degree of interaction between parameters involved in the deadlocks clearly cannot be known in advance, covering all t-way interactions may be more efficient than using random generation of inputs. In this study we tested this hypothesis for t = 2, 3, and 4 for deadlock detection in a network simulation. Achieving the same degree of coverage provided by 4-way tests would have required approximately 3.2 times as many random tests; thus combinatorial methods were more efficient for detecting deadlocks involving a higher degree of interactions. The paper reviews explanations for these results and implications for modeling and simulation.

Dynamical analysis of continuous higher-order hopfield networks for combinatorial optimization.

PubMed

Atencia, Miguel; Joya, Gonzalo; Sandoval, Francisco

2005-08-01

In this letter, the ability of higher-order Hopfield networks to solve combinatorial optimization problems is assessed by means of a rigorous analysis of their properties. The stability of the continuous network is almost completely clarified: (1) hyperbolic interior equilibria, which are unfeasible, are unstable; (2) the state cannot escape from the unitary hypercube; and (3) a Lyapunov function exists. Numerical methods used to implement the continuous equation on a computer should be designed with the aim of preserving these favorable properties. The case of nonhyperbolic fixed points, which occur when the Hessian of the target function is the null matrix, requires further study. We prove that these nonhyperbolic interior fixed points are unstable in networks with three neurons and order two. The conjecture that interior equilibria are unstable in the general case is left open.

Sample size determination in combinatorial chemistry.

PubMed Central

Zhao, P L; Zambias, R; Bolognese, J A; Boulton, D; Chapman, K

1995-01-01

Combinatorial chemistry is gaining wide appeal as a technique for generating molecular diversity. Among the many combinatorial protocols, the split/recombine method is quite popular and particularly efficient at generating large libraries of compounds. In this process, polymer beads are equally divided into a series of pools and each pool is treated with a unique fragment; then the beads are recombined, mixed to uniformity, and redivided equally into a new series of pools for the subsequent couplings. The deviation from the ideal equimolar distribution of the final products is assessed by a special overall relative error, which is shown to be related to the Pearson statistic. Although the split/recombine sampling scheme is quite different from those used in analysis of categorical data, the Pearson statistic is shown to still follow a chi2 distribution. This result allows us to derive the required number of beads such that, with 99% confidence, the overall relative error is controlled to be less than a pregiven tolerable limit L1. In this paper, we also discuss another criterion, which determines the required number of beads so that, with 99% confidence, all individual relative errors are controlled to be less than a pregiven tolerable limit L2 (0 < L2 < 1). PMID:11607586

A combinatorial morphospace for angiosperm pollen

NASA Astrophysics Data System (ADS)

Mander, Luke

2016-04-01

The morphology of angiosperm (flowering plant) pollen is extraordinarily diverse. This diversity results from variations in the morphology of discrete anatomical components. These components include the overall shape of a pollen grain, the stratification of the exine, the number and form of any apertures, the type of dispersal unit, and the nature of any surface ornamentation. Different angiosperm pollen morphotypes reflect different combinations of these discrete components. In this talk, I ask the following question: given the anatomical components of angiosperm pollen that are known to exist in the plant kingdom, how many unique biologically plausible combinations of these components are there? I explore this question from the perspective of enumerative combinatorics using an algorithm I have written in the Python programming language. This algorithm (1) calculates the number of combinations of these components; (2) enumerates those combinations; and (3) graphically displays those combinations. The result is a combinatorial morphospace that reflects an underlying notion that the process of morphogenesis in angiosperm pollen can be thought of as an n choose k counting problem. I compare the morphology of extant and fossil angiosperm pollen grains to this morphospace, and suggest that from a combinatorial point of view angiosperm pollen is not as diverse as it could be, which may be a result of developmental constraints.

Semi-local machine-learned kinetic energy density functional with third-order gradients of electron density

NASA Astrophysics Data System (ADS)

Seino, Junji; Kageyama, Ryo; Fujinami, Mikito; Ikabata, Yasuhiro; Nakai, Hiromi

2018-06-01

A semi-local kinetic energy density functional (KEDF) was constructed based on machine learning (ML). The present scheme adopts electron densities and their gradients up to third-order as the explanatory variables for ML and the Kohn-Sham (KS) kinetic energy density as the response variable in atoms and molecules. Numerical assessments of the present scheme were performed in atomic and molecular systems, including first- and second-period elements. The results of 37 conventional KEDFs with explicit formulae were also compared with those of the ML KEDF with an implicit formula. The inclusion of the higher order gradients reduces the deviation of the total kinetic energies from the KS calculations in a stepwise manner. Furthermore, our scheme with the third-order gradient resulted in the closest kinetic energies to the KS calculations out of the presented functionals.

Creative thought as blind-variation and selective-retention: Combinatorial models of exceptional creativity

NASA Astrophysics Data System (ADS)

Simonton, Dean Keith

2010-06-01

Campbell (1960) proposed that creative thought should be conceived as a blind-variation and selective-retention process (BVSR). This article reviews the developments that have taken place in the half century that has elapsed since his proposal, with special focus on the use of combinatorial models as formal representations of the general theory. After defining the key concepts of blind variants, creative thought, and disciplinary context, the combinatorial models are specified in terms of individual domain samples, variable field size, ideational combination, and disciplinary communication. Empirical implications are then derived with respect to individual, domain, and field systems. These abstract combinatorial models are next provided substantive reinforcement with respect to findings concerning the cognitive processes, personality traits, developmental factors, and social contexts that contribute to creativity. The review concludes with some suggestions regarding future efforts to explicate creativity according to BVSR theory.

The QTP family of consistent functionals and potentials in Kohn-Sham density functional theory

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

Jin, Yifan; Bartlett, Rodney J., E-mail: bartlett@qtp.ufl.edu

This manuscript presents the second, consistent density functional in the QTP (Quantum Theory Project) family, that is, the CAM-QTP(01). It is a new range-separated exchange-correlation functional in which the non-local exchange contribution is 100% at large separation. It follows the same basic principles of this family that the Kohn-Sham eigenvalues of the occupied orbitals approximately equal the vertical ionization energies, which is not fulfilled by most of the traditional density functional methods. This new CAM-QTP(01) functional significantly improves the accuracy of the vertical excitation energies especially for the Rydberg states in the test set. It also reproduces many other propertiesmore » such as geometries, reaction barrier heights, and atomization energies.« less

To Think without Thinking: The Implications of Combinatory Play and the Creative Process for Neuroaesthetics

ERIC Educational Resources Information Center

Stevens, Victoria

2014-01-01

The author considers combinatory play as an intersection between creativity, play, and neuroaesthetics. She discusses combinatory play as vital to the creative process in art and science, particularly with regard to the incubation of new ideas. She reviews findings from current neurobiological research and outlines the way that the brain activates…

A density difference based analysis of orbital-dependent exchange-correlation functionals

NASA Astrophysics Data System (ADS)

Grabowski, Ireneusz; Teale, Andrew M.; Fabiano, Eduardo; Śmiga, Szymon; Buksztel, Adam; Della Sala, Fabio

2014-03-01

We present a density difference based analysis for a range of orbital-dependent Kohn-Sham functionals. Results for atoms, some members of the neon isoelectronic series and small molecules are reported and compared with ab initio wave function calculations. Particular attention is paid to the quality of approximations to the exchange-only optimised effective potential (OEP) approach: we consider both the localised Hartree-Fock as well as the Krieger-Li-Iafrate methods. Analysis of density differences at the exchange-only level reveals the impact of the approximations on the resulting electronic densities. These differences are further quantified in terms of the ground state energies, frontier orbital energy differences and highest occupied orbital energies obtained. At the correlated level, an OEP approach based on a perturbative second-order correlation energy expression is shown to deliver results comparable with those from traditional wave function approaches, making it suitable for use as a benchmark against which to compare standard density functional approximations.

On extending Kohn-Sham density functionals to systems with fractional number of electrons.

PubMed

Li, Chen; Lu, Jianfeng; Yang, Weitao

2017-06-07

We analyze four ways of formulating the Kohn-Sham (KS) density functionals with a fractional number of electrons, through extending the constrained search space from the Kohn-Sham and the generalized Kohn-Sham (GKS) non-interacting v-representable density domain for integer systems to four different sets of densities for fractional systems. In particular, these density sets are (I) ensemble interacting N-representable densities, (II) ensemble non-interacting N-representable densities, (III) non-interacting densities by the Janak construction, and (IV) non-interacting densities whose composing orbitals satisfy the Aufbau occupation principle. By proving the equivalence of the underlying first order reduced density matrices associated with these densities, we show that sets (I), (II), and (III) are equivalent, and all reduce to the Janak construction. Moreover, for functionals with the ensemble v-representable assumption at the minimizer, (III) reduces to (IV) and thus justifies the previous use of the Aufbau protocol within the (G)KS framework in the study of the ground state of fractional electron systems, as defined in the grand canonical ensemble at zero temperature. By further analyzing the Aufbau solution for different density functional approximations (DFAs) in the (G)KS scheme, we rigorously prove that there can be one and only one fractional occupation for the Hartree Fock functional, while there can be multiple fractional occupations for general DFAs in the presence of degeneracy. This has been confirmed by numerical calculations using the local density approximation as a representative of general DFAs. This work thus clarifies important issues on density functional theory calculations for fractional electron systems.

Accurate Semilocal Density Functional for Condensed-Matter Physics and Quantum Chemistry.

PubMed

Tao, Jianmin; Mo, Yuxiang

2016-08-12

Most density functionals have been developed by imposing the known exact constraints on the exchange-correlation energy, or by a fit to a set of properties of selected systems, or by both. However, accurate modeling of the conventional exchange hole presents a great challenge, due to the delocalization of the hole. Making use of the property that the hole can be made localized under a general coordinate transformation, here we derive an exchange hole from the density matrix expansion, while the correlation part is obtained by imposing the low-density limit constraint. From the hole, a semilocal exchange-correlation functional is calculated. Our comprehensive test shows that this functional can achieve remarkable accuracy for diverse properties of molecules, solids, and solid surfaces, substantially improving upon the nonempirical functionals proposed in recent years. Accurate semilocal functionals based on their associated holes are physically appealing and practically useful for developing nonlocal functionals.

Nonlocal and Nonadiabatic Effects in the Charge-Density Response of Solids: A Time-Dependent Density-Functional Approach

NASA Astrophysics Data System (ADS)

Panholzer, Martin; Gatti, Matteo; Reining, Lucia

2018-04-01

The charge-density response of extended materials is usually dominated by the collective oscillation of electrons, the plasmons. Beyond this feature, however, intriguing many-body effects are observed. They cannot be described by one of the most widely used approaches for the calculation of dielectric functions, which is time-dependent density functional theory (TDDFT) in the adiabatic local density approximation (ALDA). Here, we propose an approximation to the TDDFT exchange-correlation kernel which is nonadiabatic and nonlocal. It is extracted from correlated calculations in the homogeneous electron gas, where we have tabulated it for a wide range of wave vectors and frequencies. A simple mean density approximation allows one to use it in inhomogeneous materials where the density varies on a scale of 1.6 rs or faster. This kernel contains effects that are completely absent in the ALDA; in particular, it correctly describes the double plasmon in the dynamic structure factor of sodium, and it shows the characteristic low-energy peak that appears in systems with low electronic density. It also leads to an overall quantitative improvement of spectra.

Nonlocal and Nonadiabatic Effects in the Charge-Density Response of Solids: A Time-Dependent Density-Functional Approach.

PubMed

Panholzer, Martin; Gatti, Matteo; Reining, Lucia

2018-04-20

The charge-density response of extended materials is usually dominated by the collective oscillation of electrons, the plasmons. Beyond this feature, however, intriguing many-body effects are observed. They cannot be described by one of the most widely used approaches for the calculation of dielectric functions, which is time-dependent density functional theory (TDDFT) in the adiabatic local density approximation (ALDA). Here, we propose an approximation to the TDDFT exchange-correlation kernel which is nonadiabatic and nonlocal. It is extracted from correlated calculations in the homogeneous electron gas, where we have tabulated it for a wide range of wave vectors and frequencies. A simple mean density approximation allows one to use it in inhomogeneous materials where the density varies on a scale of 1.6 r_{s} or faster. This kernel contains effects that are completely absent in the ALDA; in particular, it correctly describes the double plasmon in the dynamic structure factor of sodium, and it shows the characteristic low-energy peak that appears in systems with low electronic density. It also leads to an overall quantitative improvement of spectra.

Development of combinatorial chemistry methods for coatings: high-throughput adhesion evaluation and scale-up of combinatorial leads.

PubMed

Potyrailo, Radislav A; Chisholm, Bret J; Morris, William G; Cawse, James N; Flanagan, William P; Hassib, Lamyaa; Molaison, Chris A; Ezbiansky, Karin; Medford, George; Reitz, Hariklia

2003-01-01

Coupling of combinatorial chemistry methods with high-throughput (HT) performance testing and measurements of resulting properties has provided a powerful set of tools for the 10-fold accelerated discovery of new high-performance coating materials for automotive applications. Our approach replaces labor-intensive steps with automated systems for evaluation of adhesion of 8 x 6 arrays of coating elements that are discretely deposited on a single 9 x 12 cm plastic substrate. Performance of coatings is evaluated with respect to their resistance to adhesion loss, because this parameter is one of the primary considerations in end-use automotive applications. Our HT adhesion evaluation provides previously unavailable capabilities of high speed and reproducibility of testing by using a robotic automation, an expanded range of types of tested coatings by using the coating tagging strategy, and an improved quantitation by using high signal-to-noise automatic imaging. Upon testing, the coatings undergo changes that are impossible to quantitatively predict using existing knowledge. Using our HT methodology, we have developed several coatings leads. These HT screening results for the best coating compositions have been validated on the traditional scales of coating formulation and adhesion loss testing. These validation results have confirmed the superb performance of combinatorially developed coatings over conventional coatings on the traditional scale.

Comment on "Nonuniqueness of algebraic first-order density-matrix functionals"

NASA Astrophysics Data System (ADS)

Gritsenko, O. V.

2018-02-01

Wang and Knowles (WK) [Phys. Rev. A 92, 012520 (2015), 10.1103/PhysRevA.92.012520] have given a counterexample to the conventional in reduced density-matrix functional theory representation of the second-order reduced density matrix (2RDM) Γi j ,k l in the basis of the natural orbitals as a function Γi j ,k l(n ) of the orbital occupation numbers (ONs) ni. The observed nonuniqueness of Γi j ,k l for prototype systems of different symmetry has been interpreted as the inherent inability of ON functions to reproduce the 2RDM, due to the insufficient information contained in the 1RDM spectrum. In this Comment, it is argued that, rather than totally invalidating Γi j ,k l(n ) , the WK example exposes its symmetry dependence which, as well as the previously established analogous dependence in density functional theory, is demonstrated with a general formulation based on the Levy constrained search.

Novel drug metabolism indices for pharmacogenetic functional status based on combinatory genotyping of CYP2C9, CYP2C19 and CYP2D6 genes

PubMed Central

Villagra, David; Goethe, John; Schwartz, Harold I; Szarek, Bonnie; Kocherla, Mohan; Gorowski, Krystyna; Windemuth, Andreas; Ruaño, Gualberto

2011-01-01

Aims We aim to demonstrate clinical relevance and utility of four novel drug-metabolism indices derived from a combinatory (multigene) approach to CYP2C9, CYP2C19 and CYP2D6 allele scoring. Each index considers all three genes as complementary components of a liver enzyme drug metabolism system and uniquely benchmarks innate hepatic drug metabolism reserve or alteration through CYP450 combinatory genotype scores. Methods A total of 1199 psychiatric referrals were genotyped for polymorphisms in the CYP2C9, CYP2C19 and CYP2D6 gene loci and were scored on each of the four indices. The data were used to create distributions and rankings of innate drug metabolism capacity to which individuals can be compared. Drug-specific indices are a combination of the drug metabolism indices with substrate-specific coefficients. Results The combinatory drug metabolism indices proved useful in positioning individuals relative to a population with regard to innate drug metabolism capacity prior to pharmacotherapy. Drug-specific indices generate pharmacogenetic guidance of immediate clinical relevance, and can be further modified to incorporate covariates in particular clinical cases. Conclusions We believe that this combinatory approach represents an improvement over the current gene-by-gene reporting by providing greater scope while still allowing for the resolution of a single-gene index when needed. This method will result in novel clinical and research applications, facilitating the translation from pharmacogenomics to personalized medicine, particularly in psychiatry where many drugs are metabolized or activated by multiple CYP450 isoenzymes. PMID:21861665

Combinatorial evolution of site- and enantioselective catalysts for polyene epoxidation

NASA Astrophysics Data System (ADS)

Lichtor, Phillip A.; Miller, Scott J.

2012-12-01

Selectivity in the catalytic functionalization of complex molecules is a major challenge in chemical synthesis. The problem is magnified when there are several possible stereochemical outcomes and when similar functional groups occur repeatedly within the same molecule. Selective polyene oxidation provides an archetypical example of this challenge. Historically, enzymatic catalysis has provided the only precedents. Although non-enzymatic catalysts that meet some of these challenges became known, a comprehensive solution has remained elusive. Here, we describe low molecular weight peptide-based catalysts, discovered through a combinatorial synthesis and screening protocol, that exhibit site- and enantioselective oxidation of certain positions of various isoprenols. This diversity-based approach, which exhibits features reminiscent of the directed evolution of enzymes, delivers catalysts that compare favourably to the state-of-the-art for the asymmetric oxidation of these compounds. Moreover, the approach culminated in catalysts that exhibit alternative-site selectivity in comparison to oxidation catalysts previously described.

Semilocal density functional obeying a strongly tightened bound for exchange

PubMed Central

Sun, Jianwei; Perdew, John P.; Ruzsinszky, Adrienn

2015-01-01

Because of its useful accuracy and efficiency, density functional theory (DFT) is one of the most widely used electronic structure theories in physics, materials science, and chemistry. Only the exchange-correlation energy is unknown, and needs to be approximated in practice. Exact constraints provide useful information about this functional. The local spin-density approximation (LSDA) was the first constraint-based density functional. The Lieb–Oxford lower bound on the exchange-correlation energy for any density is another constraint that plays an important role in the development of generalized gradient approximations (GGAs) and meta-GGAs. Recently, a strongly and optimally tightened lower bound on the exchange energy was proved for one- and two-electron densities, and conjectured for all densities. In this article, we present a realistic “meta-GGA made very simple” (MGGA-MVS) for exchange that respects this optimal bound, which no previous beyond-LSDA approximation satisfies. This constraint might have been expected to worsen predicted thermochemical properties, but in fact they are improved over those of the Perdew–Burke–Ernzerhof GGA, which has nearly the same correlation part. MVS exchange is however radically different from that of other GGAs and meta-GGAs. Its exchange enhancement factor has a very strong dependence upon the orbital kinetic energy density, which permits accurate energies even with the drastically tightened bound. When this nonempirical MVS meta-GGA is hybridized with 25% of exact exchange, the resulting global hybrid gives excellent predictions for atomization energies, reaction barriers, and weak interactions of molecules. PMID:25561554

Semilocal density functional obeying a strongly tightened bound for exchange.

PubMed

Sun, Jianwei; Perdew, John P; Ruzsinszky, Adrienn

2015-01-20

Because of its useful accuracy and efficiency, density functional theory (DFT) is one of the most widely used electronic structure theories in physics, materials science, and chemistry. Only the exchange-correlation energy is unknown, and needs to be approximated in practice. Exact constraints provide useful information about this functional. The local spin-density approximation (LSDA) was the first constraint-based density functional. The Lieb-Oxford lower bound on the exchange-correlation energy for any density is another constraint that plays an important role in the development of generalized gradient approximations (GGAs) and meta-GGAs. Recently, a strongly and optimally tightened lower bound on the exchange energy was proved for one- and two-electron densities, and conjectured for all densities. In this article, we present a realistic "meta-GGA made very simple" (MGGA-MVS) for exchange that respects this optimal bound, which no previous beyond-LSDA approximation satisfies. This constraint might have been expected to worsen predicted thermochemical properties, but in fact they are improved over those of the Perdew-Burke-Ernzerhof GGA, which has nearly the same correlation part. MVS exchange is however radically different from that of other GGAs and meta-GGAs. Its exchange enhancement factor has a very strong dependence upon the orbital kinetic energy density, which permits accurate energies even with the drastically tightened bound. When this nonempirical MVS meta-GGA is hybridized with 25% of exact exchange, the resulting global hybrid gives excellent predictions for atomization energies, reaction barriers, and weak interactions of molecules.

Combinatorial Polymer Matrices Enhance In Vitro Maturation of Human Induced Pluripotent Cell Cell-Derived Cardiomyocytes

PubMed Central

Chun, Young Wook; Balikov, Daniel A.; Feaster, Tromondae K.; Williams, Charles H.; Sheng, Calvin C.; Lee, Jung-Bok; Boire, Timothy C.; Neely, M. Diana; Bellan, Leon M.; Ess, Kevin C.; Bowman, Aaron B.; Sung, Hak-Joon; Hong, Charles C.

2015-01-01

Cardiomyocytes derived from human induced pluripotent stem cells (iPSC-CMs) hold great promise for modeling human heart diseases. However, iPSC-CMs studied to date resemble immature embryonic myocytes and therefore do not adequately recapitulate native adult cardiomyocyte phenotypes. Since extracellular matrix plays an essential role in heart development and maturation in vivo, we sought to develop a synthetic culture matrix that could enhance functional maturation of iPSC-CMs in vitro. In this study, we employed a library of combinatorial polymers comprising of three functional subunits - poly-ε-caprolacton (PCL), polyethylene glycol (PEG), and carboxylated PCL (cPCL) - as synthetic substrates for culturing human iPSC-CMs. Of these, iPSC-CMs cultured on 4%PEG-96%PCL (each % indicates the corresponding molar ratio) exhibit the greatest contractility and mitochondrial function. These functional enhancements are associated with increased expression of cardiac myosin light chain-2v, cardiac troponin I and integrin alpha-7. Importantly, iPSC-CMs cultured on 4%PEG-95%PCL demonstrate troponin I (TnI) isoform switch from the fetal slow skeletal TnI (ssTnI) to the postnatal cardiac TnI (cTnI), the first report of such transition in vitro. Finally, culturing iPSC-CMs on 4%PEG-96%PCL also significantly increased expression of genes encoding intermediate filaments known to transduce integrin-mediated mechanical signals to the myofilaments. In summary, our study demonstrates that synthetic culture matrices engineered from combinatorial polymers can be utilized to promote in vitro maturation of human iPSC-CMs through the engagement of critical matrix-integrin interactions. PMID:26204225

Electronic Coupling Calculations for Bridge-Mediated Charge Transfer Using Constrained Density Functional Theory (CDFT) and Effective Hamiltonian Approaches at the Density Functional Theory (DFT) and Fragment-Orbital Density Functional Tight Binding (FODFTB) Level.

PubMed

Gillet, Natacha; Berstis, Laura; Wu, Xiaojing; Gajdos, Fruzsina; Heck, Alexander; de la Lande, Aurélien; Blumberger, Jochen; Elstner, Marcus

2016-10-11

In this article, four methods to calculate charge transfer integrals in the context of bridge-mediated electron transfer are tested. These methods are based on density functional theory (DFT). We consider two perturbative Green's function effective Hamiltonian methods (first, at the DFT level of theory, using localized molecular orbitals; second, applying a tight-binding DFT approach, using fragment orbitals) and two constrained DFT implementations with either plane-wave or local basis sets. To assess the performance of the methods for through-bond (TB)-dominated or through-space (TS)-dominated transfer, different sets of molecules are considered. For through-bond electron transfer (ET), several molecules that were originally synthesized by Paddon-Row and co-workers for the deduction of electronic coupling values from photoemission and electron transmission spectroscopies, are analyzed. The tested methodologies prove to be successful in reproducing experimental data, the exponential distance decay constant and the superbridge effects arising from interference among ET pathways. For through-space ET, dedicated π-stacked systems with heterocyclopentadiene molecules were created and analyzed on the basis of electronic coupling dependence on donor-acceptor distance, structure of the bridge, and ET barrier height. The inexpensive fragment-orbital density functional tight binding (FODFTB) method gives similar results to constrained density functional theory (CDFT) and both reproduce the expected exponential decay of the coupling with donor-acceptor distances and the number of bridging units. These four approaches appear to give reliable results for both TB and TS ET and present a good alternative to expensive ab initio methodologies for large systems involving long-range charge transfers.

Density-functional expansion methods: evaluation of LDA, GGA, and meta-GGA functionals and different integral approximations.

PubMed

Giese, Timothy J; York, Darrin M

2010-12-28

We extend the Kohn-Sham potential energy expansion (VE) to include variations of the kinetic energy density and use the VE formulation with a 6-31G* basis to perform a "Jacob's ladder" comparison of small molecule properties using density functionals classified as being either LDA, GGA, or meta-GGA. We show that the VE reproduces standard Kohn-Sham DFT results well if all integrals are performed without further approximation, and there is no substantial improvement in using meta-GGA functionals relative to GGA functionals. The advantages of using GGA versus LDA functionals becomes apparent when modeling hydrogen bonds. We furthermore examine the effect of using integral approximations to compute the zeroth-order energy and first-order matrix elements, and the results suggest that the origin of the short-range repulsive potential within self-consistent charge density-functional tight-binding methods mainly arises from the approximations made to the first-order matrix elements.

Scaffold architecture and pharmacophoric properties of natural products and trade drugs: application in the design of natural product-based combinatorial libraries.

PubMed

Lee, M L; Schneider, G

2001-01-01

Natural products were analyzed to determine whether they contain appealing novel scaffold architectures for potential use in combinatorial chemistry. Ring systems were extracted and clustered on the basis of structural similarity. Several such potential scaffolds for combinatorial chemistry were identified that are not present in current trade drugs. For one of these scaffolds a virtual combinatorial library was generated. Pharmacophoric properties of natural products, trade drugs, and the virtual combinatorial library were assessed using a self-organizing map. Obviously, current trade drugs and natural products have several topological pharmacophore patterns in common. These features can be systematically explored with selected combinatorial libraries based on a combination of natural product-derived and synthetic molecular building blocks.

Multiconfiguration pair-density functional theory: barrier heights and main group and transition metal energetics.

PubMed

Carlson, Rebecca K; Li Manni, Giovanni; Sonnenberger, Andrew L; Truhlar, Donald G; Gagliardi, Laura

2015-01-13

Kohn-Sham density functional theory, resting on the representation of the electronic density and kinetic energy by a single Slater determinant, has revolutionized chemistry, but for open-shell systems, the Kohn-Sham Slater determinant has the wrong symmetry properties as compared to an accurate wave function. We have recently proposed a theory, called multiconfiguration pair-density functional theory (MC-PDFT), in which the electronic kinetic energy and classical Coulomb energy are calculated from a multiconfiguration wave function with the correct symmetry properties, and the rest of the energy is calculated from a density functional, called the on-top density functional, that depends on the density and the on-top pair density calculated from this wave function. We also proposed a simple way to approximate the on-top density functional by translation of Kohn-Sham exchange-correlation functionals. The method is much less expensive than other post-SCF methods for calculating the dynamical correlation energy starting with a multiconfiguration self-consistent-field wave function as the reference wave function, and initial tests of the theory were quite encouraging. Here, we provide a broader test of the theory by applying it to bond energies of main-group molecules and transition metal complexes, barrier heights and reaction energies for diverse chemical reactions, proton affinities, and the water dimerization energy. Averaged over 56 data points, the mean unsigned error is 3.2 kcal/mol for MC-PDFT, as compared to 6.9 kcal/mol for Kohn-Sham theory with a comparable density functional. MC-PDFT is more accurate on average than complete active space second-order perturbation theory (CASPT2) for main-group small-molecule bond energies, alkyl bond dissociation energies, transition-metal-ligand bond energies, proton affinities, and the water dimerization energy.

Identities for Generalized Fibonacci Numbers: A Combinatorial Approach

ERIC Educational Resources Information Center

Plaza, A.; Falcon, S.

2008-01-01

This note shows a combinatorial approach to some identities for generalized Fibonacci numbers. While it is a straightforward task to prove these identities with induction, and also by arithmetical manipulations such as rearrangements, the approach used here is quite simple to follow and eventually reduces the proof to a counting problem. (Contains…

Combinatorial Multiobjective Optimization Using Genetic Algorithms

NASA Technical Reports Server (NTRS)

Crossley, William A.; Martin. Eric T.

2002-01-01

The research proposed in this document investigated multiobjective optimization approaches based upon the Genetic Algorithm (GA). Several versions of the GA have been adopted for multiobjective design, but, prior to this research, there had not been significant comparisons of the most popular strategies. The research effort first generalized the two-branch tournament genetic algorithm in to an N-branch genetic algorithm, then the N-branch GA was compared with a version of the popular Multi-Objective Genetic Algorithm (MOGA). Because the genetic algorithm is well suited to combinatorial (mixed discrete / continuous) optimization problems, the GA can be used in the conceptual phase of design to combine selection (discrete variable) and sizing (continuous variable) tasks. Using a multiobjective formulation for the design of a 50-passenger aircraft to meet the competing objectives of minimizing takeoff gross weight and minimizing trip time, the GA generated a range of tradeoff designs that illustrate which aircraft features change from a low-weight, slow trip-time aircraft design to a heavy-weight, short trip-time aircraft design. Given the objective formulation and analysis methods used, the results of this study identify where turboprop-powered aircraft and turbofan-powered aircraft become more desirable for the 50 seat passenger application. This aircraft design application also begins to suggest how a combinatorial multiobjective optimization technique could be used to assist in the design of morphing aircraft.

Density functional with full exact exchange, balanced nonlocality of correlations, and constraint satisfaction

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

Tao, Jianmin; Perdew, John P; Staroverov, Viktor N

2008-01-01

We construct a nonlocal density functional approximation with full exact exchange, while preserving the constraint-satisfaction approach and justified error cancellations of simpler semilocal functionals. This is achieved by interpolating between different approximations suitable for two extreme regions of the electron density. In a 'normal' region, the exact exchange-correlation hole density around an electron is semilocal because its spatial range is reduced by correlation and because it integrates over a narrow range to -1. These regions are well described by popular semilocal approximations (many of which have been constructed nonempirically), because of proper accuracy for a slowly-varying density or because ofmore » error cancellation between exchange and correlation. 'Abnormal' regions, where non locality is unveiled, include those in which exchange can dominate correlation (one-electron, nonuniform high-density, and rapidly-varying limits), and those open subsystems of fluctuating electron number over which the exact exchange-correlation hole integrates to a value greater than -1. Regions between these extremes are described by a hybrid functional mixing exact and semi local exchange energy densities locally (i.e., with a mixing fraction that is a function of position r and a functional of the density). Because our mixing fraction tends to 1 in the high-density limit, we employ full exact exchange according to the rigorous definition of the exchange component of any exchange-correlation energy functional. Use of full exact exchange permits the satisfaction of many exact constraints, but the nonlocality of exchange also requires balanced nonlocality of correlation. We find that this nonlocality can demand at least five empirical parameters (corresponding roughly to the four kinds of abnormal regions). Our local hybrid functional is perhaps the first accurate size-consistent density functional with full exact exchange. It satisfies other known exact

Exact density functional theory for ideal polymer fluids with nearest neighbor bonding constraints.

PubMed

Woodward, Clifford E; Forsman, Jan

2008-08-07

We present a new density functional theory of ideal polymer fluids, assuming nearest-neighbor bonding constraints. The free energy functional is expressed in terms of end site densities of chain segments and thus has a simpler mathematical structure than previously used expressions using multipoint distributions. This work is based on a formalism proposed by Tripathi and Chapman [Phys. Rev. Lett. 94, 087801 (2005)]. Those authors obtain an approximate free energy functional for ideal polymers in terms of monomer site densities. Calculations on both repulsive and attractive surfaces show that their theory is reasonably accurate in some cases, but does differ significantly from the exact result for longer polymers with attractive surfaces. We suggest that segment end site densities, rather than monomer site densities, are the preferred choice of "site functions" for expressing the free energy functional of polymer fluids. We illustrate the application of our theory to derive an expression for the free energy of an ideal fluid of infinitely long polymers.

Dirac Operator in Several Variables and Combinatorial Identities

NASA Astrophysics Data System (ADS)

Damiano, Alberto; Souček, Vladimír

2007-09-01

The Dolbeault sequence is a fundamental tool for many problems in the function theory of several complex variables. A lot of attention was paid in the last decades to its analogue in the function theory of several Clifford variables. The first operator in this resolution is the Dirac operator in several variables. The complete description is known in dimension 4 (i.e., in the case of quaternionic variables, see [1, 6, 4]). Much less is known in higher dimensions. The case of three variables was described completely (see [18]). The full description of the complex for all dimensions is not known at present. Even the case of the stable range (i.e., when the number of variables is less or equal to the half of dimension) is still not fully understood. There are two different approaches to the stable range case, one based on classical algebraic geometry (the Hilbert syzygy theory, see [8]), the other one on representation theory (differential invariants in certain parabolic geometries, see [14, 20]). Differential operators in these resolutions are acting on vector-valued functions. Such spaces of functions are quite complicated in general and the first problem in the description of the resolution is to understand their dimensions. Both the approaches mentioned above suggest an answer to this question, although such answers look quite different. The aim of the paper is to compare these two results and to show that they lead to complicated combinatorial identities.

Construction of a virtual combinatorial library using SMILES strings to discover potential structure-diverse PPAR modulators.

PubMed

Liao, Chenzhong; Liu, Bing; Shi, Leming; Zhou, Jiaju; Lu, Xian-Ping

2005-07-01

Based on the structural characters of PPAR modulators, a virtual combinatorial library containing 1226,625 compounds was constructed using SMILES strings. Selected ADME filters were employed to compel compounds having poor drug-like properties from this library. This library was converted to sdf and mol2 files by CONCORD 4.0, and was then docked to PPARgamma by DOCK 4.0 to identify new chemical entities that may be potential drug leads against type 2 diabetes and other metabolic diseases. The method to construct virtual combinatorial library using SMILES strings was further visualized by Visual Basic.net that can facilitate the needs of generating other type virtual combinatorial libraries.

Computational efficiency of parallel combinatorial OR-tree searches

NASA Technical Reports Server (NTRS)

Li, Guo-Jie; Wah, Benjamin W.

1990-01-01

The performance of parallel combinatorial OR-tree searches is analytically evaluated. This performance depends on the complexity of the problem to be solved, the error allowance function, the dominance relation, and the search strategies. The exact performance may be difficult to predict due to the nondeterminism and anomalies of parallelism. The authors derive the performance bounds of parallel OR-tree searches with respect to the best-first, depth-first, and breadth-first strategies, and verify these bounds by simulation. They show that a near-linear speedup can be achieved with respect to a large number of processors for parallel OR-tree searches. Using the bounds developed, the authors derive sufficient conditions for assuring that parallelism will not degrade performance and necessary conditions for allowing parallelism to have a speedup greater than the ratio of the numbers of processors. These bounds and conditions provide the theoretical foundation for determining the number of processors required to assure a near-linear speedup.

Efficient molecular density functional theory using generalized spherical harmonics expansions.

PubMed

Ding, Lu; Levesque, Maximilien; Borgis, Daniel; Belloni, Luc

2017-09-07

We show that generalized spherical harmonics are well suited for representing the space and orientation molecular density in the resolution of the molecular density functional theory. We consider the common system made of a rigid solute of arbitrary complexity immersed in a molecular solvent, both represented by molecules with interacting atomic sites and classical force fields. The molecular solvent density ρ(r,Ω) around the solute is a function of the position r≡(x,y,z) and of the three Euler angles Ω≡(θ,ϕ,ψ) describing the solvent orientation. The standard density functional, equivalent to the hypernetted-chain closure for the solute-solvent correlations in the liquid theory, is minimized with respect to ρ(r,Ω). The up-to-now very expensive angular convolution products are advantageously replaced by simple products between projections onto generalized spherical harmonics. The dramatic gain in speed of resolution enables to explore in a systematic way molecular solutes of up to nanometric sizes in arbitrary solvents and to calculate their solvation free energy and associated microscopic solvent structure in at most a few minutes. We finally illustrate the formalism by tackling the solvation of molecules of various complexities in water.

Restoring the consistency with the contact density theorem of a classical density functional theory of ions at a planar electrical double layer.

PubMed

Gillespie, Dirk

2014-11-01

Classical density functional theory (DFT) of fluids is a fast and efficient theory to compute the structure of the electrical double layer in the primitive model of ions where ions are modeled as charged, hard spheres in a background dielectric. While the hard-core repulsive component of this ion-ion interaction can be accurately computed using well-established DFTs, the electrostatic component is less accurate. Moreover, many electrostatic functionals fail to satisfy a basic theorem, the contact density theorem, that relates the bulk pressure, surface charge, and ion densities at their distances of closest approach for ions in equilibrium at a smooth, hard, planar wall. One popular electrostatic functional that fails to satisfy the contact density theorem is a perturbation approach developed by Kierlik and Rosinberg [Phys. Rev. A 44, 5025 (1991)PLRAAN1050-294710.1103/PhysRevA.44.5025] and Rosenfeld [J. Chem. Phys. 98, 8126 (1993)JCPSA60021-960610.1063/1.464569], where the full free-energy functional is Taylor-expanded around a bulk (homogeneous) reference fluid. Here, it is shown that this functional fails to satisfy the contact density theorem because it also fails to satisfy the known low-density limit. When the functional is corrected to satisfy this limit, a corrected bulk pressure is derived and it is shown that with this pressure both the contact density theorem and the Gibbs adsorption theorem are satisfied.

Correlation functional in screened-exchange density functional theory procedures.

PubMed

Chan, Bun; Kawashima, Yukio; Hirao, Kimihiko

2017-10-15

In the present study, we have explored several prospects for the further development of screened-exchange density functional theory (SX-DFT) procedures. Using the performance of HSE06 as our measure, we find that the use of alternative correlation functionals (as oppose to PBEc in HSE06) also yields adequate results for a diverse set of thermochemical properties. We have further examined the performance of new SX-DFT procedures (termed HSEB-type methods) that comprise the HSEx exchange and a (near-optimal) reparametrized B97c (c OS,0  = c SS,0  = 1, c OS,1  = -1.5, c OS,2  = -0.644, c SS,1  = -0.5, and c SS,2  = 1.10) correlation functionals. The different variants of HSEB all perform comparably to or slightly better than the original HSE-type procedures. These results, together with our fundamental analysis of correlation functionals, point toward various directions for advancing SX-DFT methods. © 2017 Wiley Periodicals, Inc. © 2017 Wiley Periodicals, Inc.

Enabling techniques in the search for new antibiotics: Combinatorial biosynthesis of sugar-containing antibiotics.

PubMed

Park, Je Won; Nam, Sang-Jip; Yoon, Yeo Joon

2017-06-15

Nature has a talent for inventing a vast number of natural products, including hybrids generated by blending different scaffolds, resulting in a myriad of bioactive chemical entities. Herein, we review the highlights and recent trends (2010-2016) in the combinatorial biosynthesis of sugar-containing antibiotics where nature's structural diversification capabilities are exploited to enable the creation of new anti-infective and anti-proliferative drugs. In this review, we describe the modern combinatorial biosynthetic approaches for polyketide synthase-derived complex and aromatic polyketides, non-ribosomal peptide synthetase-directed lipo-/glycopeptides, aminoglycosides, nucleoside antibiotics, and alkaloids, along with their therapeutic potential. Finally, we present the feasible nexus between combinatorial biosynthesis, systems biology, and synthetic biology as a toolbox to provide new antibiotics that will be indispensable in the post-antibiotic era. Copyright © 2016 Elsevier Inc. All rights reserved.

Electronic Coupling Calculations for Bridge-Mediated Charge Transfer Using Constrained Density Functional Theory (CDFT) and Effective Hamiltonian Approaches at the Density Functional Theory (DFT) and Fragment-Orbital Density Functional Tight Binding (FODFTB) Level

DOE PAGES

Gillet, Natacha; Berstis, Laura; Wu, Xiaojing; ...

2016-09-09

In this paper, four methods to calculate charge transfer integrals in the context of bridge-mediated electron transfer are tested. These methods are based on density functional theory (DFT). We consider two perturbative Green's function effective Hamiltonian methods (first, at the DFT level of theory, using localized molecular orbitals; second, applying a tight-binding DFT approach, using fragment orbitals) and two constrained DFT implementations with either plane-wave or local basis sets. To assess the performance of the methods for through-bond (TB)-dominated or through-space (TS)-dominated transfer, different sets of molecules are considered. For through-bond electron transfer (ET), several molecules that were originally synthesizedmore » by Paddon-Row and co-workers for the deduction of electronic coupling values from photoemission and electron transmission spectroscopies, are analyzed. The tested methodologies prove to be successful in reproducing experimental data, the exponential distance decay constant and the superbridge effects arising from interference among ET pathways. For through-space ET, dedicated p-stacked systems with heterocyclopentadiene molecules were created and analyzed on the basis of electronic coupling dependence on donor-acceptor distance, structure of the bridge, and ET barrier height. The inexpensive fragment-orbital density functional tight binding (FODFTB) method gives similar results to constrained density functional theory (CDFT) and both reproduce the expected exponential decay of the coupling with donor-acceptor distances and the number of bridging units. Finally, these four approaches appear to give reliable results for both TB and TS ET and present a good alternative to expensive ab initio methodologies for large systems involving long-range charge transfers.« less

Electronic Coupling Calculations for Bridge-Mediated Charge Transfer Using Constrained Density Functional Theory (CDFT) and Effective Hamiltonian Approaches at the Density Functional Theory (DFT) and Fragment-Orbital Density Functional Tight Binding (FODFTB) Level

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

Gillet, Natacha; Berstis, Laura; Wu, Xiaojing

In this paper, four methods to calculate charge transfer integrals in the context of bridge-mediated electron transfer are tested. These methods are based on density functional theory (DFT). We consider two perturbative Green's function effective Hamiltonian methods (first, at the DFT level of theory, using localized molecular orbitals; second, applying a tight-binding DFT approach, using fragment orbitals) and two constrained DFT implementations with either plane-wave or local basis sets. To assess the performance of the methods for through-bond (TB)-dominated or through-space (TS)-dominated transfer, different sets of molecules are considered. For through-bond electron transfer (ET), several molecules that were originally synthesizedmore » by Paddon-Row and co-workers for the deduction of electronic coupling values from photoemission and electron transmission spectroscopies, are analyzed. The tested methodologies prove to be successful in reproducing experimental data, the exponential distance decay constant and the superbridge effects arising from interference among ET pathways. For through-space ET, dedicated p-stacked systems with heterocyclopentadiene molecules were created and analyzed on the basis of electronic coupling dependence on donor-acceptor distance, structure of the bridge, and ET barrier height. The inexpensive fragment-orbital density functional tight binding (FODFTB) method gives similar results to constrained density functional theory (CDFT) and both reproduce the expected exponential decay of the coupling with donor-acceptor distances and the number of bridging units. Finally, these four approaches appear to give reliable results for both TB and TS ET and present a good alternative to expensive ab initio methodologies for large systems involving long-range charge transfers.« less

A Density Functional for Liquid 3He Based on the Aziz Potential

NASA Astrophysics Data System (ADS)

Barranco, M.; Hernández, E. S.; Mayol, R.; Navarro, J.; Pi, M.; Szybisz, L.

2006-09-01

We propose a new class of density functionals for liquid 3He based on the Aziz helium-helium interaction screened at short distances by the microscopically calculated two-body distribution function g(r). Our aim is to reduce to a minumum the unavoidable phenomenological ingredients inherent to any density functional approach. Results for the homogeneous liquid and droplets are presented and discussed.

Phase Transitions in Combinatorial Optimization Problems: Basics, Algorithms and Statistical Mechanics

NASA Astrophysics Data System (ADS)

Hartmann, Alexander K.; Weigt, Martin

2005-10-01

A concise, comprehensive introduction to the topic of statistical physics of combinatorial optimization, bringing together theoretical concepts and algorithms from computer science with analytical methods from physics. The result bridges the gap between statistical physics and combinatorial optimization, investigating problems taken from theoretical computing, such as the vertex-cover problem, with the concepts and methods of theoretical physics. The authors cover rapid developments and analytical methods that are both extremely complex and spread by word-of-mouth, providing all the necessary basics in required detail. Throughout, the algorithms are shown with examples and calculations, while the proofs are given in a way suitable for graduate students, post-docs, and researchers. Ideal for newcomers to this young, multidisciplinary field.

Generalized Pauli constraints in reduced density matrix functional theory.

PubMed

Theophilou, Iris; Lathiotakis, Nektarios N; Marques, Miguel A L; Helbig, Nicole

2015-04-21

Functionals of the one-body reduced density matrix (1-RDM) are routinely minimized under Coleman's ensemble N-representability conditions. Recently, the topic of pure-state N-representability conditions, also known as generalized Pauli constraints, received increased attention following the discovery of a systematic way to derive them for any number of electrons and any finite dimensionality of the Hilbert space. The target of this work is to assess the potential impact of the enforcement of the pure-state conditions on the results of reduced density-matrix functional theory calculations. In particular, we examine whether the standard minimization of typical 1-RDM functionals under the ensemble N-representability conditions violates the pure-state conditions for prototype 3-electron systems. We also enforce the pure-state conditions, in addition to the ensemble ones, for the same systems and functionals and compare the correlation energies and optimal occupation numbers with those obtained by the enforcement of the ensemble conditions alone.

Density functional theory for d- and f-electron materials and compounds

DOE PAGES

Mattson, Ann E.; Wills, John M.

2016-02-12

Here, the fundamental requirements for a computationally tractable Density Functional Theory-based method for relativistic f- and (nonrelativistic) d-electron materials and compounds are presented. The need for basing the Kohn–Sham equations on the Dirac equation is discussed. The full Dirac scheme needs exchange-correlation functionals in terms of four-currents, but ordinary functionals, using charge density and spin-magnetization, can be used in an approximate Dirac treatment. The construction of a functional that includes the additional confinement physics needed for these materials is illustrated using the subsystem-functional scheme. If future studies show that a full Dirac, four-current based, exchange-correlation functional is needed, the subsystemmore » functional scheme is one of the few schemes that can still be used for constructing functional approximations.« less

Multiconfiguration Pair-Density Functional Theory Is as Accurate as CASPT2 for Electronic Excitation.

PubMed

Hoyer, Chad E; Ghosh, Soumen; Truhlar, Donald G; Gagliardi, Laura

2016-02-04

A correct description of electronically excited states is critical to the interpretation of visible-ultraviolet spectra, photochemical reactions, and excited-state charge-transfer processes in chemical systems. We have recently proposed a theory called multiconfiguration pair-density functional theory (MC-PDFT), which is based on a combination of multiconfiguration wave function theory and a new kind of density functional called an on-top density functional. Here, we show that MC-PDFT with a first-generation on-top density functional performs as well as CASPT2 for an organic chemistry database including valence, Rydberg, and charge-transfer excitations. The results are very encouraging for practical applications.

Extending density functional embedding theory for covalently bonded systems.

PubMed

Yu, Kuang; Carter, Emily A

2017-12-19

Quantum embedding theory aims to provide an efficient solution to obtain accurate electronic energies for systems too large for full-scale, high-level quantum calculations. It adopts a hierarchical approach that divides the total system into a small embedded region and a larger environment, using different levels of theory to describe each part. Previously, we developed a density-based quantum embedding theory called density functional embedding theory (DFET), which achieved considerable success in metals and semiconductors. In this work, we extend DFET into a density-matrix-based nonlocal form, enabling DFET to study the stronger quantum couplings between covalently bonded subsystems. We name this theory density-matrix functional embedding theory (DMFET), and we demonstrate its performance in several test examples that resemble various real applications in both chemistry and biochemistry. DMFET gives excellent results in all cases tested thus far, including predicting isomerization energies, proton transfer energies, and highest occupied molecular orbital-lowest unoccupied molecular orbital gaps for local chromophores. Here, we show that DMFET systematically improves the quality of the results compared with the widely used state-of-the-art methods, such as the simple capped cluster model or the widely used ONIOM method.

Structural, Electronic and Dynamical Properties of Curium Monopnictides: Density Functional Calculations

NASA Astrophysics Data System (ADS)

Roondhe, Basant; Upadhyay, Deepak; Som, Narayan; Pillai, Sharad B.; Shinde, Satyam; Jha, Prafulla K.

2017-03-01

The structural, electronic, dynamical and thermodynamical properties of CmX (X = N, P, As, Sb, and Bi) compounds are studied using first principles calculations within density functional theory. The Perdew-Burke-Ernzerhof spin polarized generalized gradient approximation and Perdew-Wang (PW) spin polarized local density approximation as the exchange correlational functionals are used in these calculations. There is a good agreement between the present and previously reported data. The calculated electronic density of states suggests that the curium monopnictides are metallic in nature, which is consistent with earlier studies. The significant values of magnetic moment suggest their magnetic nature. The phonon dispersion curves and phonon density of states are also calculated, which depict the dynamical stability of these compounds. There is a significant separation between the optical and acoustical phonon branches. The temperature dependence of the thermodynamical functions are also calculated and discussed. Internal energy and vibrational contribution to the Helmholtz free energy increases and decreases, respectively, with temperature. The entropy increases with temperature. The specific heat at constant volume and Debye temperature obey Debye theory. The temperature variation of the considered thermodynamical functions is in line with those of other crystalline solids.

Combinatorial study of degree assortativity in networks.

PubMed

Estrada, Ernesto

2011-10-01

Why are some networks degree-degree correlated (assortative), while most of the real-world ones are anticorrelated (disassortative)? Here, we prove, by combinatorial methods, that the assortativity of a network depends only on three structural factors: transitivity (clustering coefficient), intermodular connectivity, and branching. Then, a network is assortative if the contributions of the first two factors are larger than that of the third. Highly branched networks are likely to be disassortative.

Quantum electronic stress: density-functional-theory formulation and physical manifestation.

PubMed

Hu, Hao; Liu, Miao; Wang, Z F; Zhu, Junyi; Wu, Dangxin; Ding, Hepeng; Liu, Zheng; Liu, Feng

2012-08-03

The concept of quantum electronic stress (QES) is introduced and formulated within density functional theory to elucidate extrinsic electronic effects on the stress state of solids and thin films in the absence of lattice strain. A formal expression of QES (σ(QE)) is derived in relation to deformation potential of electronic states (Ξ) and variation of electron density (Δn), σ(QE) = ΞΔn as a quantum analog of classical Hooke's law. Two distinct QES manifestations are demonstrated quantitatively by density functional theory calculations: (1) in the form of bulk stress induced by charge carriers and (2) in the form of surface stress induced by quantum confinement. Implications of QES in some physical phenomena are discussed to underlie its importance.

Lattice density functional theory for confined Ising fluids: comparison between different functional approximations in slit pore

NASA Astrophysics Data System (ADS)

Chen, Xueqian; Feng, Wei; Liu, Honglai; Hu, Ying

2016-09-01

In this paper, Lafuente and Cuesta's cluster density functional theory (CDFT) and lattice mean field approximation (LMFA) are formulated and compared within the framework of lattice density functional theory (LDFT). As a comparison, an LDFT based on our previous work on nonrandom correction to LMFA is also developed, where local density approximation is adopted on the correction. The numerical results of density distributions of an Ising fluid confined in a slit pore obtained from Monte Carlo simulation are used to check these functional approximations. Due to rational treatment on the coupling between site-excluding entropic effect and contact-attracting enthalpic effect by CDFT with Bethe-Peierls approximation (named as BPA-CDFT for short), the improvement of BPA-CDFT beyond LMFA is checked as expected. And it is interesting that our LDFT has a comparative accuracy with BPA-CDFT. Apparent differences between the profiles such as solvation force, excess adsorption quantity and interfacial tension from LMFA and non-LMFAs are found in our calculations. We also discuss some possible theoretical extensions of BPA-CDFT.

Interconfigurational energies in transition-metal atoms using gradient-corrected density-functional theory

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

Kutzler, F.W.; Painter, G.S.

1991-03-15

The rapid variation of charge and spin densities in atoms and molecules provides a severe test for local-density-functional theory and for the use of gradient corrections. In the study reported in this paper, we use the Langreth, Mehl, and Hu (LMH) functional and the generalized gradient approximation (GGA) of Perdew and Yue to calculate {ital s}-{ital d} transition energies, 4{ital s} ionization energies, and 3{ital d} ionization energies for the 3{ital d} transition-metal atoms. These calculations are compared with results from the local-density functional of Vosko, Wilk, and Nusair. By comparison with experimental energies, we find that the gradient functionalsmore » are only marginally more successful than the local-density approximation in calculating energy differences between states in transition-metal atoms. The GGA approximation is somewhat better than the LMH functional for most of the atoms studied, although there are several exceptions.« less

Two-Component Noncollinear Time-Dependent Spin Density Functional Theory for Excited State Calculations.

PubMed

Egidi, Franco; Sun, Shichao; Goings, Joshua J; Scalmani, Giovanni; Frisch, Michael J; Li, Xiaosong

2017-06-13

We present a linear response formalism for the description of the electronic excitations of a noncollinear reference defined via Kohn-Sham spin density functional methods. A set of auxiliary variables, defined using the density and noncollinear magnetization density vector, allows the generalization of spin density functional kernels commonly used in collinear DFT to noncollinear cases, including local density, GGA, meta-GGA and hybrid functionals. Working equations and derivations of functional second derivatives with respect to the noncollinear density, required in the linear response noncollinear TDDFT formalism, are presented in this work. This formalism takes all components of the spin magnetization into account independent of the type of reference state (open or closed shell). As a result, the method introduced here is able to afford a nonzero local xc torque on the spin magnetization while still satisfying the zero-torque theorem globally. The formalism is applied to a few test cases using the variational exact-two-component reference including spin-orbit coupling to illustrate the capabilities of the method.

Surface symmetry energy of nuclear energy density functionals

NASA Astrophysics Data System (ADS)

Nikolov, N.; Schunck, N.; Nazarewicz, W.; Bender, M.; Pei, J.

2011-03-01

We study the bulk deformation properties of the Skyrme nuclear energy density functionals (EDFs). 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 EDFs. 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.

Clustering and pasta phases in nuclear density functional theory

DOE PAGES

Schuetrumpf, Bastian; Zhang, Chunli; Nazarewicz, Witold

2017-05-23

Nuclear density functional theory is the tool of choice in describing properties of complex nuclei and intricate phases of bulk nucleonic matter. It is a microscopic approach based on an energy density functional representing the nuclear interaction. An attractive feature of nuclear DFT is that it can be applied to both finite nuclei and pasta phases appearing in the inner crust of neutron stars. While nuclear pasta clusters in a neutron star can be easily characterized through their density distributions, the level of clustering of nucleons in a nucleus can often be difficult to assess. To this end, we usemore » the concept of nucleon localization. We demonstrate that the localization measure provides us with fingerprints of clusters in light and heavy nuclei, including fissioning systems. Furthermore we investigate the rod-like pasta phase using twist-averaged boundary conditions, which enable calculations in finite volumes accessible by state of the art DFT solvers.« less

JDFTx: Software for joint density-functional theory

DOE PAGES

Sundararaman, Ravishankar; Letchworth-Weaver, Kendra; Schwarz, Kathleen A.; ...

2017-11-14

Density-functional theory (DFT) has revolutionized computational prediction of atomic-scale properties from first principles in physics, chemistry and materials science. Continuing development of new methods is necessary for accurate predictions of new classes of materials and properties, and for connecting to nano- and mesoscale properties using coarse-grained theories. JDFTx is a fully-featured open-source electronic DFT software designed specifically to facilitate rapid development of new theories, models and algorithms. Using an algebraic formulation as an abstraction layer, compact C++11 code automatically performs well on diverse hardware including GPUs (Graphics Processing Units). This code hosts the development of joint density-functional theory (JDFT) thatmore » combines electronic DFT with classical DFT and continuum models of liquids for first-principles calculations of solvated and electrochemical systems. In addition, the modular nature of the code makes it easy to extend and interface with, facilitating the development of multi-scale toolkits that connect to ab initio calculations, e.g. photo-excited carrier dynamics combining electron and phonon calculations with electromagnetic simulations.« less

JDFTx: Software for joint density-functional theory

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

Sundararaman, Ravishankar; Letchworth-Weaver, Kendra; Schwarz, Kathleen A.

Density-functional theory (DFT) has revolutionized computational prediction of atomic-scale properties from first principles in physics, chemistry and materials science. Continuing development of new methods is necessary for accurate predictions of new classes of materials and properties, and for connecting to nano- and mesoscale properties using coarse-grained theories. JDFTx is a fully-featured open-source electronic DFT software designed specifically to facilitate rapid development of new theories, models and algorithms. Using an algebraic formulation as an abstraction layer, compact C++11 code automatically performs well on diverse hardware including GPUs (Graphics Processing Units). This code hosts the development of joint density-functional theory (JDFT) thatmore » combines electronic DFT with classical DFT and continuum models of liquids for first-principles calculations of solvated and electrochemical systems. In addition, the modular nature of the code makes it easy to extend and interface with, facilitating the development of multi-scale toolkits that connect to ab initio calculations, e.g. photo-excited carrier dynamics combining electron and phonon calculations with electromagnetic simulations.« less

Coarse-grained density functional theories for metallic alloys: Generalized coherent-potential approximations and charge-excess functional theory

NASA Astrophysics Data System (ADS)

Bruno, Ezio; Mammano, Francesco; Fiorino, Antonino; Morabito, Emanuela V.

2008-04-01

The class of the generalized coherent-potential approximations (GCPAs) to the density functional theory (DFT) is introduced within the multiple scattering theory formalism with the aim of dealing with ordered or disordered metallic alloys. All GCPA theories are based on a common ansatz for the kinetic part of the Hohenberg-Kohn functional and each theory of the class is specified by an external model concerning the potential reconstruction. Most existing DFT implementations of CPA-based theories belong to the GCPA class. The analysis of the formal properties of the density functional defined by GCPA theories shows that it consists of marginally coupled local contributions. Furthermore, it is shown that the GCPA functional does not depend on the details of the charge density and that it can be exactly rewritten as a function of the appropriate charge multipole moments to be associated with each lattice site. A general procedure based on the integration of the qV laws is described that allows for the explicit construction of the same function. The coarse-grained nature of the GCPA density functional implies a great deal of computational advantages and is connected with the O(N) scalability of GCPA algorithms. Moreover, it is shown that a convenient truncated series expansion of the GCPA functional leads to the charge-excess functional (CEF) theory [E. Bruno , Phys. Rev. Lett. 91, 166401 (2003)], which here is offered in a generalized version that includes multipolar interactions. CEF and the GCPA numerical results are compared with status of art linearized augmented plane wave (LAPW) full-potential density functional calculations for 62 bcc- and fcc-based ordered CuZn alloys, in all the range of concentrations. Two facts clearly emerge from these extensive tests. In the first place, the discrepancies between GCPA and CEF results are always within the numerical accuracy of the calculations, both for the site charges and the total energies. In the second place, the

Expediting Combinatorial Data Set Analysis by Combining Human and Algorithmic Analysis.

PubMed

Stein, Helge Sören; Jiao, Sally; Ludwig, Alfred

2017-01-09

A challenge in combinatorial materials science remains the efficient analysis of X-ray diffraction (XRD) data and its correlation to functional properties. Rapid identification of phase-regions and proper assignment of corresponding crystal structures is necessary to keep pace with the improved methods for synthesizing and characterizing materials libraries. Therefore, a new modular software called htAx (high-throughput analysis of X-ray and functional properties data) is presented that couples human intelligence tasks used for "ground-truth" phase-region identification with subsequent unbiased verification by an algorithm to efficiently analyze which phases are present in a materials library. Identified phases and phase-regions may then be correlated to functional properties in an expedited manner. For the functionality of htAx to be proven, two previously published XRD benchmark data sets of the materials systems Al-Cr-Fe-O and Ni-Ti-Cu are analyzed by htAx. The analysis of ∼1000 XRD patterns takes less than 1 day with htAx. The proposed method reliably identifies phase-region boundaries and robustly identifies multiphase structures. The method also addresses the problem of identifying regions with previously unpublished crystal structures using a special daisy ternary plot.

A combinatorial code for pattern formation in Drosophila oogenesis.

PubMed

Yakoby, Nir; Bristow, Christopher A; Gong, Danielle; Schafer, Xenia; Lembong, Jessica; Zartman, Jeremiah J; Halfon, Marc S; Schüpbach, Trudi; Shvartsman, Stanislav Y

2008-11-01

Two-dimensional patterning of the follicular epithelium in Drosophila oogenesis is required for the formation of three-dimensional eggshell structures. Our analysis of a large number of published gene expression patterns in the follicle cells suggests that they follow a simple combinatorial code based on six spatial building blocks and the operations of union, difference, intersection, and addition. The building blocks are related to the distribution of inductive signals, provided by the highly conserved epidermal growth factor receptor and bone morphogenetic protein signaling pathways. We demonstrate the validity of the code by testing it against a set of patterns obtained in a large-scale transcriptional profiling experiment. Using the proposed code, we distinguish 36 distinct patterns for 81 genes expressed in the follicular epithelium and characterize their joint dynamics over four stages of oogenesis. The proposed combinatorial framework allows systematic analysis of the diversity and dynamics of two-dimensional transcriptional patterns and guides future studies of gene regulation.

On the existence of binary simplex codes. [using combinatorial construction

NASA Technical Reports Server (NTRS)

Taylor, H.

1977-01-01

Using a simple combinatorial construction, the existence of a binary simplex code with m codewords for all m is greater than or equal to 1 is proved. The problem of the shortest possible length is left open.

Accurate multiple sequence-structure alignment of RNA sequences using combinatorial optimization.

PubMed

Bauer, Markus; Klau, Gunnar W; Reinert, Knut

2007-07-27

The discovery of functional non-coding RNA sequences has led to an increasing interest in algorithms related to RNA analysis. Traditional sequence alignment algorithms, however, fail at computing reliable alignments of low-homology RNA sequences. The spatial conformation of RNA sequences largely determines their function, and therefore RNA alignment algorithms have to take structural information into account. We present a graph-based representation for sequence-structure alignments, which we model as an integer linear program (ILP). We sketch how we compute an optimal or near-optimal solution to the ILP using methods from combinatorial optimization, and present results on a recently published benchmark set for RNA alignments. The implementation of our algorithm yields better alignments in terms of two published scores than the other programs that we tested: This is especially the case with an increasing number of input sequences. Our program LARA is freely available for academic purposes from http://www.planet-lisa.net.

Applications of high throughput (combinatorial) methodologies to electronic, magnetic, optical, and energy-related materials

NASA Astrophysics Data System (ADS)

Green, Martin L.; Takeuchi, Ichiro; Hattrick-Simpers, Jason R.

2013-06-01

High throughput (combinatorial) materials science methodology is a relatively new research paradigm that offers the promise of rapid and efficient materials screening, optimization, and discovery. The paradigm started in the pharmaceutical industry but was rapidly adopted to accelerate materials research in a wide variety of areas. High throughput experiments are characterized by synthesis of a "library" sample that contains the materials variation of interest (typically composition), and rapid and localized measurement schemes that result in massive data sets. Because the data are collected at the same time on the same "library" sample, they can be highly uniform with respect to fixed processing parameters. This article critically reviews the literature pertaining to applications of combinatorial materials science for electronic, magnetic, optical, and energy-related materials. It is expected that high throughput methodologies will facilitate commercialization of novel materials for these critically important applications. Despite the overwhelming evidence presented in this paper that high throughput studies can effectively inform commercial practice, in our perception, it remains an underutilized research and development tool. Part of this perception may be due to the inaccessibility of proprietary industrial research and development practices, but clearly the initial cost and availability of high throughput laboratory equipment plays a role. Combinatorial materials science has traditionally been focused on materials discovery, screening, and optimization to combat the extremely high cost and long development times for new materials and their introduction into commerce. Going forward, combinatorial materials science will also be driven by other needs such as materials substitution and experimental verification of materials properties predicted by modeling and simulation, which have recently received much attention with the advent of the Materials Genome

Towards time-dependent current-density-functional theory in the non-linear regime

NASA Astrophysics Data System (ADS)

Escartín, J. M.; Vincendon, M.; Romaniello, P.; Dinh, P. M.; Reinhard, P.-G.; Suraud, E.

2015-02-01

Time-Dependent Density-Functional Theory (TDDFT) is a well-established theoretical approach to describe and understand irradiation processes in clusters and molecules. However, within the so-called adiabatic local density approximation (ALDA) to the exchange-correlation (xc) potential, TDDFT can show insufficiencies, particularly in violently dynamical processes. This is because within ALDA the xc potential is instantaneous and is a local functional of the density, which means that this approximation neglects memory effects and long-range effects. A way to go beyond ALDA is to use Time-Dependent Current-Density-Functional Theory (TDCDFT), in which the basic quantity is the current density rather than the density as in TDDFT. This has been shown to offer an adequate account of dissipation in the linear domain when the Vignale-Kohn (VK) functional is used. Here, we go beyond the linear regime and we explore this formulation in the time domain. In this case, the equations become very involved making the computation out of reach; we hence propose an approximation to the VK functional which allows us to calculate the dynamics in real time and at the same time to keep most of the physics described by the VK functional. We apply this formulation to the calculation of the time-dependent dipole moment of Ca, Mg and Na2. Our results show trends similar to what was previously observed in model systems or within linear response. In the non-linear domain, our results show that relaxation times do not decrease with increasing deposited excitation energy, which sets some limitations to the practical use of TDCDFT in such a domain of excitations.

Towards time-dependent current-density-functional theory in the non-linear regime.

PubMed

Escartín, J M; Vincendon, M; Romaniello, P; Dinh, P M; Reinhard, P-G; Suraud, E

2015-02-28

Time-Dependent Density-Functional Theory (TDDFT) is a well-established theoretical approach to describe and understand irradiation processes in clusters and molecules. However, within the so-called adiabatic local density approximation (ALDA) to the exchange-correlation (xc) potential, TDDFT can show insufficiencies, particularly in violently dynamical processes. This is because within ALDA the xc potential is instantaneous and is a local functional of the density, which means that this approximation neglects memory effects and long-range effects. A way to go beyond ALDA is to use Time-Dependent Current-Density-Functional Theory (TDCDFT), in which the basic quantity is the current density rather than the density as in TDDFT. This has been shown to offer an adequate account of dissipation in the linear domain when the Vignale-Kohn (VK) functional is used. Here, we go beyond the linear regime and we explore this formulation in the time domain. In this case, the equations become very involved making the computation out of reach; we hence propose an approximation to the VK functional which allows us to calculate the dynamics in real time and at the same time to keep most of the physics described by the VK functional. We apply this formulation to the calculation of the time-dependent dipole moment of Ca, Mg and Na2. Our results show trends similar to what was previously observed in model systems or within linear response. In the non-linear domain, our results show that relaxation times do not decrease with increasing deposited excitation energy, which sets some limitations to the practical use of TDCDFT in such a domain of excitations.

Characterizing the Spatial Density Functions of Neural Arbors

NASA Astrophysics Data System (ADS)

Teeter, Corinne Michelle

Recently, it has been proposed that a universal function describes the way in which all arbors (axons and dendrites) spread their branches over space. Data from fish retinal ganglion cells as well as cortical and hippocampal arbors from mouse, rat, cat, monkey and human provide evidence that all arbor density functions (adf) can be described by a Gaussian function truncated at approximately two standard deviations. A Gaussian density function implies that there is a minimal set of parameters needed to describe an adf: two or three standard deviations (depending on the dimensionality of the arbor) and an amplitude. However, the parameters needed to completely describe an adf could be further constrained by a scaling law found between the product of the standard deviations and the amplitude of the function. In the following document, I examine the scaling law relationship in order to determine the minimal set of parameters needed to describe an adf. First, I find that the at, two-dimensional arbors of fish retinal ganglion cells require only two out of the three fundamental parameters to completely describe their density functions. Second, the three-dimensional, volume filling, cortical arbors require four fundamental parameters: three standard deviations and the total length of an arbor (which corresponds to the amplitude of the function). Next, I characterize the shape of arbors in the context of the fundamental parameters. I show that the parameter distributions of the fish retinal ganglion cells are largely homogenous. In general, axons are bigger and less dense than dendrites; however, they are similarly shaped. The parameter distributions of these two arbor types overlap and, therefore, can only be differentiated from one another probabilistically based on their adfs. Despite artifacts in the cortical arbor data, different types of arbors (apical dendrites, non-apical dendrites, and axons) can generally be differentiated based on their adfs. In addition, within

Multireference Density Functional Theory with Generalized Auxiliary Systems for Ground and Excited States.

PubMed

Chen, Zehua; Zhang, Du; Jin, Ye; Yang, Yang; Su, Neil Qiang; Yang, Weitao

2017-09-21

To describe static correlation, we develop a new approach to density functional theory (DFT), which uses a generalized auxiliary system that is of a different symmetry, such as particle number or spin, from that of the physical system. The total energy of the physical system consists of two parts: the energy of the auxiliary system, which is determined with a chosen density functional approximation (DFA), and the excitation energy from an approximate linear response theory that restores the symmetry to that of the physical system, thus rigorously leading to a multideterminant description of the physical system. The electron density of the physical system is different from that of the auxiliary system and is uniquely determined from the functional derivative of the total energy with respect to the external potential. Our energy functional is thus an implicit functional of the physical system density, but an explicit functional of the auxiliary system density. We show that the total energy minimum and stationary states, describing the ground and excited states of the physical system, can be obtained by a self-consistent optimization with respect to the explicit variable, the generalized Kohn-Sham noninteracting density matrix. We have developed the generalized optimized effective potential method for the self-consistent optimization. Among options of the auxiliary system and the associated linear response theory, reformulated versions of the particle-particle random phase approximation (pp-RPA) and the spin-flip time-dependent density functional theory (SF-TDDFT) are selected for illustration of principle. Numerical results show that our multireference DFT successfully describes static correlation in bond dissociation and double bond rotation.

Derivative discontinuity and exchange-correlation potential of meta-GGAs in density-functional theory.

PubMed

Eich, F G; Hellgren, Maria

2014-12-14

We investigate fundamental properties of meta-generalized-gradient approximations (meta-GGAs) to the exchange-correlation energy functional, which have an implicit density dependence via the Kohn-Sham kinetic-energy density. To this purpose, we construct the most simple meta-GGA by expressing the local exchange-correlation energy per particle as a function of a fictitious density, which is obtained by inverting the Thomas-Fermi kinetic-energy functional. This simple functional considerably improves the total energy of atoms as compared to the standard local density approximation. The corresponding exchange-correlation potentials are then determined exactly through a solution of the optimized effective potential equation. These potentials support an additional bound state and exhibit a derivative discontinuity at integer particle numbers. We further demonstrate that through the kinetic-energy density any meta-GGA incorporates a derivative discontinuity. However, we also find that for commonly used meta-GGAs the discontinuity is largely underestimated and in some cases even negative.

Derivative discontinuity and exchange-correlation potential of meta-GGAs in density-functional theory

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

Eich, F. G., E-mail: eichf@missouri.edu; Hellgren, Maria

2014-12-14

We investigate fundamental properties of meta-generalized-gradient approximations (meta-GGAs) to the exchange-correlation energy functional, which have an implicit density dependence via the Kohn-Sham kinetic-energy density. To this purpose, we construct the most simple meta-GGA by expressing the local exchange-correlation energy per particle as a function of a fictitious density, which is obtained by inverting the Thomas-Fermi kinetic-energy functional. This simple functional considerably improves the total energy of atoms as compared to the standard local density approximation. The corresponding exchange-correlation potentials are then determined exactly through a solution of the optimized effective potential equation. These potentials support an additional bound state andmore » exhibit a derivative discontinuity at integer particle numbers. We further demonstrate that through the kinetic-energy density any meta-GGA incorporates a derivative discontinuity. However, we also find that for commonly used meta-GGAs the discontinuity is largely underestimated and in some cases even negative.« less

A combinatorial histidine scanning library approach to engineer highly pH-dependent protein switches

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

Murtaugh, Megan L.; Fanning, Sean W.; Sharma, Tressa M.

2012-09-05

There is growing interest in the development of protein switches, which are proteins whose function, such as binding a target molecule, can be modulated through environmental triggers. Efforts to engineer highly pH sensitive protein-protein interactions typically rely on the rational introduction of ionizable groups in the protein interface. Such experiments are typically time intensive and often sacrifice the protein's affinity at the permissive pH. The underlying thermodynamics of proton-linkage dictate that the presence of multiple ionizable groups, which undergo a pK{sub a} change on protein binding, are necessary to result in highly pH-dependent binding. To test this hypothesis, a novelmore » combinatorial histidine library was developed where every possible combination of histidine and wild-type residue is sampled throughout the interface of a model anti-RNase A single domain VHH antibody. Antibodies were coselected for high-affinity binding and pH-sensitivity using an in vitro, dual-function selection strategy. The resulting antibodies retained near wild-type affinity yet became highly sensitive to small decreases in pH, drastically decreasing their binding affinity, due to the incorporation of multiple histidine groups. Several trends were observed, such as histidine 'hot-spots,' which will help enhance the development of pH switch proteins as well as increase our understanding of the role of ionizable residues in protein interfaces. Overall, the combinatorial approach is rapid, general, and robust and should be capable of producing highly pH-sensitive protein affinity reagents for a number of different applications.« less

Structural alignment of protein descriptors - a combinatorial model.

PubMed

Antczak, Maciej; Kasprzak, Marta; Lukasiak, Piotr; Blazewicz, Jacek

2016-09-17

Structural alignment of proteins is one of the most challenging problems in molecular biology. The tertiary structure of a protein strictly correlates with its function and computationally predicted structures are nowadays a main premise for understanding the latter. However, computationally derived 3D models often exhibit deviations from the native structure. A way to confirm a model is a comparison with other structures. The structural alignment of a pair of proteins can be defined with the use of a concept of protein descriptors. The protein descriptors are local substructures of protein molecules, which allow us to divide the original problem into a set of subproblems and, consequently, to propose a more efficient algorithmic solution. In the literature, one can find many applications of the descriptors concept that prove its usefulness for insight into protein 3D structures, but the proposed approaches are presented rather from the biological perspective than from the computational or algorithmic point of view. Efficient algorithms for identification and structural comparison of descriptors can become crucial components of methods for structural quality assessment as well as tertiary structure prediction. In this paper, we propose a new combinatorial model and new polynomial-time algorithms for the structural alignment of descriptors. The model is based on the maximum-size assignment problem, which we define here and prove that it can be solved in polynomial time. We demonstrate suitability of this approach by comparison with an exact backtracking algorithm. Besides a simplification coming from the combinatorial modeling, both on the conceptual and complexity level, we gain with this approach high quality of obtained results, in terms of 3D alignment accuracy and processing efficiency. All the proposed algorithms were developed and integrated in a computationally efficient tool descs-standalone, which allows the user to identify and structurally compare

Many-Body Spectral Functions from Steady State Density Functional Theory.

PubMed

Jacob, David; Kurth, Stefan

2018-03-14

We propose a scheme to extract the many-body spectral function of an interacting many-electron system from an equilibrium density functional theory (DFT) calculation. To this end we devise an ideal scanning tunneling microscope (STM) setup and employ the recently proposed steady-state DFT formalism (i-DFT) which allows one to calculate the steady current through a nanoscopic region coupled to two biased electrodes. In our setup, one of the electrodes serves as a probe ("STM tip"), which is weakly coupled to the system we want to measure. In the ideal STM limit of vanishing coupling to the tip, the system is restored to quasi-equilibrium and the normalized differential conductance yields the exact equilibrium many-body spectral function. Calculating this quantity from i-DFT, we derive an exact relation expressing the interacting spectral function in terms of the Kohn-Sham one. As illustrative examples, we apply our scheme to calculate the spectral functions of two nontrivial model systems, namely the single Anderson impurity model and the Constant Interaction Model.

Combinatorial Histone Acetylation Patterns Are Generated by Motif-Specific Reactions.

PubMed

Blasi, Thomas; Feller, Christian; Feigelman, Justin; Hasenauer, Jan; Imhof, Axel; Theis, Fabian J; Becker, Peter B; Marr, Carsten

2016-01-27

Post-translational modifications (PTMs) are pivotal to cellular information processing, but how combinatorial PTM patterns ("motifs") are set remains elusive. We develop a computational framework, which we provide as open source code, to investigate the design principles generating the combinatorial acetylation patterns on histone H4 in Drosophila melanogaster. We find that models assuming purely unspecific or lysine site-specific acetylation rates were insufficient to explain the experimentally determined motif abundances. Rather, these abundances were best described by an ensemble of models with acetylation rates that were specific to motifs. The model ensemble converged upon four acetylation pathways; we validated three of these using independent data from a systematic enzyme depletion study. Our findings suggest that histone acetylation patterns originate through specific pathways involving motif-specific acetylation activity. Copyright © 2016 Elsevier Inc. All rights reserved.

KIDS Nuclear Energy Density Functional: 1st Application in Nuclei

NASA Astrophysics Data System (ADS)

Gil, Hana; Papakonstantinou, Panagiota; Hyun, Chang Ho; Oh, Yongseok

We apply the KIDS (Korea: IBS-Daegu-Sungkyunkwan) nuclear energy density functional model, which is based on the Fermi momentum expansion, to the study of properties of lj-closed nuclei. The parameters of the model are determined by the nuclear properties at the saturation density and theoretical calculations on pure neutron matter. For applying the model to the study of nuclei, we rely on the Skyrme force model, where the Skyrme force parameters are determined through the KIDS energy density functional. Solving Hartree-Fock equations, we obtain the energies per particle and charge radii of closed magic nuclei, namely, 16O, 28O, 40Ca, 48Ca, 60Ca, 90Zr, 132Sn, and 208Pb. The results are compared with the observed data and further improvement of the model is shortly mentioned.

Combinatorial optimization games

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

Deng, X.; Ibaraki, Toshihide; Nagamochi, Hiroshi

1997-06-01

We introduce a general integer programming formulation for a class of combinatorial optimization games, which immediately allows us to improve the algorithmic result for finding amputations in the core (an important solution concept in cooperative game theory) of the network flow game on simple networks by Kalai and Zemel. An interesting result is a general theorem that the core for this class of games is nonempty if and only if a related linear program has an integer optimal solution. We study the properties for this mathematical condition to hold for several interesting problems, and apply them to resolve algorithmic andmore » complexity issues for their cores along the line as put forward in: decide whether the core is empty; if the core is empty, find an imputation in the core; given an imputation x, test whether x is in the core. We also explore the properties of totally balanced games in this succinct formulation of cooperative games.« less

High-throughput screening for combinatorial thin-film library of thermoelectric materials.

PubMed

Watanabe, Masaki; Kita, Takuji; Fukumura, Tomoteru; Ohtomo, Akira; Ueno, Kazunori; Kawasaki, Masashi

2008-01-01

A high-throughput method has been developed to evaluate the Seebeck coefficient and electrical resistivity of combinatorial thin-film libraries of thermoelectric materials from room temperature to 673 K. Thin-film samples several millimeters in size were deposited on an integrated Al2O3 substrate with embedded lead wires and local heaters for measurement of the thermopower under a controlled temperature gradient. An infrared camera was used for real-time observation of the temperature difference Delta T between two electrical contacts on the sample to obtain the Seebeck coefficient. The Seebeck coefficient and electrical resistivity of constantan thin films were shown to be almost identical to standard data for bulk constantan. High-throughput screening was demonstrated for a thermoelectric Mg-Si-Ge combinatorial library.

Combinatorial effects of arginine and fluoride on oral bacteria.

PubMed

Zheng, X; Cheng, X; Wang, L; Qiu, W; Wang, S; Zhou, Y; Li, M; Li, Y; Cheng, L; Li, J; Zhou, X; Xu, X

2015-02-01

Dental caries is closely associated with the microbial disequilibrium between acidogenic/aciduric pathogens and alkali-generating commensal residents within the dental plaque. Fluoride is a widely used anticaries agent, which promotes tooth hard-tissue remineralization and suppresses bacterial activities. Recent clinical trials have shown that oral hygiene products containing both fluoride and arginine possess a greater anticaries effect compared with those containing fluoride alone, indicating synergy between fluoride and arginine in caries management. Here, we hypothesize that arginine may augment the ecological benefit of fluoride by enriching alkali-generating bacteria in the plaque biofilm and thus synergizes with fluoride in controlling dental caries. Specifically, we assessed the combinatory effects of NaF/arginine on planktonic and biofilm cultures of Streptococcus mutans, Streptococcus sanguinis, and Porphyromonas gingivalis with checkerboard microdilution assays. The optimal NaF/arginine combinations were selected, and their combinatory effects on microbial composition were further examined in single-, dual-, and 3-species biofilm using bacterial species-specific fluorescence in situ hybridization and quantitative polymerase chain reaction. We found that arginine synergized with fluoride in suppressing acidogenic S. mutans in both planktonic and biofilm cultures. In addition, the NaF/arginine combination synergistically reduced S. mutans but enriched S. sanguinis within the multispecies biofilms. More importantly, the optimal combination of NaF/arginine maintained a "streptococcal pressure" against the potential growth of oral anaerobe P. gingivalis within the alkalized biofilm. Taken together, we conclude that the combinatory application of fluoride and arginine has a potential synergistic effect in maintaining a healthy oral microbial equilibrium and thus represents a promising ecological approach to caries management. © International & American

Combinatorial Effects of Arginine and Fluoride on Oral Bacteria

PubMed Central

Zheng, X.; Cheng, X.; Wang, L.; Qiu, W.; Wang, S.; Zhou, Y.; Li, M.; Li, Y.; Cheng, L.; Li, J.; Zhou, X.

2015-01-01

Dental caries is closely associated with the microbial disequilibrium between acidogenic/aciduric pathogens and alkali-generating commensal residents within the dental plaque. Fluoride is a widely used anticaries agent, which promotes tooth hard-tissue remineralization and suppresses bacterial activities. Recent clinical trials have shown that oral hygiene products containing both fluoride and arginine possess a greater anticaries effect compared with those containing fluoride alone, indicating synergy between fluoride and arginine in caries management. Here, we hypothesize that arginine may augment the ecological benefit of fluoride by enriching alkali-generating bacteria in the plaque biofilm and thus synergizes with fluoride in controlling dental caries. Specifically, we assessed the combinatory effects of NaF/arginine on planktonic and biofilm cultures of Streptococcus mutans, Streptococcus sanguinis, and Porphyromonas gingivalis with checkerboard microdilution assays. The optimal NaF/arginine combinations were selected, and their combinatory effects on microbial composition were further examined in single-, dual-, and 3-species biofilm using bacterial species–specific fluorescence in situ hybridization and quantitative polymerase chain reaction. We found that arginine synergized with fluoride in suppressing acidogenic S. mutans in both planktonic and biofilm cultures. In addition, the NaF/arginine combination synergistically reduced S. mutans but enriched S. sanguinis within the multispecies biofilms. More importantly, the optimal combination of NaF/arginine maintained a “streptococcal pressure” against the potential growth of oral anaerobe P. gingivalis within the alkalized biofilm. Taken together, we conclude that the combinatory application of fluoride and arginine has a potential synergistic effect in maintaining a healthy oral microbial equilibrium and thus represents a promising ecological approach to caries management. PMID:25477312

Density-functional theory based on the electron distribution on the energy coordinate

NASA Astrophysics Data System (ADS)

Takahashi, Hideaki

2018-03-01

We developed an electronic density functional theory utilizing a novel electron distribution n(ɛ) as a basic variable to compute ground state energy of a system. n(ɛ) is obtained by projecting the electron density n({\\boldsymbol{r}}) defined on the space coordinate {\\boldsymbol{r}} onto the energy coordinate ɛ specified with the external potential {\\upsilon }ext}({\\boldsymbol{r}}) of interest. It was demonstrated that the Kohn-Sham equation can also be formulated with the exchange-correlation functional E xc[n(ɛ)] that employs the density n(ɛ) as an argument. It turned out an exchange functional proposed in our preliminary development suffices to describe properly the potential energies of several types of chemical bonds with comparable accuracies to the corresponding functional based on local density approximation. As a remarkable feature of the distribution n(ɛ) it inherently involves the spatially non-local information of the exchange hole at the bond dissociation limit in contrast to conventional approximate functionals. By taking advantage of this property we also developed a prototype of the static correlation functional E sc including no empirical parameters, which showed marked improvements in describing the dissociations of covalent bonds in {{{H}}}2,{{{C}}}2{{{H}}}4 and {CH}}4 molecules.

Combinatorial programming of human neuronal progenitors using magnetically-guided stoichiometric mRNA delivery.

PubMed

Azimi, Sayyed M; Sheridan, Steven D; Ghannad-Rezaie, Mostafa; Eimon, Peter M; Yanik, Mehmet Fatih

2018-05-01

Identification of optimal transcription-factor expression patterns to direct cellular differentiation along a desired pathway presents significant challenges. We demonstrate massively combinatorial screening of temporally-varying mRNA transcription factors to direct differentiation of neural progenitor cells using a dynamically-reconfigurable magnetically-guided spotting technology for localizing mRNA, enabling experiments on millimetre size spots. In addition, we present a time-interleaved delivery method that dramatically reduces fluctuations in the delivered transcription-factor copy-numbers per cell. We screened combinatorial and temporal delivery of a pool of midbrain-specific transcription factors to augment the generation of dopaminergic neurons. We show that the combinatorial delivery of LMX1A, FOXA2 and PITX3 is highly effective in generating dopaminergic neurons from midbrain progenitors. We show that LMX1A significantly increases TH -expression levels when delivered to neural progenitor cells either during proliferation or after induction of neural differentiation, while FOXA2 and PITX3 increase expression only when delivered prior to induction, demonstrating temporal dependence of factor addition. © 2018, Azimi et al.

Hartree and Exchange in Ensemble Density Functional Theory: Avoiding the Nonuniqueness Disaster.

PubMed

Gould, Tim; Pittalis, Stefano

2017-12-15

Ensemble density functional theory is a promising method for the efficient and accurate calculation of excitations of quantum systems, at least if useful functionals can be developed to broaden its domain of practical applicability. Here, we introduce a guaranteed single-valued "Hartree-exchange" ensemble density functional, E_{Hx}[n], in terms of the right derivative of the universal ensemble density functional with respect to the coupling constant at vanishing interaction. We show that E_{Hx}[n] is straightforwardly expressible using block eigenvalues of a simple matrix [Eq. (14)]. Specialized expressions for E_{Hx}[n] from the literature, including those involving superpositions of Slater determinants, can now be regarded as originating from the unifying picture presented here. We thus establish a clear and practical description for Hartree and exchange in ensemble systems.

Lexicographic goal programming and assessment tools for a combinatorial production problem.

DOT National Transportation Integrated Search

2008-01-01

NP-complete combinatorial problems often necessitate the use of near-optimal solution techniques including : heuristics and metaheuristics. The addition of multiple optimization criteria can further complicate : comparison of these solution technique...

Multiconfiguration Pair-Density Functional Theory: A New Way To Treat Strongly Correlated Systems.

PubMed

Gagliardi, Laura; Truhlar, Donald G; Li Manni, Giovanni; Carlson, Rebecca K; Hoyer, Chad E; Bao, Junwei Lucas

2017-01-17

The electronic energy of a system provides the Born-Oppenheimer potential energy for internuclear motion and thus determines molecular structure and spectra, bond energies, conformational energies, reaction barrier heights, and vibrational frequencies. The development of more efficient and more accurate ways to calculate the electronic energy of systems with inherently multiconfigurational electronic structure is essential for many applications, including transition metal and actinide chemistry, systems with partially broken bonds, many transition states, and most electronically excited states. Inherently multiconfigurational systems are called strongly correlated systems or multireference systems, where the latter name refers to the need for using more than one ("multiple") configuration state function to provide a good zero-order reference wave function. This Account describes multiconfiguration pair-density functional theory (MC-PDFT), which was developed as a way to combine the advantages of wave function theory (WFT) and density functional theory (DFT) to provide a better treatment of strongly correlated systems. First we review background material: the widely used Kohn-Sham DFT (which uses only a single Slater determinant as reference wave function), multiconfiguration WFT methods that treat inherently multiconfigurational systems based on an active space, and previous attempts to combine multiconfiguration WFT with DFT. Then we review the formulation of MC-PDFT. It is a generalization of Kohn-Sham DFT in that the electron kinetic energy and classical electrostatic energy are calculated from a reference wave function, while the rest of the energy is obtained from a density functional. However, there are two main differences with respent to Kohn-Sham DFT: (i) The reference wave function is multiconfigurational rather than being a single Slater determinant. (ii) The density functional is a function of the total density and the on-top pair density rather than

Density functional theory and chromium: Insights from the dimers

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

Würdemann, Rolf; Kristoffersen, Henrik H.; Moseler, Michael

2015-03-28

The binding in small Cr clusters is re-investigated, where the correct description of the dimer in three charge states is used as criterion to assign the most suitable density functional theory approximation. The difficulty in chromium arises from the subtle interplay between energy gain from hybridization and energetic cost due to exchange between s and d based molecular orbitals. Variations in published bond lengths and binding energies are shown to arise from insufficient numerical representation of electron density and Kohn-Sham wave-functions. The best functional performance is found for gradient corrected (GGA) functionals and meta-GGAs, where we find severe differences betweenmore » functionals from the same family due to the importance of exchange. Only the “best fit” from Bayesian error estimation is able to predict the correct energetics for all three charge states unambiguously. With this knowledge, we predict small bond-lengths to be exclusively present in Cr{sub 2} and Cr{sub 2}{sup −}. Already for the dimer cation, solely long bond-lengths appear, similar to what is found in the trimer and in chromium bulk.« less

Artificial cognitive memory—changing from density driven to functionality driven

NASA Astrophysics Data System (ADS)

Shi, L. P.; Yi, K. J.; Ramanathan, K.; Zhao, R.; Ning, N.; Ding, D.; Chong, T. C.

2011-03-01

Increasing density based on bit size reduction is currently a main driving force for the development of data storage technologies. However, it is expected that all of the current available storage technologies might approach their physical limits in around 15 to 20 years due to miniaturization. To further advance the storage technologies, it is required to explore a new development trend that is different from density driven. One possible direction is to derive insights from biological counterparts. Unlike physical memories that have a single function of data storage, human memory is versatile. It contributes to functions of data storage, information processing, and most importantly, cognitive functions such as adaptation, learning, perception, knowledge generation, etc. In this paper, a brief review of current data storage technologies are presented, followed by discussions of future storage technology development trend. We expect that the driving force will evolve from density to functionality, and new memory modules associated with additional functions other than only data storage will appear. As an initial step toward building a future generation memory technology, we propose Artificial Cognitive Memory (ACM), a memory based intelligent system. We also present the characteristics of ACM, new technologies that can be used to develop ACM components such as bioinspired element cells (silicon, memristor, phase change, etc.), and possible methodologies to construct a biologically inspired hierarchical system.

Automated Combinatorial Chemistry in the Organic Chemistry Majors Laboratory

ERIC Educational Resources Information Center

Nichols, Christopher J.; Hanne, Larry F.

2010-01-01

A multidisciplinary experiment has been developed in which students each synthesize a combinatorial library of 48 hydrazones with the aid of a liquid-handling robot. Each product is then subjected to a Kirby-Bauer disk diffusion assay to assess its antibacterial activity. Students gain experience working with automation and at the…

Optimal atomic structure of amorphous silicon obtained from density functional theory calculations

NASA Astrophysics Data System (ADS)

Pedersen, Andreas; Pizzagalli, Laurent; Jónsson, Hannes

2017-06-01

Atomic structure of amorphous silicon consistent with several reported experimental measurements has been obtained from annealing simulations using electron density functional theory calculations and a systematic removal of weakly bound atoms. The excess energy and density with respect to the crystal are well reproduced in addition to radial distribution function, angular distribution functions, and vibrational density of states. No atom in the optimal configuration is locally in a crystalline environment as deduced by ring analysis and common neighbor analysis, but coordination defects are present at a level of 1%-2%. The simulated samples provide structural models of this archetypal disordered covalent material without preconceived notion of the atomic ordering or fitting to experimental data.

Exact density functional and wave function embedding schemes based on orbital localization

NASA Astrophysics Data System (ADS)

Hégely, Bence; Nagy, Péter R.; Ferenczy, György G.; Kállay, Mihály

2016-08-01

Exact schemes for the embedding of density functional theory (DFT) and wave function theory (WFT) methods into lower-level DFT or WFT approaches are introduced utilizing orbital localization. First, a simple modification of the projector-based embedding scheme of Manby and co-workers [J. Chem. Phys. 140, 18A507 (2014)] is proposed. We also use localized orbitals to partition the system, but instead of augmenting the Fock operator with a somewhat arbitrary level-shift projector we solve the Huzinaga-equation, which strictly enforces the Pauli exclusion principle. Second, the embedding of WFT methods in local correlation approaches is studied. Since the latter methods split up the system into local domains, very simple embedding theories can be defined if the domains of the active subsystem and the environment are treated at a different level. The considered embedding schemes are benchmarked for reaction energies and compared to quantum mechanics (QM)/molecular mechanics (MM) and vacuum embedding. We conclude that for DFT-in-DFT embedding, the Huzinaga-equation-based scheme is more efficient than the other approaches, but QM/MM or even simple vacuum embedding is still competitive in particular cases. Concerning the embedding of wave function methods, the clear winner is the embedding of WFT into low-level local correlation approaches, and WFT-in-DFT embedding can only be more advantageous if a non-hybrid density functional is employed.

Combinatorial approach to the representation of the Schur-Weyl duality in one-dimensional spin systems

NASA Astrophysics Data System (ADS)

Jakubczyk, Dorota; Jakubczyk, Paweł

2018-02-01

We propose combinatorial approach to the representation of Schur-Weyl duality in physical systems on the example of one-dimensional spin chains. Exploiting the Robinson-Schensted-Knuth algorithm, we perform decomposition of the dual group representations into irreducible representations in a fully combinatorial way. As representation space, we choose the Hilbert space of the spin chains, but this approach can be easily generalized to an arbitrary physical system where the Schur-Weyl duality works.

Use of the rVV10 Nonlocal Correlation Functional in the B97M-V Density Functional: Defining B97M-rV and Related Functionals [On the Use of the rVV10 Nonlocal Correlation Functional in the B97M-V Density Functional: Defining B97M-rV and Related Functionals

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

Mardirossian, Narbe; Ruiz Pestana, Luis; Womack, James C.

The VV10 and rVV10 nonlocal correlation functionals are consistently implemented and assessed, with the goal of determining if the rVV10 nonlocal correlation functional can replace the VV10 nonlocal correlation functional in the recently developed B97M-V density functional, to give the B97M-rV density functional. Along the way, four density functionals are simultaneously tested: VV10, rVV10, B97M-V, and B97M-rV. An initial assessment is carried out across the S22 data set, and the short-range damping variable, b, is varied for all four density functionals in order to determine the sensitivity of the functionals to the empirical parameter. The results of this test indicatemore » that a value of b = 6 (fortuitously the same as that in B97M-V) is suitable for B97M-rV. The functionals are then compared across an extensive database of interaction energies, and it is demonstrated that B97M-rV either matches or outperforms B97M-V for all of the tests considered. Finally, the optimization of b across the S22 data set is extended to two range-separated hybrid density functionals, ωB97X-V and ωB97M-V, and a value of b = 6.2 is recommended for both ωB97X-rV and ωB97M-rV.« less

Use of the rVV10 Nonlocal Correlation Functional in the B97M-V Density Functional: Defining B97M-rV and Related Functionals [On the Use of the rVV10 Nonlocal Correlation Functional in the B97M-V Density Functional: Defining B97M-rV and Related Functionals

DOE PAGES

Mardirossian, Narbe; Ruiz Pestana, Luis; Womack, James C.; ...

2016-12-06

The VV10 and rVV10 nonlocal correlation functionals are consistently implemented and assessed, with the goal of determining if the rVV10 nonlocal correlation functional can replace the VV10 nonlocal correlation functional in the recently developed B97M-V density functional, to give the B97M-rV density functional. Along the way, four density functionals are simultaneously tested: VV10, rVV10, B97M-V, and B97M-rV. An initial assessment is carried out across the S22 data set, and the short-range damping variable, b, is varied for all four density functionals in order to determine the sensitivity of the functionals to the empirical parameter. The results of this test indicatemore » that a value of b = 6 (fortuitously the same as that in B97M-V) is suitable for B97M-rV. The functionals are then compared across an extensive database of interaction energies, and it is demonstrated that B97M-rV either matches or outperforms B97M-V for all of the tests considered. Finally, the optimization of b across the S22 data set is extended to two range-separated hybrid density functionals, ωB97X-V and ωB97M-V, and a value of b = 6.2 is recommended for both ωB97X-rV and ωB97M-rV.« less

Alternative derivation of an exchange-only density-functional optimized effective potential

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

Joubert, D. P.

2007-10-15

An alternative derivation of the exchange-only density-functional optimized effective potential equation is given. It is shown that the localized Hartree-Fock-common energy denominator Green's function approximation (LHF-CEDA) for the density-functional exchange potential proposed independently by Della Sala and Goerling [J. Chem. Phys. 115, 5718 (2001)] and Gritsenko and Baerends [Phys. Rev. A 64, 42506 (2001)] can be derived as an approximation to the OEP exchange potential in a similar way that the KLI approximation [Phys. Rev. A 45, 5453 (1992)] was derived. An exact expression for the correction term to the LHF-CEDA approximation can thus be found. The correction term canmore » be expressed in terms of the first-order perturbation-theory many-electron wave function shift when the Kohn-Sham Hamiltonian is subjected to a perturbation equal to the difference between the density-functional exchange potential and the Hartree-Fock nonlocal potential, expressed in terms of the Kohn-Sham orbitals. An explicit calculation shows that the density weighted mean of the correction term is zero, confirming that the LHF-CEDA approximation can be interpreted as a mean-field approximation. The corrected LHF-CEDA equation and the optimized effective potential equation are shown to be identical, with information distributed differently between terms in the equations. For a finite system the correction term falls off at least as fast as 1/r{sup 4} for large r.« less

Alternative derivation of an exchange-only density-functional optimized effective potential

NASA Astrophysics Data System (ADS)

Joubert, D. P.

2007-10-01

An alternative derivation of the exchange-only density-functional optimized effective potential equation is given. It is shown that the localized Hartree-Fock common energy denominator Green’s function approximation (LHF-CEDA) for the density-functional exchange potential proposed independently by Della Sala and Görling [J. Chem. Phys. 115, 5718 (2001)] and Gritsenko and Baerends [Phys. Rev. A 64, 42506 (2001)] can be derived as an approximation to the OEP exchange potential in a similar way that the KLI approximation [Phys. Rev. A 45, 5453 (1992)] was derived. An exact expression for the correction term to the LHF-CEDA approximation can thus be found. The correction term can be expressed in terms of the first-order perturbation-theory many-electron wave function shift when the Kohn-Sham Hamiltonian is subjected to a perturbation equal to the difference between the density-functional exchange potential and the Hartree-Fock nonlocal potential, expressed in terms of the Kohn-Sham orbitals. An explicit calculation shows that the density weighted mean of the correction term is zero, confirming that the LHF-CEDA approximation can be interpreted as a mean-field approximation. The corrected LHF-CEDA equation and the optimized effective potential equation are shown to be identical, with information distributed differently between terms in the equations. For a finite system the correction term falls off at least as fast as 1/r4 for large r .

A long-range-corrected density functional that performs well for both ground-state properties and time-dependent density functional theory excitation energies, including charge-transfer excited states.

PubMed

Rohrdanz, Mary A; Martins, Katie M; Herbert, John M

2009-02-07

We introduce a hybrid density functional that asymptotically incorporates full Hartree-Fock exchange, based on the long-range-corrected exchange-hole model of Henderson et al. [J. Chem. Phys. 128, 194105 (2008)]. The performance of this functional, for ground-state properties and for vertical excitation energies within time-dependent density functional theory, is systematically evaluated, and optimal values are determined for the range-separation parameter, omega, and for the fraction of short-range Hartree-Fock exchange. We denote the new functional as LRC-omegaPBEh, since it reduces to the standard PBEh hybrid functional (also known as PBE0 or PBE1PBE) for a certain choice of its two parameters. Upon optimization of these parameters against a set of ground- and excited-state benchmarks, the LRC-omegaPBEh functional fulfills three important requirements: (i) It outperforms the PBEh hybrid functional for ground-state atomization energies and reaction barrier heights; (ii) it yields statistical errors comparable to PBEh for valence excitation energies in both small and medium-sized molecules; and (iii) its performance for charge-transfer excitations is comparable to its performance for valence excitations. LRC-omegaPBEh, with the parameters determined herein, is the first density functional that satisfies all three criteria. Notably, short-range Hartree-Fock exchange appears to be necessary in order to obtain accurate ground-state properties and vertical excitation energies using the same value of omega.

Density Dependent Functional Forms Drive Compensation in Populations Exposed to Stressors

EPA Science Inventory

The interaction between density dependence (DD) and environmental stressors can result in a compensatory or synergistic response in population growth, and population models that use density-independent demographic rates or generic DD functions may be introducing bias into managem...

Magnetic behavior study of samarium nitride using density functional theory

NASA Astrophysics Data System (ADS)

Som, Narayan N.; Mankad, Venu H.; Dabhi, Shweta D.; Patel, Anjali; Jha, Prafulla K.

2018-02-01

In this work, the state-of-art density functional theory is employed to study the structural, electronic and magnetic properties of samarium nitride (SmN). We have performed calculation for both ferromagnetic and antiferromagnetic states in rock-salt phase. The calculated results of optimized lattice parameter and magnetic moment agree well with the available experimental and theoretical values. From energy band diagram and electronic density of states, we observe a half-metallic behaviour in FM phase of rock salt SmN in while metallicity in AFM I and AFM III phases. We present and discuss our current understanding of the possible half-metallicity together with the magnetic ordering in SmN. The calculated phonon dispersion curves shows dynamical stability of the considered structures. The phonon density of states and Eliashberg functional have also been analysed to understand the superconductivity in SmN.

Combinatorial screening of halide perovskite thin films and solar cells by mask-defined IR laser molecular beam epitaxy

NASA Astrophysics Data System (ADS)

Kawashima, Kazuhiro; Okamoto, Yuji; Annayev, Orazmuhammet; Toyokura, Nobuo; Takahashi, Ryota; Lippmaa, Mikk; Itaka, Kenji; Suzuki, Yoshikazu; Matsuki, Nobuyuki; Koinuma, Hideomi

2017-12-01

As an extension of combinatorial molecular layer epitaxy via ablation of perovskite oxides by a pulsed excimer laser, we have developed a laser molecular beam epitaxy (MBE) system for parallel integration of nano-scaled thin films of organic-inorganic hybrid materials. A pulsed infrared (IR) semiconductor laser was adopted for thermal evaporation of organic halide (A-site: CH3NH3I) and inorganic halide (B-site: PbI2) powder targets to deposit repeated A/B bilayer films where the thickness of each layer was controlled on molecular layer scale by programming the evaporation IR laser pulse number, length, or power. The layer thickness was monitored with an in situ quartz crystal microbalance and calibrated against ex situ stylus profilometer measurements. A computer-controlled movable mask system enabled the deposition of combinatorial thin film libraries, where each library contains a vertically homogeneous film with spatially programmable A- and B-layer thicknesses. On the composition gradient film, a hole transport Spiro-OMeTAD layer was spin-coated and dried followed by the vacuum evaporation of Ag electrodes to form the solar cell. The preliminary cell performance was evaluated by measuring I-V characteristics at seven different positions on the 12.5 mm × 12.5 mm combinatorial library sample with seven 2 mm × 4 mm slits under a solar simulator irradiation. The combinatorial solar cell library clearly demonstrated that the energy conversion efficiency sharply changes from nearly zero to 10.2% as a function of the illumination area in the library. The exploration of deposition parameters for obtaining optimum performance could thus be greatly accelerated. Since the thickness ratio of PbI2 and CH3NH3I can be freely chosen along the shadow mask movement, these experiments show the potential of this system for high-throughput screening of optimum chemical composition in the binary film library and application to halide perovskite solar cell.

Combinatorial screening of halide perovskite thin films and solar cells by mask-defined IR laser molecular beam epitaxy

PubMed Central

Kawashima, Kazuhiro; Okamoto, Yuji; Annayev, Orazmuhammet; Toyokura, Nobuo; Takahashi, Ryota; Lippmaa, Mikk; Itaka, Kenji; Suzuki, Yoshikazu; Matsuki, Nobuyuki; Koinuma, Hideomi

2017-01-01

Abstract As an extension of combinatorial molecular layer epitaxy via ablation of perovskite oxides by a pulsed excimer laser, we have developed a laser molecular beam epitaxy (MBE) system for parallel integration of nano-scaled thin films of organic–inorganic hybrid materials. A pulsed infrared (IR) semiconductor laser was adopted for thermal evaporation of organic halide (A-site: CH3NH3I) and inorganic halide (B-site: PbI2) powder targets to deposit repeated A/B bilayer films where the thickness of each layer was controlled on molecular layer scale by programming the evaporation IR laser pulse number, length, or power. The layer thickness was monitored with an in situ quartz crystal microbalance and calibrated against ex situ stylus profilometer measurements. A computer-controlled movable mask system enabled the deposition of combinatorial thin film libraries, where each library contains a vertically homogeneous film with spatially programmable A- and B-layer thicknesses. On the composition gradient film, a hole transport Spiro-OMeTAD layer was spin-coated and dried followed by the vacuum evaporation of Ag electrodes to form the solar cell. The preliminary cell performance was evaluated by measuring I-V characteristics at seven different positions on the 12.5 mm × 12.5 mm combinatorial library sample with seven 2 mm × 4 mm slits under a solar simulator irradiation. The combinatorial solar cell library clearly demonstrated that the energy conversion efficiency sharply changes from nearly zero to 10.2% as a function of the illumination area in the library. The exploration of deposition parameters for obtaining optimum performance could thus be greatly accelerated. Since the thickness ratio of PbI2 and CH3NH3I can be freely chosen along the shadow mask movement, these experiments show the potential of this system for high-throughput screening of optimum chemical composition in the binary film library and application to halide perovskite solar cell. PMID

Combinatorial screening of halide perovskite thin films and solar cells by mask-defined IR laser molecular beam epitaxy.

PubMed

Kawashima, Kazuhiro; Okamoto, Yuji; Annayev, Orazmuhammet; Toyokura, Nobuo; Takahashi, Ryota; Lippmaa, Mikk; Itaka, Kenji; Suzuki, Yoshikazu; Matsuki, Nobuyuki; Koinuma, Hideomi

2017-01-01

As an extension of combinatorial molecular layer epitaxy via ablation of perovskite oxides by a pulsed excimer laser, we have developed a laser molecular beam epitaxy (MBE) system for parallel integration of nano-scaled thin films of organic-inorganic hybrid materials. A pulsed infrared (IR) semiconductor laser was adopted for thermal evaporation of organic halide (A-site: CH 3 NH 3 I) and inorganic halide (B-site: PbI 2 ) powder targets to deposit repeated A/B bilayer films where the thickness of each layer was controlled on molecular layer scale by programming the evaporation IR laser pulse number, length, or power. The layer thickness was monitored with an in situ quartz crystal microbalance and calibrated against ex situ stylus profilometer measurements. A computer-controlled movable mask system enabled the deposition of combinatorial thin film libraries, where each library contains a vertically homogeneous film with spatially programmable A- and B-layer thicknesses. On the composition gradient film, a hole transport Spiro-OMeTAD layer was spin-coated and dried followed by the vacuum evaporation of Ag electrodes to form the solar cell. The preliminary cell performance was evaluated by measuring I - V characteristics at seven different positions on the 12.5 mm × 12.5 mm combinatorial library sample with seven 2 mm × 4 mm slits under a solar simulator irradiation. The combinatorial solar cell library clearly demonstrated that the energy conversion efficiency sharply changes from nearly zero to 10.2% as a function of the illumination area in the library. The exploration of deposition parameters for obtaining optimum performance could thus be greatly accelerated. Since the thickness ratio of PbI 2 and CH 3 NH 3 I can be freely chosen along the shadow mask movement, these experiments show the potential of this system for high-throughput screening of optimum chemical composition in the binary film library and application to halide perovskite solar cell.

Invertibility of retarded response functions for Laplace transformable potentials: Application to one-body reduced density matrix functional theory.

PubMed

Giesbertz, K J H

2015-08-07

A theorem for the invertibility of arbitrary response functions is presented under the following conditions: the time dependence of the potentials should be Laplace transformable and the initial state should be a ground state, though it might be degenerate. This theorem provides a rigorous foundation for all density-functional-like theories in the time-dependent linear response regime. Especially for time-dependent one-body reduced density matrix (1RDM) functional theory, this is an important step forward, since a solid foundation has currently been lacking. The theorem is equally valid for static response functions in the non-degenerate case, so can be used to characterize the uniqueness of the potential in the ground state version of the corresponding density-functional-like theory. Such a classification of the uniqueness of the non-local potential in ground state 1RDM functional theory has been lacking for decades. With the aid of presented invertibility theorem presented here, a complete classification of the non-uniqueness of the non-local potential in 1RDM functional theory can be given for the first time.

Path Integrals for Electronic Densities, Reactivity Indices, and Localization Functions in Quantum Systems

PubMed Central

Putz, Mihai V.

2009-01-01

The density matrix theory, the ancestor of density functional theory, provides the immediate framework for Path Integral (PI) development, allowing the canonical density be extended for the many-electronic systems through the density functional closure relationship. Yet, the use of path integral formalism for electronic density prescription presents several advantages: assures the inner quantum mechanical description of the system by parameterized paths; averages the quantum fluctuations; behaves as the propagator for time-space evolution of quantum information; resembles Schrödinger equation; allows quantum statistical description of the system through partition function computing. In this framework, four levels of path integral formalism were presented: the Feynman quantum mechanical, the semiclassical, the Feynman-Kleinert effective classical, and the Fokker-Planck non-equilibrium ones. In each case the density matrix or/and the canonical density were rigorously defined and presented. The practical specializations for quantum free and harmonic motions, for statistical high and low temperature limits, the smearing justification for the Bohr’s quantum stability postulate with the paradigmatic Hydrogen atomic excursion, along the quantum chemical calculation of semiclassical electronegativity and hardness, of chemical action and Mulliken electronegativity, as well as by the Markovian generalizations of Becke-Edgecombe electronic focalization functions – all advocate for the reliability of assuming PI formalism of quantum mechanics as a versatile one, suited for analytically and/or computationally modeling of a variety of fundamental physical and chemical reactivity concepts characterizing the (density driving) many-electronic systems. PMID:20087467

Path integrals for electronic densities, reactivity indices, and localization functions in quantum systems.

PubMed

Putz, Mihai V

2009-11-10

The density matrix theory, the ancestor of density functional theory, provides the immediate framework for Path Integral (PI) development, allowing the canonical density be extended for the many-electronic systems through the density functional closure relationship. Yet, the use of path integral formalism for electronic density prescription presents several advantages: assures the inner quantum mechanical description of the system by parameterized paths; averages the quantum fluctuations; behaves as the propagator for time-space evolution of quantum information; resembles Schrödinger equation; allows quantum statistical description of the system through partition function computing. In this framework, four levels of path integral formalism were presented: the Feynman quantum mechanical, the semiclassical, the Feynman-Kleinert effective classical, and the Fokker-Planck non-equilibrium ones. In each case the density matrix or/and the canonical density were rigorously defined and presented. The practical specializations for quantum free and harmonic motions, for statistical high and low temperature limits, the smearing justification for the Bohr's quantum stability postulate with the paradigmatic Hydrogen atomic excursion, along the quantum chemical calculation of semiclassical electronegativity and hardness, of chemical action and Mulliken electronegativity, as well as by the Markovian generalizations of Becke-Edgecombe electronic focalization functions - all advocate for the reliability of assuming PI formalism of quantum mechanics as a versatile one, suited for analytically and/or computationally modeling of a variety of fundamental physical and chemical reactivity concepts characterizing the (density driving) many-electronic systems.

Stochastic Optimally Tuned Range-Separated Hybrid Density Functional Theory.

PubMed

Neuhauser, Daniel; Rabani, Eran; Cytter, Yael; Baer, Roi

2016-05-19

We develop a stochastic formulation of the optimally tuned range-separated hybrid density functional theory that enables significant reduction of the computational effort and scaling of the nonlocal exchange operator at the price of introducing a controllable statistical error. Our method is based on stochastic representations of the Coulomb convolution integral and of the generalized Kohn-Sham density matrix. The computational cost of the approach is similar to that of usual Kohn-Sham density functional theory, yet it provides a much more accurate description of the quasiparticle energies for the frontier orbitals. This is illustrated for a series of silicon nanocrystals up to sizes exceeding 3000 electrons. Comparison with the stochastic GW many-body perturbation technique indicates excellent agreement for the fundamental band gap energies, good agreement for the band edge quasiparticle excitations, and very low statistical errors in the total energy for large systems. The present approach has a major advantage over one-shot GW by providing a self-consistent Hamiltonian that is central for additional postprocessing, for example, in the stochastic Bethe-Salpeter approach.

Dynamic kinetic energy potential for orbital-free density functional theory.

PubMed

Neuhauser, Daniel; Pistinner, Shlomo; Coomar, Arunima; Zhang, Xu; Lu, Gang

2011-04-14

A dynamic kinetic energy potential (DKEP) is developed for time-dependent orbital-free (TDOF) density function theory applications. This potential is constructed to affect only the dynamical (ω ≠ 0) response of an orbital-free electronic system. It aims at making the orbital-free simulation respond in the same way as that of a noninteracting homogenous electron gas (HEG), as required by a correct kinetic energy, therefore enabling extension of the success of orbital-free density functional theory in the static case (e.g., for embedding and description of processes in bulk materials) to dynamic processes. The potential is constructed by expansions of terms, each of which necessitates only simple time evolution (concurrent with the TDOF evolution) and a spatial convolution at each time-step. With 14 such terms a good fit is obtained to the response of the HEG at a large range of frequencies, wavevectors, and densities. The method is demonstrated for simple jellium spheres, approximating Na(9)(+) and Na(65)(+) clusters. It is applicable both to small and large (even ultralarge) excitations and the results converge (i.e., do not blow up) as a function of time. An extension to iterative frequency-resolved extraction is briefly outlined, as well as possibly numerically simpler expansions. The approach could also be extended to fit, instead of the HEG susceptibility, either an experimental susceptibility or a theoretically derived one for a non-HEG system. The DKEP potential should be a powerful tool for embedding a dynamical system described by a more accurate method (such as time-dependent density functional theory, TDDFT) in a large background described by TDOF with a DKEP potential. The type of expansions used and envisioned should be useful for other approaches, such as memory functionals in TDDFT. Finally, an appendix details the formal connection between TDOF and TDDFT.

Switched Systems and Motion Coordination: Combinatorial Challenges

NASA Technical Reports Server (NTRS)

Sadovsky, Alexander V.

2016-01-01

Problems of routing commercial air traffic in a terminal airspace encounter different constraints: separation assurance, aircraft performance limitations, regulations. The general setting of these problems is that of a switched control system. Such a system combines the differentiable motion of the aircraft with the combinatorial choices of choosing precedence when traffic routes merge and choosing branches when the routes diverge. This presentation gives an overview of the problem, the ATM context, related literature, and directions for future research.

Iconicity and the Emergence of Combinatorial Structure in Language

ERIC Educational Resources Information Center

Verhoef, Tessa; Kirby, Simon; de Boer, Bart

2016-01-01

In language, recombination of a discrete set of meaningless building blocks forms an unlimited set of possible utterances. How such combinatorial structure emerged in the evolution of human language is increasingly being studied. It has been shown that it can emerge when languages culturally evolve and adapt to human cognitive biases. How the…

Some Fundamental Issues in Ground-State Density Functional Theory: A Guide for the Perplexed.

PubMed

Perdew, John P; Ruzsinszky, Adrienn; Constantin, Lucian A; Sun, Jianwei; Csonka, Gábor I

2009-04-14

Some fundamental issues in ground-state density functional theory are discussed without equations: (1) The standard Hohenberg-Kohn and Kohn-Sham theorems were proven for a Hamiltonian that is not quite exact for real atoms, molecules, and solids. (2) The density functional for the exchange-correlation energy, which must be approximated, arises from the tendency of electrons to avoid one another as they move through the electron density. (3) In the absence of a magnetic field, either spin densities or total electron density can be used, although the former choice is better for approximations. (4) "Spin contamination" of the determinant of Kohn-Sham orbitals for an open-shell system is not wrong but right. (5) Only to the extent that symmetries of the interacting wave function are reflected in the spin densities should those symmetries be respected by the Kohn-Sham noninteracting or determinantal wave function. Functionals below the highest level of approximations should however sometimes break even those symmetries, for good physical reasons. (6) Simple and commonly used semilocal (lower-level) approximations for the exchange-correlation energy as a functional of the density can be accurate for closed systems near equilibrium and yet fail for open systems of fluctuating electron number. (7) The exact Kohn-Sham noninteracting state need not be a single determinant, but common approximations can fail when it is not. (8) Over an open system of fluctuating electron number, connected to another such system by stretched bonds, semilocal approximations make the exchange-correlation energy and hole-density sum rule too negative. (9) The gap in the exact Kohn-Sham band structure of a crystal underestimates the real fundamental gap but may approximate the first exciton energy in the large-gap limit. (10) Density functional theory is not really a mean-field theory, although it looks like one. The exact functional includes strong correlation, and semilocal approximations often

Phase space explorations in time dependent density functional theory

NASA Astrophysics Data System (ADS)

Rajam, Aruna K.

Time dependent density functional theory (TDDFT) is one of the useful tools for the study of the dynamic behavior of correlated electronic systems under the influence of external potentials. The success of this formally exact theory practically relies on approximations for the exchange-correlation potential which is a complicated functional of the co-ordinate density, non-local in space and time. Adiabatic approximations (such as ALDA), which are local in time, are most commonly used in the increasing applications of the field. Going beyond ALDA, has been proved difficult leading to mathematical inconsistencies. We explore the regions where the theory faces challenges, and try to answer some of them via the insights from two electron model systems. In this thesis work we propose a phase-space extension of the TDDFT. We want to answer the challenges the theory is facing currently by exploring the one-body phase-space. We give a general introduction to this theory and its mathematical background in the first chapter. In second chapter, we carryout a detailed study of instantaneous phase-space densities and argue that the functionals of distributions can be a better alternative to the nonlocality issue of the exchange-correlation potentials. For this we study in detail the interacting and the non-interacting phase-space distributions for Hookes atom model. The applicability of ALDA-based TDDFT for the dynamics in strongfields can become severely problematic due to the failure of single-Slater determinant picture.. In the third chapter, we analyze how the phase-space distributions can shine some light into this problem. We do a comparative study of Kohn-Sham and interacting phase-space and momentum distributions for single ionization and double ionization systems. Using a simple model of two-electron systems, we have showed that the momentum distribution computed directly from the exact KS system contains spurious oscillations: a non-classical description of the

Combinatorial computational chemistry approach for materials design: applications in deNOx catalysis, Fischer-Tropsch synthesis, lanthanoid complex, and lithium ion secondary battery.

PubMed

Koyama, Michihisa; Tsuboi, Hideyuki; Endou, Akira; Takaba, Hiromitsu; Kubo, Momoji; Del Carpio, Carlos A; Miyamoto, Akira

2007-02-01

Computational chemistry can provide fundamental knowledge regarding various aspects of materials. While its impact in scientific research is greatly increasing, its contributions to industrially important issues are far from satisfactory. In order to realize industrial innovation by computational chemistry, a new concept "combinatorial computational chemistry" has been proposed by introducing the concept of combinatorial chemistry to computational chemistry. This combinatorial computational chemistry approach enables theoretical high-throughput screening for materials design. In this manuscript, we review the successful applications of combinatorial computational chemistry to deNO(x) catalysts, Fischer-Tropsch catalysts, lanthanoid complex catalysts, and cathodes of the lithium ion secondary battery.

Single cell systems biology by super-resolution imaging and combinatorial labeling

PubMed Central

Lubeck, Eric; Cai, Long

2012-01-01

Fluorescence microscopy is a powerful quantitative tool for exploring regulatory networks in single cells. However, the number of molecular species that can be measured simultaneously is limited by the spectral separability of fluorophores. Here we demonstrate a simple but general strategy to drastically increase the capacity for multiplex detection of molecules in single cells by using optical super-resolution microscopy (SRM) and combinatorial labeling. As a proof of principle, we labeled mRNAs with unique combinations of fluorophores using Fluorescence in situ Hybridization (FISH), and resolved the sequences and combinations of fluorophores with SRM. We measured the mRNA levels of 32 genes simultaneously in single S. cerevisiae cells. These experiments demonstrate that combinatorial labeling and super-resolution imaging of single cells provides a natural approach to bring systems biology into single cells. PMID:22660740

A classical density-functional theory for describing water interfaces.

PubMed

Hughes, Jessica; Krebs, Eric J; Roundy, David

2013-01-14

We develop a classical density functional for water which combines the White Bear fundamental-measure theory (FMT) functional for the hard sphere fluid with attractive interactions based on the statistical associating fluid theory variable range (SAFT-VR). This functional reproduces the properties of water at both long and short length scales over a wide range of temperatures and is computationally efficient, comparable to the cost of FMT itself. We demonstrate our functional by applying it to systems composed of two hard rods, four hard rods arranged in a square, and hard spheres in water.

Functional connectivity density mapping: comparing multiband and conventional EPI protocols.

PubMed

Cohen, Alexander D; Tomasi, Dardo; Shokri-Kojori, Ehsan; Nencka, Andrew S; Wang, Yang

2018-06-01

Functional connectivity density mapping (FCDM) is a newly developed data-driven technique that quantifies the number of local and global functional connections for each voxel in the brain. In this study, we evaluated reproducibility, sensitivity, and specificity of both local functional connectivity density (lFCD) and global functional connectivity density (gFCD). We compared these metrics using the human connectome project (HCP) compatible high-resolution (2 mm isotropic, TR = 0.8 s) multiband (MB), and more typical, lower resolution (3.5 mm isotropic, TR = 2.0 s) single-band (SB) resting state functional MRI (rs-fMRI) acquisitions. Furthermore, in order to be more clinically feasible, only rs-fMRI scans that lasted seven minutes were tested. Subjects were scanned twice within a two-week span. We found sensitivity and specificity increased and reproducibility either increased or did not change for the MB compared to the SB acquisitions. The MB scans also showed improved gray matter/white matter contrast compared to the SB scans. The lFCD and gFCD patterns were similar across MB and SB scans and confined predominantly to gray matter. We also observed a strong spatial correlation of FCD between MB and SB scans indicating the two acquisitions provide similar information. These findings indicate high-resolution MB acquisitions improve the quality of FCD data, and seven minute rs-fMRI scan can provide robust FCD measurements.

Work-function calculations for a symmetrical total-charge-density profile at the metallic surface

NASA Astrophysics Data System (ADS)

Wojciechowski, K. F.; Sobańska-Nowotnik, M.

1983-07-01

It is shown that, if the total-charge-density profile nT(x) at the surface of jellium satisfies the Budd-Vannimenus constraint and also is a symmetrical function of x, relative to the ordinate axis, then the work-function variation versus the Wigner-Seitz radius rs does not depend on the form of nT(x). Also the simple linear-density profile is used to calculate the work function by application of the variational principle for the energy, including the first and second density-gradient corrections to the kinetic energy and the first gradient correction to the exchange and correlation energy. The results for the work function are in good agreement with the polycrystalline values for low-density metals.

Semiclassical neutral atom as a reference system in density functional theory.

PubMed

Constantin, Lucian A; Fabiano, E; Laricchia, S; Della Sala, F

2011-05-06

We use the asymptotic expansions of the semiclassical neutral atom as a reference system in density functional theory to construct accurate generalized gradient approximations (GGAs) for the exchange-correlation and kinetic energies without any empiricism. These asymptotic functionals are among the most accurate GGAs for molecular systems, perform well for solid state, and overcome current GGA state of the art in frozen density embedding calculations. Our results also provide evidence for the conjointness conjecture between exchange and kinetic energies of atomic systems.

FDE-vdW: A van der Waals inclusive subsystem density-functional theory.

PubMed

Kevorkyants, Ruslan; Eshuis, Henk; Pavanello, Michele

2014-07-28

We present a formally exact van der Waals inclusive electronic structure theory, called FDE-vdW, based on the Frozen Density Embedding formulation of subsystem Density-Functional Theory. In subsystem DFT, the energy functional is composed of subsystem additive and non-additive terms. We show that an appropriate definition of the long-range correlation energy is given by the value of the non-additive correlation functional. This functional is evaluated using the fluctuation-dissipation theorem aided by a formally exact decomposition of the response functions into subsystem contributions. FDE-vdW is derived in detail and several approximate schemes are proposed, which lead to practical implementations of the method. We show that FDE-vdW is Casimir-Polder consistent, i.e., it reduces to the generalized Casimir-Polder formula for asymptotic inter-subsystems separations. Pilot calculations of binding energies of 13 weakly bound complexes singled out from the S22 set show a dramatic improvement upon semilocal subsystem DFT, provided that an appropriate exchange functional is employed. The convergence of FDE-vdW with basis set size is discussed, as well as its dependence on the choice of associated density functional approximant.

FDE-vdW: A van der Waals inclusive subsystem density-functional theory

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

Kevorkyants, Ruslan; Pavanello, Michele, E-mail: m.pavanello@rutgers.edu; Eshuis, Henk

2014-07-28

We present a formally exact van der Waals inclusive electronic structure theory, called FDE-vdW, based on the Frozen Density Embedding formulation of subsystem Density-Functional Theory. In subsystem DFT, the energy functional is composed of subsystem additive and non-additive terms. We show that an appropriate definition of the long-range correlation energy is given by the value of the non-additive correlation functional. This functional is evaluated using the fluctuation–dissipation theorem aided by a formally exact decomposition of the response functions into subsystem contributions. FDE-vdW is derived in detail and several approximate schemes are proposed, which lead to practical implementations of the method.more » We show that FDE-vdW is Casimir-Polder consistent, i.e., it reduces to the generalized Casimir-Polder formula for asymptotic inter-subsystems separations. Pilot calculations of binding energies of 13 weakly bound complexes singled out from the S22 set show a dramatic improvement upon semilocal subsystem DFT, provided that an appropriate exchange functional is employed. The convergence of FDE-vdW with basis set size is discussed, as well as its dependence on the choice of associated density functional approximant.« less

Orthogonality of embedded wave functions for different states in frozen-density embedding theory

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

Zech, Alexander; Wesolowski, Tomasz A.; Aquilante, Francesco

2015-10-28

Other than lowest-energy stationary embedded wave functions obtained in Frozen-Density Embedding Theory (FDET) [T. A. Wesolowski, Phys. Rev. A 77, 012504 (2008)] can be associated with electronic excited states but they can be mutually non-orthogonal. Although this does not violate any physical principles — embedded wave functions are only auxiliary objects used to obtain stationary densities — working with orthogonal functions has many practical advantages. In the present work, we show numerically that excitation energies obtained using conventional FDET calculations (allowing for non-orthogonality) can be obtained using embedded wave functions which are strictly orthogonal. The used method preserves the mathematicalmore » structure of FDET and self-consistency between energy, embedded wave function, and the embedding potential (they are connected through the Euler-Lagrange equations). The orthogonality is built-in through the linearization in the embedded density of the relevant components of the total energy functional. Moreover, we show formally that the differences between the expectation values of the embedded Hamiltonian are equal to the excitation energies, which is the exact result within linearized FDET. Linearized FDET is shown to be a robust approximation for a large class of reference densities.« less

Polymer surface functionalities that control human embryoid body cell adhesion revealed by high throughput surface characterization of combinatorial material microarrays

PubMed Central

Yang, Jing; Mei, Ying; Hook, Andrew L.; Taylor, Michael; Urquhart, Andrew J.; Bogatyrev, Said R.; Langer, Robert; Anderson, Daniel G.; Davies, Martyn C.; Alexander, Morgan R.

2010-01-01

High throughput materials discovery using combinatorial polymer microarrays to screen for new biomaterials with new and improved function is established as a powerful strategy. Here we combine this screening approach with high throughput surface characterisation (HT-SC) to identify surface structure-function relationships. We explore how this combination can help to identify surface chemical moieties that control protein adsorption and subsequent cellular response. The adhesion of human embryoid body (hEB) cells to a large number (496) of different acrylate polymers synthesized in a microarray format is screened using a high throughput procedure. To determine the role of the polymer surface properties on hEB cell adhesion, detailed HT-SC of these acrylate polymers is carried out using time of flight secondary ion mass spectrometry (ToF SIMS), x-ray photoelectron spectroscopy (XPS), pico litre drop sessile water contact angle (WCA) measurement and atomic force microscopy (AFM). A structure-function relationship is identified between the ToF SIMS analysis of the surface chemistry after a fibronectin (Fn) pre-conditioning step and the cell adhesion to each spot using the multivariate analysis technique partial least squares (PLS) regression. Secondary ions indicative of the adsorbed Fn correlate with increased cell adhesion whereas glycol and other functionalities from the polymers are identified that reduce cell adhesion. Furthermore, a strong relationship between the ToF SIMS spectra of bare polymers and the cell adhesion to each spot is identified using PLS regression. This identifies a role for both the surface chemistry of the bare polymer and the pre-adsorbed Fn, as-represented in the ToF SIMS spectra, in controlling cellular adhesion. In contrast, no relationship is found between cell adhesion and wettability, surface roughness, elemental or functional surface composition. The correlation between ToF SIMS data of the surfaces and the cell adhesion demonstrates

Combinatorial Strategies for the Development of Bulk Metallic Glasses

NASA Astrophysics Data System (ADS)

Ding, Shiyan

The systematic identification of multi-component alloys out of the vast composition space is still a daunting task, especially in the development of bulk metallic glasses that are typically based on three or more elements. In order to address this challenge, combinatorial approaches have been proposed. However, previous attempts have not successfully coupled the synthesis of combinatorial libraries with high-throughput characterization methods. The goal of my dissertation is to develop efficient high-throughput characterization methods, optimized to identify glass formers systematically. Here, two innovative approaches have been invented. One is to measure the nucleation temperature in parallel for up-to 800 compositions. The composition with the lowest nucleation temperature has a reasonable agreement with the best-known glass forming composition. In addition, the thermoplastic formability of a metallic glass forming system is determined through blow molding a compositional library. Our results reveal that the composition with the largest thermoplastic deformation correlates well with the best-known formability composition. I have demonstrated both methods as powerful tools to develop new bulk metallic glasses.

Importance of the Kinetic Energy Density for Band Gap Calculations in Solids with Density Functional Theory.

PubMed

Tran, Fabien; Blaha, Peter

2017-05-04

Recently, exchange-correlation potentials in density functional theory were developed with the goal of providing improved band gaps in solids. Among them, the semilocal potentials are particularly interesting for large systems since they lead to calculations that are much faster than with hybrid functionals or methods like GW. We present an exhaustive comparison of semilocal exchange-correlation potentials for band gap calculations on a large test set of solids, and particular attention is paid to the potential HLE16 proposed by Verma and Truhlar. It is shown that the most accurate potential is the modified Becke-Johnson potential, which, most noticeably, is much more accurate than all other semilocal potentials for strongly correlated systems. This can be attributed to its additional dependence on the kinetic energy density. It is also shown that the modified Becke-Johnson potential is at least as accurate as the hybrid functionals and more reliable for solids with large band gaps.

Application of combinatorial biocatalysis for a unique ring expansion of dihydroxymethylzearalenone

USDA-ARS?s Scientific Manuscript database

Combinatorial biocatalysis was applied to generate a diverse set of dihydroxymethylzearalenone derivatives with modified ring structure. In one chemoenzymatic reaction sequence, dihydroxymethylzearalenone was first subjected to a unique enzyme-catalyzed oxidative ring opening reaction that creates ...

Probability density function approach for compressible turbulent reacting flows

NASA Technical Reports Server (NTRS)

Hsu, A. T.; Tsai, Y.-L. P.; Raju, M. S.

1994-01-01

The objective of the present work is to extend the probability density function (PDF) tubulence model to compressible reacting flows. The proability density function of the species mass fractions and enthalpy are obtained by solving a PDF evolution equation using a Monte Carlo scheme. The PDF solution procedure is coupled with a compression finite-volume flow solver which provides the velocity and pressure fields. A modeled PDF equation for compressible flows, capable of treating flows with shock waves and suitable to the present coupling scheme, is proposed and tested. Convergence of the combined finite-volume Monte Carlo solution procedure is discussed. Two super sonic diffusion flames are studied using the proposed PDF model and the results are compared with experimental data; marked improvements over solutions without PDF are observed.

Tunable non-interacting free-energy functionals: development and applications to low-density aluminum

NASA Astrophysics Data System (ADS)

Trickey, Samuel; Karasiev, Valentin

We introduce the concept of tunable orbital-free non-interacting free-energy density functionals and present a generalized gradient approximation (GGA) with a subset of parameters defined from constraints and a few free parameters. Those free parameters are tuned to reproduce reference Kohn-Sham (KS) static-lattice pressures for Al at T=8 kK for bulk densities between 0.6 and 2 g/cm3. The tuned functional then is used in OF molecular dynamics (MD) simulations for Al with densities between 0.1 and 2 g/cm3 and T between 6 and 50 kK to calculate the equation of state and generate configurations for electrical conductivity calculations. The tunable functional produces accurate results. Computationally it is very effective especially at elevated temperature. Kohn-Shiam calculations for such low densities are affordable only up to T=10 kK, while other OF approximations, including two-point functionals, fail badly in that regime. Work supported by US DoE Grant DE-SC0002139.

A density functional theory for colloids with two multiple bonding associating sites.

PubMed

Haghmoradi, Amin; Wang, Le; Chapman, Walter G

2016-06-22

Wertheim's multi-density formalism is extended for patchy colloidal fluids with two multiple bonding patches. The theory is developed as a density functional theory to predict the properties of an associating inhomogeneous fluid. The equation of state developed for this fluid depends on the size of the patch, and includes formation of cyclic, branched and linear clusters of associated species. The theory predicts the density profile and the fractions of colloids in different bonding states versus the distance from one wall as a function of bulk density and temperature. The predictions from our theory are compared with previous results for a confined fluid with four single bonding association sites. Also, comparison between the present theory and Monte Carlo simulation indicates a good agreement.

Modulation Based on Probability Density Functions

NASA Technical Reports Server (NTRS)

Williams, Glenn L.

2009-01-01

A proposed method of modulating a sinusoidal carrier signal to convey digital information involves the use of histograms representing probability density functions (PDFs) that characterize samples of the signal waveform. The method is based partly on the observation that when a waveform is sampled (whether by analog or digital means) over a time interval at least as long as one half cycle of the waveform, the samples can be sorted by frequency of occurrence, thereby constructing a histogram representing a PDF of the waveform during that time interval.

Gas phase electrodeposition: a programmable multimaterial deposition method for combinatorial nanostructured device discovery.

PubMed

Lin, En-Chiang; Cole, Jesse J; Jacobs, Heiko O

2010-11-10

This article reports and applies a recently discovered programmable multimaterial deposition process to the formation and combinatorial improvement of 3D nanostructured devices. The gas-phase deposition process produces charged <5 nm particles of silver, tungsten, and platinum and uses externally biased electrodes to control the material flux and to turn deposition ON/OFF in selected domains. Domains host nanostructured dielectrics to define arrays of electrodynamic 10 × nanolenses to further control the flux to form <100 nm resolution deposits. The unique feature of the process is that material type, amount, and sequence can be altered from one domain to the next leading to different types of nanostructures including multimaterial bridges, interconnects, or nanowire arrays with 20 nm positional accuracy. These features enable combinatorial nanostructured materials and device discovery. As a first demonstration, we produce and identify in a combinatorial way 3D nanostructured electrode designs that improve light scattering, absorption, and minority carrier extraction of bulk heterojunction photovoltaic cells. Photovoltaic cells from domains with long and dense nanowire arrays improve the relative power conversion efficiency by 47% when compared to flat domains on the same substrate.

Thermodynamics of technetium: Reconciling theory and experiment using density functional perturbation analysis

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

Weck, Philippe F.; Kim, Eunja

The structure, lattice dynamics and thermodynamic properties of bulk technetium were investigated within the framework of density functional theory. The phonon density of states spectrum computed with density functional perturbation theory closely matches inelastic coherent neutron scattering measurements. The thermal properties of technetium were derived from phonon frequencies calculated within the quasi-harmonic approximation (QHA), which introduces a volume dependence of phonon frequencies as a part of the anharmonic effect. As a result, the predicted thermal expansion and isobaric heat capacity of technetium are in excellent agreement with available experimental data for temperatures up to ~1600 K.

Thermodynamics of technetium: Reconciling theory and experiment using density functional perturbation analysis

DOE PAGES

Weck, Philippe F.; Kim, Eunja

2015-06-11

The structure, lattice dynamics and thermodynamic properties of bulk technetium were investigated within the framework of density functional theory. The phonon density of states spectrum computed with density functional perturbation theory closely matches inelastic coherent neutron scattering measurements. The thermal properties of technetium were derived from phonon frequencies calculated within the quasi-harmonic approximation (QHA), which introduces a volume dependence of phonon frequencies as a part of the anharmonic effect. As a result, the predicted thermal expansion and isobaric heat capacity of technetium are in excellent agreement with available experimental data for temperatures up to ~1600 K.

Density-functional theory applied to d- and f-electron systems

NASA Astrophysics Data System (ADS)

Wu, Xueyuan

Density functional theory (DFT) has been applied to study the electronic and geometric structures of prototype d- and f-electron systems. For the d-electron system, all electron DFT with gradient corrections to the exchange and correlation functionals has been used to investigate the properties of small neutral and cationic vanadium clusters. Results are in good agreement with available experimental and other theoretical data. For the f-electron system, a hybrid DFT, namely, B3LYP (Becke's 3-parameter hybrid functional using the correlation functional of Lee, Yang and Parr) with relativistic effective core potentials and cluster models has been applied to investigate the nature of chemical bonding of both the bulk and the surfaces of plutonium monoxide and dioxide. Using periodic models, the electronic and geometric structures of PuO2 and its (110) surface, as well as water adsorption on this surface have also been investigated using DFT in both local density approximation (LDA) and generalized gradient approximation (GGA) formalisms.

Grid-free density functional calculations on periodic systems.

PubMed

Varga, Stefan

2007-09-21

Density fitting scheme is applied to the exchange part of the Kohn-Sham potential matrix in a grid-free local density approximation for infinite systems with translational periodicity. It is shown that within this approach the computational demands for the exchange part scale in the same way as for the Coulomb part. The efficiency of the scheme is demonstrated on a model infinite polymer chain. For simplicity, the implementation with Dirac-Slater Xalpha exchange functional is presented only. Several choices of auxiliary basis set expansion coefficients were tested with both Coulomb and overlap metric. Their effectiveness is discussed also in terms of robustness and norm preservation.

Grid-free density functional calculations on periodic systems

NASA Astrophysics Data System (ADS)

Varga, Štefan

2007-09-01

Density fitting scheme is applied to the exchange part of the Kohn-Sham potential matrix in a grid-free local density approximation for infinite systems with translational periodicity. It is shown that within this approach the computational demands for the exchange part scale in the same way as for the Coulomb part. The efficiency of the scheme is demonstrated on a model infinite polymer chain. For simplicity, the implementation with Dirac-Slater Xα exchange functional is presented only. Several choices of auxiliary basis set expansion coefficients were tested with both Coulomb and overlap metric. Their effectiveness is discussed also in terms of robustness and norm preservation.

Evaluation of the Current Status of the Combinatorial Approach for the Study of Phase Diagrams

PubMed Central

Wong-Ng, W.

2012-01-01

This paper provides an evaluation of the effectiveness of using the high throughput combinatorial approach for preparing phase diagrams of thin film and bulk materials. Our evaluation is based primarily on examples of combinatorial phase diagrams that have been reported in the literature as well as based on our own laboratory experiments. Various factors that affect the construction of these phase diagrams are examined. Instrumentation and analytical approaches needed to improve data acquisition and data analysis are summarized. PMID:26900530

Combinatorial events of insertion sequences and ICE in Gram-negative bacteria.

PubMed

Toleman, Mark A; Walsh, Timothy R

2011-09-01

The emergence of antibiotic and antimicrobial resistance in Gram-negative bacteria is incremental and linked to genetic elements that function in a so-called 'one-ended transposition' manner, including ISEcp1, ISCR elements and Tn3-like transposons. The power of these elements lies in their inability to consistently recognize one of their own terminal sequences, while recognizing more genetically distant surrogate sequences. This has the effect of mobilizing the DNA sequence found adjacent to their initial location. In general, resistance in Gram-negatives is closely linked to a few one-off events. These include the capture of the class 1 integron by a Tn5090-like transposon; the formation of the 3' conserved segment (3'-CS); and the fusion of the ISCR1 element to the 3'-CS. The structures formed by these rare events have been massively amplified and disseminated in Gram-negative bacteria, but hitherto, are rarely found in Gram-positives. Such events dominate current resistance gene acquisition and are instrumental in the construction of large resistance gene islands on chromosomes and plasmids. Similar combinatorial events appear to have occurred between conjugative plasmids and phages constructing hybrid elements called integrative and conjugative elements or conjugative transposons. These elements are beginning to be closely linked to some of the more powerful resistance mechanisms such as the extended spectrum β-lactamases, metallo- and AmpC type β-lactamases. Antibiotic resistance in Gram-negative bacteria is dominated by unusual combinatorial mistakes of Insertion sequences and gene fusions which have been selected and amplified by antibiotic pressure enabling the formation of extended resistance islands. © 2011 Federation of European Microbiological Societies. Published by Blackwell Publishing Ltd. All rights reserved.

Ranked solutions to a class of combinatorial optimizations—with applications in mass spectrometry based peptide sequencing and a variant of directed paths in random media

NASA Astrophysics Data System (ADS)

Doerr, Timothy P.; Alves, Gelio; Yu, Yi-Kuo

2005-08-01

Typical combinatorial optimizations are NP-hard; however, for a particular class of cost functions the corresponding combinatorial optimizations can be solved in polynomial time using the transfer matrix technique or, equivalently, the dynamic programming approach. This suggests a way to efficiently find approximate solutions-find a transformation that makes the cost function as similar as possible to that of the solvable class. After keeping many high-ranking solutions using the approximate cost function, one may then re-assess these solutions with the full cost function to find the best approximate solution. Under this approach, it is important to be able to assess the quality of the solutions obtained, e.g., by finding the true ranking of the kth best approximate solution when all possible solutions are considered exhaustively. To tackle this statistical issue, we provide a systematic method starting with a scaling function generated from the finite number of high-ranking solutions followed by a convergent iterative mapping. This method, useful in a variant of the directed paths in random media problem proposed here, can also provide a statistical significance assessment for one of the most important proteomic tasks-peptide sequencing using tandem mass spectrometry data. For directed paths in random media, the scaling function depends on the particular realization of randomness; in the mass spectrometry case, the scaling function is spectrum-specific.

A path-oriented knowledge representation system: Defusing the combinatorial system

NASA Technical Reports Server (NTRS)

Karamouzis, Stamos T.; Barry, John S.; Smith, Steven L.; Feyock, Stefan

1995-01-01

LIMAP is a programming system oriented toward efficient information manipulation over fixed finite domains, and quantification over paths and predicates. A generalization of Warshall's Algorithm to precompute paths in a sparse matrix representation of semantic nets is employed to allow questions involving paths between components to be posed and answered easily. LIMAP's ability to cache all paths between two components in a matrix cell proved to be a computational obstacle, however, when the semantic net grew to realistic size. The present paper describes a means of mitigating this combinatorial explosion to an extent that makes the use of the LIMAP representation feasible for problems of significant size. The technique we describe radically reduces the size of the search space in which LIMAP must operate; semantic nets of more than 500 nodes have been attacked successfully. Furthermore, it appears that the procedure described is applicable not only to LIMAP, but to a number of other combinatorially explosive search space problems found in AI as well.

Extension of many-body theory and approximate density functionals to fractional charges and fractional spins.

PubMed

Yang, Weitao; Mori-Sánchez, Paula; Cohen, Aron J

2013-09-14

The exact conditions for density functionals and density matrix functionals in terms of fractional charges and fractional spins are known, and their violation in commonly used functionals has been shown to be the root of many major failures in practical applications. However, approximate functionals are designed for physical systems with integer charges and spins, not in terms of the fractional variables. Here we develop a general framework for extending approximate density functionals and many-electron theory to fractional-charge and fractional-spin systems. Our development allows for the fractional extension of any approximate theory that is a functional of G(0), the one-electron Green's function of the non-interacting reference system. The extension to fractional charge and fractional spin systems is based on the ensemble average of the basic variable, G(0). We demonstrate the fractional extension for the following theories: (1) any explicit functional of the one-electron density, such as the local density approximation and generalized gradient approximations; (2) any explicit functional of the one-electron density matrix of the non-interacting reference system, such as the exact exchange functional (or Hartree-Fock theory) and hybrid functionals; (3) many-body perturbation theory; and (4) random-phase approximations. A general rule for such an extension has also been derived through scaling the orbitals and should be useful for functionals where the link to the Green's function is not obvious. The development thus enables the examination of approximate theories against known exact conditions on the fractional variables and the analysis of their failures in chemical and physical applications in terms of violations of exact conditions of the energy functionals. The present work should facilitate the calculation of chemical potentials and fundamental bandgaps with approximate functionals and many-electron theories through the energy derivatives with respect to the